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1

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability | Department of  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

098: ISC BIND Deleted Domain Name Resolving Vulnerability 098: ISC BIND Deleted Domain Name Resolving Vulnerability U-098: ISC BIND Deleted Domain Name Resolving Vulnerability February 8, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to bypass certain security restrictions. PLATFORM: ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ABSTRACT: The vulnerability is caused due to an error within the cache update policy. reference LINKS: Original Advisory Secunia Advisory SA47884 CVE-2012-1033 IMPACT ASSESSMENT: High Discussion: Researchers discovered a vulnerability affecting the large majority of popular DNS implementations which allows a malicious domain name to stay resolvable long after it has been removed from the upper level servers. The

2

Cellulose binding domain proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

1998-01-01T23:59:59.000Z

3

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1998-01-01T23:59:59.000Z

4

Cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1998-02-17T23:59:59.000Z

5

Nucleic acids encoding a cellulose binding domain  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 15 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1996-03-05T23:59:59.000Z

6

Nucleic acids encoding a cellulose binding domain  

SciTech Connect

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1996-01-01T23:59:59.000Z

7

A chromatin binding site in the tail domain of nuclear lamins that interacts with core histones  

E-Print Network (OSTI)

Abstract. Interaction of chromatin with the nuclear envelope and lamina is thought to help determine higher order chromosome organization in the interphase nucleus. Previous studies have shown that nuclear lamins bind chromatin directly. Here we have localized a chromatin binding site to the carboxyl-terminal tail domains of both A- and B-type mammalian lamins, and have characterized the biochemical properties of this binding in detail. Recombinant glutathione-S-transferase fusion proteins containing the tail domains of mammalian lamins C, BI, and B 2 were analyzed for their ability to associate with rat liver chromatin fragments immobi-lized on microtiter plate wells. We found that all three lamin tails specifically bind to chromatin with apparent Kds of 120-300 nM. By examining a series of deletion

Hideo Taniura; Charles Glass; Larry Gerace

1995-01-01T23:59:59.000Z

8

Methods of detection using a cellulose binding domain fusion product  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Shimshon, IL); Shpiegl, Itai (North Gallilea, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1999-01-01T23:59:59.000Z

9

Methods of use of cellulose binding domain proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1997-09-23T23:59:59.000Z

10

Methods of detection using a cellulose binding domain fusion product  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 34 figs.

Shoseyov, O.; Shpiegl, I.; Goldstein, M.A.; Doi, R.H.

1999-01-05T23:59:59.000Z

11

Methods of use of cellulose binding domain proteins  

SciTech Connect

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

1997-01-01T23:59:59.000Z

12

U-183: ISC BIND DNS Resource Records Handling Vulnerability ...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

U-098: ISC BIND Deleted Domain Name Resolving Vulnerability U-038: BIND 9 Resolver crashes after logging an error in query.c T-617: BIND RPZ Processing Flaw Lets Remote Users...

13

IQGAP Proteins Reveal an Atypical Phosphoinositide (aPI) Binding Domain with a Pseudo C2 Domain Fold  

SciTech Connect

Class I phosphoinositide (PI) 3-kinases act through effector proteins whose 3-PI selectivity is mediated by a limited repertoire of structurally defined, lipid recognition domains. We describe here the lipid preferences and crystal structure of a new class of PI binding modules exemplified by select IQGAPs (IQ motif containing GTPase-activating proteins) known to coordinate cellular signaling events and cytoskeletal dynamics. This module is defined by a C-terminal 105-107 amino acid region of which IQGAP1 and -2, but not IQGAP3, binds preferentially to phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3). The binding affinity for PtdInsP3, together with other, secondary target-recognition characteristics, are comparable with those of the pleckstrin homology domain of cytohesin-3 (general receptor for phosphoinositides 1), an established PtdInsP3 effector protein. Importantly, the IQGAP1 C-terminal domain and the cytohesin-3 pleckstrin homology domain, each tagged with enhanced green fluorescent protein, were both re-localized from the cytosol to the cell periphery following the activation of PI 3-kinase in Swiss 3T3 fibroblasts, consistent with their common, selective recognition of endogenous 3-PI(s). The crystal structure of the C-terminal IQGAP2 PI binding module reveals unexpected topological similarity to an integral fold of C2 domains, including a putative basic binding pocket. We propose that this module integrates select IQGAP proteins with PI 3-kinase signaling and constitutes a novel, atypical phosphoinositide binding domain that may represent the first of a larger group, each perhaps structurally unique but collectively dissimilar from the known PI recognition modules.

Dixon, Miles J.; Gray, Alexander; Schenning, Martijn; Agacan, Mark; Tempel, Wolfram; Tong, Yufeng; Nedyalkova, Lyudmila; Park, Hee-Won; Leslie, Nicholas R.; van Aalten, Daan M.F.; Downes, C. Peter; Batty, Ian H. (Toronto); (Dundee)

2012-10-16T23:59:59.000Z

14

Crystal Structure of the Simian Virus 40 Large T-Antigen Origin-Binding Domain  

Science Conference Proceedings (OSTI)

The origins of replication of DNA tumor viruses have a highly conserved feature, namely, multiple binding sites for their respective initiator proteins arranged as inverted repeats. In the 1.45- Angstroms crystal structure of the simian virus 40 large T-antigen (T-ag) origin-binding domain (obd) reported herein, T-ag obd monomers form a left-handed spiral with an inner channel of 30 Angstroms having six monomers per turn. The inner surface of the spiral is positively charged and includes residues known to bind DNA. Residues implicated in hexamerization of full-length T-ag are located at the interface between adjacent T-ag obd monomers. These data provide a high-resolution model of the hexamer of origin-binding domains observed in electron microscopy studies and allow the obd's to be oriented relative to the hexamer of T-ag helicase domains to which they are connected.

Meinke,G.; Bullock, P.; Bohm, A.

2006-01-01T23:59:59.000Z

15

Crystal Structure of the Chromodomain Helicase DNA-binding Protein 1 (Chd1) DNA-binding Domain in Complex with DNA  

Science Conference Proceedings (OSTI)

Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.

Sharma A.; Heroux A.; Jenkins K. R.; Bowman G. D.

2011-12-09T23:59:59.000Z

16

Structure of the C-terminal heme-binding domain of THAP domain containing protein 4 from Homo sapiens  

SciTech Connect

The thanatos (the Greek god of death)-associated protein (THAP) domain is a sequence-specific DNA-binding domain that contains a C2-CH (Cys-Xaa{sub 2-4}-Cys-Xaa{sub 35-50}-Cys-Xaa{sub 2}-His) zinc finger that is similar to the DNA domain of the P element transposase from Drosophila. THAP-containing proteins have been observed in the proteome of humans, pigs, cows, chickens, zebrafish, Drosophila, C. elegans, and Xenopus. To date, there are no known THAP domain proteins in plants, yeast, or bacteria. There are 12 identified human THAP domain-containing proteins (THAP0-11). In all human THAP protein, the THAP domain is located at the N-terminus and is {approx}90 residues in length. Although all of the human THAP-containing proteins have a homologous N-terminus, there is extensive variation in both the predicted structure and length of the remaining protein. Even though the exact function of these THAP proteins is not well defined, there is evidence that they play a role in cell proliferation, apoptosis, cell cycle modulation, chromatin modification, and transcriptional regulation. THAP-containing proteins have also been implicated in a number of human disease states including heart disease, neurological defects, and several types of cancers. Human THAP4 is a 577-residue protein of unknown function that is proposed to bind DNA in a sequence-specific manner similar to THAP1 and has been found to be upregulated in response to heat shock. THAP4 is expressed in a relatively uniform manner in a broad range of tissues and appears to be upregulated in lymphoma cells and highly expressed in heart cells. The C-terminal domain of THAP4 (residues 415-577), designated here as cTHAP4, is evolutionarily conserved and is observed in all known THAP4 orthologs. Several single-domain proteins lacking a THAP domain are found in plants and bacteria and show significant levels of homology to cTHAP4. It appears that cTHAP4 belongs to a large class of proteins that have yet to be fully functionally characterized. On the basis of prior work, we predicted that cTHAP4 is composed of a heme-binding nitrobindin domain, making THAP4 the only human THAP protein predicted to bind a cofactor. Nitrobindin, a recently characterized protein from Arabidopsis thaliana, is structurally similar and exhibits nitric oxide (NO)-binding properties that resemble the heme-binding nitrophorins. Nitrophorins use a heme moiety to store, transport, and release NO in a pH-specific manner. Although the exact function of nitrobindin is not fully known, the similarities between the well-characterized nitrophorins imply a role in NO transport, sensing, or metabolism. To better elucidate the possible function of THAP4, we solved the hemebound structure of cTHAP4 to a resolution of 1.79 {angstrom}.

Bianchetti, Christopher M.; Bingman, Craig A.; Phillips, Jr., George N. (UW)

2012-03-15T23:59:59.000Z

17

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

Shoseyov, Oded (Karmey Yosef, IL)

1998-01-01T23:59:59.000Z

18

Kits and methods of detection using cellulose binding domain fusion proteins  

DOE Patents (OSTI)

A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques. 16 figs.

Shoseyov, O.; Yosef, K.

1998-04-14T23:59:59.000Z

19

LINC Complexes Form by Binding of Three KASH Peptides to Domain Interfaces of Trimeric SUN Proteins  

Science Conference Proceedings (OSTI)

Linker of nucleoskeleton and cytoskeleton (LINC) complexes span the nuclear envelope and are composed of KASH and SUN proteins residing in the outer and inner nuclear membrane, respectively. LINC formation relies on direct binding of KASH and SUN in the perinuclear space. Thereby, molecular tethers are formed that can transmit forces for chromosome movements, nuclear migration, and anchorage. We present crystal structures of the human SUN2-KASH1/2 complex, the core of the LINC complex. The SUN2 domain is rigidly attached to a trimeric coiled coil that prepositions it to bind three KASH peptides. The peptides bind in three deep and expansive grooves formed between adjacent SUN domains, effectively acting as molecular glue. In addition, a disulfide between conserved cysteines on SUN and KASH covalently links both proteins. The structure provides the basis of LINC complex formation and suggests a model for how LINC complexes might arrange into higher-order clusters to enhance force-coupling.

Sosa, Brian A.; Rothballer, Andrea; Kutay, Ulrike; Schwartz, Thomas U. (MIT); (ETH Zurich)

2012-08-31T23:59:59.000Z

20

Structure of Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain  

NLE Websites -- All DOE Office Websites (Extended Search)

Human Toll-like Receptor Human Toll-like Receptor 3 (TLR3) Ligand-binding Domain Jungwoo Choe1, Matthew S. Kelker1, and Ian A. Wilson1 1Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 Figure 1. Overall structure of human TLR3 ECD. The N-terminal region is colored blue, the 23 canonical LRRs are in yellow and the C-terminal region is in pink. N-linked sugars that are observed in the electron density maps are shown in ball-and-stick. (From Choe et al. 2005). Innate immunity is the front line host defense that acts within minutes of infection to counter invasion by microorganisms. Members of the Toll-like receptor (TLR) family recognize conserved pathogen-associated molecular

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


21

Reversibly Bound Chloride in the Atrial Natriuretic Peptide Receptor Hormone Binding Domain: Possible Allosteric Regulation and a Conserved Structural Motif for the Chloride-binding Site  

SciTech Connect

The binding of atrial natriuretic peptide (ANP) to its receptor requires chloride, and it is chloride concentration dependent. The extracellular domain (ECD) of the ANP receptor (ANPR) contains a chloride near the ANP-binding site, suggesting a possible regulatory role. The bound chloride, however, is completely buried in the polypeptide fold, and its functional role has remained unclear. Here, we have confirmed that chloride is necessary for ANP binding to the recombinant ECD or the full-length ANPR expressed in CHO cells. ECD without chloride (ECD(-)) did not bind ANP. Its binding activity was fully restored by bromide or chloride addition. A new X-ray structure of the bromide-bound ECD is essentially identical to that of the chloride-bound ECD. Furthermore, bromide atoms are localized at the same positions as chloride atoms both in the apo and in the ANP-bound structures, indicating exchangeable and reversible halide binding. Far-UV CD and thermal unfolding data show that ECD(-) largely retains the native structure. Sedimentation equilibrium in the absence of chloride shows that ECD(-) forms a strongly associated dimer, possibly preventing the structural rearrangement of the two monomers that is necessary for ANP binding. The primary and tertiary structures of the chloride-binding site in ANPR are highly conserved among receptor-guanylate cyclases and metabotropic glutamate receptors. The chloride-dependent ANP binding, reversible chloride binding, and the highly conserved chloride-binding site motif suggest a regulatory role for the receptor bound chloride. Chloride-dependent regulation of ANPR may operate in the kidney, modulating ANP-induced natriuresis.

Ogawa, H.; Qiu, Y; Philo, J; Arakawa, T; Ogata, C; Misono, K

2010-01-01T23:59:59.000Z

22

Structural Insights into the Functional Role of the Hcn Sub-domain of the Receptor-Binding Domain of the Botulinum Neurotoxin Mosaic Serotype C/D  

SciTech Connect

Botulinum neurotoxin (BoNT), the causative agent of the deadly neuroparalytic disease botulism, is the most poisonous protein known for humans. Produced by different strains of the anaerobic bacterium Clostridium botulinum, BoNT effects cellular intoxication via a multistep mechanism executed by the three modules of the activated protein. Endocytosis, the first step of cellular intoxication, is triggered by the ~50 kDa, heavy-chain receptor-binding module (HCR) that is specific for a ganglioside and a protein receptor on neuronal cell surfaces. This dual receptor recognition mechanism between BoNT and the host cells membrane is well documented and occurs via specific intermolecular interactions with the C-terminal sub-domain, Hcc, of BoNT-HCR. The N-terminal sub-domain of BoNT-HCR, Hcn, comprises ~50% of BoNT-HCR and adopts a B-sheet jelly roll fold. While suspected in assisting cell surface recognition, no unambiguous function for the Hcn sub-domain in BoNT has been indentified. To obtain insights into the potential function of the Hcn sub-domain in BoNT, the first crystal structure of a BoNT with an organic ligand bound to the Hcn sub-domain has been obtained. Here, we describe the crystal structure of BoNT/CD-HCR determined at 1.70 resolution with a tetraethylene glycol (PG4) molecule bound in an hydrophobic cleft between B-strands in the B-sheet jelly fold roll of the Hcn sub-domain. The molecule is completely engulfed in the cleft, making numerous hydrophobic (Y932, S959, W966, and D1042) and hydrophilic (S935, W977, L979, N1013, and I1066) contacts with the proteins side chain and backbone that may mimic in vivo interactions with the phospholipid membranes on neuronal cell surfaces. A sulfate ion was also observed bound to residues T1176, D1177, K1196, and R1243 in the Hcc sub-domain of BoNT/CD-HCR. In the crystal structure of a similar protein, BoNT/D-HCR, a sialic acid

Zhang, Yanfeng; Gardberg, Anna; Edwards, Tom E.; Sankaran, Banumathi; Robinson, Howard; Varnum, Susan M.; Buchko, Garry W.

2013-07-01T23:59:59.000Z

23

Embargoed Deletion  

NLE Websites -- All DOE Office Websites (Extended Search)

PNAS proof PNAS proof Embargoed Deletion of Cel48S Q:1 from Clostridium thermocellum ; 2 Daniel G. Olson a,b,c , Shital A. Tripathi a,c , Richard J. Giannone c,d , Jonathan Lo b,c , Nicky C. Caiazza a,c , David A. Hogsett a,c , Robert Hettich c,d , Adam M. Guss b,c , Genia Dubrovsky b,c , and Lee R. Lynd a,b,c,e,1 a Mascoma Corporation, NH 03766; b Thayer School of Engineering and e Department of Biological Sciences, Dartmouth College, NH 03755; and c BioEnergy Science Center, d Oak Ridge National Laboratory, TN 37830 Q:3 Edited* by Lonnie O'Neal Ingram, University of Florida, Gainesville, FL, and approved August 16, 2010 (received for review April 9, 2010) Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cel- lulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, S S , and S8), the most abundant cellulosome

24

Chain-specific Protein Kinase C Activity by a Direct Interaction: Identification of the 143-3 Binding Domain  

E-Print Network (OSTI)

Myosin II heavy chain (MHC) specific protein kinase C (MHC-PKC), isolated from Dictyostelium discoideum, regulates myosin II assembly and localization in response to the chemoattractant cyclic AMP. Immunoprecipitation of MHC-PKC revealed that it resides as a complex with several proteins. We show herein that one of these proteins is a homologue of the 143-3 protein (Dd143-3). This protein has recently been implicated in the regulation of intracellular signaling pathways via its interaction with several signaling proteins, such as PKC and Raf-1 kinase. We demonstrate that the mammalian 143-3 ? isoform inhibits the MHC-PKC activity in vitro and that this inhibition is carried out by a direct interaction between the two proteins. Furthermore, we found that the cytosolic MHC-PKC, which is inactive, formed a complex with Dd143-3 in the cytosol in a cyclic AMP-dependent manner, whereas the membrane-bound active MHC-PKC was not found in a complex with Dd143-3. This suggests that Dd143-3 inhibits the MHC-PKC in vivo. We further show that MHC-PKC binds Dd143-3 as well as 143-3? through its C1 domain, and the interaction between these two proteins does not involve a peptide containing phosphoserine as was found for Raf-1 kinase. Our experiments thus show an in vivo function for a member of the 143-3 family and demonstrate that MHC-PKC interacts directly with Dd143-3 and 143-3 ? through its C1 domain both in vitro and in vivo, resulting in the inhibition of the kinase.

Meirav Matto-yelin; Alastair Aitken; Shoshana Ravid; James A. Spudich

1997-01-01T23:59:59.000Z

25

Rotations of the 2B Sub-domain of E. coli UvrD Helicase/Translocase Coupled to Nucleotide and DNA Binding  

Science Conference Proceedings (OSTI)

Escherichia coli UvrD is a superfamily 1 DNA helicase and single-stranded DNA (ssDNA) translocase that functions in DNA repair and plasmid replication and as an anti-recombinase by removing RecA protein from ssDNA. UvrD couples ATP binding and hydrolysis to unwind double-stranded DNA and translocate along ssDNA with 3'-to-5' directionality. Although a UvrD monomer is able to translocate along ssDNA rapidly and processively, DNA helicase activity in vitro requires a minimum of a UvrD dimer. Previous crystal structures of UvrD bound to a ssDNA/duplex DNA junction show that its 2B sub-domain exists in a 'closed' state and interacts with the duplex DNA. Here, we report a crystal structure of an apo form of UvrD in which the 2B sub-domain is in an 'open' state that differs by an {approx} 160{sup o} rotation of the 2B sub-domain. To study the rotational conformational states of the 2B sub-domain in various ligation states, we constructed a series of double-cysteine UvrD mutants and labeled them with fluorophores such that rotation of the 2B sub-domain results in changes in fluorescence resonance energy transfer. These studies show that the open and closed forms can interconvert in solution, with low salt favoring the closed conformation and high salt favoring the open conformation in the absence of DNA. Binding of UvrD to DNA and ATP binding and hydrolysis also affect the rotational conformational state of the 2B sub-domain, suggesting that 2B sub-domain rotation is coupled to the function of this nucleic acid motor enzyme.

Jia, Haifeng; Korolev, Sergey; Niedziela-Majka, Anita; Maluf, Nasib K.; Gauss, George H.; Myong, Sua; Ha, Taekjip; Waksman, Gabriel; Lohman, Timothy M. (UIUC); (St. Louis-MED); (WU-MED); (UCL)

2011-11-02T23:59:59.000Z

26

Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor  

Science Conference Proceedings (OSTI)

We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe (UPENN)

2012-05-08T23:59:59.000Z

27

Crystallographic Analysis of Murine Constitutive Androstane Receptor Ligand-Binding Domain Complexed with 5[alpha]-androst-16-en-3[alpha]-ol  

Science Conference Proceedings (OSTI)

The constitutive androstane receptor (CAR) is a member of the nuclear receptor superfamily. In contrast to classical nuclear receptors, which possess small-molecule ligand-inducible activity, CAR exhibits constitutive transcriptional activity in the apparent absence of ligand. CAR is among the most important transcription factors; it coordinately regulates the expression of microsomal cytochrome P450 genes and other drug-metabolizing enzymes. The murine CAR ligand-binding domain (LBD) was coexpressed with the steroid receptor coactivator protein (SRC-1) receptor-interacting domain (RID) in Escherichia coli. The mCAR LBD subunit was purified away from SRC-1 by affinity, anion-exchange and size-exclusion chromatography, crystallized with androstenol and the structure of the complex determined by molecular replacement.

Vincent, J.; Shan, L.; Fan, M.; Brunzelle, J.S.; Forman, B.M.; Fernandez, E.J. (Tennessee-K); (NWU); (CHNMC)

2010-03-08T23:59:59.000Z

28

HH Domain of Alzheimers Disease Ab Provides Structural Basis for Neuronal Binding in PC12 and Mouse Cortical/Hippocampal Neurons  

E-Print Network (OSTI)

A key question in understanding AD is whether extracellular Ab deposition of parenchymal amyloid plaques or intraneuronal Ab accumulation initiates the AD process. Amyloid precursor protein (APP) is endocytosed from the cell surface into endosomes where it is cleaved to produce soluble Ab which is then released into the brain interstitial fluid. Intraneuronal Ab accumulation is hypothesized to predominate from the neuronal uptake of this soluble extracellular Ab rather than from ER/Golgi processing of APP. We demonstrate that substitution of the two adjacent histidine residues of Ab40 results in a significant decrease in its binding with PC12 cells and mouse cortical/hippocampal neurons. These substitutions also result in a dramatic enhancement of both thioflavin-T positive fibril formation and binding to preformed Ab fibrils while maintaining its plaque-binding ability in AD transgenic mice. Hence, alteration of the histidine domain of Ab prevented neuronal binding and drove Ab to enhanced fibril formation and subsequent amyloid plaque deposition- a potential mechanism for removing toxic species of Ab. Substitution or even masking of these Ab histidine residues might provide a new therapeutic direction for minimizing neuronal uptake and subsequent neuronal degeneration and

Joseph F. Poduslo; Emily J. Gilles; Muthu Ramakrishnan; Kyle G. Howell; Thomas M. Wengenack; Geoffry L. Curran; Karunya K. K

2010-01-01T23:59:59.000Z

29

Improving the fidelity of deletion  

Science Conference Proceedings (OSTI)

In this work we study the quantum deletion machine with two transformers, and show that the deletion machine with a single transformer performs better than the deletion machine with more than two transformers. We also observe that the fidelity of deletion depends on the blank state used in the deleter, and so for different blank states the fidelity is different. Further, we study the Pati-Braunsein deleter with transformer.

Adhikari, Satyabrata; Choudhury, B. S. [Department of Mathematics, Bengal Engineering and Science University, Howrah-711103, West Bengal (India)

2006-05-15T23:59:59.000Z

30

[3H]Azidodantrolene photoaffinity labeling, synthetic domain peptides and monoclonal antibody reactivity identify the dantrolene binding sequence on RyR1  

DOE Green Energy (OSTI)

Dantrolene is a drug that suppresses intracellular Ca2+ release from sarcoplasmic reticulum in normal skeletal muscle and is used as a therapeutic agent in individuals susceptible to malignant hyperthermia. Though its precise mechanism of action has not been elucidated, we have identified the N-terminal region (amino acids 1-1400) of the skeletal muscle isoform of the ryanodine receptor (RyR1), the primary Ca2+ release channel in sarcoplasmic reticulum, as a molecular target for dantrolene using the photoaffinity analog [3H]azidodantrolene(1). Here, we demonstrate that heterologously expressed RyR1 retains its capacity to be specifically labeled with [3H]azidodantrolene,indicating that muscle specific factors are not required for this ligand-receptor interaction. Synthetic domain peptides of RyR1, previously shown to affect RyR1 function in vitro and in vivo, were exploited as potential drug binding site mimics and used in photoaffinity labeling experiments. Only DP1 and DP1-2, peptide s containing the amino acid sequence corresponding to RyR1 residues 590-609, were specifically labeled by [3H]azidodantrolene. A monoclonal anti-RyR1 antibody which recognizes RyR1 and its 1400 amino acid N-terminal fragment, recognizes DP1 and DP1-2 in both Western blots and immunoprecipitation assays, and specifically inhibits [3H]azidodantrolene photolabeling of RyR1 and its N-terminal fragment in sarcoplasmic reticulum. Our results indicate that synthetic domain peptides can mimic a native, ligand binding conformation in vitro, and that the dantrolene binding site and the epitope for the monoclonal antibody on RyR1 are equivalent and composed of amino-acids 590-609.

Paul-Pletzer, Kalanethee; Yamamoto, Takeshi; Bhat, Manju B.; Ma, Jianjie; Ikemoto, Noriaki; Jimenez, Leslie S.; Morimoto, Hiromi; Williams, Philip G.; Parness, Jerome

2002-06-14T23:59:59.000Z

31

High-level expression, purification, crystallization and preliminary X-ray crystallographic studies of the receptor binding domain of botulinum neurotoxin serotype D  

SciTech Connect

Botulinum neurotoxins (BoNTs) are highly toxic proteins for humans and can cause neuroparalytic disease botulism. Due to the limitations of production and manipulation of holoenzymes, expressing non-toxic heavy chain receptor binding domains (HCR) has become a common strategy for vaccine and antibody development. Meanwhile, large quantities and highly purified soluble proteins are required for research areas such as antibody maturation and structural biology. We present high level expression and purification of the BoNT serotype D HCR in E. coli using a codon-optimized cDNA. By varying expression conditions, especially at low temperature, the protein was expressed at a high level with high solubility. About 150-200 mg protein was purified to >90% purity from 1 L cell culture. The recombinant D_HCR was crystallized and the crystals diffracted to 1.65 resolution. The crystals belong to space group P212121 with unit cell dimensions a = 60.8 , b = 89.7 , c = 93.9 . Preliminary crystallographic data analysis revealed one molecule in asymmetric unit.

Zhang, Yanfeng; Gao, Xiaoli; Qin, Lin; Buchko, Garry W.; Robinson, Howard; Varnum, Susan M.

2010-12-01T23:59:59.000Z

32

Brief Communication: Design of multiplex PCR primers using heuristic algorithm for sequential deletion applications  

Science Conference Proceedings (OSTI)

The sequential deletion method is commonly applied to locate the functional domain of a protein. Unfortunately, manually designing primers for multiplex polymerase chain reaction (PCR) is a labor-intensive task. In order to speed up the experimental ... Keywords: Multiplex polymerase chain reaction (PCR), N-terminal truncated mutants, Polyacrylamide gel electrophoresis (PAGE), Sequential deletion

Yung-Fu Chen; Rung-Ching Chen; Yung-Kuan Chan; Ren-Hao Pan; You-Cheng Hseu; Elong Lin

2009-04-01T23:59:59.000Z

33

Yet Another Sanitizable and Deletable Signatures  

Science Conference Proceedings (OSTI)

In 2008, Izu et al. introduced a concept of the sanitizable and deletable signature as a combination of the sanitizable signature and the deletable signature in which the partial information (e.g. privacy information) can be sanitized or deleted with ... Keywords: Digital signature, sanitizable signature, deletable signature, sanitizable, deletable signature

Tetsuya Izu; Masami Izumi; Noboru Kunihiro; Kazuo Ohta

2011-03-01T23:59:59.000Z

34

Cdc73 subunit of the Paf1 complex contains a C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin  

Science Conference Proceedings (OSTI)

The conserved Paf1 complex localizes to the coding regions of genes and facilitates multiple processes during transcription elongation, including the regulation of histone modifications. However, the mechanisms that govern Paf1 complex recruitment to active genes are undefined. Here we describe a previously unrecognized domain within the Cdc73 subunit of the Paf1 complex, the Cdc73 C-domain, and demonstrate its importance for Paf1 complex occupancy on transcribed chromatin. Deletion of the C-domain causes phenotypes associated with elongation defects without an apparent loss of complex integrity. Simultaneous mutation of the C-domain and another subunit of the Paf1 complex, Rtf1, causes enhanced mutant phenotypes and loss of histone H3 lysine 36 trimethylation. The crystal structure of the C-domain reveals unexpected similarity to the Ras family of small GTPases. Instead of a deep nucleotide-binding pocket, the C-domain contains a large but comparatively flat surface of highly conserved residues, devoid of ligand. Deletion of the C-domain results in reduced chromatin association for multiple Paf1 complex subunits. We conclude that the Cdc73 C-domain probably constitutes a protein interaction surface that functions with Rtf1 in coupling the Paf1 complex to the RNA polymerase II elongation machinery.

Amrich C. G.; Heroux A.; Davis, C. P.; Rogal, W. P.; Shirra, M. K.; Gardner, R. G.; Arndt, K. M.; VanDemark, A. P.

2012-03-30T23:59:59.000Z

35

Help:Deleting pages | Open Energy Information  

Open Energy Info (EERE)

pages pages Jump to: navigation, search See Category:Proposed deletion for the listing of all articles currently proposed for deletion. Proposed deletion is the way to suggest that an article is a candidate for uncontroversial deletion. If nobody objects, the article is deleted after seven days. An article may not be proposed for deletion ("PRODed") if it has been PRODed before. Proposed deletion is only applicable to mainspace articles, lists, and disambiguation pages; it cannot be used with redirects, userspace pages, templates, categories, or pages in any other namespace. There are three steps to the PROD process An article or disambiguation page is nominated when an editor carefully reviews the article and inserts the {{subst:proposed deletion}} tag by placing {{subst:proposed deletion}} on the page. This lists the

36

Help:Sysop deleting and undeleting | Open Energy Information  

Open Energy Info (EERE)

Sysop deleting and undeleting Sysop deleting and undeleting Jump to: navigation, search Deleting a page is a straightforward operation for anyone with sysop permissions. Users without such permissions can still remove text from wiki pages, or propose/request that a page should be deleted. See Help:Deleting a page. Contents 1 Before deleting 2 Use the 'delete' tab 3 Undeleting 4 Configuring deletion reasons Before deleting Sysops should also be aware of the general advice given on Help:Deleting a page (In particular, note that there are many situations where a deleting is too drastic. Often a redirect is more appropriate for example) Before deleting you could perform various checks: Use the "What links here" tool. This gives an indication as to how important a page is, and what subjects it relates to. Perhaps the page is

37

An environment-mediated quantum deleter  

E-Print Network (OSTI)

Environment-induced decoherence presents a great challenge to realizing a quantum computer. We point out the somewhat surprising fact that decoherence can be useful, indeed necessary, for practical quantum computation, in particular, for the effective erasure of quantum memory in order to initialize the state of the quantum computer. The essential point behind the deleter is that the environment, by means of a dissipative interaction, furnishes a contractive map towards a pure state. We present a specific example of an amplitude damping channel provided by a two-level system's interaction with its environment in the weak Born-Markov approximation. This is contrasted with a purely dephasing, non-dissipative channel provided by a two-level system's interaction with its environment by means of a quantum nondemolition interaction. We point out that currently used state preparation techniques, for example using optical pumping, essentially perform as quantum deleters.

R. Srikanth; Subhashish Banerjee

2006-11-27T23:59:59.000Z

38

Synthetic heparin-binding factor analogs  

DOE Patents (OSTI)

The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

Pena, Louis A. (Poquott, NY); Zamora, Paul O. (Gaithersburg, MD); Lin, Xinhua (Plainview, NY); Glass, John D. (Shoreham, NY)

2010-04-20T23:59:59.000Z

39

Eminent Domain Law (Iowa)  

Energy.gov (U.S. Department of Energy (DOE))

These regulations confer the power of eminent domain and describe procedures for exercising eminent domain in Iowa.

40

Deletion of ultraconserved elements yields viable mice  

SciTech Connect

Ultraconserved elements have been suggested to retainextended perfect sequence identity between the human, mouse, and ratgenomes due to essential functional properties. To investigate thenecessities of these elements in vivo, we removed four non-codingultraconserved elements (ranging in length from 222 to 731 base pairs)from the mouse genome. To maximize the likelihood of observing aphenotype, we chose to delete elements that function as enhancers in amouse transgenic assay and that are near genes that exhibit markedphenotypes both when completely inactivated in the mouse as well as whentheir expression is altered due to other genomic modifications.Remarkably, all four resulting lines of mice lacking these ultraconservedelements were viable and fertile, and failed to reveal any criticalabnormalities when assayed for a variety of phenotypes including growth,longevity, pathology and metabolism. In addition more targeted screens,informed by the abnormalities observed in mice where genes in proximityto the investigated elements had been altered, also failed to revealnotable abnormalities. These results, while not inclusive of all thepossible phenotypic impact of the deleted sequences, indicate thatextreme sequence constraint does not necessarily reflect crucialfunctions required for viability.

Ahituv, Nadav; Zhu, Yiwen; Visel, Axel; Holt, Amy; Afzal, Veena; Pennacchio, Len A.; Rubin, Edward M.

2007-07-15T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


41

Deletion discussions in Wikipedia: decision factors and outcomes  

Science Conference Proceedings (OSTI)

Deletion of articles is a common process in Wikipedia, in order to ensure the overall quality of the encyclopedia. Yet, there is a need to better understand the procedures in order to promote the best decisions without unnecessary community work. In ... Keywords: Wikipedia, articles for deletion, collaboration and conflict, decision-making, factors analysis, novices, online argumentation, values

Jodi Schneider; Alexandre Passant; Stefan Decker

2012-08-01T23:59:59.000Z

42

Flag rates for deletion? | OpenEI Community  

Open Energy Info (EERE)

Flag rates for deletion? Flag rates for deletion? Home > Groups > Utility Rate I found some "rates" that don't belong; they are one-time connection fees instead of rates (e.g. with a $2,500 connection fee as a "fixed monthly charge"). Is there some way to flag rates for suggested deletion? Submitted by Ewilson on 22 June, 2012 - 11:27 1 answer Points: 1 Hi Ewilson, Thank you for pointing this out! We are currently working on a way for users to propose deletion: http://en.openei.org/wiki/Help:Deleting_pages. Let me know if you have any questions! Wzeng on 12 July, 2012 - 08:19 Groups Menu You must login in order to post into this group. Recent content There is currently no way to s... ranking of utilities by demand charge? FYI, OpenEI now accommodates t... Very useful information. Thank...

43

Help:Deleting a page | Open Energy Information  

Open Energy Info (EERE)

page page Jump to: navigation, search Contents 1 When not to delete a page 1.1 Proposing changes 1.2 Unlinking a page 2 Deletion itself 3 See also When not to delete a page Typically you would delete a page if the contents are entirely inappropriate and do not match the purposes of the Wiki. In other situations, you would take a less extreme course of action, for example: The page should have a different title -- See Help:Moving a page The contents should have been placed on a different page -- Add the contents to the other page, and then supply a redirect. See Help:Redirects The contents are already on a different page -- Delete the duplicate content and leave a redirect. That way, the page title, which made sense to somebody, will helpfully redirect to the information. See Help:Redirects

44

Random Context and Semi-Conditional Insertion-Deletion Systems  

E-Print Network (OSTI)

In this article we introduce the operations of insertion and deletion working in a random-context and semi-conditional manner. We show that the conditional use of rules strictly increase the computational power. In the case of semi-conditional insertion-deletion systems context-free insertion and deletion rules of one symbol are sufficient to get the computational completeness. In the random context case our results expose an asymmetry between the computational power of insertion and deletion rules: systems of size $(2,0,0; 1,1,0)$ are computationally complete, while systems of size $(1,1,0;2,0,0)$ (and more generally of size $(1,1,0;p,1,1)$) are not. This is particularly interesting because other control mechanisms like graph-control or matrix control used together with insertion-deletion systems do not present such asymmetry.

Ivanov, Sergiu

2011-01-01T23:59:59.000Z

45

Ectrodactyly and proximal/intermediate interstitial deletion 7q  

Science Conference Proceedings (OSTI)

We report on an individual with severe mental retardation, seizures, microcephaly, unusual face, scoliosis, and cleft feet and cleft right hand. The chromosomal study showed a proximal interstitial deletion 7q (q11.23q22). From our review of the literature, 11 patients have been reported with ectrodactyly (split hand/split foot malformation) and proximal/intermediate interstitial deletions or rearrangements of 7q. The critical segment for ectrodactyly seems to be located between 7q21.2 and 7q22.1. This malformation is present in 41% of the patients whose deletion involves the critical segment. 37 refs., 3 figs., 1 tab.

McElveen, C.; Carvajal, M.V.; Moscatello, D. [Louisiana State Univ. Medical Center, New Orleans, LA (United States)] [and others

1995-03-13T23:59:59.000Z

46

Making abstract domains condensing  

Science Conference Proceedings (OSTI)

In this article, we show that reversible analyses of logic languages by abstract interpretation can be performed without loss of precision by systematically refining abstract domains. This is obtained by adding to the abstract domain the minimal amount ... Keywords: Abstract domain, abstract interpretation, completeness, condensation, linear logic, logic program analysis

Roberto Giacobazzi; Francesco Ranzato; Francesca Scozzari

2005-01-01T23:59:59.000Z

47

Stochastic Chemical Reactions in Micro-domains  

E-Print Network (OSTI)

Traditional chemical kinetics may be inappropriate to describe chemical reactions in micro-domains involving only a small number of substrate and reactant molecules. Starting with the stochastic dynamics of the molecules, we derive a master-diffusion equation for the joint probability density of a mobile reactant and the number of bound substrate in a confined domain. We use the equation to calculate the fluctuations in the number of bound substrate molecules as a function of initial reactant distribution. A second model is presented based on a Markov description of the binding and unbinding and on the mean first passage time of a molecule to a small portion of the boundary. These models can be used for the description of noise due to gating of ionic channels by random binding and unbinding of ligands in biological sensor cells, such as olfactory cilia, photo-receptors, hair cells in the cochlea.

D. Holcman; Z. Schuss

2004-12-25T23:59:59.000Z

48

Quantum Fusion of Domain Walls with Fluxes  

E-Print Network (OSTI)

We study how fluxes on the domain wall world volume modify quantum fusion of two distant parallel domain walls into a composite wall. The elementary wall fluxes can be separated into parallel and antiparallel components. The parallel component affects neither the binding energy nor the process of quantum merger. The antiparallel fluxes, instead, increase the binding energy and, against naive expectations, suppress quantum fusion. In the small flux limit we explicitly find the bounce solution and the fusion rate as a function of the flux. We argue that at large (antiparallel) fluxes there exists a critical value of the flux (versus the difference in the wall tensions), which switches off quantum fusion altogether. This phenomenon of flux-related wall stabilization is rather peculiar: it is unrelated to any conserved quantity. Our consideration of the flux-related all stabilization is based on substantiated arguments that fall short of complete proof.

S. Bolognesi; M. Shifman; M. B. Voloshin

2009-07-20T23:59:59.000Z

49

Domain analysis for estrogen receptor/Sp1-mediated transactivation and detection of estrogen receptor/Sp1 protein interactions in living cells  

E-Print Network (OSTI)

Estrogen Receptor ? (ER?)/Sp1 activation of GC-rich gene promoters in breast cancer cells is dependent, in part, on the activation function 1 (AF1) of ER?. This study investigates contributions of the DNA binding domain (C) and AF2 (DEF) regions of ER? on activation of ER?/Sp1. 17Beta-estradiol (E2) and the antiestrogens 4-hydroxytamoxifen and ICI 182,780 induced reporter gene activity in MCF-7 and MDA-MB-231 cells cotransfected with human or mouse ER? (hER? or MOR), but not ER? and GC-rich constructs containing three tandem Sp1 binding sites (pSp13) or other E2-responsive GC-rich promoters. Estrogen and antiestrogen activation of hER?/Sp1 was dependent on overlapping and different regions of the C, D, E, and F domains of ER?. Antiestrogen-induced activation of hER?/Sp1 was lost using hER? mutants deleted in zinc finger 1 (amino acids (aa) 185-205), zinc finger 2 (aa 218-245), and the hinge/helix 1 (aa 265-330) domains. In contrast with antiestrogens, E2-dependent activation of hER?/Sp1 required the C-terminal F domain (aa 579-595), which contains a ?-strand structural motif. Moreover, in peptide competition experiments overexpression of NR-box peptides inhibits E2-induced luciferase activity of pERE3, which contains three tandem repeats of consensus ERE sites, whereas E2-induced hER?/Sp1 action was not inhibited by NR-box peptide expression. In contrast, overexpression of a C-terminal (aa 575-595) F domain peptide specifically blocked E2-dependent activation of hER?/Sp1, but not on activation of pERE3, suggesting that F domain interactions with nuclear cofactors are specifically required for ER?/Sp1 action. Furthermore, direct physical interactions between hER? and Sp1 protein in vivo have been investigated by using Fluorescence Resonance Energy Transfer (FRET) microscopy and image analysis. Consistent with results from transient transfection assay, E2, 4OHT, and ICI enhanced hER?/Sp1 interactions in living cells and these interactions were also confirmed by coimmunoprecipitation. In addition, endogenous hER?/Sp1 action was evaluated by using si RNA for Sp1 and a significant decrease in ligand-induced hER?/Sp1 action was observed after decreased Sp1 expression.

Kim, KyoungHyun

2004-08-01T23:59:59.000Z

50

Nested Domain Defects  

E-Print Network (OSTI)

An example of a supersymmetric model involving two interacting chiral superfields is presented here which allows for solutions describing string-like ``domain ribbon'' defects embedded within a domain wall. It is energetically favorable for the fermions within the wall to populate the domain ribbons, and an explicit solution is found for the fermion zero modes. The Fermi gas within ribbons can allow them to stabilize in the form of small loops.

J. R. Morris

1997-07-30T23:59:59.000Z

51

Tweets are forever: a large-scale quantitative analysis of deleted tweets  

Science Conference Proceedings (OSTI)

This paper describes an empirical study of 1.6M deleted tweets collected over a continuous one-week period from a set of 292K Twitter users. We examine several aggregate properties of deleted tweets, including their connections to other tweets (e.g., ... Keywords: deletion, privacy, social networks

Hazim Almuhimedi; Shomir Wilson; Bin Liu; Norman Sadeh; Alessandro Acquisti

2013-02-01T23:59:59.000Z

52

Deletion (11)(q14.1q21)  

Science Conference Proceedings (OSTI)

The authors report on a 4-year-old girl with moderate development delay, horseshoe kidney, bilateral duplication of the ureters with right upper pole obstruction, hydronephrosis and nonfunction, and subsequent Wilms tumor of the right lower pole. She had an interstitial deletion of the long arm of chromosome 11 involving the region 11(q14.1q21). 22 refs., 2 figs., 1 tab.

Stratton, R.F.; Lazarus, K.H.; Ritchie, E.J.L. [Southwest Texas Methodist Hospital, San Antonio, TX (United States); Bell, A.M. [Nichols Institute, Los Angeles, CA (United States)

1994-02-01T23:59:59.000Z

53

Domain bias in web search  

Science Conference Proceedings (OSTI)

This paper uncovers a new phenomenon in web search that we call domain bias --- a user's propensity to believe that a page is more relevant just because it comes from a particular domain. We provide evidence of the existence of domain bias in click activity ... Keywords: domain bias, user behavior, web search

Samuel Ieong; Nina Mishra; Eldar Sadikov; Li Zhang

2012-02-01T23:59:59.000Z

54

Simplified parallel domain traversal  

Science Conference Proceedings (OSTI)

Many data-intensive scientific analysis techniques require global domain traversal, which over the years has been a bottleneck for efficient parallelization across distributed-memory architectures. Inspired by MapReduce and other simplified parallel ... Keywords: atmospheric ensemble analysis, data-intensive analysis, parallel particle tracing, parallel processing

Wesley Kendall; Jingyuan Wang; Melissa Allen; Tom Peterka; Jian Huang; David Erickson

2011-11-01T23:59:59.000Z

55

Data Domain to Model Domain Conversion Package | Argonne National  

NLE Websites -- All DOE Office Websites (Extended Search)

Data Domain to Model Domain Conversion Package Data Domain to Model Domain Conversion Package Data Domain to Model Domain Conversion Package The Data Domain to Model Domain Conversion Package project will develop methods and implement a novel approach for generating data ensembles by using the latest available statistical modeling tools and knowledge of relevant physical and chemical process to develop climatologically aware methods for processing ACRF and other spatially sparse data sets. Data collected at the Atmospheric Radiation Measurement Program Climate Research Facility (ACRF) sites are employed mainly in column radiation models, to validate the models and develop new parameterizations. Currently, no single methodology can be used with data collected at the spatial scale of the ACRF sites or from specific AmeriFlux locations, to

56

The trace partitioning abstract domain  

Science Conference Proceedings (OSTI)

In order to achieve better precision of abstract interpretation-based static analysis, we introduce a new generic abstract domain, the trace partitioning abstract domain. We develop a theoretical framework allowing a wide range of instantiations of the ...

Xavier Rival; Laurent Mauborgne

2007-08-01T23:59:59.000Z

57

Product Binding Varies Dramatically between Processive and Nonprocessive Cellulase Enzymes  

DOE Green Energy (OSTI)

Cellulases hydrolyze {beta}-1,4 glycosidic linkages in cellulose, which are among the most prevalent and stable bonds in Nature. Cellulases comprise many glycoside hydrolase families and exist as processive or nonprocessive enzymes. Product inhibition negatively impacts cellulase action, but experimental measurements of product-binding constants vary significantly, and there is little consensus on the importance of this phenomenon. To provide molecular level insights into cellulase product inhibition, we examine the impact of product binding on processive and nonprocessive cellulases by calculating the binding free energy of cellobiose to the product sites of catalytic domains of processive and nonprocessive enzymes from glycoside hydrolase families 6 and 7. The results suggest that cellobiose binds to processive cellulases much more strongly than nonprocessive cellulases. We also predict that the presence of a cellodextrin bound in the reactant site of the catalytic domain, which is present during enzymatic catalysis, has no effect on product binding in nonprocessive cellulases, whereas it significantly increases product binding to processive cellulases. This difference in product binding correlates with hydrogen bonding between the substrate-side ligand and the cellobiose product in processive cellulase tunnels and the additional stabilization from the longer tunnel-forming loops. The hydrogen bonds between the substrate- and product-side ligands are disrupted by water in nonprocessive cellulase clefts, and the lack of long tunnel-forming loops results in lower affinity of the product ligand. These findings provide new insights into the large discrepancies reported for binding constants for cellulases and suggest that product inhibition will vary significantly based on the amount of productive binding for processive cellulases on cellulose.

Bu, L.; Nimlos, M. R.; Shirts, M. R.; Stahlberg, J.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-07-13T23:59:59.000Z

58

Structural and functional analyses of minimal phosphopeptides targeting the polo-box domain of polo-like kinase 1  

E-Print Network (OSTI)

Polo-like kinase-1 (Plk1) has a pivotal role in cell proliferation and is considered a potential target for anticancer therapy. The noncatalytic polo-box domain (PBD) of Plk1 forms a phosphoepitope binding module for ...

Yun, Sang-Moon

59

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides a system for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, this system can be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Carolyn (Albany, CA)

1999-10-05T23:59:59.000Z

60

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

1999-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


61

Inhibition of selectin binding  

DOE Patents (OSTI)

This invention provides compositions for inhibiting the binding between two cells, one expressing P- or L-selectin on the surface and the other expressing the corresponding ligand. A covalently crosslinked lipid composition is prepared having saccharides and acidic group on separate lipids. The composition is then interposed between the cells so as to inhibit binding. Inhibition can be achieved at an effective oligosaccharide concentration as low as 10.sup.6 fold below that of the free saccharide. Since selectins are involved in recruiting cells to sites of injury, these composition scan be used to palliate certain inflammatory and immunological conditions.

Nagy, Jon O. (Rodeo, CA); Spevak, Wayne R. (Albany, CA); Dasgupta, Falguni (New Delhi, IN); Bertozzi, Caroline (Albany, CA)

2001-10-09T23:59:59.000Z

62

Radon Binding to Water-Soluble Cryptophane  

Science Conference Proceedings (OSTI)

Radon Binding to Water-Soluble Cryptophane. Summary: Collaboration on investigating the thermodynamics of radon binding ...

2012-06-27T23:59:59.000Z

63

Deletion of the Cel48S cellulase from Clostridium thermocellum  

Science Conference Proceedings (OSTI)

Clostridium thermocellum is a thermophilic anaerobic bacterium that rapidly solubilizes cellulose with the aid of a multienzyme cellulosome complex. Creation of knockout mutants for Cel48S (also known as CelS, SS, and S8), the most abundant cellulosome subunit, was undertaken to gain insight into its role in enzymatic and microbial cellulose solubilization. Cultures of the Cel48S deletion mutant (S mutant) were able to completely solubilize 10 g/L crystalline cellulose. The cellulose hydrolysis rate of the S mutant strain was 60% lower than the parent strain, with the S mutant strain also exhibiting a 40% reduction in cell yield. The cellulosome produced by the S mutant strain was purified by affinity digestion, characterized enzymatically, and found to have a 35% lower specific activity on Avicel. The composition of the purified cellulosome was analyzed by tandem mass spectrometry with APEX quantification and no significant changes in abundance were observed in any of the major (>1% of cellulosomal protein) enzymatic subunits. Although most cellulolytic bacteria have one family 48 cellulase, C. thermocellum has two, Cel48S and Cel48Y. Cellulose solubilization by a Cel48S and Cel48Y double knockout was essentially the same as that of the Cel48S single knockout. Our results indicate that solubilization of crystalline cellulose by C. thermocellum can proceed to completion without expression of a family 48 cellulase.

Olson, Daniel G [Mascoma Corporation; Tripathi, Shital A. [Mascoma Corporation; Giannone, Richard J [ORNL; Lo, Jonathan [Dartmouth College; Caiazza, Nicky [ORNL; Hogsett, David A [ORNL; Hettich, Robert {Bob} L [ORNL; Guss, Adam M [ORNL; Dubrovsky, Genia [Dartmouth College; Lynd, Lee R [ORNL

2010-01-01T23:59:59.000Z

64

V-204: A specially crafted query can cause BIND to terminate abnormally |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

V-204: A specially crafted query can cause BIND to terminate V-204: A specially crafted query can cause BIND to terminate abnormally V-204: A specially crafted query can cause BIND to terminate abnormally July 27, 2013 - 4:35am Addthis PROBLEM: A specially crafted query that includes malformed rdata can cause named to terminate with an assertion failure while rejecting the malformed query. PLATFORM: BIND 9.7 ABSTRACT: A specially crafted query sent to a BIND nameserver can cause it to crash (terminate abnormally). REFERENCE LINKS: ISC Knowledge Base CVE-2013-4854 IMPACT ASSESSMENT: High DISCUSSION: BIND is an implementation of the Domain Name System (DNS) protocols. Authoritative and recursive servers are equally vulnerable. Intentional exploitation of this condition can cause a denial of service in all nameservers running affected versions of BIND 9. Access Control Lists do

65

Vector-field domain walls  

Science Conference Proceedings (OSTI)

We argue that spontaneous Lorentz violation may generally lead to metastable domain walls related to the simultaneous violation of some accompanying discrete symmetries. Remarkably, such domain-wall solutions exist for spacelike Lorentz violation and do not exist for the timelike violation. Because a preferred space direction is spontaneously induced, these domain walls have no planar symmetry and produce a peculiar static gravitational field at small distances, while their long-distance gravity appears the same as for regular scalar-field walls. Some possible applications of vector-field domain walls are briefly discussed.

Chkareuli, J. L. [E. Andronikashvili Institute of Physics, 0177 Tbilisi, Georgia (United States); I. Chavchavadze State University, 0162 Tbilisi (Georgia); Kobakhidze, Archil [E. Andronikashvili Institute of Physics, 0177 Tbilisi (Georgia); School of Physics, University of Melbourne, Victoria 3010 (Australia); Volkas, Raymond R. [School of Physics, University of Melbourne, Victoria 3010 (Australia)

2009-09-15T23:59:59.000Z

66

Structure of the cytoplasmic domain of Yersinia pestis YscD, an essential component of the type III secretion system  

Science Conference Proceedings (OSTI)

The Yersinia pestis YscD protein is an essential component of the type III secretion system. YscD consists of an N-terminal cytoplasmic domain (residues 1-121), a transmembrane linker (122-142) and a large periplasmic domain (143-419). Both the cytoplasmic and the periplasmic domains are required for the assembly of the type III secretion system. Here, the structure of the YscD cytoplasmic domain solved by SAD phasing is presented. Although the three-dimensional structure is similar to those of forkhead-associated (FHA) domains, comparison with the structures of canonical FHA domains revealed that the cytoplasmic domain of YscD lacks the conserved residues that are required for binding phosphothreonine and is therefore unlikely to function as a true FHA domain.

Lountos, George T.; Tropea, Joseph E.; Waugh, David S. (SAIC); (NCI)

2012-09-17T23:59:59.000Z

67

JORDAN DOMAINS ARE CAT(0)  

E-Print Network (OSTI)

Abstract. For a Jordan domain in the plane the length metric space of points connected to an interior point by a curve of finite length is a cat(0) space. With respect to the cone topology, that space plus its boundary at infinity is topologically the same as the original Jordan domain. 1.

Richard L. Bishop

2005-01-01T23:59:59.000Z

68

Domain assignments for FSSP representative set using DomainParser  

NLE Websites -- All DOE Office Websites (Extended Search)

Domain assignments for the FSSP representative set Domain assignments for the FSSP representative set The following are the domain assignments for the FSSP representative set (released on January 31, 2000, 1987 chains in total) using DomainParser. Each line shows a PDB entry (with a chain identifier if any), total number of residues, number of domains, and domain assignments. The result is obtained fully automatically without manual editing. 12asa 327 2 (33-86; 271-288) (4-32; 87-270; 289-330) 153l 185 1 16pk 415 2 (5-205; 409-419) (206-408) 16vpa 311 2 (47-130; 164-233; 324-349) (131-163; 234-323; 395-402) 1914 171 1 19hca 292 2 (45-107) (1-44; 108-292) 1a02f 53 1 1a02j 52 1 1a02n 280 2 (399-569) (570-678) 1a04a 205 2 (5-126) (127-216) 1a0aa 63 1 1a0ca 437 1 1a0fa 201 2 (1-81) (82-201) 1a0ha 159 1 1a0i 332 2 (2-239) (240-349)

69

Total alpha-globin gene cluster deletion has high frequency in Filipinos  

SciTech Connect

Most {alpha}-thalassemias [Thal] are due to large deletions. In Southeast Asians, the (--{sup SEA}) double {alpha}-globin gene deletion is common, 3 (--{sup Tot}) total {alpha}-globin cluster deletions are known: Filipino (--{sup Fil}), Thai (--{sup Thai}), and Chinese (--{sup Chin}). In a Hawaii Thal project, provisional diagnosis of {alpha}-Thal-1 heterozygotes was based on microcytosis, normal isoelectric focusing, and no iron deficiency. One in 10 unselected Filipinos was an {alpha}-Thal-1 heterozygote, 2/3 of these had a (--{sup Tot}) deletion: a {var_sigma}-cDNA probe consistently showed fainter intensity of the constant 5.5 kb {var_sigma}{sub 2} BamHI band, with no heterzygosity for {var_sigma}-globin region polymorphisms; {alpha}-cDNA or {var_sigma}-cDNA probes showed no BamHI or BglII bands diagnostic of the (--{sup SEA}) deletion; bands for the (-{alpha}) {alpha}-Thal-2 single {alpha}-globin deletions were only seen in Hb H cases. A reliable monoclonal anti-{var_sigma}-peptide antibody test for the (--{sup SEA}) deletion was always negative in (--{sup Tot}) samples. Southern digests with the Lo probe, a gift from D. Higgs of Oxford Univ., confirmed that 49 of 50 (--{sup Tot}) chromosomes in Filipinos were (--{sup Fil}). Of 20 {alpha}-Thal-1 hydrops born to Filipinos, 11 were (--{sup Fil}/--{sup SEA}) compound heterozygotes; 9 were (--{sup SEA}/--{sup SEA}) homozygotes, but none was a (--{sup Fil}/--{sup Fil}).

Hunt, J.A.; Haruyama, A.Z.; Chu, B.M. [Kapiolani Medical Center, Honolulu, HI (United States)] [and others

1994-09-01T23:59:59.000Z

70

Keys, nominals, and concrete domains  

Science Conference Proceedings (OSTI)

Many description logics (DLs) combine knowledge representation on an abstract, logical level with an interface to "concrete" domains like numbers and strings with built-in predicates such as <, +, and prefix-of. These hybrid DLs have turned out to ...

Carsten Lutz; Carlos Areces; Ian Horrocks; Ulrike Sattler

2005-01-01T23:59:59.000Z

71

Plan recognition in exploratory domains  

Science Conference Proceedings (OSTI)

This paper describes a challenging plan recognition problem that arises in environments in which agents engage widely in exploratory behavior, and presents new algorithms for effective plan recognition in such settings. In exploratory domains, agents@? ... Keywords: Plan recognition, User modeling

Yaakov Gal; Swapna Reddy; Stuart M. Shieber; Andee Rubin; Barbara J. Grosz

2012-01-01T23:59:59.000Z

72

How Dynein Binds to Microtubules  

NLE Websites -- All DOE Office Websites (Extended Search)

with binding. Confirmation was provided by docking the crystal structure into an electron-density map of a dynein stalk bound to microtubules that was obtained by...

73

Non-virulence of a recombinant shrimp nidovirus is associated with its non structural gene sequence and not a large structural gene deletion  

SciTech Connect

RT-PCR using a commercial kit for yellow head virus (YHV) detection in growth-retarded shrimp yielded an unusual 777 bp amplicon instead of expected amplicons of 277 bp for YHV type-1 (YHV-1) or 406 bp for YHV type-2 (YHV-2). Cloning and sequencing (GenBank (EU170438)) revealed approximately 80% identity to non-structural (NS) ORF1b sequences of both YHV-1 (GenBank (AA083987)) and YHV-2 (GenBank (AF227196)), indicating an atypical YHV type (A-YHV) phylogenetically equidistant from both types. An RT-PCR test specifically designed for A-YHV revealed that it was uncommon and that its occurrence in shrimp culture ponds did not correlate with growth retardation or mortality. By immunohistochemistry with YHV-specific monoclonal antibodies, the A-YHV gave positive reactions for envelope protein gp64 and capsid protein p20, but not for envelope protein gp116, even though gp116 and gp64 originate from a polyprotein of ORF3. Lack of gp116 immunoreactivity correlated with a large ORF3 deletion (GenBank (EU123854)) in the region of the protein targeted by an MAb against gp116. Transmission electron microscopy of A-YHV-infected shrimp revealed only unenveloped pre-virions. During manuscript revision, information received revealed that typing of YHV isolates based on sequences of ORF1b and ORF3 had yielded several geographical types, including one virulent type (YHV-1b) with an ORF3 deletion sequence that matched the sequence of A-YHV. Using these sequences and an additional A-YHV sequence ( (EU853170)) from the ORF1b typing region, A-YHV potentially represents a recombinant between type 1b and type 5. SDS-PAGE and Western blot analysis revealed that type 1b produced a gp116 deletion protein that did not bind with the MAb or polyclonal Ab to normal gp116. Overall, the information suggested that lack of A-YHV virulence was associated with the NS gene sequence linked to ORF1b rather than the deletion in ORF3.

Gangnonngiw, Warachin [National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, Klong Luang Pratumthani 12120 (Thailand); Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Anantasomboon, Gun [Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Department of Anatomy, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Anatomy Unit, Department of Medical Science, Faculty of Science, Rangsit University, Patumthani 12000 (Thailand); Sang-oum, Wiwat; Sriurairatana, Siriporn [Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Sritunyalucksana, Kallaya [National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Thailand Science Park, Klong Luang Pratumthani 12120 (Thailand); Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Flegel, Timothy W. [Centex Shrimp, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand); Department of Biotechnology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400 (Thailand)], E-mail: sctwf@mucc.mahidol.ac.th

2009-03-01T23:59:59.000Z

74

Uterine deletion of Trp53 compromises antioxidant responses in mouse decidua  

Science Conference Proceedings (OSTI)

Preterm birth is a global health issue impacting both mothers and children. However, the etiology of preterm birth is not clearly understood. From our recent finding that premature decidual senescence with terminal differentiation is a cause of preterm birth in mice with uterine Trp53 deletion, encoding p53 protein, led us to explore other potential factors that are related to preterm birth. Utilizing proteomics approaches, here we show that 183 candidate proteins cause significant changes in decidua with Trp53 deletion as compared to normal decidua. Functional categorization of these proteins unveiled new pathways that are influenced by p53. In particular, downregulation of a cluster of antioxidant proteins in p53 deficient decidua suggests that increased oxidative stress could be one cause of preterm birth in mice with uterine deletion of Trp53.

Burnum, Kristin E.; Hirota, Yasushi; Baker, Erin Shammel; Yoshie, Mikihiro; Ibrahim, Yehia M.; Monroe, Matthew E.; Anderson, Gordon A.; Smith, Richard D.; Daikoku, Takiko; Dey, Sudhansu K.

2012-09-01T23:59:59.000Z

75

Domain walls riding the wave.  

SciTech Connect

Recent years have witnessed a rapid proliferation of electronic gadgets around the world. These devices are used for both communication and entertainment, and it is a fact that they account for a growing portion of household energy consumption and overall world consumption of electricity. Increasing the energy efficiency of these devices could have a far greater and immediate impact than a gradual switch to renewable energy sources. The advances in the area of spintronics are therefore very important, as gadgets are mostly comprised of memory and logic elements. Recent developments in controlled manipulation of magnetic domains in ferromagnet nanostructures have opened opportunities for novel device architectures. This new class of memories and logic gates could soon power millions of consumer electronic devices. The attractiveness of using domain-wall motion in electronics is due to its inherent reliability (no mechanical moving parts), scalability (3D scalable architectures such as in racetrack memory), and nonvolatility (retains information in the absence of power). The remaining obstacles in widespread use of 'racetrack-type' elements are the speed and the energy dissipation during the manipulation of domain walls. In their recent contribution to Physical Review Letters, Oleg Tretiakov, Yang Liu, and Artem Abanov from Texas A&M University in College Station, provide a theoretical description of domain-wall motion in nanoscale ferromagnets due to the spin-polarized currents. They find exact conditions for time-dependent resonant domain-wall movement, which could speed up the motion of domain walls while minimizing Ohmic losses. Movement of domain walls in ferromagnetic nanowires can be achieved by application of external magnetic fields or by passing a spin-polarized current through the nanowire itself. On the other hand, the readout of the domain state is done by measuring the resistance of the wire. Therefore, passing current through the ferromagnetic wire is the preferred method, as it combines manipulation and readout of the domain-wall state. The electrons that take part in the process of readout and manipulation of the domain-wall structure in the nanowire do so through the so-called spin transfer torque: When spin-polarized electrons in the ferromagnet nanowire pass through the domain wall they experience a nonuniform magnetization, and they try to align their spins with the local magnetic moments. The force that the electrons experience has a reaction force counterpart that 'pushes' the local magnetic moments, resulting in movement of the domain wall in the direction of the electron flow through the spin-transfer torque. The forces between the electrons and the local magnetic moments in the ferromagnet also create additional electrical resistance for the electrons passing through the domain wall. By measuring resistance across a segment of the nanowire, one determines if a domain wall is present; i.e., one can read the stored information. The interaction of the spin-polarized electrons with the domain wall in the ferromagnetic nanowire is not very efficient. Even for materials achieving high polarization of the free electrons, it is very difficult to move the magnetic domain wall. Several factors contribute to this problem, with imperfections of the ferromagnetic nanowire that cause domain-wall pinning being the dominant one. Permalloy nanowires, one of the best candidates for domain-wall-based memory and logic devices, require current densities of the order of 10{sup 8} A/cm{sup 2} in order to move a domain wall from a pinning well. Considering that this current has to pass through a relatively long wire, it is not very difficult to imagine that most of the energy will go to Joule heating. The efficiency of the process - the ratio of the energy converted to domain-wall motion to the total energy consumed - is comparable to that of an incandescent light bulb converting electricity to light. A step towards more efficient domain-wall-based memory devices is the advance of using alternating currents or curren

Karapetrov, G.; Novosad, V.; Materials Science Division

2010-11-01T23:59:59.000Z

76

The C-Terminal RpoN Domain of sigma54 Forms an unpredictedHelix-Turn-Helix Motif Similar to domains of sigma70  

SciTech Connect

The ''{delta}'' subunit of prokaryotic RNA-polymerase allows gene-specific transcription initiation. Two {sigma} families have been identified, {sigma}{sup 70} and {sigma}{sup 54}, which use distinct mechanisms to initiate transcription and share no detectable sequence homology. Although the {sigma}{sup 70}-type factors have been well characterized structurally by x-ray crystallography, no high-resolution structural information is available for the {sigma}{sup 54}-type factors. Here we present the NMR derived structure of the C-terminal domain of {sigma}{sup 54} from Aquifex aeolicus. This domain (Thr323 to Gly389), which contains the highly conserved RpoN box sequence, consists of a poorly structured N-terminal tail followed by a three-helix bundle, which is surprisingly similar to domains of the {sigma}{sup 70}-type proteins. Residues of the RpoN box, which have previously been shown to be critical for DNA binding, form the second helix of an unpredicted helix-turn-helix motif. This structure's homology with other DNA binding proteins, combined with previous biochemical data, suggest how the C-terminal domain of {sigma}{sup 54} binds to DNA.

Doucleff, Michaeleen; Malak, Lawrence T.; Pelton, Jeffrey G.; Wemmer, David E.

2005-11-01T23:59:59.000Z

77

Anchored Clathrate Waters Bind Antifreeze Proteins to Ice  

DOE Green Energy (OSTI)

The mechanism by which antifreeze proteins (AFPs) irreversibly bind to ice has not yet been resolved. The ice-binding site of an AFP is relatively hydrophobic, but also contains many potential hydrogen bond donors/acceptors. The extent to which hydrogen bonding and the hydrophobic effect contribute to ice binding has been debated for over 30 years. Here we have elucidated the ice-binding mechanism through solving the first crystal structure of an Antarctic bacterial AFP. This 34-kDa domain, the largest AFP structure determined to date, folds as a Ca{sup 2+}-bound parallel beta-helix with an extensive array of ice-like surface waters that are anchored via hydrogen bonds directly to the polypeptide backbone and adjacent side chains. These bound waters make an excellent three-dimensional match to both the primary prism and basal planes of ice and in effect provide an extensive X-ray crystallographic picture of the AFP{vert_ellipsis}ice interaction. This unobstructed view, free from crystal-packing artefacts, shows the contributions of both the hydrophobic effect and hydrogen bonding during AFP adsorption to ice. We term this mode of binding the 'anchored clathrate' mechanism of AFP action.

C Garnham; R Campbell; P Davies

2011-12-31T23:59:59.000Z

78

True costs of cheap labor are hard to measure: edge deletion and VCG payments in graphs  

Science Conference Proceedings (OSTI)

We address the problem of lowering the buyer's expected payments in shortest path auctions, where the buyer's goal is to purchase a path in a graph in which edges are owned by selfish agents. We show that by deleting some of the edges of the graph, one ... Keywords: auction, mechanism design, shortest paths

Edith Elkind

2005-06-01T23:59:59.000Z

79

Characterization of national Web domains  

Science Conference Proceedings (OSTI)

During the last few years, several studies on the characterization of the public Web space of various national domains have been published. The pages of a country are an interesting set for studying the characteristics of the Web because at the same ... Keywords: Web characterization, Web measurement

Ricardo Baeza-Yates; Carlos Castillo; Efthimis N. Efthimiadis

2007-05-01T23:59:59.000Z

80

Tandem SAM Domain Structure of Human Caskin1: A Presynaptic, Self-Assembling Scaffold for CASK  

Science Conference Proceedings (OSTI)

The synaptic scaffolding proteins CASK and Caskin1 are part of the fibrous mesh of proteins that organize the active zones of neural synapses. CASK binds to a region of Caskin1 called the CASK interaction domain (CID). Adjacent to the CID, Caskin1 contains two tandem sterile a motif (SAM) domains. Many SAM domains form polymers so they are good candidates for forming the fibrous structures seen in the active zone. We show here that the SAM domains of Caskin1 form a new type of SAM helical polymer. The Caskin1 polymer interface exhibits a remarkable segregation of charged residues, resulting in a high sensitivity to ionic strength in vitro. The Caskin1 polymers can be decorated with CASK proteins, illustrating how these proteins may work together to organize the cytomatrix in active zones.

Stafford, Ryan L.; Hinde, Elizabeth; Knight, Mary Jane; Pennella, Mario A.; Ear, Jason; Digman, Michelle A.; Gratton, Enrico; Bowie, James U. (UCI); (UCLA)

2012-02-07T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
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they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


81

Structural Analysis of Rtt106p Reveals a DNA Binding Role Required for Heterochromatin Silencing  

Science Conference Proceedings (OSTI)

Rtt106p is a Saccharomyces cerevisiae histone chaperone with roles in heterochromatin silencing and nucleosome assembly. The molecular mechanism by which Rtt106p engages in chromatin dynamics remains unclear. Here, we report the 2.5 {angstrom} crystal structure of the core domain of Rtt106p, which adopts an unusual 'double pleckstrin homology' domain architecture that represents a novel structural mode for histone chaperones. A histone H3-H4-binding region and a novel double-stranded DNA-binding region have been identified. Mutagenesis studies reveal that the histone and DNA binding activities of Rtt106p are involved in Sir protein-mediated heterochromatin formation. Our results uncover the structural basis of the diverse functions of Rtt106p and provide new insights into its cellular roles.

Liu, Y.; Huang, H; Zhou, B; Wang, S; Hu, Y; Li, X; Liu, J; Niu, L; Wu, J; et. al.

2010-01-01T23:59:59.000Z

82

Characterization of the functional domains of the natriuretic peptide receptor/guanylate cyclase by radiation inactivation  

SciTech Connect

Radiation inactivation has been used to evaluate the molecular size of domains responsible for atrial natriuretic peptide (ANP)-binding and cyclase functions of the ANP receptor/guanylate cyclase. Two types of inactivation curves were observed for cyclase function in both adrenal cortex and aortic smooth muscle cells: (1) biphasic with enhanced guanylate cyclase activity after exposure to low radiation doses and (2) linear after preincubation of membrane proteins with 0.5 microM ANP or solubilization with Triton X-100. The existence of an inhibitory component was the simplest model that best explained the types of radiation curves obtained. Activation of guanylate cyclase by ANP or Triton X-100 could occur via the dissociation of this inhibitory component from the catalytic domain. On the other hand, the loss of ANP-binding activity was linear with increasing radiation exposures under basal, ANP treatment, and Triton X-100 solubilization conditions. Radiation inactivation sizes of about 30 kDa for cyclase function, 20 kDa for ANP-binding function, and 90 kDa for inhibitory function were calculated. These studies suggest that the ANP receptor/guanylate cyclase behaves as a multidomain protein. The results obtained by radiation inactivation of the various biological functions of this receptor are compatible with the hypothesis of an intramolecular inhibitory domain repressing the guanylate cyclase catalytic domain within its membrane environment.

Tremblay, J.; Huot, C.; Koch, C.; Potier, M. (Univ. of Montreal, Quebec, (Canada))

1991-05-05T23:59:59.000Z

83

Structure of the Membrane Proximal Oxioreductase Domain of Human Steap3, the Dominant Ferrireductase of the Erythroid Transferrin Cycle  

SciTech Connect

The daily production of 200 billion erythrocytes requires 20 mg of iron, accounting for nearly 80% of the iron demand in humans. Thus, erythroid precursor cells possess an efficient mechanism for iron uptake in which iron loaded transferrin (Tf) binds to the transferrin receptor (TfR) at the cell surface. The Tf:TfR complex then enters the endosome via receptor-mediated endocytosis. Upon endosomal acidification, iron is released from Tf, reduced to Fe{sup 2+} by Steap3, and transported across the endosomal membrane by divalent metal iron transporter 1. Steap3, the major ferrireductase in erythrocyte endosomes, is a member of a unique family of reductases. Steap3 is comprised of an N-terminal cytosolic oxidoreductase domain and a C-terminal heme-containing transmembrane domain. Cytosolic NADPH and a flavin are predicted cofactors, but the NADPH/flavin binding domain differs significantly from those in other eukaryotic reductases. Instead, Steap3 shows remarkable, although limited homology to FNO, an archaeal oxidoreductase. We have determined the crystal structure of the human Steap3 oxidoreductase domain in the absence and presence of NADPH. The structure reveals an FNO-like domain with an unexpected dimer interface and substrate binding sites that are well positioned to direct electron transfer from the cytosol to a heme moiety predicted to be fixed within the transmembrane domain. Here, we discuss possible gating mechanisms for electron transfer across the endosomal membrane.

Sendamarai, A.K.; Ohgami, R.S.; Fleming, M.D.; Lawrence, C.M.

2009-05-27T23:59:59.000Z

84

PRF Domain Extension Using DAGs  

E-Print Network (OSTI)

We prove a general domain extension theorem for pseudo-random functions (PRFs). Given a PRF F from n bits to n bits, it is well known that employing F in a chaining mode (CBC-MAC) yields a PRF on the bigger domain of mn bits. One can view each application of F in this chaining mode to be a node in a graph, and the chaining as the edges between the node. The resulting graph is just a line graph. In this paper, we show that the underlying graph can be an arbitrary directed acyclic graph (DAG), and the resulting function on the larger domain is still a PRF. The only requirement on the graph is that it have unique source and sink nodes, and no two nodes have the same set of incident nodes. A new highly parallelizable MAC construction follows which has a critical path of only m applications of F . If we allow Galois field arithmetic, we can consider edge-colored DAGs, where the colors represent multiplication in the field by the color. We prove an even more general theorem, where the only restriction on the colored DAGs is that if two nodes (u and v) have the same set of incident nodes W , then at least one w in W is incident on u and v with a different colored edge. PMAC (parallelizable message authentication [5]) is a simple example of such graphs. Finally, to handle variable length domain extension, we extend our theorem to a collection of DAGs. The general theorem allows one to have further optimizations over PMAC, and many modes which deal with variable lengths. All the results proven are under the adaptive adversary model. Keywords: PRF, MAC, DAG, partial order, Galois field 1

Charanjit S. Jutla

2005-01-01T23:59:59.000Z

85

How to Run DomainParser  

NLE Websites -- All DOE Office Websites (Extended Search)

Run DomainParser Run DomainParser The structure for partition needs to be prepared in the PDB format. In most cases, running DomainParser using defaults should give satisfactory partitions. However, several options offered in DomainParser can provide a partition that a user desires or correct some overcut/undercut partitions. Here, we use a PDB file 1atna.pdb as an example to show how to use the DomainParser program. Run DomainParser using defaults: domainparser 1atna.pdb The output shows the partition for each domain in terms of ranges of residue numbers: 4 domains have been found for 1atna: Domain 1 : 34-96. Domain 2 : 181-272. Domain 3 : 148-180; 273-336. Domain 4 : 0-33; 97-147; 337-372. The program also generates a new file 1atna_dom.pdb, with the "temperature factor" column (column 61-66 of an "ATOM" entry) showing domain numbers. A

86

Mutations in the consensus helicase domains of the Werner syndrome gene  

Science Conference Proceedings (OSTI)

Werner syndrome (WS) is an autosomal recessive disease with a complex phenotype that is suggestive of accelerated aging. WS is caused by mutations in a gene, WRN, that encodes a predicted 1,432-amino-acid protein with homology to DNA and RNA helicases. Previous work identified four WS mutations in the 3{prime} end of the gene, which resulted in predicted truncated protein products of 1,060-1,247 amino acids but did not disrupt the helicase domain region (amino acids 569-859). Here, additional WS subjects were screened for mutations, and the intron-exon structure of the gene was determined. A total of 35 exons were defined, with the coding sequences beginning in the second exon. Five new WS mutations were identified: two nonsense mutations at codons 369 and 889; a mutation at a splice-junction site, resulting in a predicted truncated protein of 760 amino acids; a 1-bp deletion causing a frameshift; and a predicted truncated protein of 391 amino acids. Another deletion is >15 kb of genomic DNA, including exons 19-23; the predicted protein is 1,186 amino acids long. Four of these new mutations either partially disrupt the helicase domain region or result in predicted protein products completely missing the helicase region. These results confirm that mutations in the WRN gene are responsible for WS. Also, the location of the mutations indicates that the presence or absence of the helicase domain does not influence the WS phenotype and suggests that WS is the result of complete loss of function of the WRN gene product. 63 refs., 1 fig., 5 tabs.

Yu, Chang-En; Oshima, Junko; Wijsman, E.M. [Univ. of Washington, Seattle, WA (United States)] [and others

1997-02-01T23:59:59.000Z

87

In Vitro Evolution of a Peptide with a Hematite Binding Motif That May Constitute a Natural Metal-Oxide Binding Archetype  

DOE Green Energy (OSTI)

Phage-display technology was used to evolve peptides that selectively bind to the metal-oxide hematite (Fe2O3) from a library of approximately 3 billion different polypeptides. The sequences of these peptides contained the highly conserved amino acid motif, Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr. To better understand the nature of the peptide?metal oxide binding demonstrated by these experiments, molecular dynamics simulations were carried out for Ser-Pro-Ser at a hematite surface. These simulations show that hydrogen bonding occurs between the two serine amino acids and the hydroxylated hematite surface and that the presence of proline between the hydroxide residues restricts the peptide flexibility, thereby inducing a structural-binding motif. A search of published sequence data revealed that the binding motif (Ser/Thr-Pro-Ser/Thr) is adjacent to the terminal heme-binding domain of both OmcA and MtrC, which are outer membrane cytochromes from the metal-reducing bacterium Shewanella oneidensis MR-1. The entire five amino acid consensus sequence (Ser/Thr-hydrophobic/aromatic-Ser/Thr-Pro-Ser/Thr) was also found as multiple copies in the primary sequences of metal-oxide binding proteins Sil1 and Sil2 from Thalassiosira pseudonana. We suggest that this motif constitutes a natural metal-oxide binding archetype that could be exploited in enzyme-based biofuel cell design and approaches to synthesize tailored metal-oxide nanostructures.

Lower, Brian H.; Lins, Roberto D.; Oestreicher, Zachery W.; Straatsma, TP; Hochella Jr., Michael F.; Shi, Liang; Lower, Steven

2008-05-15T23:59:59.000Z

88

Improving abstract interpretations by combining domains  

Science Conference Proceedings (OSTI)

In this paper we consider static analyses based on abstract interpretation of logic programs over combined domains. It is known that analyses over combined domains potentially provide more information than obtainable by performing the independent abstract ...

M. Codish; A. Mulkers; M. Bruynooghe; M. Garca de la Banda; M. Hermenegildo

1993-08-01T23:59:59.000Z

89

Patterning Nano-Domains with Orthogonal Functionalities ...  

Science Conference Proceedings (OSTI)

Page 1. Patterning Nano-Domains with Orthogonal Functionalities: Solventless Synthesis of Self-Sorting Surfaces Karen ...

2013-10-27T23:59:59.000Z

90

DEVELOPMENT AND DISEASE An Fgf8 mouse mutant phenocopies human 22q11 deletion syndrome  

E-Print Network (OSTI)

microdeletion detected in humans, is associated with a lifethreatening array of birth defects. Although 90 % of affected individuals share the same three megabase deletion, their phenotype is highly variable and includes craniofacial and cardiovascular anomalies, hypoplasia or aplasia of the thymus with associated deficiency of T cells, hypocalcemia with hypoplasia or aplasia of the parathyroids, and a variety of central nervous system abnormalities. Because ablation of neural crest in chicks produces many features of the deletion 22q11 syndrome, it has been proposed that haploinsufficiency in this region impacts neural crest function during cardiac and pharyngeal arch development. Few factors required for migration, survival, proliferation and subsequent differentiation of pharyngeal arch neural crest and

Deborah U. Frank; Lori K. Fotheringham; Judson A. Brewer; Louis J. Muglia; Martin Tristani-firouzi; Mario R. Capecchi; Anne M. Moon

2002-01-01T23:59:59.000Z

91

Effects of Deletions of High Molecular Weight Glutenin Subunit Alleles on Dough Properties and Wheat Flour Tortilla Quality  

E-Print Network (OSTI)

In wheat (Triticum aestivum L), high molecular weight glutenin subunits (HMW -GS) are synthesized by the loci Glu-A1, Glu-B1, and Glu-D1 on the long arm of group 1 chromosome, and their variants play a significant role in the functional properties of flour; hence dough properties and tortilla quality. This study was conducted to understand the effects of HMW-GS on dough properties and tortilla quality using 40 different wheat lines from two different locations; Texas Agrilife Experiment Station at McGregor, and at Castroville, Texas, in 2010. Wheat lines in which one or more of these loci were absent (deletion lines) and non-deletion lines were used. Flours were evaluated for insoluble polymeric protein (IPP) content and mixograph properties. Dough properties; compression force, stress relaxation test, and dough extensibility, were determined using a texture analyzer. Tortillas were produced by hot-pressed method and evaluated for physical properties and textural change during 16 days of storage. Flour from deletion lines had lower average IPP content (38.4%) than non-deletion lines (41.9%). Dough from deletion lines were more extensible (44.8 mm) and required lower equilibrium force from stress relaxation test (4.91 N) compared to non-deletion lines (34.2 mm, and 6.56 N, respectively). Deletion lines produced larger diameter tortillas (177 mm) than non-deletion lines (165 mm) and had lighter color (L* = 82.3) than tortillas from non-deletion lines (L* = 81.0). Most of the deletion lines interestingly produced tortillas with acceptable flexibility scores on day 16 of storage (>= 3.0). Flour IPP content (r = -0.57) and equilibrium force (r = -0.80) were negatively correlated with tortilla diameter, but positively correlated with 16 day flexibility scores (r = 0.72, and r = 0.68, respectively). In general, deletion at Glu-A1 or Glu-D1 or presence of 2+12 instead of 5+10 allelic pair at Glu-D1 locus produced large diameter tortillas, but with poor day 16 flexibility. However, combination of 7+9 at Glu-B1 locus with deletions at Glu-A1 or Glu-D1 or 2+12 at Glu-D1 consistently produced tortillas that had large diameter and retained good flexibility scores during 16 days of storage. The results indicate the presence of 7+9 at Glu-B1 may play a crucial role in selection of wheat varieties for tortilla making.

Tuncil, Yunus

2012-08-01T23:59:59.000Z

92

Labelling Heuristics for CSP Application Domains  

E-Print Network (OSTI)

Labelling Heuristics for CSP Application Domains Zeynep K#16;z#16;ltan Computer Science Division an application domain as a family of CSP models, so as to exhibit the generic constraint store for all models store and the domain propagation during search is analysed, so as to infer | before modelling any CSP

Rossi, Francesca

93

Free biholomorphic classification of noncommutative domains  

E-Print Network (OSTI)

In this paper we develop a theory of free holomorphic functions on noncommutative Reinhardt domains generated by positive regular free holomorphic functions in n noncommuting variables. We show that the free biholomorphic classification of these domains is the same as the classification, up to unital completely isometric isomorphisms, of the corresponding noncommutative domain algebras.

Popescu, Gelu

2010-01-01T23:59:59.000Z

94

Architecture for mobile Heterogeneous Multi Domain networks  

Science Conference Proceedings (OSTI)

Multi domain networks can be used in several scenarios including military, enterprize networks, emergency networks and many other cases. In such networks, each domain might be under its own administration. Therefore, the cooperation among domains is ... Keywords: Network architecture, heterogeneous networks, mobility, policy based networking

Arjan Durresi; Ping Zhang; Mimoza Durresi; Leonard Barolli

2010-01-01T23:59:59.000Z

95

Crystal Structures of the S. cerevisiae Spt6 Core and C-terminal Tandem SH2 Domain  

SciTech Connect

The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the {approx} 900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.

D Close; S Johnson; M Sdano; S McDonald; H Robinson; T Formosa; C Hill

2011-12-31T23:59:59.000Z

96

Crystal Structures of the S. cerevisiae Spt6 Core and C-Terminal Tandem SH2 Domain  

Science Conference Proceedings (OSTI)

The conserved and essential eukaryotic protein Spt6 functions in transcription elongation, chromatin maintenance, and RNA processing. Spt6 has three characterized functions. It is a histone chaperone capable of reassembling nucleosomes, a central component of transcription elongation complexes, and is required for recruitment of RNA processing factors to elongating RNA polymerase II (RNAPII). Here, we report multiple crystal structures of the 168-kDa Spt6 protein from Saccharomyces cerevisiae that together represent essentially all of the ordered sequence. Our two structures of the {approx} 900-residue core region reveal a series of putative nucleic acid and protein-protein interaction domains that fold into an elongated form that resembles the bacterial protein Tex. The similarity to a bacterial transcription factor suggests that the core domain performs nucleosome-independent activities, and as with Tex, we find that Spt6 binds DNA. Unlike Tex, however, the Spt6 S1 domain does not contribute to this activity. Crystal structures of the Spt6 C-terminal region reveal a tandem SH2 domain structure composed of two closely associated SH2 folds. One of these SH2 folds is cryptic, while the other shares striking structural similarity with metazoan SH2 domains and possesses structural features associated with the ability to bind phosphorylated substrates including phosphotyrosine. Binding studies with phosphopeptides that mimic the RNAPII C-terminal domain revealed affinities typical of other RNAPII C-terminal domain-binding proteins but did not indicate a specific interaction. Overall, these findings provide a structural foundation for understanding how Spt6 encodes several distinct functions within a single polypeptide chain.

Close, D.; Robinson, H.; Johnson, S. J.; Sdano, M. A.; McDonald, S. M.; Formosa, T.; Hill, C. P.

2011-05-13T23:59:59.000Z

97

Domain Bubbles of Extra Dimensions  

E-Print Network (OSTI)

``Dimension bubbles'' of the type previously studied by Blau and Guendelman [S.K. Blau and E.I. Guendelman, Phys. Rev. D40, 1909 (1989)], which effectively enclose a region of 5d spacetime and are surrounded by a region of 4d spacetime, can arise in a 5d theory with a compact extra dimension that is dimensionally reduced to give an effective 4d theory. These bubbles with thin domain walls can be stabilized against total collapse in a rather natural way by a scalar field which, as in the case with ``ordinary'' nontopological solitons, traps light scalar particles inside the bubble.

J. R. Morris

2002-11-19T23:59:59.000Z

98

Domain wall conduction in multiaxial ferroelectrics  

Science Conference Proceedings (OSTI)

The conductance of domain wall structures consisting of either stripes or cylindrical domains in multiaxial ferroelectric-semiconductors is analyzed. The effects of the flexoelectric coupling, domain size, wall tilt, and curvature on charge accumulation are analyzed using the Landau-Ginsburg Devonshire theory for polarization vector combined with the Poisson equation for charge distributions. The proximity and size effect of the electron and donor accumulation/depletion by thin stripe domains and cylindrical nanodomains are revealed. In contrast to thick domain stripes and wider cylindrical domains, in which the carrier accumulation (and so the static conductivity) sharply increases at the domain walls only, small nanodomains of radii less than 5-10 correlation lengths appeared conducting across the entire cross-section. Implications of such conductive nanosized channels may be promising for nanoelectronics.

Eliseev, E. A. [National Academy of Science of Ukraine, Kiev, Ukraine; Morozovska, A. N. [National Academy of Science of Ukraine, Kiev, Ukraine; Svechnikov, S. V. [National Academy of Science of Ukraine, Kiev, Ukraine; Maksymovych, Petro [ORNL; Kalinin, Sergei V [ORNL

2012-01-01T23:59:59.000Z

99

The chlorophyll-binding protein CP47 in photosystem II. Final report  

DOE Green Energy (OSTI)

Generally, light-harvesting chlorophyll-binding proteins (LHCP) of the Cab family that are prevalent antenna systems in plants are thought to be absent in cyanobacteria. Therefore, it often is tacitly assumed that in cyanobacteria all chlorophyll is associated with the PS II and PS I core antenna. For this reason, it was of interest to investigate what the effect would be of genetic deletion of both the PS I core complex and the PS II core antenna in Synechocystis. Therefore, a mutant was made in which the psaAB genes for the PS I core were deleted, in addition to deletion or inactivation of psbB and/or psbC (coding for CP43). In this series of mutants, also apcE was deleted. In the absence of both CP47 and CP43, also the PS II reaction center proteins D1 and D2 were not detectable in the thylakoid membrane. Thus, both PS II and PS I were deleted in the resulting strains. Nonetheless, a significant amount of chlorophyll (about 15% of that present when PS II was left intact) was found to remain in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant. This chlorophyll had fluorescence characteristics resembling those of LHC II in higher plants, with a 678 nm emission maximum at 77 K. The properties of this chlorophyll remaining in the absence of PS II and PS I in Synechocystis did not resemble those of chlorophyll bound to a CP43-like protein that has been found in cyanobacteria and that is expressed under iron-stress conditions. However, some similarities in terms of fluorescence emission were observed with the isolated 22 kDa protein encoded by psbS. The role and association of the remaining chlorophyll in the PS I-less, psbB{sup {minus}}, psbC{sup {minus}}, apcE{sup {minus}} mutant remains unclear, however, this chlorophyll protein is expected to be functionally connected to PS II when this photosystem is present.

Vermaas, W.F.J.

1995-12-31T23:59:59.000Z

100

Evidence for a distinct region causing a cat-like cry in patients with 5p deletions  

SciTech Connect

The cri-du-chat syndrome is a contiguous gene syndrome that results from a deletion of the short arm of chromosome 5 (5p). Patients present with a cat-like cry at birth, which is usually considered diagnostic of this syndrome. Additional features of the syndrome include failure to thrive, microcephaly, hypertelorism, epicanthal folds, hypotonia, and severe mental retardation. We report on four families in which patients with 5p deletions have only the characteristic cat-like cry, with normal to mildly delayed development. The precise locations of the deletions in each family were determined by FISH using lambda phage and cosmic clones. All of the deletion breakpoints map distal to a chromosomal region that is implicated with the facial features and severe mental and developmental delay in the cri-du-chat syndrome. DNA clones mapping in the chromosomal region associated with the cat-like cry feature will be useful diagnostic tools. They will allow for the distinction between 5p deletions that will result in the severe delay observed in most cri-du-chat syndrome patients and those deletions that result in the isolated cat-like cry feature, which is associated with a better prognosis. 19 refs., 5 figs., 1 tab.

Gersh, M.; Goodart, S.A.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States)] [and others

1995-06-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
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101

Truncated atrial natriuretic peptide (ANP) analogs: relationship between receptor binding and cyclic GMP accumulation  

SciTech Connect

The authors have shown that cultured bovine aortic smooth muscle (BASM) cells contain high affinity receptor sites for the ANP, auriculin (ANP(4-28)). Furthermore, ANP(4-28) causes cyclic GMP (cGMP) levels to increase in BASM. In the present study, the authors synthesized a series of NH/sub 2/ and/or COOH truncated ANP(4-28) analogs and examined their ability to compete for /sup 125/I-ANP(4-28) binding to BASM and increase cGMP levels. ANP-mediated cGMP responses were reduced when amino acids were deleted from the NH/sub 2/ and/or COOH termini of ANP(4-28). Removal of the NH/sub 2/ terminal R, R-S, or R-S-S residues resulted in a 10X decrease in potency for cGMP stimulation. Deletion of the COOH terminal R-Y and F-R-Y residues resulted in a marked decline in potency. ANP's lacking the F-R-Y tripeptide were nearly inactive in stimulating cGMP accumulation. In contrast to the cGMP effects, NH/sub 2/ and/or COOH truncations of ANP(4-28) did not alter apparent receptor binding affinities (Ki(app)). All of these peptide analogs exhibited Ki(app)'s of 1-5 nM. Furthermore, peptides that bound effectively and failed to elicit cGMP responses did not antagonize ANP(4-28)-mediated cGMP increases. These binding and functional data suggest the presence of a single class of ANP receptors on BASM is insufficient to explain the actions of ANP's in these cells.

Scarborough, R.; Schenk, D.; Schwartz, K.; Kang, L.L.; McEnroe, G.; Arfsten, A.; Lewicki, J.

1986-03-01T23:59:59.000Z

102

Bindings  

E-Print Network (OSTI)

With Debian or Ubuntu the installation is very simple apt-get install python Versions Several versions of Python are available 2.4, 2.5 and 2.6. ? python-V gives the version of Python that will be used % python-V Python 2.5.4Outline

Francois Faure

2009-01-01T23:59:59.000Z

103

DSC: Public Domain Protein Secondary Structure Prediction  

E-Print Network (OSTI)

This paper describes the public domain versions of DSC (ftp://ftp.icnet.uk/icrfpublic /bmm/king/dsc/dsc.tar.z.).

Ross D. King; Mansoor Saqi; Roger Sayle; Michael J. E. Sternberg

1997-01-01T23:59:59.000Z

104

A structure-based database of antibody variable domain diversity  

Science Conference Proceedings (OSTI)

The diversity of natural antibodies is limited by the genetic mechanisms that engender diversity and the functional requirements of antigen binding. Using an in vitro-evolved autonomous heavy chain variable domain (V{sub H}H-RIG), we have investigated the limits of structurally-tolerated diversity in the three complementarity-determining regions and a fourth loop within the third framework region. We determined the X-ray crystal structure of the V{sub H}H-RIG domain at 1.9 {angstrom} resolution and used it to guide the design of phage-displayed libraries encompassing the four loops. The libraries were subjected to selections for structural stability, and a database of structurally-tolerated sequences was compiled from the sequences of approximately 1000 unique clones. The results reveal that all four loops accommodate significantly greater diversity than is observed in nature. Thus, it appears that most sequence biases in the natural immune repertoire arise from factors other than structural constraints and, consequently, it should be possible to enhance the functions of antibodies significantly through in vitro evolution.

Bond, C.J.; Wiesmann, C.; Marsters, Jr., J.C.; Sidhu, S.S. (Genentech)

2010-07-13T23:59:59.000Z

105

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described.

Clemons, Gisela K. (Berkeley, CA)

1997-01-01T23:59:59.000Z

106

Erythropoietin binding protein from mammalian serum  

DOE Patents (OSTI)

Purified mammalian erythropoietin binding-protein is disclosed, and its isolation, identification, characterization, purification, and immunoassay are described. The erythropoietin binding protein can be used for regulation of erythropoiesis by regulating levels and half-life of erythropoietin. A diagnostic kit for determination of level of erythropoietin binding protein is also described. 11 figs.

Clemons, G.K.

1997-04-29T23:59:59.000Z

107

Optical coherence domain reflectometry guidewire  

DOE Patents (OSTI)

A guidewire with optical sensing capabilities is based on a multiplexed optical coherence domain reflectometer (OCDR), which allows it to sense location, thickness, and structure of the arterial walls or other intra-cavity regions as it travels through the body during minimally invasive medical procedures. This information will be used both to direct the guidewire through the body by detecting vascular junctions and to evaluate the nearby tissue. The guidewire contains multiple optical fibers which couple light from the proximal to distal end. Light from the fibers at the distal end of the guidewire is directed onto interior cavity walls via small diameter optics such as gradient index lenses and mirrored corner cubes. Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers, which are multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The guidewire can also be used in nonmedical applications.

Colston, Billy W. (Livermore, CA); Everett, Matthew (Pleasanton, CA); Da Silva, Luiz B. (Danville, CA); Matthews, Dennis (Moss Beach, CA)

2001-01-01T23:59:59.000Z

108

Genomic deletion of a long-range bone enhancer misregulatessclerostin in Van Buchem disease  

Science Conference Proceedings (OSTI)

Mutations in distant regulatory elements can negatively impact human development and health, yet due to the difficulty of detecting these critical sequences we predominantly focus on coding sequences for diagnostic purposes. We have undertaken a comparative sequence-based approach to characterize a large noncoding region deleted in patients affected by Van Buchem disease (VB), a severe sclerosing bone dysplasia. Using BAC recombination and transgenesis we characterized the expression of human sclerostin (sost) from normal (hSOSTwt) or Van Buchem(hSOSTvb D) alleles. Only the hSOSTwt allele faithfully expressed high levels of human sost in the adult bone and impacted bone metabolism, consistent with the model that the VB noncoding deletion removes a sost specific regulatory element. By exploiting cross-species sequence comparisons with in vitro and in vivo enhancer assays we were able to identify a candidate enhancer element that drives human sost expression in osteoblast-like cell lines in vitro and in the skeletal anlage of the E14.5 mouse embryo, and discovered a novel function for sclerostin during limb development. Our approach represents a framework for characterizing distant regulatory elements associated with abnormal human phenotypes.

Loots, Gabriela G.; Kneissel, Michaela; Keller, Hansjoerg; Baptist, Myma; Chang, Jessie; Collette, Nicole M.; Ovcharenko, Dmitriy; Plajzer-Frick, Ingrid; Rubin, Edward M.

2005-04-15T23:59:59.000Z

109

Full abstraction for nominal Scott domains  

Science Conference Proceedings (OSTI)

We develop a domain theory within nominal sets and present programming language constructs and results that can be gained from this approach. The development is based on the concept of orbit-finite subset, that is, a subset of a nominal sets that is ... Keywords: denotational semantics, domain theory, full abstraction, nominal sets, symmetry

Steffen Lsch; Andrew M. Pitts

2013-01-01T23:59:59.000Z

110

A logical model for relational abstract domains  

Science Conference Proceedings (OSTI)

In this article we introduce the notion of Heyting completion in abstract interpretation. We prove that Heyting completion provides a model for Cousot's reduced cardinal power of abstract domains and that it supplies a logical basis to specify relational ... Keywords: Heyting completion, abstract interpretation, closure operators, condensing analysis, constraint logic programming, directional types, domains, intuitionistic logic, reduced cardinal power, static analysis

Roberto Giacobazzi; Francesca Scozzari

1998-09-01T23:59:59.000Z

111

Improving abstract interpretations by combining domains  

Science Conference Proceedings (OSTI)

This article considers static analysis based on abstract interpretation of logic programs over combined domains. It is known that analyses over combined domains provide more information potentially than obtained by the independent analyses. However, ... Keywords: abstract interpretation, logic programming, program analysis

Michael Codish; Anne Mulkers; Maurice Bruynooghe; Maria Garca de la Banda; Manuel Hermenegildo

1995-01-01T23:59:59.000Z

112

Domain reduction method for atomistic simulations  

Science Conference Proceedings (OSTI)

In this paper, a quasi-static formulation of the method of multi-scale boundary conditions (MSBCs) is derived and applied to atomistic simulations of carbon nano-structures, namely single graphene sheets and multi-layered graphite. This domain reduction ... Keywords: atomistic simulation, carbon nano-structures, deformable boundary, domain reduction, graphite, multi-scale modeling, nano-indentation

Sergey N. Medyanik; Eduard G. Karpov; Wing Kam Liu

2006-11-01T23:59:59.000Z

113

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Affinities  

E-Print Network (OSTI)

Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein-Ligand Binding Jersey 08854 Received June 2, 2010 Abstract: The binding energy distribution analysis method (BEDAM of the probability distribution of the binding energy obtained in the canonical ensemble in which the ligand

114

Hidden Rotational Symmetries in Magnetic Domain Patterns  

NLE Websites -- All DOE Office Websites (Extended Search)

Hidden Rotational Symmetries in Magnetic Domain Patterns Print Hidden Rotational Symmetries in Magnetic Domain Patterns Print Magnetic thin films have complicated domain patterns that may or may not repeat with each cycle through a hysteresis loop. A magnetic thin film with perpendicular anisotropy, such as that used in computer hard drives, for example, commonly exhibits labyrinthine domain patterns. These patterns are disordered over a macroscopic length scale, and intuitively we do not expect to observe any symmetry in such systems. Scientists at the ALS, the University of Oregon, and the University of California, San Diego, have recently used coherent soft x-ray scattering with angular Fourier analysis to discover that the disordered domain patterns do, in fact, exhibit rotational symmetries, which can be as small as two-fold or as large as 30-fold. Their study of magnetic symmetries gives scientists a toolbox for discovering hidden symmetries in diverse material systems.

115

Slow Dynamics of Orbital Domains in Manganite  

NLE Websites -- All DOE Office Websites (Extended Search)

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

116

Slow Dynamics of Orbital Domains in Manganite  

NLE Websites -- All DOE Office Websites (Extended Search)

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

117

Hidden Rotational Symmetries in Magnetic Domain Patterns  

NLE Websites -- All DOE Office Websites (Extended Search)

Hidden Rotational Symmetries in Hidden Rotational Symmetries in Magnetic Domain Patterns Hidden Rotational Symmetries in Magnetic Domain Patterns Print Wednesday, 27 June 2012 00:00 Magnetic thin films have complicated domain patterns that may or may not repeat with each cycle through a hysteresis loop. A magnetic thin film with perpendicular anisotropy, such as that used in computer hard drives, for example, commonly exhibits labyrinthine domain patterns. These patterns are disordered over a macroscopic length scale, and intuitively we do not expect to observe any symmetry in such systems. Scientists at the ALS, the University of Oregon, and the University of California, San Diego, have recently used coherent soft x-ray scattering with angular Fourier analysis to discover that the disordered domain patterns do, in fact, exhibit rotational symmetries, which can be as small as two-fold or as large as 30-fold. Their study of magnetic symmetries gives scientists a toolbox for discovering hidden symmetries in diverse material systems.

118

Slow Dynamics of Orbital Domains in Manganite  

NLE Websites -- All DOE Office Websites (Extended Search)

Slow Dynamics of Orbital Domains in Manganite Print Slow Dynamics of Orbital Domains in Manganite Print At the ALS, an international team of researchers has used low-energy coherent x rays to extract new knowledge about the correlated motion of groups of self-assembled, outer-lying electrons in the extremely complex electronic system found in manganites. The manganite family of materials has puzzled physicists for years by defying standard models for the motion of electrons in crystals. By controlling the properties of the incident x rays, the researchers were able to map the complexity of a "half-doped" manganite into a far-field speckle diffraction pattern to study the manganite's domain dynamics. Their results suggest the material undergoes a transition characterized by the competition between a pinned orbital domain topology that remains static and mobile domain boundaries that exhibit slow, temporal fluctuations.

119

ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome  

SciTech Connect

ATR-X (alpha-thalassemia/mental retardation, X-linked) syndrome is a human congenital disorder that causes severe intellectual disabilities. Mutations in the ATRX gene, which encodes an ATP-dependent chromatin-remodeler, are responsible for the syndrome. Approximately 50% of the missense mutations in affected persons are clustered in a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, ADD{sub ATRX}), whose function has remained elusive. Here we identify ADD{sub ATRX} as a previously unknown histone H3-binding module, whose binding is promoted by lysine 9 trimethylation (H3K9me3) but inhibited by lysine 4 trimethylation (H3K4me3). The cocrystal structure of ADD{sub ATRX} bound to H3{sub 1-15}K9me3 peptide reveals an atypical composite H3K9me3-binding pocket, which is distinct from the conventional trimethyllysine-binding aromatic cage. Notably, H3K9me3-pocket mutants and ATR-X syndrome mutants are defective in both H3K9me3 binding and localization at pericentromeric heterochromatin; thus, we have discovered a unique histone-recognition mechanism underlying the ATR-X etiology.

Iwase, Shigeki; Xiang, Bin; Ghosh, Sharmistha; Ren, Ting; Lewis, Peter W.; Cochrane, Jesse C.; Allis, C. David; Picketts, David J.; Patel, Dinshaw J.; Li, Haitao; Shi, Yang (Harvard-Med); (Ottawa Hosp.); (MSKCC); (Rockefeller); (CH-Boston); (Tsinghua); (Mass. Gen. Hosp.)

2011-07-19T23:59:59.000Z

120

ATRX ADD Domain Links an Atypical Histone Methylation Recognition Mechanism to Human Mental-Retardation Syndrome  

SciTech Connect

ATR-X (alpha-thalassemia/mental retardation, X-linked) syndrome is a human congenital disorder that causes severe intellectual disabilities. Mutations in the ATRX gene, which encodes an ATP-dependent chromatin-remodeler, are responsible for the syndrome. Approximately 50% of the missense mutations in affected persons are clustered in a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, ADD{sub ATRX}), whose function has remained elusive. Here we identify ADD{sub ATRX} as a previously unknown histone H3-binding module, whose binding is promoted by lysine 9 trimethylation (H3K9me3) but inhibited by lysine 4 trimethylation (H3K4me3). The cocrystal structure of ADD{sub ATRX} bound to H3{sub 1-15}K9me3 peptide reveals an atypical composite H3K9me3-binding pocket, which is distinct from the conventional trimethyllysine-binding aromatic cage. Notably, H3K9me3-pocket mutants and ATR-X syndrome mutants are defective in both H3K9me3 binding and localization at pericentromeric heterochromatin; thus, we have discovered a unique histone-recognition mechanism underlying the ATR-X etiology.

S Iwase; B Xiang; S Ghosh; T Ren; P Lewis; J Cochrane; C Allis; D Picketts; D Patel; et al.

2011-12-31T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


121

The Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A  

NLE Websites -- All DOE Office Websites (Extended Search)

Unique Unique Binding Mode of Cellulosomal CBM4 from Clostridium thermocellum Cellobiohydrolase A Markus Alahuhta, Qi Xu, Yannick J. Bomble, Roman Brunecky, William S. Adney, Shi-You Ding, Michael E. Himmel and Vladimir V. Lunin⁎ National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, CO 80401, USA Received 26 April 2010; received in revised form 12 July 2010; accepted 14 July 2010 Available online 21 July 2010 The crystal structure of the carbohydrate-binding module (CBM) 4 Ig fused domain from the cellulosomal cellulase cellobiohydrolase A (CbhA) of Clostridium thermocellum was solved in complex with cellobiose at 2.11 Å resolution. This is the first cellulosomal CBM4 crystal structure reported to date. It is similar to the previously solved noncellulosomal soluble oligosaccharide-binding CBM4 structures. However, this new structure possesses a significant

122

Structures of Adnectin/Protein Complexes Reveal an Expanded Binding Footprint  

Science Conference Proceedings (OSTI)

Adnectins are targeted biologics derived from the tenth type III domain of human fibronectin ({sup 10}Fn3), a member of the immunoglobulin superfamily. Target-specific binders are selected from libraries generated by diversifying the three {sup 10}Fn3 loops that are analogous to the complementarity determining regions of antibodies. The crystal structures of two Adnectins were determined, each in complex with its therapeutic target, EGFR or IL-23. Both Adnectins bind different epitopes than those bound by known monoclonal antibodies. Molecular modeling suggests that some of these epitopes might not be accessible to antibodies because of the size and concave shape of the antibody combining site. In addition to interactions from the Adnectin diversified loops, residues from the N terminus and/or the {beta} strands interact with the target proteins in both complexes. Alanine-scanning mutagenesis confirmed the calculated binding energies of these {beta} strand interactions, indicating that these nonloop residues can expand the available binding footprint.

Ramamurthy, Vidhyashankar; Krystek, Jr., Stanley R.; Bush, Alexander; Wei, Anzhi; Emanuel, Stuart L.; Gupta, Ruchira Das; Janjua, Ahsen; Cheng, Lin; Murdock, Melissa; Abramczyk, Bozena; Cohen, Daniel; Lin, Zheng; Morin, Paul; Davis, Jonathan H.; Dabritz, Michael; McLaughlin, Douglas C.; Russo, Katie A.; Chao, Ginger; Wright, Martin C.; Jenny, Victoria A.; Engle, Linda J.; Furfine, Eric; Sheriff, Steven (BMS)

2012-11-09T23:59:59.000Z

123

Involvement of the Rab27 binding protein Slac2c/MyRIP in insulin exocytosis  

E-Print Network (OSTI)

Rab27a is a GTPase associated with insulin-containing secretory granules of pancreatic ?-cells. Selective reduction of Rab27a expression by RNA interference did not alter granule distribution and basal secretion but impaired exocytosis triggered by insulin secretagogues. Screening for potential effectors of the GTPase revealed that the Rab27a-binding protein Slac2c/MyRIP is associated with secretory granules of ?-cells. Attenuation of Slac2c/MyRIP expression by RNA interference did not modify basal secretion but severely impaired hormone release in response to secretagogues. Although ?-cells express Myosin-Va, a potential partner of Slac2c/MyRIP, no functional link between the two proteins could be demonstrated. In fact, overexpression of the Myosin-Va binding domain of Slac2c/MyRIP did not affect granule localization and hormone exocytosis. In contrast, overexpression of the actin-binding domain of Slac2c/MyRIP led to a potent inhibition of exocytosis without detectable alteration in granule distribution. This effect was prevented by point mutations that abolish actin binding. Taken together our data suggest that Rab27a and Slac2c/MyRIP are part of a complex mediating the interaction of secretory granules with cortical actin cytoskeleton and participate to the regulation of the final steps of insulin exocytosis.

Laurent Waselle; Mitsunori Fukuda; Mariella Iezzi; Aziz El-amraoui; Christine Petit; Romano Regazzi

2003-01-01T23:59:59.000Z

124

Time-Domain Electromagnetics | Open Energy Information  

Open Energy Info (EERE)

Time-Domain Electromagnetics Time-Domain Electromagnetics Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Time-Domain Electromagnetics Details Activities (10) Areas (10) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Electrical Techniques Parent Exploration Technique: Electromagnetic Sounding Techniques Information Provided by Technique Lithology: Detection of rock units or geological features with contrasting apparent resistivity. Stratigraphic/Structural: Structural information may be inferred from TDEM data. Hydrological: Hydrological information such as depth to groundwater table may be determined. Thermal: Extent of hydrothermal alteration mineralogy may be inferred. Cost Information

125

Unfurling of the band 4.1, ezrin, radixin, moesin (FERM) domain of the merlin tumor suppressor  

Science Conference Proceedings (OSTI)

The merlin-1 tumor suppressor is encoded by the Neurofibromatosis-2 (Nf2) gene and loss-of-function Nf2 mutations lead to nervous system tumors in man and to several tumor types in mice. Merlin is an ERM (ezrin, radixin, moesin) family cytoskeletal protein that interacts with other ERM proteins and with components of cell-cell adherens junctions (AJs). Merlin stabilizes the links of AJs to the actin cytoskeleton. Thus, its loss destabilizes AJs, promoting cell migration and invasion, which in Nf2{sup +/-} mice leads to highly metastatic tumors. Paradoxically, the 'closed' conformation of merlin-1, where its N-terminal four-point-one, ezrin, radixin, moesin (FERM) domain binds to its C-terminal tail domain, directs its tumor suppressor functions. Here we report the crystal structure of the human merlin-1 head domain when crystallized in the presence of its tail domain. Remarkably, unlike other ERM head-tail interactions, this structure suggests that binding of the tail provokes dimerization and dynamic movement and unfurling of the F2 motif of the FERM domain. We conclude the 'closed' tumor suppressor conformer of merlin-1 is in fact an 'open' dimer whose functions are disabled by Nf2 mutations that disrupt this architecture.

Yogesha, S.D.; Sharff, Andrew J.; Giovannini, Marco; Bricogne, Gerard; Izard, Tina (House Ear); (Globel Phasing); (Scripps)

2012-03-26T23:59:59.000Z

126

Enhanced Hydrogen Production in Escherichia coli Through Chemical Mutagenesis, Gene Deletion, and Transposon Mutagenesis  

E-Print Network (OSTI)

We demonstrate that hydrogen production can be increased by random mutagenesis using N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and that hydrogen production can be further increased in the chemically-mutagenized strain by targeted gene deletion and overexpression of genes related to formate metabolism. Chemical mutagenesis of Escherichia coli BW25113 hyaB hybC hycE::kan/pBS(Kan)-HycE to form strain 3/86 resulted in 109 +/- 0.5- fold more hydrogen; 3/86 lacks functional hydrogen uptake hydrogenases 1 and 2, has hydrogenproducing hydrogenase 3 inactivated from the chromosome, and has constitutively active hydrogenase 3 based on expression of the large subunit of hydrogenase 3 from a high copy number plasmid. Deleting fdoG, which encodes formate dehydrogenase O, (that diverts formate from hydrogen), from chemical mutagen 3/86 increased hydrogen production 188 +/- 0.50-fold (relative to the unmutagenized strain), and deletion of hycA, which encodes the repressor of formate hydrogen lyase (FHL), increased hydrogen production 232 +/- 0.50-fold. Deleting both fdoG and hycA increased hydrogen production 257 +/- 0.50-fold, and overexpressing fhlA along with the fdoG hycA mutations increased hydrogen 308 +/- 0.52-fold. Whole-transcriptome analysis of chemical mutagen 3/86 revealed 89 genes were induced and 31 genes were repressed. In an effort to identify chromosomal mutations in chemical mutagen 3/86, we performed comparative genome sequencing and identified two chromosomal loci with mutations in coding regions of ftnA and yebJ; however, neither gene was related to the increased hydrogen production as determined by the close vial (short) hydrogen assay. In addition, transposon mutagenesis, which is one of the most efficient strategies for creating random mutations in the genomic DNA, was performed in two different strains: E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA and E. coli MG1655 to identify beneficial mutations for hydrogen production. As a result of screening 461 E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA transformants and 1000 E. coli MG1655 transformants, three interesting mutations have been discovered in E. coli BW25113 hyaB hybC hycA fdoG::kan/pCA24N-FhlA transformants (gpsA, dipZ, glgP) and 1 beneficial mutation in E. coli MG1655 transformants (malT). When any of these genes gpsA, dipZ, or glgP is disrupted by Tn5 insertion, hydrogen production decreases 17, 3 and 8-fold, respectively. Additionally, when malT gene is disrupted by Tn5 insertion, hydrogen increases 3.4-fold.

Garzon Sanabria, Andrea Juliana

2010-05-01T23:59:59.000Z

127

Targeted deletion of the 9p21 noncoding coronary artery disease risk interval in mice  

SciTech Connect

Sequence polymorphisms in a 58kb interval on chromosome 9p21 confer a markedly increased risk for coronary artery disease (CAD), the leading cause of death worldwide 1,2. The variants have a substantial impact on the epidemiology of CAD and other life?threatening vascular conditions since nearly a quarter of Caucasians are homozygous for risk alleles. However, the risk interval is devoid of protein?coding genes and the mechanism linking the region to CAD risk has remained enigmatic. Here we show that deletion of the orthologous 70kb noncoding interval on mouse chromosome 4 affects cardiac expression of neighboring genes, as well as proliferation properties of vascular cells. Chr4delta70kb/delta70kb mice are viable, but show increased mortality both during development and as adults. Cardiac expression of two genes near the noncoding interval, Cdkn2a and Cdkn2b, is severely reduced in chr4delta70kb/delta70kb mice, indicating that distant-acting gene regulatory functions are located in the noncoding CAD risk interval. Allelespecific expression of Cdkn2b transcripts in heterozygous mice revealed that the deletion affects expression through a cis-acting mechanism. Primary cultures of chr4delta70kb/delta70kb aortic smooth muscle cells exhibited excessive proliferation and diminished senescence, a cellular phenotype consistent with accelerated CAD pathogenesis. Taken together, our results provide direct evidence that the CAD risk interval plays a pivotal role in regulation of cardiac Cdkn2a/b expression and suggest that this region affects CAD progression by altering the dynamics of vascular cell proliferation.

Visel, Axel; Zhu, Yiwen; May, Dalit; Afzal, Veena; Gong, Elaine; Attanasio, Catia; Blow, Matthew J.; Cohen, Jonathan C.; Rubin, Edward M.; Pennacchio, Len A.

2010-01-01T23:59:59.000Z

128

Function of the ATR N-terminal domain revealed by an ATM/ATR chimera  

SciTech Connect

The ATM and ATR kinases function at the apex of checkpoint signaling pathways. These kinases share significant sequence similarity, phosphorylate many of the same substrates, and have overlapping roles in initiating cell cycle checkpoints. However, they sense DNA damage through distinct mechanisms. ATR primarily senses single stranded DNA (ssDNA) through its interaction with ATRIP, and ATM senses double strand breaks through its interaction with Nbs1. We determined that the N-terminus of ATR contains a domain that binds ATRIP. Attaching this domain to ATM allowed the fusion protein (ATM*) to bind ATRIP and associate with RPA-coated ssDNA. ATM* also gained the ability to localize efficiently to stalled replication forks as well as double strand breaks. Despite having normal kinase activity when tested in vitro and being phosphorylated on S1981 in vivo, ATM* is defective in checkpoint signaling and does not complement cellular deficiencies in either ATM or ATR. These data indicate that the N-terminus of ATR is sufficient to bind ATRIP and to promote localization to sites of replication stress.

Chen Xinping [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Zhao Runxiang [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Glick, Gloria G. [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States); Cortez, David [Department of Biochemistry, Vanderbilt University, 613 Light Hall, 23rd, Pierce Avenue, Nashville, TN 37232 (United States)]. E-mail: david.cortez@vanderbilt.edu

2007-05-01T23:59:59.000Z

129

Inferring evolutionary scenarios for protein domain compositions  

Science Conference Proceedings (OSTI)

Essential cellular processes are controlled by functional interactions of protein domains, which can be inferred from their evolutionary histories. Methods to reconstruct these histories are challenged by the complexity of reconstructing macroevolutionary ...

John Wiedenhoeft; Roland Krause; Oliver Eulenstein

2010-05-01T23:59:59.000Z

130

Casimir forces in the time domain: Applications  

E-Print Network (OSTI)

Our previous article [Phys. Rev. A 80, 012115 (2009)] introduced a method to compute Casimir forces in arbitrary geometries and for arbitrary materials that was based on a finite-difference time-domain (FDTD) scheme. In ...

Johnson, Steven G.

131

Improving abstract interpretations by combining domains  

E-Print Network (OSTI)

This article considers static analysis based on abstract interpretation of logic programs over combined domains. It is known that analyses over combined domains provide more information potentially than obtained by the independent analyses. However, the construction of a combined analysis often requires redefining the basic operations for the combined domain. A practical ap-proach to maintain precision in combined analyses of logic programs which reuses the individual analyses and does not redefine the basic operations is illustrated, The advantages of the approach are that (1) proofs of correctness for the new domains are not required and (2) implementations can be reused. The approach is demonstrated by showing that a combined sharing analysis constructed from old proposals compares well with other new proposals suggested in recent

Michael Codish; Anne Mulkers; Maurice Bruynooghe; Maria Garcia De La Banda; Manuel Hermenegildo

1995-01-01T23:59:59.000Z

132

Indexing Flower Patent Images Using Domain Knowledge  

Science Conference Proceedings (OSTI)

The authors describe a new approach to indexing a specialized database using the color and spatial domain knowledge available for the database. They illustrate their approach by using it to solve the problem of indexing flower images when searching a ...

Madirakshi Das; R. Manmatha; Edward M. Riseman

1999-09-01T23:59:59.000Z

133

Domain constants associated with Schwarzian derivative  

Science Conference Proceedings (OSTI)

we note that every Jordan domain is M6bius equivalent to a subdomain of H having 0 ... Since the boundary of f(A) is not a Jordan curve, S~A(A)-Ao(A). Thus (

134

Structured hints : extracting and abstracting domain expertise.  

SciTech Connect

We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

2009-03-16T23:59:59.000Z

135

The Complexity of Description Logics with Concrete Domains  

E-Print Network (OSTI)

of Concrete Domains . . . . . . . . . . . . . . . . . . . . . . 31 2.4.1 Unary Concrete Domains and ALCf Domains . . . . . . . . . . . . . . . . . . . 36 3 Reasoning with ALCF(D) 41 3.1 Concept Satis#12;ability: ALCF . . . . . . . . . . . . . . . . . . . . . . . . 78 4.3 The Upper Bound

Baader, Franz

136

The Complexity of Description Logics with Concrete Domains  

E-Print Network (OSTI)

of Concrete Domains . . . . . . . . . . . . . . . . . . . . . . 31 2.4.1 Unary Concrete Domains and ALCf Domains . . . . . . . . . . . . . . . . . . . 36 3 Reasoning with ALCF(D) 41 3.1 Concept Satisfiability: ALCF . . . . . . . . . . . . . . . . . . . . . . . . 78 4.3 The Upper Bound

Baader, Franz

137

*Revisions to POS List, i.e. updates, additions and/or deletions NILAND GAS TURBINE PLANT, DOCKET NO.O6-SPPE-1  

E-Print Network (OSTI)

*Revisions to POS List, i.e. updates, additions and/or deletions NILAND GAS TURBINE PLANT, DOCKET OF CALIFORNIA SMALL POWER PLANT EXEMPTION FOR THE NILAND GAS TURBINE PLANT DOCKET NO. 06-SPPE-1 (Imperial_hahn@urscorp.com #12;*Revisions to POS List, i.e. updates, additions and/or deletions NILAND GAS TURBINE PLANT, DOCKET

138

Identifying binding sites in sequential genomic data  

Science Conference Proceedings (OSTI)

The identification of cis-regulatory binding sites in DNA is a difficult problem in computational biology. To obtain a full understanding of the complex machinery embodied in genetic regulatory networks it is necessary to know both the identity of the ... Keywords: computational biology, imbalanced data, sampling, support vector machine, transcription factor binding sites

Mark Robinson; Cristina Gonzlez Castellano; Rod Adams; Neil Davey; Yi Sun

2007-09-01T23:59:59.000Z

139

Complexity measures for binding-blocking automata  

Science Conference Proceedings (OSTI)

We define three complexity measures for binding-blocking automata (BBA) namely, blocking number, blocking instant and blocking quotient. We also study some hierarchical structures of BBA arising out of it. Keywords: binding-blocking automata, complexity measures, peptide-antibody interaction

M. Sakthi Balan

2008-04-01T23:59:59.000Z

140

A single mutation in the core domain of the lac repressor reduces leakiness  

E-Print Network (OSTI)

of allosteric control. Protein engineering has brought about LacI var- iants with altered inducibility: directed evolution yielded variants with 100-fold tighter affinity for IPTG that car- ried mutations in both the DNA and inducer binding domains [40... . Biochemistry 2008, 47:80588069. 39. Meinhardt S, Manley MW Jr, Becker NA, Hessman JA, Maher LJ 3rd, Swint-Kruse L: Novel insights from hybrid LacI/GalR proteins: family-wide functional attributes and biologically significant variation in transcription...

Gatti-Lafranconi, Pietro; Dijkman, Willem P; Devenish, Sean RA; Hollfelder, Florian

2013-07-08T23:59:59.000Z

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141

A Tcl Binding to Motif  

E-Print Network (OSTI)

Tcl is a type--free interpreted language intended for use as an embedded command language for applications. Motif is the standard GUI for the XWindow System, but this has a complex C--based API. This paper discusses a binding of tcl to Motif which allows for a simpler API. 1. Introduction The XWindow System is now accepted as the standard windowing systems for Unix graphics workstations and terminals [1]. It provides a low--level set of tools to build applications. Most applications now are built using a higher--level toolkit which typically supplies objects usually known as widgets. There are a number of such toolkits, but the one that has achieved the major success is the Motif toolkit [] based on the Xt Intrinsics [8]. Motif has defined a look--and--feel that is copied to a greater or lesser extent by other toolkits, and forms a component of specifications such as COSE. The specification for Motif [7] basically assumes a C--like language, and the only implementation of that specif...

Jan Newmarch

1994-01-01T23:59:59.000Z

142

Domain-specific abstractions and compiler transformations  

NLE Websites -- All DOE Office Websites (Extended Search)

Domain-specific abstractions and compiler Domain-specific abstractions and compiler transformations Domain-specific abstractions and compiler transformations March 4, 2013 sadayappan Saday Sadayappan Department of Computer Science and Engineering, Ohio State University Recent trends in architecture are making multicore parallelism as well as heterogeneity ubiquitous. This creates significant chalenges to application developers as well as compiler implementations. Currently it is virtually impossible to achieve performance portability of high-performance applications, i.e., develop a single version of source code for an application that achieves high performance on different parallel computer platforms. Different implementations of compute intensive core functions are generally needed for different target platforms, e.g., for multicore

143

Domain-wall branes in Lifshitz theories  

E-Print Network (OSTI)

We analyze whether or not Lifshitz field theories in 4 + 1 dimensions may provide ultraviolet-complete domain-wall brane models. We first show that Lifshitz scalar field theory can admit topologically stable domain wall solutions. A Lifshitz fermion field is then added to the toy model, and we demonstrate that 3+1- dimensional Kaluza-Klein zero mode solutions do not exist when the four spatial dimensions are treated isotropically. To recover 3 + 1-dimensional chiral fermions dynamically localized to the domain wall, we must postulate the breaking of full 4-dimensional rotational symmetry down to the subgroup of rotations which mix the usual 3-dimensional spatial directions and fix the extra-dimensional axis in addition to the anisotropy between space and time.

Jayne E. Thompson; Raymond R. Volkas

2010-08-12T23:59:59.000Z

144

Thermodynamics of free Domain Wall fermions  

E-Print Network (OSTI)

Studying various thermodynamic quantities for the free domain wall fermions for both finite and infinite fifth dimensional extent N_5, we find that the lattice corrections are minimum for $N_T\\geq10$ for both energy density and susceptibility, for its irrelevant parameter M in the range 1.45-1.50. The correction terms are, however, quite large for small lattice sizes of $N_T\\leq8$. We propose modifications of the domain wall operator, as well as the overlap operator, to reduce the finite cut-off effects to within 10% of the continuum results of the thermodynamic quantities for the currently used N_T=6-8 lattices. Incorporating chemical potential, we show that \\mu^2 divergences are absent for a large class of such domain wall fermion actions although the chiral symmetry is broken for $\\mu\

R. V. Gavai; Sayantan Sharma

2008-11-19T23:59:59.000Z

145

Eminent Domain (Indiana) | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

(Indiana) (Indiana) Eminent Domain (Indiana) < Back Eligibility Agricultural Commercial Construction Fed. Government Fuel Distributor General Public/Consumer Industrial Installer/Contractor Institutional Investor-Owned Utility Local Government Low-Income Residential Multi-Family Residential Municipal/Public Utility Nonprofit Residential Retail Supplier Rural Electric Cooperative Schools State/Provincial Govt Systems Integrator Transportation Tribal Government Utility Savings Category Alternative Fuel Vehicles Hydrogen & Fuel Cells Buying & Making Electricity Water Home Weatherization Solar Wind Program Info State Indiana Program Type Siting and Permitting Provider Indiana Association of Cities and Towns Utilities, corporations, and gas storage facilities may invoke the law of eminent domain in certain circumstances, as provided for in this

146

Standing gravitational waves from domain walls  

SciTech Connect

We construct a plane symmetric, standing gravitational wave for a domain wall plus a massless scalar field. The scalar field can be associated with a fluid which has the properties of 'stiff' matter, i.e., matter in which the speed of sound equals the speed of light. Although domain walls are observationally ruled out in the present era, the solution has interesting features which might shed light on the character of exact nonlinear wave solutions to Einstein's equations. Additionally this solution may act as a template for higher dimensional 'brane-world' model standing waves.

Gogberashvili, Merab [Andronikashvili Institute of Physics, 6 Tamarashvili Street, Tbilisi 0177 (Georgia); Javakhishvili Tbilisi State University, 3 Chavchavadze Avenue, Tbilisi 0128 (Georgia); California State University, Fresno, Physics Department, Fresno, California 93740-8031 (United States); Myrzakul, Shynaray [Department of General and Theoretical Physics, Gumilev Eurasian National University, Astana, 010008 (Kazakhstan); California State University, Fresno, Physics Department, Fresno, California 93740-8031 (United States); Singleton, Douglas [California State University, Fresno, Physics Department, Fresno, California 93740-8031 (United States); Institute of Gravitation and Cosmology, Peoples' Friendship University of Russia, Moscow 117198 (Russian Federation)

2009-07-15T23:59:59.000Z

147

Parallel computation for shallow water flow: a domain decomposition approach  

Science Conference Proceedings (OSTI)

Keywords: additive Schwarz preconditioning, domain decomposition, finite elements, parallelization, shallow water

L. Paglieri; D. Ambrosi; L. Formaggia; A. Quarteroni; A. L. Scheinine

1997-09-01T23:59:59.000Z

148

Assignment of human myocyte-specific enhancer binding factor 2C (hMEF2C) to human chromosome 5q14 and evidence that MEF2C is evolutionarily conserved  

SciTech Connect

Human myocyte-specific enhancer binding factor 2C (hMEF2C) belongs to the MEF2 subfamily of the MADS (MCM1, AGAMOUS, DEF A, serum response factor) family of transcription factors. Members of the MADS family share a conserved domain - the MADS domain - that is necessary for DNA binding. Highly conserved versions of the MADS domain and of an adjacent domain that is known as the MEF2 domain are found in members of the MEF2 subfamily. Both of these domains are necessary for binding to the MEF2 regulatory element. This regulatory element is known to be functionally important in a variety of muscle-specific genes and possibly in the brain creatine kinase gene. The MEF2C gene product activates transcription by binding to the MEF2 element. hMEF2C is expressed at high levels in postmitotic neurons in the brain, where it is most abundant in the cerebral cortex, and is also expressed in differentiated myotubes. Several lines of evidence suggest the existence of a rat homologue of MEF2C, and a mouse homologue has been cloned. The mouse gene was mapped to mouse chromosome 13 in a region that is syntenic to human 5q13-q15. 12 refs., 1 fig.

Krainc, D.; Lipton, S.A. [Harvard Medical School, Boston, MA (United States); Haas, M.; Ward, D.C. [Yale Univ. School of Medicine, New Haven, CT (United States)] [and others

1995-10-10T23:59:59.000Z

149

Sgf29 binds histone H3K4me2/3 and is required for SAGA complex recruitment and histone H3 acetylation  

SciTech Connect

The SAGA (Spt-Ada-Gcn5 acetyltransferase) complex is an important chromatin modifying complex that can both acetylate and deubiquitinate histones. Sgf29 is a novel component of the SAGA complex. Here, we report the crystal structures of the tandem Tudor domains of Saccharomyces cerevisiae and human Sgf29 and their complexes with H3K4me2 and H3K4me3 peptides, respectively, and show that Sgf29 selectively binds H3K4me2/3 marks. Our crystal structures reveal that Sgf29 harbours unique tandem Tudor domains in its C-terminus. The tandem Tudor domains in Sgf29 tightly pack against each other face-to-face with each Tudor domain harbouring a negatively charged pocket accommodating the first residue alanine and methylated K4 residue of histone H3, respectively. The H3A1 and K4me3 binding pockets and the limited binding cleft length between these two binding pockets are the structural determinants in conferring the ability of Sgf29 to selectively recognize H3K4me2/3. Our in vitro and in vivo functional assays show that Sgf29 recognizes methylated H3K4 to recruit the SAGA complex to its targets sites and mediates histone H3 acetylation, underscoring the importance of Sgf29 in gene regulation.

Bian, Chuanbing; Xu, Chao; Ruan, Jianbin; Lee, Kenneth K.; Burke, Tara L.; Tempel, Wolfram; Barsyte, Dalia; Li, Jing; Wu, Minhao; Zhou, Bo O.; Fleharty, Brian E.; Paulson, Ariel; Allali-Hassani, Abdellah; Zhou, Jin-Qiu; Mer, Georges; Grant, Patrick A.; Workman, Jerry L.; Zang, Jianye; Min, Jinrong (Toronto); (Stowers); (UST - China); (UV); (Chinese Aca. Sci.); (MCCM)

2011-09-28T23:59:59.000Z

150

Adaptive mesh generation for curved domains  

Science Conference Proceedings (OSTI)

This paper considers the technologies needed to support the creation of adaptively constructed meshes for general curved three-dimensional domains and outlines one set of solutions for providing them. A brief review of an effective way to integrate mesh ... Keywords: adaptive meshes, anisotropic meshes, curved meshes

Mark S. Shephard; Joseph E. Flaherty; Kenneth E. Jansen; Xiangrong Li; Xiaojuan Luo; Nicolas Chevaugeon; Jean-Franois Remacle; Mark W. Beall; Robert M. O'Bara

2005-02-01T23:59:59.000Z

151

Combinational domain encryption for still visual data  

Science Conference Proceedings (OSTI)

Image data has distinct regions of different importance. This property of image data has extensively been used to develop partial encryption techniques, but it is still unnoticed for total encryption. Providing similar security level to data of varied ... Keywords: Arnold cat map, Combinational domain, Edge detection, Net pixel change ratio, Statistical analysis

Nidhi Taneja; Balasubramanian Raman; Indra Gupta

2012-08-01T23:59:59.000Z

152

Diversification for multi-domain result sets  

Science Conference Proceedings (OSTI)

Multi-domain search answers to queries spanning multiple entities, like "Find a hotel in Milan close to a concert venue, a museum and a good restaurant", by producing ranked sets of entity combinations that maximize relevance, measured by a function ...

Alessandro Bozzon; Marco Brambilla; Piero Fraternali; Marco Tagliasacchi

2012-07-01T23:59:59.000Z

153

Learning conjunctive concepts in structural domains  

Science Conference Proceedings (OSTI)

We study the problem of learning conjunctive concepts from examples on structural domains like the blocks world. nus class of concepts is formally defined and it is shown that even for samples in which each example (positive or negative) is a two-object ...

David Haussler

1987-07-01T23:59:59.000Z

154

Spectral Domain Boundaries in Cellular Automata  

Science Conference Proceedings (OSTI)

Let A^{Z^D} be the Cantor space of Z^D-indexed configurations in a finite alphabet A, and let ? be the Z^D-action of shifts on A^{Z^D}. A cellular automaton is a continuous, ?-commuting self-map ? of A^{Z^D}, and a ?-invariant ... Keywords: Cellular automaton, defect, domain boundary, kink, subshift

Marcus Pivato

2007-11-01T23:59:59.000Z

155

Analysis of interrogatives in different domains  

Science Conference Proceedings (OSTI)

The aim of this work is twofold: to quantify the distinct interrogative types in different domains for European Portuguese, and to discuss the weight of the linguistic features that best describe these structures, in order to model interrogatives in ... Keywords: interrogatives, prosody, punctuation

Helena Moniz; Fernando Batista; Isabel Trancoso; Ana Isabel Mata

2010-03-01T23:59:59.000Z

156

Data challenges of time domain astronomy  

Science Conference Proceedings (OSTI)

Astronomy has been at the forefront of the development of the techniques and methodologies of data intensive science for over a decade with large sky surveys and distributed efforts such as the Virtual Observatory. However, it faces a new data deluge ... Keywords: Astronomy, Classification, Time domain, Virtual observatory

Matthew J. Graham; S. G. Djorgovski; Ashish Mahabal; Ciro Donalek; Andrew Drake; Giuseppe Longo

2012-10-01T23:59:59.000Z

157

Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding  

Science Conference Proceedings (OSTI)

Ash2L is a core component of the MLL family histone methyltransferases and has an important role in regulating the methylation of histone H3 on lysine 4. Here, we report the crystal structure of the N-terminal domain of Ash2L and reveal a new function of Ash2L. The structure shows that Ash2L contains an atypical PHD finger that does not have histone tail-binding activity. Unexpectedly, the structure shows a previously unrecognized winged-helix motif that directly binds to DNA. The DNA-binding-deficient mutants of Ash2L reduced Ash2L localization to the HOX locus. Strikingly, a single mutation in Ash2L{sub WH} (K131A) breaks the chromatin domain boundary, suggesting that Ash2L also has a role in chromosome demarcation.

Chen, Yong; Wan, Bingbing; Wang, Kevin C.; Cao, Fang; Yang, Yuting; Protacio, Angeline; Dou, Yali; Chang, Howard Y.; Lei, Ming (Michigan-Med); (HHMI)

2011-09-06T23:59:59.000Z

158

Ovine placental lactogen binds specifically to endometrial glands of the ovine uterus  

E-Print Network (OSTI)

A hormonal servomechanism has been proposed to regulate differentiation and function of the endometrial glandular epithelium (GE) in the ovine uterus during pregnancy that involves sequential actions of estrogen, progesterone, ovine interferon tau (IFN[T]), placental lactogen (oPL), and placental growth hormone (oGH). The biological actions of oPL in vitro are mediated by homodimerization of the PRL receptor (oPRLR) as well as heterodimerization of the oPRLR and oGH receptor (oGHR). The objectives of this study were to: (1) determine effects of intrauterine oPL, oGH and their combination on endometrial histoarchitecture and gene expression; (2) localize and characterize binding sites for oPL in the ovine uterus in vivo using an in situ ligand binding assay; and (3) determine temporal and spatial alterations in STAT 1, 3 and 5 expression in the pregnant ovine uterus. Intrauterine infusion of oPL and/or oGH following IFN[T] into ovariectomized ewes treated daily with progesterone differentially affected endometrial gland number and expression of uterine milk proteins and osteopontin. However, neither hormone affected PRLR, IGF-I or IGF-II mRNA levels in the endometrium. A chimeric protein of placental secretory alkaline phosphatase (SEAP) and oPL (SEAP-oPL) was used to identify and characterize binding sites for oPL in frozen sections of interplacentomal endometrium from pregnant ewes. Specific binding of SEAP-oPL was detected in the endometrial GE on Days 30, 60, 90, and 120 of pregnancy. In Day 90 endometrium, SEAP-oPL binding to the endometrial GE was displaced completely by oPL and oPRL, but only partially by oGH. Binding experiments using the extracellular domain of the oPRLR also showed that iodinated oPL binding could be competed by oPRL and oPL, but not by oGH. Collectively, results indicate that oPL binds to receptors in the endometrial glands and that PRL is more effective than GH for competing these binding sites. Thus, effects of oPL on the endometrial glands may be mediated by both PRLR and GHR.

Noel, Sekoni Daouda

2002-01-01T23:59:59.000Z

159

Zebrafish homologs of 16p11.2, a genomic region associated with brain disorders, are active during brain development, and include two deletion dosage sensor genes  

E-Print Network (OSTI)

Deletion or duplication of one copy of the human 16p11.2 interval is tightly associated with impaired brain function, including autism spectrum disorders (ASDs), intellectual disability disorder (IDD) and other phenotypes, ...

Blaker-Lee, Alicia

160

RNA binding protein and binding site useful for expression of recombinant molecules  

DOE Patents (OSTI)

The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

Mayfield, Stephen (Cardiff, CA)

2000-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


161

Use of Cre/loxP recombination to swap cell binding motifs on the adenoviral capsid protein IX  

Science Conference Proceedings (OSTI)

We used Cre/loxP recombination to swap targeting ligands present on the adenoviral capsid protein IX (pIX). A loxP-flanked sequence encoding poly-lysine (pK-binds heparan sulfate proteoglycans) was engineered onto the 3'-terminus of pIX, and the resulting fusion protein allowed for routine virus propagation. Growth of this virus on Cre-expressing cells removed the pK coding sequence, generating virus that could only infect through alternative ligands, such as a tyrosine kinase receptor A (TrkA)-binding motif engineered into the capsid fibre protein for enhanced infection of neuronal cells. We used a similar approach to swap the pK motif on pIX for a sequence encoding a single-domain antibody directed towards CD66c for targeted infection of cancer cells; Cre-mediated removal of the pK-coding sequence simultaneously placed the single-domain antibody coding sequence in frame with pIX. Thus, we have developed a simple method to propagate virus lacking native viral tropism but containing cell-specific binding ligands. - Highlights: > We describe a method to grow virus lacking native tropism but containing novel cell-binding ligands. > Cre/loxP recombination was used to modify the adenovirus genome. > A targeting ligand present on capsid protein IX was removed or replaced using recombination. > Cre-loxP was also used to 'swap' the identity of the targeting ligand present on pIX.

Poulin, Kathy L. [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Tong, Grace; Vorobyova, Olga [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Pool, Madeline [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Kothary, Rashmi [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Parks, Robin J., E-mail: rparks@ohri.ca [Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario (Canada); Centre for Neuromuscular Disease, University of Ottawa, Ottawa, Ontario (Canada); Department of Medicine, University of Ottawa, Ottawa, Ontario (Canada); Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario (Canada)

2011-11-25T23:59:59.000Z

162

A Novel Fold in the Tral Relaxase-Helicase C-Terminal Domain Is Essential for Conjugative DNA Transfer  

Science Conference Proceedings (OSTI)

TraI relaxase-helicase is the central catalytic component of the multiprotein relaxosome complex responsible for conjugative DNA transfer (CDT) between bacterial cells. CDT is a primary mechanism for the lateral propagation of microbial genetic material, including the spread of antibiotic resistance genes. The 2.4-{angstrom} resolution crystal structure of the C-terminal domain of the multifunctional Escherichia coli F (fertility) plasmid TraI protein is presented, and specific structural regions essential for CDT are identified. The crystal structure reveals a novel fold composed of a 28-residue N-terminal {alpha}-domain connected by a proline-rich loop to a compact {alpha}/{beta}-domain. Both the globular nature of the {alpha}/{beta}-domain and the presence as well as rigidity of the proline-rich loop are required for DNA transfer and single-stranded DNA binding. Taken together, these data establish the specific structural features of this noncatalytic domain that are essential to DNA conjugation.

Guogas, Laura M.; Kennedy, Sarah A.; Lee, Jin-Hyup; Redinbo, Matthew R.; (UNC)

2009-06-04T23:59:59.000Z

163

Reasoning with Concrete Domains Carsten Lutz  

E-Print Network (OSTI)

and fea­ ture disagreement. This leads to the new logic ALCF(D), which combines ALC(D) with the logic ALCF problems for the logic ALCF(D) are given. Furthermore, the complexity of rea­ soning with ALCF(D) is formally analyzed. Since reason­ ing with ALCF(D) involves a satisfiability check for the concrete domain

Baader, Franz

164

HYDRATE DISSOCIATION IN A 1-D DOMAIN  

NLE Websites -- All DOE Office Websites (Extended Search)

HYDRATE DISSOCIATION IN A 1-D DOMAIN HYDRATE DISSOCIATION IN A 1-D DOMAIN I. Domain Description 1-D Cartesian system, L x W x H = 1.5 m x 1.0 m x 1.0 m Discretization: 30 x 1 x 1 in (x,y,z) Uniform Δx = 0.05 m each; Δy = Δz = 1 m II. Initial Conditions Pressure: P i = 8 MPa Temperature: T i = 2 o C (for thermal stimulation), T i = 6 o C (for depressurization) Saturations: S H = 0.5, S A = 0.5, S G = 0.0 III. Boundary Conditions At x = X max : No mass or heat flow At x = 0: Constant S A = 1.0 (1) Constant P 0 = P i Constant T 0 = 45 o C Thermal stimulation (2) Constant T 0 = T i = 6 o C Constant P 0 = 2.8 MPa Depressurization to a pressure above the Q-point, no ice formation (3) Constant T 0 = T i = 6 o C Constant P 0 = 0.5 MPa Depressurization to a pressure below the Q-point,

165

Crystal structure of the anti-viral APOBEC3G catalytic domain and functional implications  

SciTech Connect

The APOBEC family members are involved in diverse biological functions. APOBEC3G restricts the replication of human immunodeficiency virus (HIV), hepatitis B virus and retroelements by cytidine deamination on single-stranded DNA or by RNA binding. Here we report the high-resolution crystal structure of the carboxy-terminal deaminase domain of APOBEC3G (APOBEC3G-CD2) purified from Escherichia coli. The APOBEC3G-CD2 structure has a five-stranded {beta}-sheet core that is common to all known deaminase structures and closely resembles the structure of another APOBEC protein, APOBEC2. A comparison of APOBEC3G-CD2 with other deaminase structures shows a structural conservation of the active-site loops that are directly involved in substrate binding. In the X-ray structure, these APOBEC3G active-site loops form a continuous 'substrate groove' around the active centre. The orientation of this putative substrate groove differs markedly (by 90 degrees) from the groove predicted by the NMR structure. We have introduced mutations around the groove, and have identified residues involved in substrate specificity, single-stranded DNA binding and deaminase activity. These results provide a basis for understanding the underlying mechanisms of substrate specificity for the APOBEC family.

Holden, Lauren G.; Prochnow, Courtney; Chang, Y. Paul; Bransteitter, Ronda; Chelico, Linda; Sen, Udayaditya; Stevens, Raymond C.; Goodman, Myron F.; Chen, Xiaojiang S. (USC); (Scripps)

2009-04-07T23:59:59.000Z

166

A Few Graph-Based Relational Numerical Abstract Domains  

Science Conference Proceedings (OSTI)

This article presents the systematic design of a class of relational numerical abstract domains from non-relational ones. Constructed domains represent sets of invariants of the form (vj - vi C), where vj ...

Antoine Min

2002-09-01T23:59:59.000Z

167

Smart Grid Conceptual Actors/Data Flow Diagram- Cross Domain...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Smart Grid Conceptual ActorsData Flow Diagram- Cross Domain Network Focued- Open SGSG-Network TF Smart Grid Conceptual ActorsData Flow Diagram- Cross Domain Network Focued- Open...

168

Structural basis of substrate discrimination and integrin binding by autotaxin  

SciTech Connect

Autotaxin (ATX, also known as ectonucleotide pyrophosphatase/phosphodiesterase-2, ENPP2) is a secreted lysophospholipase D that generates the lipid mediator lysophosphatidic acid (LPA), a mitogen and chemoattractant for many cell types. ATX-LPA signaling is involved in various pathologies including tumor progression and inflammation. However, the molecular basis of substrate recognition and catalysis by ATX and the mechanism by which it interacts with target cells are unclear. Here, we present the crystal structure of ATX, alone and in complex with a small-molecule inhibitor. We have identified a hydrophobic lipid-binding pocket and mapped key residues for catalysis and selection between nucleotide and phospholipid substrates. We have shown that ATX interacts with cell-surface integrins through its N-terminal somatomedin B-like domains, using an atypical mechanism. Our results define determinants of substrate discrimination by the ENPP family, suggest how ATX promotes localized LPA signaling and suggest new approaches for targeting ATX with small-molecule therapeutic agents.

Hausmann, Jens; Kamtekar, Satwik; Christodoulou, Evangelos; Day, Jacqueline E.; Wu, Tao; Fulkerson, Zachary; Albers, Harald M.H.G.; van Meeteren, Laurens A.; Houben, Anna J.S.; van Zeijl, Leonie; Jansen, Silvia; Andries, Maria; Hall, Troii; Pegg, Lyle E.; Benson, Timothy E.; Kasiem, Mobien; Harlos, Karl; Vander Kooi, Craig W.; Smyth, Susan S.; Ovaa, Huib; Bollen, Mathieu; Morris, Andrew J.; Moolenaar, Wouter H.; Perrakis, Anastassis (Pfizer); (Leuven); (Oxford); (NCI-Netherlands); (Kentucky)

2013-09-25T23:59:59.000Z

169

Cooperative Dynamics of a 'Conjugated' Domain Wall in Giant ...  

Science Conference Proceedings (OSTI)

Presentation Title, Cooperative Dynamics of a 'Conjugated' Domain Wall in Giant ... Appropriately designed, such a superstructure can cooperatively move...

170

Exciton binding energy in semiconductor quantum dots  

Science Conference Proceedings (OSTI)

In the adiabatic approximation in the context of the modified effective mass approach, in which the reduced exciton effective mass {mu} = {mu}(a) is a function of the radius a of the semiconductor quantum dot, an expression for the exciton binding energy E{sub ex}(a) in the quantum dot is derived. It is found that, in the CdSe and CdS quantum dots with the radii a comparable to the Bohr exciton radii a{sub ex}, the exciton binding energy E{sub ex}(a) is substantially (respectively, 7.4 and 4.5 times) higher than the exciton binding energy in the CdSe and CdS single crystals.

Pokutnii, S. I., E-mail: Pokutnyi_Sergey@inbox.ru [National Academy of Sciences of Ukraine, G.V. Kurdjumov Institute for Metal Physics (Ukraine)

2010-04-15T23:59:59.000Z

171

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain  

E-Print Network (OSTI)

Ken Chen 1,2 , William A. McLaughlin 1,2 , Benzhuo Lu 1,2 ,Citation: Hou T, Chen K, McLaughlin WA, Lu B, Wang W (2006)

Hou, T J; Chen, K; McLaughlin, W A; Lu, B Z; Wang, W

2006-01-01T23:59:59.000Z

172

Binding energies of hypernuclei and hypernuclear interactions  

SciTech Connect

In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

1996-05-01T23:59:59.000Z

173

Deletions within COL11A1 in Type 2 stickler syndrome detected by multiplex ligation-dependent probe amplification (MLPA)  

E-Print Network (OSTI)

peak ratios romosomes (far left) may differ depending upon the gender of the DNA e deleted region, are not included in either kit. AB E DC P382 del 39 P382 del 49 P381 del 41-42 P382 del 6-43P381 del 8-42 del Exons 6-43 P381 del 15-25 P382 del 16... , Moran RT, Warman M, Ala-Kokko L: Stickler syndrome. In GeneReviews [internet]. Edited by Pagon RA, Bird TC, Dolan CR, Stephens K. Seattle, WA: University of Washington; 2000. updated 2010. 10. Schouten JP, McElgunn CJ, Waaijer R, Zwijnenburg D, Diepvens...

Vijzelaar, Raymon; Waller, Sarah; Errami, Abdellatif; Donaldson, Alan; Lourenco, Teresa; Rodrigues, Marcia; McConnell, Vivienne; Fincham, Gregory; Snead, Martin; Richards, Allan

2013-04-26T23:59:59.000Z

174

Glycosylation Helps Cellulase Enzymes Bind to Plant Cell Walls (Fact Sheet)  

DOE Green Energy (OSTI)

Computer simulations suggest a new strategy to design enhanced enzymes for biofuels production. Large-scale computer simulations predict that the addition of glycosylation on carbohydrate-binding modules can dramatically improve the binding affinity of these protein domains over amino acid mutations alone. These simulations suggest that glycosylation can be used as a protein engineering tool to enhance the activity of cellulase enzymes, which are a key component in the conversion of cellulose to soluble sugars in the production of biofuels. Glycosylation is the covalent attachment of carbohydrate molecules to protein side chains, and is present in many proteins across all kingdoms of life. Moreover, glycosylation is known to serve a wide variety of functions in biological recognition, cell signaling, and metabolism. Cellulase enzymes, which are responsible for deconstructing cellulose found in plant cell walls to glucose, contain glycosylation that when modified can affect enzymatic activity-often in an unpredictable manner. To gain insight into the role of glycosylation on cellulase activity, scientists at the National Renewable Energy Laboratory (NREL) used computer simulation to predict that adding glycosylation on the carbohydrate-binding module of a cellulase enzyme dramatically boosts the binding affinity to cellulose-more than standard protein engineering approaches in which amino acids are mutated. Because it is known that higher binding affinity in cellulases leads to higher activity, this work suggests a new route to designing enhanced enzymes for biofuels production. More generally, this work suggests that tuning glycosylation in cellulase enzymes is a key factor to consider when engineering biochemical conversion processes, and that more work is needed to understand how glycosylation affects cellulase activity at the molecular level.

Not Available

2012-06-01T23:59:59.000Z

175

Communicating oscillatory networks: Frequency Domain Analysis  

E-Print Network (OSTI)

-deterministic models and used the presented techni- que of frequency domain analysis to investigate the differ- ences. The quasi-deterministic models are constructed from exactly the same reaction scheme and kinetic para- meters, however the kinetic functions... significant role in our findings. Note in particular from Additional file 1 Table S4 that the two species that directly perturb the cell cycle (namely p53a and NF-#1;Bn) have low stochasticity, so any noise inherent in their respective net- works does...

Ihekwaba, Adaoha E C; Sedwards, Sean

2011-12-22T23:59:59.000Z

176

Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) | Department  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) Petroleum Pipeline Eminent Domain Permit Procedures (Georgia) < Back Eligibility Commercial Construction Developer Fuel Distributor General Public/Consumer Industrial Investor-Owned Utility Municipal/Public Utility Utility Program Info State Georgia Program Type Environmental Regulations Siting and Permitting Provider Georgia Department of Natural Resources The Petroleum Pipeline Eminent Domain Permit Procedures serve to protect Georgia's natural and environmental resources by requiring permits be issued by the Director of the Environmental Protection Division prior to any petroleum or petroleum product pipe company acquiring property or interests by eminent domain. Monitoring conditions will be issued with

177

Hydrogen Bonding Penalty upon Ligand Binding  

E-Print Network (OSTI)

Ligand binding involves breakage of hydrogen bonds with water molecules and formation of new hydrogen bonds between protein and ligand. In this work, the change of hydrogen bonding energy in the binding process, namely hydrogen bonding penalty, is evaluated with a new method. The hydrogen bonding penalty can not only be used to filter unrealistic poses in docking, but also improve the accuracy of binding energy calculation. A new model integrated with hydrogen bonding penalty for free energy calculation gives a root mean square error of 0.7 kcal/mol on 74 inhibitors in the training set and of 1.1 kcal/mol on 64 inhibitors in the test set. Moreover, an application of hydrogen bonding penalty into a high throughput docking campaign for EphB4 inhibitors is presented, and remarkably, three novel scaffolds are discovered out of seven tested. The binding affinity and ligand efficiency of the most potent compound is about 300 nM and 0.35 kcal/mol per non-hydrogen atom, respectively.

Hongtao Zhao; Danzhi Huang

2011-01-01T23:59:59.000Z

178

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning Stochastic Domain-Wall Depinning in Magnetic Nanowires Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Wednesday, 29 July 2009 00:00 Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

179

Using Non-Government Domain Names | Department of Energy  

NLE Websites -- All DOE Office Websites (Extended Search)

Using Non-Government Domain Names Using Non-Government Domain Names Using Non-Government Domain Names There may be occasion where it is necessary to utilize a non-government domain. The OMB Policies for Federal Agency Public Websites states: Your agency must use only .gov, .mil, or Fed.us domains unless the agency head explicitly determines another domain is necessary for the proper performance of an agency function. This requirement recognizes the proper performance of agency functions includes an obligation for clear and unambiguous public notification of the agency's involvement in or sponsorship of its information dissemination products including public websites. It also recognizes in certain limited circumstances other domains may be necessary for the proper performance of an agency function.

180

Impact on the steam electric power industry of deleting Section 316(a) of the Clean Water Act: Capital costs  

Science Conference Proceedings (OSTI)

Many power plants discharge large volumes of cooling water. In some cases, the temperature of the discharge exceeds state thermal requirements. Section 316(a) of the Clean Water Act (CWA) allows a thermal discharger to demonstrate that less stringent thermal effluent limitations would still protect aquatic life. About 32% of total US steam electric generating capacity operates under Section 316(a) variances. In 1991, the US Senate proposed legislation that would delete Section 316(a) from the CWA. This study, presented in two companion reports, examines how this legislation would affect the steam electric power industry. This report describes alternatives available to nuclear and coal-fired plants currently operating under variances. Data from 38 plants representing 14 companies are used to estimate the national cost of implementing such alternatives. Although there are other alternatives, most affected plants would be retrofitted with cooling towers. Assuming that all plants currently operating under variances would install cooling towers, the national capital cost estimate for these retrofits ranges from $22.7 billion to $24.4 billion (in 1992 dollars). The second report quantitatively and qualitatively evaluates the energy and environmental impacts of deleting the variance. Little justification has been found for removing the Section 316(a) variance from the CWA.

Veil, J.A.

1993-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


181

Study of ferroelectric domain switching by domain wall induced light scattering  

E-Print Network (OSTI)

of an unipolarity in a polydomain ther- mally de-poled SBN crystal is supported by electrical measurements.8 We now- der repolarizing fields the crystal becomes depoled, the de- gree of depoling increasing, partially depoled by +E pulses, is now restored to its single-domain state. We mention that in a single

Osnabrück, Universität

182

Atomic structure of nitrate-binding protein crucial for photosynthetic productivity  

DOE Green Energy (OSTI)

Cyanobacteria, blue-green algae, are the most abundant autotrophs in aquatic environments and form the base of all aquatic food chains by fixing carbon and nitrogen into cellular biomass. The single most important nutrient for photosynthesis and growth is nitrate, which is severely limiting in many aquatic environments particularly the open ocean (1, 2). It is therefore not surprising that NrtA, the solute-binding component of the high-affinity nitrate ABC transporter, is the single-most abundant protein in the plasma membrane of these bacteria (3). Here we describe the first structure of a nitratespecific receptor, NrtA from Synechocystis sp. PCC 6803, complexed with nitrate and determined to a resolution of 1.5. NrtA is significantly larger than other oxyanionbinding proteins, representing a new class of transport proteins. From sequence alignments, the only other solute-binding protein in this class is CmpA, a bicarbonatebinding protein. Therefore, these organisms created a novel solute-binding protein for two of the most important nutrients; inorganic nitrogen and carbon. The electrostatic charge distribution of NrtA appears to force the protein off of the membrane while the flexible tether facilitates the delivery of nitrate to the membrane pore. The structure not only details the determinants for nitrate selectivity in NrtA, but also the bicarbonate specificity in CmpA. Nitrate and bicarbonate transport are regulated by the cytoplasmic proteins NrtC and CmpC, respectively. Interestingly, the residues lining the ligand binding pockets suggest that they both bind nitrate. This implies that the nitrogen and carbon uptake pathways are synchronized by intracellular nitrate and nitrite.3 The nitrate ABC transporter of cyanobacteria is composed of four polypeptides (Figure 1): a high-affinity periplasmic solute-binding lipoprotein (NrtA), an integral membrane permease (NrtB), a cytoplasmic ATPase (NrtD), and a unique ATPase/solute-binding fusion protein (NrtC) that regulates transport (4). NrtA binds both nitrate and nitrite (Kd = 0.3 mM) and is necessary for cell survival when nitrate is the primary nitrogen source (5). The role of NrtA is to scavenge nitrate/nitrite from the periplasm for delivery to the membrane permease, NrtB. The passage of solute through the transmembrane pore is linked to ATP hydrolysis by NrtC and NrtD. NrtD consists of a single ATPase domain. In contrast, NrtC contains both an ATPase domain and a Cterminal solute-binding domain that shares 50% amino acid sequence similarity with NrtA, and is required for the ammonium-mediated inhibition of nitrate transport (6, 7). Aside from the homologous transporter for bicarbonate, CmpABCD, there are no other known examples of ABC transporters that have an ATPase/solute-binding fusion component. The specificity of the nitrate transporter is conferred by NrtA (4). NrtA is ~49% identical (60% similar) in amino acid sequence to the bicarbonate receptor CmpA. In its entirety, it does not have significant homology to any other known protein. To elucidate the molecular determinants of nitrate specificity, we determined the crystal structure of the Synechocystis 6803 NrtA to 1.5 . While the general shape of NrtA is akin to that of other solute binding proteins, NrtA clearly represents a new and unique structural variant of these C clamp proteins. From this structure and sequence alignments of other bicarbonate and nitrate transporters, the molecular basis for solute selectivity is clear and suggests that regulatory domains of both icarbonate and nitrate transport systems bind nitrate. Based on these findings, a model is presented that 4 demonstrates how such synergistic regulation of bicarbonate and nitrate transport is important in conserving energy during the process of carbon fixation and nitrogen assimilation.

Koropatkin, Nicole M.; Pakrasi, Himadri B.; Smith, Thomas J.

2006-06-27T23:59:59.000Z

183

The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier?Gorlin syndrome  

Science Conference Proceedings (OSTI)

The recognition of distinctly modified histones by specialized 'effector' proteins constitutes a key mechanism for transducing molecular events at chromatin to biological outcomes. Effector proteins influence DNA-templated processes, including transcription, DNA recombination and DNA repair; however, no effector functions have yet been identified within the mammalian machinery that regulate DNA replication. Here we show that ORC1 - a component of ORC (origin of replication complex), which mediates pre-DNA replication licensing - contains a bromo adjacent homology (BAH) domain that specifically recognizes histone H4 dimethylated at lysine 20 (H4K20me2). Recognition of H4K20me2 is a property common to BAH domains present within diverse metazoan ORC1 proteins. Structural studies reveal that the specificity of the BAH domain for H4K20me2 is mediated by a dynamic aromatic dimethyl-lysine-binding cage and multiple intermolecular contacts involving the bound peptide. H4K20me2 is enriched at replication origins, and abrogating ORC1 recognition of H4K20me2 in cells impairs ORC1 occupancy at replication origins, ORC chromatin loading and cell-cycle progression. Mutation of the ORC1 BAH domain has been implicated in the aetiology of Meier-Gorlin syndrome (MGS), a form of primordial dwarfism, and ORC1 depletion in zebrafish results in an MGS-like phenotype. We find that wild-type human ORC1, but not ORC1-H4K20me2-binding mutants, rescues the growth retardation of orc1 morphants. Moreover, zebrafish depleted of H4K20me2 have diminished body size, mirroring the phenotype of orc1 morphants. Together, our results identify the BAH domain as a novel methyl-lysine-binding module, thereby establishing the first direct link between histone methylation and the metazoan DNA replication machinery, and defining a pivotal aetiological role for the canonical H4K20me2 mark, via ORC1, in primordial dwarfism.

Kuo, Alex J.; Song, Jikui; Cheung, Peggie; Ishibe-Murakami, Satoko; Yamazoe, Sayumi; Chen, James K.; Patel, Dinshaw J.; Gozani, Or (Stanford); (MSKCC); (Stanford-MED)

2012-07-11T23:59:59.000Z

184

Interaction of the 4S polycyclic hydrocarbon-binding protein with the cytochrome P450c gene  

SciTech Connect

The 4S polycyclic hydrocarbon binding protein has been purified from rat liver and its properties examined. The protein was incubated with subclones from the P450c gene; it specifically interacted with a plasmid that contained the 5'-half of intron 1, exon 1 and 5'-flanking sequences. Exonuclease foot-printing after binding of the 4S protein to portions of the P450c gene showed protection at -200 and -400 bp from exon 1. The region -882 to +2545bp was constructed before a reporter, chloramphenicol acetyl transferase (CAT) gene in a plasmid that contained the SV40 ori, polyA signals, ampicillin resist gene. The P450c region contained promoter and putative regulatory sequences. The construct was transfected into rat hepatocytes, RL-PR-C and into rat hepatoma cells, H-4-11-E. After addition of 3-methylcholanthrene (3MC), CAT expression was induced. When the plasmid was constructed with the P450c fragment inverted, no CAT expression was seen. Deletion of -95 to -665 or from -238 to -660 bp eliminated the expression of CAT in response to 3MC. These experiments indicated the importance of this region in the induction of P450c by 3MC.

Houser, W.H.; Cunningham, C.K.; Hines, R.N.; Bresnick, E.

1987-05-01T23:59:59.000Z

185

Birefringence insensitive optical coherence domain reflectometry system  

DOE Patents (OSTI)

A birefringence insensitive fiber optic optical coherence domain reflectometry (OCDR) system is provided containing non-polarization maintaining (non-PM) fiber in the sample arm and the reference arm without suffering from signal degradation caused by birefringence. The use of non-PM fiber significantly reduces the cost of the OCDR system and provides a disposable or multiplexed section of the sample arm. The dispersion in the reference arm and sample arm of the OCDR system are matched to achieve high resolution imaging. This system is useful in medical applications or for non-medical in situ probes. The disposable section of non-PM fiber in the sample arm can be conveniently replaced when contaminated by a sample or a patient.

Everett, Matthew J. (Livermore, CA); Davis, Joseph G. (Lafayette, CA)

2002-01-01T23:59:59.000Z

186

SO(10) domain-wall brane models  

E-Print Network (OSTI)

We construct domain-wall brane models based on the grand-unification group SO(10), generalising the SU(5) model of Davies, George and Volkas. Motivated by the Dvali-Shifman proposal for the dynamical localisation of gauge bosons, the SO(10) symmetry is spontaneously broken inside the wall. We present two scenarios: in the first, the unbroken subgroup inside the wall is SU(5) x U(1)X, and in the second it is the left-right symmetry group SU(3) x SU(2)L x SU(2)R x U(1)B-L. In both cases we demonstrate that the phenomenologically-correct fermion zero modes can be localised to the wall, and we briefly discuss how the symmetry-breaking dynamics may be extended to induce breaking to the standard model group with subsequent electroweak breaking. Dynamically localised gravity is realised through the type 2 Randall-Sundrum mechanism.

Jayne E. Thompson; Raymond R. Volkas

2009-08-28T23:59:59.000Z

187

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

188

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

189

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

190

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

191

Stochastic Domain-Wall Depinning in Magnetic Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Stochastic Domain-Wall Depinning in Magnetic Nanowires Print Reliably controlling the motion of magnetic domain walls along magnetic nanowires is a key requirement for current technological development of novel classes of logic and storage devices, but understanding the nature of non-deterministic domain-wall motion remains a scientific challenge. A statistical analysis of high-resolution magnetic soft x-ray microscopy images by a Berkeley Lab-University of Hamburg group has now revealed that the stochastic behavior of the domain-wall depinning field in notch-patterned Ni80Fe20 (permalloy) nanowires depends strongly on the wire width and the notch depth. This result both provides valuable insight into the motion of magnetic-domain walls and opens a path to further technological developments in spintronics applications.

192

Physical analysis of the region deleted in the t{sup w18} allele of the mouse tcl-4 complementation group  

SciTech Connect

We have generated a YAC config of at least 3.3 Mb from the proximal region of In(17)4 of mouse chromosome 17. This region corresponds to DNA lost in the gastrulation mutant t{sup w18}, which belongs to the tcl-4 complementation group. Our most proximal and distal probes lie within the deletion-3.3 Mb apart-indicating that we have not cloned the entire region. The deleted region is contained in a genetic interval of less than 1 cM, suggesting that some suppression of recombination must occur. 36 refs., 5 figs., 2 tabs.

Barclay, J.; King, T.F.; Crossley, P.H. [Imperial College of Science, Technology and Medicine, London (United Kingdom)] [and others] [Imperial College of Science, Technology and Medicine, London (United Kingdom); and others

1996-08-15T23:59:59.000Z

193

V-079: ISC BIND AAAA Record Lookup Handling Assertion Failure...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Lets Remote Users Deny Service T-633: BIND RRSIG RRsets Negative Caching Off-by-one Bug Lets Remote Users Deny Service U-183: ISC BIND DNS Resource Records Handling Vulnerability...

194

U-101: Mozilla Firefox / Thunderbird / SeaMonkey XBL Binding...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

to a use-after-free error in the "nsXBLDocumentInfo::ReadPrototypeBindings()" method when handling XBL bindings in a hash table and can be exploited to cause a cycle collector to...

195

Interactions of the chondroitin sulfate proteoglycan phosphacan, the extracellular domain of a receptor-type protein tyrosine phosphatase, with neurons, glia, and neural cell adhesion molecules  

E-Print Network (OSTI)

Abstract. Phosphacan is a chondroitin sulfate proteoglycan produced by glial cells in the central nervous system, and represents the extracellular domain of a receptor-type protein tyrosine phosphatase (RPTPg'/B). We previously demonstrated that soluble phosphacan inhibited the aggregation of microbeads coated with N-CAM or Ng-CAM, and have now found that soluble ~25I-phosphacan bound reversibly to these neural cell adhesion molecules, but not to a number of other cell surface and extracellular matrix proteins. The binding was saturable, and Scatchard plots indicated a single high affinity binding site with a Kd of,~0.1 nM. Binding was reduced by "~15 % after chondroitinase treatment, and free chondroitin sulfate was only moderately inhibitory, indicating that the phosphacan core glycoprotein accounts for most of the

Peter Milev; David R. Friedl; Takeshi Sakurai; Laina Karthikeyan; Manuela Flad; Ren K. Margolis; Martin Grumet; Richard U. Margolis

1994-01-01T23:59:59.000Z

196

Definition: Time-Domain Electromagnetics | Open Energy Information  

Open Energy Info (EERE)

Definition Definition Edit with form History Facebook icon Twitter icon » Definition: Time-Domain Electromagnetics Jump to: navigation, search Dictionary.png Time-Domain Electromagnetics Time-domain electromagnetic (TDEM) surveys are active-source soundings which provide information about the electrical structure of the shallow subsurface.[1] View on Wikipedia Wikipedia Definition Transient electromagnetics, (also time-domain electromagnetics / TDEM), is a geophysical exploration technique in which electric and magnetic fields are induced by transient pulses of electric current and the subsequent decay response measured. TEM / TDEM methods are generally able to determine subsurface electrical properties, but are also sensitive to subsurface magnetic properties in applications like UXO detection and

197

Organic Solar Cells: Absolute Measurement of Domain Composition...  

NLE Websites -- All DOE Office Websites (Extended Search)

Organic Solar Cells: Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in Solar Cells Organic Solar Cells: Absolute Measurement of...

198

Time-Domain Electromagnetics At Long Valley Caldera Area (Sorey...  

Open Energy Info (EERE)

released results from 158 time-domain electromagnetic (TDEM) soundings and, with Chevron Resources, a total of 77 magnetotelluric (MT) stations. Reinterpretations of the...

199

The domain structure of Helicobacter pylori DnaB  

E-Print Network (OSTI)

helicase: the N-terminal domain can be dispensable for helicase activity whereas the extreme C-terminal region is essential for its function

Ram Gopal Nitharwal; Subhankar Paul; Ashraf Dar; Nirupam Roy Choudhury; Rajesh K Soni; Dhaneswar Prusty; Sukrat Sinha; Tara Kashav; Gauranga Mukhopadhyay; Tapan Kumar Chaudhuri; Samudrala Gourinath; Suman Kumar Dhar

2006-01-01T23:59:59.000Z

200

Iran Thomas Auditorium, 8600 Charged Domain Walls in Ferroelectrics  

NLE Websites -- All DOE Office Websites (Extended Search)

Monday, February 4, 2013 11:00 am Iran Thomas Auditorium, 8600 Charged Domain Walls in Ferroelectrics Alexander K. Tagantsev Ceramics Laboratory, Swiss Federal Institute of...

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


201

Applying pomdps to dialog systems in the troubleshooting domain  

E-Print Network (OSTI)

This paper reports on progress applying partially observable Markov decision processes (POMDPs) to a commercial dialog domain: troubleshooting. In the troubleshooting domain, a spoken dialog system helps a user to fix a product such as a failed DSL connection. Past work has argued that a POMDP is a principled approach to building spoken dialog systems in the simpler slot-filling domain; this paper explains how the POMDPs formulation can be extended to the more complex troubleshooting domain. Results from dialog simulation verify that a POMDP outperforms a handcrafted baseline. 1

Jason D. Williams

2007-01-01T23:59:59.000Z

202

National Geothermal Data System (NGDS) Geothermal Data Domain...  

Open Energy Info (EERE)

National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Jump to: navigation, search OpenEI Reference LibraryAdd to library...

203

Jamming Behavior of Domains in a Spiral Antiferromagnetic System  

NLE Websites -- All DOE Office Websites (Extended Search)

spectroscopy, this research shows that the domains of a spiral antiferromagnet enter a jammed state at the onset of long-range order. Researchers found that slow thermal...

204

Hepatocyte-specific deletion of the keap1 gene activates Nrf2 and confers potent resistance against acute drug toxicity  

Science Conference Proceedings (OSTI)

Nrf2 is a key regulator of many detoxifying enzyme genes, and cytoplasmic protein Keap1 represses the Nrf2 activity under quiescent conditions. Germ line deletion of the keap1 gene results in constitutive activation of Nrf2, but the pups unexpectedly died before weaning. To investigate how constitutive activation of Nrf2 influences the detoxification system in adult mice, we generated mice bearing a hepatocyte-specific disruption of the keap1 gene. Homozygous mice were viable and their livers displayed no apparent abnormalities, but nuclear accumulation of Nrf2 is elevated. Microarray analysis revealed that, while many detoxifying enzyme genes are highly expressed, some of the typical Nrf2-dependent genes are only marginally increased in the Keap1-deficient liver. The mutant mice were significantly more resistant to toxic doses of acetaminophen than control animals. These results demonstrate that chronic activation of Nrf2 confers animals with resistance to xenobiotics without affecting the morphological and physiological integrity of hepatocytes.

Okawa, Hiromi [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Motohashi, Hozumi [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Kobayashi, Akira [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan); Aburatani, Hiroyuki [Research Center for Advance Science and Technology, University of Tokyo, Tokyo 153-8904 (Japan); Kensler, Thomas W. [Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205 (United States); Yamamoto, Masayuki [Graduate School of Comprehensive Human Sciences, Center for Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan) and ERATO Environmental Response Project, Japan Science and Technology Corporation, 1-1-1 Tennoudai, Tsukuba 305-8577 (Japan)]. E-mail: masi@tara.tsukuba.ac.jp

2006-01-06T23:59:59.000Z

205

A nuclear cap-binding complex binds Balbiani ring pre-mRNA cotranscriptionally and accompanies the ribonucleoprotein particle during nuclear export  

E-Print Network (OSTI)

Abstract. In vertebrates, a nuclear cap-binding complex (CBC) formed by two cap-binding proteins, CBP20 and CBP80, is involved in several steps of RNA metabolism, including pre-mRNA splicing and nuclear export of some RNA polymerase II-transcribed U snRNAs. The CBC is highly conserved, and antibodies against human CBP20 cross-react with the CBP20 counterpart in the dipteran Chironomus tentans. Using immunoelectron microscopy, the in situ association of CBP20 with a specific pre-mRNP particle, the Balbiani ring particle, has been analyzed at different stages of pre-mRNA synthesis, maturation, and nucleo-cytoplasmic transport. We demonstrate that CBP20 binds to the nascent pre-mRNA shortly after transcription initiation, stays in the RNP particles after splicing has been completed, and remains attached to the 5 ' domain during translocation of the RNP through the nuclear pore complex (NPC). The rapid association of CBP20 with nascent RNA transcripts in situ is consistent with the role of CBC in splicing, and the retention of CBC on the RNP during translocation through the NPC supports its proposed involvement in RNA export. "~'N the nucleus of eukaryotic cells, messenger RNA pre-1 / cursors (pre-mRNAs) undergo a series of maturation- ~ reactions before they are exported to the cytoplasm where the mature messenger RNAs (mRNAs) can direct protein synthesis. One of these maturation events is the addition of a monomethylated guanosine residue to the first encoded nucleotide of the RNA via a 5'-5 ' triphosphate linkage (Shatkin, 1976). This reaction occurs on all transcripts synthesized by RNA polymerase II shortly after the start of transcription (Salditt-Georgieff et al., 1980; Rasmussen and Lis, 1993). The resulting cap structure is implicated in several aspects of pre-mRNA and mRNA metabolism. The cap structure increases RNA stability, and is required for efficient translation initiation, premRNA

Neus Visa; Elisa Izaurralde; Bertil Daneholt; Iain W. Mattaj

1996-01-01T23:59:59.000Z

206

Characterization of a baculovirus nuclear localization signal domain in the late expression factor 3 protein  

Science Conference Proceedings (OSTI)

The baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) single-stranded DNA binding protein LEF-3 is a multi-functional protein that is required to transport the helicase protein P143 into the nucleus of infected cells where they function to replicate viral DNA. The N-terminal 56 amino acid region of LEF-3 is required for nuclear transport. In this report, we analyzed the effect of site-specific mutagenesis of LEF-3 on its intracellular distribution. Fluorescence microscopy of expression plasmid-transfected cells demonstrated that the residues 28 to 32 formed the core nuclear localization signal, but other adjacent positively-charged residues augmented these sequences. Comparison with other group I Alphabaculoviruses suggested that this core region functionally duplicated residues including 18 and 19. This was demonstrated by the loss of nuclear localization when the equivalent residues (18 to 20) in Choristoneura fumiferana nucleopolyhedrovirus (CfMNPV) LEF-3 were mutated. The AcMNPV LEF-3 nuclear localization domain was also shown to drive nuclear transport in mammalian cells indicating that the protein nuclear import systems in insect and mammalian cells are conserved. We also demonstrated by mutagenesis that two conserved cysteine residues located at 82 and 106 were not essential for nuclear localization or for interaction with P143. However, by using a modified construct of P143 that localized on its own to the nucleus, we demonstrated that a functional nuclear localization domain on LEF-3 was required for interaction between LEF-3 and P143.

Au, Victoria; Yu Mei [Department of Microbiology and Immunology, Queen's University, Kingston, ON, K7L 3N6 (Canada); Carstens, Eric B. [Department of Microbiology and Immunology, Queen's University, Kingston, ON, K7L 3N6 (Canada)], E-mail: Carstens@queensu.ca

2009-03-01T23:59:59.000Z

207

NMR structure of the N-terminal domain of the replication initiator protein DnaA  

DOE Green Energy (OSTI)

DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 Angstrom based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.

Wemmer, David E.; Lowery, Thomas J.; Pelton, Jeffrey G.; Chandonia, John-Marc; Kim, Rosalind; Yokota, Hisao; Wemmer, David E.

2007-08-07T23:59:59.000Z

208

Catheter guided by optical coherence domain reflectometry  

DOE Patents (OSTI)

A guidance and viewing system based on multiplexed optical coherence domain reflectometry is incorporated into a catheter, endoscope, or other medical device to measure the location, thickness, and structure of the arterial walls or other intra-cavity regions at discrete points on the medical device during minimally invasive medical procedures. The information will be used both to guide the device through the body and to evaluate the tissue through which the device is being passed. Multiple optical fibers are situated along the circumference of the device. Light from the distal end of each fiber is directed onto the interior cavity walls via small diameter optics (such as gradient index lenses and mirrored corner cubes). Both forward viewing and side viewing fibers can be included. The light reflected or scattered from the cavity walls is then collected by the fibers and multiplexed at the proximal end to the sample arm of an optical low coherence reflectometer. The system may also be implemented in a nonmedical inspection device.

Everett, Matthew (Pleasanton, CA); Colston, Billy W. (Livermore, CA); Da Silva, Luiz B. (Danville, CA); Matthews, Dennis (Moss Beach, CA)

2002-01-01T23:59:59.000Z

209

Visualisation of Tensor Time Domain Electromagnetic Data  

DOE Green Energy (OSTI)

Long Offset Time Domain Electromagnetic (LOTEM) measurements traditionally use a single current source. By using a second source, a tensor analysis technique analogous to that used in DC resistivity multiple-source bipole-dipole surveying, is possible. An instantaneous apparent resistivity tensor is defined as the relationship between the time varying (total) electric field and the DC half space current density vectors due to each source. If the sources are dipoles the three coordinate invariant apparent resistivities of the tensor are independent of source orientation. For a uniform half space, one of the invariants is virtually constant in time, deviating from the half space resistivity by a maximum of 6%. This method provides a way in which the complicated data set obtained during a tensor LOTEM survey can be presented in a compact and intelligible form, and has many advantages over conventional methods of analyzing LOTEM data particularly where the resistivity distribution is three dimensional (3D). Results from a 3D resistivity model of an idealized geothermal reservoir and outflow structure are used to illustrate the power of this analysis.

Caldwell, T.G.; Bibby, H.M.

1995-01-01T23:59:59.000Z

210

WHERE MULTIFUNCTIONAL DNA REPAIR PROTEINS MEET: MAPPING THE INTERACTION DOMAINS BETWEEN XPG AND WRN  

Science Conference Proceedings (OSTI)

The rapid recognition and repair of DNA damage is essential for the maintenance of genomic integrity and cellular survival. Multiple complex and interconnected DNA damage responses exist within cells to preserve the human genome, and these repair pathways are carried out by a specifi c interplay of protein-protein interactions. Thus a failure in the coordination of these processes, perhaps brought about by a breakdown in any one multifunctional repair protein, can lead to genomic instability, developmental and immunological abnormalities, cancer and premature aging. This study demonstrates a novel interaction between two such repair proteins, Xeroderma pigmentosum group G protein (XPG) and Werner syndrome helicase (WRN), that are both highly pleiotropic and associated with inherited genetic disorders when mutated. XPG is a structure-specifi c endonuclease required for the repair of UV-damaged DNA by nucleotide excision repair (NER), and mutations in XPG result in the diseases Xeroderma pigmentosum (XP) and Cockayne syndrome (CS). A loss of XPG incision activity results in XP, whereas a loss of non-enzymatic function(s) of XPG causes CS. WRN is a multifunctional protein involved in double-strand break repair (DSBR), and consists of 35 DNA-dependent helicase, 35 exonuclease, and single-strand DNA annealing activities. Nonfunctional WRN protein leads to Werner syndrome, a premature aging disorder with increased cancer incidence. Far Western analysis was used to map the interacting domains between XPG and WRN by denaturing gel electrophoresis, which separated purifi ed full length and recombinant XPG and WRN deletion constructs, based primarily upon the length of each polypeptide. Specifi c interacting domains were visualized when probed with the secondary protein of interest which was then detected by traditional Western analysis using the antibody of the secondary protein. The interaction between XPG and WRN was mapped to the C-terminal region of XPG as well as the C-terminal region of WRN. The physical interaction between XPG and WRN links NER, (made evident by the disease XP) with DSBR, which imparts additional knowledge of the overlapping nature of these two proteins and the previously distinct DNA repair pathways they are associated with. Since genomic integrity is constantly threatened by both endogenous and exogenous (internal and external) damage, understanding the roles of these proteins in coordinating DNA repair processes with replication will signifi cantly further understanding how defects instigate physiological consequences in response to various DNA damaging sources. This ultimately contributes to our understanding of cancer and premature aging.

Rangaraj, K.; Cooper, P.K.; Trego, K.S.

2009-01-01T23:59:59.000Z

211

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM DO BIOFUELS LIFE CYCLE  

E-Print Network (OSTI)

ANDERSON-TEIXEIRA FINAL PROOF.DOCX (DO NOT DELETE) 3/7/2011 9:29 AM 589 DO BIOFUELS LIFE CYCLE ANALYSES ACCURATELY QUANTIFY THE CLIMATE IMPACTS OF BIOFUELS-RELATED LAND USE CHANGE? Kristina J. Anderson in determining the sustainability of biofuels. To ensure that legal standards are effective in limiting climate

DeLucia, Evan H.

212

A domain of spacetime intervals in general relativity  

E-Print Network (OSTI)

Beginning from only a countable dense set of events and the causality relation, it is possible to reconstruct a globally hyperbolic spacetime in a purely order theoretic manner. The ultimate reason for this is that globally hyperbolic spacetimes belong to a category that is equivalent to a special category of domains called interval domains.

Keye Martin; Prakash Panangaden

2004-07-26T23:59:59.000Z

213

Domain analysis on an electronic health records system  

Science Conference Proceedings (OSTI)

Electronic Health Records (EHR) have been proposed as a means for managing the technical and organisational complexity that arises in modern healthcare. Different EHR systems are being developed around the world, and within individual countries, different ... Keywords: electronic health record, feature oriented domain analysis, healthcare domain

Xiaocheng Ge; Richard F. Paige; John A. McDermid

2009-10-01T23:59:59.000Z

214

Frequency-domain constructed redundant bases for denoising  

Science Conference Proceedings (OSTI)

In this paper, redundant bases for denoising are constructed completely in the frequency-domain. The advantage of the frequency-domain bases construction approach is that it provides much more flexibility. As a result, the filterbank (basis) can be constructed ... Keywords: denoising, redundant basis, wavelet frames, wavelets

Jianyu Lin; Graham C. Goodwin

2007-04-01T23:59:59.000Z

215

Scholarly research and information practices: a domain analytic approach  

Science Conference Proceedings (OSTI)

This paper deals with information needs, seeking, searching, and uses within scholarly communities by introducing theory from the field of science and technology studies. In particular it contributes to the domain-analytic approach in information science ... Keywords: Computer-mediated communication, Domain-analysis, Information practices, Scientific collaboration, Scientific communication, Writing in the disciplines

J. Fry

2006-01-01T23:59:59.000Z

216

HLP: a next generation inter-domain routing protocol  

Science Conference Proceedings (OSTI)

It is well-known that BGP, the current inter-domain routing protocol, has many deficiencies. This paper describes a hybrid link-state and path-vector protocol called HLP as an alternative to BGP that has vastly better scalability, isolation and convergence ... Keywords: BGP, convergence, inter-domain routing, scalability

Lakshminarayanan Subramanian; Matthew Caesar; Cheng Tien Ee; Mark Handley; Morley Mao; Scott Shenker; Ion Stoica

2005-08-01T23:59:59.000Z

217

Nodal domains on graphs - How to count them and why?  

E-Print Network (OSTI)

The purpose of the present manuscript is to collect known results and present some new ones relating to nodal domains on graphs, with special emphasize on nodal counts. Several methods for counting nodal domains will be presented, and their relevance as a tool in spectral analysis will be discussed.

Ram Band; Idan Oren; Uzy Smilansky

2007-11-21T23:59:59.000Z

218

Nodal domains on graphs - How to count them and why?  

E-Print Network (OSTI)

The purpose of the present manuscript is to collect known results and present some new ones relating to nodal domains on graphs, with special emphasize on nodal counts. Several methods for counting nodal domains will be presented, and their relevance as a tool in spectral analysis will be discussed.

Band, Ram; Smilansky, Uzy

2007-01-01T23:59:59.000Z

219

One-Way Nested Regional Climate Simulations and Domain Size  

Science Conference Proceedings (OSTI)

The impact of domain size on regional climate simulations is explored in the context of a state-of-the-art regional model centered over western Europe. It is found that the quality of the climate simulations is highly dependent on the domain ...

S. Vannitsem; F. Chom

2005-01-01T23:59:59.000Z

220

NEXP TIME-complete description logics with concrete domains  

Science Conference Proceedings (OSTI)

Concrete domains are an extension of Description Logics (DLs) that allow one to integrate reasoning about conceptual knowledge with reasoning about "concrete qualities" of real-world entities such as their sizes, weights, and durations. In this article, ... Keywords: Computational complexity, NExpTime-completeness, concrete domains, description logic, domino problem, post correspondence problem

Carsten Lutz

2004-10-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


221

Using domain-independent problems for introducing formal methods  

Science Conference Proceedings (OSTI)

The key to the integration of formal methods into engineering practice is education. In teaching, domain-independent problems i.e., not requiring prior engineering background offer many advantages. Such problems are widely available, but ... Keywords: domain-independent problems, formal methods, functional predicate calculus, funmath, generic functionals, specification, teaching, word problems

Raymond Boute

2006-08-01T23:59:59.000Z

222

Domain decomposition strategies for nonlinear flow problems in porous media  

Science Conference Proceedings (OSTI)

Domain decomposition (DD) methods, such as the additive Schwarz method, are almost exclusively applied to linearized equations. In the context of nonlinear problems, these linear systems appear as part of a Newton iteration. However, applying DD methods ... Keywords: ASPIN, Domain decomposition, Nonlinear multiphase flow, Nonlinear preconditioning, Nonlinear solvers, Porous media

Jan Ole Skogestad; Eirik Keilegavlen; Jan M. Nordbotten

2013-02-01T23:59:59.000Z

223

A debug interface for debugging multiple domain specific aspect languages  

Science Conference Proceedings (OSTI)

Research in the area of multi-DSAL development has been mainly devoted to enabling the interoperability of multiple aspect mechanisms. Less attention has been given to making programming with multiple aspect languages practical. For domain specific aspect ... Keywords: AspectJ, aspect-oriented programming (AOP), aspect-oriented software engineering (AOSE), awesome, cool, debugging, domain specific languages (DSLs), validate

Yoav Apter; David H. Lorenz; Oren Mishali

2012-03-01T23:59:59.000Z

224

Face recognition in JPEG and JPEG2000 compressed domain  

Science Conference Proceedings (OSTI)

In this paper we investigate the potential of performing face recognition in JPEG and JPEG2000 compressed domain. This is achieved by avoiding full decompression and using transform coefficients as input to face recognition algorithms. We propose a new ... Keywords: Compressed Domain, DCT, DWT, Face Recognition, JPEG, JPEG2000

Kresimir Delac; Mislav Grgic; Sonja Grgic

2009-07-01T23:59:59.000Z

225

Important Cognitive Components of Domain-Specific Search Knowledge  

E-Print Network (OSTI)

the subject-specific terms to enter in a query. For example, many university students often buy electronicImportant Cognitive Components of Domain-Specific Search Knowledge Suresh K. Bhavnani School Many users have acquired a sophisticated understanding of searching the Web in specific domains

Bhavnani, Suresh K.

226

Identification of signatures in biomedical spectra using domain knowledge  

Science Conference Proceedings (OSTI)

Objective: Demonstrate that incorporating domain knowledge into feature selection methods helps identify interpretable features with predictive capability comparable to a state-of-the-art classifier. Methods: Two feature selection methods, one using ... Keywords: Classification of biomedical spectra, Consensus feature sets, Dimensionality reduction, Domain knowledge, Feature selection, Genetic algorithm, L1-norm SVM, Spectral signature

Erinija Pranckeviciene; Ray Somorjai; Richard Baumgartner; Moon-Gu Jeon

2005-11-01T23:59:59.000Z

227

Semantic data integration and monitoring in the railway domain  

Science Conference Proceedings (OSTI)

Information integration is a key for further growth of efficiency in management decisions for the railway domain. In the context of the EU project InteGRail (funded in the 6th Framework Programme) an integration approach leveraged by ontologies known ... Keywords: data and system integration, distributed reasoning, information reuse, monitoring and maintenance, ontology, railway domain, semantic modeling

Jan-Gregor Fischer; Mikhail Roshchin; Gerhard Langer; Michael Pirker

2009-08-01T23:59:59.000Z

228

Decision support for the software product line domain engineering lifecycle  

Science Conference Proceedings (OSTI)

Software product line engineering is a paradigm that advocates the reusability of software engineering assets and the rapid development of new applications for a target domain. These objectives are achieved by capturing the commonalities and variabilities ... Keywords: Domain engineering, Feature models, NLP model inference, Software product lines

Ebrahim Bagheri; Faezeh Ensan; Dragan Gasevic

2012-09-01T23:59:59.000Z

229

Reducing the beta-shift in domain wall fermion simulations  

E-Print Network (OSTI)

The beta-shift induced from dynamical domain wall quarks leads to increased roughness of the gauge field, thus reversing the effect of smoothing from the gauge action improvement. By exploiting the relation of overlap and domain wall fermions in greater detail,we propose an algorithm which reduces the beta-shift to the level of dynamical overlap fermions.

Alban Allkoci; Artan Borici

2006-01-24T23:59:59.000Z

230

Gene encoding herbicide safener binding protein  

DOE Patents (OSTI)

The cDNA encoding safener binding protein (SafBP), also referred to as SBP1, is set forth in FIG. 5 and SEQ ID No. 1. The deduced amino acid sequence is provided in FIG. 5 and SEQ ID No. 2. Methods of making and using SBP1 and SafBP to alter a plant's sensitivity to certain herbicides or a plant's responsiveness to certain safeners are also provided, as well as expression vectors, transgenic plants or other organisms transfected with said vectors and seeds from said plants.

Walton, Jonathan D. (East Lansing, MI); Scott-Craig, John S. (East Lansing, MI)

1999-01-01T23:59:59.000Z

231

Definition: Controlled Source Frequency-Domain Magnetics | Open Energy  

Open Energy Info (EERE)

Frequency-Domain Magnetics Frequency-Domain Magnetics Jump to: navigation, search Dictionary.png Controlled Source Frequency-Domain Magnetics AquaTrackTM, a controlled-source frequency domain magnetics tool (CS-FDM), is a patented invention by Willowstick Technologies. This technique is meant to characterize groundwater conditions and flow patterns up to 1,000 m depth.[1] References ↑ http://pangea.stanford.edu/ERE/pdf/IGAstandard/SGW/2006/kofoed.pdf Ret LikeLike UnlikeLike You like this.Sign Up to see what your friends like. rieved from "http://en.openei.org/w/index.php?title=Definition:Controlled_Source_Frequency-Domain_Magnetics&oldid=590084" Category: Definitions What links here Related changes Special pages Printable version Permanent link Browse properties 429 Throttled (bot load)

232

Controlled Source Frequency-Domain Magnetics At Salt Wells Area  

Open Energy Info (EERE)

Controlled Source Frequency-Domain Magnetics At Salt Wells Area Controlled Source Frequency-Domain Magnetics At Salt Wells Area (Montgomery, Et Al., 2005) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Controlled Source Frequency-Domain Magnetics At Salt Wells Area (Montgomery, Et Al., 2005) Exploration Activity Details Location Salt Wells Area Exploration Technique Controlled Source Frequency-Domain Magnetics Activity Date 2004 - 2004 Usefulness useful DOE-funding Unknown Exploration Basis AMP Resource contracted Willowstick Technologies, LLC to conduct a Controlled Source-Frequency Domain Magnetics (CS-FDM) geophysical investigation at Salt Wells in order to characterize and delineate areas showing the greatest concentrations and highest temperatures of geothermal groundwater. The investigation also sought to map blind faults beneath the

233

Diffusion of liquid domains in lipid bilayer membranes  

E-Print Network (OSTI)

We report diffusion coeffcients of micron-scale liquid domains in giant unilamellar vesicles of phospholipids and cholesterol. The trajectory of each domain is tracked, and the mean square displacement grows linearly in time as expected for Brownian motion. We study domain dffusion as a function of composition and temperature, and measure how diffusion depends on domain size. We find mechanisms of domain diffusion which are consistent with membrane-dominated drag in viscous Lo phases [P.G. Saffman and M. Delbruck, PNAS 72, 3111 (1975)], and bulk-dominated drag for less viscous L$_\\alpha$ phases [B.D.Hughes et al., J. Fluid Mech. 110, 349 (1981)]. Where applicable, we obtain the membrane viscosity and report activation energies of diffusion.

Pietro Cicuta; Sarah L. Keller; Sarah L. Veatch

2006-11-18T23:59:59.000Z

234

Stripe Domain-Structures in a Thin Ferromagnetic Film  

E-Print Network (OSTI)

We present a theory of the stripe domain structure in a thin ferromagnetic film with single-ion easy-axis magnetic anisotropy and long-range dipole interactions, for a wide range of temperatures and applied magnetic field. The domains exist at temperatures below the reorientational phase transition from out-of-plane to in-plane magnetization. The system of stripes can be described as a liquid crystal with a preferred domain-wall orientation. The positional order is destroyed by both thermodynamical meandering of domain walls and by the proliferation of dislocations. Spatial anisotropy generated by the fourth-order exchange energy stabilizes the stripe domain structure and pins its orientation. For any temperature below the reorientational phase transition there exists a critical perpendicular-to-plane magnetic field, which separates multidomain and monodomain states of the film. The theory explains recent experimental observations.

KASHUBA, AB; Pokrovsky, Valery L.

1993-01-01T23:59:59.000Z

235

Domain Decomposition via Explicit/Implicit Time Marching 1 Polynomial Collocation Using a Domain Decomposition Solution to Parabolic  

E-Print Network (OSTI)

Decomposition Solution to Parabolic PDE's via the Penalty Method and Explicit/Implicit Time Marching Kelly Black 1 Abstract A domain decomposition method is examined to solve a time dependent parabolic equation05. (1) Introduction We examine a domain decomposition method for solving a parabolic equation using

236

Reflection-Based Python-C++ Bindings  

Science Conference Proceedings (OSTI)

Python is a flexible, powerful, high-level language with excellent interactive and introspective capabilities and a very clean syntax. As such, it can be a very effective tool for driving physics analysis. Python is designed to be extensible in low-level C-like languages, and its use as a scientific steering language has become quite widespread. To this end, existing and custom-written C or C++ libraries are bound to the Python environment as so-called extension modules. A number of tools for easing the process of creating such bindings exist, such as SWIG and Boost. Python. Yet, the process still requires a considerable amount of effort and expertise. The C++ language has few built-in introspective capabilities, but tools such as LCGDict and CINT add this by providing so-called dictionaries: libraries that contain information about the names, entry points, argument types, etc. of other libraries. The reflection information from these dictionaries can be used for the creation of bindings and so the process can be fully automated, as dictionaries are already provided for many end-user libraries for other purposes, such as object persistency. PyLCGDict is a Python extension module that uses LCG dictionaries, as PyROOT uses CINT reflection information, to allow /cwPython users to access C++ libraries with essentially no preparation on the users' behalf. In addition, and in a similar way, PyROOT gives ROOT users access to Python libraries.

Generowicz, Jacek; Lavrijsen, Wim T.L.P.; Marino, Massimo; Mato, Pere

2004-10-14T23:59:59.000Z

237

HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of apobec  

Science Conference Proceedings (OSTI)

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, represent adaptation for rapid growth in a newly infected host, or reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV -I env coding sequences in 81 very early B SUbtype infections previously shown to have resulted from transmission or expansion of single viruses (n=78) or two closely related viruses (n=3). In these cases the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 envand identified a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either (i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or (ii) in a nucleotide context indicative of APOBEC mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was both embedded in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp4l. We also examined the distribution, extent, and sequence context of insertions and deletions and provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not mutational hotspots. These results provide a detailed view of the process of diversification of HIV-1 following transmission.

Korber, Bette [Los Alamos National Laboratory; Bhattacharya, Tanmoy [Los Alamos National Laboratory; Giorgi, Elena [Los Alamos National Laboratory; Gaschen, B [Los Alamos National Laboratory; Daniels, M [Los Alamos National Laboratory

2009-01-01T23:59:59.000Z

238

Characterization of STIP, a multi-domain nuclear protein, highly conserved in metazoans, and essential for embryogenesis in Caenorhabditis elegans  

Science Conference Proceedings (OSTI)

We report here the identification and characterization of STIP, a multi-domain nuclear protein that contains a G-patch, a coiled-coil, and several short tryptophan-tryptophan repeats highly conserved in metazoan species. To analyze their functional role in vivo, we cloned nematode stip-1 genes and determined the spatiotemporal pattern of Caenorhabditis elegans STIP-1 protein. RNA analyses and Western blots revealed that stip-1 mRNA was produced via trans-splicing and translated as a 95-kDa protein. Using reporter constructs, we found STIP-1 to be expressed at all developmental stages and in many tissue/cell types including worm oocyte nuclei. We found that STIP-1 is targeted to the nucleus and forms large polymers with a rod-like shape when expressed in mammalian cells. Using deletion mutants, we mapped the regions of STIP-1 involved in nuclear import and polymer assembly. We further showed that knockdown of C. elegans stip-1 by RNA interference arrested development and resulted in morphologic abnormalities around the 16-cell stage followed by 100% lethality, suggesting its essential role in worm embryogenesis. Importantly, the embryonic lethal phenotype could be faithfully rescued with Drosophila and human genes via transgenic expression. Our data provide the first direct evidence that STIP have a conserved essential nuclear function across metazoans from worms to humans.

Ji Qiongmei [Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10021 (United States); Huang, C.-H. [Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10021 (United States)]. E-mail: chuang@nybloodcenter.org; Peng Jianbin [Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10021 (United States); Hashmi, Sarwar [Developmental Biology, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10021 (United States); Ye Tianzhang [Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10021 (United States); Chen Ying [Laboratory of Biochemistry and Molecular Genetics, Lindsley F. Kimball Research Institute, New York Blood Center, 310 E 67th Street, New York, NY 10021 (United States)

2007-04-15T23:59:59.000Z

239

Atomic structure of the nuclear pore complex targeting domain of a Nup116 homologue from the yeast, Candida glabrata  

SciTech Connect

The nuclear pore complex (NPC), embedded in the nuclear envelope, is a large, dynamic molecular assembly that facilitates exchange of macromolecules between the nucleus and the cytoplasm. The yeast NPC is an eightfold symmetric annular structure composed of {approx}456 polypeptide chains contributed by {approx}30 distinct proteins termed nucleoporins. Nup116, identified only in fungi, plays a central role in both protein import and mRNA export through the NPC. Nup116 is a modular protein with N-terminal 'FG' repeats containing a Gle2p-binding sequence motif and a NPC targeting domain at its C-terminus. We report the crystal structure of the NPC targeting domain of Candida glabrata Nup116, consisting of residues 882-1034 [CgNup116(882-1034)], at 1.94 {angstrom} resolution. The X-ray structure of CgNup116(882-1034) is consistent with the molecular envelope determined in solution by small-angle X-ray scattering. Structural similarities of CgNup116(882-1034) with homologous domains from Saccharomyces cerevisiae Nup116, S. cerevisiae Nup145N, and human Nup98 are discussed.

Sampathkumar, Parthasarathy; Kim, Seung Joong; Manglicmot, Danalyn; Bain, Kevin T.; Gilmore, Jeremiah; Gheyi, Tarun; Phillips, Jeremy; Pieper, Ursula; Fernandez-Martinez, Javier; Franke, Josef D.; Matsui, Tsutomu; Tsuruta, Hiro; Atwell, Shane; Thompson, Devon A.; Emtage, J. Spencer; Wasserman, Stephen R.; Rout, Michael P.; Sali, Andrej; Sauder, J. Michael; Almo, Steven C.; Burley, Stephen K. (Einstein); (SLAC); (Rockefeller); (UCSF); (Lilly)

2012-10-23T23:59:59.000Z

240

Structure and Mutagenesis of the Parainfluenza Virus 5 Hemagglutinin-Neuraminidase Stalk Domain Reveals a Four-Helix Bundle and the Role of the Stalk in Fusion Promotion  

SciTech Connect

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 {angstrom}, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.

Bose, Sayantan; Welch, Brett D.; Kors, Christopher A.; Yuan, Ping; Jardetzky, Theodore S.; Lamb, Robert A. (NWU); (Stanford-MED)

2012-08-31T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
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We encourage you to perform a real-time search of NLEBeta
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241

Distributed grooming in multi-domain IP/MPLS-DWDM networks  

Science Conference Proceedings (OSTI)

This paper studies distributed multi-domain, multi-layer provisioning (grooming) in IP/MPLS-DWDM networks. Although many multi-domain studies have emerged over the years, these have primarily considered "homogeneous" network layers. Meanwhile, most grooming ... Keywords: inter-domain routing, multi-domain IP-DWDM, multi-domain grooming

Q. Liu; T. Frangieh; F. Xu; C. Xie; N. Ghani; A. Gumaste; T. Lehman; Chin Guok; S. Klasky

2009-11-01T23:59:59.000Z

242

Functionalized Polymers For Binding To Solutes In Aqueous Solutions  

NLE Websites -- All DOE Office Websites (Extended Search)

Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. Available for thumbnail of Feynman Center (505) 665-9090 Email Functionalized Polymers For Binding To Solutes In Aqueous Solutions A functionalized polymer for binding a dissolved molecule in an aqueous solution is presented. The polymer has a backbone polymer to which one or more functional groups are covalently linked. The backbone polymer can be such polymers as polyethylenimine, polyvinylamine, polyallylamine, and polypropylamine. These polymers are generally water-soluble, but can be insoluble when cross-linked. The functional group can be for example diol

243

Hardware device to physical structure binding and authentication  

Science Conference Proceedings (OSTI)

Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

2013-08-20T23:59:59.000Z

244

Method and apparatus for detecting chemical binding  

DOE Patents (OSTI)

The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

2007-07-10T23:59:59.000Z

245

Electrical Currents and Adhesion of Edge-Delete Regions of EVA-to-Glass Module Packaging: Preprint  

DOE Green Energy (OSTI)

Presented at the 2001 NCPV Program Review Meeting: Electrical conductivity pathways from the grounded frame to the cell area in a PV module are reviewed here. Electrical conductivity pathways from the grounded frame to the cell area in a PV module are reviewed here. Measurements are made on 4 inch x 8 inch soda lime (SL) glass substrates with contact patterns defined using 3-mil and 10-mil diameter bead-blast removal of the SnO{sub 2} coating to study the dominant path, which is the EVA/glass interface. The remaining SnO{sub 2} contact strips are separated by what would simulate the module edge delete regions. EVA encapsulated bead-blast surface resistances are 8 x 10{sup 15} ohm/sq compared to 8 x 10{sup 12} ohm/sq for native SL glass surfaces. Adhesion strengths to bead-blast surfaces are 25 to 30 lbs/in. Stress test results on these interfaces after removal from damp heat suggest corrosion of the glass at the glass-EVA interface.

McMahon, T. J.; Jorgensen, G. J.

2001-10-01T23:59:59.000Z

246

Clinical polyomavirus BK variants with agnogene deletion are non-functional but rescued by trans-complementation  

SciTech Connect

High-level replication of polyomavirus BK (BKV) in kidney transplant recipients is associated with the emergence of BKV variants with rearranged (rr) non-coding control region (NCCR) increasing viral early gene expression and cytopathology. Cloning and sequencing revealed the presence of a BKV quasispecies which included non-functional variants when assayed in a recombinant virus assay. Here we report that the rr-NCCR of BKV variants RH-3 and RH-12, both bearing a NCCR deletion including the 5' end of the agnoprotein coding sequence, mediated early and late viral reporter gene expression in kidney cells. However, in a recombinant virus they failed to produce infectious progeny despite large T-antigen and VP1 expression and the formation of nuclear virus-like particles. Infectious progeny was generated when the agnogene was reconstructed in cis or agnoprotein provided in trans from a co-existing BKV rr-NCCR variant. We conclude that complementation can rescue non-functional BKV variants in vitro and possibly in vivo.

Myhre, Marit Renee; Olsen, Gunn-Hege [Department of Microbiology and Virology, Institute of Medical Biology, University of Tromso, Tromso (Norway); Gosert, Rainer [Transplantation Virology, Institute for Medical Microbiology, Department of Biomedicine, University of Basel, Basel (Switzerland); Hirsch, Hans H. [Transplantation Virology, Institute for Medical Microbiology, Department of Biomedicine, University of Basel, Basel (Switzerland); Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel (Switzerland); Rinaldo, Christine Hanssen, E-mail: christine.rinaldo@unn.n [Department of Microbiology and Infection Control, University Hospital of North Norway, P.O. Box 56, N-9038 Tromso (Norway)

2010-03-01T23:59:59.000Z

247

A Thousand Invisible Cords Binding Astronomy and High-Energy Physics  

E-Print Network (OSTI)

The traditional realm of astronomy is the observation and study of the largest objects in the Universe, while the traditional domain of high-energy physics is the study of the smallest things in nature. But these two sciences concerned with opposite ends of the size spectrum are, in Muir's words, bound fast by a thousand invisible cords that cannot be broken. In this essay I propose that collaborations of astronomers and high-energy physicists on common problems are beneficial for both fields, and that both astronomy and high-energy physics can advance by this close and still growing relationship. Dark matter and dark energy are two of the binding cords I will use to illustrate how collaborations of astronomers and high-energy physicists on large astronomical projects can be good for astronomy, and how discoveries in astronomy can guide high-energy physicists in their quest for understanding nature on the smallest scales. Of course, the fields have some different intellectual and collaborative traditions, neither of which is ideal. The cultures of the different fields cannot be judged to be right or wrong; they either work or they don't. When astronomers and high-energy physicists work together, the binding cords can either encourage or choke creativity. The challenge facing the astronomy and high-energy physics communities is to adopt the best traditions of both fields. It is up to us to choose wisely.

Rocky Kolb

2007-08-09T23:59:59.000Z

248

A-84: Tight Binding Understanding of Carbon Defects in Steel  

Science Conference Proceedings (OSTI)

Thus, a coherent transferable tight-binding (TB) parameterization was developed for Fe-C by ... A-54: Used Foundry Sand Reclamation in New Vibratory Unit.

249

Comprehensive investigation of the non-covalent binding of MRI ...  

Science Conference Proceedings (OSTI)

of MRI contrast agents with human serum albumin. Virginie ... binding between human serum albumin (HSA) and MRI contrast .... The relative error on the T1...

250

Sequestering Uranium from Seawater: Binding Strength and Modes...  

NLE Websites -- All DOE Office Websites (Extended Search)

YouTube: AdvancedLightSource Home Science Highlights Journal Covers Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime...

251

Definition: Frequency-Domain Electromagnetics Survey | Open Energy  

Open Energy Info (EERE)

Frequency-Domain Electromagnetics Survey Frequency-Domain Electromagnetics Survey Jump to: navigation, search Dictionary.png Frequency-Domain Electromagnetics Survey Frequency-domain electromagnetic techniques are continuous wave field methods which enable the mapping of the electrical conductivity of the subsurface through electromagnetic induction.[1] View on Wikipedia Wikipedia Definition Electromagnetic induction is the production of a potential difference (voltage) across a conductor when it is exposed to a varying magnetic field. Michael Faraday is generally credited with the discovery of induction in 1831 though it may have been anticipated by the work of Francesco Zantedeschi in 1829. Around 1830 to 1832, Joseph Henry made a similar discovery, but did not publish his findings until later. Faraday's

252

Time-Domain Electromagnetics At Haleakala Volcano Area (Thomas, 1986) |  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Haleakala Volcano Time-Domain Electromagnetics At Haleakala Volcano Area (Thomas, 1986) Exploration Activity Details Location Haleakala Volcano Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes Controlled-source electromagnetic soundings were found to be substantially more successful in the southwest rift than either the Schlumberger or the self-potential studies. This was largely due to the ability of time-domain methods to penetrate high-resistivity surface layers and thus to define lower-resistivity sections at depth. The results of this sounding study, which was conducted at elevations ranging from 75 to 497 m a.s.l., generally indicated moderate- to lowresistivity (6 - 7 ohm.m) sections to depths of 1 km on the lower rift zone and higher resistivities (12-16

253

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

NLE Websites -- All DOE Office Websites (Extended Search)

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported...

254

Analysis of multi-domain complex simulation studies  

Science Conference Proceedings (OSTI)

Complex simulations are increasingly important in systems analysis and design. In some cases simulations can be exhaustively validated against experiment and taken to be implicitly accurate. However, in domains where only limited validation of the simulations ...

James R. Gattiker; Earl Lawrence; David Higdon

2006-05-01T23:59:59.000Z

255

Minimally supervised domain-adaptive parse reranking for relation extraction  

Science Conference Proceedings (OSTI)

The paper demonstrates how the generic parser of a minimally supervised information extraction framework can be adapted to a given task and domain for relation extraction (RE). For the experiments a generic deep-linguistic parser was employed that works ...

Feiyu Xu; Hong Li; Yi Zhang; Hans Uszkoreit; Sebastian Krause

2011-10-01T23:59:59.000Z

256

Observed and Simulated Energy Cycles in the Frequency Domain  

Science Conference Proceedings (OSTI)

The analysis of spectral energetics in the frequency domain has been applied to several observed datasets and those simulated by a GFDL general circulation model. There exists good agreement on the directions of energy flows between the observed ...

Jian Sheng; Yoshikazu Hayashi

1990-05-01T23:59:59.000Z

257

The Complexity of Reasoning with Concrete Domains Revised Version  

Science Conference Proceedings (OSTI)

Description logics are knowledge representation and reasoning formalisms which represent conceptual knowledge on an abstract logical level. Concrete domains are a theoretically well-founded approach to the integration of description logic reasoning with ...

C. Lutz

1999-08-01T23:59:59.000Z

258

NEXPTIME-Complete Description Logics with Concrete Domains  

Science Conference Proceedings (OSTI)

Concrete domains are an extension of Description Logics (DLs) allowing to integrate reasoning about conceptual knowledge with reasoning about "concrete properties" of objects such as sizes, weights, and durations. It is known that reasoning with ALC(D), ...

Carsten Lutz

2001-06-01T23:59:59.000Z

259

Domain wall induced magnetoresistance in a superconductor/ferromagnet nanowire  

E-Print Network (OSTI)

In a nanowire consisting of a ferromagnet/insulator/superconductor multilayer structure, the superconductivity is shown to depend strongly on the configuration of the magnetic domain walls in the neighboring ferromagnetic ...

Miao, G. X.

260

Embedding domain-specific modelling languages in maude specifications  

Science Conference Proceedings (OSTI)

We propose an approach for embedding Domain-Specific Modelling Languages (DSML) into Maude, based on representing models and metamodels as Maude specifications, and on representing operational semantics and model transformations as computable functions/relations ...

Vlad Rusu

2011-01-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


261

Aspen: a domain specific language for performance modeling  

Science Conference Proceedings (OSTI)

We present a new approach to analytical performance modeling using Aspen, a domain specific langauge. Aspen (Abstract Scalable Performance Engineering Notation) fills an important gap in existing performance modeling techniques and is designed to enable ...

Kyle L. Spafford; Jeffrey S. Vetter

2012-11-01T23:59:59.000Z

262

Learning semantic structures from in-domain documents  

E-Print Network (OSTI)

Semantic analysis is a core area of natural language understanding that has typically focused on predicting domain-independent representations. However, such representations are unable to fully realize the rich diversity ...

Chen, Harr

2011-01-01T23:59:59.000Z

263

Two families with isolated cat cry without the cri-du-chat syndrome phenotype have an inherited 5p15.3 deletion: Delineation of the larynx malformation region  

SciTech Connect

The cri-du-chat syndrome is a contiguous gene syndrome that results from a deletion of the short arm of chromosome 5 (5p). Patients present with a cat-like cry at birth that is usually considered diagnostic of this syndrome. Additional features of the syndrome include failure to thrive, microcephaly, hypertelorism, epicanthal folds, hypotonia, and severe mental retardation. We report on two families in which the patients with 5p deletions have only the characteristic cat-like cry with normal to mildly delayed development. One family has three children with varying levels of developmental delay and a deletion of 5p15.3 that was inherited from the father. The second family has a mother and daughter both presenting with a cat-like cry and normal intelligence. A de novo deletion in a patient with isolated cat cry and mild developmental delay was also identified. The precise locations of the deletions in each family were determined by fluorescent in situ hybridization using lambda phage, cosmids, and YAC clones. Cryptic translocations and mosaicism were not detected in the parents transmitting the deletion. All of the deletion breakpoints map distal to the previously defined cri-du-chat critical region. A YAC contig has been constructed for the chromosomal region implicated in the larynx malformation. DNA clones mapping in this region will be useful diagnostic tools for delineating 5p deletions that result in the typical features of cri-du-chat syndrome with deletions that result in the isolated cat-like cry feature which is associated with a better prognosis.

Gersh, M.; Overhauser, J. [Thomas Jefferson Univ., Philadelphia, PA (United States); Pasztor, L.M. [Children`s Mercy Hospital, Kansas City, MO (United States)] [and others

1994-09-01T23:59:59.000Z

264

Using multiple sources to construct a sentiment sensitive thesaurus for cross-domain sentiment classification  

Science Conference Proceedings (OSTI)

We describe a sentiment classification method that is applicable when we do not have any labeled data for a target domain but have some labeled data for multiple other domains, designated as the source domains. We automatically create a ...

Danushka Bollegala; David Weir; John Carroll

2011-06-01T23:59:59.000Z

265

Hypothesis for a serine proteinase-like domain at the COOH terminus of Slowpoke calcium-activated potassium channels  

E-Print Network (OSTI)

A B S T RA C T Bovine pancreatic trypsin inhibitor (BPTI) is a 58-residue protein with three disulfide bonds that belongs to the Kunitz family of serine proteinase inhibitors. BPTI is an extremely potent inhibitor of trypsin, but it also specifically binds to various active and inactive serine proteinase homologs with KD values that range over eight orders of magnitude. We previously described an interaction of BPTI at an intracellular site that results in the production of discrete subconductance events in large conductance Ca 2+ activated K + channels (Moss, G.W.J., and E. Moczydlowski. 1996. J. Gen. Physiol. 107:47-68). In this paper, we summarize a variety of accumulated evidence which suggests that BPTI binds to a site on the Kca channel protein that structurally resembles a serine proteinase. One line of evidence includes the finding that the complex of BPTI and trypsin, in which the inhibitory loop of BPTI is masked by interaction with trypsin, is completely ineffective in the production of substate events in the gca channel. To further investigate this notion, we performed a sequence analysis of the ~x-subunit of cloned slowpoke I~: a channels from Drosophila and mammals. This analysis suggests that a region of ~250 residues near the COOH terminus of the Kca channel is homologous to members of the serine proteinase family, but is catalytically inactive because of various substitutions of key catalytic residues. The sequence analysis also predicts the location of a Ca2+-binding loop that is found in many serine proteinase enzymes. We hypothesize that this COOH-terminal domain of the slowpoke Kca channel adopts the characteristic double-barrel fold of serine proteinases, is involved in Ca2+-activation of the channel, and may also bind other intracellular components that regulate Kca channel activity. KEY WORD S " bovine pancreatic trypsin inhibitor * planar bilayer sequence alignment sequence homology single channel recording

Guy W. J. Moss; John Marshall; Edward Moczydlowski

1996-01-01T23:59:59.000Z

266

Attraction Domains of Delay Systems: Construction by the Lyapunov Function Method  

Science Conference Proceedings (OSTI)

Description of attraction domains of delay systems is studied. Attraction domains are estimated by the Lyapunov functions method and a method of determining the required Lyapunov function.

A. V. Gorbunov; V. A. Kamenetskii

2005-10-01T23:59:59.000Z

267

Enumeration Algorithm for Determination of Binding Constants in Capillary Electrophoresis  

E-Print Network (OSTI)

result in the new migration time. Because the true binding constant and complex mobility values have. With the enumeration algorithm, all possible combinations of the binding constant and the complex mobility in certain and the mobility of the complex formed between the interacting pair, to form a 2-D curve. When the experimental

Chen, David D.Y.

268

Babel Fortran 2003 Binding for Structured Data Types  

SciTech Connect

Babel is a tool aimed at the high-performance computing community that addresses the need for mixing programming languages (Java, Python, C, C++, Fortran 90, FORTRAN 77) in order to leverage the specific benefits of those languages. Scientific codes often rely on structured data types (structs, derived data types) to encapsulate data, and Babel has been lacking in this type of support until recently. We present a new language binding that focuses on their interoperability of C/C++ with Fortran 2003. The new binding builds on the existing Fortran 90 infrastructure by using the iso-c-binding module defined in the Fortran 2003 standard as the basis for C/C++ interoperability. We present the technical approach for the new binding and discuss our initial experiences in applying the binding in FACETS (Framework Application for Core-Edge Transport Simulations) to integrate C++ with legacy Fortran codes.

Muszala, S; Epperly, T; Wang, N

2008-05-02T23:59:59.000Z

269

BPA FINAL Binding Arbitration policy | Department of Energy  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy BPA FINAL Binding Arbitration policy Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited

270

Assessment of current cybersecurity practices in the public domain : cyber indications and warnings domain.  

SciTech Connect

This report assesses current public domain cyber security practices with respect to cyber indications and warnings. It describes cybersecurity industry and government activities, including cybersecurity tools, methods, practices, and international and government-wide initiatives known to be impacting current practice. Of particular note are the U.S. Government's Trusted Internet Connection (TIC) and 'Einstein' programs, which are serving to consolidate the Government's internet access points and to provide some capability to monitor and mitigate cyber attacks. Next, this report catalogs activities undertaken by various industry and government entities. In addition, it assesses the benchmarks of HPC capability and other HPC attributes that may lend themselves to assist in the solution of this problem. This report draws few conclusions, as it is intended to assess current practice in preparation for future work, however, no explicit references to HPC usage for the purpose of analyzing cyber infrastructure in near-real-time were found in the current practice. This report and a related SAND2010-4766 National Cyber Defense High Performance Computing and Analysis: Concepts, Planning and Roadmap report are intended to provoke discussion throughout a broad audience about developing a cohesive HPC centric solution to wide-area cybersecurity problems.

Hamlet, Jason R.; Keliiaa, Curtis M.

2010-09-01T23:59:59.000Z

271

Three-dimensional transient electromagnetic modeling in the Laplace Domain  

Science Conference Proceedings (OSTI)

In modeling electromagnetic responses, Maxwell's equations in the frequency domain are popular and have been widely used (Nabighian, 1994; Newman and Alumbaugh, 1995; Smith, 1996, to list a few). Recently, electromagnetic modeling in the time domain using the finite difference (FDTD) method (Wang and Hohmann, 1993) has also been used to study transient electromagnetic interactions in the conductive medium. This paper presents a new technique to compute the electromagnetic response of three-dimensional (3-D) structures. The proposed new method is based on transforming Maxwell's equations to the Laplace domain. For each discrete Laplace variable, Maxwell's equations are discretized in 3-D using the staggered grid and the finite difference method (FDM). The resulting system of equations is then solved for the fields using the incomplete Cholesky conjugate gradient (ICCG) method. The new method is particularly effective in saving computer memory since all the operations are carried out in real numbers. For the same reason, the computing speed is faster than frequency domain modeling. The proposed approach can be an extremely useful tool in developing an inversion algorithm using the time domain data.

Mizunaga, H.; Lee, Ki Ha; Kim, H.J.

1998-09-01T23:59:59.000Z

272

Cerenkov radio pulses from electromagnetic showers in the time domain  

Science Conference Proceedings (OSTI)

The electric field of the Cerenkov radio pulse produced by a single charged particle track in a dielectric medium is derived from first principles. An algorithm is developed to obtain the pulse in the time domain for numerical calculations. The algorithm is implemented in a Monte Carlo simulation of electromagnetic showers in dense media (specifically designed for coherent radio emission applications) as might be induced by interactions of ultrahigh energy neutrinos. The coherent Cerenkov radio emission produced by such showers is obtained simultaneously both in the time and frequency domains. A consistency check performed by Fourier transforming the pulse in time and comparing it to the frequency spectrum obtained directly in the simulations yields, as expected, fully consistent results. The reversal of the time structure inside the Cerenkov cone and the signs of the corresponding pulses are addressed in detail. The results, besides testing algorithms used for reference calculations in the frequency domain, shed new light into the properties of the radio pulse in the time domain. The shape of the pulse in the time domain is directly related to the depth development of the excess charge in the shower and its width to the observation angle with respect to the Cerenkov direction. This information can be of great practical importance for interpreting actual data.

Alvarez-Muniz, Jaime; Romero-Wolf, Andres; Zas, Enrique [Depto. de Fisica de Particulas and Instituto Galego de Fisica de Altas Enerxias, Universidade de Santiago de Compostela, 15782 Santiago de Compostela (Spain); Department of Physics and Astronomy, University of Hawaii at Manoa, Honolulu, Hawaii 96822 (United States); Depto. de Fisica de Particulas and Instituto Galego de Fisica de Altas Enerxias, Universidad de Santiago de Compostela, 15782 Santiago de Compostela (Spain)

2010-06-15T23:59:59.000Z

273

Angiotensin II receptor binding sites in brain microvessels  

SciTech Connect

The authors assessed the specific binding of /sup 125/I-labeled angiotensin II (/sup 125/I-Ang II) to particulate fractions of the cerebral cortex and cerebellum and to microvessels obtained by bulk isolation from these two brain regions in the dog. /sup 125/I-Ang II binds to cerebral and cerebellar microvessels in a specific, saturable, and reversible manner and with high affinity (dissociation constant about 1 nM). Maximal binding of /sup 125/I-Ang II to brain microvessels was about 2-fold higher than the maximal binding to particulate fractions of the cerebellum and more than 15-fold higher than that of the cerebral cortex. Furthermore, finding that analogues of Ang II displace specific /sup 125/I-Ang II binding to brain microvessels in a rank order that correlates with their pharmacological activities confers biological relevance on the ligand-binding studies. These results strongly suggest that specific Ang II receptor binding sites are present in brain microvessels. Such Ang II receptors may have an important role in regulating the microcirculation of the brain.

Speth, R.C.; Harik, S.I.

1985-09-01T23:59:59.000Z

274

Frequency-Domain Electromagnetic Survey | Open Energy Information  

Open Energy Info (EERE)

Frequency-Domain Electromagnetic Survey Frequency-Domain Electromagnetic Survey Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Frequency-Domain Electromagnetic Survey Details Activities (0) Areas (0) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Electrical Techniques Parent Exploration Technique: Electromagnetic Profiling Techniques Information Provided by Technique Lithology: Detection of high-conductivity bodies in the subsurface. Stratigraphic/Structural: Hydrological: Thermal: Detection of the presence of a thermal anomaly through its resistivity signature. Cost Information Low-End Estimate (USD): 2,928.38292,838 centUSD 2.928 kUSD 0.00293 MUSD 2.92838e-6 TUSD / mile Median Estimate (USD): 4,505.20450,520 centUSD

275

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

NLE Websites -- All DOE Office Websites (Extended Search)

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

276

National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment  

Open Energy Info (EERE)

National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Jump to: navigation, search OpenEI Reference LibraryAdd to library Conference Paper: National Geothermal Data System (NGDS) Geothermal Data Domain: Assessment of Geothermal Community Data Needs Abstract To satisfy the critical need for geothermal data to advance geothermal energy as a viable renewable energy contender, the U.S. Department of Energy is in-vesting in the development of the National Geothermal Data System (NGDS). This paper outlines efforts among geothermal data providers nationwide to sup-ply cutting edge geoinformatics. NGDS geothermal data acquisition, delivery, and methodology are dis-cussed. In particular, this paper addresses the various types of data required to effectively assess

277

Controlled Source Frequency-Domain Magnetics | Open Energy Information  

Open Energy Info (EERE)

Controlled Source Frequency-Domain Magnetics Controlled Source Frequency-Domain Magnetics Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Technique: Controlled Source Frequency-Domain Magnetics Details Activities (2) Areas (2) Regions (0) NEPA(0) Exploration Technique Information Exploration Group: Geophysical Techniques Exploration Sub Group: Magnetic Techniques Parent Exploration Technique: Magnetic Techniques Information Provided by Technique Lithology: Stratigraphic/Structural: Hydrological: Locate geothermal groundwater and flow patterns. Thermal: Cost Information Low-End Estimate (USD): 12,000.001,200,000 centUSD 12 kUSD 0.012 MUSD 1.2e-5 TUSD / mile Median Estimate (USD): 18,000.001,800,000 centUSD 18 kUSD 0.018 MUSD 1.8e-5 TUSD / mile High-End Estimate (USD): 25,000.002,500,000 centUSD

278

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

NLE Websites -- All DOE Office Websites (Extended Search)

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

279

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

NLE Websites -- All DOE Office Websites (Extended Search)

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

280

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress  

NLE Websites -- All DOE Office Websites (Extended Search)

Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Dynein Motor Domain Shows Ring-Shaped Motor, Buttress Print Movement is fundamental to life. It takes place even at the cellular level where cargo is continually being transported by motor proteins. These tiny machines convert the energy gained from hydrolysing ATP into a series of small conformational changes that allow them to literally "walk" along microscopic tracks. Motor proteins (in the kinesin and myosin families) have been extensively studied by x-ray crystallography, but until recently there was little molecular structural information for dyneins, another type of motor protein. A group from the University of California, San Francisco, working at ALS Beamline 8.3.1 has reported the 6-Å-resolution structure of the motor domain of dynein in yeast. It reveals details of the ring-shaped motor as well as a new, unanticipated feature called the buttress that may play an important role in dynein's mechanical cycle.

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


281

Definition: Frequency-Domain Electromagnetic Survey | Open Energy  

Open Energy Info (EERE)

Electromagnetic Survey Electromagnetic Survey Jump to: navigation, search Dictionary.png Frequency-Domain Electromagnetic Survey Frequency-domain electromagnetic techniques are continuous wave field methods which enable the mapping of the electrical conductivity of the subsurface through electromagnetic induction.[1] Also Known As Controlled-Source EM References ↑ http://library.seg.org/doi/pdf/10.1190/1.1441531 Ret LikeLike UnlikeLike You like this.Sign Up to see what your friends like. rieved from "http://en.openei.org/w/index.php?title=Definition:Frequency-Domain_Electromagnetic_Survey&oldid=591411" Category: Definitions What links here Related changes Special pages Printable version Permanent link Browse properties About us Disclaimers Energy blogs Linked Data Developer services

282

Improved time-domain accuracy standards for model gravitational waveforms  

Science Conference Proceedings (OSTI)

Model gravitational waveforms must be accurate enough to be useful for detection of signals and measurement of their parameters, so appropriate accuracy standards are needed. Yet these standards should not be unnecessarily restrictive, making them impractical for the numerical and analytical modelers to meet. The work of Lindblom, Owen, and Brown [Phys. Rev. D 78, 124020 (2008)] is extended by deriving new waveform accuracy standards which are significantly less restrictive while still ensuring the quality needed for gravitational-wave data analysis. These new standards are formulated as bounds on certain norms of the time-domain waveform errors, which makes it possible to enforce them in situations where frequency-domain errors may be difficult or impossible to estimate reliably. These standards are less restrictive by about a factor of 20 than the previously published time-domain standards for detection, and up to a factor of 60 for measurement. These new standards should therefore be much easier to use effectively.

Lindblom, Lee [Theoretical Astrophysics 350-17, California Institute of Technology, Pasadena, California 91125 (United States); Baker, John G. [Gravitational Astrophysics Laboratory, NASA/GSFC, Greenbelt, Maryland 20771 (United States); Owen, Benjamin J. [Institute for Gravitation and the Cosmos, Center for Gravitational Wave Physics, Department of Physics, Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

2010-10-15T23:59:59.000Z

283

Bilayer Thickness Mismatch Controls Domain Size in Model Membranes  

Science Conference Proceedings (OSTI)

The observation of lateral phase separation in lipid bilayers has received considerable attention, especially in connection to lipid raft phenomena in cells. It is widely accepted that rafts play a central role in cellular processes, notably signal transduction. While micrometer-sized domains are observed with some model membrane mixtures, rafts much smaller than 100 nm beyond the reach of optical microscopy are now thought to exist, both in vitro and in vivo. We have used small-angle neutron scattering, a probe free technique, to measure the size of nanoscopic membrane domains in unilamellar vesicles with unprecedented accuracy. These experiments were performed using a four-component model system containing fixed proportions of cholesterol and the saturated phospholipid 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), mixed with varying amounts of the unsaturated phospholipids 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and 1,2-dioleoylsn- glycero-3-phosphocholine (DOPC). We find that liquid domain size increases with the extent of acyl chain unsaturation (DOPC:POPC ratio). Furthermore, we find a direct correlation between domain size and the mismatch in bilayer thickness of the coexisting liquid-ordered and liquid-disordered phases, suggesting a dominant role for line tension in controlling domain size. While this result is expected from line tension theories, we provide the first experimental verification in free-floating bilayers. Importantly, we also find that changes in bilayer thickness, which accompany changes in the degree of lipid chain unsaturation, are entirely confined to the disordered phase. Together, these results suggest how the size of functional domains in homeothermic cells may be regulated through changes in lipid composition.

Heberle, Frederick A [ORNL; Petruzielo, Robin S [ORNL; Pan, Jianjun [ORNL; Drazba, Paul [ORNL; Kucerka, Norbert [Canadian Neutron Beam Centre and Comelius University (Slovakia); Feigenson, Gerald [Cornell University; Katsaras, John [ORNL

2013-01-01T23:59:59.000Z

284

Binding Parameters of Alkaloids Berberine and Sanguinarine with DNA  

E-Print Network (OSTI)

We study the interaction of berberine and sanguinarine (plant alkaloids) with DNA in aqueous solutions, by using optical spectroscopy methods (absorption and fluorescence). The dependencies of alkaloid spectral characteristics on the concentration ratio N/c between the DNA base pairs and alkaloid molecules in the solutions are considered, and the manifestations of the alkaloid-DNA binding are revealed. The character of binding is found to depend on N/c. The parameters of the binding of berberine and sanguinarine with DNA are determined, by using the modified Scatchard and McGhee-von Hippel equations

Gumenyuk, V G; Kutovyy, S Yu; Yashchuk, V M; Zaika, L A

2012-01-01T23:59:59.000Z

285

Time-domain determination of transmission in quantum nanostructures  

SciTech Connect

The finite-difference time-domain method is being used to calculate transmission through nanoscale quantum structures. This is determined by first taking the Fourier transform of a waveform before it enters a channel and then taking the Fourier transform of the portion of the waveform that is transmitted through the channel. By storing the time-domain waveforms at the input and output, a very small total problem space is required. This is significant, because it is intended that this one-dimensional method be extended to three dimensions.

Sullivan, Dennis M.; Wilson, Paul M. [Department of Electrical and Computer Engineering, University of Idaho, Moscow, Idaho 83844-1023 (United States)

2012-09-15T23:59:59.000Z

286

Observation and implications of magnetic domains in lateral spin valves  

Science Conference Proceedings (OSTI)

Co/Cu/Co lateral spin valves (LSV), with Co being the topmost layer, are in situ prepared and measured under ultrahigh vacuum conditions. The clean process yields a non-local spin signal of 0.9 m{Omega}. Scanning electron microscopy with polarization analysis (SEMPA) reveals domain structures in both magnetic electrodes that depend on the LSV dimensions. The spin signal correlates to SEMPA images as well as the anisotropic magnetoresistance of both Co magnets, revealing a strong impact of multi-domain states on the spin signal.

Mennig, J.; Matthes, F.; Buergler, D. E.; Schneider, C. M. [Peter Gruenberg Institute, Electronic Properties (PGI-6) and Juelich-Aachen Research Alliance, Fundamentals of Future Information Technology (JARA-FIT), Forschungszentrum Juelich GmbH, Juelich D-52425 (Germany)

2012-04-01T23:59:59.000Z

287

Current Domain Challenges in the Emergency Response Community  

SciTech Connect

This paper describes the development of a framework targeted to technology providers in order to better understand the grand domain challenges of the emergency response and management community (EM). In developing this framework, Pacific Northwest National Laboratory researchers interviewed subject matter experts (SMEs) across the EM domain and corroborated these findings with current literature. We are currently examining relationships and dependencies within the framework. A thorough understanding of these gaps and dependencies will allow for a more informed approach prioritizing research, developing tools, and applying technology to enhance performance in the EM community.

Barr, Jonathan L.; Peddicord, Annie M Boe; Burtner, Edwin R.; Mahy, Heidi A.

2011-05-08T23:59:59.000Z

288

Crystal Structure of the N-Terminal Domain of the Human Protooncogene Nup214/CAN  

Science Conference Proceedings (OSTI)

The mammalian nuclear pore complex (NPC) is an {approx}120-MDa proteinaceous assembly consisting of {approx}30 proteins and is the sole gate in the nuclear envelope. The human protooncogene Nup214 was first identified as a target for chromosomal translocation involved in leukemogenesis. Nup214 is located on the cytoplasmic face of the NPC and is implicated in anchoring the cytoplasmic filaments of the NPC and recruiting the RNA helicase Ddx19. Here, we present the crystal structure of the human Nup214 N-terminal domain at 1.65-{angstrom} resolution. The structure reveals a seven-bladed {beta}-propeller followed by a 30-residue C-terminal extended peptide segment, which folds back onto the {beta}-propeller and binds to its bottom face. The {beta}-propeller repeats lack any recognizable sequence motif and are distinguished by extensive insertions between the canonical {beta}-strands. We propose a mechanism by which the C-terminal peptide extension is involved in NPC assembly.

Napetschnig,J.; Blobel, G.; Hoelz, A.

2007-01-01T23:59:59.000Z

289

Binding Preferences, Surface Attachment, Diffusivity, and Orientation of a Family 1 Carbohydrate-Binding Module on Cellulose  

DOE Green Energy (OSTI)

Cellulase enzymes often contain carbohydrate-binding modules (CBMs) for binding to cellulose. The mechanisms by which CBMs recognize specific surfaces of cellulose and aid in deconstruction are essential to understand cellulase action. The Family 1 CBM from the Trichoderma reesei Family 7 cellobiohydrolase, Cel7A, is known to selectively bind to hydrophobic surfaces of native cellulose. It is most commonly suggested that three aromatic residues identify the planar binding face of this CBM, but several recent studies have challenged this hypothesis. Here, we use molecular simulation to study the CBM binding orientation and affinity on hydrophilic and hydrophobic cellulose surfaces. Roughly 43 {mu}s of molecular dynamics simulations were conducted, which enables statistically significant observations. We quantify the fractions of the CBMs that detach from crystal surfaces or diffuse to other surfaces, the diffusivity along the hydrophobic surface, and the overall orientation of the CBM on both hydrophobic and hydrophilic faces. The simulations demonstrate that there is a thermodynamic driving force for the Cel7A CBM to bind preferentially to the hydrophobic surface of cellulose relative to hydrophilic surfaces. In addition, the simulations demonstrate that the CBM can diffuse from hydrophilic surfaces to the hydrophobic surface, whereas the reverse transition is not observed. Lastly, our simulations suggest that the flat faces of Family 1 CBMs are the preferred binding surfaces. These results enhance our understanding of how Family 1 CBMs interact with and recognize specific cellulose surfaces and provide insights into the initial events of cellulase adsorption and diffusion on cellulose.

Nimlos, M. R.; Beckham, G. T.; Matthews, J. F.; Bu, L.; Himmel, M. E.; Crowley, M. F.

2012-06-08T23:59:59.000Z

290

A Fortran binding for the GNU scientific library  

Science Conference Proceedings (OSTI)

The GNU scientific library is a collection of numerical routines for scientific computing. This article discusses some aspects of the design of a fully standard-conforming Fortran binding for GSL via incremental usage of Fortran 2003 features, in particular ...

Reinhold Bader

2007-08-01T23:59:59.000Z

291

Bayesian unsupervised learning of DNA regulatory binding regions  

Science Conference Proceedings (OSTI)

Identification of regulatory binding motifs, that is, short specific words, within DNA sequences is a commonly occurring problem in computational bioinformatics. A wide variety of probabilistic approaches have been proposed in the literature to either ...

Jukka Corander; Magnus Ekdahl; Timo Koski

2009-01-01T23:59:59.000Z

292

Assessing phylogenetic motif models for predicting transcription factor binding sites  

Science Conference Proceedings (OSTI)

Motivation: A variety of algorithms have been developed to predict transcription factor binding sites (TFBSs) within the genome by exploiting the evolutionary information implicit in multiple alignments of the genomes of related species. One such ...

John Hawkins; Charles Grant; William Stafford Noble; Timothy L. Bailey

2009-06-01T23:59:59.000Z

293

Reversible and irreversible binding of nanoparticles to polymeric surfaces  

Science Conference Proceedings (OSTI)

Reversible and irreversible binding of CdSe-nanoparticles and nanorods to polymeric surfaces via a strong, multiple hydrogen bond (= Hamilton-receptor/barbituric acid) is described. Based on ROMP-copolymers, the supramolecular interaction on a thin polymer ...

Wolfgang H. Binder; Marina Lomoschitz; Robert Sachsenhofer; Gernot Friedbacher

2009-01-01T23:59:59.000Z

294

Neutron Electric Dipole Moment with Domain Wall Quarks  

E-Print Network (OSTI)

We present preliminary results for nucleon dipole moments computed with domain wall fermions. Our main target is the electric dipole moment of the neutron arising from the theta term in the gauge part of the QCD lagrangian. The calculated magnetic dipole moments of the proton and neutron are in rough accord with experimental values.

F. Berruto; T. Blum; K. Orginos; A. Soni

2004-11-02T23:59:59.000Z

295

A core reference ontology for the customer relationship domain  

Science Conference Proceedings (OSTI)

Customer Relationship Management (CRM) has emerged as an important strategy that companies should implement in order to build profitable and stable relationships with their customer. The domain of CRM has peculiar characteristics: a CRM strategy is largely ... Keywords: CRM, Customer relationship management, business activities, business knowledge, customer relationships, software

Diego Magro; Anna Goy

2012-01-01T23:59:59.000Z

296

Experiences from identifying software reuse opportunities by domain analysis  

Science Conference Proceedings (OSTI)

In a large corporate organization there are sometimes similar software products in certain subdomains with a perceived functional overlap. This promises to be an opportunity for systematic reuse to reduce software development and maintenance costs. In ... Keywords: business case, domain analysis, software product lines

Heiko Koziolek, Thomas Goldschmidt, Thijmen de Gooijer, Dominik Domis, Stephan Sehestedt

2013-08-01T23:59:59.000Z

297

Representing a robotic domain using temporal description logics  

Science Conference Proceedings (OSTI)

A temporal logic for representing and reasoning on a robotic domain is presented. Actions are represented by describing what is true while the action itself is occurring, and plans are constructed by temporally relating actions and world states. The ... Keywords: Action Representation, Description Logic, Robotics, Temporal Logic

Alessandro Artale; Enrico Franconi

1999-04-01T23:59:59.000Z

298

Semantics-aware open information extraction in the biomedical domain  

Science Conference Proceedings (OSTI)

The increasing amount of biomedical scientific literature published on the Web is demanding new tools and methods to automatically process and extract relevant information. Traditional information extraction has focused on recognizing well-defined entities ... Keywords: biomedical domain, relation extraction, semantic annotation

Victoria Nebot; Rafael Berlanga

2011-12-01T23:59:59.000Z

299

Domain-dependent single-agent search enhancements  

Science Conference Proceedings (OSTI)

AI research has developed an extensive collection of methods to solve state-space problems. Using the challenging domain of Sokoban, this paper studies the effect of search enhancements on program performance. We show that the current state of the art ... Keywords: IDA, Sokoban, single-agent search

Andreas Junghanns; Jonathan Schaeffer

1999-07-01T23:59:59.000Z

300

Discovering common outcomes of agents' communicative actions in various domains  

Science Conference Proceedings (OSTI)

We explore the common patterns of human behavior, expressed via communicative actions, and displayed in various domains of human activities associated with conflicts. We build the generic methodology based on machine learning and reasoning to predict ... Keywords: Agents, Conflict scenarios, Emotions, Learning human behavior, Mental states, Outcomes of communicative actions, Scenarios as graphs

Boris Galitsky; Josep-Lluis de la Rosa; Boris Kovalerchuk

2011-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


301

Knowledge mapping for rapidly evolving domains: A design science approach  

Science Conference Proceedings (OSTI)

Knowledge mapping can provide comprehensive depictions of rapidly evolving scientific domains. Taking the design science approach, we developed a Web-based knowledge mapping system (i.e., Nano Mapper) that provides interactive search and analysis on ... Keywords: Design science, Information systems, Knowledge mapping

Yan Dang; Yulei Zhang; Paul Jen-Hwa Hu; Susan A. Brown; Hsinchun Chen

2011-01-01T23:59:59.000Z

302

Continuous time domain properties of causal cubic splines  

Science Conference Proceedings (OSTI)

The paper studies the continuous time domain properties of causal cubic splines with equidistant knots. Causality is achieved by truncating the impulse response of the ideal interpolator to a chosen length. The introduced error affects the final interpolation ... Keywords: Cardinal spline functions, Causality, Cubic spline, Interpolation, Signal reconstruction, Signal resampling

D. Petrinovic

2009-10-01T23:59:59.000Z

303

A Collaborative Filtering Algorithm Based on Global and Domain Authorities  

Science Conference Proceedings (OSTI)

Collaborative filtering has been very successful in both applications and researches. In real situation, different users may have different influences on other users' decisions. Those authoritative users usually play more important roles. But few existing ... Keywords: Collaboration Filtering, Domain Authority, Global Authority

Li Zhou; Yong Zhang; Chun-Xiao Xing

2008-12-01T23:59:59.000Z

304

Face images feature extraction analysis for recognition in frequency domain  

Science Conference Proceedings (OSTI)

In this paper a novel technique to extract facial features for recognition in frequency domain using Discrete Fourier Transform (DFT) is presented. In pre processing phase facial tilt and varying image background challenges have been addressed to improve ... Keywords: DFT, dimension reduction, face recognition, facial tilt, image background, image decimation

M. Almas Anjum; M. Younus Javed

2006-08-01T23:59:59.000Z

305

MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel  

SciTech Connect

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.; Iyer, VenkyN.; Eisen, Michael B.

2004-10-28T23:59:59.000Z

306

Calculation of HVDC-converter harmonics in frequency domain with regard to asymmetries and comparison with time domain simulations  

SciTech Connect

In order to study the effects of large HVDC converters to the feeding ac networks, it is of importance to explain and to calculate harmonic phenomena which are a result of converter operation. During commissioning of real HVDC converters it could be seen, that harmonics resulting from unsymmetries in the system voltages or from unsymmetries in converter operation led to significant difficulties concerning the system design. For this reason, not only the effects of characteristic but also the effects of noncharacteristic converter harmonics must be taken into account. The aim is to describe the steady state harmonic behavior of the converter. The harmonic spectra are not determined by time domain analysis but instead the solution is found by frequency domain calculations. This can result in reduced calculation time in comparison to conventional fourier analysis of the time functions. The converter is interpreted as an amplitude modulator with voltage and current converter functions which describe the coupling of the dc circuit and the ac network through the converter. To verify the theory, comparison of frequency domain with time domain calculations were carried out.

Rittiger, J. [Siemens AG, Erlangen (Germany); Kulicke, B. [Technische Univ. Berlin (Germany)

1995-10-01T23:59:59.000Z

307

MANAGING TIGHT BINDING RECEPTORS FOR NEW SPEARATIONS TECHNOLOGIES  

DOE Green Energy (OSTI)

Much of the earth's pollution involves compounds of the metallic elements, including actinides, strontium, cesium, technetium, and RCRA metals. Metal ions bind to molecules called ligands, which are the molecular tools that can manipulate the metal ions under most conditions. This DOE-EMSP sponsored program strives (1) to provide the foundations for using the most powerful ligands in transformational separations technologies and (2) to produce seminal examples of their applications to separations appropriate to the DOE EM mission. These ultra tight-binding ligands can capture metal ions in the most competitive of circumstances (from mineralized sites, lesser ligands, and even extremely dilute solutions), but they react so slowly that they are useless in traditional separations methodologies. Two attacks on this problem are underway. The first accommodates to the challenging molecular lethargy by developing a seminal slow separations methodology termed the soil poultice. The second designs ligands that are only tight-binding while wrapped around the targeted metal ion, but can be put in place by switch-binding and removed by switch-release. We envision a kind of molecular switching process to accelerate the union between metal ion and tight-binding ligand. Molecular switching processes are suggested for overcoming the slow natural equilibration rate with which ultra tight-binding ligands combine with metal ions. Ligands that bind relatively weakly combine with metal ions rapidly, so the trick is to convert a ligand from a weak, rapidly binding species to a powerful, slow releasing ligand--during the binding of the ligand to the metal ion. Such switch-binding ligands must react with themselves, and the reaction must take place under the influence of the metal ion. For example, our generation 1 ligands showed that a well-designed linear ligand with ends that readily combine, forms a cyclic molecule when it wraps around a metal ion. Our generation 2 ligands are even more interesting. They convert from rings to structures that wrap around a metal ion to form a cage. These ligands are called cryptands. Switch release is accomplished by photolytic cleavage of a bond to convert a cyclic ligand into a linear ligand or to break similar bonds in a cryptate. Our studies have demonstrated switch binding and switch release with cryptates of calcium. These remarkable cyclic ligands and cage-like ligands are indeed tight-binding and may, in principle, be incorporated in various separations methodologies, including the soil poultice. The soil poultice mimics the way in which microbes secrete extremely powerful ligands into the soil in order to harvest iron. The cellular membrane of the microbe recognizes the iron/ligand complex and admits it into the cell. The soil poultice uses molecularly imprinted polymers (MIPs) to play the role of the cellular membrane. Imprinting involves creation of the polymer in the presence of the metal/ligand complex. In principle, a well design ligand/MIP combination can be highly selective toward almost any targeted metal ion. The principles for that design are the focus of these investigations. An imprinting molecule can interact with the polymer through any, some, or all of the so-called supramolecular modes; e.g., hydrogen bonding, electrostatic charge, minor ligand bonding, Pi-Pi stacking, and hydrophobic and van der Waals interactions. Historically these modes of binding have given MIPs only small re-binding capacities and very limited selectivities. This program has shown that each mode of interaction can be made more powerful than previously suspected and that combinations of different supramolecular interaction modes can produce remarkable synergisms. The results of this systematic study provide a firm foundation for tailoring molecular imprinted polymers for reclamation of specific metal ion, including those important to the DOE EM mission.

DARYLE H BUSCH RICHARD S GIVENS

2004-12-10T23:59:59.000Z

308

Impact on the steam electric power industry of deleting Section 316(a) of the Clean Water Act: Energy and environmental impacts  

Science Conference Proceedings (OSTI)

Many power plants discharge large volumes of cooling water. In some cases, the temperature of the discharge exceeds state thermal requirements. Section 316(a) of the Clean Water Act (CWA) allows a thermal discharger to demonstrate that less stringent thermal effluent limitations would still protect aquatic life. About 32% of the total steam electric generating capacity in the United States operates under Section 316(a) variances. In 1991, the US Senate proposed legislation that would delete Section 316(a) from the CWA. This study, presented in two companion reports, examines how this legislation would affect the steam electric power industry. This report quantitatively and qualitatively evaluates the energy and environmental impacts of deleting the variance. No evidence exists that Section 316(a) variances have caused any widespread environmental problems. Conversion from once-through cooling to cooling towers would result in a loss of plant output of 14.7-23.7 billion kilowatt-hours. The cost to make up the lost energy is estimated at $12.8-$23.7 billion (in 1992 dollars). Conversion to cooling towers would increase emission of pollutants to the atmosphere and water loss through evaporation. The second report describes alternatives available to plants that currently operate under the variance and estimates the national cost of implementing such alternatives. Little justification has been found for removing the 316(a) variance from the CWA.

Veil, J.A.; VanKuiken, J.C.; Folga, S.; Gillette, J.L.

1993-01-01T23:59:59.000Z

309

Thick planar domain wall: its thin wall limit and dynamics  

E-Print Network (OSTI)

We consider a planar gravitating thick domain wall of the $\\lambda \\phi^4$ theory as a spacetime with finite thickness glued to two vacuum spacetimes on each side of it. Darmois junction conditions written on the boundaries of the thick wall with the embedding spacetimes reproduce the Israel junction condition across the wall in the limit of infinitesimal thickness. The thick planar domain wall located at a fixed position is then transformed to a new coordinate system in which its dynamics can be formulated. It is shown that the wall's core expands as if it were a thin wall. The thickness in the new coordinates is not constant anymore and its time dependence is given.

S. Ghassemi; S. Khakshournia; R. Mansouri

2006-09-28T23:59:59.000Z

310

Domain-independent information extraction in unstructured text  

SciTech Connect

Extracting information from unstructured text has become an important research area in recent years due to the large amount of text now electronically available. This status report describes the findings and work done during the second year of a two-year Laboratory Directed Research and Development Project. Building on the first-year`s work of identifying important entities, this report details techniques used to group words into semantic categories and to output templates containing selective document content. Using word profiles and category clustering derived during a training run, the time-consuming knowledge-building task can be avoided. Though the output still lacks in completeness when compared to systems with domain-specific knowledge bases, the results do look promising. The two approaches are compatible and could complement each other within the same system. Domain-independent approaches retain appeal as a system that adapts and learns will soon outpace a system with any amount of a priori knowledge.

Irwin, N.H. [Sandia National Labs., Albuquerque, NM (United States). Software Surety Dept.

1996-09-01T23:59:59.000Z

311

Information Retrieval Systems Adapted to the Biomedical Domain  

E-Print Network (OSTI)

The terminology used in Biomedicine shows lexical peculiarities that have required the elaboration of terminological resources and information retrieval systems with specific functionalities. The main characteristics are the high rates of synonymy and homonymy, due to phenomena such as the proliferation of polysemic acronyms and their interaction with common language. Information retrieval systems in the biomedical domain use techniques oriented to the treatment of these lexical peculiarities. In this paper we review some of the techniques used in this domain, such as the application of Natural Language Processing (BioNLP), the incorporation of lexical-semantic resources, and the application of Named Entity Recognition (BioNER). Finally, we present the evaluation methods adopted to assess the suitability of these techniques for retrieving biomedical resources.

Marrero, Mnica; Urbano, Julin; Morato, Jorge; Moreiro, Jos-Antonio; 10.3145/epi.2010.may.04

2012-01-01T23:59:59.000Z

312

Slurry line eminent domain urged over rail lands  

Science Conference Proceedings (OSTI)

According to C.E. Bagge of the National Coal Association (NCA), Congress should pass a bill that would grant coal slurry pipelines the right-of-eminent-domain across land held by railroads. An NCA study determined that 85% of the coal shipped by U.S. railroads in 1977 could not have been shipped in any other way, and the NCA feels that the coal market would be improved if the railroads' transport dominance were reduced by the presence of slurry lines. NCA and Senator D. Bumpers would prefer that the bill under consideration be broadened to give slurry lines eminent domain over private lands, but this expansion of powers is considered politically infeasible. According to Senator W. Ford, the proposed bill would be applied primarily in eastern states, rather than in western states, as is generally thought, since eastern railroads usually own their track beds but western railroads are built on federal easements which slurry lines can cross.

Bagge, C.E.

1980-06-09T23:59:59.000Z

313

Workshop on Time Domain Science Using X-ray Techniques  

NLE Websites -- All DOE Office Websites (Extended Search)

Time-Resolved Beamlines Time-Resolved Beamlines Advisory Committee Workshop Home Workshop Chairs: Lin Chen (Argonne National Laboratory) Steve Milton (Advanced Photon Source) David Reis (University of Michigan) Linda Young (Argonne National Laboratory) Workshop on Time Domain Science Using X-ray Techniques August 29 September 1, 2004, The Abbey, Fontana, Lake Geneva Area, Wisconsin A workshop on "Time Domain Science Using X-ray Techniques" was held from August 29 September 1, 2004 , welcoming both experts and beginners in the field. This is one of the concurrently held workshops in the series on "Future Scientific Directions for the Advanced Photon Source." The goal of the workshop was to identify future directions in scientific research using time resolved x-ray techniques and to address possiblities to produce ps

314

Investigation of Unusual Albedos in the SGP Domain  

NLE Websites -- All DOE Office Websites (Extended Search)

Investigation of Unusual Albedos in the SGP Domain Investigation of Unusual Albedos in the SGP Domain Groff, David ARM SGP Duchon, Claude University Of Oklahoma Category: Atmospheric State and Surface We investigate the cause of unusually high albedos at an Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) extended facility near Morris, OK. In a previous study, daily albedos were calculated at several SGP extended facilities for 1998 and 1999 using broadband (.28 to 3 microns) pyranometers. The average daily albedo during this period was calculated to be at least about 5% higher at Morris than at any of the other SGP extended facilities. Surface based measurements of daily albedos at Morris and two nearby SGP extended facilities during 2004 and 2005 suggest the unusually high albedo measurements at Morris are real.

315

An angiogenin-binding protein from endothelial cells  

SciTech Connect

A 42-kDa bovine protein that binds bovine angiogenin (angiogenin binding protein (AngBP)) has been identified as a dissociable cell-surface component of calf pulmonary artery endothelial cells and a transformed bovine endothelial cell line, GM7373. {sup 125}I-Ang can be crosslinked efficiently to AngBP by a water-soluble carbodiimide, 1-ethyl-3-(3-dimethylaminopropyl)carbo-diimide. Bovine ribonuclease A competes with the binding of {sup 125}I-Ang to AngBP, but lysozyme does not. Direct binding to AngBP of {sup 125}I-labeled bovine ribonuclease A is, however, much weaker than that of {sup 125}I-Ang. Two enzymatically active derivatives of angiogenin cleaved at residues 60-61 and 67-68, respectively, fail to induce angiogenesis and also bind to AngBP only weakly. AngBP has been isolated by treatment of cells with heparan sulfate, affinity chromatography on angiogenin-Sepharose of the material dissociated from the cell surface, and gel filtration HPLC. The results suggest that AngBP has the characteristics of a receptor that may likely function in angiogenesis.

Hu, Guofu; Chang, Sooik; Riordan, J.F.; Vallee, B.L. (Harvard Medical School, Boston, MA (United States))

1991-03-15T23:59:59.000Z

316

Acid Gas Capture Using CO2-Binding Organic Liquids  

SciTech Connect

Current chemical CO2 scrubbing technology is primarily aqueous alkanolamine based. These systems rapidly bind CO2 (forming water-soluble carbamate and bicarbonate salts) however, the process has serious disadvantages. The concentration of monoethanolamine rarely exceeds 30 wt % due to the corrosive nature of the solution, and this reduces the maximum CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the CO2 scrubber. The ?30 wt % loading of ethanolamine also means that a large excess of water must be pumped and heated during CO2 capture and release, and this greatly increases the energy requirements especially considering the high specific heat of water (4 j/g-1K-1). Our approach is to switch to organic systems that chemically bind CO2 as liquid alkylcarbonate salts. Our CO2-binding organic liquids have higher CO2 solubility, lower specific heats, potential for less corrosion and lower binding energies for CO2 than aqueous systems. CO2BOLs also reversibly bind and release mixed sulfur oxides. Furthermore the CO2BOL system can be direct solvent replacements for any solvent based CO2 capture systems because they are commercially available reagents and because they are fluids they would not require extensive process re-engineering.

Heldebrant, David J.; Koech, Phillip K.; Rainbolt, James E.; Zheng, Feng

2010-11-10T23:59:59.000Z

317

Adding statistics routines to the SLATEC public domain subprogram library  

SciTech Connect

The SLATEC library is a public-domain portable library of FORTRAN subroutines organized by several DOE and DOD laboratories. SLATEC includes a comprehensive set of mathematical routines, including special functions, linear algebra, and differential equation solvers. These routines will run on most computers which support FORTRAN. It was decided to include statistical routines in SLATEC, and some routines are being added. This paper discusses the nature of SLATEC, indicate plans for the statistics routines, and call for further contributions to SLATEC.

Durst, M.J.; Margolies, D.S.; Fong, K.

1983-01-01T23:59:59.000Z

318

Superradiant instabilities of rotating black holes in the time domain  

E-Print Network (OSTI)

Bosonic fields on rotating black hole spacetimes are subject to amplification by superradiance, which induces exponentially-growing instabilities (the `black hole bomb') in two scenarios: if the black hole is enclosed by a mirror, or if the bosonic field has rest mass. Here we present a time-domain study of the scalar field on Kerr spacetime which probes ultra-long timescales up to $t \\lesssim 5 \\times 10^6 M$, to reveal the growth of the instability. We describe an highly-efficient method for evolving the field, based on a spectral decomposition into a coupled set of 1+1D equations, and an absorbing boundary condition inspired by the `perfectly-matched layers' paradigm. First, we examine the mirror case to study how the instability timescale and mode structure depend on mirror radius. Next, we examine the massive-field, whose rich spectrum (revealed through Fourier analysis) generates `beating' effects which disguise the instability. We show that the instability is clearly revealed by tracking the stress-energy of the field in the exterior spacetime. We calculate the growth rate for a range of mass couplings, by applying a frequency-filer to isolate individual modal contributions to the time-domain signal. Our results are in accord with previous frequency-domain studies which put the maximum growth rate at $\\tau^{-1} \\approx 1.72 \\times 10^{-7} (GM/c^3)^{-1}$ for the massive scalar field on Kerr spacetime.

Sam R. Dolan

2012-12-06T23:59:59.000Z

319

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

320

BPA GUIDANCE ON THE USE OF BINDING ARBITRATION  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

BONNEVILLE POWER ADMINISTRATION'S BONNEVILLE POWER ADMINISTRATION'S GUIDANCE ON THE USE OF BINDING ARBITRATION FOR BPA CONTRACTS Introduction Alternative dispute resolution (ADR) encompasses a variety of methods that parties may use to resolve disputes without litigation. Arbitration is a private, less formal process in which parties agree to submit a dispute to one or more impartial arbitrators who then render a decision or award. In non-binding arbitration a party is not required to accept the arbitrator's decision. In contrast, a decision or award in binding arbitration is final and subject to only very limited rights of appeal. See Federal Arbitration Act, 9 U.S.C. §§ 1-16 (FAA). Both types of arbitration can provide benefits to BPA, its customers, and other stakeholders including the public, such as greater flexibility, limited discovery, a

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


321

ac and dc current-induced motion of a 360 degrees domain wall  

E-Print Network (OSTI)

he response of 360 [360 degrees]domain walls in narrow magnetic stripes to applied dc and ac currents, investigated by micromagnetic simulation, differs qualitatively from the response of 180 [180 degrees] domain walls. ...

Mascaro, Mark D.

322

From top-level to domain ontologies: ecosystem classifications as a case study  

Science Conference Proceedings (OSTI)

This paper shows how to use a top-level ontology to create robust and logically coherent domain ontology in a way that facilitates computational implementation and interoperability. It uses a domain ontology of ecosystem classification and delineation ...

Thomas Bittner

2007-09-01T23:59:59.000Z

323

Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate  

E-Print Network (OSTI)

Phenomenological theory of a single domain wall in uniaxial trigonal ferroelectrics: Lithium niobate and lithium tantalate David A. Scrymgeour and Venkatraman Gopalan Department of Materials Science, lithium niobate and lithium tantalate. The contributions to the domain- wall energy from polarization

Gopalan, Venkatraman

324

Magnetic behavior of 360 domain walls in patterned magnetic thin films  

E-Print Network (OSTI)

360 transverse domain walls (360DWs), which form readily from transverse 180 domain walls (180DWs) of opposite sense, demonstrate qualitatively distinct behaviors from their constituent 180DWs and are therefore of interest ...

Mascaro, Mark Daniel

2012-01-01T23:59:59.000Z

325

Time-domain non-Monte Carlo noise simulation for nonlinear dynamic circuits with arbitrary excitations  

Science Conference Proceedings (OSTI)

A new, time-domain, non-Monte Carlo method for computer simulation of electrical noise in nonlinear dynamic circuits with arbitrary excitations is presented. This time-domain noise simulation ...

Alper Demir; Edward W. Y. Liu; Alberto L. Sangiovanni-Vincentelli

1994-11-01T23:59:59.000Z

326

Towards an understanding of human alpha-7 nicotinic acetylcholine receptor selectivity : the creation and characterization of a soluble ligand binding domain template  

E-Print Network (OSTI)

red label beside the button changes to green and the word Editable button, which changes a label from red to greentwo green arrows). Clicking on the query structure button (

Nemecz, kos

2011-01-01T23:59:59.000Z

327

Structure of the FHA1 Domain of Yeast Rad53 and Identification of Binding Sites for both FHA1 and its  

E-Print Network (OSTI)

-hydroxysulfosuccinimide; Nle, norleucine; NOE, nuclear Overhauser effect; NOESY, nuclear Overhauser enhancement correlated by 18 natural amino acid residues (except for Cys and Met) plus norleucine (Nle), which is used, we searched the sequence of Rad9 for these features and found a match for residues 192 TEAD195 . We

Tsai, Ming-Daw

328

Decreased angiotensin II binding affinity and binding capacity in the anterior pituitary gland of adult spontaneously hypertensive rats  

SciTech Connect

Angiotensin II (ANG) binding sites were quantified in single pituitary glands from 4-week-old and 14-week-old male spontaneously hypertensive rats (SHR) and age-matched male normotensive Wistar-Kyoto (WKY) control rats after incubation with /sup 125/I-(Sar/sup 1/)-ANG, autoradiography with computerized densitometry, and comparison to /sup 125/I-standards. The maximum binding capacity (B/sub max/) decreased while the dissociation constant (K/sub d/) for ANG increased in 14-week-old SHR when compared to age-matched WKY control rats. Conversely, no difference between rat strains was found in 4-week-old animals. Our results suggest that pituitary ANG binding sites may play a role in the pathophysiology of established genetic hypertension.

Gutkind, J.S.; Castren, E.; Saavedra, J.M.

1988-01-01T23:59:59.000Z

329

Multi-physical simulations of current-induced domain wall motion using graphics processing units  

Science Conference Proceedings (OSTI)

Micromagnetic simulations of current- induced domain wall motion are presented. Domain walls are prominent candidates for concepts of storing binary data by the magnetization of ferromagnetic nanostructures. Influences of the spin-torque and the Oersted ... Keywords: current-induced domain wall motion, graphics processing units, multi-physical micromagnetic modelling and simulations, racetrack memory

Andr Drews; Gunnar Selke; Dietmar P. F. Mller

2010-07-01T23:59:59.000Z

330

Secure interoperable digital content distribution mechanisms in a multi-domain architecture  

Science Conference Proceedings (OSTI)

Current DRM systems use the Authorized Domain concept to allow sharing of DRM-enabled multimedia contents across multiple devices. However, some devices in an authorized domain may support only a limited number of DRM systems of the content providers ... Keywords: Authorized domain, DRM, Interoperability, Personal content sharing, TPM

Lei Lei Win; Tony Thomas; Sabu Emmanuel

2012-09-01T23:59:59.000Z

331

Local Electromechanical Response at a Single Ferroelectric Domain Wall in Lithium Niobate  

E-Print Network (OSTI)

Local Electromechanical Response at a Single Ferroelectric Domain Wall in Lithium Niobate DAVID A electromechanical response across a single ferroelectric domain wall in congruent lithium niobate at room in the crystal, which interact with the domain wall. I. INTRODUCTION FERROELECTRIC lithium niobate and lithium

Gopalan, Venkatraman

332

Analysing the effect of out-of-domain data on SMT systems  

Science Conference Proceedings (OSTI)

In statistical machine translation (SMT), it is known that performance declines when the training data is in a different domain from the test data. Nevertheless, it is frequently necessary to supplement scarce in-domain training data with out-of-domain ...

Barry Haddow; Philipp Koehn

2012-06-01T23:59:59.000Z

333

Pounamu: A meta-tool for exploratory domain-specific visual language tool development  

Science Conference Proceedings (OSTI)

Domain-specific visual language tools have become important in many domains of software engineering and end user development. However building such tools is very challenging with a need for multiple views of information and multi-user support, the ability ... Keywords: Domain-specific languages, Meta-CASE, Meta-tools, Visual design environments

Nianping Zhu; John Grundy; John Hosking; Na Liu; Shuping Cao; Akhil Mehra

2007-08-01T23:59:59.000Z

334

Modular and deformable touch-sensitive surfaces based on time domain reflectometry  

Science Conference Proceedings (OSTI)

Time domain reflectometry, a technique originally used in diagnosing cable faults, can also locate where a cable is being touched. In this paper, we explore how to extend time domain reflectometry in order to touch-enable thin, modular, and deformable ... Keywords: TDR, capacitive sensing, deformable, input, time domain reflectometry, touch sensing, wearable

Raphael Wimmer; Patrick Baudisch

2011-10-01T23:59:59.000Z

335

DNA-Binding Mechanism in Prokaryotic Partition Complex Formation  

NLE Websites -- All DOE Office Websites (Extended Search)

DNA-Binding Mechanism in DNA-Binding Mechanism in Prokaryotic Partition Complex Formation DNA-Binding Mechanism in Prokaryotic Partition Complex Formation Print Wednesday, 29 March 2006 00:00 The faithful inheritance of genetic information, essential for all organisms, requires accurate movement and positioning of replicated DNA to daughter cells during cell division. In cells without distinct nuclei (prokaryotes), this process, called partition or segregation, is mediated by par systems. The prototype system of prokaryotic partition is the Escherichia coli P1 plasmid par system, which consists of a centromere site (parS) on the plasmid DNA and two proteins, ParA and ParB. The initial formation of the so-called partition complex between ParB and the centromere is a critical step in partition. To understand the DNA-binding mechanism utilized by ParB, Schumacher and Funnell determined crystal structures of the C-terminal region of ParB, known as ParB(142-333), bound to centromere sites.

336

Scheduling and resource binding algorithm considering timing variation  

Science Conference Proceedings (OSTI)

The timing closure problem (e.g., meeting timing/ clock period constraint) is one of the most important problems in the design automation. However, the rapid increase of the impact of the process variation on circuit timing makes the problem much more ... Keywords: binding, high-level synthesis, scheduling, timing analysis, timing variation

Jongyoon Jung; Taewhan Kim

2011-02-01T23:59:59.000Z

337

PHYS 551 Lecture #27 Title: TightBinding  

E-Print Network (OSTI)

PHYS 551 Lecture #27 Title: Tight­Binding Now that we have shown that /( ~ k; ~r) = \\Gamma P ~ R e i ~ k \\Delta ~ R OE A (~r \\Gamma ~ R) satisfies the Bloch condition, all that remains is to grind the calculation explicitly. First, the wave­function /( ~ k; ~r) must be normalized. Thus Z / \\Lambda / dV = 1 = j

Winokur, Michael

338

Automatic Generation of Tcl Bindings for C and C++ Libraries  

E-Print Network (OSTI)

Automatic Generation of Tcl Bindings for C and C++ Libraries Wolfgang Heidrich Computer Graphics@informatik.uni-erlangen.de Abstract In the past few years Tcl has found widespread in- terest as a extensible scripting language. Numerous Tcl interfaces for a variety of C libraries have been created. While most of these language

Heidrich, Wolfgang

339

Automatic Generation of Tcl Bindings for C and C++ Libraries  

E-Print Network (OSTI)

In the past few years Tcl has found widespread interest as a extensible scripting language. Numerous Tcl interfaces for a variety of C libraries have been created. While most of these language bindings have been created by hand, others have made use of dedicated code generators designed for the specific library. In this paper we present a tool for the automatic generation of Tcl language bindings for arbitrary C libraries. Moreover, the mapping of C++ class hierarchies to [incr Tcl] classes will be described. 1 Introduction 1.1 Prior Work One of the reasons for the recent success of Tcl is its powerful API to C and C++, which allows the extension of the core language with commands implemented as C functions. This facility has been used to create a variety of language bindings for C libraries, ranging from different 3D graphics libraries (iris gl, OpenGL, vogle, sipp) to several X widget sets, for example Wafe and tclMotif. While most of this work has been done manually, other bind...

Wolfgang Heidrich; Philipp Slusallek

1995-01-01T23:59:59.000Z

340

Inhibition of cell-cell binding by lipid assemblies  

DOE Patents (OSTI)

This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

Nagy, Jon O. (Rodeo, CA); Bargatze, Robert F. (Bozeman, MT)

2001-05-22T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


341

AAAS Office of Opportunities in Science The Double Bind  

E-Print Network (OSTI)

of scientists regardless of race, ethnicity or gender. Conserving of their time and energies, they tackled. Science careers in the context of gender and race or ethnic bias have been a major part of our lives of biases related to both their race or ethnicity and gender, constituting a double bind. Programs

Ortiz, Christine

342

A Unitary Anesthetic Binding Site at High Resolution  

DOE Green Energy (OSTI)

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.

Vedula, L. Sangeetha; Brannigan, Grace; Economou, Nicoleta J.; Xi, Jin; Hall, Michael A.; Liu, Renyu; Rossi, Matthew J.; Dailey, William P.; Grasty, Kimberly C.; Klein, Michael L.; Eckenhoff, Roderic G.; Loll, Patrick J.; (Drexel-MED); (UPENN)

2009-10-21T23:59:59.000Z

343

Workshop on gate valve pressure locking and thermal binding  

SciTech Connect

The purpose of the Workshop on Gate Valve Pressure Locking and Thermal Binding was to discuss pressure locking and thermal binding issues that could lead to inoperable gate valves in both boiling water and pressurized water reactors. The goal was to foster exchange of information to develop the technical bases to understand the phenomena, identify the components that are susceptible, discuss actual events, discuss the safety significance, and illustrate known corrective actions that can prevent or limit the occurrence of pressure locking or thermal binding. The presentations were structured to cover U.S. Nuclear Regulatory Commission staff evaluation of operating experience and planned regulatory activity; industry discussions of specific events, including foreign experience, and efforts to determine causes and alleviate the affects; and valve vendor experience and recommended corrective action. The discussions indicated that identifying valves susceptible to pressure locking and thermal binding was a complex process involving knowledge of components, systems, and plant operations. The corrective action options are varied and straightforward.

Brown, E.J.

1995-07-01T23:59:59.000Z

344

Inhibition Of Call-Cell Binding By Kipid Assemblies  

DOE Patents (OSTI)

This invention relates generally to the field of therapeutic compounds designed to interfere between the binding of ligands and their receptors on cell surface. More specifically, it provides products and methods for inhibiting cell migration and activation using lipid assemblies with surface recognition elements that are specific for the receptors involved in cell migration and activation.

Nagy, Jon O. (Rodeo, CA), Bargatze, Robert F. (Bozeman, MT)

2003-12-16T23:59:59.000Z

345

A Unitary Anesthetic Binding Site at High Resolution  

DOE Green Energy (OSTI)

Propofol is the most widely used injectable general anesthetic. Its targets include ligand-gated ion channels such as the GABA{sub A} receptor, but such receptor-channel complexes remain challenging to study at atomic resolution. Until structural biology methods advance to the point of being able to deal with systems such as the GABA{sub A} receptor, it will be necessary to use more tractable surrogates to probe the molecular details of anesthetic recognition. We have previously shown that recognition of inhalational general anesthetics by the model protein apoferritin closely mirrors recognition by more complex and clinically relevant protein targets; here we show that apoferritin also binds propofol and related GABAergic anesthetics, and that the same binding site mediates recognition of both inhalational and injectable anesthetics. Apoferritin binding affinities for a series of propofol analogs were found to be strongly correlated with the ability to potentiate GABA responses at GABA{sub A} receptors, validating this model system for injectable anesthetics. High resolution x-ray crystal structures reveal that, despite the presence of hydrogen bond donors and acceptors, anesthetic recognition is mediated largely by van der Waals forces and the hydrophobic effect. Molecular dynamics simulations indicate that the ligands undergo considerable fluctuations about their equilibrium positions. Finally, apoferritin displays both structural and dynamic responses to anesthetic binding, which may mimic changes elicited by anesthetics in physiologic targets like ion channels.

L Vedula; G Brannigan; N Economou; J Xi; M Hall; R Liu; M Rossi; W Dailey; K Grasty; et. al.

2011-12-31T23:59:59.000Z

346

Temperature-profile determination using frequency-domain reflectometry  

DOE Green Energy (OSTI)

The temperature distribution along a coaxial electrical cable can be determined by means of frequency-domain reflectometry if the cable has an inner sheath of a suitable temperature-sensitive dielectric material. Such a technique would have advantages in cost and convenience over the conventional method of placing a separate thermocouple at each point where the temperature is to be measured. It would be especially useful for underground applications in assessing geothermal reservoirs and in instrumenting in situ coal-gasification and oil-shale-retorting experiments.

Lytle, R.J.; Myers, G.K.

1976-04-02T23:59:59.000Z

347

Expert System Models in the Companies' Financial and Accounting Domain  

E-Print Network (OSTI)

The present paper is based on studying, analyzing and implementing the expert systems in the financial and accounting domain of the companies, describing the use method of the informational systems that can be used in the multi-national companies, public interest institutions, and medium and small dimension economical entities, in order to optimize the managerial decisions and render efficient the financial-accounting functionality. The purpose of this paper is aimed to identifying the economical exigencies of the entities, based on the already used accounting instruments and the management software that could consent the control of the economical processes and patrimonial assets.

Mates, D; Bostan, I; Grosu, V

2010-01-01T23:59:59.000Z

348

Both common variations and rare non-synonymous substitutions and small insertion/deletions in CLU are associated with increased Alzheimer risk  

E-Print Network (OSTI)

[9]. Moreover, CLU enhances endocytosis of Ab aggre- gates to brain phagocytes [10]. Taking its variety of phy- siological functions, CLU could be a guardian or enemy in AD [11]. The CLU transcriptional unit is located in the chro- mosomal region 8p21... only in green. All predicted pathogenic variants are indicated in bold. After cleavage of the signal peptide, the secreted CLU form (449 AA) contains two coiled-coiled domains (pink), three amphipathic domains (blue) and a cysteine rich region (yellow...

Bettens, Karolien; Brouwers, Nathalie; Engelborghs, Sebastiaan; Lambert, Jean-Charles; Rogaeva, Ekaterina; Vandenberghe, Rik; Le Bastard, Nathalie; Pasquier, Florence; Vermeulen, Steven; Van Dongen, Jasper; Mattheijssens, Maria; Peeters, Karin; Mayeux, Richard; St George-Hyslop, Peter; Amouyel, Philippe; De Deyn, Peter P; Sleegers, Kristel; Van Broeckhoven, Christine

2012-01-16T23:59:59.000Z

349

2.0 Closed-Domain Hydrate Dissociation (Base Case w/ Hydrate  

NLE Websites -- All DOE Office Websites (Extended Search)

Closed-Domain Hydrate Dissociation (Base Case w/ Hydrate) Closed-Domain Hydrate Dissociation (Base Case w/ Hydrate) 2.1 Problem Description One half of a 20-m, one-dimensional horizontal domain, discretized using uniformly spaced 1-m grid cells (optionally 0.1-m grid cells) is initialized with aqueous-hydrate conditions; whereas, the other half of the domain is initialized with gas-aqueous conditions. As with the Base Case problem, a closed horizontal domain is used to eliminate gravitational body forces and boundary condition effects. The initial conditions are specified to yield complete dissociation of the hydrate, via the thermal capacitance of the domain-half initialized with gas-aqueous conditions. To initialize the aqueous-hydrate half of the domain, temperature, pressure, and hydrate saturation are

350

Transcription of domain patterns in near-stoichiometric magnesium-doped lithium niobate  

SciTech Connect

Recently, light-induced domain reversal has been developed to a promising method for domain engineering, but the depth of reversed domain is only of several tens of microns, which greatly limits its practical applications. In this Letter, we fabricated domain patterns on the -z face of 1.0 mol % Mg doped near-stoichiometric lithium niobate with the assistance of a focal 532 nm laser, and then succeeded to transcribe these domain patterns from the -z to the +z face by applying external field without laser illumination. The transcribed domains have much larger depths, can sustain more than 100 times of the transcription cycles without large deformation, and can be erased by one transcription cycle with illumination of 532 nm laser. Finally, a light-induced ferroelectric domain transcription model was proposed.

Zeng Hao; Tian Tian; Sun Tongqing [School of Physics, Nankai University, Tianjin 300071 (China); Kong Yongfa; Chen Shaolin; Zhang Ling; Rupp, Romano [MOE Key Laboratory of Weak-Light Nonlinear Photonics and TEDA Applied Physics School, Nankai University, Tianjin 300457 (China); Xu Jingjun [School of Physics, Nankai University, Tianjin 300071 (China); MOE Key Laboratory of Weak-Light Nonlinear Photonics and TEDA Applied Physics School, Nankai University, Tianjin 300457 (China)

2010-11-15T23:59:59.000Z

351

The Australian domain name registration system : a more efficient system for the promotion of liberalisation, consumer protection and growth.  

E-Print Network (OSTI)

??This thesis is about the Australian domain name system and, in particular, the principles governing the registration of domain names in the '.au' country code (more)

Ng, Jenny Swee Gaik

2009-01-01T23:59:59.000Z

352

Organic Solar Cells: Absolute Measurement of Domain Composition and  

NLE Websites -- All DOE Office Websites (Extended Search)

Organic Solar Cells: Absolute Organic Solar Cells: Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in Solar Cells Organic Solar Cells: Absolute Measurement of Domain Composition and Nanoscale Size Distribution Explains Performance in Solar Cells Print Tuesday, 22 January 2013 00:00 This front cover represents the morphology and resulting device dynamics in organic solar cell blend films of PTB7 and PC71BM, as revealed by combined resonant x-ray scattering and microscopy done at the Advanced Light Source. Harald Ade and co-workers find that the fullerene molecules (red) are miscible in the polymer (blue) up to 30 wt.%, above which they begin to agglomerate (bottom). This agglomeration is important for the optoelectronic processes within the device, but the agglomerates must be kept to small sizes by the solvent processing additive diiodooctane (DIO). Correlation of this morphology with the spectrally resolved quantum efficiency shows that the yellow excitons created upon photoabsorption must arrive at the agglomerate interface for charge separation to occur. The blue electrons and green holes can then percolate through appropriate molecules in the mixed matrix to the electrodes for harvesting of electrical energy. Article Link (PDF)

353

Domain-Specific Languages for Composing Signature Discovery Workflows  

SciTech Connect

Domain-agnostic signature discovery entails investigation across multiple scientific disciplines. The breadth and cross-disciplinary nature of this work requires that existing executables be integrated with new capabilities into workflows, representing a wide range of user tasks. An algorithm may be written in multiple programming languages for various hardware platforms, and so workflow composition requires integrating executables from any number of remote hosts. This raises an engineering issue on how to generate web service wrappers for these heterogeneous executables and to compose them into a scientific workflow environment (e.g., Taverna). In this paper, we introduce two simple Domain-Specific Languages (DSLs) to automate these processes. Our Service Description Language (SDL) describes key elements of a signature discovery service and automatically generates its implementation code. The Workflow Description Language (WDL) describes the pipeline of services and generates deployable artifacts for the Taverna workflow management system. We demonstrate our approach with a real-world workflow composed of services wrapping remote executables.

Jacob, Ferosh; Gray, Jeff; Wynne, Adam S.; Liu, Yan (Jenny) [Jenny; Baker, Nathan A.

2012-10-23T23:59:59.000Z

354

Domain Wall QCD with Near-Physical Pions  

E-Print Network (OSTI)

We present physical results for a variety of light hadronic quantities obtained via a combined analysis of three 2+1 flavour domain wall fermion ensemble sets. For two of our ensemble sets we used the Iwasaki gauge action with beta=2.13 (a^-1=1.75(4) GeV) and beta=2.25 (a^-1=2.31(4) GeV) and lattice sizes of 24^3 x 64 and 32^3 x 64 respectively, with unitary pion masses in the range 293(5)-417(10) MeV. The extent L_s for the 5^th dimension of the domain wall fermion formulation is L_s=16 in these ensembles. In this analysis we include a third ensemble set that makes use of the novel Iwasaki+DSDR (Dislocation Suppressing Determinant Ratio) gauge action at beta = 1.75 (a^-1=1.37(1) GeV) with a lattice size of 32^3 x 64 and L_s=32 to reach down to partially-quenched pion masses as low as 143(1) MeV and a unitary pion mass of 171(1) MeV, while retaining good chiral symmetry and topological tunneling. We demonstrate a significant improvement in our control over the chiral extrapolation, resulting in much improved ...

Arthur, R; Boyle, P A; Christ, N H; Garron, N; Hudspith, R J; Izubuchi, T; Jung, C; Kelly, C; Lytle, A T; Mawhinney, R D; Murphy, D; Ohta, S; Sachrajda, C T; Soni, A; Zanotti, J M

2012-01-01T23:59:59.000Z

355

Quantifying the mechanisms of domain gain in animal proteins  

E-Print Network (OSTI)

-3#7;#7;#7;MF#7;inositol-polyphosphate 5-phosphatase activity#7;1.9 x10-4#7;6.7 x10-3#7;#7;Annotation Cluster 6#7;MF#7;helicase activity#7;1.2 x10-4#7;4.5 x10-3#7;#7;#7;MF#7;purine NTP-dependent helicase activity#7;2.1 x10-3#7;3.6 x10-2#7;#7;#7;MF#7;ATP... -dependent helicase activity#7;2.1 x10-3#7;3.6 x10-2#7;#7;Other significant GO terms#7;MF#7;scavenger receptor activity#7;2.6 x10-6#7;1.2 x10-3#7;#7;#7;MF#7;diacylglycerol binding#7;3.6 x10-5#7;1.8 x10-3#7;#7;#7;MF#7;binding#7;6.7 x10-5#7;3.0 x10-3#7;#7;#7;MF#7...

Buljan, Marija; Frankish, Adam; Bateman, Alex

2010-07-15T23:59:59.000Z

356

Allosteric Activation of E2-RING Finger-Mediated Ubiquitylation by a Structurally Defined Specific E2-Binding Region of gp78  

SciTech Connect

The activity of RING finger ubiquitin ligases (E3) is dependent on their ability to facilitate transfer of ubiquitin from ubiquitin-conjugating enzymes (E2) to substrates. The G2BR domain within the E3 gp78 binds selectively and with high affinity to the E2 Ube2g2. Through structural and functional analyses, we determine that this occurs on a region of Ube2g2 distinct from binding sites for ubiquitin-activating enzyme (E1) and RING fingers. Binding to the G2BR results in conformational changes in Ube2g2 that affect ubiquitin loading. The Ube2g2:G2BR interaction also causes an 50-fold increase in affinity between the E2 and RING finger. This results in markedly increased ubiquitylation by Ube2g2 and the gp78 RING finger. The significance of this G2BR effect is underscored by enhanced ubiquitylation observed when Ube2g2 is paired with other RING finger E3s. These findings uncover a mechanism whereby allosteric effects on an E2 enhance E2-RING finger interactions and, consequently, ubiquitylation.

Das, Ranabir; Mariano, Jennifer; Tsai, Yien Che; Kalathur, Ravi C.; Kostova, Zlatka; Li, Jess; Tarasov, Sergey G.; McFeeters, Robert L.; Altieri, Amanda S.; Ji, Xinhua; Byrd, R. Andrew; Weissman, Allan M.; (NCI)

2010-11-12T23:59:59.000Z

357

U-183: ISC BIND DNS Resource Records Handling Vulnerability | Department of  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

3: ISC BIND DNS Resource Records Handling Vulnerability 3: ISC BIND DNS Resource Records Handling Vulnerability U-183: ISC BIND DNS Resource Records Handling Vulnerability June 5, 2012 - 7:00am Addthis PROBLEM: A vulnerability has been reported in ISC BIND, which can be exploited by malicious people to disclose potentially sensitive information or cause a DoS (Denial of Service). PLATFORM: Version(s): ISC BIND 9.2.x ISC BIND 9.3.x ISC BIND 9.4.x ISC BIND 9.5.x ISC BIND 9.6.x ISC BIND 9.7.x ISC BIND 9.8.x ISC BIND 9.9.x ABSTRACT: This problem was uncovered while testing with experimental DNS record types. It is possible to add records to BIND with null (zero length) rdata fields. Reference List: Secunia Advisory 49338 CVE-2012-1667 Original Advisory IMPACT ASSESSMENT: High Discussion: Recursive servers may crash or disclose some portion of memory to the

358

Nuclear deformation effect on the binding energies in heavy ions  

E-Print Network (OSTI)

Nuclear deformation effects on the binding energies in heavy ions are investigated. Approximate formulas for the nuclear-size correction and the isotope shift for deformed nuclei are derived. Combined with direct numerical evaluations, these formulas are employed to reanalyse experimental data on the nuclear-charge-distribution parameters in $^{238}\\textrm{U}$ and to revise the nuclear-size corrections to the binding energies in H- and Li-like $^{238}\\textrm{U}$. As a result, the theoretical uncertainties for the ground-state Lamb shift in $^{238}\\textrm{U}^{91+}$ and for the $2p_{1/2}-2s$ transition energy in $^{238}\\textrm{U}^{89+}$ are significantly reduced. The isotope shift of the $2p_{j}-2s$ transition energies for $^{142}\\textrm{Nd}^{57+}$ and $^{150}\\textrm{Nd}^{57+}$ is also evaluated including nuclear size and nuclear recoil effects within a full QED treatment.

Kozhedub, Y S; Shabaev, V M; Tupitsyn, I I; Brandau, C; Kozhuharov, C; Plunien, G; Sthlker, T

2007-01-01T23:59:59.000Z

359

Nuclear binding energies from a BPS Skyrme model  

E-Print Network (OSTI)

Recently, within the space of generalized Skyrme models, a BPS submodel was identified which reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classical soliton energies, the excitation energies from the collective coordinate quantization of spin and isospin, the electrostatic Coulomb energies and a small explicit isospin symmetry breaking, which accounts for the mass difference between proton and neutron. The integrability properties of the BPS Skyrme model allow, in fact, for an analytical calculation of all contributions, which may then be compared with the semi-empirical mass formula. We find that for heavier nuclei, where the model is expected to be more accurate o...

Adam, C; Sanchez-Guillen, J; Wereszczynski, A

2013-01-01T23:59:59.000Z

360

Reversible Acid Gas Capture Using CO2-Binding Organic Liquids  

SciTech Connect

Acid gas scrubbing technology is predominantly aqueous alkanolamine based. Of the acid gases, CO2, H2S and SO2 have been shown to be reversible, however there are serious disadvantages with corrosion and high regeneration costs. The primary scrubbing system composed of monoethanolamine is limited to 30% by weight because of the highly corrosive solution. This gravimetric limitation limits the CO2 volumetric (?108 g/L) and gravimetric capacity (?7 wt%) of the system. Furthermore the scrubbing system has a large energy penalty from pumping and heating the excess water required to dissolve the MEA bicarbonate salt. Considering the high specific heat of water (4 j/g-1K-1), low capacities and the high corrosion we set out to design a fully organic solvent that can chemically bind all acid gases i.e. CO2 as reversible alkylcarbonate ionic liquids or analogues thereof. Having a liquid acid gas carrier improves process economics because there is no need for excess solvent to pump and to heat. We have demonstrated illustrated in Figure 1, that CO2-binding organic liquids (CO2BOLs) have a high CO2 solubility paired with a much lower specific heat (<1.5 J/g-1K-1) than aqueous systems. CO2BOLs are a subsection of a larger class of materials known as Binding Organic Liquids (BOLs). Our BOLs have been shown to reversibly bind and release COS, CS2, and SO2, which we denote COSBOLS, CS2BOLs and SO2BOLs. Our BOLs are highly tunable and can be designed for post or pre-combustion gas capture. The design and testing of the next generation zwitterionic CO2BOLs and SO2BOLs are presented.

Heldebrant, David J.; Koech, Phillip K.; Yonker, Clement R.; Rainbolt, James E.; Zheng, Feng

2010-08-31T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


361

High-resolution DNA-binding specificity analysis of yeast transcription factors  

E-Print Network (OSTI)

Transcription factors (TFs) regulate the expression of genes through sequence-specific interactions with DNA-binding sites. However, despite recent progress in identifying in vivo TF binding sites by microarray readout of ...

Zhu, Cong

362

V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote Users Execute Arbitrary Code V-058: Microsoft Internet Explorer CDwnBindInfo Object Reuse Flaw Lets Remote...

363

A hypothesis driven approach to condition specific transcription factor binding site characterization in S.c.  

Science Conference Proceedings (OSTI)

We demonstrate a computational process by which transcription factor binding sites can be elucidated using genome-wide expression and binding profiles. The profiles direct us to the intergenic locations likely to contain the promoter regions for a given ...

Rhonda Harrison; Charles DeLisi

2002-03-01T23:59:59.000Z

364

V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Addthis Related Articles U-038: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c T-662:...

365

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service...  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

Off-by-one Bug Lets Remote Users Deny Service U-260: ISC BIND RDATA Processing Flaw Lets Remote Users Deny Service U-183: ISC BIND DNS Resource Records Handling Vulnerability...

366

Transferable tight-binding parameters: An application to Ni and Ni-Al alloys  

Science Conference Proceedings (OSTI)

Two approaches for obtaining tight-binding parameters for metallic alloys are compared and contrasted with special regard for the application to large scale simulations such as may occur in tight-binding molecular dynamics studies.

Sluiter, M.H.F.; Singh, P.P.

1993-07-01T23:59:59.000Z

367

T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service | Department  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

7: BIND RPZ Processing Flaw Lets Remote Users Deny Service 7: BIND RPZ Processing Flaw Lets Remote Users Deny Service T-617: BIND RPZ Processing Flaw Lets Remote Users Deny Service May 6, 2011 - 7:00am Addthis PROBLEM: A vulnerability has been reported in BIND, which can be exploited by malicious people to cause a DoS (Denial of Service). PLATFORM: ISC BIND version 9.8.0. ABSTRACT: When a name server is configured with a response policy zone (RPZ), queries for type RRSIG can trigger a server crash. REFERENCE LINKS: ISC Advisory: CVE-2011-1907 Secunia Advisory: SA44416 Vulnerability Report: ISC BIND CVE-2011-1907 SecurityTracker Alert ID: 1025503 IMPACT ASSESSMENT: High Discussion: This advisory only affects BIND users who are using the RPZ feature configured for RRset replacement. BIND 9.8.0 introduced Response Policy Zones (RPZ), a mechanism for modifying DNS responses returned by a

368

Angiotensin receptor binding and pressor effects in cat subretrofacial nucleus  

SciTech Connect

Central administration of angiotensin II (ANG II) increases arterial blood pressure via increased sympathetic activity. The authors have examined the possibility that one site of action of ANG II is the subretrofacial (SRF) nucleus in the rostral ventrolateral medulla, since this nucleus is known to play a critical role in the tonic and phasic control of arterial pressure. In vitro autoradiography, employing {sup 125}I-labeled (Sar{sup 1}, Ile{sup 8})ANG II as radioligand, was used to localize binding sites for ANG-II in the cat ventrolateral medulla. A high density of ANG II-receptor binding sites was found confined to the SRF nucleus. In a second group of experiments in anesthetized cats, microinjections of ANG II, in doses ranging from 10 to 50 pmol, were made into histologically identified sites within and outside the SRF nucleus. Microinjections into the nucleus resulted in a dose-dependent increase in arterial pressure, which was abolished by systemic administration of the ganglion-blocking drug hexamethonium bromide. In contrast, microinjections just outside the SRF nucleus had no effect on arterial pressure. It is concluded that activation of ANG II-receptor binding sites within the SRF nucleus leads to an increase in arterial pressure via increased sympathetic efferent activity.

Allen, A.M.; Dampney, R.A.L.; Mendelsohn, F.A.O. (Univ. of Melbourne (Australia) Univ. of Sydney (Australia))

1988-11-01T23:59:59.000Z

369

Stereoselective Binding of Ruthenium Complexes to Cytochrome c  

NLE Websites -- All DOE Office Websites (Extended Search)

Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Site-Dependent Stereoselective Binding of Ruthenium Aquobipyridine Complexes to Histidine Side Chains in Horse Heart Cytochrome c Jian Luo, James F. Wishart, and Stephan S. Isied J. Am. Chem. Soc. 120, 12970-12971 (1998) [Find paper at ACS Publications] Abstract: Stereoselective covalent binding of the ruthenium complexes cis-[Ru(bpy)2(H2O)2]2+ (bpy = 2,2'-bipyridine) and cis-[Ru(dmbpy)2(H2O)2]2+ (dmbpy = 4,4'-dimethyl-2,2'-bipyridine) to the surface His 33 residue and the more buried His 26 residues of Horse heart cytochrome c (Hh cyt c) to form large enantiomeric excess of D-[Ru(dmbpy)2(H2O)]-His 26-cyt c (38%), but little or no excess of D-[Ru(bpy)2(H2O)]-His 26-cyt c (6%). At the surface exposed His 33 site, equal entiomeric excess of L-[Ru(dmbpy)2(H2O)]-His 33-cyt c and L-[Ru(bpy)2(H2O)]-His 33-cyt c (34%)

370

Thermodynamics and Kinetics of Carbon Dioxide Binding to Two Stereoisomers  

NLE Websites -- All DOE Office Websites (Extended Search)

Binding to Stereoisomers of a Cobalt(I) Macrocycle Binding to Stereoisomers of a Cobalt(I) Macrocycle Carol Creutz, Harold A. Schwarz, James F. Wishart, Etsuko Fujita and Norman Sutin J. Am. Chem. Soc. 113, 3361-3371 (1991) Abstract: The thermodynamics and kinetics of binding of CO2, CO, and H+ to N-racemic and N-meso stereoisomers of the cobalt(I) macrocycle CoL+ (L=5,7,7,12,14,14-hexamethyl-1,4,8,11-tetraazacyclotetradeca-4,11-diene) have been determined in aqueous media with use of the pulse radiolysis technique and transient ultraviolet-visible spectroscopy. N-rac or N-meso-CoL+ was produced by the hydrated electron reduction of N-rac or N-meso-CoL2+, with tert-butyl alcohol generally added to scavenge hydroxyl radicals. Reactions of both N-rac- and N-meso CoL+ are readily followed by the disappearance of intense ([epsilon] 1 x 104 M-1 cm-1) absorption bands

371

Comparison of Four Parallel Algorithms for Domain Decomposed  

National Nuclear Security Administration (NNSA)

Comparison of Four Parallel Comparison of Four Parallel Algorithms for Domain Decomposed Implicit Monte Carlo Thomas A Brunner (SNL) Thomas A Brunner (SNL) Todd J. Todd J. Urbatsch Urbatsch and Thomas M. Evans (LANL) and Thomas M. Evans (LANL) Nicholas A. Gentile (LLNL) Nicholas A. Gentile (LLNL) Joint Russian-American Five-Laboratory Conference on Computational Mathematics/Physics 19-23 June 2005 Vienna, Austria Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. Los Alamos National Laboratory, an affirmative action/equal opportunity employer, is operated by the University of Californian for the United States Department of Energy under contract W-7405-ENG-36.

372

Numerical study of domain coarsening in anisotropic stripe patterns  

E-Print Network (OSTI)

We study the coarsening of two-dimensional smectic polycrystals characterized by grains of oblique stripes with only two possible orientations. For this purpose, an anisotropic Swift-Hohenberg equation is solved. For quenches close enough to the onset of stripe formation, the average domain size increases with time as $t^{1/2}$. Further from onset, anisotropic pinning forces similar to Peierls stresses in solid crystals slow down defects, and growth becomes anisotropic. In a wide range of quench depths, dislocation arrays remain mobile and dislocation density roughly decays as $t^{-1/3}$, while chevron boundaries are totally pinned. We discuss some agreements and disagreements found with recent experimental results on the coarsening of anisotropic electroconvection patterns.

Denis Boyer

2004-03-09T23:59:59.000Z

373

Domain Decomposition for Flow in Porous Media with Fractures  

E-Print Network (OSTI)

this article. The fractures that we are concerned with are filled with debris so we consider them as porous media. The permeability in the fracture is large in comparison with that in the surrounding rock, so the fluid circulates faster in the fracture. Thus we have a highly heterogeneous porous medium. One idea that has been used to take this into account is to treat the fracture as an interface and to assume that the fluid that flows into the fracture stays in the fracture. In fact, in many models the contrast in permeabilities is of such an order that the flow outside of the fracture is neglected. However, here we are concerned with the situation in which the exchange between the fracture and the rest of the domain is significant. To deal with this case we need to model both what happens in the fracture and what happens outside the fracture. One

Clarisse Alboin; Jerome Jaffre; Jean Roberts; Christophe Serres

1999-01-01T23:59:59.000Z

374

Ion mobility spectrometer using frequency-domain separation  

DOE Patents (OSTI)

An apparatus and method are provided for separating and analyzing chemical species in an ion mobility spectrometer using a frequency-domain technique wherein the ions generated from the chemical species are selectively transported through an ion flow channel having a moving electrical potential therein. The moving electrical potential allows the ions to be selected according to ion mobility, with certain of the ions being transported to an ion detector and other of the ions being effectively discriminated against. The apparatus and method have applications for sensitive chemical detection and analysis for monitoring of exhaust gases, hazardous waste sites, industrial processes, aerospace systems, non-proliferation, and treaty verification. The apparatus can be formed as a microelectromechanical device (i.e. a micromachine). 6 figs.

Martin, S.J.; Butler, M.A.; Frye, G.C.; Schubert, W.K.

1998-08-04T23:59:59.000Z

375

Ion mobility spectrometer using frequency-domain separation  

DOE Patents (OSTI)

An apparatus and method is provided for separating and analyzing chemical species in an ion mobility spectrometer using a frequency-domain technique wherein the ions generated from the chemical species are selectively transported through an ion flow channel having a moving electrical potential therein. The moving electrical potential allows the ions to be selected according to ion mobility, with certain of the ions being transported to an ion detector and other of the ions being effectively discriminated against. The apparatus and method have applications for sensitive chemical detection and analysis for monitoring of exhaust gases, hazardous waste sites, industrial processes, aerospace systems, non-proliferation, and treaty verification. The apparatus can be formed as a microelectromechanical device (i.e. a micromachine).

Martin, Stephen J. (Albuquerque, NM); Butler, Michael A. (Albuquerque, NM); Frye, Gregory C. (Cedar Crest, NM); Schubert, W. Kent (Albuquerque, NM)

1998-01-01T23:59:59.000Z

376

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)  

E-Print Network (OSTI)

Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method are described to predict the free energies of binding of a series of anaesthetic drugs to a recently. The correlation coefficient between computed and measured binding free energies is 70% with high statistical

377

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Danzhi Huang and Amedeo Caflisch*  

E-Print Network (OSTI)

Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation Danzhi Huang of the absolute free energy of binding. A predictive accuracy of about 1.0 kcal/mol is obtained for 13 and 29 into proteins of known structure require fast and accurate methods for the evaluation of binding free energies.1

Caflisch, Amedeo

378

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*,  

E-Print Network (OSTI)

Theory of Free Energy and Entropy in Noncovalent Binding Huan-Xiang Zhou*, and Michael K. Gilson, Rockville, Maryland 20850 Received December 23, 2008 Contents 1. Introduction 4092 2. Free Energy, Partition.4. Solvation and a Temperature-Dependent Energy Function 4096 3. Binding Free Energy and Binding Constant 4096

Weston, Ken

379

Computational Investigation of Glycosylation Effects on a Family 1 Carbohydrate-Binding Module  

DOE Green Energy (OSTI)

Carbohydrate-binding modules (CBMs) are ubiquitous components of glycoside hydrolases, which degrade polysaccharides in nature. CBMs target specific polysaccharides, and CBM binding affinity to cellulose is known to be proportional to cellulase activity, such that increasing binding affinity is an important component of performance improvement. To ascertain the impact of protein and glycan engineering on CBM binding, we use molecular simulation to quantify cellulose binding of a natively glycosylated Family 1 CBM. To validate our approach, we first examine aromatic-carbohydrate interactions on binding, and our predictions are consistent with previous experiments, showing that a tyrosine to tryptophan mutation yields a 2-fold improvement in binding affinity. We then demonstrate that enhanced binding of 3-6-fold over a nonglycosylated CBM is achieved by the addition of a single, native mannose or a mannose dimer, respectively, which has not been considered previously. Furthermore, we show that the addition of a single, artificial glycan on the anterior of the CBM, with the native, posterior glycans also present, can have a dramatic impact on binding affinity in our model, increasing it up to 140-fold relative to the nonglycosylated CBM. These results suggest new directions in protein engineering, in that modifying glycosylation patterns via heterologous expression, manipulation of culture conditions, or introduction of artificial glycosylation sites, can alter CBM binding affinity to carbohydrates and may thus be a general strategy to enhance cellulase performance. Our results also suggest that CBM binding studies should consider the effects of glycosylation on binding and function.

Taylor, C. B.; Talib, M. F.; McCabe, C.; Bu, L.; Adney, W. S.; Himmel, M. E.; Crowley, M. F.; Beckham, G. T.

2012-01-27T23:59:59.000Z

380

Structural Characterization of a 140 Degree Domain Movement in the Two-Step Reaction Catalyzed By 4-Chlorobenzoate:CoA Ligase  

Science Conference Proceedings (OSTI)

Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PP{sub 1}, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140{sup o} to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue [Wu et al. (2008) Biochemistry 47, 8026-8039]. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

Reger, A.S.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.M.

2009-05-21T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


381

Structural Characterization of a 140 degrees Domain Movement in the Two-Step Reaction Catalyzed by 4-Chlorobenzoate:CoA Ligase  

Science Conference Proceedings (OSTI)

Members of the adenylate-forming family of enzymes play a role in the metabolism of halogenated aromatics and of short, medium, and long chain fatty acids, as well as in the biosynthesis of menaquinone, peptide antibiotics, and peptide siderophores. This family includes a subfamily of acyl- and aryl-CoA ligases that catalyze thioester synthesis through two half-reactions. A carboxylate substrate first reacts with ATP to form an acyl-adenylate. Subsequent to the release of the product PPi, the enzyme binds CoA, which attacks the activated acyl group to displace AMP. Structural and functional studies on different family members suggest that these enzymes alternate between two conformations during catalysis of the two half-reactions. Specifically, after the initial adenylation step, the C-terminal domain rotates by 140 to adopt a second conformation for thioester formation. Previously, we determined the structure of 4-chlorobenzoate:CoA ligase (CBL) in the adenylate forming conformation bound to 4-chlorobenzoate. We have determined two new crystal structures. We have determined the structure of CBL in the original adenylate-forming conformation, bound to the adenylate intermediate. Additionally, we have used a novel product analogue, 4-chlorophenacyl-CoA, to trap the enzyme in the thioester-forming conformation and determined this structure in a new crystal form. This work identifies a novel binding pocket for the CoA nucleotide. The structures presented herein provide the foundation for biochemical analyses presented in the accompanying manuscript in this issue. The complete characterization of this enzyme allows us to provide an explanation for the use of the domain alternation strategy by these enzymes.

Reger,A.; Wu, R.; Dunaway-Mariano, D.; Gulick, A.

2008-01-01T23:59:59.000Z

382

A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano,  

Open Energy Info (EERE)

A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano, A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano, Hawaii Jump to: navigation, search OpenEI Reference LibraryAdd to library == A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano, HawaiiThesis/Dissertation == Author Catherine King Skokan Organization Colorado School of Mines Published Publisher Not Provided, 1974 DOI Not Provided Check for DOI availability: http://crossref.org Online Internet link for A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano, Hawaii Citation [[Citation::Catherine King Skokan. 1974. A Time-Domain Electromagnetic Survey of the East Rift Zone Kilauea Volcano, Hawaii []. [ (!) ]: Colorado School of Mines.]] Retrieved from "http://en.openei.org/w/index.php?title=A_Time-Domain_Electromagnetic_Survey_of_the_East_Rift_Zone_Kilauea_Volcano,_Hawaii&oldid=682585"

383

Domain Engineered Configuration Control Mark Ardis, Peter Dudak, Liz Dor, Wen-jenq Leu, Lloyd Nakatani, Bob Olsen,  

E-Print Network (OSTI)

, application engineering, domain specific language, configuration control, FAST, InfoWiz, VFSM, Tcl/Tk Abstract

Ardis, Mark

384

Crystal Structures of the Outer Membrane Domain of Intimin and Invasin from Enterohemorrhagic E. coli and Enteropathogenic Y. pseudotuberculosis  

SciTech Connect

Intimins and invasins are virulence factors produced by pathogenic Gram-negative bacteria. They contain C-terminal extracellular passenger domains that are involved in adhesion to host cells and N-terminal {beta} domains that are embedded in the outer membrane. Here, we identify the domain boundaries of an E. coli intimin {beta} domain and use this information to solve its structure and the {beta} domain structure of a Y. pseudotuberculosis invasin. Both {beta} domain structures crystallized as monomers and reveal that the previous range of residues assigned to the {beta} domain also includes a protease-resistant domain that is part of the passenger. Additionally, we identify 146 nonredundant representative members of the intimin/invasin family based on the boundaries of the highly conserved intimin and invasin {beta} domains. We then use this set of sequences along with our structural data to find and map the evolutionarily constrained residues within the {beta} domain.

Fairman, James W.; Dautin, Nathalie; Wojtowicz, Damian; Liu, Wei; Noinaj, Nicholas; Barnard, Travis J.; Udho, Eshwar; Przytycka, Teresa M.; Cherezov, Vadim; Buchanan, Susan K. (CUA); (Einstein); (NIH); (Scripps)

2012-12-10T23:59:59.000Z

385

The Importance of Domain Size and Purity in High-Efficiency Organic...  

NLE Websites -- All DOE Office Websites (Extended Search)

The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The efficiency of polymerorganic photovoltaic cells hinges on excitons-electronhole pairs...

386

Characterization of III-V/Si(100) Anti-Phase Domains  

Science Conference Proceedings (OSTI)

Due to the specific surface orientation of APDs, evaluations of the domain composition by surface sensitive probes like low energy electron diffraction (

387

The FUN30 Chromatin Remodeler, Fft3, Protects Centromeric and Subtelomeric Domains from Euchromatin Formation  

E-Print Network (OSTI)

The chromosomes of eukaryotes are organized into structurally and functionally discrete domains. This implies the presence of insulator elements that separate adjacent domains, allowing them to maintain different chromatin structures. We show that the Fun30 chromatin remodeler, Fft3, is essential for maintaining a proper chromatin structure at centromeres and subtelomeres. Fft3 is localized to insulator elements and inhibits euchromatin assembly in silent chromatin domains. In its absence, euchromatic histone modifications and histone variants invade centromeres and subtelomeres, causing a misregulation of gene expression and severe chromosome segregation defects. Our data strongly suggest that Fft3 controls the identity of chromatin domains by protecting these regions from euchromatin assembly.

Julian Walfridsson; Hasanuzzaman Bhuiyan; Karl Ekwall

2011-01-01T23:59:59.000Z

388

Study of the structure of ferroelectric domain walls in barium titanate ceramics  

Science Conference Proceedings (OSTI)

Structure of 90{degree} ferroelectric domain boundaries in barium titanate ceramics has been studied by means of Transmission Electron Microscopy and High Resolution TEM. Tilts of specific fringes across domain walls are measured on HREM images and Selected Area Diffraction Patterns. They are in a good agreement with the twin model admitted for these domain boundaries. A computerized method has been developed to give access to quantitative information about atomic displacements across these ferroelectric domain walls. The so calculated displacement field is then compared with Landau-Ginzburg based theoretical predictions.

Normand, L.; Thorel, A. [Centre des Materiaux, Evry cedex (France) ; Kilaas, R. [Lawrence Berkeley Lab., CA (United States); Montardi, Y. [Rhone-Poulenc, CRA, Aubervilliers (France)

1995-02-01T23:59:59.000Z

389

Application and modeling of frequency-domain lifetime spectroscopy for microsphere-based optical glucose sensors  

E-Print Network (OSTI)

A new glucose affinity sensor based on a homogeneous fluorescence resonance energy transfer (FRET) assay system was developed to monitor the competitive binding between concanavalin A (ConA) and dextran. The FRET quenching kinetics of the donor were analyzed from frequency-domain (FD) measurements as functions of both glucose and acceptor-protein concentrations using a Frster-type decay kinetics model. The results showed that the FD measurements and donor decay kinetics can indicate quantitative changes in the presence of glucose at concentrations ranging from 0 to 224 mg/dL. The second set of experiments proved the feasibility of performing analyte sensing with FD lifetime spectroscopy using microsphere-based sensors in multiple scattering solutions. A well characterized pH-sensitive fluorophore was entrapped in poly(ethylene glycol) microspheres. The particles were then immersed in a buffered polystyrene solution of various pH. Measurements of phase shift and modulation of the generated and multiply scattered fluorescent light were acquired as the modulation frequency of the incident excitation light varied from 10 to 120 MHz. After the measured data were analyzed with the coupled diffusion equations, the obtained lifetimes from the scattering measurements matched values from non-scattering measurements. Lastly, a new two-speed Monte Carlo (MC) simulation was developed to predict light propagation through the sensors and thus was used to evaluate these sensors and to design these sensors for implantation. The model used random packing structure and considered geometric optics and two light propagation speeds. Experimental measurements of phase-shift and modulation of excitation light were made on a cubic phantom with non-fluorescent resin microspheres of 74 m diameter, and compared to those computed from the MC simulation. The results showed that the mean phase shift (PS) deviation was 0.736 and the mean amplitude deviation was 42%. Quantitative changes in detected fluorescence phase-shift and modulation were investigated for microsphere diameter, volume fraction, refractive index, and fluorophore lifetime. We also found that even though the sensitivity of PS change in the presence of scattering was the same as the value without scattering, the values of PS were magnified due to the scattering effects.

Liang, Feng

2006-12-01T23:59:59.000Z

390

U-039: ISC Update: BIND 9 Resolver crashes after logging an error in  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

9: ISC Update: BIND 9 Resolver crashes after logging an error 9: ISC Update: BIND 9 Resolver crashes after logging an error in query.c U-039: ISC Update: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 2:30pm Addthis PROBLEM: ISC Update: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Versions of BIND, 9.4-ESV, 9.6-ESV, 9.7.x, 9.8.x ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

391

U-038: BIND 9 Resolver crashes after logging an error in query.c |  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

8: BIND 9 Resolver crashes after logging an error in query.c 8: BIND 9 Resolver crashes after logging an error in query.c U-038: BIND 9 Resolver crashes after logging an error in query.c November 16, 2011 - 8:37am Addthis PROBLEM: BIND 9 Resolver crashes after logging an error in query.c. PLATFORM: Multiple version of BIND 9. Specific versions under investigation ABSTRACT: A remote server can cause the target connected client to crash. Organizations across the Internet are reporting crashes interrupting service on BIND 9 nameservers performing recursive queries. Affected servers crash after logging an error in query.c with the following message: "INSIST(! dns_rdataset_isassociated(sigrdataset))" Multiple versions are reported as being affected, including all currently supported release versions of ISC BIND 9. ISC is actively investigating the root cause and

392

PHYS 551 Lecture #27 Title: Tight-Binding  

E-Print Network (OSTI)

PHYS 551 Lecture #27 Title: Tight-Binding Now that we have shown that (~k;~r) = P ~R ei~k~RA(~r ~R-function (~k;~r) must be normalized. Thus Z dV = 1 = j j2 X R X R0 ei~k~R ~R0 Z A(~r ~R0)A(~r ~R)dV Now for each ~R0, the sum over ~R must be the same since the crystal has the same distribution of neighbors

Winokur, Michael

393

Tight-binding model for hydrogen-silicon interactions  

SciTech Connect

We have developed an empirical tight-binding model for use in molecular-dynamics simulations to study hydrogen-silicon systems. The hydrogen-silicon interaction is constructed to reproduce the electronic energy levels and vibration frequencies of silane (SiH{sub 4}). Further use of the model in the studies of disilane (Si{sub 2}H{sub 6}) and of hydrogen on the Si(111) surface also yields results in good agreement with first-principles calculations and experiments.

Min, B.J.; Lee, Y.H.; Wang, C.Z.; Chan, C.T.; Ho, K.M. (Microelectronics Research Center, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States) Department of Physics and Astronomy, Ames Laboratory, Iowa State University, Ames, Iowa 50011 (United States))

1992-03-15T23:59:59.000Z

394

Stability of atoms in the anionic domain (Z  

E-Print Network (OSTI)

We study the stability and universal behaviour of the ionization energy of N-electron atoms with nuclear charge Z in the anionic domain (Z

Gil, G

2013-01-01T23:59:59.000Z

395

Audio enabled information extraction system for cricket and hockey domains  

E-Print Network (OSTI)

The proposed system aims at the retrieval of the summarized information from the documents collected from web based search engine as per the user query related to cricket and hockey domain. The system is designed in a manner that it takes the voice commands as keywords for search. The parts of speech in the query are extracted using the natural language extractor for English. Based on the keywords the search is categorized into 2 types: - 1.Concept wise - information retrieved to the query is retrieved based on the keywords and the concept words related to it. The retrieved information is summarized using the probabilistic approach and weighted means algorithm.2.Keyword search - extracts the result relevant to the query from the highly ranked document retrieved from the search by the search engine. The relevant search results are retrieved and then keywords are used for summarizing part. During summarization it follows the weighted and probabilistic approaches in order to identify the data comparable to the k...

Saraswathi, S; B., Sai Vamsi Krishna; S, Suresh Reddy

2010-01-01T23:59:59.000Z

396

Quantum Fusion of Strings (Flux Tubes) and Domain Walls  

E-Print Network (OSTI)

We consider formation of composite strings and domain walls as a result of fusion of two elementary objects (elementary strings in the first case and elementary walls in the second) located at a distance from each other. The tension of the composite object T_2 is assumed to be less than twice the tension of the elementary object T_1, so that bound states are possible. If in the initial state the distance d between the fusing strings or walls is much larger than their thickness and satisfies the conditions T_1 d^2 >> 1 (in the string case) and T_1 d^3 >> 1 (in the wall case), the problem can be fully solved quasiclassically. The fusion probability is determined by the first, "under the barrier" stage of the process. We find the bounce configuration and its extremal action S_B. In the wall problem e^{-S_B} gives the fusion probability per unit time per unit area. In the string case, due to a logarithmic infrared divergence, the problem is well formulated only for finite-length strings. The fusion probability per unit time can be found in the limit in which the string length is much larger than the distance between two merging strings.

S. Bolognesi; M. Shifman; M. B. Voloshin

2009-05-11T23:59:59.000Z

397

SIMPLICITY OF NONCOMMUTATIVE DEDEKIND DOMAINS K. R. Goodearl and J. T. Stafford  

E-Print Network (OSTI)

SIMPLICITY OF NONCOMMUTATIVE DEDEKIND DOMAINS K. R. Goodearl and J. T. Stafford Abstract X 1 #12; 2 K. R. GOODEARL AND J. T. STAFFORD pR = Rp and (ii) R=P is a domain. These exist. STAFFORD We note that Lemma 4 also holds if the hypothesis \\dim k R

Akhmedov, Azer

398

A domain specific language to define gestures for multi-touch applications  

Science Conference Proceedings (OSTI)

It is increasingly common for software and hardware systems to support touch-based interaction. While the technology to support this interaction is still evolving, common protocols for providing consistent communication between hardware and software ... Keywords: TouchToolkit, domain specific language, domain-specific language, gesture, gesture definition language (GDL), multi-touch, multi-user, touch interaction

Shahedul Huq Khandkar; Frank Maurer

2010-10-01T23:59:59.000Z

399

Time-domain Fatigue Response and Reliability Analysis of Offshore Wind Turbines with  

E-Print Network (OSTI)

-domain based simulation model of 750 kW land-based wind turbine Gear contact fatigue analysis of a wind of 750 kW land-based wind turbine Gear contact fatigue analysis of a wind turbine drive train under response and reliability analysis #12;Time domain based simulation model of 750 kW land-based wind turbine

Nørvåg, Kjetil

400

Ontology-Driven construction of domain corpus with frame semantics annotations  

Science Conference Proceedings (OSTI)

Semantic Role Labeling plays a key role in many text mining applications. The development of SRL systems for the biomedical domain is frustrated by the lack of large domain specific corpora that are labeled with semantic roles. In this paper we proposed ...

He Tan; Rajaram Kaliyaperumal; Nirupama Benis

2012-03-01T23:59:59.000Z

Note: This page contains sample records for the topic "bind deleted domain" from the National Library of EnergyBeta (NLEBeta).
While these samples are representative of the content of NLEBeta,
they are not comprehensive nor are they the most current set.
We encourage you to perform a real-time search of NLEBeta
to obtain the most current and comprehensive results.


401

Building frame-based corpus on the basis of ontological domain knowledge  

Science Conference Proceedings (OSTI)

Semantic Role Labeling (SRL) plays a key role in many NLP applications. The development of SRL systems for the biomedical domain is frustrated by the lack of large domain-specific corpora that are labeled with semantic roles. Corpus development has been ...

He Tan; Rajaram Kaliyaperumal; Nirupama Benis

2011-06-01T23:59:59.000Z

402

A new domain decomposition method with overlapping patches for ultrascale simulations: Application to biological flows  

Science Conference Proceedings (OSTI)

We address the failure in scalability of large-scale parallel simulations that are based on (semi-)implicit time-stepping and hence on the solution of linear systems on thousands of processors. We develop a general algorithmic framework based on domain ... Keywords: Arterial network, CFD, Multi-domain decomposition, Petaflop computing, Scalability, Spectral element method

L. Grinberg; G. E. Karniadakis

2010-08-01T23:59:59.000Z

403

Quality in use of domain-specific languages: a case study  

Science Conference Proceedings (OSTI)

Domain-Specific Languages (DSLs) are claimed to increment productivity, while reducing the required maintenance and programming expertise. In this context, DSLs usability is a key factor for its successful adoption. In this paper, we propose a systematic ... Keywords: domain-specific languages, experimental software engineering, language evaluation, software language engineering, usability

Ankica Barii?; Vasco Amaral; Miguel Goulo; Bruno Barroca

2011-10-01T23:59:59.000Z

404

End-to-end QoS of X-domain pipes  

Science Conference Proceedings (OSTI)

Multi-media services and other critical multi-site services (e.g. VPN) are becoming mainstream, and require a guaranteed Quality of Service (QoS). Services need to be established across several domains, often to connect multi-domain end-users. Thus, ...

Hlia Pouyllau; Stefan Haar

2007-08-01T23:59:59.000Z

405

EXACT SOLUTION OF THE SIXVERTEX MODEL WITH DOMAIN WALL BOUNDARY CONDITIONS. DISORDERED PHASE  

E-Print Network (OSTI)

EXACT SOLUTION OF THE SIX­VERTEX MODEL WITH DOMAIN WALL BOUNDARY CONDITIONS. DISORDERED PHASE PAVEL M. BLEHER AND VLADIMIR V. FOKIN Abstract. The six­vertex model, or the square ice model, with domain to obtain the large N asymptotics of the six­vertex model with DWBC in the disordered phase. The solution

406

Micro-and nanoscale domain engineering in lithium niobate and lithium tantalate  

E-Print Network (OSTI)

Micro- and nanoscale domain engineering in lithium niobate and lithium tantalate Vladimir Ya. Shur investigation of the domain evolution in lithium niobate and lithium tantalate during backswitched electric sources based on quasi-phase matching.11 Lithium niobate LiNbO3 (LN) and lithium tantalate LiTaO3 (LT

Byer, Robert L.

407

Policy-based self-adaptive architectures: a feasibility study in the robotics domain  

Science Conference Proceedings (OSTI)

Robotics is a challenging domain which sometimes exhibits a clear need for self-adaptive capabilities, as such functionality offers the potential for robots to account for their unstable and unpredictable deployment domains. This paper focuses on a feasibility ... Keywords: robotic architectures, self-adaptive software

John C. Georgas; Richard N. Taylor

2008-05-01T23:59:59.000Z

408

SafeCap Domain Language for Reasoning about Safety and Capacity  

Science Conference Proceedings (OSTI)

The on-going UK SAFECAP project develops modeling techniques and tools for improving railway capacity while ensuring that safety standards are maintained. This paper reports recent SAFECAP results on designing a Domain Specific Language (DSL) that will ... Keywords: railway modelling, formal verification, domain language, route-based signalling, safety

Alexei Iliasov; Alexander Romanovsky

2012-11-01T23:59:59.000Z

409

An efficient, robust, domain-decomposition algorithm for particle Monte Carlo  

Science Conference Proceedings (OSTI)

A previously described algorithm [T.A. Brunner, T.J. Urbatsch, T.M. Evans, N.A. Gentile, Comparison of four parallel algorithms for domain decomposed implicit Monte Carlo, Journal of Computational Physics 212 (2) (2006) 527-539] for doing domain decomposed ... Keywords: Monte Carlo methods, Neutron transport, Parallel computation, Radiative transfer

Thomas A. Brunner; Patrick S. Brantley

2009-06-01T23:59:59.000Z

410

Magnetic thin-film split-domain current sensor-recorder  

DOE Patents (OSTI)

A sensor-recorder for recording a representation of the direction and peak amplitude of a transient current. A magnetic thin film is coated on a glass substrate under the influence of a magnetic field so that the finished film is magnetically uniaxial and anisotropic. The film is split into two oppositely magnetized contiguous domains with a central boundary by subjecting adjacent portions of the film simultaneously to magnetic fields that are opposed 180.degree.. With the split-domain sensor-recorder placed with the film plane and domain boundary either perpendicular or parallel to the expected conductive path of a transient current, the occurrence of the transient causes switching of a portion of one domain to the direction of the other domain. The amount of the switched domain portion is indicative of the amplitude of the peak current of the transient, while the particular domain that is switched is indicative of the direction of the current. The resulting domain patterns may be read with a passive magnetic tape viewer.

Hsieh, Edmund J. (Livermore, CA)

1979-01-01T23:59:59.000Z

411

Transaction-based authentication and key agreement protocol for inter-domain VoIP  

Science Conference Proceedings (OSTI)

We present an authentication and key agreement protocol to secure Voice over IP call establishment between interconnection proxies of different domains. The protocol operates on a transaction basis. Each transaction is defined as the set of operations ... Keywords: Authentication, DDoS Protection, Inter-domain VoIP, Synchronisation, VoIP security

Patrick Battistello; Joaquin Garcia-Alfaro; Cyril DelTr

2012-09-01T23:59:59.000Z

412

Quasineutral limit of the Euler-Poisson system for ions in a domain with boundaries  

E-Print Network (OSTI)

We study the quasineutral limit of the isothermal Euler-Poisson system describing a plasma made of ions and massless electrons. The analysis is achieved in a domain of $\\R^3$ and thus extends former results by Cordier and Grenier [Comm. Partial Differential Equations, 25 (2000), pp.~1099--1113], who dealt with the same problem in a one-dimensional domain without boundary.

Grard-Varet, David; Rousset, Frdric

2011-01-01T23:59:59.000Z

413

Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and  

NLE Websites -- All DOE Office Websites (Extended Search)

Defining How Botulinum Toxin Binds to Defining How Botulinum Toxin Binds to the Synaptotagmin Receptor and Creating Improved Therapeutics to Block Toxicity Botulinum neurotoxin (BoNT), the most potent toxin known, induces a potentially fatal paralytic condition known as "botulism". Botulism can occur when toxin-producing bacteria infect wounds (wound botulism) or the intestinal tract (infant/intestinal botulism), or following the ingestion of contaminated food in which toxin has been produced (food-borne botulism). In the USA, infant botulism represents the most common manifestation of the disease, where its prevalence has led to speculation of a link to sudden infant death syndrome. BoNTs are subdivided into seven distinct serotypes (types A through G), and an increasingly large number of subtypes continue to be identified within each serotype, highlighting the need to produce broad-spectrum therapeutics. BoNT variants are an important biochemical set of tools for understanding nerve function, and important therapeutic agents in current clinical use to provide relief to patients with a wide spectrum of neurological disorders.

414

Relativistic Nuclear Energy Density Functionals: adjusting parameters to binding energies  

E-Print Network (OSTI)

We study a particular class of relativistic nuclear energy density functionals in which only nucleon degrees of freedom are explicitly used in the construction of effective interaction terms. Short-distance (high-momentum) correlations, as well as intermediate and long-range dynamics, are encoded in the medium (nucleon density) dependence of the strength functionals of an effective interaction Lagrangian. Guided by the density dependence of microscopic nucleon self-energies in nuclear matter, a phenomenological ansatz for the density-dependent coupling functionals is accurately determined in self-consistent mean-field calculations of binding energies of a large set of axially deformed nuclei. The relationship between the nuclear matter volume, surface and symmetry energies, and the corresponding predictions for nuclear masses is analyzed in detail. The resulting best-fit parametrization of the nuclear energy density functional is further tested in calculations of properties of spherical and deformed medium-heavy and heavy nuclei, including binding energies, charge radii, deformation parameters, neutron skin thickness, and excitation energies of giant multipole resonances.

T. Niksic; D. Vretenar; P. Ring

2008-09-08T23:59:59.000Z

415

Dendroaspis natriuretic peptide binds to the natriuretic peptide clearance receptor  

SciTech Connect

Dendroaspis natriuretic peptide (DNP) is a newly-described natriuretic peptide which lowers blood pressure via vasodilation. The natriuretic peptide clearance receptor (NPR-C) removes natriuretic peptides from the circulation, but whether DNP interacts with human NPR-C directly is unknown. The purpose of this study was to test the hypothesis that DNP binds to NPR-C. ANP, BNP, CNP, and the NPR-C ligands AP-811 and cANP(4-23) displaced [{sup 125}I]-ANP from NPR-C with pM-to-nM K {sub i} values. DNP displaced [{sup 125}I]-ANP from NPR-C with nM potency, which represents the first direct demonstration of binding of DNP to human NPR-C. DNP showed high pM affinity for the GC-A receptor and no affinity for GC-B (K {sub i} > 1000 nM). DNP was nearly 10-fold more potent than ANP at stimulating cGMP production in GC-A expressing cells. Blockade of NPR-C might represent a novel therapeutic approach in augmenting the known beneficial actions of DNP in cardiovascular diseases such as hypertension and heart failure.

Johns, Douglas G. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States)]. E-mail: Douglas.G.Johns@gsk.com; Ao, Zhaohui [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Heidrich, Bradley J. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Hunsberger, Gerald E. [Respiratory and Inflammatory Diseases Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Graham, Taylor [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Payne, Lisa [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Elshourbagy, Nabil [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Lu, Quinn [Gene Expression and Protein Biochemistry, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Aiyar, Nambi [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States); Douglas, Stephen A. [Vascular Biology and Thrombosis Department, Cardiovascular and Urogenital Center for Excellence in Drug Discovery, GlaxoSmithKline, King of Prussia, PA 19406 (United States)

2007-06-22T23:59:59.000Z

416

Argonne CNM News: Study of Ferroelectric Domain Walls Offers a New  

NLE Websites -- All DOE Office Websites (Extended Search)

Study of Ferroelectric Domain Walls Offers a New Nanoscale Conduction Path Study of Ferroelectric Domain Walls Offers a New Nanoscale Conduction Path Scanning tunneling microscopy tips SPM images of the (110) surface of cleaved h-HoMnO3. (top) PFM image showing in-plane ferroelectric domains (oriented vertically, red arrows). (bottom) cAFM image showing enhanced conduction along tail-to-tail domain walls; images are 4 microns per side. Facility users from Rutgers University together with the Center for Nanoscale Materials' Electronic & Magnetic Materials & Devices Group have identified two-dimensional sheets of charge formed at the boundaries of ferroelectric domains in a multiferroic material. These two-dimensional charged sheets are not pinned by unstable defects, chemical dopants, or structural interface, but are formed naturally as the inevitable

417

The Importance of Domain Size and Purity in High-Efficiency Organic Solar  

NLE Websites -- All DOE Office Websites (Extended Search)

The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The efficiency of polymer/organic photovoltaic cells hinges on excitons-electron/hole pairs energized by sunlight-getting to the interfaces of donor and acceptor domains quickly, before recombining. At the interfaces, they become free charges that must then reach device electrodes. With the discovery of mixed domains of donor and acceptor molecules, many have pictured the excitons' journey as easy (interfaces are everywhere) but the charges' journey as precarious (interfaces are everywhere). Instead, using a combination of x-ray scattering and microscopy techniques, researchers have found that excitons may actually not fare so well in mixed domains but need access to pure aggregates to efficiently convert into charges. The smaller the aggregates, the better, allowing increased interfacial area and dramatic increases in device performance.

418

Time-Domain Electromagnetics At Soda Lake Area (Combs 2006) | Open Energy  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Soda Lake Area (Combs 2006) Time-Domain Electromagnetics At Soda Lake Area (Combs 2006) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Time-Domain Electromagnetics At Soda Lake Area (Combs 2006) Exploration Activity Details Location Soda Lake Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness not indicated DOE-funding Unknown Notes "EM sounding, MT, CSAMT, dipole-dipole resistivity; reservoir model?" References Jim Combs (1 January 2006) Historical Exploration And Drilling Data From Geothermal Prospects And Power Generation Projects In The Western United States Retrieved from "http://en.openei.org/w/index.php?title=Time-Domain_Electromagnetics_At_Soda_Lake_Area_(Combs_2006)&oldid=388133" Category:

419

The Importance of Domain Size and Purity in High-Efficiency Organic Solar  

NLE Websites -- All DOE Office Websites (Extended Search)

The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The efficiency of polymer/organic photovoltaic cells hinges on excitons-electron/hole pairs energized by sunlight-getting to the interfaces of donor and acceptor domains quickly, before recombining. At the interfaces, they become free charges that must then reach device electrodes. With the discovery of mixed domains of donor and acceptor molecules, many have pictured the excitons' journey as easy (interfaces are everywhere) but the charges' journey as precarious (interfaces are everywhere). Instead, using a combination of x-ray scattering and microscopy techniques, researchers have found that excitons may actually not fare so well in mixed domains but need access to pure aggregates to efficiently convert into charges. The smaller the aggregates, the better, allowing increased interfacial area and dramatic increases in device performance.

420

Non-equilibrium raft-like membrane domains under continuous recycling  

E-Print Network (OSTI)

We present a model for the kinetics of spontaneous membrane domain (raft) assembly that includes the effect of membrane recycling ubiquitous in living cells. We show that the domains have a broad power-law distribution with an average radius that scales with the 1/4 power of the domain lifetime when the line tension at the domain edges is large. For biologically reasonable recycling and diffusion rates the average domain radius is in the tens of nm range, consistent with observations. This represents one possible link between signaling (involving rafts) and traffic (recycling) in cells. Finally, we present evidence that suggests that the average raft size may be the same for all scale-free recycling schemes.

Matthew S. Turner; Pierre Sens; Nicholas D. Socci

2005-03-30T23:59:59.000Z

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421

Scaling Behavior of the First Arrival Time of a Random-Walking Magnetic Domain  

SciTech Connect

We report a universal scaling behavior of the first arrival time of a traveling magnetic domain wall into a finite space-time observation window of a magneto-optical microscope enabling direct visualization of a Barkhausen avalanche in real time. The first arrival time of the traveling magnetic domain wall exhibits a nontrivial fluctuation and its statistical distribution is described by universal power-law scaling with scaling exponents of 1.34 {+-} 0.07 for CoCr and CoCrPt films, despite their quite different domain evolution patterns. Numerical simulation of the first arrival time with an assumption that the magnetic domain wall traveled as a random walker well matches our experimentally observed scaling behavior, providing an experimental support for the random-walking model of traveling magnetic domain walls.

Im, M.-Y.; Lee, S.-H.; Kim, D.-H.; Fischer, P.; Shin, S.-C.

2008-02-04T23:59:59.000Z

422

The Importance of Domain Size and Purity in High-Efficiency Organic Solar  

NLE Websites -- All DOE Office Websites (Extended Search)

The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The Importance of Domain Size and Purity in High-Efficiency Organic Solar Cells Print The efficiency of polymer/organic photovoltaic cells hinges on excitons-electron/hole pairs energized by sunlight-getting to the interfaces of donor and acceptor domains quickly, before recombining. At the interfaces, they become free charges that must then reach device electrodes. With the discovery of mixed domains of donor and acceptor molecules, many have pictured the excitons' journey as easy (interfaces are everywhere) but the charges' journey as precarious (interfaces are everywhere). Instead, using a combination of x-ray scattering and microscopy techniques, researchers have found that excitons may actually not fare so well in mixed domains but need access to pure aggregates to efficiently convert into charges. The smaller the aggregates, the better, allowing increased interfacial area and dramatic increases in device performance.

423

Structure, Function, and Evolution of Biogenic Amine-binding Proteins in Soft Ticks  

Science Conference Proceedings (OSTI)

Two highly abundant lipocalins, monomine and monotonin, have been isolated from the salivary gland of the soft tick Argas monolakensis and shown to bind histamine and 5-hydroxytryptamine (5-HT), respectively. The crystal structures of monomine and a paralog of monotonin were determined in the presence of ligands to compare the determinants of ligand binding. Both the structures and binding measurements indicate that the proteins have a single binding site rather than the two sites previously described for the female-specific histamine-binding protein (FS-HBP), the histamine-binding lipocalin of the tick Rhipicephalus appendiculatus. The binding sites of monomine and monotonin are similar to the lower, low affinity site of FS-HBP. The interaction of the protein with the aliphatic amine group of the ligand is very similar for the all of the proteins, whereas specificity is determined by interactions with the aromatic portion of the ligand. Interestingly, protein interaction with the imidazole ring of histamine differs significantly between the low affinity binding site of FS-HBP and monomine, suggesting that histamine binding has evolved independently in the two lineages. From the conserved features of these proteins, a tick lipocalin biogenic amine-binding motif could be derived that was used to predict biogenic amine-binding function in other tick lipocalins. Heterologous expression of genes from salivary gland libraries led to the discovery of biogenic amine-binding proteins in soft (Ornithodoros) and hard (Ixodes) tick genera. The data generated were used to reconstruct the most probable evolutionary pathway for the evolution of biogenic amine-binding in tick lipocalins.

Mans, Ben J.; Ribeiro, Jose M.C.; Andersen, John F. (NIH)

2008-08-19T23:59:59.000Z

424

The adenovirus E4 11 k protein binds and relocalizes the cytoplasmic P-body component Ddx6 to aggresomes  

Science Conference Proceedings (OSTI)

The adenovirus E4 11 k protein, product of E4 ORF3, is required in infection for processes including normal accumulation of viral late mRNAs. 11 k restructures both the nucleus and cytoplasm of infected cells by relocalizing specific host cell target proteins, most strikingly components of nuclear PML oncogenic domains. It is likely that in many cases relocalization inactivates target proteins to produce 11 k's effects, although the mechanism and targets for stimulation of late mRNA accumulation is unknown. We have identified a new set of proteins relocalized by 11 k: at least five protein components of cytoplasmic mRNA processing bodies (p-bodies) are found in 11 k-induced cytoplasmic aggresomes, sites where proteins are inactivated or destroyed. One of these p-body proteins, RNA helicase Ddx6, binds 11 k, suggesting a mechanism for relocalization. Because p-bodies are sites for mRNA degradation, their modification by 11 k may provide an explanation for the role of 11 k in viral late mRNA accumulation.

Greer, Amy E. [Division of Medical Microbiology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD 21205 (United States); Hearing, Patrick [Department of Molecular Genetics and Microbiology, School of Medicine, Stony Brook University, Stony Brook, NY 11794 (United States); Ketner, Gary, E-mail: gketner@jhsph.edu [W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore MD 21205 (United States)

2011-08-15T23:59:59.000Z

425

Test Please delete this record  

Science Conference Proceedings (OSTI)

This measurement characterizes the types of BC emissions that result in nearsurface BC containing particles in a region that is dominated by biomass and open pit/stove cooking. Specifically, examine three primary BC emission sources: (i) urban setting (e.g., fossil fuel emissions); and (ii) biomass burning. Source (i) are captured at the Indian Institute of Science (IISc) in Bangalore. Biomass emissions (ii) contains a series of 12 day measurement excursions to the rural area surrounding Bangalore.

Arthur Sedlacek; Satheesh S; Stephen Springston; ,

2013-11-06T23:59:59.000Z

426

Test Please delete this record  

DOE Data Explorer (OSTI)

This measurement characterizes the types of BC emissions that result in nearsurface BC containing particles in a region that is dominated by biomass and open pit/stove cooking. Specifically, examine three primary BC emission sources: (i) urban setting (e.g., fossil fuel emissions); and (ii) biomass burning. Source (i) are captured at the Indian Institute of Science (IISc) in Bangalore. Biomass emissions (ii) contains a series of 12 day measurement excursions to the rural area surrounding Bangalore.

Arthur Sedlacek; Satheesh S; Stephen Springston

427

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network (OSTI)

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

I. Casinos

2008-05-22T23:59:59.000Z

428

On the nuclear interaction. Potential, binding energy and fusion reaction  

E-Print Network (OSTI)

The nuclear interaction is responsible for keeping neutrons and protons joined in an atomic nucleus. Phenomenological nuclear potentials, fitted to experimental data, allow one to know about the nuclear behaviour with more or less success where quantum mechanics is hard to be used. A nuclear potential is suggested and an expression for the potential energy of two nuclear entities, either nuclei or nucleons, is developed. In order to estimate parameters in this expression, some nucleon additions to nuclei are considered and a model is suggested as a guide of the addition process. Coulomb barrier and energy for the addition of a proton to each one of several nuclei are estimated by taking into account both the nuclear and electrostatic components of energy. Studies on the binding energies of several nuclei and on the fusion reaction of two nuclei are carried out.

Casinos, I

2008-01-01T23:59:59.000Z

429

Does nuclear matter bind at large $N_c$?  

E-Print Network (OSTI)

The existence of nuclear matter at large $N_c$ is investigated in the framework of effective hadronic models of the Walecka type. This issue is strongly related to the nucleon-nucleon attraction in the scalar channel, and thus to the nature of the light scalar mesons. Different scenarios for the light scalar sector correspond to different large $N_c$ scaling properties of the parameters of the hadronic models. In all realistic phenomenological scenarios for the light scalar field(s) responsible for the attraction in the scalar channel it is found that nuclear matter does not bind in the large $N_c$ world. We thus conclude that $N_c = 3$ is in this respect special: 3 is fortunately not large at all and allows for nuclear matter, while large $N_c$ would not.

Bonanno, Luca

2011-01-01T23:59:59.000Z

430

Unveiling Residual Molecular Binding in Triply Charged Hydrogen Bromide  

Science Conference Proceedings (OSTI)

We present an experimental and theoretical study of triply charged hydrogen bromide ions formed by photoionization of the inner 3d shell of Br. The experimental results, obtained by detecting the 3d photoelectron in coincidence with the two subsequent Auger electrons, are analyzed using calculated potential energy curves of HBr{sup 3+}. The competition between the short-range chemical binding potential and the Coulomb repulsion in the dissociative process is shown. Two different mechanisms are observed for double Auger decay: one, a direct process with simultaneous ejection of two Auger electrons to final HBr{sup 3+} ionic states and the other, a cascade process involving double Auger decay characterized by the autoionization of Br*{sup +} ion subsequent to the HBr{sup 2+} fragmentation.

Penent, F.; Lablanquie, P.; Palaudoux, J.; Gamblin, G.; Carniato, S. [UPMC, Universite Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Andric, L. [UPMC, Universite Paris 06, LCPMR, 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [CNRS, LCPMR (UMR 7614), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France)] [Universite Paris-Est, 5 boulevard Descartes, 77454 Marne-la-Vallee Cedex 2 (France); Hikosaka, Y. [Department of Environmental Science, Niigata University, Niigata 950-2181 (Japan); Ito, K. [Photon Factory, Institute of Materials Structure Science, Oho, Tsukuba 305-0801 (Japan)

2011-03-11T23:59:59.000Z

431

Characterization of Selective Binding of Alkali Cations with Carboxylate  

NLE Websites -- All DOE Office Websites (Extended Search)

Characterization of Selective Characterization of Selective Binding of Alkali Cations with Carboxylate Characterization of Selective Binding of Alkali Cations with Carboxylate Print Wednesday, 24 September 2008 00:00 During its lifetime, a cell spends a considerable fraction of its energy pumping sodium and calcium out and potassium in. This balancing process is similar to that found in the coils of the DNA double helix, where specific ions nestle and help stabilize this macromolecule. These are only two examples of selective ion interactions in biology; there are many others also vital to life. The existence of these interactions has been known since the early 20th century, when Franz Hofmeister observed that some salts (ionic compounds) aided the solution of proteins in egg, some caused proteins to destabilize and precipitate, and others ranged in activity between the two extremes. Hofmeister then ranked "salt-out" (destabilizing) ions versus "salt-in" (stabilizing) ions according to the magnitude of their effects (the "Hofmeister effects"). However, despite enormous effort, why certain interactions are preferred over others is not completely understood. Recently, a team of researchers from UC Berkeley used the model systems of acetate and formate (two simple carboxylic acids) with a series of cations to test predictions made in the literature for preferential interactions. Near-edge x-ray absorption fine structure (NEXAFS) spectroscopy was used as this technique is highly sensitive to the chemical environments around a molecule. Experiments at ALS Beamline 8.0.1 confirmed strengthening of the interaction between the cations and the carboxylate group in the following order: potassium, sodium, and lithium.

432

A = 4 0/sup +/ - 1/sup +/ binding-energy difference  

DOE Green Energy (OSTI)

The A = 4 ..lambda..-hypernuclei provide a rich source of information about the s-wave properties of the fundamental hyperon-nucleon (YN) force as well as offer a unique opportunity to investigate the complications that arise in calculations of the properties of bound systems in which one baryon (here the ..lambda..) with a given isospin couples strongly to another (the ..sigma..) with a different isospin. The ..lambda../sup 4/H - ..lambda../sup 4/He isodoublet ground-state energies are not consistent with a charge symmetry hypothesis for the YN interaction. The (spin-flip) excitation energies are quite sensitive to the ..lambda..N - ..sigma..N coupling of the YN interaction. In particular, when one represents the free YN interaction in terms of one-channel effective ..lambda..N potentials, the resulting 0/sup +/ (ground) state and 1/sup +/ (excited) spin-flip state are inversely ordered in terms of binding energies, the 1/sup +/ state being more bound. It is the ..sigma.. suppression that results from the reduced strength of the ..lambda..N - ..sigma..N off-diagonal coupling potential when the trinucleon core is restricted to isospin-1/2 which we study here. We find this spin-isospin suppression of the ..lambda..-..sigma.. conversion, which is due to the composite nature of the nuclear cores of the ..lambda../sup 4/H and ..lambda../sup 4/He hypernuclei, to be a significant factor in understanding the 0/sup +/ - 1 /sup +/ binding energy relationship.

Gibson, B.F.; Lehman, D.R.

1982-01-01T23:59:59.000Z

433

A domain flip as a result of a single amino-acid substitution.  

DOE Green Energy (OSTI)

BACKGROUND: The self-assembly properties of beta domains are important features of diverse classes of proteins that include cell-adhesion molecules, surface receptors and the immunoglobulin superfamily. Immunoglobulin light-chain variable domains are well suited to the study of structural factors that determine dimerization, including how residues at the interface influence the preferred dimer arrangement. RESULTS: Single-site mutants of light-chain variable domain Len, designated LenQ38E and LenK30T, formed 'flipped' dimers in which one domain was rotated by about 180 degrees compared with the native protein. The dimer in the native protein is similar to that found between variable domains in Fab immunoglobulin fragments. When compared to the native dimer, more surface area is buried, and more hydrogen bonds and salt bridges are formed between the monomers in the flipped conformation. CONCLUSIONS: Immunoglobulin light-chain variable domains can form a minimum of two distinct quaternary structures. Single-site mutations resulting from changes of one base, such as the exchange of Gln38 to Glu or Lys30 to Thr, change the 'conventional' dimer of protein Len to a flipped arrangement. Native Len is not found in the flipped-domain dimer conformation because it would have excess positive electrostatic potential at the dimer interface that is not compensated by other forces. Excess negative or positive electrostatic potential at the dimer interface can have a determining effect on the mode of dimerization.

Polluluri, P. R.; Huang, D.-B.; Raffen, R.; Cai, X.; Johnson, G.; Wilkins-Stevens, P.; Stevens, F. J.; Schiffer, M.; Center for Mechanistic Biology and Biotechnology

1998-08-15T23:59:59.000Z

434

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

435

U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service  

Energy.gov (U.S. Department of Energy (DOE)) Indexed Site

1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service 1: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability U-221: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability July 26, 2012 - 7:00am Addthis PROBLEM: ISC BIND 9 DNSSEC Validation CVE-2012-3817 Denial of Service Vulnerability PLATFORM: BIND 9.6-ESV-R1 through versions 9.6-ESV-R7-P1 BIND 9.7.1 through versions 9.7.6-P1 BIND 9.8.0 through versions 9.8.3-P1 BIND 9.9.0 through versions 9.9.1-P1 ABSTRACT: ISC BIND is prone to a denial-of-service vulnerability. reference LINKS: The Vendor's Advisory CVE-2012-3817 Bugtraq ID: 54658 SecurityTracker Alert ID: 1027296 IMPACT ASSESSMENT: High Discussion: When DNSSEC validation is enabled, does not properly initialize the failing-query cache, which allows remote attackers to cause a denial of

436

V-172: ISC BIND RUNTIME_CHECK Error Lets Remote Users Deny Service Against Recursive Resolvers  

Energy.gov (U.S. Department of Energy (DOE))

A defect exists which allows an attacker to crash a BIND 9 recursive resolver with a RUNTIME_CHECK error in resolver.c

437

Sequestering Uranium from Seawater: Binding Strength and Modes of Uranyl Complexes with Glutarimidedioxime  

E-Print Network (OSTI)

data_request/cif. OECD, Uranium 2009: Resources, Productionthermodynamics of uranium, (H. Wanner and I. Forest,of California. Sequestering uranium from seawater: binding

Tian, Guoxin

2013-01-01T23:59:59.000Z

438

Reproducible domain wall pinning by linear non-topographic features in a ferromagnetic nanowire  

Science Conference Proceedings (OSTI)

We demonstrate that for multilayered magnetic nanowires, where the thickness and composition of the individual layers have been carefully chosen, domain walls can be pinned at non-topographic sites created purely by ion irradiation in a focused ion beam system. The pinning results from irradiation induced alloying leading to magnetic property modification only in the affected regions. Using Lorentz transmission electron microscopy, we have studied the pinning behavior of domain walls at the irradiation sites. Depending on the irradiation dose, a single line feature not only pinned the domain walls but also acted to control their structure and the strength of their pinning.

Basith, M. A.; McVitie, S.; McGrouther, D.; Chapman, J. N. [School of Physics and Astronomy, University of Glasgow, Glasgow G12 8QQ (United Kingdom)

2012-06-04T23:59:59.000Z

439

Monte Carlo simulation of ferroelectric domain structure: Electrostatic and elastic strain energy contributions  

DOE Green Energy (OSTI)

A lattice-Monte Carlo approach was developed to simulate ferroelectric domain behavior. The model utilizes a Hamiltonian for the total energy that includes electrostatic terms (involving dipole-dipole interactions, local polarization gradients, and applied electric field), and elastic strain energy. The contributions of these energy components to the domain structure and to the overall applied field response of the system were examined. In general, the model exhibited domain structure characteristics consistent with those observed in a tetragonally distorted ferroelectric. Good qualitative agreement between the appearance of simulated electrical hysteresis loops and those characteristic of real ferroelectric materials was found.

POTTER JR.,BARRETT G.; TUTTLE,BRUCE A.; TIKARE,VEENA

2000-04-04T23:59:59.000Z

440

Semantic Filtering by inference on domain knowledge in spoken language dialogue systems  

E-Print Network (OSTI)

General natural dialogue processing requires large amounts of domain knowledge as well as linguistic knowledge in order to ensure acceptable coverage and understanding. There are several ways of integrating lexical resources (e.g. dictionaries, thesauri) and knowledge bases or ontologies at different levels of dialogue processing. We concentrate in this paper on how to exploit domain knowledge for filtering interpretation hypotheses generated by a robust semantic parser. We use domain knowledge to semantically constrain the hypothesis space. Moreover, adding an inference mechanism allows us to complete the interpretation when information is not explicitly available. Further, we discuss briefly how this can be generalized towards a predictive natural interactive system.

Afzal Ballim; Vincenzo Pallotta

2000-01-01T23:59:59.000Z

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441

Australasian Medical Journal [AMJ 2012, 5, 9, 478-481] Extractive summarisation of medical documents using domain knowledge and  

E-Print Network (OSTI)

Australasian Medical Journal [AMJ 2012, 5, 9, 478-481] 478 Extractive summarisation of medical documents using domain knowledge and corpus. Extractive summarisation of medical documents using domain knowledge and corpus

Aliod, Diego Mollá

442

How to Determine if Your Computer is Part of a Domain -Windows XP Page 1 of 3 How to Determine if Your Computer is Part of a Domain -Windows XP  

E-Print Network (OSTI)

How to Determine if Your Computer is Part of a Domain - Windows XP Page 1 of 3 How to Determine if Your Computer is Part of a Domain - Windows XP Last Update: 11/28/2011 1. Click the Windows Start: #12;How to Determine if Your Computer is Part of a Domain - Windows XP Page 2 of 3 4. From the popup

Mladenoff, David

443

Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum.  

E-Print Network (OSTI)

??From opportunistic protist Cryptosporidium parvum we identified and functionally assayed a fatty acyl-CoA-binding protein (ACBP) gene. The CpACBP1 gene encodes a protein of 268 aa (more)

Zeng, Bin

2009-01-01T23:59:59.000Z

444

Creating a specific domain ontology for supporting R&D in the science-based sector - The case of biosensors  

Science Conference Proceedings (OSTI)

In science-based and technology-intensive projects, knowledge management challenges require a tentative and cautious review of the technological domains, as well as, venues to monitor and assess the way those domains evolve, emerge, mature, and decline. ... Keywords: Biosensor, Domain ontology, Engineering knowledge, Meta-modeling

Fragiskos A. Batzias; Christina G. Siontorou

2012-09-01T23:59:59.000Z

445

Time-Domain Electromagnetics At Kilauea East Rift Area (Thomas, 1986) |  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Kilauea East Rift Time-Domain Electromagnetics At Kilauea East Rift Area (Thomas, 1986) Exploration Activity Details Location Kilauea East Rift Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes A series of time-domain electromagnetic (TDEM) soundings were also performed in the lower East Rift Zone as part of the HGP exploration program (Klein and Kauahikaua, 1975; Kauahikaua and Klein, 1977); this work was recently expanded to include additional TDEM and vertical electrical soundings, and the entire data set was reinterpreted (Kauahikaua, 1981b; Kauahikaua and Mattice, 1981). The resistivity model presented by Kauahikaua (1981b) suggests that moderate to high basement resistivities, corresponding to cold freshwater saturated basalts, are present north of

446

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print The quest to increase both computer data-storage density and the speed at which one can read and write the information remains unconsummated. One novel concept is based on the use of a local electric current to push magnetic domain walls along a thin nanowire. A German, Korean, Berkeley Lab team has used the x-ray microscope XM-1 at the ALS to demonstrate that magnetic domain walls in curved permalloy nanowires can be moved at high speed by injecting nanosecond pulses of spin-polarized currents into the wires, but the motion is largely stochastic. This result will have an impact on the current development of magnetic storage devices in which data is moved electronically rather than mechanically as in computer disk drives.

447

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print The quest to increase both computer data-storage density and the speed at which one can read and write the information remains unconsummated. One novel concept is based on the use of a local electric current to push magnetic domain walls along a thin nanowire. A German, Korean, Berkeley Lab team has used the x-ray microscope XM-1 at the ALS to demonstrate that magnetic domain walls in curved permalloy nanowires can be moved at high speed by injecting nanosecond pulses of spin-polarized currents into the wires, but the motion is largely stochastic. This result will have an impact on the current development of magnetic storage devices in which data is moved electronically rather than mechanically as in computer disk drives.

448

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print The quest to increase both computer data-storage density and the speed at which one can read and write the information remains unconsummated. One novel concept is based on the use of a local electric current to push magnetic domain walls along a thin nanowire. A German, Korean, Berkeley Lab team has used the x-ray microscope XM-1 at the ALS to demonstrate that magnetic domain walls in curved permalloy nanowires can be moved at high speed by injecting nanosecond pulses of spin-polarized currents into the wires, but the motion is largely stochastic. This result will have an impact on the current development of magnetic storage devices in which data is moved electronically rather than mechanically as in computer disk drives.

449

Time-Domain Electromagnetics At Long Valley Caldera Area (Sorey, Et Al.,  

Open Energy Info (EERE)

1991) 1991) Jump to: navigation, search GEOTHERMAL ENERGYGeothermal Home Exploration Activity: Time-Domain Electromagnetics At Long Valley Caldera Area (Sorey, Et Al., 1991) Exploration Activity Details Location Long Valley Caldera Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes In 1986, Unocal Geothermal Division released results from 158 time-domain electromagnetic (TDEM) soundings and, with Chevron Resources, a total of 77 magnetotelluric (MT) stations. Reinterpretations of the Unocal and Chevron data (Park and Torres-Verdin, 1988 ) and the recent public-domain MT studies (e.g. Hermance et al., 1988) outline similar shallow low-resistivity regions. At shallow depths in the caldera References Michael L. Sorey, Gene A. Suemnicht, Neil C. Sturchio, Gregg A.

450

Time-Domain Electromagnetics At Hualalai Northwest Rift Area (Thomas, 1986)  

Open Energy Info (EERE)

Time-Domain Electromagnetics At Hualalai Northwest Time-Domain Electromagnetics At Hualalai Northwest Rift Area (Thomas, 1986) Exploration Activity Details Location Hualalai Northwest Rift Area Exploration Technique Time-Domain Electromagnetics Activity Date Usefulness useful DOE-funding Unknown Notes Three time-domain electromagnetic soundings were conducted on the middle northwest rift at elevations of 280-320 m (Fig. 40) (Kauahikaua and Mattice, 1981). These soundings penetrated to a greater depth than the Schlumberger soundings and two of them were able to resolve basement resistivities ranging from 9 to 12 ohm-m at depths of 1500 to 1800 m. One sounding detected a 9 ohm.m layer at 600 m depth that was underlain by a more resistive basement. These results suggest that thermal fluids may be responsible for the low-resistivity basement, whereas the high-resistivity

451

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print The quest to increase both computer data-storage density and the speed at which one can read and write the information remains unconsummated. One novel concept is based on the use of a local electric current to push magnetic domain walls along a thin nanowire. A German, Korean, Berkeley Lab team has used the x-ray microscope XM-1 at the ALS to demonstrate that magnetic domain walls in curved permalloy nanowires can be moved at high speed by injecting nanosecond pulses of spin-polarized currents into the wires, but the motion is largely stochastic. This result will have an impact on the current development of magnetic storage devices in which data is moved electronically rather than mechanically as in computer disk drives.

452

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires  

NLE Websites -- All DOE Office Websites (Extended Search)

X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print X-Ray Imaging Current-Driven Magnetic Domain-Wall Motion in Nanowires Print The quest to increase both computer data-storage density and the speed at which one can read and write the information remains unconsummated. One novel concept is based on the use of a local electric current to push magnetic domain walls along a thin nanowire. A German, Korean, Berkeley Lab team has used the x-ray microscope XM-1 at the ALS to demonstrate that magnetic domain walls in curved permalloy nanowires can be moved at high speed by injecting nanosecond pulses of spin-polarized currents into the wires, but the motion is largely stochastic. This result will have an impact on the current development of magnetic storage devices in which data is moved electronically rather than mechanically as in computer disk drives.

453