11 Search Results

Here in this work, we revisit the marking decisions made in the standard adaptive finite element method (AFEM). Experience shows that a naïve marking policy leads to inefficient use of computational resources for adaptive mesh refinement (AMR). Consequently, using AMR in practice often involves ad-hoc or time-consuming offline parameter tuning to set appropriate parameters for the marking subroutine. To address these practical concerns, we recast AMR as a Markov decision process in which refinement parameters can be selected on-the-fly at run time, without the need for pre-tuning by expert users. In this new paradigm, the refinement parameters are also chosenmore » adaptively via a marking policy that can be optimized using methods from reinforcement learning. We use the Poisson equation to demonstrate our techniques on h- and hp-refinement benchmark problems, and our experiments suggest that superior marking policies remain undiscovered for many classical AFEM applications. Furthermore, an unexpected observation from this work is that marking policies trained on one family of PDEs are sometimes robust enough to perform well on problems far outside the training family. For illustration, we show that a simple hp-refinement policy trained on 2D domains with only a single re-entrant corner can be deployed on far more complicated 2D domains, and even 3D domains, without significant performance loss. For reproduction and broader adoption, we accompany this work with an open-source implementation of our methods.« less

Na⁺ is the most abundant ion in living organisms and plays essential roles in regulating nutrient uptake, muscle contraction, and neurotransmission. The identification of Na⁺ in protein structures is crucial for gaining a deeper understanding of protein function in a physiological context. LeuT, a bacterial homolog of the neurotransmitter:sodium symporter family, uses the Na⁺ gradient to power the uptake of amino acids into cells and has been used as a paradigm for the study of Na⁺-dependent transport systems. We have devised a low-energy multi-crystal approach for characterizing low-Z (Z ≤ 20) anomalous scattering ions such as Na⁺, Mg²⁺, K⁺, andmore » Ca²⁺ by combining Bijvoet-difference Fourier syntheses for ion detection and f” refinements for ion speciation. Using the approach, we experimentally identify two Na⁺ bound near the central leucine binding site in LeuT. Using LeuT microcrystals, we also demonstrate that Na⁺ may be depleted to study conformational changes in the LeuT transport cycle.« less

A simple, fast, and economical alcohol penetration method for assessing the solid oxide cell to metal window frame seal in a typical planar design is presented. An alcohol such as ethanol or isopropanol is placed into the cavity of a cell sealed to the window frame. Within 3–5 min, one can determine if the glass seal is hermetic by visual observation along the seal edges on the side of the sealed frame. Cross bubbling and open circuit voltage methods for determining whether the seal failed or cracked at high temperature after final stack firing are also discussed.

ABSTRACT The distribution and abundance of metals in the diffuse intergalactic medium (IGM) have implications for galaxy formation and evolution models, and has been argued to be sensitive to the Universe’s reionization history. However, reduced sensitivity in the near-IR implies that probing IGM metals at z > 4 is currently out of reach with the traditional method of detecting individual absorbers. We present a new technique based on clustering analysis that enables the detection of these weak IGM absorbers. We investigate the two-point correlation function (2PCF) of the $${\rm C\, {\small IV}}$$ forest as a probe of IGM metallicity andmore » enrichment topology by simulating the z = 4.5 IGM with models of inhomogeneous metal distributions. The 2PCF of the $${\rm C\, {\small IV}}$$ forest demonstrates a clear peak at a characteristic separation corresponding to the doublet separation of the $${\rm C\, {\small IV}}$$ line.The peak amplitude scales quadratically with metallicity, while enrichment topology affects both the shape and amplitude of the 2PCF. For models consistent with the distribution of metals at z ∼ 3, we find that we can constrain [C/H] to within 0.2 dex, log$$\, M_{\rm {min}}$$ to within 0.4 dex, and R to within 15 per cent. We show that CGM absorbers can be reliably identified and masked, thus recovering the underlying IGM signal. The auto-correlation of the metal-line forest presents a compelling avenue to constrain the IGM metallicity and enrichment topology with high precision at z > 4, thereby pushing such measurements into the Epoch of Reionization.« less

The transcription factor WRINKLED1 ( WRI1 ) is known as a master regulator of fatty acid synthesis in developing oilseeds of Arabidopsis thaliana and other species. WRI1 is known to directly stimulate the expression of many fatty acid biosynthetic enzymes and a few targets in the lower part of the glycolytic pathway. However, it remains unclear to what extent and how the conversion of sugars into fatty acid biosynthetic precursors is controlled by WRI 1. To shortlist possible gene targets for future in-planta experimental validation, here we present a strategy that combines phylogenetic foot printing of cis-regulatory elements with additionalmore » layers of evidence. Upstream regions of protein-encoding genes in A. thaliana were searched for the previously described DNA-binding consensus for WRI1, the ASML1/WRI1 (AW)-box. For about 900 genes, AW-box sites were found to be conserved across orthologous upstream regions in 11 related species of the crucifer family. For 145 select potential target genes identified this way, affinity of upstream AW-box sequences to WRI1 was assayed by Microscale Thermophoresis. This allowed definition of a refined WRI1 DNA-binding consensus. We find that known WRI1 gene targets are predictable with good confidence when upstream AW-sites are phylogenetically conserved, specifically binding WRI1 in the in vitro assay, positioned in proximity to the transcriptional start site, and if the gene is co-expressed with WRI1 during seed development. When targets predicted in this way are mapped to central metabolism, a conserved regulatory blueprint emerges that infers concerted control of contiguous pathway sections in glycolysis and fatty acid biosynthesis by WRI1. Several of the newly predicted targets are in the upper glycolysis pathway and the pentose phosphate pathway. Of these, plastidic isoforms of fructokinase ( FRK 3) and of phosphoglucose isomerase ( PGI 1) are particularly corroborated by previously reported seed phenotypes of respective null mutations.« less

A number of non-standard finite element methods have been proposed in recent years, each of which derives from a specific class of PDE-constrained norm minimization problems. The most notable examples are LL* methods. In this work, we argue that all high-order methods in this class should be expected to deliver substandard uniform h-refinement convergence rates. In fact, one may not even see rates proportional to the polynomial order p > 1 when the exact solution is a constant function. Here, we show that the convergence rate is limited by the regularity of an extraneous Lagrange multiplier variable which naturally appearsmore » via a saddle-point analysis. In turn, limited convergence rates appear because the regularity of this Lagrange multiplier is determined, in part, by the geometry of the domain. Numerical experiments support our conclusions.« less

This technical note describes synchrotron x-ray fluorescence microscopy (XFM) as a method for measuring the concentrations of various elements in cross-sections of the ear at extremely high resolution. This method could be of great importance for addressing many open questions in hearing research. XFM uses synchrotron radiation to evoke emissions from many biologically relevant elements in the tissue. The intensity and wavelength of the emitted radiation provide a fingerprint of the tissue composition that can be used to measure the concentration of the elements in the sampled location. Here, we focus on energies that target biologically-relevant elements of the periodicmore » table between magnesium and zinc. Since a highly focused x-ray beam is used, the spot size is well below 1 mu m and the samples can be scanned at a nanometer lateral resolution. This study shows that measurement of the concentrations of different elements is possible in a mid-modiolar cross-section of a mouse cochlea. Images are presented that indicate potassium and chloride "hot spots" in the spiral ligament and the spiral limbus, providing experimental evidence for the potassium recycling pathway and showing the cochlear structures involved. Scans of a section obtained from the incus, one of the middle ear ossicles, in a developing mouse have shown that zinc is not uniformly distributed This supports the hypothesis that zinc plays a special role in the process of ossification. Although limited by sophisticated sample preparation and sectioning, the method provides ample exciting opportunities, to understand the role of genetics and epigenetics on hearing mechanisms in ontogeny and phylogeny.« less

In this work, we present a measurement of the cosmic microwave background (CMB) lensing potential using 500 deg$^2$ of 150 GHz data from the SPTpol receiver on the South Pole Telescope. The lensing potential is reconstructed with signal-to-noise per mode greater than unity at lensing multipoles $$L \lesssim 250$$, using a quadratic estimator on a combination of CMB temperature and polarization maps. We report measurements of the lensing potential power spectrum in the multipole range of $100< L < 2000$ from sets of temperature-only, polarization-only, and minimum-variance estimators. We measure the lensing amplitude by taking the ratio of the measuredmore » spectrum to the expected spectrum from the best-fit $$\Lambda$$CDM model to the $$\textit{Planck}$$ 2015 TT+lowP+lensing dataset. For the minimum-variance estimator, we find $$A_{\rm{MV}} = 0.944 \pm 0.058{\rm (Stat.)}\pm0.025{\rm (Sys.)}$$; restricting to only polarization data, we find $$A_{\rm{POL}} = 0.906 \pm 0.090 {\rm (Stat.)} \pm 0.040 {\rm (Sys.)}$$. Considering statistical uncertainties alone, this is the most precise polarization-only lensing amplitude constraint to date (10.1 $$\sigma$$), and is more precise than our temperature-only constraint. We perform null tests and consistency checks and find no evidence for significant contamination.« less

Accurate estimates of population density are a critical component of effective wildlife conservation and management. However, many snake species are so secretive that their density cannot be determined using traditional methods such as capture–mark–recapture. Thus, the status of most terrestrial snake populations remains completely unknown. We developed a novel simulation-based technique for estimating density of secretive snakes that combined behavioural observations of snake road-crossing behaviour (crossing speed), effort-corrected road-survey data, and simulations of spatial movement patterns derived from radio-telemetry, without relying on mark–recapture. Here, we used radio-telemetry data to parameterise individual-based movement models that estimate the frequency with which individualmore » snakes cross roads and used information on survey vehicle speed and snake crossing speed to determine the probability of detecting a snake, given that it crosses the road transect during a survey. Snake encounter frequencies during systematic road surveys were then interpreted in light of detection probabilities and simulation model results to estimate snake densities and to assess various factors likely to affect abundance estimates. We demonstrated the broad applicability of this approach through a case study of the imperiled southern hognose snake (Heterodon simus) in the North Carolina (USA) Sandhills. We estimated that H. simus occurs at average densities of 0.17 ha^–1 in the North Carolina Sandhills and explored the sensitivity of this estimate to assumptions and variation in model parameters. Our novel method allowed us to generate the first abundance estimates for H. simus. We found that H. simus exists at low densities relative to congeners and other mid-sized snake species, raising concern that this species may not only have declined in geographic range, but may also occur at low densities or be declining in their strongholds, such as the North Carolina Sandhills. We present a framework for estimating density of species that have traditionally been considered too secretive to study at the population level. This method will greatly enhance our ability to study and manage a wide variety of snake species and could be applied to other secretive wildlife species that are most frequently encountered during road surveys.« less

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) thatmore » simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.« less