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At least 1,045 records · Page 58

Properties of protein unfolded states suggest broad selection for expanded conformational ensembles

Much attention is being paid to conformational biases in the ensembles of intrinsically disordered proteins. However, it is currently unknown whether or how conformational biases within the disordered ensembles of foldable proteins affect function in vivo. Recently, we demonstrated that water can be a good solvent for unfolded polypeptide chains, even those with a hydrophobic and charged sequence composition typical of folded proteins. These results run counter to the generally accepted model that protein folding begins with hydrophobicity-driven chain collapse. Here we investigate what other features, beyond amino acid composition, govern chain collapse. We found that local clustering of hydrophobic and/or charged residues leads to significant collapse of the unfolded ensemble of pertactin, a secreted autotransporter virulence protein from Bordetella pertussis , as measured by small angle X-ray scattering (SAXS). Sequence patterns that lead to collapse also correlate with increased intermolecular polypeptide chain association and aggregation. Crucially, sequence patterns that support an expanded conformational ensemble enhance pertactin secretion to the bacterial cell surface. Similar sequence pattern features are enriched across the large and diverse family of autotransporter virulence proteins, suggesting sequence patterns that favor an expanded conformational ensemble are under selection for efficient autotransporter protein secretion, a necessary prerequisite for virulence. More broadly, we found that sequence patterns that lead to more expanded conformational ensembles are enriched across water-soluble proteins in general, suggesting protein sequences are under selection to regulate collapse and minimize protein aggregation, in addition to their roles in stabilizing folded protein structures.

59 BASIC BIOLOGICAL SCIENCES↗

Uncovering interpretable relationships in high-dimensional scientific data through function preserving projections

Abstract In many fields of science and engineering, we frequently encounter experiments or simulations datasets that describe the behavior of complex systems and uncovering human interpretable patterns between their inputs and outputs via exploratory data analysis is essential for building intuition and facilitating discovery. Often, we resort to 2D embeddings for examining these high-dimensional relationships (e.g. dimensionality reduction). However, most existing embedding methods treat the dimensions as coordinates for samples in a high-dimensional space, which fail to capture the potential functional relationships, and the few methods that do take function into consideration either only focus on linear patterns or produce non-linear embeddings that are hard to interpret. To address these challenges, we proposed function preserving projections (FPP), which construct 2D linear embeddings optimized to reveal interpretable yet potentially non-linear patterns between the domain and the range of a high-dimensional function. The intuition here is that humans are good at understanding potentially non-linear patterns in 2D but unable to interpret non-linear mapping from high-dimensional space to 2D. Therefore, we should restrict the projection to linear but not the pattern we are seeking. Using FPP on real-world datasets, one can obtain fundamentally new insights about high-dimensional relationships in extremely large datasets that could not be processed with existing dimension reduction methods.

97 MATHEMATICS AND COMPUTING↗

Clonality, local population structure, and gametophyte sex ratios in cryptic species of the Sphagnum magellanicum complex

Sphagnum (peatmoss) comprises a moss (Bryophyta) clade with approximately 300-500 species. The genus has unparalleled ecological importance because Sphagnum-dominated peatlands store almost a third of the terrestrial carbon pool and peatmosses engineer the formation and microtopography of peatlands. Genomic resources for Sphagnum are being actively expanded, but many aspects of their biology are still poorly known. Among these are the degree to which Sphagnum species reproduce asexually, and the relative frequencies of male and female gametophytes in these haploid-dominant plants. Here, we assess clonality and gametophyte sex ratios and test hypotheses about the local-scale distribution of clones and sexes in four North American species of the S. magellanicum complex. These four species are difficult to distinguish morphologically and are very closely related. We also assess microbial communities associated with Sphagnum host plant clones and sexes at two sites. 405 samples of the four species, representing 57 populations, were subjected to RADseq. Analyses of population structure and clonality based on the molecular data utilized both phylogenetic and phenetic approaches. Multi-locus genotypes (genets) were identified using the RADseq data. Sexes of sampled ramets were determined using a molecular approach that utilized coverage of loci on the sex chromosomes after the method was validated using a sample of plants that expressed sex phenotypically. Sex ratios were estimated for each species, and populations within species. Differences in fitness between genets was estimated as the numbers of ramets each genet comprised. Degree of clonality (numbers of genets/numbers of ramets [samples]) within species, among sites, and between gametophyte sexes were estimated. Sex ratios were estimated for each species, and populations within species. Sphagnum-associated microbial communities were assessed at two sites in relation to Sphagnum clonality and sex. All four species appear to engage in a mixture of sexual and asexual (clonal) reproduction. A single ramet represents most genets but 2-8 ramets were detected for some genets. Only one genet is represented by ramets in multiple populations; all other genets are restricted to a single population. Within populations ramets of individual genets are spatially clustered, suggesting limited dispersal even within peatlands. Sex ratios are male-biased in S. diabolicum but female-biased in the other three species, although significantly so only in S. divinum. Neither species nor males/females differ in levels of clonal propagation. At St. Regis Lake (NY) and Franklin Bog (VT), microbial community composition is strongly differentiated between the sites, but differences between species, genets, and sexes were not detected. Within S. divinum, however, female gametophytes harbored 2-3 times the number oi of microbial taxa as males. These four Sphagnum species all exhibit a similar reproductive patterns that result from a mixture of sexual and asexual reproduction. The spatial patterns of clonally replicated ramets of genets suggest that these species fall between the so-called phalanx patterns where genets abut one another but do not extensively mix, because of limited ramet fragmentation, and the guerrilla patterns where extensive genet fragmentation and dispersal results in greater mixing of different genets. Although sex ratios in bryophytes are most often female-biased, both male and female biases occur in this complex of closely related species. The association of far greater microbial diversity for female gametophytes in S. divinum, which has a female-biased sex ratio, suggests additional research to determine if levels of microbial diversity are consistently correlated with differing patterns of sex ratio biases.

59 BASIC BIOLOGICAL SCIENCES↗

Propagation of statistical uncertainties of Skyrme mass models to simulations of r -process nucleosynthesis

Uncertainties in nuclear models have a major impact on simulations that aim at understanding the origin of heavy elements in the universe through the rapid neutron capture process ( r process) of nucleosynthesis. Within the framework of the nuclear density functional theory, we use results of Bayesian statistical analysis to propagate uncertainties in the parameters of energy density functionals to the predicted r -process abundance pattern, by way not only of the nuclear masses but also through the influence of the masses on β -decay and neutron capture rates. We point out the importance of the nonequilibrium end stage of the r process in determining the width of the resulting abundance pattern uncertainty bands. We additionally make the first identifications of specific parameters of Skyrme-like energy density functionals which show tentative correlations with particular aspects of the r -process abundance pattern. While previous studies have explored the reduction in the abundance pattern uncertainties due to anticipated new measurements of neutron-rich nuclei, here we point out that an even larger reduction will occur when these new measurements are used to reduce the uncertainty of model predictions of masses, which are then propagated through to the abundance pattern. We make a quantitative prediction for how large this reduction will be.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Time series methods for the analysis of soundscapes and other cyclical ecological data

Biodiversity monitoring has entered an era of ‘big data’, exemplified by a near-continuous collection of sounds, images, chemical and other signals from organisms in diverse ecosystems. Such data streams have the potential to help identify new threats, assess the effectiveness of conservation interventions, as well as generate new ecological insights. However, appropriate analytical methods are often still missing, particularly with respect to characterizing cyclical temporal patterns. Here, we present a framework for characterizing and analysing ecological responses that represent nonstationary, complex temporal patterns and demonstrate the value of using Fourier transforms to decorrelate continuous data points. In our example, we use a framework based on three approaches (spectral analysis, magnitude squared coherence, and principal component analysis) to characterize differences in tropical forest soundscapes within and across sites and seasons in Gabon. By reconstructing the underlying, cyclic behaviour of the soundscape for each site, we show how one can identify circadian patterns in acoustic activity. Soundscapes in the dry season had a complex diel cycle, requiring multiple harmonics to represent daily variation, while in the wet season there was less variance attributable to the daily cyclic patterns. Our framework can be applied to most continuous, or near-continuous ecological data collected at a fine temporal resolution, allowing ecologists to explore patterns of temporal autocorrelation at multiple levels for biologically meaningful trends. Such methods will become indispensable as biological big data are used to understand the impact of anthropogenic pressures on biodiversity and to inform efforts to mitigate them.

54 ENVIRONMENTAL SCIENCES↗

Implications of gnomonic distortion on electron backscatter diffraction and transmission Kikuchi diffraction

The effect of gnomonic distortion on orientation indexing of electron backscatter diffraction patterns is explored through simulation of electron diffraction patterns for sample-to-detector geometries associated with transmission Kikuchi diffraction (TKD) and electron backscatter diffraction (EBSD). Simulated data were analysed by computing a similarity index for both Hough transformed data and simulated patterns to determine the sensitivity of each method for detecting subtle differences in the effect of gnomonic distortions on electron diffraction patterns. These results indicate that the increased gnomonic distortions in electron diffraction patterns for a TKD geometry enhance the sensitivity for detecting subtle differences in interband angles. Additionally, the utilisation of a Hough transform-based indexing approach further enhances the sensitivity.

36 MATERIALS SCIENCE↗

Results From Invoking Artificial Neural Networks to Measure Insider Threat Detection & Mitigation

Advances on differentiating between malicious intent and natural “organizational evolution” to explain observed anomalies in operational workplace patterns suggest benefit from evaluating collective behaviors observed in the facilities to improve insider threat detection and mitigation (ITDM). Advances in artificial neural networks (ANN) provide more robust pathways for capturing, analyzing, and collating disparate data signals into quantitative descriptions of operational workplace patterns. In response, a joint study by Sandia National Laboratories and the University of Texas at Austin explored the effectiveness of commercial artificial neural network (ANN) software to improve ITDM. Overall, this research demonstrates the benefit of learning patterns of organizational behaviors, detecting off-normal (or anomalous) deviations from these patterns, and alerting when certain types, frequencies, or quantities of deviations emerge for improving ITDM. Evaluating nearly 33,000 access control data points and over 1,600 intrusion sensor data points collected over a nearly twelve-month period, this study's results demonstrated the ANN could recognize operational patterns at the Nuclear Engineering Teaching Laboratory (NETL) and detect off-normal behaviors—suggesting that ANNs can be used to support a data-analytic approach to ITDM. Several representative experiments were conducted to further evaluate these conclusions, with the resultant insights supporting collective behavior-based analytical approaches to quantitatively describe insider threat detection and mitigation.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

Regional biogeography versus intra-annual dynamics of the root and soil microbiome

Abstract Background Root and soil microbial communities constitute the below-ground plant microbiome, are drivers of nutrient cycling, and affect plant productivity. However, our understanding of their spatiotemporal patterns is confounded by exogenous factors that covary spatially, such as changes in host plant species, climate, and edaphic factors. These spatiotemporal patterns likely differ across microbiome domains (bacteria and fungi) and niches (root vs. soil). Results To capture spatial patterns at a regional scale, we sampled the below-ground microbiome of switchgrass monocultures of five sites spanning > 3 degrees of latitude within the Great Lakes region. To capture temporal patterns, we sampled the below-ground microbiome across the growing season within a single site. We compared the strength of spatiotemporal factors to nitrogen addition determining the major drivers in our perennial cropping system. All microbial communities were most strongly structured by sampling site, though collection date also had strong effects; in contrast, nitrogen addition had little to no effect on communities. Though all microbial communities were found to have significant spatiotemporal patterns, sampling site and collection date better explained bacterial than fungal community structure, which appeared more defined by stochastic processes. Root communities, especially bacterial, were more temporally structured than soil communities which were more spatially structured, both across and within sampling sites. Finally, we characterized a core set of taxa in the switchgrass microbiome that persists across space and time. These core taxa represented < 6% of total species richness but > 27% of relative abundance, with potential nitrogen fixing bacteria and fungal mutualists dominating the root community and saprotrophs dominating the soil community. Conclusions Our results highlight the dynamic variability of plant microbiome composition and assembly across space and time, even within a single variety of a plant species. Root and soil fungal community compositions appeared spatiotemporally paired, while root and soil bacterial communities showed a temporal lag in compositional similarity suggesting active recruitment of soil bacteria into the root niche throughout the growing season. A better understanding of the drivers of these differential responses to space and time may improve our ability to predict microbial community structure and function under novel conditions.

59 BASIC BIOLOGICAL SCIENCES↗

X-ray Irradiance Distribution for an Interferometer with a Curved Biprism Array

The development of interferometry-based X-ray phase contrast imaging systems that provide highly resolved X-rays with spatially-modulated intensity is enabling the full potential of X-ray optics to image phase, attenuation, and small angle scatter properties of soft tissue. In this work we present analytical formulations of a new hardware concept for X-ray phase contrast imaging wherein the phase grating is replaced with an array of Fresnel biprisms. We derive expressions for the irradiance distribution pattern of a biprism interferometer composed of a curved biprism array with multiple biprisms and multiple point sources. These expressions are used to plot fringe patterns for X-ray design parameters, including 1) size, number, and period of X-ray point sources; 2) biprism parameters of material composition, angle, number, and period; and 3) biprism array to X-ray source and detector distances. Analytical results show that the biprism interferometer provides a longitudinally-nonperiodic pattern of spatially modulated intensity different from the Talbot longitudinally-periodic pattern common in grating interferometry. The curvature of the biprism array brings a sharper longitudinal fringe pattern. Experiments are being performed to verify the analytical calculations for a biprism plastic material of SU-8 using a synchrotron source. X-ray biprism material has widely varied indexes of refraction relative to wavelength and thus the separation of the virtual sources and resulting interference fringe period also varies with X-ray wavelength. Our aim is to develop biprism interferometry imaging systems with excellent polychromatic performance that produce high-contrast fringes with spatially incoherent X-ray illumination. Biprism interferometry will potentially provide higher fringe visibility with better image quality to that of diffraction grating interferometry.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Optimizing DOE Opportunities to Research Land–Atmosphere Interactions in the U.S. Southeast (Workshop Report)

The southeastern United States (Southeast), with its complex and varied environments, is an area of tremendous economic, ecological, and societal importance to the country. The region is characterized by heterogeneous landscapes (i.e., geology and soil type) and a long history of human land use coupled with a warm temperature regime and high precipitation. As a result, soil erosion and deposition are pronounced, vegetation recovery is rapid, and human modification is extensive across the region. To better understand land–atmosphere interactions in this important and complex region, research communities supported by the U.S. Department of Energy’s Biological and Environmental Research (BER) program identified the Southeast as a priority region of interest. In fall 2024, the third Atmospheric Radiation Measurement Mobile Facility (AMF3), one of three mobile monitoring facilities designed to collect atmospheric and climate data from undersampled regions around the world, will begin operations in northwestern Alabama’s Bankhead National Forest (BNF). The AMF3-BNF 5-year deployment, from 2024–2029, will monitor the effects of feedbacks among aerosols, clouds, and precipitation on plant physiology and canopy-scale fluxes. It will also focus on scale aggregation to resolve the role of local forcing on larger-scale processes. To enable broader AMF3 involvement by the science community, the BER Environmental System Science (ESS) program organized the Southeast Land– Atmosphere Research Opportunities (SELARO) workshop in August 2023. The purpose was to identify gaps in scientific understanding of terrestrial processes in the Southeast (defined as states bounded by the Gulf of Mexico to the south, the Atlantic Ocean to east, the Mississippi River to the west, and extending through Tennessee and North Carolina to the north) and explore opportunities to use the AMF3-BNF deployment to coordinate and leverage research efforts across the region. Many parts of the Southeast have experienced repeated anthropogenic forcings. Farming, hunting, burning, and settlement of the region by Indigenous Peoples first shaped the distribution of plant communities, which in turn influenced European colonization patterns. Timber harvesting was common during the expansion of European settlements, and production forestry continues today. Agricultural production was extensive and then waned through the 20th century, creating a period of afforestation following agricultural abandonment. Today, many formerly agricultural landscapes are undergoing rapid urbanization and suburbanization. Overlying these patterns of anthropogenic land use are frequent disturbances from hurricanes, tornadoes, wildfires, drought, flooding, ice storms, and the occasional blizzard. An additional characteristic of the Southeast is its overall landscape complexity. Unlike the western United States, where broad expanses may share similar characteristics, Southeast topography, drainage patterns, vegetation, and development patterns vary widely across relatively small spatial scales (<1 km). This is due to the region’s underlying geology and soil development, species biodiversity patterns, and land ownership and use coupled with strong forces of erosion, weathering, and rapid plant growth in the warm, wet climate.

54 ENVIRONMENTAL SCIENCES↗

A computational modeling framework for pre-clinical evaluation of cardiac mapping systems

There are a variety of difficulties in evaluating clinical cardiac mapping systems, most notably the inability to record the transmembrane potential throughout the entire heart during patient procedures which prevents the comparison to a relevant “gold standard”. Cardiac mapping systems are comprised of hardware and software elements including sophisticated mathematical algorithms, both of which continue to undergo rapid innovation. The purpose of this study is to develop a computational modeling framework to evaluate the performance of cardiac mapping systems. The framework enables rigorous evaluation of a mapping system’s ability to localize and characterize (i.e., focal or reentrant) arrhythmogenic sources in the heart. The main component of our tool is a library of computer simulations of various dynamic patterns throughout the entire heart in which the type and location of the arrhythmogenic sources are known. Our framework allows for performance evaluation for various electrode configurations, heart geometries, arrhythmias, and electrogram noise levels and involves blind comparison of mapping systems against a “silver standard” comprised of computer simulations in which the precise transmembrane potential patterns throughout the heart are known. A feasibility study was performed using simulations of patterns in the human left atria and three hypothetical virtual catheter electrode arrays. Activation times (AcT) and patterns (AcP) were computed for three virtual electrode arrays: two basket arrays with good and poor contact and one high-resolution grid with uniform spacing. The average root mean squared difference of AcTs of electrograms and those of the nearest endocardial action potential was less than 1 ms and therefore appears to be a poor performance metric. In an effort to standardize performance evaluation of mapping systems a novel performance metric is introduced based on the number of AcPs identified correctly and those considered spurious as well as misclassifications of arrhythmia type; spatial and temporal localization accuracy of correctly identified patterns was also quantified. This approach provides a rigorous quantitative analysis of cardiac mapping system performance. Proof of concept of this computational evaluation framework suggests that it could help safeguard that mapping systems perform as expected as well as provide estimates of system accuracy.

59 BASIC BIOLOGICAL SCIENCES↗

Impact of Intersection Control on Battery Electric Vehicle Energy Consumption

Battery electric vehicle (BEV) sales have significantly increased in recent years. They have different energy consumption patterns compared to the fuel consumption patterns of internal combustion engine vehicles (ICEVs). This study quantified the impact of intersection control approaches—roundabout, traffic signal, and two-way stop controls—on BEVs’ energy consumption. The paper systematically investigates BEVs’ energy consumption patterns compared to the fuel consumption of ICEVs. The results indicate that BEVs’ energy consumption patterns are significantly different than ICEVs’ patterns. For example, for BEVs approaching a high-speed intersection, the roundabout was found to be the most energy-efficient intersection control, while the two-way stop sign was the least efficient. In contrast, for ICEVs, the two-way stop sign was the most fuel-efficient control, while the roundabout was the least efficient. Findings also indicate that the energy saving of traffic signal coordination was less significant for BEVs compared to the fuel consumption of ICEVs since more regenerative energy is produced when partial or poorly coordinated signal plans are implemented. The study confirms that BEV regenerative energy is a major factor in energy efficiency, and that BEVs recover different amounts of energy in different urban driving environments. The study suggests that new transportation facilities and control strategies should be designed to enhance BEVs’ energy efficiency, particularly in zero emission zones.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Circuit board interconnect decals

A circuit component decal comprising a transparent sheet and an opaque circuit pattern. The transparent sheet includes opposing top and bottom surfaces and a number of edges. The opaque circuit pattern includes an electronic component footprint and a number of circuit lead paths. The electronic component footprint includes a number of contact points representing the location of leads of the electronic component. The circuit lead paths extend from the contact points to the edges of the transparent sheet. The opaque circuit pattern corresponds to only a section of a complete circuit pattern and is configured to block energy from reaching a first portion of the intermediate substrate when the transparent sheet is positioned on the intermediate substrate so as to form the section of the complete circuit pattern.

42 ENGINEERING↗

Heat treatment to anneal residual stresses during additive manufacturing

The present disclosure relates to a method of producing a product through additive manufacturing with heat treatment. The method involves using a fusing beam to melt powder particles disposed on a substrate, where the fusing beam is impressed with a two dimensional pattern containing image information from a first layer to be printed. The fused powder particles are then heat treated with a beam impressed with an additional two dimensional pattern. The additional two dimensional pattern has image information from the first layer to achieve heat treatment of the product. The heat treatment is completed prior to laying down additional new layers of material. The heat treatment is an annealing operation. The method may further involve providing a new layer of powdered material on top of the layer of fused powder particles subsequent to the heat treatment, and repeating the melting and heat treating operations in a layer-by-layer fashion using the two dimensional pattern and the additional two dimensional pattern, until the part is completed.

DeMuth, James A.↗

Controlled wetting and spreading of metals on substrates using porous interlayers and related articles

The disclosure generally relates to a method of creating patterned metallic circuits (e.g., silver circuits) on a substrate (e.g., a ceramic substrate). A porous metal interlayer (e.g., porous nickel) is applied to the substrate to improve wetting and adhesion of the patterned metal circuit material to the substrate. The substrate is heated to a temperature sufficient to melt the patterned metal circuit material but not the porous metal interlayer. Spreading of molten metal circuit material on the substrate is controlled by the porous metal interlayer, which can itself be patterned, such as having a defined circuit pattern. Thick-film silver or other metal circuits can be custom designed in complicated shapes for high temperature/high power applications. The materials designated for the circuit design allows for a low-cost method of generating silver circuits other metal circuits on a ceramic substrate.

Nicholas, Jason Dale↗

A Generalizable Approach to Direct the Self-Assembly of Functional Blue-Phase Liquid Crystals

Blue phases (BPs) are soft and stimuli-responsive photonic crystals that are interesting for sensing, display, and lasing applications. Polycrystallinity has, however, limited both the study and applicability of BPs. Continuum simulations, which lack molecule-specific details, predict that striped chemical patterns, consisting of alternating homeotropic and planar regions, can be used to nucleate single crystals of BPs. Here it is experimentally demonstrated that, independent of the chemistry and complexity of the BP forming material, chemical patterns direct the self-assembly of BPs; these results indicate that a general, thermodynamics-based continuum description of BP self-assembly is adequate for a broad range of materials. When the pattern periodicity equals the BPII unit cell size, single crystals with (100) orientation form for all studied materials. Chemical patterns also promote the growth of BPI crystals with (110) orientation. Importantly, the self-assembly of a photopolymerizable BP is directed and thermally stable, UV-polymerized single crystals are prepared. As a result, the ability to create arbitrarily large, polymeric photonic single crystals with uniform lattice orientation, may have broad implications for optical applications.

36 MATERIALS SCIENCE↗

Zinc‐Imidazolate Films as an All‐Dry Resist Technology

Here, motivated by the drawbacks of solution phase processing, an all‐dry resist formation process is presented that utilizes amorphous zinc‐imidazolate (aZnMIm) films deposited by atomic/molecular layer deposition (ALD/MLD), patterned with electron beam lithography (EBL), and developed by novel low temperature (120 °C) gas phase etching using 1,1,1,5,5,5‐hexafluoroacetylacetone (hfacH) to achieve well‐resolved 22 nm lines with a pitch of 30 nm. The effects of electron beam irradiation on the chemical structure and hfacH etch resistance of aZnMIm films are investigated, and it is found that electron irradiation degrades the 2‐methylimidazolate ligands and transforms aZnMIm into a more dense material that is resistant to etching by hfacH and has a C:N:Zn ratio effectively identical to that of unmodified aZnMIm. These findings showcase the potential for aZnMIm films to function in a dry resist technology. Sensitivity, contrast, and critical dimensions of the patterns are determined to be 37 mC cm −2 , 0.87, and 29 nm, respectively, for aZnMIm deposited on silicon substrates and patterned at 30 keV. This work introduces a new direction for solvent‐free resist processing, offering the prospect of scalable, high‐resolution patterning techniques for advanced semiconductor fabrication processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗