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At least 1,495 records · Page 83

Energy‐aware relay positioning in flying networks

Summary The ability to move and hover has made rotary‐wing unmanned aerial vehicles (UAVs) suitable platforms to act as flying communications relays (FCRs), aiming at providing on‐demand, temporary wireless connectivity when there is no network infrastructure available or a need to reinforce the capacity of existing networks. However, since UAVs rely on their on‐board batteries, which can be drained quickly, they typically need to land frequently for recharging or replacing them, limiting their endurance and the flying network availability. The problem is exacerbated when a single FCR UAV is used. The FCR UAV energy is used for two main tasks: Communications and propulsion. The literature has been focused on optimizing both the flying network performance and energy efficiency from the communications point of view, overlooking the energy spent for the UAV propulsion. Yet, the energy spent for communications is typically negligible when compared with the energy spent for the UAV propulsion. In this article, we propose energy‐aware relay positioning (EREP), an algorithm for positioning the FCR taking into account the energy spent for the UAV propulsion. Building upon the conclusion that hovering is not the most energy‐efficient state, EREP defines the trajectory and speed that minimize the energy spent by the FCR UAV on propulsion, without compromising in practice the quality of service offered by the flying network. The EREP algorithm is evaluated using simulations. The obtained results show gains up to 26% in the FCR UAV endurance for negligible throughput and delay degradation.

Rodrigues, Hugo↗

Synchrotron‐source micro‐x‐ray computed tomography for examining butterfly eyes

Comparative anatomy is an important tool for investigating evolutionary relationships among species, but the lack of scalable imaging tools and stains for rapidly mapping the microscale anatomies of related species poses a major impediment to using comparative anatomy approaches for identifying evolutionary adaptations. We describe a method using synchrotron source micro-x-ray computed tomography (syn-μXCT) combined with machine learning algorithms for high-throughput imaging of Lepidoptera (i.e., butterfly and moth) eyes. Our pipeline allows for imaging at rates of ~15 min/mm 3 at 600 nm 3 resolution. Image contrast is generated using standard electron microscopy labeling approaches (e.g., osmium tetroxide) that unbiasedly labels all cellular membranes in a species-independent manner thus removing any barrier to imaging any species of interest. To demonstrate the power of the method, we analyzed the 3D morphologies of butterfly crystalline cones, a part of the visual system associated with acuity and sensitivity and found significant variation within six butterfly individuals. Despite this variation, a classic measure of optimization, the ratio of interommatidial angle to resolving power of ommatidia, largely agrees with early work on eye geometry across species. We show that this method can successfully be used to determine compound eye organization and crystalline cone morphology. Our novel pipeline provides for fast, scalable visualization and analysis of eye anatomies that can be applied to any arthropod species, enabling new questions about evolutionary adaptations of compound eyes and beyond.

59 BASIC BIOLOGICAL SCIENCES↗

Benchmark Dose Analysis of DNA Damage Biomarker Responses Provides Compound Potency and Adverse Outcome Pathway Information for the Topoisomerase II Inhibitor Class of Compounds

Genetic toxicology data have traditionally been utilized for hazard identification to provide a binary call for a compound's risk. Recent advances in the scientific field, especially with the development of high‐throughput methods to quantify DNA damage, have influenced a change of approach in genotoxicity assessment. The in vitro MultiFlow® DNA Damage Assay is one such method which multiplexes γH2AX, p53, phospho‐histone H3 biomarkers into a single‐flow cytometric analysis (Bryce et al., [2016]: Environ Mol Mutagen 57:546–558). This assay was used to study human TK6 cells exposed to each of eight topoisomerase II poisons for 4 and 24 hr. Using PROAST v65.5, the Benchmark Dose approach was applied to the resulting flow cytometric datasets. With “compound” serving as covariate, all eight compounds were combined into a single analysis, per time point and endpoint. The resulting 90% confidence intervals, plotted in Log scale, were considered as the potency rank for the eight compounds. The in vitro MultiFlow data showed a maximum confidence interval span of 1Log, which indicates data of good quality. Patterns observed in the compound potency rank were scrutinized by using the expert rule‐based software program Derek Nexus, developed by Lhasa Limited. Compound sub‐classification and structural alerts were considered contributory to the potencies observed for the topoisomerase II poisons studied herein. The Topo II poison Adverse Outcome Pathway was evaluated with MultiFlow endpoints serving as Key Events. The step‐wise approach described herein can be considered as a foundation for risk assessment of compounds within a specific mode of action of interest. Environ. Mol. Mutagen. 2020. © 2020 Wiley Periodicals, Inc.

Wheeldon, Ryan P.↗

Transcriptomics-Based Points of Departure for Daphnia magna Exposed to 18 Per- and Polyfluoroalkyl Substances

Here, per- and polyfluoroalkyl substances (PFAS) represent a large group of contaminants of concern based on their widespread use, environmental persistence, and potential toxicity. Many traditional models for estimating toxicity, bioaccumulation, and other toxicological properties are not well suited for PFAS. Consequently, there is a need to generate hazard information for PFAS in an efficient and cost-effective manner. In the present study, Daphnia magna were exposed to multiple concentrations of 22 different PFAS for 24 h, in 96-well plate format. Following exposure, whole body RNA was extracted and extracts, each representing five exposed individuals, were subjected to RNA sequencing. Following analytical measurements to verify PFAS exposure concentrations, and quality control on processed cDNA libraries for sequencing, concentration-response modeling was applied to the data sets for 18 of the tested compounds, and the concentration at which a concerted molecular response occurred (transcriptomic point of departure; tPOD) was calculated. The tPODs, based on measured concentrations of PFAS, generally ranged from 0.03-0.58 µM (9.9-350 µg/L; interquartile range). In most cases, these concentrations were two orders of magnitude lower than similarly calculated tPODs for human cell lines exposed to PFAS. They were also lower than apical effect concentrations reported for seven PFAS for which some crustacean or invertebrate toxicity data were available, although there were a few exceptions. Despite being lower than most other available hazard benchmarks, Daphnia magna tPODs were, on average, four orders of magnitude greater than the maximum aqueous concentrations of PFAS measured in Great Lakes tributaries. Overall, this high throughput transcriptomics assay with Daphnia magna holds promise as a component of a tiered hazard evaluation strategy employing new approach methodologies.

59 BASIC BIOLOGICAL SCIENCES↗

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand‐Binding Cavity

Abstract Stabilization of amyloidogenic immunoglobulin light chains (LCs) by binding of small molecule “kinetic stabilizers” is under development as a novel treatment for light chain amyloidosis. From a high‐throughput screen, we previously identified 16 full‐length (FL) LC stabilizers from five distinct chemotypes. We then obtained structural biological information on two classes of hits, coumarins and hydantoins, revealing that both chemotypes bind to a pocket at the V L −V L interface of the FL LC dimer. Here, we report crystal structures of three screening hits from two other chemotypes, diaryl hydrazones and sulfones, in complex with an amyloidogenic FL LC. While two of these hits bind to the previously identified pocket, one diaryl hydrazone binds to a different pocket bisected by the C 2 symmetry axis of the dimer. These data further expand on the FL LC stabilizer‐binding surface that could be used in design of more potent FL LC aggregation inhibitors.

Chemistry↗

Protein3D: Enabling analysis and extraction of metal‐containing sites from the Protein Data Bank with molSimplify

Abstract Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing a key role in modulating chemical reactivity and selectivity. Unlike smaller synthetic catalysts, a metalloenzyme active site is embedded in a larger protein, which makes interrogation of electronic properties and geometric features with quantum mechanical calculations challenging. Here we implement the ability to fetch crystallographic structures from the Protein Data Bank and analyze the metal binding sites in the program molSimplify. We show the usefulness of the newly created protein3D class to extract the local environment around non‐heme iron enzymes containing a two histidine motif and prepare 372 structures for quantum mechanical calculations. Our implementation of protein3D serves to expand the range of systems molSimplify can be used to analyze and will enable high‐throughput study of metal‐containing active sites in proteins.

Edholm, Freya↗

Erratum to: Soft- and reactive landing of ions onto surfaces: concepts and applications

Soft- and reactive landing of mass-selected ions is gaining attention as a promising approach for the precisely-controlled preparation of materials on surfaces that are not amenable to deposition using conventional methods. A broad range of ionization sources and mass filters are available that make ion soft-landing a versatile tool for surface modification using beams of hyperthermal (<100?eV) ions. The ability to select the mass-to-charge ratio of the ion, its kinetic energy and charge state, along with precise control of the size, shape, and position of the ion beam on the deposition target distinguishes ion soft landing from other surface modification techniques. Soft- and reactive landing have been used to prepare interfaces for practical applications as well as precisely-defined model surfaces for fundamental investigations in chemistry, physics, and materials science. For instance, soft- and reactive landing have been applied to study the surface chemistry of ions isolated in the gas-phase, prepare arrays of proteins for high-throughput biological screening, produce novel carbon-based and polymer materials, enrich the secondary structure of peptides and the chirality of organic molecules, immobilize electrochemically-active proteins and organometallics on electrodes, create thin films of complex molecules, and immobilize catalytically active organometallics as well as ligated metal clusters. In addition, soft landing has enabled investigation of the size-dependent behavior of bare metal clusters in the critical subnanometer size regime where chemical and physical properties do not scale predictably with size. The morphology, aggregation, and immobilization of larger bare metal nanoparticles, which are directly relevant to the design of catalysts as well as improved memory and electronic devices, have also been studied using ion soft landing. This review article begins in section 1 with a brief introduction to the existing applications of ion soft- and reactive landing. Section 2 provides an overview of the ionization sources and mass filters that have been used to date for soft landing of mass-selected ions. A discussion of the competing processes that occur during ion deposition as well as the types of ions and surfaces that have been investigated follows in section 3. Section 4 discusses the physical phenomena that occur during and after ion soft landing, including retention and reduction of ionic charge along with factors that impact the efficiency of ion deposition. The influence of soft landing on the secondary structure and biological activity of complex ions is addressed in section 5. Lastly, an overview of the structure and mobility as well as the catalytic, optical, magnetic, and redox properties of bare ionic clusters and nanoparticles deposited onto surfaces is presented in section 6. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:439–479, 2016.

Johnson, Grant E.↗

Metagenomic strategies identify diverse integron–integrase and antibiotic resistance genes in the Antarctic environment

The objective of this study is to identify and analyze integrons and antibiotic resistance genes (ARGs) in samples collected from diverse sites in terrestrial Antarctica. Integrons were studied using two independent methods. One involved the construction and analysis of intI gene amplicon libraries. In addition, we sequenced 17 metagenomes of microbial mats and soil by high-throughput sequencing and analyzed these data using the IntegronFinder program. As expected, the metagenomic analysis allowed for the identification of novel predicted intI integrases and gene cassettes (GCs), which mostly encode unknown functions. However, some intI genes are similar to sequences previously identified by amplicon library analysis in soil samples collected from non-Antarctic sites. ARGs were analyzed in the metagenomes using ABRIcate with CARD database and verified if these genes could be classified as GCs by IntegronFinder. We identified 53 ARGs in 15 metagenomes, but only four were classified as GCs, one in MTG12 metagenome (Continental Antarctica), encoding an aminoglycoside-modifying enzyme (AAC(6´)acetyltransferase) and the other three in CS1 metagenome (Maritime Antarctica). One of these genes encodes a class D β-lactamase (blaOXA-205) and the other two are located in the same contig. One is part of a gene encoding the first 76 amino acids of aminoglycoside adenyltransferase (aadA6), and the other is a qacG2 gene.

59 BASIC BIOLOGICAL SCIENCES↗

Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina

Abstract Structure‐based virtual high‐throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the ‘docking power’. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein‐ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.

Agarwal, Rupesh↗

Identifying Suitable Front Contacts for High‐Efficiency Cd(Se,Te) Solar Cells on Space‐Qualified Cover Glass

Deployment of photovoltaics in space requires devices that combine high-efficiency, low areal mass, and resilience to harsh environments. Historically, high-efficiency multijunction III–V materials have dominated space power systems; however, their high cost and limited manufacturing throughput motivate the exploration of scalable alternatives. While CdTe-based thin-film photovoltaics offer an attractive option, their performance on non-conventional substrates can suffer from front contact instability under higher-temperature processing. Here, the role of front contact chemistry in limiting cell performance is investigated using CdTe-based devices fabricated on 150 μm thick Ceria-doped space-qualified 0214 Corning glass. A matrix of four transparent conducting oxides (TCOs: CTO, AZO, ITO, IZO) combined with two n-type emitters (MZO, IGO) reveals chemical stability at the front interface—rather than absorber composition alone—governs recombination losses, voltage deficits, and device reproducibility. Chemically stable front contact combinations suppress elemental diffusion and interfacial degradation, resulting in significantly improved carrier lifetimes and junction quality. These insights are validated through record-certified Cd(Se,Te) cell efficiencies of 18.4% under AM1.5G and 16.2% under AM0 illumination on ultra-thin glass. Beyond CdTe, this work provides a general framework for the rational selection of TCO/emitter interfaces in superstrate thin-film photovoltaics, including emerging technologies like metal halide perovskites, while enabling high-efficiency, lightweight photovoltaics for space applications.

14 SOLAR ENERGY↗

Mechanically robust hydrophobized double network hydrogels and their fundamental salt transport properties

Abstract Water swollen polymer networks are attractive for applications ranging from tissue regeneration to water purification. For water purification, charged polymers provide excellent ion separation properties. However, many ion exchange membranes (IEMs) are brittle, necessitating the use of thick support materials that ultimately decrease throughput. To this end, novel double network hydrogels (DNHs) with variable water content are prepared and characterized in terms of mechanical and ion transport properties to evaluate their potential utility as tough membrane materials. The first network contains fixed anionic charges, while the other is comprised of a copolymer with varied ratios of hydrophobic ethyl acrylate (EA) and hydrophilic dimethyl acrylamide (DMA) repeat units. Characterization of freestanding DNH films reveals a reduction in water content from 88 to 53 wt% and a simultaneous increase in ultimate stress and strain by ~3.5× and ~4.5×, respectively, for 95%/5% EA/DMA, relative to 100% DMA. Fundamental salt transport properties relevant to water purification, including permeability, solubility, and diffusivity, are measured and systematically compared with conventional membrane materials to inform the development of DNHs for membrane applications. The ability to simultaneously reduce water content and increase mechanical integrity highlights the potential of DNHs as a synthetic platform for future membrane applications.

Allen, Marshall J.↗

Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel

Abstract Estimates of plant traits derived from hyperspectral reflectance data have the potential to efficiently substitute for traits, which are time or labor intensive to manually score. Typical workflows for estimating plant traits from hyperspectral reflectance data employ supervised classification models that can require substantial ground truth datasets for training. We explore the potential of an unsupervised approach, autoencoders, to extract meaningful traits from plant hyperspectral reflectance data using measurements of the reflectance of 2151 individual wavelengths of light from the leaves of maize ( Zea mays ) plants harvested from 1658 field plots in a replicated field trial. A subset of autoencoder‐derived variables exhibited significant repeatability, indicating that a substantial proportion of the total variance in these variables was explained by difference between maize genotypes, while other autoencoder variables appear to capture variation resulting from changes in leaf reflectance between different batches of data collection. Several of the repeatable latent variables were significantly correlated with other traits scored from the same maize field experiment, including one autoencoder‐derived latent variable (LV8) that predicted plant chlorophyll content modestly better than a supervised model trained on the same data. In at least one case, genome‐wide association study hits for variation in autoencoder‐derived variables were proximal to genes with known or plausible links to leaf phenotypes expected to alter hyperspectral reflectance. In aggregate, these results suggest that an unsupervised, autoencoder‐based approach can identify meaningful and genetically controlled variation in high‐dimensional, high‐throughput phenotyping data and link identified variables back to known plant traits of interest.

Tross, Michael C.↗

Spatial analysis of cell patterning to aid genetic and phenotypic understanding of grass stomatal density: A case study in maize

Biological processes involve complex hierarchies where composite traits result from multiple component traits. However, holistically understanding of how sets of component traits interact to underpin genotype-to-phenotype relationships is generally lacking. Stomatal density (SD) is a tractable model system for exploring how high-throughput phenotyping (HTP) data could be exploited by a new spatial analysis approach to better understand a developmentally and functionally important trait. SD is a composite trait, resulting from various components related to cell identity and size, which are themselves governed by a series of spatio-developmental processes. Data from 192 recombinant inbred lines of maize [Zea mays (L.)] were analyzed by a new stomatal patterning phenotype (SPP) to (1) describe the average spatial probability distribution of the nearest neighboring stomata; (2) derive a core set of component traits related to cell size, cell packing, and positional probabilities; (3) build a structural equation model of component traits underlying SD; and (4) identify stomatal patterning quantitative trait loci (QTL). The core set of SPP-derived traits explained 74% of the variation in SD. Analyzing SPP component traits allowed some loci previously identified as generic SD QTL to be recognized as specific to lateral versus longitudinal elements of stomatal patterning. Therefore, this study highlights how novel insights can be gained by decomposing a composite trait (e.g., SD) into a set of component traits that were present in HTP data but not previously exploited.

59 BASIC BIOLOGICAL SCIENCES↗

Shock Initiation Microscopy with High Time and Space Resolution

In this paper, we describe studies of shock initiation and shock-to-detonation transitions in energetic materials using a tabletop shock compression microscope with nanosecond time resolution and micrometer spatial resolution. Planar input shocks with durations of 4–20 ns are produced using 0–4.5 km/s laser-launched flyer plates. Emphasis is on measurements of temperature, velocities, pressure, and microstructure using photon Doppler velocimetry (PDV), optical pyrometry and high-speed videography. Techniques are discussed for fabricating disposable shock target arrays of tiny plastic-bonded explosives (PBX), liquid and powder explosives, and single-crystal explosives for high-throughput studies. Optical temperature measurements of shocked triaminotrinitrobenzene (TATB) are discussed. Since TATB is yellow, we developed methods to correct for the blue absorption to obtain more accurate temperatures. Hot spots in shocked polymer-encased HMX (octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine) crystals are observed in real-time, showing a hot spot produced in a collapsing void that ignites a deflagration. Despite the small dimensions of our explosive charges (typically 1 mm diameter and 250 μm length), we produced reproducible detonation states in solid and liquid explosives using short-duration shocks near the von Neumann spike (VNS) pressure. We show the VNS pressure is associated with a transition to high-efficiency gas production from the explosives. In studies of NM, prior to detonation, we see reaction originating at hot spots which coalesce to form a superdetonation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Ultrasound Characterization of Plastic Bonded Explosives With Varied Binder Content and Density

Advanced explosive formulations and methods of production require rapid characterization for both processes and materials. Here, we present results for ultrasound characterization of a plastic bonded explosive (PBX) formulation as a function of binder weight percent and pressing density using through-transmission sound speed measurements. The explosive in this study was composed of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) combined with the fluoropolymer binder Kynar Ultraflex B. Binder content ranged from 2.6 wt.% to 11.5 wt.% with associated explosive formulation densities from 1.69 g/cc to 1.89 g/cc. We find linear and nonlinear changes in longitudinal and shear sound speeds, peak frequencies, and measured elastic properties for the different PBX formulations. These measured changes can differentiate the tested formulations, highlighting the potential for ultrasound as a nondestructive characterization method for newly-formulated PBXs. We also demonstrate through-transmission measurements using different coupling media and present results from an ultrasound technique called resonant ultrasound spectroscopy (RUS). Both transmission and RUS approaches may allow for rapid and even automated characterization of PBX components suitable for high-throughput manufacturing operations.

Engineering↗

Adaptable SEC‐SAXS data collection for higher quality structure analysis in solution

Abstract The two major challenges in synchrotron size‐exclusion chromatography coupled in‐line with small‐angle x‐ray scattering (SEC‐SAXS) experiments are the overlapping peaks in the elution profile and the fouling of radiation‐damaged materials on the walls of the sample cell. In recent years, many post‐experimental analyses techniques have been developed and applied to extract scattering profiles from these problematic SEC‐SAXS data. Here, we present three modes of data collection at the BioSAXS Beamline 4–2 of the Stanford Synchrotron Radiation Lightsource (SSRL BL4‐2). The first mode, the High‐Resolution mode, enables SEC‐SAXS data collection with excellent sample separation and virtually no additional peak broadening from the UHPLC UV detector to the x‐ray position by taking advantage of the low system dispersion of the UHPLC. The small bed volume of the analytical SEC column minimizes sample dilution in the column and facilitates data collection at higher sample concentrations with excellent sample economy equal to or even less than that of the conventional equilibrium SAXS method. Radiation damage problems during SEC‐SAXS data collection are evaded by additional cleaning of the sample cell after buffer data collection and avoidance of unnecessary exposures through the use of the x‐ray shutter control options, allowing sample data collection with a clean sample cell. Therefore, accurate background subtraction can be performed at a level equivalent to the conventional equilibrium SAXS method without requiring baseline correction, thereby leading to more reliable downstream structural analysis and quicker access to new science. The two other data collection modes, the High‐Throughput mode and the Co‐Flow mode, add agility to the planning and execution of experiments to efficiently achieve the user's scientific objectives at the SSRL BL4‐2.

Matsui, Tsutomu↗

Magneto-Optical Sensing Beyond the Shot Noise Limit

Magneto-optical sensors including spin noise spectroscopies and magneto-optical Kerr effect microscopies are now ubiquitous tools for materials characterization that can provide new understanding of spin dynamics, hyperfine interactions, spin-orbit interactions, and charge-carrier g-factors. Both interferometric and intensity-difference measurements can provide photon-shot-noise-limited sensitivity, but further improvements in sensitivity with classical resources require either increased laser power that can induce unwanted heating and electronic perturbations or increased measurement times that can obscure out-of-equilibrium dynamics and slow experimental throughput. Proof-of-principle measurements have already demonstrated quantum enhanced spin noise measurements with a squeezed readout field that are likely to be critical to the nonperturbative characterization of spin excitations in quantum materials that emerge at low temperatures. Here, a truncated nonlinear interferometric readout for low-temperature magneto-optical Kerr effect and related magneto-optical microscopies that is accessible with today's quantum optical resources is proposed. 10 nrad/$\sqrt{Hz}$ sensitivity is achievable with optical power as small as 1 µW. As a result, measurements may be performed at temperatures as low as 83 mK in commercially available dilution refrigerators. This combination of high sensitivity and low operating temperature is impossible to achieve with any classical measurement. The quantum advantage for the proposed measurements persists even in the limit of large loss and small squeezing parameters.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗