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At least 991 records · Page 55
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Grandparent Inference from Genetic Data: The Potential for Parentage-Based Tagging Programs to Identify Offspring of Hatchery Strays

Abstract Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent–grandchild trios by using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false-positive and false-negative error rates and showed that genetic panels containing 500–700 single-nucleotide polymorphisms or 200–300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

Delomas, Thomas A. (ORCID:000000015154759X)↗
DOE OSTI2026

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↗
DOE OSTI2020

Voxel carving–based 3D reconstruction of sorghum identifies genetic determinants of light interception efficiency

Changes in canopy architecture traits have been shown to contribute to yield increases. Optimizing both light interception and light interception efficiency of agricultural crop canopies will be essential to meeting the growing food needs. Canopy architecture is inherently three-dimensional (3D), but many approaches to measuring canopy architecture component traits treat the canopy as a two-dimensional (2D) structure to make large scale measurement, selective breeding, and gene identification logistically feasible. We develop a high throughput voxel carving strategy to reconstruct 3D representations of sorghum from a small number of RGB photos. Our approach builds on the voxel carving algorithm to allow for fully automatic reconstruction of hundreds of plants. It was employed to generate 3D reconstructions of individual plants within a sorghum association population at the late vegetative stage of development. Light interception parameters estimated from these reconstructions enabled the identification of known and previously unreported loci controlling light interception efficiency in sorghum. The approach is generalizable and scalable, and it enables 3D reconstructions from existing plant high throughput phenotyping datasets. We also propose a set of best practices to increase 3D reconstructions’ accuracy.

3D plant reconstruction↗
DOE OSTI2023

A cellular selection identifies elongated flavodoxins that support electron transfer to sulfite reductase

Flavodoxins (Flds) mediate the flux of electrons between oxidoreductases in diverse metabolic pathways. To investigate whether Flds can support electron transfer to a sulfite reductase (SIR) that evolved to couple with a ferredoxin, we evaluated the ability of Flds to transfer electrons from a ferredoxin-NADP reductase (FNR) to a ferredoxin-dependent SIR using growth complementation of an Escherichia coli strain with a sulfur metabolism defect. We show that Flds from cyanobacteria complement this growth defect when coexpressed with an FNR and an SIR that evolved to couple with a plant ferredoxin. When we evaluated the effect of peptide insertion on Fld-mediated electron transfer, we observed a sensitivity to insertions within regions predicted to be proximal to the cofactor and partner binding sites, while a high insertion tolerance was detected within loops distal from the cofactor and within regions of helices and sheets that are proximal to those loops. Bioinformatic analysis showed that natural Fld sequence variability predicts a large fraction of the motifs that tolerate insertion of the octapeptide SGRPGSLS. In conclusion, these results represent the first evidence that Flds can support electron transfer to assimilatory SIRs, and they suggest that the pattern of insertion tolerance is influenced by interactions with oxidoreductase partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Identifying apparent local stable isotope equilibrium in a complex non-equilibrium system

Although being out of equilibrium, biomolecules in organisms have the potential to approach isotope equilibrium locally because enzymatic reactions are intrinsically reversible. A rigorous approach that can describe isotope distribution among biomolecules and their apparent deviation from equilibrium state is lacking, however. Applying the concept of distance matrix in graph theory, we propose that apparent local isotope equilibrium among a subset of biomolecules can be assessed using an apparent fractionation difference (|Δα|) matrix, in which the differences between the observed isotope composition (δ') and the calculated equilibrium fractionation factor (1000lnβ) can be more rigorously evaluated than by using a previous approach for multiple biomolecules. We tested our |Δα| matrix approach by re-analyzing published data of different amino acids (AAs) in potato and in green alga. Our re-analysis shows that biosynthesis pathways could be the reason for an apparently close-to-equilibrium relationship inside AA families in potato leaves. Different biosynthesis/degradation pathways in tubers may have led to the observed isotope distribution difference between potato leaves and tubers. The analysis of data from green algae does not support the conclusion that AAs are further from equilibrium in glucose-cultured green algae than in the autotrophic ones. Application of the |Δα| matrix can help us to locate potential reversible reactions or reaction networks in a complex system such as a metabolic system. The same approach can be broadly applied to all complex systems that have multiple components, e.g. geochemical or atmospheric systems of early Earth or other planets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identifying build orientation of 3D-printed materials using convolutional neural networks

The advent of additive manufacturing (AM) processes brought with it intense research into various materials and manufacturing processes. At the same time, the need for validation of material properties, as well as study and forecasting of aging, has arisen. Modern imaging techniques, like X-ray computed tomography (XCT), are a convenient vehicle for such studies; however, the large datasets they produce require novel analysis techniques to efficiently extract critical information. Here, we present our work on developing a 3D extension of the ResNet architecture to distinguish between two build orientations of tensile bars produced by AM. Using only information from XCT, our method achieves a 99.3% correct classification at a misidentification of 1%.

36 MATERIALS SCIENCE↗
DOE OSTI2018

An overview of methods to identify and manage uncertainty for modelling problems in the water-environment-agriculture cross-sector

Uncertainty pervades the representation of systems in the water–environment–agriculture cross-sector. Successful methods to address uncertainties have largely focused on standard mathematical formulations of biophysical processes in a single sector, such as partial or ordinary differential equations. More attention to integrated models of such systems is warranted. Model components representing the different sectors of an integrated model can have less standard, and different, formulations to one another, as well as different levels of epistemic knowledge and data informativeness. Thus, uncertainty is not only pervasive but also crosses boundaries and propagates between system components. Uncertainty assessment (UA) cries out for more eclectic treatment in these circumstances, some of it being more qualitative and empirical. Here in this paper, we discuss the various sources of uncertainty in such a cross-sectoral setting and ways to assess and manage them. We have outlined a fast-growing set of methodologies, particularly in the computational mathematics literature on uncertainty quantification (UQ), that seem highly pertinent for uncertainty assessment. There appears to be considerable scope for advancing UA by integrating relevant UQ techniques into cross-sectoral problem applications. Of course this will entail considerable collaboration between domain specialists who often take first ownership of the problem and computational methods experts.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

How to identify different new neutrino oscillation physics scenarios at DUNE

Next generation neutrino oscillation experiments are expected to measure the remaining oscillation parameters with very good precision. They will have unprecedented capabilities to search for new physics that modify oscillations. DUNE, with its broad band beam, good particle identification, and relatively high energies will provide an excellent environment to search for new physics. If deviations from the standard three-flavor oscillation picture are seen however, it is crucial to know which new physics scenario is found so that it can be verified elsewhere and theoretically understood. We investigate several benchmark new physics scenarios by looking at existing long-baseline accelerator neutrino data from NOvA and T2K and determine at what sensitivity DUNE can differentiate among them. We consider sterile neutrinos and both vector and scalar non-standard neutrino interactions, all with new complex phases, the latter of which could conceivably provide absolute neutrino mass scale information. We find that, in many interesting cases, DUNE will have good model discrimination. We also perform a new fit to NOvA and T2K data with scalar NSI.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2018

Anisotropic flow of identified particles in Pb-Pb collisions at $ {\sqrt{s}}_{\mathrm{NN}}=5.02 $ TeV

The elliptic (v 2 ), triangular (v 3 ), and quadrangular (v 4 ) flow coefficients of π ± , K ± , p+$ \overline{p}\ $,Λ+$ \overline{Λ}\ $,K S 0 , and the Φ-meson are measured in Pb-Pb collisions at $ {\sqrt{s}}_{\mathrm{NN}}=5.02 $ TeV. Results obtained with the scalar product method are reported for the rapidity range |y| < 0.5 as a function of transverse momentum, p T , at different collision centrality intervals between 0–70%, including ultra-central (0–1%) collisions for π ± , K ± , and p + $ \overline{p}\ $. For p T < 3 GeV/c, the flow coefficients exhibit a particle mass dependence. At intermediate transverse momenta (3 < p T < 8–10 GeV/c), particles show an approximate grouping according to their type (i.e., mesons and baryons). The Φ-meson v 2 , which tests both particle mass dependence and type scaling, follows p + $ \overline{p}\ $ v 2 at low p T and π ± v 2 at intermediate p T . The evolution of the shape of v n (p T ) as a function of centrality and harmonic number n is studied for the various particle species. Flow coefficients of π ± , K ± , and p + $ \overline{p}\ $ for p T < 3 GeV/c are compared to iEBE-VISHNU and MUSIC hydrodynamical calculations coupled to a hadronic cascade model (UrQMD). The iEBE-VISHNU calculations describe the results fairly well for p T < 2.5 GeV/c, while MUSIC calculations reproduce the measurements for p T < 1 GeV/c. A comparison to v n coefficients measured in Pb-Pb collisions at $ {\sqrt{s}}_{\mathrm{NN}}=2.76 $ TeV is also provided. [Figure not available: see fulltext.].

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Anisotropic flow of identified hadrons in $\mathrm{X}$e-$\mathrm{X}$e collisions at $\sqrt{s_{NN}}$ = 5.44 $\mathrm{T}$e$\mathrm{V}$

Measurements of elliptic (v 2 ) and triangular (v 3 ) flow coefficients of π ± , K ± , $p+\bar{p}$, $K$$^{0}_{S}$, and $Λ+\bar{Λ}$ obtained with the scalar product method in Xe-Xe collisions at $\sqrt{s_{NN}}$ = 5.44 TeV are presented. The results are obtained in the rapidity range |y| < 0.5 and reported as a function of transverse momentum, p T , for several collision centrality classes. The flow coefficients exhibit a particle mass dependence for p T < 3 GeV/c, while a grouping according to particle type (i.e., meson and baryon) is found at intermediate transverse momenta (3 < p T < 8 GeV/c). The magnitude of the baryon v 2 is larger than that of mesons up to p T = 6 GeV/c. The centrality dependence of the shape evolution of the p T -differential v 2 is studied for the various hadron species. The v 2 coefficients of π ± , K ± , and $p+\bar{p}$ are reproduced by MUSIC hydrodynamic calculations coupled to a hadronic cascade model (UrQMD) for p T < 1 GeV/c. A comparison with v n measurements in the corresponding centrality intervals in Pb-Pb collisions at $\sqrt{s_{NN}}$ = 5.02 TeV yields an enhanced v 2 in central collisions and diminished value in semicentral collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Comprehensive characterization of hepatocyte-derived extracellular vesicles identifies direct miRNA-based regulation of hepatic stellate cells and DAMP-based hepatic macrophage IL-1ß and IL-17 upregulation in alcoholic hepatitis mice.

Extracellular vesicles (EVs) have been growingly recognized as biomarkers and mediators of alcoholic liver disease (ALD) in human and mice. Here we characterized hepatocyte-derived EVs (HC-EVs) and their cargo for their biological functions in a novel murine model that closely resembles liver pathology observed in patients with alcoholic hepatitis (AH), the most severe spectrum of ALD. The number of circulating EVs and HC-EVs were significantly increased by 10-fold in AH mice compared to control mice. The miRNA(miR)-seq analysis detected 20 up-regulated and 4 down-regulated miRNAs (P < 0.001-0.05) in AH-HC-EVs. Treatment of murine primary hepatic stellate cells (HSCs) with AH-HC-EVs induced ?-SMA (P < 0.05) and Col1a1 (P < 0.001). Smad7, Nr1d2, and Rora genes which regulate HSC activation were predicted targets of 17 miRs up-regulated in AH-HC-EVs. Among them were miR-27a and miR-181 which upon transfection in HSCs, repressed Nr1d2, the HSC quiescence marker. AH-HC-EVs were also enriched in organelle proteins and mitochondrial DNA (10-fold, P < 0.05) and upregulated IL-1??and IL-17 production by hepatic macrophages (HMs) from AH mice in a TLR9-dependent manner. These results demonstrate HC-EV release is intensified in AH and suggest that AH-HC-EVs orchestrate liver fibrogenesis by directly targeting HSC quiescence transcripts via a unique set of miRNAs and by amplifying HSC activation via DAMP-based induction of profibrogenic IL-1? and IL-17 by HMs.

AH, hepatocyte-derived EVs, miRNAs, DAMPs, HSC act↗
DOE OSTI2018

Breaking the curse of dimensionality to identify causal variants in Breeding 4

In the past, plant breeding has undergone three major transformations and is currently transitioning to a new technological phase, Breeding 4. This phase is characterized by the development of methods for biological design of plant varieties, including transformation and gene editing techniques directed toward causal loci. The application of such technologies will require to reliably estimate the effect of loci in plant genomes by avoiding the situation where the number of loci assayed ($p$) surpasses the number of plant genotypes (n). Here, we discuss approaches to avoid this curse of dimensionality ($n\ll p$), which will involve analyzing intermediate phenotypes such as molecular traits and component traits related to plant morphology or physiology. Because these approaches will rely on novel data types such as DNA sequences and high-throughput phenotyping images, Breeding 4 will call for analyses that are complementary to traditional quantitative genetic studies, being based on machine learning techniques which make efficient use of sequence and image data. In this article, we will present some of these techniques and their application for prioritizing causal loci and developing improved varieties in Breeding 4.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Low Cerebral Blood Volume Identifies Poor Outcome in Stent Retriever Thrombectomy

BackgroundMechanical thrombectomy (MT) is an efficient treatment of acute stroke caused by large-vessel occlusion. We evaluated the factors predicting poor clinical outcome (3-month modified Rankin Scale, mRS >2) although MT performed with modern stent retrievers.MethodsWe prospectively collected the clinical and imaging data of 105 consecutive anterior circulation stroke patients who underwent MT after multimodal CT imaging. Patients with occlusion of the internal carotid artery and/or middle cerebral artery up to the M2 segment were included. We recorded baseline clinical, procedural and imaging variables, technical outcome, 24-h imaging outcome and the clinical outcome. Differences between the groups were studied with appropriate statistical tests and binary logistic regression analysis.ResultsLow cerebral blood volume Alberta stroke program early CT score (CBV-ASPECTS) was associated with poor clinical outcome (median 7 vs. 9, p = 0.01). Lower collateral score (CS) significantly predicted poor outcome in regression modelling with CS = 0 increasing the odds of poor outcome 4.4-fold compared to CS = 3 (95% CI 1.27–15.5, p = 0.02). Lower CBV-ASPECTS significantly predicted poor clinical outcome among those with moderate or severe stroke (OR 0.82, 95% CI 0.68–1, p = 0.05) or poor collateral circulation (CS 0–1, OR 0.66, 95% CI 0.48–0.90, p = 0.009) but not among those with mild strokes or good collaterals.ConclusionsCBV-ASPECTS estimating infarct core is a significant predictor of poor clinical outcome among anterior circulation stroke patients treated with MT, especially in the setting of poor collateral circulation and/or moderate or severe stroke.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2017

A groundwater salinity hotspot and its connection to an intermittent stream identified by environmental tracers (Mt Lofty Ranges, South Australia)

High and variable levels of salinity were investigated in an intermittent stream in a high-rainfall area (∼800 mm/year) of the Mt. Lofty Ranges of South Australia. The groundwater system was found to have a local, upslope saline lens, referred to here as a groundwater salinity ‘hotspot’. Environmental tracer analyses (δ{sup 18}O, δ{sup 2}H, {sup 87/86}Sr, and major elements) of water from the intermittent stream, a nearby permanent stream, shallow and deep groundwater, and soil-water/runoff demonstrate seasonal groundwater input of very saline composition into the intermittent stream. This input results in large salinity increases of the stream water because the winter wet-season stream flow decreases during spring in this Mediterranean climate. Furthermore, strontium and water isotope analyses demonstrate: (1) the upslope-saline-groundwater zone (hotspot) mixes with the dominant groundwater system, (2) the intermittent-stream water is a mixture of soil-water/runoff and the upslope saline groundwater, and (3) the upslope-saline-groundwater zone results from the flushing of unsaturated-zone salts from the thick clayey regolith and soil which overlie the metamorphosed shale bedrock. The preferred theory on the origin of the upslope-saline-groundwater hotspot is land clearing of native deep-rooted woodland, followed by flushing of accumulated salts from the unsaturated zone due to increased recharge. This cause of elevated groundwater and surface-water salinity, if correct, could be widespread in Mt. Lofty Ranges areas, as well as other climatically and geologically similar areas with comparable hydrogeologic conditions.

58 GEOSCIENCES↗