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DOE OSTI2017

Identification of Hip BMD Loss and Fracture Risk Markers Through Population-Based Serum Proteomics: HIP BMD LOSS & FRACTURE RISK MARKERS BY POPULATION-BASED SERUM PROTEOMICS

Accelerated bone loss significantly increases the risk of osteoporosis and fracture. The mechanisms underlying bone loss remain incompletely understood, and there are few available biomarkers. We utilized a novel proteomics approach to identify serum peptides and proteins associated with bone loss in 1967 older men who were randomly chosen from the Osteoporotic Fracture in Men Study (MrOS study) (age ≥ 65 yrs). Men had 2-3 measures of femoral neck BMD over an average follow-up of 4.6 years. Change in BMD was estimated and then categorized into three groups: maintained BMD (n=453), expected loss (n=1185) and accelerated loss (n=237). A liquid chromatography–ion mobility separation-mass spectrometry (LC-IMS-MS) proteomics platform was used to identify and quantify peptides from serum proteins. The whole cohort was randomly divided into discovery (N= 960) and validation (N= 915) sub-cohorts. Linear regression models and a random forest approach were used to discover differentially abundant individual peptides and a proteomic signature that distinguished individuals with accelerated bone loss from those who maintained BMD. Network analyses were performed using the MetaCore knowledgebase. We identified 12 peptides that were associated with BMD loss in both discovery (P< 0.1 FDR) and replication sub-cohorts (P<0.05). Those 12 peptides mapped to the following proteins: ALS, LYVE1, RNAS1, C2, ICOSL, C163A, C7, HEMO, CD14, CERU, CRAC1 and CD59. Meta-analysis of peptidesassociated with bone loss identified 6 additional proteins including GRP78, IGF-2, SHBG, ENPP2, IBP2 and IBP6. We also identified a proteomic signature that was predictive of BMD loss with a discriminative value similar to serum bone marker carboxy-terminal collagen crosslink peptide (CTX). Interestingly, combining the proteomic signature with CTX significantly improved the ability to discriminate men with accelerated loss. In summary, we have identified potential new biomarkers for bone loss that provide a more in depth understanding of its pathophysiology.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Raman chemical imaging of the rhizosphere bacterium Pantoea sp. YR343 and its co-culture with Arabidopsis thaliana

Chemical imaging of plant-bacteria co-cultures renders it possible to characterize bacterial populations and behaviors and their interactions with proximal organisms, under conditions closest to the environment in the rhizosphere. Here Raman micro-spectroscopy and confocal Raman imaging are used as minimally invasive probes to study the rhizosphere bacterial isolate, Pantoea sp. YR343, and its co-culture with model plant Arabidopsis thaliana by combining enhanced Raman spectroscopies with electron microscopy and principal component analysis (PCA). In this work, the presence of carotenoid pigments in the wild type Pantoea sp. YR343 was characterized using resonance Raman scattering, which was also used to confirm successful disruption of the crtB gene in an engineered carotenoid mutant strain. Other components of the Pantoea sp. YR343 cells were imaged in the presence of resonantly enhanced pigments using a combination of surface enhanced Raman imaging and PCA. Pantoea sp. YR343 cells decorated with Ag colloid synthesized ex situ gave spectra dominated by carotenoid scattering, whereas colloids synthesized in situ produced spectral signatures characteristic of flavins in the cell membrane. Scanning electron microscopy (SEM) of whole cells and transmission electron microscopy (TEM) images of thinly sliced cross-sections were used to assess structural integrity of the coated cells and to establish the origin of spectral signatures based on the position of Ag nanoparticles in the cells. Finally, raman imaging was also used to characterize senescent green Arabidopsis thaliana plant roots inoculated with Pantoea sp. YR343, and PCA was used to distinguish spectral contributions from plant and bacterial cells, thereby establishing the potential of Raman imaging to visualize the distribution of rhizobacteria on plant roots.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Chemical diversity in angiosperms − monoterpene synthases control complex reactions that provide the precursors for ecologically and commercially important monoterpenoids

SUMMARY Monoterpene synthases (MTSs) catalyze the first committed step in the biosynthesis of monoterpenoids, a class of specialized metabolites with particularly high chemical diversity in angiosperms. In addition to accomplishing a rate enhancement, these enzymes manage the formation and turnover of highly reactive carbocation intermediates formed from a prenyl diphosphate substrate. At each step along the reaction path, a cationic intermediate can be subject to cyclization, migration of a proton, hydride, or alkyl group, or quenching to terminate the sequence. However, enzymatic control of ligand folding, stabilization of specific intermediates, and defined quenching chemistry can maintain the specificity for forming a signature product. This review article will discuss our current understanding of how angiosperm MTSs control the reaction environment. Such knowledge allows inferences about the origin and regulation of chemical diversity, which is pertinent for appreciating the role of monoterpenoids in plant ecology but also for aiding commercial efforts that harness the accumulation of these specialized metabolites for the food, cosmetic, and pharmaceutical industries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models

Abstract Background A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. Results Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp 614 Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro 323 Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. Conclusions These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

A robust gene expression-based prognostic risk score predicts overall survival of lung adenocarcinoma patients

Identification of reliable predictive biomarkers and new therapeutic targets is a critical step for significant improvement in patient outcomes. Here, we developed a multi-step bioinformatics analytic strategy to mine large omics and clinical data to build a prognostic scoring system for predicting the overall survival (OS) of lung adenocarcinoma (LuADC) patients. In latter we first identified 1327 significantly and robustly deregulated genes, 600 of which were significantly associated with the OS of LuADC patients. Gene co-expression network analysis revealed the biological functions of these 600 genes in normal lung and LuADCs, which were found to be enriched for cell cycle-related processes, blood vessel development, cell-matrix adhesion and metabolic processes. Finally, we implemented a multiple resampling method combined with Cox regression analysis to identify a 27-gene signature associated with OS, and then created a prognostic scoring system based on this signature. This scoring system robustly predicted OS of LuADC patients in 100 sampling test sets and was further validated in four independent LuADC cohorts. In addition, in comparison to other existing prognostic gene signatures published in the literature, our signature was significantly superior in predicting OS of LuADC patients. In summary, our multiomics and clinical data integration study created a 27-gene prognostic risk score that can predict OS of LuADC patients independent of age, gender and clinical stage. This score could guide therapeutic selection and allow stratification in clinical trials.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2002

Remote Sensing Information Science Research

This document is the final report summarizing research conducted by the Remote Sensing Research Unit, Department of Geography, University of California, Santa Barbara under National Aeronautics and Space Administration Research Grant NAG5-10457. This document describes work performed during the period of 1 March 2001 thorough 30 September 2002. This report includes a survey of research proposed and performed within RSRU and the UCSB Geography Department during the past 25 years. A broad suite of RSRU research conducted under NAG5-10457 is also described under themes of Applied Research Activities and Information Science Research. This research includes: 1. NASA ESA Research Grant Performance Metrics Reporting. 2. Global Data Set Thematic Accuracy Analysis. 3. ISCGM/Global Map Project Support. 4. Cooperative International Activities. 5. User Model Study of Global Environmental Data Sets. 6. Global Spatial Data Infrastructure. 7. CIESIN Collaboration. 8. On the Value of Coordinating Landsat Operations. 10. The California Marine Protected Areas Database: Compilation and Accuracy Issues. 11. Assessing Landslide Hazard Over a 130-Year Period for La Conchita, California Remote Sensing and Spatial Metrics for Applied Urban Area Analysis, including: (1) IKONOS Data Processing for Urban Analysis. (2) Image Segmentation and Object Oriented Classification. (3) Spectral Properties of Urban Materials. (4) Spatial Scale in Urban Mapping. (5) Variable Scale Spatial and Temporal Urban Growth Signatures. (6) Interpretation and Verification of SLEUTH Modeling Results. (7) Spatial Land Cover Pattern Analysis for Representing Urban Land Use and Socioeconomic Structures. 12. Colorado River Flood Plain Remote Sensing Study Support. 13. African Rainfall Modeling and Assessment. 14. Remote Sensing and GIS Integration.

Clarke, Keith C.↗

NASA NTRS2023

Reconfigurations in Brain Networks Upon Awakening From Slow Wave Sleep: Interventions and Implications in Neural Communication

Sleep inertia is the brief period of impaired alertness and performance experienced immediately after waking. Little is known about the neural mechanisms underlying this phenomenon. A better understanding of the neural processes during sleep inertia may offer insight into the awakening process. We observed brain activity every 15 min for 1 hr following abrupt awakening from slow wave sleep during the biological night. Using 32-channel electroencephalography, a network science approach, and a within-subject design, we evaluated power, clustering coefficient, and path length across frequency bands under both a control and a polychromatic short-wavelength-enriched light intervention condition. We found that under control conditions, the awakening brain is typified by an immediate reduction in global theta, alpha, and beta power. Simultaneously, we observed a decrease in the clustering coefficient and an increase in path length within the delta band. Exposure to light immediately after awakening ameliorated changes in clustering. Our results suggest that long-range network communication within the brain is crucial to the awakening process and that the brain may prioritize these long-range connections during this transitional state. Our study highlights a novel neurophysiological signature of the awakening brain and provides a potential mechanism by which light improves performance after waking.

EEG↗

NASA NTRS2026

A Review of Pump Package Assembly Anomalies and Demonstration to Gain Motor Controller Replacement Capability

The International Space Station (ISS) generates heat within the US modules from systems used to operate the station, maintain crew health, and conduct science experiments in the orbiting laboratory. The Internal Thermal Control System (ITCS) collects this heat in water loops and transfers it to the external ammonia system for rejection to space. The ITCS uses six Pump Package Assemblies (PPA) as the motive force to circulate the water within the Lab, Node 2, and Node 3 (Node 1 is parasitic to the Lab and Node 3 ITCS loops). In the life of ISS, 3 PPAs have had to be replaced and 2 PPAs are currently showing signs of degradation. The first PPA to fail in 2003 was due to early coolant chemistry issues; the remaining pump failures and current pump degradations are determined to be related to the Pump/Fan Motor Controller (PFMC), with their individual signatures all being unique to this point. The PFMC of one of the failed PPAs was returned and testing confirmed its sub-components to be the root cause of the PPA failure. Due to the relative size and weight of the standalone PFMC in comparison to the integrated assembly, it is desired, from a launch and on-orbit stowage perspective, to replace the PFMC component of the degraded PPA instead of the entire PPA. The PPA was not designed for this capability, so on the ground demonstrations are planned using crew tools to show that the PFMC can be replaced on-orbit while maintaining full functionality. This paper will focus on the signatures of the two most recent PPA failures and the two PPAs showing signs of degradation, in addition to presenting the findings from the PFMC demonstration effort.

Aaron Rodriguez↗

NASA NTRS2026

A Review of Pump Package Assembly Anomalies and Demonstration to Gain Motor Controller Replacement Capability

Aaron Rodriguez↗

NASA NTRS2004

Lunar and Planetary Science XXXV: Impacts on Mars and Earth

The session "Impacts on Mars and Earth" included the following reports:A Timescale for Major Events in Early Mars Crustal Evolution; Impact Craters in Arabia Terra, Mars; Ancient Giant Basin/Aquifer System in the Arabia Region, Mars; Small Crater Morphology Within Gusev Crater and Isidis Planitia: Evidence for Widespread Secondaries on Mars; Martian Surface Properties: Inferences from Resolved Differences in Crater Geometries; Asymmetric Ramparts of Secondary Craters in Cerberus, Mars: Interpretation and Implications for Local Stratigraphy; Depth to Diameter Relationships of Craters in the High Latitudes (70 -80 ) of Mars: Implications for Geologic History of Those Areas; Impact Cratering on Mars: Search for Target Influence on Morphology; Starting Conditions for Hydrothermal Systems Underneath Martian Craters: Hydrocode Modeling; Impact-induced Hydrothermal System at the Sudbury Crater: Duration, Temperatures, Mechanics, and Biological Implications; Major and Trace Element Variations in Impact Crater Clay from Chicxulub, Lonar, and Mistastin, Implications for the Martian Soil; Stable Isotopes and Hydrothermal Fluid Source in the Yaxcopoil-1 Borehole, Chicxulub Impact Structure, Mexico; and Chicxulub Impact Melts: Geochemical Signatures of Target Lithology Mixing and Post-Impact Hydrothermal Fluid Processes.

Source record↗

DOE OSTI2020

Discovery of a Nearby Young Brown Dwarf Disk

We report the discovery of the youngest brown dwarf with a disk at 102 pc from the Sun, WISEA J120037.79−784508.3 (W1200−7845), via the Disk Detective citizen science project. We establish that W1200−7845 is located in the 3.7{sub −1.4}{sup +4.6} Myr old ε Cha association. Its spectral energy distribution (SED) exhibits clear evidence of an infrared (IR) excess, indicative of the presence of a warm circumstellar disk. Modeling this warm disk, we find the data are best fit using a power-law description with a slope α = −0.94, which suggests that it is a young, Class II type disk. Using a single blackbody disk fit, we find T{sub eff,disk}=521 K and L{sub IR}/L{sub ∗}=0.14. The near-IR spectrum of W1200−7845 matches a spectral type of M6.0 γ ± 0.5, which corresponds to a low surface gravity object, and lacks distinctive signatures of strong Paβ or Brγ accretion. Both our SED fitting and spectral analysis indicate that the source is cool (T {sub eff} = 2784–2850 K), with a mass of 42–58 M {sub Jup}, well within the brown dwarf regime. The proximity of this young brown dwarf disk makes the system an ideal benchmark for investigating the formation and early evolution of brown dwarfs.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Direct Exciton Harvesting from a Bound Triplet Pair

Abstract Singlet fission is commonly defined as the generation of two triplet excitons from a single absorbed photon. However, ambiguities within this definition arise due to the complexity of the various double triplet states that exist in SF chromophores and the corresponding interconversion processes. To clarify this process, singlet fission is frequently depicted as sequential two‐step conversion in which a singlet exciton decays into a bound triplet‐pair biexciton state that dissociates into two “free” triplet excitons. However, this model discounts the potential for direct harvesting from the coupled biexciton state. Here, it is demonstrated that individual triplet excitons can be extracted directly from a bound triplet pair. It is demonstrated that due to the requirement for geminate triplet–triplet annihilation in intramolecular singlet fission compounds, unique spectral and kinetic signatures can be used to quantify triplet‐pair harvesting yields. An internal quantum efficiency for triplet exciton transfer from the triplet pair of >50%, limited only by the solubility of the compounds is achieved. The harvesting process is not dependent on the net multiplicity of the triplet‐pair state, suggesting that an explicit, independent dissociation step is not a requirement for using triplet pairs to do chemical or electrical work.

Chemistry↗

DOE OSTI2022

Proteomic Profiling of Intra-Islet Features Reveals Substructure-Specific Protein Signatures

Despite their diminutive size, islets of Langerhans play a large role in maintaining systemic energy balance in the body. New technologies have enabled us to go from studying the whole pancreas, to isolated whole islets, to partial islet sections, and now to islet substructures isolated from within the islet. Using a microfluidic nanodroplet-based proteomics platform coupled with laser capture microdissection (LCM), we present an in-depth investigation of protein profiles specific to regions within the islet. These regions studied include the vascular tissue containing interface boundary, micro-vascular tissue internal to the islet, isolated endocrine cells, islet sections with vasculature intact, and finally acinar tissue from around the islet. Unique protein signatures observed in the inner vasculature potentially indicate increased innervation and intra-islet neuron-like crosstalk compared to external vasculature. We also demonstrate the utility of these data for isolating localized structure-specific drug-target interactions using existing protein/drug binding databases.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2016

Colossal magnetic phase transition asymmetry in mesoscale FeRh stripes

Coupled order parameters in phase-transition materials can be controlled using various driving forces such as temperature, magnetic and electric field, strain, spin-polarized currents and optical pulses. Tuning the material properties to achieve efficient transitions would enable fast and low-power electronic devices. Here we show that the first-order metamagnetic phase transition in FeRh films becomes strongly asymmetric in mesoscale structures. In patterned FeRh stripes we observed pronounced supercooling and an avalanche-like abrupt transition from the ferromagnetic to the antiferromagnetic phase, while the reverse transition remains nearly continuous over a broad temperature range. Although modest asymmetry signatures have been found in FeRh films, the effect is dramatically enhanced at the mesoscale. The activation volume of the antiferromagnetic phase is more than two orders of magnitude larger than typical magnetic heterogeneities observed in films. Finally, the collective behaviour upon cooling results from the role of long-range ferromagnetic exchange correlations that become important at the mesoscale and should be a general property of first-order metamagnetic phase transitions.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Spectroscopic analysis reveals that soil phosphorus availability and plant allocation strategies impact feedstock quality of nutrient-limited switchgrass

Abstract The perennial native switchgrass adapts better than other plant species do to marginal soils with low plant-available nutrients, including those with low phosphorus (P) content. Switchgrass roots and their associated microorganisms can alter the pools of available P throughout the whole soil profile making predictions of P availability in situ challenging. Plant P homeostasis makes monitoring of P limitation via measurements of plant P content alone difficult to interpret. To address these challenges, we developed a machine-learning model trained with high accuracy using the leaf tissue chemical profile, rather than P content. By applying this learned model in field trials across two sites with contrasting extractable soil P, we observed that actual plant available P in soil was more similar than expected, suggesting that adaptations occurred to alleviate the apparent P constraint. These adaptations come at a metabolic cost to the plant that have consequences for feedstock chemical components and quality. We observed that other biochemical signatures of P limitation, such as decreased cellulose-to-lignin ratios, were apparent, indicating re-allocation of carbon resources may have contributed to increased P acquisition. Plant P allocation strategies also differed across sites, and these differences were correlated with the subsequent year’s biomass yields.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Magnetism in Mn-nanowires and -clusters as δ-doped layers in group IV semiconductors (Si, Ge)

Mn doping of group-IV semiconductors (Si/Ge) is achieved by embedding nanostructured Mn-layers in group-IV matrix. The Mn-nanostructures are monoatomic Mn-wires or Mn-clusters and capped with an amorphous Si or Ge layer. The precise fabrication of δ-doped Mn-layers is combined with element-specific detection of the magnetic signature with x-ray magnetic circular dichroism. The largest moment (2.5 μ B /Mn) is measured for Mn-wires with ionic bonding character and a-Ge overlayer cap; a-Si capping reduces the moment due to variations of bonding in agreement with theoretical predictions. The moments in δ-doped layers dominated by clusters is quenched with an antiferromagnetic component from Mn–Mn bonding.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Embrace the darkness: An experimental perspective on organic exciton–polaritons

Organic polaritonics has emerged as a captivating interdisciplinary field that marries the complexities of organic photophysics with the fundamental principles of quantum optics. By harnessing strong light–matter coupling in organic materials, exciton–polaritons offer unique opportunities for advanced device performance, including enhanced energy transport and low-threshold lasing, as well as new functionalities like polariton chemistry. In this review, we delve into the foundational principles of exciton–polaritons from an experimental perspective, highlighting the key states, processes, and timescales that govern polariton phenomena. Our review centers on the spectroscopy of exciton–polaritons. We overview the primary spectroscopic approaches that reveal polariton phenomena, and we discuss the challenges in disentangling polaritonic signatures from spectral artifacts. We discuss how organic materials, due to their complex photophysics and disordered nature, not only present challenges to the conventional polariton models but also provide opportunities for new physics, like manipulating dark electronic states. As the research field continues to grow, with increasingly complex materials and devices, this review serves as a valuable introductory guide for researchers navigating the intricate landscape of organic polaritonics.

36 MATERIALS SCIENCE↗

DOE OSTI2024

HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies

Changing the course of the human immunodeficiency virus type I (HIV-1) pandemic is a high public health priority with approximately 39 million people currently living with HIV-1 (PLWH) and about 1.5 million new infections annually worldwide. Broadly neutralizing antibodies (bnAbs) typically target highly conserved sites on the HIV-1 envelope glycoproteins (Envs), which mediate viral entry, and block the infection of diverse HIV-1 strains. But different mechanisms of HIV-1 resistance to bnAbs prevent robust application of bnAbs for therapeutic and preventive interventions. Here we report the development of a new database that provides data and computational tools to aid the discovery of resistant features and may assist in analysis of HIV-1 resistance to bnAbs. Bioinformatic tools allow identification of specific patterns in Env sequences of resistant strains and development of strategies to elucidate the mechanisms of HIV-1 escape; comparison of resistant and sensitive HIV-1 strains for each bnAb; identification of resistance and sensitivity signatures associated with specific bnAbs or groups of bnAbs; and visualization of antibody pairs on cross-sensitivity plots. The database has been designed with a particular focus on user-friendly and interactive interface. Our database is a valuable resource for the scientific community and provides opportunities to investigate patterns of HIV-1 resistance and to develop new approaches aimed to overcome HIV-1 resistance to bnAbs.

60 APPLIED LIFE SCIENCES↗