Deep learning for identifying personal and family history of suicidal thoughts and behaviors from EHRs
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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning
Agricultural practices affect soil microbes which are critical to soil health and sustainable agriculture. To understand prokaryotic and fungal assembly under agricultural practices, we use machine learning-based methods. We show that fertility source is the most pronounced factor for microbial assembly especially for fungi, and its effect decreases with soil depths. Fertility source also shapes microbial co-occurrence patterns revealed by machine learning, leading to fungi-dominated modules sensitive to fertility down to 30 cm depth. Tillage affects soil microbiomes at 0-20 cm depth, enhancing dispersal and stochastic processes but potentially jeopardizing microbial interactions. Cover crop effects are less pronounced and lack depth-dependent patterns. Machine learning reveals that the impact of agricultural practices on microbial communities is multifaceted and highlights the role of fertility source over the soil depth. Machine learning overcomes the linear limitations of traditional methods and offers enhanced insights into the mechanisms underlying microbial assembly and distributions in agriculture soils.
60 APPLIED LIFE SCIENCES↗
Targeted proteomic assays for quantitation of proteins identified by proteogenomic analysis of ovarian cancer
Here, mass spectrometry (MS) based targeted proteomic methods such as selected reaction monitoring (SRM) are becoming the method of choice for preclinical verification of candidate protein biomarkers. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute has investigated the standardization and analytical validation of the SRM assays and demonstrated robust analytical performance on different instruments across different laboratories. An Assay Portal has also been established by CPTAC to provide the research community a resource consisting of large set of targeted MS-based assays, and a depository to share assays publicly, providing that assays meet the guidelines proposed by CPTAC. Herein, we report 98 SRM assays covering 70 candidate protein biomarkers previously reported as associated with ovarian cancer that have been thoroughly characterized according to the CPTAC Assay Characterization Guidance Document. The experiments, methods and results for characterizing these SRM assays for their MS response, repeatability, selectivity, stability, and reproducible detection of endogenous analytes are described in detail.
60 APPLIED LIFE SCIENCES↗
Identifying Cu( ii )–amyloid peptide binding intermediates in the early stages of aggregation by resonance Raman spectroscopy: a simulation study
The aggregation of amyloid beta (Aβ) peptides plays a crucial role in the pathology and etiology of Alzheimer's disease. Experimental evidence shows that copper ion is an aggregation-prone species with the ability to coordinately bind to Aβ and further induce the formation of neurotoxic Aβ oligomers. However, the detailed structures of Cu(II)–Aβ complexes have not been illustrated, and the kinetics and dynamics of the Cu(II) binding are not well understood. Two Cu(II)–Aβ complexes have been proposed to exist under physiological conditions, and another two might exist at higher pH values. By using ab initio simulations for the spontaneous resonance Raman and time domain stimulated resonance Raman spectroscopy signals, we obtained the characteristic Raman vibronic features of each complex. Finally, these signals contain rich structural information with high temporal resolution, enabling the characterization of transient states during the fast Cu–Aβ binding and interconversion processes.
59 BASIC BIOLOGICAL SCIENCES↗
Towards identifying the active sites on RuO 2 (110) in catalyzing oxygen evolution
While the surface atomic structure of RuO 2 has been well studied in ultra high vacuum, much less is known about the interaction between water and RuO 2 in aqueous solution. In this work, in situ surface X-ray scattering measurements combined with density functional theory (DFT) were used to determine the surface structural changes on single-crystal RuO2(110) as a function of potential in acidic electrolyte. The redox peaks at 0.7, 1.1 and 1.4 V vs. reversible hydrogen electrode (RHE) could be attributed to surface transitions associated with the successive deprotonation of –H 2 O on the coordinatively unsaturated Ru sites (CUS) and hydrogen adsorbed to the bridging oxygen sites. At potentials relevant to the oxygen evolution reaction (OER), an –OO species on the Ru CUS sites was detected, which was stabilized by a neighboring –OH group on the Ru CUS or bridge site. Combining potential-dependent surface structures with their energetics from DFT led to a new OER pathway, where the deprotonation of the –OH group used to stabilize –OO was found to be rate-limiting.
36 MATERIALS SCIENCE↗
Identifying the first folded alkylbenzene via ultraviolet, infrared, and Raman spectroscopy of pentylbenzene through decylbenzene
The conformational preferences of pentyl- through decylbenzene are studied under jet-cooled conditions in the gas phase. Laser-induced fluorescence excitation spectra, fluorescence-dip infrared spectra in the alkyl CH stretch region, and Raman spectra are combined to provide assignments for the observed conformers. Density functional theory calculations at the B3LYP-D3BJ/def2TZVP level of theory provide relative energies and normal mode vibrations that serve as inputs for an anharmonic local mode theory introduced in earlier work on alkylbenzenes with n = 2–4. This model explicitly includes anharmonic mixing of the CH stretch modes with the overtones of scissors/bend modes of the CH 2 and CH 3 groups in the alkyl chain, and is used to assign and interpret the single-conformation IR spectra. In octylbenzene, a pair of LIF transitions shifted -92 and -78 cm -1 from the all-trans electronic origin have unique alkyl CH stretch transitions that are fit by the local model to a g1g3g4 conformation in which the alkyl chain folds back over the aromatic ring π cloud. Its calculated energy is only 1.0 kJ mol -1 above the all-trans global minimum. This fold is at an alkyl chain length less than half that of the pure alkanes (n = 18), consistent with a smaller energy cost for the g1 dihedral and the increased dispersive interaction of the chain with the π cloud. Local site frequencies for the entire set of conformers from the local mode model show ‘edge effects’ that raise the site frequencies of CH 2 (1) and CH 2 (2) due to the phenyl ring and CH 2 (n - 1) due to the methyl group. The g1g3g4 conformer also shows local sites shifted up in frequency at CH 2 (3) and CH 2 (6) due to interaction with the π cloud.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Identifying key descriptors in surface binding: interplay of surface anchoring and intermolecular interactions for carboxylates on Au(110)
The relative stability of carboxylates on Au(110) was investigated as part of a comprehensive study of adsorbate binding on Group IB metals that can be used to predict and understand how to control reactivity in heterogeneous catalysis.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Identifying the chemical and structural irreversibility in LiNi 0.8 Co 0.15 Al 0.05 O 2 – a model compound for classical layered intercalation
In this work, we extracted 95% of the electrochemically available Li from LiNi 0.8 Co 0.15 Al 0.05 O 2 (NCA) by galvanostatically charging the NCA/MCMB full cell to 4.7 V. Joint powder X-ray and neutron diffraction (XRD & ND) studies were undertaken for NCA at highly charged states at the first cycle, and discharged states at different cycles. The results indicate that the bulk structure of NCA maintains the O3 structure up to the extraction of 0.90 Li per formula unit. In addition, we found that the transition metal layer becomes more disordered along the c-axis than along the a- and b-axes upon charging. This anisotropic disorder starts to develop no later than 4.3 V on charge and continues to grow until the end of charge. As Li is re-inserted during discharge, the structure that resembles the pristine NCA is recovered. The irreversible loss of Li and the migration of Ni to the Li layer have been quantified by the joint XRD and ND refinement and the results were further verified by solid state 7 Li NMR and magnetic measurements. Thus, our work clearly demonstrates that the NCA bulk retains a robust, single phase O3 structure throughout the wide delithiation range (up to 0.9 Li per formula unit of NCA) and is suitable for higher energy density usage with proper modifications.
25 ENERGY STORAGE↗
Identifying the acceptor state in NiO hole collection layers: direct observation of exciton dissociation and interfacial hole transfer across a Fe 2 O 3 /NiO heterojunction
NiO is widely utilized as a hole transport layer in solar energy devices where light absorption in a photoactive layer is followed by charge separation and hole injection into a NiO collection layer. Due to the complex electronic structure of the hybridized valence band in NiO, the chemical nature of the hole acceptor state has remained an open question, despite the fact that hole localization in this material significantly influences device efficiency. To comment on this, we present results of ultrafast charge carrier dynamics in a NiO based model heterojunction (Fe 2 O 3 /NiO) using extreme ultraviolet reflection–absorption (XUV-RA) spectroscopy. Element specific XUV-RA spectroscopy demonstrates the formation of transient Ni 3+ within 10 ps following selective photoexcitation of the underlying Fe 2 O 3 substrate. This indicates that hole transfer in this system occurs to NiO valence band states composed of significant Ni 3d character. Additionally, we show that this hole injection process proceeds via a two-step sequential mechanism where fast, field-driven exciton dissociation occurs in Fe 2 O 3 in 680 ± 60 fs, followed by subsequent hole injection to NiO in 9.2 ± 2.9 ps. Furthermore, these results reveal the chemical nature of the hole acceptor state in widely used NiO hole transport layers and provides a direct observation of exciton dissociation and interfacial hole transfer in this model system.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Can machine learning identify the next high-temperature superconductor? Examining extrapolation performance for materials discovery
Traditional machine learning (ML) metrics overestimate model performance for materials discovery.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Vibrational energy redistribution during donor–acceptor electronic energy transfer: criteria to identify subsets of active normal modes
Photoinduced electronic energy transfer in conjugated donor–acceptor systems is naturally accompanied by intramolecular vibrational energy redistributions accepting an excess of electronic energy.
Alfonso-Hernandez, L.↗
High-temperature decomposition of Cu 2 BaSnS 4 with Sn loss reveals newly identified compound Cu 2 Ba 3 Sn 2 S 8
The decomposition mechanism of Cu 2 BaSnS 4 is studied by in situ diffraction and fluorescence analysis revealing “Sn loss” and Cu 2 Ba 3 Sn 2 S 8 at high temperatures.
36 MATERIALS SCIENCE↗
Development of a PFAS reaction library: identifying plausible transformation pathways in environmental and biological systems
We have developed reaction libraries for predicting transformation products of PFAS in a variety of environmental and biological reaction systems.
Chemistry↗
Identifying hydroxylated copper dimers in SSZ-13 via UV-vis-NIR spectroscopy
Cu-Exchanged zeolites are promising materials for the selective conversion of methane to methanol. Their activity is attributed to the presence of small Cu-oxo and Cu-hydroxy clusters, but the nature of active centers in various zeolite structures is still under debate. In this contribution, we combine time dependent density functional theory with spin–orbit coupling to predict the optical spectra of various Cu monomers and dimers in SSZ-13. As a result, we furthermore compare theoretical results to experimental measurements and find that the presence of Cu-hydroxy dimers and Cu monomers could potentially explain the experimentally observed UV-vis-NIR spectra.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High-voltage deprotonation of layered-type materials as a newly identified cause of electrode degradation
Herein, we report the transition metal dependent deprotonation of layered type materials during their high voltage (>4.5 V vs. Li/Li + ) operation as a potential degradation cause in an electrochemical system.
25 ENERGY STORAGE↗
Identifying biochemical constituents involved in the mycosynthesis of zinc oxide nanoparticles
Filamentous fungi are known to secrete biochemicals that drive the synthesis of nanoparticles (NPs) that vary in composition, size, and shape; a process deemed mycosynthesis. Following the introduction of precursor salts directly to the fungal mycelia or their exudates, mycosynthesis proceeds at ambient temperature and pressure, and near neutral pH, presenting significant energy and cost savings over traditional chemical or physical approaches. The mycosynthesis of zinc oxide (ZnO) NPs by various fungi exhibited a species dependent morphological preference for the resulting NPs, suggesting that key differences in the biochemical makeup of their individual exudates may regulate the controlled nucleation and growth of these different morphologies. Metabolomics and proteomics of the various fungal exudates suggest that metal chelators, such as hexamethylenetetramine, present in high concentrations in exudates of Aspergillus versicolor are critical for the production dense, well-formed, spheroid nanoparticles. Further, the results also corroborate that the proteinaceous material in the production of ZnO NPs serves as a surface modifier, or protein corona, preventing excessive coagulation of the NPs. Collectively, these findings suggest that NP morphology is regulated by the small molecule metabolites, and not proteins, present in fungal exudates, establishing a deeper understanding of the factors and mechanism underlying mycosynthesis of NPs.
59 BASIC BIOLOGICAL SCIENCES↗
Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity
Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Distribution system versus bulk power system: identifying the source of electric service interruptions in the US
This study reports on the results from efforts by the Institute of Electric and Electronics Engineers (IEEE) Distribution Reliability Working Group (DRWG) and the U.S. Energy Information Administration (EIA) to improve the usefulness of reliability metrics by developing and then applying consistent, yet distinct measures of the continuity of supply based on the portion of the electric power system from which power interruptions originate: the lower voltage distribution system versus the high‐voltage bulk power system. The modified metrics better support reliability planning in the US because they separately measure the effectiveness of actions to improve reliability made by the two distinct groups of firms (and their regulators or oversight bodies) that are responsible for planning and operating each portion of the US electric power system. The authors then present for the first time quantitative information on the reliability of each portion of the US electric power system. When reliability is measured using the system average interruption duration index and the system average interruption frequency index, they find that the distribution system accounts for at least 94 and 92%, respectively, of all interruptions. They also find that these relationships have been stable over the recent past.
24 POWER TRANSMISSION AND DISTRIBUTION↗