Search NASA⌕ Search

SEARCH · Search NASA

Results for “Score function”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5

Gray matter volume drives the brain age gap in schizophrenia: a SHAP study

Neuroimaging-based brain age is a biomarker that is generated by machine learning (ML) predictions. The brain age gap (BAG) is typically defined as the difference between the predicted brain age and chronological age. Studies have consistently reported a positive BAG in individuals with schizophrenia (SCZ). However, there is little understanding of which specific factors drive the ML-based brain age predictions, leading to limited biological interpretations of the BAG. We gathered data from three publicly available databases - COBRE, MCIC, and UCLA - and an additional dataset (TOPSY) of early-stage schizophrenia (82.5% untreated first-episode sample) and calculated brain age with pre-trained gradient-boosted trees. Then, we applied SHapley Additive Explanations (SHAP) to identify which brain features influence brain age predictions. We investigated the interaction between the SHAP score for each feature and group as a function of the BAG. These analyses identified total gray matter volume (group × SHAP interaction term β = 1.71 [0.53; 3.23]; p corr < 0.03) as the feature that influences the BAG observed in SCZ among the brain features that are most predictive of brain age. Other brain features also presented differences in SHAP values between SCZ and HC, but they were not significantly associated with the BAG. We compared the findings with a non-psychotic depression dataset (CAN-BIND), where the interaction was not significant. This study has important implications for the understanding of brain age prediction models and the BAG in SCZ and, potentially, in other psychiatric disorders.

60 APPLIED LIFE SCIENCES↗

Consequence-driven cyber-informed engineering and related systems and methods

Embodiments of the disclosure relate to a computer-implemented consequence-driven cyber-informed engineering tool for performing and reporting consequence-based prioritization, system-of-systems breakdown, consequence-based targeting, and mitigations and protections. Embodiments of a CCE tool may perform one or more steps of defining a target industrial control system (ICS), wherein the target ICS includes operational goals, critical functions, and critical services; determining one or more scored high consequence events (HCE) associated with the defined target ICS; prioritizing the scored HCEs according to an HCE severity index; and updating a dashboard with one or more representations of the prioritized HCEs, wherein the updated dashboard is associated with the CCE tool and presented at a display.

Assante, Michael↗

Designing optimal core–shell MOFs for direct air capture

Metal–organic frameworks (MOFs), along with other novel adsorbents, are frequently proposed as candidate materials to selectively adsorb CO 2 for carbon capture processes. However, adsorbents designed to strongly bind CO 2 nearly always bind H 2 O strongly (sometimes even more so). Given that water is present in significant quantities in the inlet streams of most carbon capture processes, a method that avoids H 2 O competition for the CO 2 binding sites would be technologically valuable. Here, in this paper, we consider a novel core–shell MOF design strategy, where a high-CO 2 -capacity MOF “core” is protected from competitive H 2 O-binding via a MOF “shell” that has very slow water diffusion. We consider a high-frequency adsorption/desorption cycle that regenerates the adsorbents before water can pass through the shell and enter the core. To identify optimal core–shell MOF pairs, we use a combination of experimental measurements, computational modeling, and multiphysics modeling. Our library of MOFs is created from two starting MOFs-UiO-66 and UiO-67-augmented with 30 possible functional group variations, yielding 1740 possible core–shell MOF pairs. After defining a performance score to rank these pairs, we identified 10 core–shell MOF candidates that significantly outperform any of the MOFs functioning alone.

42 ENGINEERING↗

Disturbance and diversity: Lichen species richness decreases with increasing anthropogenic disturbance

Anthropogenic disturbance is rapidly increasing through habitat degradation, development, and deforestation. Gaps remain in understanding the effects of this disturbance on diverse and ecologically important organisms such as lichens. In North America, studies have focused on epiphytic macrolichens and catastrophic disturbance, largely ignoring microlichens and less severe disturbances. The Intermediate Disturbance Hypothesis predicts these moderate disturbances will lead to higher species richness. Here we examine the effects of anthropogenic disturbance in the form of land management on overall lichen richness, including microlichens, and on the species richness of eight lichen functional groups. The study draws on a comprehensive data set of 872 species, in 208 one-hectare plots throughout the Southern Appalachian Mountains, a global biodiversity hotspot in eastern North America. A habitat quality index based on an established forestry metric was used as a proxy for anthropogenic disturbance and was quantified using a 10-part score including categories such as percent native tree canopy cover and degree of fragmentation. Linear models were used to compare habitat quality scores to overall species richness and to species richness of functional groups. Rather than following the Intermediate Disturbance Hypothesis, all groups uniformly follow a negative linear relationship: as disturbance increases, species richness decreases. This pattern held even for widely variable functional groups such as morphotype. Effective conservation of lichen richness should prioritize the maintenance of existing older, less-disturbed stands within large, contiguously forested areas.

59 BASIC BIOLOGICAL SCIENCES↗

The soil health assessment protocol and evaluation applied to soil organic carbon

The concept of soil health has evolved over the past several decades, recognizing that dynamic soil property response to management and land use is highly dependent on site-specific factors that must be considered when interpreting soil health measurements. Initially, the Soil Management Assessment Framework (SMAF) and Comprehensive Assessment of Soil Health (CASH) were developed and used globally for scoring soil health indicators. However, both SMAF and CASH frameworks were developed using a relatively small dataset and their interpretation curves were not validated at the nationwide scale. Expanding upon these concepts, we propose the Soil Health Assessment Protocol and Evaluation (SHAPE) tool. The SHAPE was developed using 14,680 soil organic C (SOC) observations from across the United States, and accounts for edaphic and climate factors at the continental scale. Data were compiled from the literature, the Cornell Soil Health Laboratory, and the Kellogg Soil Survey Laboratory. In this approach, scoring curves are Bayesian model-based estimates of the conditional cumulative distribution function (CDF) for defined soil peer groups reflecting five soil texture and five soil suborder classes adjusted for mean annual temperature and precipitation. Specifically, SHAPE produces scores between 0 and 1 (0–100%) for measured SOC values that reflect the quantile or position within the conditional CDF along with measures of uncertainty. Herein, we focus on development of the SHAPE scoring curve for SOC with our case studies. SHAPE is a flexible, quantitative tool that provides a regionally relevant interpretation of this key soil health indicator.

54 ENVIRONMENTAL SCIENCES↗

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for an electronic structure that is designed as a drop-in replacement for groundstate density functional theory (DFT) energy calculations. The model is a message-passing graph neural network that uses symmetryadapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 × 10 6 DFT calculations on molecules and geometries. This dataset covers the most common elements in biochemistry and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, and I) and charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformer benchmark set, OrbNet Denali has a median correlation coefficient of R 2 = 0.90 compared to the reference DLPNO-CCSD(T) calculation and R 2 = 0.97 compared to the method used to generate the training data (ωB97X-D3/def2- TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for noncovalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of ωB97X-D3/def2-TZVP with an average mean absolute error of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Optimizing Earthquake Nowcasting With Machine Learning: The Role of Strain Hardening in the Earthquake Cycle

Abstract Nowcasting is a term originating from economics, finance, and meteorology. It refers to the process of determining the uncertain state of the economy, markets or the weather at the current time by indirect means. In this paper, we describe a simple two‐parameter data analysis that reveals hidden order in otherwise seemingly chaotic earthquake seismicity. One of these parameters relates to a mechanism of seismic quiescence arising from the physics of strain‐hardening of the crust prior to major events. We observe an earthquake cycle associated with major earthquakes in California, similar to what has long been postulated. An estimate of the earthquake hazard revealed by this state variable time series can be optimized by the use of machine learning in the form of the Receiver Operating Characteristic skill score. The ROC skill is used here as a loss function in a supervised learning mode. Our analysis is conducted in the region of 5° × 5° in latitude‐longitude centered on Los Angeles, a region which we used in previous papers to build similar time series using more involved methods (Rundle & Donnellan, 2020, https://doi.org/10.1029/2020EA001097 ; Rundle, Donnellan et al., 2021, https://doi.org/10.1029/2021EA001757 ; Rundle, Stein et al., 2021, https://doi.org/10.1088/1361-6633/abf893 ). Here we show that not only does the state variable time series have forecast skill, the associated spatial probability densities have skill as well. In addition, use of the standard ROC and Precision (PPV) metrics allow probabilities of current earthquake hazard to be defined in a simple, straightforward, and rigorous way.

58 GEOSCIENCES↗

Grid Optimization Competition on Synthetic and Industrial Power Systems

This paper summarizes a grid optimization (GO) competition effort in the United States to find the best solution strategies for up to interconnect-scale power system networks with around 32,000 buses. The optimization problem is a mixedinteger, non-convex non-linear problem, (MINLP) and includes discrete variables such as unit commitment and line switching, control settings (transformer taps and phase shifters with impedance correction tables), and bus shunts. The case study includes six actual industry grids as well as 16 realistic synthetic grids created by three different dataset teams. The winners are selected and ranked based on scoring criteria, which consider the solution quality (such as objective functions) within time limits. Nine winner teams are selected from 26 competitor teams. The results achieved by different teams are described and the performance of different algorithms on synthetic grids and actual industry grids are compared and analyzed.

mixed-integer non-linear programming↗

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes

Interpreting changes in patient genomes, understanding how viruses evolve and engineering novel protein function all depend on accurately predicting the functional outcomes that arise from amino acid substitutions. To that end, the development of first-generation prediction algorithms was guided by historic experimental datasets. However, these datasets were heavily biased toward substitutions at positions that have not changed much throughout evolution (i.e. conserved). Although newer datasets include substitutions at positions that span a range of evolutionary conservation scores, these data are largely derived from assays that agglomerate multiple aspects of function. To facilitate predictions from the foundational chemical properties of proteins, large substitution databases with biochemical characterizations of function are needed. We report here a database derived from mutational, biochemical, bioinformatic, structural, pathological and computational studies of a highly studied protein family—pyruvate kinase (PYK). A centerpiece of this database is the biochemical characterization—including quantitative evaluation of allosteric regulation—of the changes that accompany substitutions at positions that sample the full conservation range observed in the PYK family. We have used these data to facilitate critical advances in the foundational studies of allosteric regulation and protein evolution and as rigorous benchmarks for testing protein predictions. We trust that the collected dataset will be useful for the broader scientific community in the further development of prediction algorithms.

59 BASIC BIOLOGICAL SCIENCES↗

Distinct Clinical Impact and Biological Function of Angiopoietin and Angiopoietin-like Proteins in Human Breast Cancer

Secreted angiopoietin/angiopoietin-like (ANGPT/ANGPTL) proteins are involved in many biological processes. However, the role of these proteins in human breast cancers (BCs) remains largely unclear. Here, we conducted integrated omics analyses to evaluate the clinical impact of ANGPT/ANGPTL proteins and to elucidate their biological functions. In BCs, we identified rare mutations in ANGPT/ANGPTL genes, frequent gains of ANGPT1, ANGPT4, and ANGPTL1, and frequent losses of ANGPT2, ANGPTL5, and ANGPTL7, but observed that ANGPTL1, 2, and 4 were robustly downregulated in multiple datasets. The expression levels of ANGPTL1, 5, and 8 were positively correlated with overall survival (OS), while the expression levels of ANGPTL4 were negatively correlated with OS. Additionally, the expression levels of ANGPTL1 and 7 were positively correlated with distant metastasis-free survival (DMFS), while the expression levels of ANGPT2 and ANGPTL4 were negatively correlated with DMFS. The prognostic impacts of ANGPT/ANGPTL genes depended on the molecular subtypes and on clinical factors. We discovered that various ANGPT/ANGPTL genes were co-expressed with various genes involved in different pathways. Finally, with the exception of ANGPTL3, the remaining genes showed significant correlations with cancer-associated fibroblasts, endothelial cells, and microenvironment score, whereas only ANGPTL6 was significantly correlated with immune score. Our findings provide strong evidence for the distinct clinical impact and biological function of ANGPT/ANGPTL proteins, but the question of whether some of them could be potential therapeutic targets still needs further investigation in BCs.

60 APPLIED LIFE SCIENCES↗

Sequence-structure-function characterization of the emerging tetracycline destructase family of antibiotic resistance enzymes

Tetracycline destructases (TDases) are flavin monooxygenases which can confer resistance to all generations of tetracycline antibiotics. The recent increase in the number and diversity of reported TDase sequences enables a deep investigation of the TDase sequence-structure-function landscape. Here, we evaluate the sequence determinants of TDase function through two complementary approaches: (1) constructing profile hidden Markov models to predict new TDases, and (2) using multiple sequence alignments to identify conserved positions important to protein function. Using the HMM-based approach we screened 50 high-scoring candidate sequences in Escherichia coli, leading to the discovery of 13 new TDases. The X-ray crystal structures of two new enzymes from Legionella species were determined, and the ability of anhydrotetracycline to inhibit their tetracycline-inactivating activity was confirmed. Using the MSA-based approach we identified 31 amino acid positions 100% conserved across all known TDase sequences. The roles of these positions were analyzed by alanine-scanning mutagenesis in two TDases, to study the impact on cell and in vitro activity, structure, and stability. These results expand the diversity of TDase sequences and provide valuable insights into the roles of important residues in TDases, and flavin monooxygenases more broadly.

60 APPLIED LIFE SCIENCES↗

Population‐level gene expression can repeatedly link genes to functions in maize

SUMMARY Transcriptome‐wide association studies (TWAS) can provide single gene resolution for candidate genes in plants, complementing genome‐wide association studies (GWAS) but efforts in plants have been met with, at best, mixed success. We generated expression data from 693 maize genotypes, measured in a common field experiment, sampled over a 2‐h period to minimize diurnal and environmental effects, using full‐length RNA‐seq to maximize the accurate estimation of transcript abundance. TWAS could identify roughly 10 times as many genes likely to play a role in flowering time regulation as GWAS conducted data from the same experiment. TWAS using mature leaf tissue identified known true‐positive flowering time genes known to act in the shoot apical meristem, and trait data from a new environment enabled the identification of additional flowering time genes without the need for new expression data. eQTL analysis of TWAS‐tagged genes identified at least one additional known maize flowering time gene through trans ‐eQTL interactions. Collectively these results suggest the gene expression resource described here can link genes to functions across different plant phenotypes expressed in a range of tissues and scored in different experiments.

Torres‐Rodríguez, J. Vladimir↗

PROACTIVE Focus Area 4: Structured Decision Metrics Analysis (Final Report)

A structured decision metrics analysis was developed as one of the tasks under PROACTIVE’s Focus Area 4 (FA4) and used structured decision metrics for processes, items, and facilities (PIF) to determine the efficacy of an M&V system in meeting treaty goals and technical objectives. The method starts with the functional decomposition of a “treaty” with the M&V system overlaid on it. A Functional Decomposition Rubric (FDR) for each PIF is used to determine a score ranging from 0 (weak) to 4 (strong) for assurance, security, and burden. The individual scores are combined to provide an overall Verification System Score (VSS) which assesses the overall verification system’s suitability given goals; scores for each step of the process are also given. The outcome of the evaluation is to identify needs or modifications to the enterprise model, verification system, or proposed testbed capabilities. VeriScore was used to evaluate FA4’s Spiral 0 exercise; those results are included in this report. The VeriScore and FDR framework can also be used in a non-treaty environment, as any goal/objective/method structure will work, thus expanding its applicability beyond traditional arms control structures.

99 GENERAL AND MISCELLANEOUS↗

V1G Frequency Regulation: Algorithm Development, Validation & Analysis at Scale

Researchers at Argonne National Laboratory developed and validated a high-fidelity digital twin of a smart charging (V1G) ecosystem to model the participation of up to 1,000 unique electric vehicles (EVs) in the PJM frequency regulation market. Utilizing a discrete-event framework, the simulation models complex interactions, from dynamic grid signals (updated every 2 seconds) to individual EV charging dynamics. The simulation incorporates multiple EV models created from real-world lab test data. Researchers tested multiple control algorithms to balance the dual objectives of maximizing aggregator’s revenue and driver charging needs. Results demonstrate that aggregated EVs function as a controllable, highly effective grid resource, achieving high PJM Performance Scores (80–90%). Additionally, an optimized, market-aware bidding strategy was identified as key to profitability. The platform was shown to provide drivers with an average charging discount of nearly 50%. The algorithm was further validated in the lab using production EVs and charging stations to compare simulation results with real-world performance.

Manne, Nithin↗

Plasma proteomic biomarkers of physical frailty in heart failure: a propensity score matched discovery-based pilot study

Background: Physical frailty is highly prevalent in heart failure (HF), but we lack an understanding of the underlying pathophysiology. Proteomics evaluation of plasma samples may elucidate potential mechanisms and biomarkers of physical frailty in HF. We aimed to identify plasma proteomic biomarkers that are differentially expressed between physically frail and non physically frail adults with HF. Methods: This was a secondary analysis of a subset of data and plasma samples from a study of frailty among patients with New York Heart Association (NYHA) Functional Classification I-IV HF. Physical frailty was measured using the Frailty Phenotype Criteria. Propensity score matching was used to match pairs of physically frail (n = 20) vs. non-physically frail (n = 20) patients on clinical characteristics. Plasma samples were processed using a sensitive liquid chromatography mass spectrometry platform, utilizing a multiplexed tandem mass tag-labeled quantitative proteomics approach. Differentially expressed proteins were quantified individually using paired t tests with associated log fold change of 0.3 and Fisher’s combined p values. Results: The sample (n = 40) was 62.8±16.9 years old, 58% female, and 55% NYHA Class III/IV. Proteomics analysis revealed 7 proteins differentially expressed using full differential criteria: matrix metalloproteinase-14 was downregulated in frailty, and copine-1, low affinity immunoglobulin gamma Fc region receptor III-A and III-B, probable non-functional immunoglobulin kappa variable 2D-24, glutathione S-transferase Mu 1, and argininosuccinate lyase were upregulated in frailty. Conclusions: Proteomic biomarkers related to the immune system, stress response, and detoxification were differentially expressed between physically frail and non-physically frail adults with HF.

Biomarkers↗

Photometric redshifts for the S-PLUS Survey: Is machine learning up to the task?

The Southern Photometric Local Universe Survey (S-PLUS) is a novel project that aims to map the Southern Hemisphere using a twelve filter system, comprising five broad-band SDSS-like filters and seven narrow-band filters optimized for important stellar features in the local universe. In this paper we use the photometry and morphological information from the first S-PLUS data release (S-PLUS DR1) cross-matched to unWISE data and spectroscopic redshifts from Sloan Digital Sky Survey DR15. We explore three different machine learning methods (Gaussian Processes with GPz and two Deep Learning models made with TensorFlow) and compare them with the currently used template-fitting method in the S-PLUS DR1 to address whether machine learning methods can take advantage of the twelve filter system for photometric redshift prediction. Using tests for accuracy for both single-point estimates such as the calculation of the scatter, bias, and outlier fraction, and probability distribution functions (PDFs) such as the Probability Integral Transform (PIT), the Continuous Ranked Probability Score (CRPS) and the Odds distribution, we conclude that a deep-learning method using a combination of a Bayesian Neural Network and a Mixture Density Network offers the most accurate photometric redshifts for the current test sample. In conclusion, it achieves single-point photometric redshifts with scatter (σ NMAD ) of 0.023, normalized bias of -0.001, and outlier fraction of 0.64% for galaxies with r_auto magnitudes between 16 and 21.

79 ASTRONOMY AND ASTROPHYSICS↗

Powering the Blue Economy - Ocean Observing Use Cases Report

The "Powering the Blue Economy" (PBE) Report identified ocean observing and autonomous underwater vehicle (AUV) recharge as near-term markets with significant potential for marine energy integration when specified qualitative and quantitative assessment criteria were used. The ocean observing market (including AUVs) scored high relative to other markets analyzed in the PBE Report with respect to market size, marine renewable energy (MRE) compatibility with functional requirements, competitive positioning (i.e., MRE versus other power sources), path to market, and alignment to the Department of Energy Water Power Technologies Office (WPTO) and other agencies' objectives. Based on this scoring, Pacific Northwest National Laboratory (PNNL) and the National Renewable Energy Laboratory (NREL) pursued the development of five use cases that represent a spectrum of ocean observation platforms, fixed and mobile, to explore the present and future power needs that might be satisfied by marine energy. The use cases were described and analyzed for this potential by examining current missions and future needs, evaluating the mix of renewable energy sources that might satisfy those needs at sea, and understanding the overall cost drivers that might enable this application.

14 SOLAR ENERGY↗