Search NASA⌕ Search

SEARCH · Search NASA

Results for “host data”

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 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WLN002

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for mRNA and miRNA expression analysis. See Experiment WLN003 for corresponding omics analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Transcriptomics dataset downloads have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Metis – A Tool to Harmonize and Analyze Multi-Sectoral Data and Linkages at Variable Spatial Scales

Metis was developed to allow users to analyze regional and sub-regional multi-sector dynamics by providing a platform to harmonize and amalgamate data from different models and stakeholders operating at variable spatial scales. Metis is an open-source R package hosted on GitHub. Metis functions collectively allow users to compare, manipulate, and harmonize multi-sector data at user-specified spatial scales, and to identify and quantify sectoral inter-linkages. Each Metis function can also be used independently to support an array of other research applications, such as spatial analysis and data visualization.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Syntrophic bacterial and host–microbe interactions in bacterial vaginosis

Bacterial vaginosis (BV) is a common, polymicrobial condition of the vaginal microbiota that is associated with symptoms such as malodor and excessive discharge, along with increased risk of various adverse sequelae. Host–bacteria and bacteria–bacteria interactions are thought to contribute to the condition, but many of these functions have yet to be elucidated. Using untargeted metaproteomics, we identified 1068 host and 1418 bacterial proteins in a set of cervicovaginal lavage samples collected from 20 participants with BV and 9 who were negative for the condition. We identified Dialister micraerophilus as a major producer of malodorous polyamines and identified a syntrophic interaction between this organism and Fannyhessea vaginae that leads to increased production of putrescine, a metabolite characteristic of BV. Although formate synthesis has not previously been noted in BV, we discovered diverse bacteria associated with the condition express pyruvate formate-lyase enzymes in vivo and confirm these organisms secrete formic acid in vitro. Sodium hypophosphite efficiently inhibited this function in multiple taxa. We also found that the fastidious organism Coriobacteriales bacterium DNF00809 can metabolize formic acid secreted by Gardnerella vaginalis, representing another syntrophic interaction. We noted an increased abundance of the host epithelial repair protein transglutaminase 3 in the metaproteomic data, which we confirmed by enzyme-linked immunosorbent assay. Other proteins identified in our samples implicate Finegoldia magna and Parvimonas micra in the production of malodorous trimethylamine. Some bacterial proteins identified represent novel targets for future therapeutics to disrupt BV communities and promote vaginal colonization by commensal lactobacilli.

bacterial vaginosis↗
DOE OSTI2021

Omics-Lethal Human Viruses, Influenza A Experiment ICL102

The purpose of this experiment was to evaluate the human host cellular response to wild-type Influenza A/Anhui/1/2013 (H7N9; "AH1-WT") virus and mutant viruses NS1-L103F/I106M ("AH1-F/M") and partially ferret-adapted ("AH1-691") infection. Sample data was obtained from human lung adenocarcinoma cells (Calu-3) and processed for mRNA, miRNA, proteomics, lipidomics, and metabolomics expression analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, lipidomics, and transcriptomics dataset download each have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WLN003

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus infectious clone (WNV-NY99 clone 382) and mutant WNV-E218A (WNV-NY99 382 E218A 2 nt) virus infection. Sample data was obtained from mouse popliteal draining lymph nodes for proteomics, metabolomics, and lipidomics expression analysis. See Experiment WLN002 for corresponding transcriptome analysis. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, and lipidomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Energy Materials Chemistry Integrating Theory, Experiment and Data Science (Final Report)

The Energy Materials Chemistry Integrating Theory, Experiment and Data Science (EM-CITED) project is a multidisciplinary research effort focused on accelerating discovery of scientific knowledge via incorporation of data science and artificial intelligence in materials chemistry research. The project aims to advance materials chemistry-aware data science to unify theory and experiment knowledge streams. The work resulted in foundational AI frameworks for materials chemistry – Deep Reasoning Networks (DRNets), Hierarchical Correlation Learning for Multi-property Prediction (H-CLMP), and Material-to-Spectrum (Mat2Spec) prediction – as well as a host of strategies for accelerated scientific discoveries through principled incorporation of data science in computational and experimental research.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Limited impact of jet-induced feedback in the multi-phase nuclear interstellar medium of 4C12.50

4C12.50 (IRAS 13451+1232) at z = 0.122 is an ultraluminous infared radio galaxy that has often been proposed as a prime candidate for the link between ultraluminous infared galaxies and young radio galaxies. It is also an interesting target to investigate whether and how radio-induced feedback affects the evolution of galaxies in the early phases of radio activity. We study, in detail for the first time, the hot (≥1500 K) molecular gas in 4C12.50. The potential impact of the radio jet on this gas phase, as well as on the star formation activity, are investigated. We also study the ionised (including coronal) gas as traced by the near-infrared lines. Using near-infrared long slit spectroscopy obtained with EMIR on GTC and X-shooter on VLT, we analyse the emission line spectrum of the ionised, coronal, and, specially, the hot molecular gas in the western nucleus hosting the compact radio jet. Based on high spatial resolution ALMA CO(2–1) data, we also revise the location of 4C12.50 in the Kennicutt-Schmidt diagram in order to investigate whether star formation is suppressed. 4C12.50 hosts (2.1 ± 0.4) × 10 4 M ⊙ of hot molecular gas. An unusually high rotational temperature T rot = 3020 ± 160 K is inferred. The molecular gas mass obeys a power-law temperature distribution, dM H2 /dT ∝ T –5 , from T ~300 K and up to ~3000 K. Both results support the idea that shocks (probably induced by the radio jet) contribute to the heating and excitation of the hot molecular gas. A molecular outflow is not detected. The coupling of the outflowing ionised and neutral outflows with the hot molecular gas is poor. Contrary to other studies, we claim that there is no evidence for star formation suppression in this object. If radio-induced feedback can regulate the star formation activity in galaxies, 4C12.50 is a promising candidate to reveal this phenomenon in action. However, we find no solid evidence for a current or past impact of this mechanism on the evolution of this system, neither by clearing out the dusty central cocoon efficiently, nor by suppressing the star formation activity.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Distributed out-of-memory NMF on CPU/GPU architectures

We propose an efficient distributed out-of-memory implementation of the non-negative matrix factorization (NMF) algorithm for heterogeneous high-performance-computing systems. The proposed implementation is based on prior work on NMFk, which can perform automatic model selection and extract latent variables and patterns from data. In this work, we extend NMFk by adding support for dense and sparse matrix operation on multi-node, multi-GPU systems. The resulting algorithm is optimized for out-of-memory problems where the memory required to factorize a given matrix is greater than the available GPU memory. Memory complexity is reduced by batching/tiling strategies, and sparse and dense matrix operations are significantly accelerated with GPU cores (or tensor cores when available). Input/output latency associated with batch copies between host and device is hidden using CUDA streams to overlap data transfers and compute asynchronously, and latency associated with collective communications (both intra-node and inter-node) is reduced using optimized NVIDIA Collective Communication Library (NCCL) based communicators. Benchmark results show significant improvement, from 32X to 76x speedup, with the new implementation using GPUs over the CPU-based NMFk. Good weak scaling was demonstrated on up to 4096 multi-GPU cluster nodes with approximately 25,000 GPUs when decomposing a dense 340 Terabyte-size matrix and an 11 Exabyte-size sparse matrix of density 10 -6 .

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Omics-Lethal Human Viruses, West Nile Experiment WCB001

The purpose of this experiment was to evaluate the host response to wild-type West Nile virus (WNV-NY99 382) and mutant WNV-E218A virus infection. Sample data was obtained from mouse cerebellum tissue and processed for mRNA, miRNA, proteomics, metabolomics, and lipidomics expression analysis. Tissues from this experiment were matched to tissues from GSE77193 (WCT001), using 1/4 of the cortex and 1/2 of cerebellum from the same mice. Secondary host-associated viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics, metabolomics, lipidomics, and transcriptomics dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific West Nile virus infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Analysis of twelve genomes of the bacterium Kerstersia gyiorum from brown-throated sloths ( Bradypus variegatus ), the first from a non-human host

Kerstersia gyiorum is a Gram-negative bacterium found in various animals, including humans, where it has been associated with various infections. Knowledge of the basic biology of K. gyiorum is essential to understand the evolutionary strategies of niche adaptation and how this organism contributes to infectious diseases; however, genomic data about K. gyiorum is very limited, especially from non-human hosts. In this work, we sequenced 12 K. gyiorum genomes isolated from healthy free-living brown-throated sloths (Bradypus variegatus) in the Parque Estadual das Fontes do Ipiranga (São Paulo, Brazil), and compared them with genomes from isolates of human origin, in order to gain insights into genomic diversity, phylogeny, and host specialization of this species. Phylogenetic analysis revealed that these K. gyiorum strains are structured according to host. Despite the fact that sloth isolates were sampled from a single geographic location, the intra-sloth K. gyiorum diversity was divided into three clusters, with differences of more than 1,000 single nucleotide polymorphisms between them, suggesting the circulation of various K. gyiorum lineages in sloths. Genes involved in mobilome and defense mechanisms against mobile genetic elements were the main source of gene content variation between isolates from different hosts. Sloth-specific K. gyiorum genome features include an IncN2 plasmid, a phage sequence, and a CRISPR-Cas system. The broad diversity of defense elements in K. gyiorum (14 systems) may prevent further mobile element flow and explain the low amount of mobile genetic elements in K. gyiorum genomes. Gene content variation may be important for the adaptation of K. gyiorum to different host niches. This study furthers our understanding of diversity, host adaptation, and evolution of K. gyiorum, by presenting and analyzing the first genomes of non-human isolates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Geochemical-hydromechanical couplings during water-serpentinized harzburgite interactions at 20° C and 30 bars

Interaction of groundwater with the serpentinized harzburgites of the upper mantle plays an important role in the geologic carbon cycle and serpentinization processes. Here, in this study, an intact serpentinized harzburgite with more than 60% lizardite from the Semail ophiolite in Oman was reacted with water at near neutral pH and low PCO 2 to observe its dissolution behavior and reaction path within the CaO-MgO-SiO 2 -CO 2 -H 2 O system at 20 °C and 30 bars. In the experiment, mass (i.e. H 2 O, ions) transfer is by diffusion and the selected temperature and pressure conditions mimic water-rock interactions at the shallow portions of most ultramafic rock hosted aquifers. Equilibrium activity-activity diagrams and thermodynamic data were used to compare the experimentally determined reaction path with the theoretical stability boundaries for minerals involved to investigate the evolution of bulk chemical composition, mineralogy, and water composition. The experiments demonstrated that (i) the water-rock interactions increased the pH of the aqueous phase from 5.9 to 7.5 over a period of 18 weeks; (ii) the dissolution of lizardite, orthopyroxene (enstatite), and clinopyroxene (diopside and augite) increased the concentration of Mg, Ca, and Si in the aqueous phase; (iii) the dissolution was incongruent with respect to Mg and Si, favoring Si release at pH > 6 due to (a) breaking of more reactive cation‑oxygen bonds that is consistent with the stoichiometry of magnesium for proton exchange reaction which favors a surface that is enriched in Mg at basic conditions, and (b) preferential dissolution of clinopyroxene Mg 1.30 Ca 0.52 Fe 0.06 Si 2 O 6 ; (iv) the aqueous phase was undersaturated with respect to carbonate (e.g. calcite, magnesite, and hydromagnesite) and hydrous (e.g. lizardite, chrysotile, brucite, and talc) minerals; (v) the bulk chemical composition and mineralogy of the intact serpentinized harzburgite matrix did not change; (vi) the thermodynamic data can successfully predict water-intact serpentinized harzburgite behavior if the water chemical composition can be constrained; and (vii) no detectable macroscopic form of damage (e.g. microcracks forming as a result of differential stress fields due to changes in volume during chemical reaction) was observed.

Carbonation↗
DOE OSTI2025

Microscopic scattering approach to in-gap states: Cr adatoms on superconducting 𝛽−Bi 2 ⁢Pd

We develop a microscopic scattering formalism to describe Yu-Shiba-Rusinov (YSR) states due to a single Cr adatom on the Bi-terminated surface of 𝛽−Bi 2 ⁢Pd, by combining ab initio Wannier functions with a real-space Green's function approach in the Bogoliubov–de Gennes formalism. Our framework reproduces key scanning tunneling spectroscopy features, including a single particle-hole asymmetric YSR peak and isotropic 𝑑⁢𝐼/𝑑⁢𝑉 maps around the impurity. Decomposing the YSR states reveals contributions from four nearly degenerate 𝐶 4⁢𝑣 representations, with energy broadening masking their individual signatures. Spin-orbit coupling induces partial spin polarization, while the spatial asymmetry between particle and hole components arises from Cr 𝑑−Bi 𝑝 hybridization. These results highlight the importance of realistic band structures and microscopic modeling for interpreting STM data and provide a foundation for studying impurity chains hosting topological excitations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Software For Detecting, Analyzing, And Mitigating Anomalous Network Packets Through A Multi Dimensional Latent Space Representation

The code ingests network packet payloads, classifies the payload as anomalous or normal, and plots the payload in a 3-D latent space representation. It also enables user interaction with the representation to allow for the user to click on the packet payload in the latent space and determine host id, network topology, and access the raw packet data.

Anderson, MatthewW.↗
DOE OSTI2020

Within-Host Phenotypic Evolution and the Population-Level Control of Chronic Viral Infections by Treatment and Prophylaxis

Chronic viral infections can persist for decades spanning thousands of viral generations, leading to a highly diverse population of viruses with its own complex evolutionary history. We propose an expandable mathematical framework for understanding how the emergence of genetic and phenotypic diversity affects the population-level control of those infections by both non-curative treatment and chemo-prophylactic measures. Our frameworks allows both neutral and phenotypic evolution, and we consider the specific evolution of contagiousness, resistance to therapy, and efficacy of prophylaxis. We compute both the controlled and uncontrolled, population-level basic reproduction number accounting for the within-host evolutionary process where new phenotypes emerge and are lost in infected persons, which we also extend to include both treatment and prophylactic control efforts. We used these results to discuss the conditions under which the relative efficacy of prophylactic versus therapeutic methods of control are superior. Finally, we give expressions for the endemic equilibrium of these models for certain constrained versions of the within-host evolutionary model providing a potential method for estimating within-host evolutionary parameters from population-level genetic sequence data.

sensitivity analysis↗
DOE OSTI2023

COOL–LAMPS. III. Discovery of a 25."9 Separation Quasar Lensed by a Merging Galaxy Cluster*

In the third paper from the COOL–LAMPS Collaboration, we report the discovery of COOL J0542-2125, a gravitationally lensed quasar at z = 1.84, observed as three images due to an intervening massive galaxy cluster at z = 0.61. The lensed quasar images were identified in a search for lens systems in recent public optical imaging data and have separations on the sky up to 25farcs9, wider than any previously known lensed quasar. The galaxy cluster acting as a strong lens appears to be in the process of merging, with two subclusters separated by ~1 Mpc in the plane of the sky, and their central galaxies showing a radial velocity difference of ~1000 km s-1. Both cluster cores show strongly lensed images of an assortment of background sources, as does the region between them. A preliminary strong lens model implies masses of $M_{<250kpc} = 1.79^{+0.16}_{-0.01}$ x $10^{14} M_⊙$ and $M_{<250kpc} = 1.48^{+0.04}_{-0.10}$ x $10^{14} M_⊙$ for the east and west subclusters, respectively. This line of sight is also coincident with an ROSAT ALL-sky Survey source, centered between the two confirmed cluster halos reminiscent of other major cluster-scale mergers. Archival and new follow-up imaging show flux variability in the quasar images of up to 0.4 mag within ~1 yr, and new multicolor imaging data reveal a 2σ detection of the underlying quasar host. A lens system with this configuration offers rare opportunities for a range of future studies of both the lensed quasar and its host and the foreground cluster merger causing the lensing.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Data-Centric AI and the Open Energy Data Initiative (OEDI)

This presentation emphasizes the critical importance of data-centric AI. The limitations of model-centric AI when dealing with poor or insufficient data are highlighted, and it is illustrated how training models on inaccurate or noisy data leads to suboptimal results. This talk advocates for a hybrid approach that combines a focus on data quality and model parameters to achieve optimal results. The Open Energy Data Initiative (OEDI) is introduced as a valuable resource for obtaining high-quality energy-related datasets, hosting nearly 2,000 publicly accessible datasets, including 99 solar-related datasets, totaling over 2.7 petabytes of data. OEDI's data lakes enable users to query and work with data without extensive transfers. In conclusion, the significance of data-centric AI and adherence to data curation best practices is emphasized, positioning OEDI as a prime source of high-quality data for AI and machine learning in the renewable energy sector.

AI↗
DOE OSTI2021

Conflation of Geospatial POI Data and Ground-level Imagery via Link Prediction on Joint Semantic Graph

With the proliferation of smartphone cameras and social networks, we have rich, multi-modal data about points of interest (POIs) - like cultural landmarks, institutions, businesses, etc. - within a given areas of interest (AOI) (e.g., a county, city or a neighborhood) available to us. Data conflation across multiple modalities of data sources is one of the key challenges in maintaining a geographical information system (GIS) which accumulate data about POIs. Given POI data from nine different sources, and ground-level geo-tagged and scene-captioned images from two different image hosting platforms, in this work we explore the application of graph neural networks (GNNs) to perform data conflation, while leveraging a natural graph structure evident in geospatial data. The preliminary results demonstrate the capacity of a GNN operation to learn distributions of entity (POIs and images) features, coupled with topological structure of entity's local neighborhood in a semantic nearest neighbor graph, in order to predict links between a pair of entities.

Gurav, Rutuja↗
DOE OSTI2021

PNNL DataHub Project: Omics Lethal Human Viruses Project Profiling of the Host Response to Influenza A Virus Infection, Processed Experimental Dataset Catalog

Influenza A virus (IAV) is a high risk biological agent, classified as a Category C priority pathogen (Orthomyxoviridae) by the National Institute of Allergy and Infectious Diseases (NIAID), and is known to cause severe respiratory disease with high mortality rates in humans. Lethal host-pathogen invasion mechanisms and the cellular intricacies behind these fatal infections still remain unclear. The NIAID Modeling Host Responses to Understand Severe Human Virus Infections Research Program project (2013-2018) aimed to develop an improved comprehensive understanding of the host response to a suite of viruses causing lethal infections leveraging a systems biology approach. Herein, PNNL sub-projects provide a never before released comprehensive infectious disease collection of primary and secondary transformation multi-Omics data profiling a series of priority pathogen primary experimental studies for enhanced open-access to viral Omics datasets and project lifecycle metadata. Secondary host-pathogen viral dataset downloads contain one or more statistically processed (normalization data transformation) quantitative dataset collections resulting in qualitative expression analyses of primary host-pathogen experimental study designs. Leveraging unique high-resolution Omics capabilities for proteomics (P), metabolomics (M), lipidomics (L), and transcriptomics (T) dataset downloads each have a direct relationship to a primary sample submission corresponding to a specific Influenza A virus [NCBITAXON:11320] experimental infection study. Host sample types include human lung adenocarcinoma cells ["Calu-3", BTO:0002750] and whole mouse lung [BTO:0000763] tissue collections.

59 BASIC BIOLOGICAL SCIENCES↗