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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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230 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Status of genome function annotation in model organisms and crops

Abstract Since the entry into genome‐enabled biology several decades ago, much progress has been made in determining, describing, and disseminating the functions of genes and their products. Yet, this information is still difficult to access for many scientists and for most genomes. To provide easy access and a graphical summary of the status of genome function annotation for model organisms and bioenergy and food crop species, we created a web application ( https://genomeannotation.rheelab.org ) to visualize, search, and download genome annotation data for 28 species. The summary graphics and data tables will be updated semi‐annually, and snapshots will be archived to provide a historical record of the progress of genome function annotation efforts. Clear and simple visualization of up‐to‐date genome function annotation status, including the extent of what is unknown, will help address the grand challenge of elucidating the functions of all genes in organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Complex eigenvalue instantons and the Fredholm determinant expansion in the Gross-Witten-Wadia model

We study the leading nonperturbative corrections to the strong-coupling (ungapped) phase of the Gross-Witten-Wadia (GWW) integral over unitary matrices, to one-loop order. We compute these corrections directly in terms of eigenvalue tunneling in a holomorphic presentation of the integral over eigenvalues. The leading nonperturbative contribution to the partition function comes from a pair of complex eigenvalue instantons. We show that these are in fact “ghost instantons”, which are extrema of the one-eigenvalue effective potential on the “unphysical sheet” of the spectral curve and have been discussed in detail recently by Mariño, Schiappa, and Schwick. Further, we discuss the relationship of these instantons to the Fredholm determinant expansion of the unitary matrix integral, which has recently become an object of interest in the computations of BPS indices of supersymmetric gauge theories and black holes. We find that, after taking the ’t Hooft limit, the first correction given by the Fredholm determinant expansion of the GWW integral agrees precisely with the leading nonperturbative correction, to one-loop order.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

EPIsembleVis: A geo-visual analysis and comparison of the prediction ensembles of multiple COVID-19 models

In this work, we present EPIsembleVis, a web-based comparative visual analysis tool for evaluating the consistency of multiple COVID-19 prediction models. Our approach analyzes a collection of COVID-19 predictions from different epidemiological models as an ensemble and utilizes two metrics to quantify model performance. These metrics include (a) prediction uncertainty (represented as the dispersion of predictions in each ensemble) and (b) prediction error (calculated by comparing individual model predictions with the recorded data). Through an interactive visual interface, our approach provides a data-driven workflow for (a) selecting and constructing the COVID-19 model prediction ensemble based on the spatiotemporal overlap of available predictions of multiple epidemiological models, (b) quantifying the model performance using both the uncertainty of each model prediction ensemble, and the error of each ensemble member that represents individual model predictions, and (c) visualizing the spatiotemporal variability in the projection performance of individual models using a suite of novel ensemble visualization techniques, such as the data availability map, a spatiotemporal textured-tile calendar, multivariate rose chart, and time-series leaflet glyph. We demonstrate the capability of our ensemble visual interface through a case study that investigates the performance of weekly COVID-19 predictions, which are provided through the COVID-19 Forecast Hub UMass-Amherst Influenza Forecasting Center of Excellence [47] for the United States and United States Territories. The EPIsembleVis tool is implemented using open-source web technologies and adaptive system design, rendering it interoperable with Elasticsearch and Kibana for automatically ingesting COVID-19 predictions from online repositories, and it is generalizable for analyzing worldwide projections from more epidemiological models.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

A deep learning approach to identify missing is-a relations in SNOMED CT

Abstract Objective SNOMED CT is the largest clinical terminology worldwide. Quality assurance of SNOMED CT is of utmost importance to ensure that it provides accurate domain knowledge to various SNOMED CT-based applications. In this work, we introduce a deep learning-based approach to uncover missing is-a relations in SNOMED CT. Materials and Methods Our focus is to identify missing is-a relations between concept-pairs exhibiting a containment pattern (ie, the set of words of one concept being a proper subset of that of the other concept). We use hierarchically related containment concept-pairs as positive instances and hierarchically unrelated containment concept-pairs as negative instances to train a model predicting whether an is-a relation exists between 2 concepts with containment pattern. The model is a binary classifier leveraging concept name features, hierarchical features, enriched lexical attribute features, and logical definition features. We introduce a cross-validation inspired approach to identify missing is-a relations among all hierarchically unrelated containment concept-pairs. Results We trained and applied our model on the Clinical finding subhierarchy of SNOMED CT (September 2019 US edition). Our model (based on the validation sets) achieved a precision of 0.8164, recall of 0.8397, and F1 score of 0.8279. Applying the model to predict actual missing is-a relations, we obtained a total of 1661 potential candidates. Domain experts performed evaluation on randomly selected 230 samples and verified that 192 (83.48%) are valid. Conclusions The results showed that our deep learning approach is effective in uncovering missing is-a relations between containment concept-pairs in SNOMED CT.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Shepherding Metadata Through the Building Lifecycle

Many different digital representations of a building are produced over the course of its lifecycle. These representations contain the metadata required to support different stages of the building, from initial planning and design, to construction and commissioning, through operations, audits, retrofits and maintenance. However, because of differences in the semantics, structure and syntax of these representations, the metadata they contain is not interoperable. We present a novel method for leveraging these representations to create a unified, authoritative Brick metadata model for a building that can be continually maintained over the course of the building lifecycle. A simple synchronization protocol relays inferred Brick metadata from existing metadata sources such as gbXML, BuildingSync, Project Haystack and Modelica to a central integration server, which merges the metadata into a valid Brick model.

Fierro, Gabe↗
DOE OSTI2020

Interactive Metadata Integration with Brick

Many different digital representations of a building are produced over the course of its lifecycle. While these representations individually contain metadata required to support different stages of the building's lifecycle, they are largely not interoperable due to differences in structure, syntax and semantics. This impedes the development and deployment of data-driven applications providing fault detection and diagnosis, virtual metering or optimal control. [4] introduces a new platform for the continuous curation of a unified, Brick [1]-based metadata model that can be maintained throughout the building lifecycle. In this demonstration, we present a live proof-of-concept implementation of the platform with support for several metadata representations in the context of a simulated building lifecycle.

Fierro, Gabe↗
DOE OSTI2022

Application-Driven Creation of Building Metadata Models with Semantic Sufficiency

Semantic metadata models such as Brick, RealEstateCore, Project Haystack, and BOT promise to simplify and lower the cost of developing software for smart buildings, enabling the widespread deployment of energy efficiency applications. However, creating these models remains a challenge. Despite recent advances in creating models from existing digital representations like point labels and architectural models, there is still no feedback mechanism to ensure that the human input to these methods results in a model that can actually support the desired software. In this paper, we introduce the notion of semantic sufficiency, a practical principle for semantic metadata model creation that asserts that a model is "finished" when it contains the metadata necessary to support a given set of applications. To support semantic sufficiency, we design a standard representation for capturing application metadata requirements and a templating system for generating common metadata model components with limited user input. We then construct an iterative model creation workflow that integrates metadata requirements to direct the model creation effort, and present several novel optimizations that increase the model utility while minimizing the effort by a human operator. These new abstractions for model creation and validation lower model development costs and ensure the utility of the resulting model, thus facilitating the adoption of intelligent building applications.

applications↗
DOE OSTI2024

Multi-Omics integration can be used to rescue metabolic information for some of the dark region of the Pseudomonas putida proteome

In every omics experiment, genes or their products are identified for which even state of the art tools are unable to assign a function. In the biotechnology chassis organism Pseudomonas putida, these proteins of unknown function make up 14% of the proteome. This missing information can bias analyses since these proteins can carry out functions which impact the engineering of organisms. As a consequence of predicting protein function across all organisms, function prediction tools generally fail to use all of the types of data available for any specific organism, including protein and transcript expression information. Additionally, the release of Alphafold predictions for all Uniprot proteins provides a novel opportunity for leveraging structural information. We constructed a bespoke machine learning model to predict the function of recalcitrant proteins of unknown function in Pseudomonas putida based on these sources of data, which annotated 1079 terms to 213 proteins. Among the predicted functions supplied by the model, we found evidence for a significant overrepresentation of nitrogen metabolism and macromolecule processing proteins. These findings were corroborated by manual analyses of selected proteins which identified, among others, a functionally unannotated operon that likely encodes a branch of the shikimate pathway.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

BioHackathon 2015: Semantics of data for life sciences and reproducible research

We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.

97 MATHEMATICS AND COMPUTING↗