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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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DOE OSTI2017

The metagenomic data life-cycle: standards and best practices

Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described in a harmonised way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (1) material sampling, (2) material sequencing (3) data analysis and (4) data archiving & publishing. Taking examples from marine research, we summarise essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. These aspects of metagenomics dataset generation have been to some extent addressed by the scientific community but greater awareness and adoption is still needed. We emphasise the lack of standards relating to reporting how metagenomics datasets are analysed and how the metagenomics data analysis outputs should be archived and published. We propose best practice as a foundation for a community standard to enable reproducibility and better sharing of metagenomics datasets, leading ultimately to greater metagenomics data reuse and repurposing.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2020

Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization

Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

In with the old, in with the new: machine learning for time to event biomedical research

The predictive modeling literature for biomedical applications is dominated by biostatistical methods for survival analysis, and more recently some out of the box machine learning approaches. In this article, we show a presentation of a machine learning method appropriate for time-to-event modeling in the area of prostate cancer long-term disease progression. Using XGBoost adapted to long-term disease progression, we developed a predictive model for 118 788 patients with localized prostate cancer at diagnosis from the Department of Veterans Affairs (VA). Our model accounted for patient censoring. Harrell’s c-index for our model using only features available at the time of diagnosis was 0.757 95% confidence interval [0.756, 0.757]. Our results show that machine learning methods like XGBoost can be adapted to use accelerated failure time (AFT) with censoring to model long-term risk of disease progression. Furthermore, the long median survival justifies and requires censoring. Overall, we show that an existing machine learning approach can be used for AFT outcome modeling in prostate cancer, and more generally for other chronic diseases with long observation times.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2019

Automatic extraction of cancer registry reportable information from free-text pathology reports using multitask convolutional neural networks

Objective: In this work we implement 2 different multitask learning (MTL) techniques, hard parameter sharing and cross-stitch, to train a word-level convolutional neural network (CNN) specifically designed for automatic extraction of cancer data from unstructured text in pathology reports. We show the importance of learning related information extraction (IE) tasks leveraging shared representations across the tasks to achieve state-of-the-art performance in classification accuracy and computational efficiency. Materials and Methods: Multitask CNN (MTCNN) attempts to tackle document information extraction by learning to extract multiple key cancer characteristics simultaneously. We trained our MTCNN to perform 5 information extraction tasks: (1) primary cancer site (65 classes), (2) laterality (4 classes), (3) behavior (3 classes), (4) histological type (63 classes), and (5) histological grade (5 classes). We evaluated the performance on a corpus of 95 231 pathology documents (71 223 unique tumors) obtained from the Louisiana Tumor Registry. We compared the performance of the MTCNN models against single-task CNN models and 2 traditional machine learning approaches, namely support vector machine (SVM) and random forest classifier (RFC). Results: MTCNNs offered superior performance across all 5 tasks in terms of classification accuracy as compared with the other machine learning models. Based on retrospective evaluation, the hard parameter sharing and cross-stitch MTCNN models correctly classified 59.04% and 57.93% of the pathology reports respectively across all 5 tasks. The baseline models achieved 53.68% (CNN), 46.37% (RFC), and 36.75% (SVM). Based on prospective evaluation, the percentages of correctly classified cases across the 5 tasks were 60.11% (hard parameter sharing), 58.13% (cross-stitch), 51.30% (single-task CNN), 42.07% (RFC), and 35.16% (SVM). Moreover, hard parameter sharing MTCNNs outperformed the other models in computational efficiency by using about the same number of trainable parameters as a single-task CNN. Conclusions: The hard parameter sharing MTCNN offers superior classification accuracy for automated coding support of pathology documents across a wide range of cancers and multiple information extraction tasks while maintaining similar training and inference time as those of a single task–specific model.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2018

Studying language evolution in the age of big data

The increasing availability of large digital corpora of cross-linguistic data is revolutionizing many branches of linguistics. Overall, it has triggered a shift of attention from detailed questions about individual features to more global patterns amenable to rigorous, but statistical, analyses. This engenders an approach based on successive approximations where models with simplified assumptions result in frameworks that can then be systematically refined, always keeping explicit the methodological commitments and the assumed prior knowledge. Therefore, they can resolve disputes between competing frameworks quantitatively by separating the support provided by the data from the underlying assumptions. These methods, though, often appear as a ‘black box’ to traditional practitioners. In fact, the switch to a statistical view complicates comparison of the results from these newer methods with traditional understanding, sometimes leading to misinterpretation and overly broad claims. We describe here this evolving methodological shift, attributed to the advent of big, but often incomplete and poorly curated, data, emphasizing the underlying similarity of the newer quantitative to the traditional comparative methods and discussing when and to what extent the former have advantages over the latter. In this review, we cover briefly both randomization tests for detecting patterns in a largely model-independent fashion and phylolinguistic methods for a more model-based analysis of these patterns. We foresee a fruitful division of labor between the ability to computationally process large volumes of data and the trained linguistic insight declaring worthy prior commitments and interesting hypotheses in need of comparison.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2021

Measurement of the anisotropy power spectrum of the radio synchrotron background

We present the first targeted measurement of the power spectrum of anisotropies of the radio synchrotron background, at 140 MHz, where it is the overwhelmingly dominant photon background. This measurement is important for understanding the background level of radio sky brightness, which is dominated by steep-spectrum synchrotron radiation at frequencies below ν ~ 0.5 GHz and has been measured to be significantly higher than that produced by known classes of extragalactic sources and most models of Galactic halo emission. We determine the anisotropy power spectrum on scales ranging from 2° to 0.2 arcmin with Low-Frequency Array observations of two 18-deg 2 fields – one centred on the Northern hemisphere’s coldest patch of radio sky where the Galactic contribution is smallest and the other offset from that location by 15°. We find that the anisotropy power is higher than that attributable to the distribution of point sources above 100 μJy in flux. Furthermore, this level of radio anisotropy power indicates that if it results from point sources, those sources are likely at low fluxes and incredibly numerous, and likely clustered in a specific manner.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Islander: A database of precisely mapped genomic islands in tRNA and tmRNA genes

Genomic islands are mobile DNAs that are major agents of bacterial and archaeal evolution. Integration into prokaryotic chromosomes usually occurs site-specifically at tRNA or tmRNA gene (together, tDNA) targets, catalyzed by tyrosine integrases. This splits the target gene, yet sequences within the island restore the disrupted gene; the regenerated target and its displaced fragment precisely mark the endpoints of the island. We applied this principle to search for islands in genomic DNA sequences. Our algorithm identifies tDNAs, finds fragments of those tDNAs in the same replicon and removes unlikely candidate islands through a series of filters. A search for islands in 2168 whole prokaryotic genomes produced 3919 candidates. The website Islander (recently moved to http://bioinformatics.sandia.gov/islander/) presents these precisely mapped candidate islands, the gene content and the island sequence. The algorithm further insists that each island encode an integrase, and attachment site sequence identity is carefully noted; therefore, the database also serves in the study of integrase site-specificity and its evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The tmRNA website

We report that the transfer-messenger RNA (tmRNA) and its partner protein SmpB act together in resolving problems arising when translating bacterial ribosomes reach the end of mRNA with no stop codon. Their genes have been found in nearly all bacterial genomes and in some organelles. The tmRNA Website serves tmRNA sequences, alignments and feature annotations, and has recently moved to http: //bioinformatics.sandia.gov/tmrna/. New features include software used to find the sequences, an update raising the number of unique tmRNA sequences from 492 to 1716, and a database of SmpB sequences which are served along with the tmRNA sequence from the same organism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

RNAcentral: an international database of ncRNA sequences

The field of non-coding RNA biology has been hampered by the lack of availability of a comprehensive, up-to-date collection of accessioned RNA sequences. Here we present the first release of RNAcentral, a database that collates and integrates information from an international consortium of established RNA sequence databases. The initial release contains over 8.1 million sequences, including representatives of all major functional classes. A web portal (http://rnacentral.org) provides free access to data, search functionality, cross-references, source code and an integrated genome browser for selected species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

The MG-RAST Metagenomics Database and Portal in 2015

MG-RAST (http://metagenomics.anl.gov) is an opensubmission data portal for processing, analyzing, sharing and disseminating metagenomic datasets. Currently, the system hosts over 200 000 datasets and is continuously updated. The volume of submissions has increased 4-fold over the past 24 months, now averaging 4 terabasepairs per month. In addition to several new features, we report changes to the analysis workflow and the technologies used to scale the pipeline up to the required throughput levels. Lastly, to show possible uses for the data from MG-RAST, we present several examples integrating data and analyses from MG-RAST into popular third-party analysis tools or sequence alignment tools.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2016

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Upon the first publication of the fifth iteration of the Functional Annotation of Mammalian Genomes collaborative project, FANTOM5, we gathered a series of primary data and database systems into the FANTOM web resource (http://fantom.gsc.riken.jp) to facilitate researchers to explore transcriptional regulation and cellular states. In the course of the collaboration, primary data and analysis results have been expanded, and functionalities of the database systems enhanced. We believe that our data and web systems are invaluable resources, and we think the scientific community will benefit for this recent update to deepen their understanding of mammalian cellular organization. We introduce the contents of FANTOM5 here, report recent updates in the web resource and provide future perspectives.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Oak Ridge Reservation Environmental Protection Rad Neshaps Radionuclide Inventory Web Database and Rad Neshaps Source and Dose Database

The U.S. Environmental Protection Agency promulgated national emission standards for emissions of radionuclides other than radon from US Department of Energy facilities in Chapter 40 of the Code of Federal Regulations (CFR) 61, Subpart H. This regulatory standard limits the annual effective dose that any member of the public can receive from Department of Energy facilities to 0.1 mSv. As defined in the preamble of the final rule, all of the facilities on the Oak Ridge Reservation, i.e., the Y–12 National Security Complex, Oak Ridge National Laboratory, East Tennessee Technology Park, and any other U.S. Department of Energy operations on Oak Ridge Reservation, combined, must meet the annual dose limit of 0.1 mSv. At Oak Ridge National Laboratory, there are monitored sources and numerous unmonitored sources. To maintain radiological source and inventory information for these unmonitored sources, e.g., laboratory hoods, equipment exhausts, and room exhausts not currently venting to monitored stacks on the Oak Ridge National Laboratory campus, the Environmental Protection Rad NESHAPs Inventory Web Database was developed. This database is updated annually and is used to compile emissions data for the annual Radionuclide National Emission Standards for Hazardous Air Pollutants (Rad NESHAPs) report required by 40 CFR 61.94. It also provides supporting documentation for facility compliance audits. In addition, a Rad NESHAPs source and dose database was developed to import the source and dose summary data from Clean Air Act Assessment Package—1988 computer model files. As a result, this database provides Oak Ridge Reservation and facility-specific source inventory; doses associated with each source and facility; and total doses for the Oak Ridge Reservation dose.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

Why don't we share data and code? Perceived barriers and benefits to public archiving practices

The biological sciences community is increasingly recognizing the value of open, reproducible and transparent research practices for science and society at large. Despite this recognition, many researchers fail to share their data and code publicly. This pattern may arise from knowledge barriers about how to archive data and code, concerns about its reuse, and misaligned career incentives. Here, we define, categorize and discuss barriers to data and code sharing that are relevant to many research fields. We explore how real and perceived barriers might be overcome or reframed in the light of the benefits relative to costs. By elucidating these barriers and the contexts in which they arise, we can take steps to mitigate them and align our actions with the goals of open science, both as individual scientists and as a scientific community.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2019

Continuous-time quantum walks on dynamic graphs

Continuous-time quantum walks (CTQWs) on static graphs provide efficient methods for search and sampling as well as a model for universal quantum computation. We consider an extension of CTQWs to the case of dynamic graphs, in which an ordered sequence of graphs governs free evolution of the quantum walk. We then consider how perfect state transfer during the quantum walk can be used to design dynamic graphs that implement a universal set of quantum logic gates. We give explicit examples for a complete logical basis, and we validate implementations using numerical simulations for quantum teleportation and addition circuits. Lastly, we discuss the potential for realizing CTQWs on dynamic graphs using actively controlled quantum optical waveguides.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2017

New measurements of low-energy resonances in the Ne 22 ( p , γ ) Na 23 reaction

The Ne 22 ( p , γ ) Na 23 reaction is one of the most uncertain reactions in the NeNa cycle and plays a crucial role in the creation of Na 23 , the only stable Na isotope. Uncertainties in the low-energy rates of this and other reactions in the NeNa cycle lead to ambiguities in the nucleosynthesis predicted from models of thermally pulsing asymptotic giant branch (AGB) stars. This in turn complicates the interpretation of anomalous Na-O trends in globular cluster evolutionary scenarios. Prior studies of the Ne 22 ( p , γ ) Na 23 , Ne 22 ( He 3 , d ) Na 23 , and C 12 ( C 12 , p ) Na 23 reactions disagree on the strengths, spins, and parities of low-energy resonances in Na 23 and the direct-capture Ne 22 ( p , γ ) Na 23 reaction rate contains large uncertainties as well. Here, we present new measurements of resonances at E r c.m. = 417 , 178, and 151 keV and of the direct-capture process in the Ne 22 ( p , γ ) Na 23 reaction. The resulting total Ne 22 ( p , γ ) Na 23 rate is approximately a factor of 20 higher than the rate listed in a recent compilation at temperatures relevant to hot-bottom burning in AGB stars. Although our rate is close to that derived from a recent Ne 22 ( p , γ ) Na 23 measurement by Cavanna et al. in 2015, we find that this large rate increase results in only a modest 18% increase in the Na 23 abundance predicted from a 5 M ⊙ thermally pulsing AGB star model from Ventura and D'Antona (2005). The estimated astrophysical impact of this rate increase is in marked contrast to the factor of ~ 3 increase in Na 23 abundance predicted by Cavanna et al. and is attributed to the interplay between the Na 23 ( p , α ) Ne 20 and Ne 20 ( p , γ ) Na 21 reactions, both of which remain fairly uncertain at the relevant temperature range.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗