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At least 1,063 records · Page 59

Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA

Tens-of-thousands of chemicals are registered in the U.S. for use in countless processes and products. Recent evidence suggests that many of these chemicals are measureable in environmental and/or biological systems, indicating the potential for widespread exposures. Traditional public health research tools, including in vivo studies and targeted analytical chemistry methods, have been unable to meet the needs of screening programs designed to evaluate chemical safety. As such, new tools have been developed to enable rapid assessment of potentially harmful chemical exposures and their attendant biological responses. One group of tools, known as “nontargeted analysis” (NTA) methods, allows the rapid characterization of thousands of never-before-studied compounds in a wide variety of environmental, residential, and biological media. This article discusses current applications of NTA methods, challenges to their effective use in chemical screening studies, and ways in which shared resources (e.g., chemical standards, databases, model predictions, and media measurements) can advance their use in risk-based chemical prioritization. A brief review is provided of resources and projects within EPA’s Office of Research and Development (ORD) that provide benefit to, and receive benefits from, NTA research endeavors. A summary of EPA’s Non-Targeted Analysis Collaborative Trial (ENTACT) is also given, which makes direct use of ORD resources to benefit the global NTA research community. Finally, a research framework is described that shows how NTA methods will bridge chemical prioritization efforts within ORD. This framework exists as a guide for institutions seeking to understand the complexity of chemical exposures, and the impact of these exposures on living systems.

54 ENVIRONMENTAL SCIENCES↗

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

Large language models (LLMs) show promise in supporting differential diagnosis, but their performance is challenging to evaluate due to the unstructured nature of their responses, and their accuracy compared to existing diagnostic tools is not well characterized. To assess the current capabilities of LLMs to diagnose genetic diseases, we benchmarked these models on 5213 previously published case reports using the Phenopacket Schema, the Human Phenotype Ontology and Mondo disease ontology. Prompts generated from each phenopacket were sent to seven LLMs, including four generalist models and three LLMs specialized for medical applications. The same phenopackets were used as input to a widely used diagnostic tool, Exomiser, in phenotype-only mode. The best LLM ranked the correct diagnosis first in 23.6% of cases, whereas Exomiser did so in 35.5% of cases. While the performance of LLMs for supporting differential diagnosis has been improving, it has not reached the level of commonly used traditional bioinformatics tools. Future research is needed to determine the best approach to incorporate LLMs into diagnostic pipelines.

Reese, Justin T. [Lawrence Berkeley National Labor↗

Resonant inelastic X-ray scattering tools to count 5 $f$ electrons of actinides and probe bond covalency

The actinides possess a complex electronic structure, making their chemical and physical properties among the least understood in the periodic table. Advanced spectroscopic tools, able to obtain deep insights into the electronic structure and binding properties of the actinides, are highly desirable. Here, we introduce two sensitive spectroscopic tools: one determines the number of localized 5f electrons on an actinide atom, and another assesses the covalent character of actinide-ligand bonding. Both tools are based on the multiplet structure present in actinide M 4 edge core-to-core resonant inelastic X-ray scattering (CC-RIXS) maps. The spectral intensity of different many-body final-state multiplets directly depends on the local many-electron ground-state symmetry including the local 5 f spin configuration. By comparing U M 4 edge CC-RIXS data for 21 U, Np, Pu and Am compounds, we demonstrate the ability to compare the number of localized 5 f electrons and bond covalency across the actinide series.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

A solar energy desalination analysis tool, sedat, with data and models for selecting technologies and regions

Abstract There is interest for desalination technologies powered by solar energy as arid areas are typically bestowed with good solar potential. In response to a US DOE call for solar desalination analysis tools, we developed an open-source solar energy desalination analysis tool, sedat , for techno-economical evaluation of desalination technologies and selection of regions with the highest potential for using solar energy to power desalination plants. It is expected that this software will simplify the planning, design, and valuation of solar desalination systems in the U.S. and worldwide. Sedat uses Dash for integrating various layers of large volumes of GIS data with Python-based models of solar energy generation and desalination technologies. It derives time-series of energy generation and water production, with details of plant performance and suggestions for improving the solar-desalination coupling. This paper summarizes the various phases of the tool’s development, presents example results showing the potential, under multiple objectives, of solar desalination in parts of the U.S. southwest, and discusses method details that would be useful for future model development.

14 SOLAR ENERGY↗

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Bolduc, Benjamin (ORCID:0000000324200755)↗

CyPhyR: a cyber‐physical analysis tool for measuring and enabling resiliency in microgrids

This study presents a tool to study the cyber‐physical resiliency (CyPhyR) of critical energy infrastructure system, in particular the effect of cyber attacks on the microgrid's resiliency. The developed tool enables measuring resiliency using data from cyber and physical systems and suggests control decisions for resilient planning and operation of the microgrid. The microgrid resiliency is formulated based on graph theory based indices and cyber‐power system characteristics. A Common Vulnerability Scoring System based metric called the Cyber Asset Impact Potential is developed and used in the planning phase, and another metric, Cyber Impact Severity is introduced to study the system performance in the operational phase. The information from these two phases is provided to the operator to make informed and proactive decisions to ensure the resilient operation of the microgrid. The performance of the developed tool has been tested using comprehensive real‐time cyber‐power testbed for a Consortium for Electric Reliability Technology Solutions microgrid test system.

Venkataramanan, Venkatesh↗

Tool path influence on electric pulse aided deformation during incremental sheet metal forming

Titanium and its alloys are difficult to form at room temperature due to their high flow stress. Super plastic deformation of Ti alloys involves low strain rate forming at very high temperatures which need special tooling which can withstand high temperatures. It was observed that when high current density electric pulse is applied during deformation it reduces the flow stress through electron-dislocation interaction. This phenomenon is known as electro-plasticity. In the present work, importance of tool configuration to enhance the formability without much resistive heating is demonstrated for Incremental Sheet Metal Forming (ISMF). Tool configuration is selected to minimize the current carrying zone in DC pulse aided incremental forming to enhance the formability due to electro plasticity and the same is demonstrated by forming two pyramid shaped components of 30° and 45° wall angles using a Titanium alloy sheet of 0.6 mm thickness. Load measurement indicated that a critical current density is essential for the electro-plasticity to be effective and the same is realized with the load and temperature measurements.

36 MATERIALS SCIENCE↗

Nearside-farside, local angular momentum and resummation theories: Useful tools for understanding the dynamics of complex-mode reactions

A valuable tool for understanding the dynamics of direct reactions is Nearside-Farside (NF) scattering theory. It makes a decomposition of the (resummed) partial wave series for the scattering amplitude, both for the differential cross section (DCS) and the Local Angular Momentum (LAM). This paper makes the first combined application of these techniques to complex-mode reactions. We ask if NF theory is a useful tool for their identification, in particular, can it distinguish complex-mode from direct-mode reactions? We also ask whether NF theory can identify NF interference oscillations in the full DCSs of complex-mode reactions. Our investigation exploits the fact that accurate quantum scattering matrix elements have recently become available for complex-mode reactions. We first apply NF theory to two simple models for the scattering amplitude of a complex-mode reaction: One involves a single Legendre polynomial; the other involves a single Legendre function of the first kind, whose form is suggested by complex angular momentum theory. We then study, at fixed translational energies, four state-to-state complex-mode reactions. They are: S({sup 1}D) + HD → SH + D, S({sup 1}D) + DH → SD + H, N({sup 2}D) +H{sub 2} → NH + H, and H{sup +} + D{sub 2} → HD + D{sup +}. We compare the NF results for the DCSs and LAMs with those for a state-to-state direct reaction, namely, F + H{sub 2} → FH + H. We demonstrate that NF theory is a valuable tool for identifying and analyzing the dynamics of complex-mode reactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

S&T converging trends in dealing with disaster: A review on AI tools

Science and Technology (S&T) has been able to help mankind to solve or minimize problems when arise. Different methodologies, techniques and tools were developed or used for specific cases by researchers, engineers, scientists throughout the world, and numerous papers and articles have been written by them. Nine selected cases such as flash flood, earthquakes, workplace accident, fault in aircraft industry, seismic vulnerability, disaster mitigation and management, and early fault detection in nuclear industry have been studied. This paper looked at those cases, and their results showed nearly 60% uses artificial intelligence (AI) as a tool. This paper also did some review that will help young researchers in deciding the types of AI tools to be selected; thus proving the future trends in S&T.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Charge breeders: Development of diagnostic tools to probe the underlying physics

Charge breeders were developed more than 20 years ago in the context of radioactive ion beam (RIB) production. The main goal is to boost the charge state of a singly charged RIB to a higher value matching the A/Q of a post-accelerator. In that way, the RIB produced at some tens of keV can efficiently be accelerated to energies in a range of few MeV/u up to several tens of MeV/u, which is of interest for nuclear structure and nuclear astrophysics experiments. Two families of charge breeders have been developed: one based on Electron Cyclotron Resonance Ion Sources (ECRISs) suitable for Continuous Wave (CW) operation and another built around Electron Beam Ion Sources (EBISs) used for pulsed post-accelerators. For many years, experimental studies have been carried out to enhance the charge breeding process and improve the extracted beam quality, i.e., purity, intensity, emittance, and time structure. The evolution of the charge breeders is also closely related to the emergence of new facilities delivering even more exotic beams. Diagnostic tools, such as Faraday cups, beam profile monitors, and emittance scanners, are mandatory to tune the machines and evaluate their performances. However, to go beyond that, a better understanding of plasma physics (in ECRIS) and electron-ion interactions (in EBIS), as well as the 1+ beam characteristics, for instance, energy spread transverse emittance, is needed. Therefore, simulation codes modeling the physics phenomena in both type of charge breeders were developed to support the understanding of experimental outputs and to gain insights into non-observable parameters. Nevertheless, more sophisticated diagnostic tools are required to improve the charge breeding performance and to extend the potential applications toward new RIB facilities. This Review will present the two kinds of charge breeders and their technical evolutions. It will review the diagnostic tools and simulation codes employed for operation and evaluation of the internal physics processes.

47 OTHER INSTRUMENTATION↗

Flexible visualization of a 3rd party Intrusion Prevention (Security) tool: A use case with the ELK stack

A difficult aspect of cyber security is the ability to achieve automated real time intrusion prevention across various sets of systems. To this extent, several companies are offering comprehensive solutions that leverage an "accuracy of scale" and moving much of the intelligence and detection on the Cloud, relying on an ever-growing set of data and analytics to increase decision accuracy. Often, they provide tools to visualize the decision workflows in attack prevention (as well as tune the algorithm) but those solutions are not always practical as companies see the problem as "global" that is, from a unified Cyber-security standpoint. However, a key to a successful Cyber-security program is transparency and trust: from an experimental team viewpoint, this specifically means having the ability to immediately see what and from where, who has been blocked and being able to inform the community in case of a revoked access without the need for filing a "ticket" (that may eventually be answered) – in other words, rapid response to their user-base is essential but solutions targeting "sub-groups" in an organization are not often available. We have come up with a versatile solution leveraging the ELK stack (Elasticsearch, Logstash, & Kibana) and an IPS (Intrusion Prevention System) based WAF (Web Application Firewall) from Signal Sciences. Signal Science allows the streaming of detailed logs in a Logstash format suitable for custom solutions for visualization. By combining these two tools, we have strengthened our security posture and enabled individual experiments to monitor their own traffic. Specifically, the IPS WAF provides unique data such as country of origin, protocol, response code, source IP, and paths accessed. In this contribution, we will show how we engineered a visualization solution so experiment groups could access a dashboard with predefined graphs but also, where they can create individual customizable dashboards used to display blocked traffic and troubleshoot latency issues. We will discuss the details and procedures for developing and configuring these tools and how it benefits cyber security postures across our scientific based environment.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

The 'last mile' of data handling: Fermilab's IFDH tools

IFDH (Intensity Frontier Data Handling), is a suite of tools for data movement tasks for Fermilab experiments and is an important part of the FIFE[2] (Fabric for Intensity Frontier [1] Experiments) initiative described at this conference. IFDH encompasses moving input data from caches or storage elements to compute nodes (the 'last mile' of data movement) and moving output data potentially to those caches as part of the journey back to the user. IFDH also involves throttling and locking to ensure that large numbers of jobs do not cause data movement bottlenecks. IFDH is realized as an easy to use layer that users call in their job scripts (e.g. 'ifdh cp'), hiding the low level data movement tools. One advantage of this layer is that the underlying low level tools can be selected or changed without the need for the user to alter their scripts. Logging and performance monitoring can also be added easily. This system will be presented in detail as well as its impact on the ease of data handling at Fermilab experiments.

Lyon, Adam L.↗

Calibration and validation of a spar-type floating offshore wind turbine model using the FAST dynamic simulation tool

In this study, high-quality computer simulations are required when designing floating wind turbines because of the complex dynamic responses that are inherent with a high number of degrees of freedom and variable metocean conditions. In 2007, the FAST wind turbine simulation tool, developed and maintained by the U.S. Department of Energy's (DOE's) National Renewable Energy Laboratory (NREL), was expanded to include capabilities that are suitable for modeling floating offshore wind turbines. In an effort to validate FAST and other offshore wind energy modeling tools, DOE funded the DeepCwind project that tested three prototype floating wind turbines at 1/50 th scale in a wave basin, including a semisubmersible, a tension-leg platform, and a spar buoy. This paper describes the use of the results of the spar wave basin tests to calibrate and validate the FAST offshore floating simulation tool, and presents some initial results of simulated dynamic responses of the spar to several combinations of wind and sea states. Wave basin tests with the spar attached to a scale model of the NREL 5-megawatt reference wind turbine were performed at the Maritime Research Institute Netherlands under the DeepCwind project. This project included free-decay tests, tests with steady or turbulent wind and still water (both periodic and irregular waves with no wind), and combined wind/wave tests. The resulting data from the 1/50th model was scaled using Froude scaling to full size and used to calibrate and validate a full-size simulated model in FAST. Results of the model calibration and validation include successes, subtleties, and limitations of both wave basin testing and FAST modeling capabilities.

17 WIND ENERGY↗

Open access to high-level data and analysis tools in the CMS experiment at the LHC

The CMS experiment, in recognition of its commitment to data preservation and open access as well as to education and outreach, has made its first public release of high-level data under the CC0 waiver: up to half of the proton-proton collision data (by volume) at 7 TeV from 2010 in CMS Analysis Object Data format. CMS has prepared, in collaboration with CERN and the other LHC experiments, an open-data web portal based on Invenio. The portal provides access to CMS public data as well as to analysis tools and documentation for the public. The tools include an event display and histogram application that run in the browser. In addition a virtual machine containing a CMS software environment along with XRootD access to the data is available. Within the virtual machine the public can analyse CMS data, example code is provided. As a result, we describe the accompanying tools and documentation and discuss the first experiences of data use.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Lipid Mini-On: mining and ontology tool for enrichment analysis of lipidomic data

Abstract Summary Here we introduce Lipid Mini-On, an open-source tool that performs lipid enrichment analyses and visualizations of lipidomics data. Lipid Mini-On uses a text-mining process to bin individual lipid names into multiple lipid ontology groups based on the classification (e.g. LipidMaps) and other characteristics, such as chain length. Lipid Mini-On provides users with the capability to conduct enrichment analysis of the lipid ontology terms using a Shiny app with options of five statistical approaches. Lipid classes can be added to customize the user’s database and remain updated as new lipid classes are discovered. Visualization of results is available for all classification options (e.g. lipid subclass and individual fatty acid chains). Results are also visualized through an editable network of relationships between the individual lipids and their associated lipid ontology terms. The utility of the tool is demonstrated using biological (e.g. human lung endothelial cells) and environmental (e.g. peat soil) samples. Availability and implementation Rodin (R package: https://github.com/PNNL-Comp-Mass-Spec/Rodin), Lipid Mini-On Shiny app (https://github.com/PNNL-Comp-Mass-Spec/LipidMiniOn) and Lipid Mini-On online tool (https://omicstools.pnnl.gov/shiny/lipid-mini-on/). Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

RAG-3D: A search tool for RNA 3D substructures

In this study, to address many challenges in RNA structure/function prediction, the characterization of RNA's modular architectural units is required. Using the RNA-As-Graphs (RAG) database, we have previously explored the existence of secondary structure (2D) submotifs within larger RNA structures. Here we present RAG-3D—a dataset of RNA tertiary (3D) structures and substructures plus a web-based search tool—designed to exploit graph representations of RNAs for the goal of searching for similar 3D structural fragments. The objects in RAG-3D consist of 3D structures translated into 3D graphs, cataloged based on the connectivity between their secondary structure elements. Each graph is additionally described in terms of its subgraph building blocks. The RAG-3D search tool then compares a query RNA 3D structure to those in the database to obtain structurally similar structures and substructures. This comparison reveals conserved 3D RNA features and thus may suggest functional connections. Though RNA search programs based on similarity in sequence, 2D, and/or 3D structural elements are available, our graph-based search tool may be advantageous for illuminating similarities that are not obvious; using motifs rather than sequence space also reduces search times considerably. Ultimately, such substructuring could be useful for RNA 3D structure prediction, structure/function inference and inverse folding.

59 BASIC BIOLOGICAL SCIENCES↗

Comprehensive High Throughput One‐Pot Analysis of Glycoproteins through Tool for Rapid Analysis of Glycopeptide by Permethylation (TRAP) Method.

Glycoproteins plays key roles in various cellular functions such as protein folding, protein targeting, receptor function, cell–cell recognition, protein stability, signaling, and other cellular functions. Currently a comprehensive and universal tool for the automated analysis of glycopeptides through their tandem mass spectrometry and data processing is a tedious process. We recently developed a method, Tool for Rapid Analysis of glycopeptide by Permethylation (TRAP), that simplifies glycoprotein analysis by integrating glycan sequencing and glycopeptide analysis in a single experiment. We employed this approach for the detailed analysis of glycosidic linkages, composition, glycan sequencing, glycosylation site mapping and sequencing of peptide moiety of glycopeptides of glycoproteins from both prokaryotes and eukaryotes. Here we are presenting an easy to use, robust, suitable for large as well as small sample sets and also cost‐effective glycoprotein analysis tool through TRAP approach. A permethylation protocol which can be automated and suitable for reliable permethylation of glycopeptides from the protease digest of glycoproteins was developed. Initial studies on glycopeptides from a model glycoprotein bovine RNAse B indicates that improved sensitivity and throughput of permethylation reactions can be achieved in conducting the reaction in microscale. This approach would enable convenient, rapid, and reliable high‐throughput screening of protein glycosylation and can be employed as a cost‐effective kit for glycosylated biomarker discoveries. In order to improvise the comprehensive glycosylation analysis and throughput, we have also developed an LC‐MS/MS platform for the analysis of glycopeptides processed through TRAP. We have conducted the analysis of standard glycoproteins such as bovine RNase B, human transferrin, and bovine fetuin and our preliminary results indicate that TRAP hyphened with LC‐MS/MS enables characterization of isomers of each glycoform at each glycosylation sites of complex glycoprotein mixtures. Support or Funding Information This research was supported by the National Institutes of Health (NIH) funded research, Grant R21GM122633; resource for biomedical glycomics, Grant P41GM103490; instrument grant, Grant S10OD018530; and U.S. Department of Energy grant, Grant DE‐SC0015662, to the Complex Carbohydrate Research Center. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Shajahan, Asif↗