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At least 739 records · Page 41

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

Complex morphological traits are the product of many genes with transient or lasting developmental effects that interact in anatomical context. Mouse models are a key resource for disentangling such effects, because they offer myriad tools for manipulating the genome in a controlled environment. Unfortunately, phenotypic data are often obtained using laboratory-specific protocols, resulting in self-contained datasets that are difficult to relate to one another for larger scale analyses. To enable meta-analyses of morphological variation, particularly in the craniofacial complex and brain, we created MusMorph, a database of standardized mouse morphology data spanning numerous genotypes and developmental stages, including E10.5, E11.5, E14.5, E15.5, E18.5, and adulthood. To standardize data collection, we implemented an atlas-based phenotyping pipeline that combines techniques from image registration, deep learning, and morphometrics. Alongside stage-specific atlases, we provide aligned micro-computed tomography images, dense anatomical landmarks, and segmentations (if available) for each specimen (N = 10,056). Our workflow is open-source to encourage transparency and reproducible data collection.

59 BASIC BIOLOGICAL SCIENCES↗

Probabilistic estimation of depth-resolved profiles of soil thermal diffusivity from temperature time series: Supporting Data

This dataset consists of soil temperature time series that were used to estimate soil thermal diffusivity and its uncertainty trough the probabilistic modelling approach developed and presented in the article named "Probabilistic estimation of depth-resolved profiles of soil thermal diffusivity from temperature time series" and published in Earth Surface Dynamics. There are two compressed (.zip) files that contains synthetic (Synthetic_soiltemp_Teller.zip) and field (Field_soiltemp_Teller.zip) data. There is one MATLAB file that requires MATLAB to execute but any text editor can open it. The Synthetic_soiltemp_Teller.zip file includes 5 comma-delimited data files (.csv) each of which contains soil temperature time series generated through forward modeling (i.e., heat-conduction process in a heterogeneous medium using an explicit finite difference method) to mimic various types of temperature gradients, trend and fluctuations. These synthetic soil temperatures were used to investigate the impact of different environmental conditions on the uncertainty of thermal diffusivity estimates. The Field_soiltemp_Teller.zip file contains 28 comma-delimited data files (.csv) out of which (a) 27 files includes soil temperature time series recorded from 27 temperature probes located in a site along Teller Road about 40 km northwest of Nome, Alaska (64.72°N, 165.94°W), (b) one includes the name and coordinates of the 27 probes. These field soil temperatures were used to infer soil thermal diffusivity at numerous locations and depths in a discontinuous permafrost environment, and to evaluate the links between the estimated soil thermal diffusivity values and soil physical properties. The comma-delimited data files (.csv) of the synthetic and field soil temperature time series includes date and time (UTC) in the first column and soil temperature from 5 cm below the ground surface to 1.05 m depth (with 5 or 10 cm spacing between sensors) in the other columns. The measurements were acquired every 15 minutes. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

54 ENVIRONMENTAL SCIENCES↗

Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three-dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB, RCSB.org) and Protein Data Bank in Europe (PDBe, PDBe.org) as an open-source, web-based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. Across RCSB.org, the RCSB PDB research-focused web portal, Mol* has been implemented to support single-mouse-click atomic-level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small-molecule ligands, ions, water molecules, or other macromolecules. RCSB.org Mol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within various RCSB.org tools—allowing users to view polymer sequence and structure-based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available at RCSB.org, Standalone Mol* is freely available for visualizing any atomic-level or multi-scale biostructure at rcsb.org/3d-view.

3D biostructure↗

One step removed shadow network

A system and method includes an operational network that communicates with an external network by opening a first transmission protocol socket. A data diode coupled to the operational network and a gateway enables the one-way transfer of all information received from the external network and transmitted by the operational network to the gateway such that no information travels from the gateway to the operational network or the external network. The gateway opens a second transmission protocol socket by mapping a sequence number to an acknowledgement number and increasing that mapped acknowledgement number by a value of one. A transmitter then transmits the acknowledgment to a remote network or a gateway.

Park, Brent K.↗

Automating Traffic Microsimulation from SYNCHRO UTDF to SUMO

Modern transportation research relies on seamlessly integrating traffic signal data with robust network representation and simulation tools. This study presents utdf2gmns, an open-source Python tool that automates conversion of the Universal Traffic Data Format, including network representation, signalized intersections, and turning volumes into the General Modeling Network Specification (GMNS) Standard. The resulting GMNS-compliant network can be converted for microsimulation in SUMO. By automatically extracting intersection control parameters and aligning them with GMNS conventions, utdf2gmns minimizes manual preprocessing and data loss. utdf2gmns also integrates with the Sigma-X engine to extract and visualize key traffic control metrics, such as phasing diagrams, turning volumes, volume-tocapacity ratios, and control delays. This streamlined workflow enables efficient scenario testing, accurate model building, and consistent data management. Validated through case studies, utdf2gmns reliably models complex urban corridors, promoting reproducibility and standardization. Documentation is available on GitHub and PyPI, supporting easy integration and community engagement.

Luo, Roy [ORNL] (ORCID:0009000312909983)↗

Models and Processes to Extract Drug-like Molecules From Natural Language Text

Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of viral research. However, this literature is too large for human review and features unusual vocabularies for which existing named entity recognition (NER) models are ineffective. We report here on a project that leverages both human and artificial intelligence to detect references to such molecules in free text. We present 1) a iterative model-in-the-loop method that makes judicious use of scarce human expertise in generating training data for a NER model, and 2) the application and evaluation of this method to the problem of identifying drug-like molecules in the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198,875 papers. We show that by repeatedly presenting human labelers only with samples for which an evolving NER model is uncertain, our human-machine hybrid pipeline requires only modest amounts of non-expert human labeling time (tens of hours to label 1778 samples) to generate an NER model with an F-1 score of 80.5%—on par with that of non-expert humans—and when applied to CORD’19, identifies 10,912 putative drug-like molecules. This enriched the computational screening team’s targets by 3,591 molecules, of which 18 ranked in the top 0.1% of all 6.6 million molecules screened for docking against the 3CLPro protein.

60 APPLIED LIFE SCIENCES↗

ARES I: WASP-76 b, A Tale of Two HST Spectra

We analyze the transmission and emission spectra of the ultra-hot Jupiter WASP-76 b, observed with the G141 grism of the Hubble Space Telescope’s (HST) Wide Field Camera 3 (WFC3). We reduce and fit the raw data for each observation using the open-source software Iraclis before performing a fully Bayesian retrieval using the publicly available analysis suite TauREx 3. Previous studies of the WFC3 transmission spectra of WASP-76 b found hints of titanium oxide (TiO) and vanadium oxide (VO) or non-gray clouds. Accounting for a fainter stellar companion to WASP-76, we reanalyze this data and show that removing the effects of this background star changes the slope of the spectrum, resulting in these visible absorbers no longer being detected, eliminating the need for a non-gray cloud model to adequately fit the data but maintaining the strong water feature previously seen. However, our analysis of the emission spectrum suggests the presence of TiO and an atmospheric thermal inversion, along with a significant amount of water. Given the brightness of the host star and the size of the atmospheric features, WASP-76 b is an excellent target for further characterization with HST, or with future facilities, to better understand the nature of its atmosphere, to confirm the presence of TiO and to search for other optical absorbers.

79 ASTRONOMY AND ASTROPHYSICS↗

Kinetics Data of Iron(II), Manganese(II), Dissolved Organic Carbon and Nitrate from Batch Incubation Experiments Using Hyporheic Sediments from the East River Watershed, Colorado.

Hyporheic zones act as critical ecological links between terrestrial and aquatic systems where redox-sensitive metals of iron (Fe) and manganese (Mn) significantly impact nutrient cycling and water quality. In order to understand the production, release and speciation of Fe(II) and Mn(II) in groundwater, we conducted batch incubation experiments using sediment samples from a hyporheic zone of the East River floodplain in Colorado. The East River is part of the Watershed Function Scientific Focus Area (WFSFA) located in the Upper Colorado River Basin, United States. Collection and processing of the data is described in the Methods, along with details of data file contents. There are 6 data files provided in two formats: 1 zip-folder of .csv (open source) files, and 1 zip-folder of .xlsx (Excel) files. The data tables provided in the two formats are the exact same.

54 ENVIRONMENTAL SCIENCES↗

Narrow-Band Least-Squares Infrasound Array Processing

Infrasound data from arrays can be used to detect, locate, and quantify a variety of natural and anthropogenic sources from local to remote distances. However, many array processing methods use a single broad frequency range to process the data, which can lead to signals of interest being missed due to the choice of frequency limits or simultaneous clutter sources. In this work, we introduce a new open-source Python code that processes infrasound array data in multiple sequential narrow frequency bands using the least-squares approach. We test our algorithm on a few examples of natural sources (volcanic eruptions, mass movements, and bolides) for a variety of array configurations. Our method reduces the need to choose frequency limits for processing, which may result in missed signals, and it is parallelized to decrease the computational burden. Improvements of our narrow-band least-squares algorithm over broad-band least-squares processing include the ability to distinguish between multiple simultaneous sources if distinct in their frequency content (e.g., microbarom or surf vs. volcanic eruption), the ability to track changes in frequency content of a signal through time, and a decreased need to fine-tune frequency limits for processing. We incorporate a measure of planarity of the wavefield across the array (sigma tau, στ) as well as the ability to utilize the robust least trimmed squares algorithm to improve signal processing and insight into array performance. Our implementation allows for more detailed characterization of infrasound signals recorded at arrays that can improve monitoring and enhance research capabilities.

58 GEOSCIENCES↗

Convergent Manufacturing of Large-Scale Components for Nuclear Applications, via Additive Manufacturing and Powder Metallurgy Hot Isostatic Pressing

Powder metallurgy (PM)–hot isostatic pressing (PM-HIP) has long been recognized as a powerful route for producing fully dense, near net shape metallic components. By consolidating powders under high temperature and pressure, HIP provides isotropic properties, uniform microstructures, and scalability to complex geometries that are vital for sectors such as aerospace, energy, and nuclear power. Yet despite these advantages, the technology has remained constrained by costly trial and error canister fabrication, limitations of conventional forging, and incomplete knowledge about how the canister design influences final part properties. Additive manufacturing (AM), by contrast, thrives on design freedom and geometric flexibility but struggles with speed, scalability, and cost when applied to very large structures. The research presented in this report investigated how a convergent manufacturing approach, combining AM with PM-HIP, can merge the strengths of both technologies, leveraging AM’s flexibility for canister design and HIP’s consolidation capability to deliver reliable, large, and complex parts. The work progressed through three case studies that built on one another in scale and complexity. Small cylindrical canisters fabricated by conventional methods, laser powder bed fusion, and directed energy deposition were filled with stainless steel powders and subjected to HIP. The resulting parts demonstrated near-full density and mechanical properties on par with wrought stainless steel, showing for the first time that AM canisters can be a direct substitute for conventional ones without sacrificing quality. The next step involved a medium-scale, noncentrosymmetric T-valve, which is an enclosed, multibranch geometry that tested the limits of AM + PM-HIP integration. The T-valve achieved predictable shrinkage and uniform densification, confirming feasibility for enclosed designs. However, this study also revealed oxide inclusions and interfacial challenges at the AM + HIP boundary, underscoring the critical importance of controlling interface chemistry and employing robust, in situ strategies, such as melt pool monitoring and thermal monitoring, coupled with nondestructive evaluation techniques such as x-ray computed tomography. Finally, the effort culminated in fabricating a large-scale impeller weighing nearly 2000 lb and spanning 5 ft in diameter. Produced via multirobot wire arc AM and hot isostatic pressed to near-full density, the impeller validated industrial-scale feasibility. Predictive models closely matched experimental shrinkage, tensile properties were spatially uniform across the component, and the AM + PM-HIP interface proved mechanically sound despite the presence of oxide-decorated prior particle boundaries. This large-scale demonstration is a major milestone, showing that hybrid AM + PM‑HIP can reliably deliver components at reactor-relevant scales. Collectively, these studies charted a logical pathway: small-scale work built scientific confidence, medium-scale work highlighted opportunities and challenges, and large-scale work proved industrial impact. The overarching conclusion of this report is that AM + PM-HIP should not be seen as a replacement for forging but as a complementary pathway that provides the US with flexibility, resilience, and new options for manufacturing nuclear-grade components. Looking ahead, several directions emerge as critical to sustaining progress. Predictive modeling must become faster, more accessible, and more accurate, with digital twins and machine learning reducing reliance on trial and error. Powders and alloys must be optimized for HIP, with improved cleanliness, reduced oxides, and tailored chemistries that enhance creep, fatigue, and irradiation resistance. Interfaces between AM and HIP regions must be better engineered through coatings, machining strategies, and surface treatments to mitigate oxide formation and ensure reliable bonding to explore opportunities for HIP of targeted compositional parts, as well as multimaterial HIP cladding applications. Monitoring and nondestructive evaluation need to expand, incorporating multimodal sensors, x-ray computed tomography, and real-time data integration through platforms such as Pelican. At the same time, the pathway to industrial adoption requires techno-economic analysis, machinability studies, and qualification frameworks aligned with industry and regulatory standards. Finally, workforce and academic engagement must be strengthened. Programs that train technicians and engineers for US Navy and US Department of Energy manufacturing challenges should be paired with academic partnerships to support fundamental research, with open sharing of non-export-controlled data to accelerate innovation and build the next generation of experts. In conclusion, this report demonstrates that hybrid AM + PM-HIP is scientifically viable and strategically important. By combining the design agility of AM with the consolidation strength of HIP and embedding modeling, monitoring, and workforce development, this approach provided a transformative new capability for US manufacturing. The path forward is clear: hybrid AM + PM-HIP is not just a promising research direction but is also potentially an industrially relevant pathway that can reshape how nuclear-grade components are designed, qualified, and deployed.

36 MATERIALS SCIENCE↗

fluxfinder: An R Package for Reproducible Calculation and Initial Processing of Greenhouse Gas Fluxes From Static Chamber Measurements

Fluxes of greenhouse gases are a critical component of the earth's natural climate, but anthropogenic emissions have created an imbalance and resulted in global climate change. Quantifying the emission of these gases is vital to our understanding of their sources and sinks, both natural and anthropogenic. The static chamber method, in which a system of interest is enclosed, and gas concentrations are measured over time, is widely used to estimate fluxes of greenhouse gases. With the development of instruments such as infrared gas analyzers (IRGAs) supporting high-frequency concentration data, there is a growing need for open-source workflows to calculate fluxes. Here we present fluxfinder, an R package designed to support reproducible calculations and processing of greenhouse gas fluxes measured with the static chamber method. The package includes raw data file parsing from widely used IRGAs, metadata matching, unit conversion, flux estimations, and initial quality assurance/quality control (QA/QC). Diagnostic graphical plots provide a transparent way to differentiate between measurement issues and nonlinear behavior. The package is also designed to be easily integrated with the gasfluxes package for further fitting of nonlinear concentration-time models, allowing alternative or additional flux QA/QC. The fluxfinder package offers a flexible workflow that is easily adaptable to promote open and reproducible greenhouse gas flux estimations.

Wilson, Stephanie J.↗

Common Information Model for Electromagnetic Transients (CIM for EMT): CRADA 533 [Abstract only}

The control and protection functions of inverter-based resources (IBR) have raised concerns with bulk system reliability. Most of the current interest lies with solar photovoltaic generation but increasing amounts of storage would pose the same risks. Newer North American Electric Reliability Corporation (NERC) guidelines call for electromagnetic transient (EMT) studies of IBR and recommend that transmission operators collect distributed energy resource (DER) data to support such modeling. IEEE Standard P2800.1 is defining tests for model parameterization, so good model data should become available from inverter vendors. (EMT studies also apply to large power transformer reliability, and transformer vendors can provide EMT models.) Utilities don’t currently have the rest of the bulk system represented for EMT studies at large scale. An International Electrotechnical Commission (IEC) standard Common Information Model (CIM) provides a way of supporting these detailed models from physical asset data, e.g., conductors, towers, transformer data sheets, control block diagrams, while avoiding software vendor lock-in. CIM-for-EMT, with proposed schema extensions and open-source converters, provides a way to exchange EMT data between organizations and tools. This project leverages Office of Electricity (OE) funding of CIM-for-EMT code base through the GridAPPS-DTM project, and of GridPACKTM (parallelized transmission solver), for interoperability testing in CIM-for-EMT. The project also leverages partner PGSTech investments in EMTP® interoperability with CIM.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Review of searches for vector-like quarks, vector-like leptons, and heavy neutral leptons in proton–proton collisions at $\sqrt{s} = 13$ TeV at the CMS experiment

The LHC has provided an unprecedented amount of proton–proton collision data, bringing forth exciting opportunities to address fundamental open questions in particle physics. These questions can potentially be answered by performing searches for very rare processes predicted by models that attempt to extend the standard model of particle physics. The data collected by the CMS experiment in 2015–2018 at a center-of-mass energy of 13 TeV can be used to test the standard model with high precision and potentially uncover evidence for new particles or interactions. An interesting possibility is the existence of new fermions with masses ranging from the MeV to the TeV scale. Such new particles appear in many possible extensions of the standard model and are well motivated theoretically. New fermions may explain the appearance of three generations of leptons and quarks, the mass hierarchy across these generations, and the nonzero neutrino masses. In this report, the results of searches targeting vectorlike quarks, vector-like leptons, and heavy neutral leptons at the CMS experiment are summarized. The complementarity of current searches for each type of new fermion is discussed, and combinations of several searches for vector-like quarks are presented. The discovery potential for some of these searches at the High-Luminosity LHC is also discussed.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Review of searches for vector-like quarks, vector-like leptons, and heavy neutral leptons in proton-proton collisions at $\sqrt{s}$ = 13 TeV at the CMS experiment

The LHC has provided an unprecedented amount of proton-proton collision data, bringing forth exciting opportunities to address fundamental open questions in particle physics. These questions can potentially be answered by performing searches for very rare processes predicted by models that attempt to extend the standard model of particle physics. The data collected by the CMS experiment in 2015-2018 at a center-of-mass energy of 13 TeV can be used to test the standard model with high precision and potentially uncover evidence for new particles or interactions. An interesting possibility is the existence of new fermions with masses ranging from the MeV to the TeV scale. Such new particles appear in many possible extensions of the standard model and are well motivated theoretically. New fermions may explain the appearance of three generations of leptons and quarks, the mass hierarchy across the generations, and the nonzero neutrino masses. In this report, the results of searches targeting vector-like quarks, vector-like leptons, and heavy neutral leptons at the CMS experiment are summarized. The complementarity of current searches for each type of new fermion is discussed, and combinations of several searches for vector-like quarks are presented. The discovery potential for some of these searches at the High-Luminosity LHC is also discussed.

FOS: Physical sciences↗

Heterogeneous estimations of non-pharmaceutical mitigation behavior during the COVID-19 pandemic

The COVID-19 pandemic highlighted the importance of human behavior in mitigating the spread of disease. Nonetheless, human behavior is often overlooked in models of disease spread, particularly by underutilizing real-world data. We address this by estimating probabilities that individuals engage in behaviors that influence SARS-CoV-2 transmission risk during the COVID-19 pandemic, between September 2020 and June 2022. These behaviors include wearing a mask, using public transportation, spending time with others, avoiding contact with others, and going to work. Our estimates account for the age and sex of individuals and are generated for every county in the United States. We utilized multiple open-source datasets and United States Census data to produce these estimates. Multiple datasets were used for validation, showing our estimates demonstrated comparable accuracy and robustness. Our estimates aid in understanding human behavior dynamics during the COVID-19 pandemic and could be used to inform monthly or longer-term behavior in simulations of COVID-19. Moreover, the methods presented can be applied to other behaviors and features for future simulations of infectious disease.

97 MATHEMATICS AND COMPUTING↗

Open Chemistry, JupyterLab, REST, and quantum chemistry

Quantum chemistry must evolve if it wants to fully leverage the benefits of the internet age, where the worldwide web offers a vast tapestry of tools that enable users to communicate and interact with complex data at the speed and convenience of a button press. The Open Chemistry project has developed an open-source framework that offers an end-to-end solution for producing, sharing, and visualizing quantum chemical data interactively on the web using an array of modern tools and approaches. These tools build on some of the best open-source community projects such as Jupyter for interactive online notebooks, coupled with 3D accelerated visualization, state-of-the-art computational chemistry codes including NWChem and Psi4, and emerging machine learning and data mining tools such as ChemML and ANI. They offer flexible formats to import and export data, along with approaches to compare computational and experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Integration of Wi-Fi Location-Based Services to Optimize Energy Efficient Commercial Building Operations

This project investigated and demonstrated the use of Wi-Fi Location-Based Services (LBS) to perform occupancy sensing in commercial buildings. Wi-Fi LBS can be used to detect the presence of Wi-Fi enabled mobile devices and laptops that accompany occupants as they move through the building. These signals can be used to determine occupant presence, head count, and location. When integrated with the building automation system, this emerging technology approach can be used to manage other connected systems such as lighting and HVAC to reduce energy usage in the building and improve occupant comfort. An open source location detection algorithm was developed, which uses data collected from three or more Wi-Fi access points to determine the presence and estimate the location of mobile devices and laptops. Access points can detect Wi-Fi enabled devices even if they are not connected to the existing Wi-Fi network. Building occupancy is determined based on the presence, location, and movement of these devices through the space. From lab and small-scale in-situ testing, the Location Detection Algorithm (LDA) was found to be accurate to within 10 feet and could be further refined by tuning the algorithm for the specific space characteristics such as layout and obstructions (walls, furniture, etc.). An open source method to integrate the occupancy data with existing building automations systems was investigated. The Wi-Fi occupancy sensing approach was then demonstrated and validated at commercial buildings located in Saint Paul, MN; Madison, WI; New York City; and Fort Worth, TX.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗