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At least 37 records · Page 2

Visual Brick model authoring tool for building metadata standardization

In this study, the Brick ontology is a unified semantic metadata standard for building assets and their relationships, serving as a key enabler for effective interoperability and automation of building systems and analytics. However, creating a Brick model, in other words, standard semantic metadata based on the Brick ontology for a building dataset, can be a complex task. This paper presents two case studies of the creation of Brick models for real-world residential and commercial building datasets, highlighting the challenges during the Brick model creation process. Additionally, the paper introduces VizBrick, an interactive authoring tool for creating semantic building metadata. VizBrick facilitates the creation of Brick models by providing an intuitive visual interface and interactive capabilities, such as keyword search, automatic mapping suggestions, and recommendations. The use of VizBrick is shown to significantly reduce the time and effort required during the Brick model creation process.

42 ENGINEERING↗

Coupling Surface Flow with High-performance Subsurface Reactive Flow and Transport Code PFLOTRAN

Water exchange between the surface and subsurface is important for both water resource management and environmental protection. In this paper, we develop coupled surface and subsurface flow simulation capability in a parallel subsurface flow and reactive transport code PFLOTRAN. We sequentially couple the diffusion wave-based surface flow with the subsurface flow governedby the Richards equation in PFLOTRAN. These two flow domains are linked with a boundary condition switching method that ensures continuity of pressure and flux at the surface-subsurface interface. We verify the coupled code against other existing hydrologic models and observation data using a number of numerical experiments. The coupled hydrological model exhibits good performance in strong parallel scaling tests. The new coupled surface and subsurface simulator significantly advance community simulation capability towards improving integrated hydrologic and biogeochemical understanding of complex systems such as watersheds and river corridors. Keywords: Surface flow, Integrated hydrological modeling, Boundary condition switching, Parallel computing

Wu, Runjian↗

Tikiri—Towards a lightweight blockchain for IoT

Internet of Things (IoT) platforms have been deployed in several domains to enhance efficiency of business process and improve productivity. Most IoT platforms comprise of heterogeneous software and hardware components which can potentially introduce security and privacy challenges. Blockchain technology has been proposed as one of the solutions to realize IoT security by leveraging the (a) Immutable ledger, (b) Decentralized architecture and (c) Strong cryptography primitives. However, integrating blockchain platforms with IoT based applications presents several challenges due to lack of (a) acceptable performance on resource-constrained devices, (b) high transaction throughput, (c) keyword-based search and retrieve, (d) transaction back pressure operations, and (e) real-time response. In this paper, we propose a lightweight blockchain platform, “Tikiri”, for resource-constrained IoT devices. Tikiri uses Apache Kafka for the consensus and proposes new blockchain architecture to handle real-time transaction execution on the blockchain. Tikiri is characterized by functional programming and actor-based smart contract platform that realizes concurrent execution of transactions in the blockchain. Tikiri realizes a lightweight and scalable blockchain that can provides performance on the resource-constrained IoT devices.

97 MATHEMATICS AND COMPUTING↗

The spore coat is essential for Bacillus subtilis spore resistance to pulsed light, and pulsed light treatment eliminates some spore coat proteins

Microbial surface contamination of equipment or of food contact material is a recurring problem in the food industry. Spore-forming bacteria are far more resistant to a wide variety of treatments than their vegetative forms. Understanding the mechanisms underlying decontamination processes is needed to improve surface decontamination strategies against endospores potentially at the source of foodborne diseases or food-spoilage. Pulsed light (PL) with xenon lamps delivers high-energy short-time pulses of light with wavelengths in the range 200 nm-1100 nm and a high UV-C fraction. Bacillus subtilis spores were exposed to either PL or to continuous UV-C. Gel electrophoresis and western blotting revealed elimination of various proteins of the spore coat, an essential outer structure that protects spores from a wide variety of environmental conditions and inactivation treatments. Proteomic analysis confirmed the elimination of some spore coat proteins after PL treatment. Transmission electron microscopy of PL treated spores revealed a gap between the lamellar inner spore coat and the outer spore coat. Overall, spores of mutant strains with defects in genes coding for spore coat proteins were more sensitive to PL than to continuous UV-C. This study demonstrates that radiations delivered by PL contribute to specific damage to the spore coat, and overall to spore inactivation. Keywords Decontamination, UV, proteins, proteomics, microscopy Journal Pre-proof

59 BASIC BIOLOGICAL SCIENCES↗

Estimated capital costs of fish exclusion technologies for hydropower facilities

Hydropower is a reliable source of renewable energy, and its future expansion is likely to be in the form of either smaller new stream development (NSD) projects or powering existing non-powered dams. Thresholds for entrainment risk to fish and the requirements for fish exclusion at hydropower facilities often differ depending on the species involved, the characteristics of the facility, and the goals of stakeholders, but little quantitative information is present within the literature regarding the specific costs of fish exclusion measures. Cost data associated with protection, mitigation, and enhancement (PM&E) measures related to positive barrier screening were identified using keyword searches of an existing environmental mitigation cost data set and manual extraction from regulatory licensing documents available in the Federal Energy Regulatory Commission (FERC) eLibrary. This approach yielded a total of 50 p.m.&E mitigation measures with estimated capital construction costs pertaining to positive barrier screens and represented <10% of the 171 total FERC project dockets available in the data set. These data were highly skewed toward conventional relicensing projects, as <7% were associated with NSD projects. Results indicate highly variable costs are associated with fish screening, with flow-normalized costs one to two orders of magnitude higher for screening with the highest exclusion capability (≤0.09 in. spacing) compared with coarser screening (1–2 in.). These data provide an initial baseline for estimating exclusion costs for hydropower development and may help developers consider options for more fish-friendly generation technologies, though gaps remain relating to a lack of data, particularly for NSD projects.

13 HYDRO ENERGY↗

Improved production and purification of 240Am by deuteron-induced activation of 240Pu target

An optimized method for production of 240Am via the 240Pu(d,2n)240Am reaction is reported. The optimized method produced 7.94 × 108 ± 7% atoms 240Am/mg 240Pu/µA-h. The yield and purity of the products from the optimized method are evaluated in context of the intended application to produce material to measure the cross-section for the 240Am(n,f) reaction. The presented method is also compared with other production methods available in the literature. Keywords—240Am production, deuteron-induced reactions, cross-section, target preparation, post-irradiation purification Abbreviations GEA—Gamma Energy Analysis

Morrison, Erin C.↗

Depletion of atmospheric neutrino fluxes from parton energy loss

The phenomenon of fully coherent energy loss (FCEL) in the collisions of protons on light ions affects the physics of cosmic ray air showers. As an illustration, we address two closely related observables: hadron production in forthcoming proton-oxygen collisions at the LHC, and the atmospheric neutrino fluxes induced by the semileptonic decays of hadrons produced in proton-air collisions. In both cases, a significant nuclear suppression due to FCEL is predicted. The conventional and prompt neutrino fluxes are suppressed by ~10...25% in their relevant neutrino energy ranges. Previous estimates of atmospheric neutrino fluxes should be scaled down accordingly to account for FCEL. Keywords: Atmospheric neutrinos, Parton energy loss

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format

The layout of portable document format (PDF) files is constant to any screen, and the metadata therein are latent, compared to mark-up languages such as HTML and XML. No semantic tags are usually provided, and a PDF file is not designed to be edited or its data interpreted by software. However, data held in PDF files need to be extracted in order to comply with opensource data requirements that are now government-regulated. In the chemical domain, related chemical and property data also need to be found, and their correlations need to be exploited to enable data science in areas such as data-driven materials discovery. Such relationships may be realized using text-mining software such as the “chemistry-aware” natural-language-processing tool, ChemDataExtractor; however, this tool has limited data-extraction capabilities from PDF files. This study presents the PDFDataExtractor tool, which can act as a plug-in to ChemDataExtractor. It outperforms other PDF-extraction tools for the chemical literature by coupling its functionalities to the chemical-named entityrecognition capabilities of ChemDataExtractor. The intrinsic PDF-reading abilities of ChemDataExtractor are much improved. The system features a template-based architecture. This enables semantic information to be extracted from the PDF files of scientific articles in order to reconstruct the logical structure of articles. While other existing PDF-extracting tools focus on quantity mining, this template-based system is more focused on quality mining on different layouts. PDFDataExtractor outputs information in JSON and plain text, including the metadata of a PDF file, such as paper title, authors, affiliation, email, abstract, keywords, journal, year, document object identifier (DOI), reference, and issue number. With a self-created evaluation article set, PDFDataExtractor achieved promising precision for all key assessed metadata areas of the document text.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Systems Engineering and Analysis in Support of a US Federal Staging Facility for UNF

The US Department of Energy Office of Nuclear Energy (DOE-NE) Office of Spent Fuel and High-Level Waste Disposition is examining a set of system options and conducting supporting analyses to inform the development of an integrated waste management system, which may include one or more federal staging facilities (FSFs) for used nuclear fuel (UNF ) sited using a collaborative siting process. This paper focuses on the ongoing activities in two systems engineering and analysis work areas: (1) data and tools development, validation, and maintenance and (2) systems engineering execution. Within the first work area, the STANDARDS 5.0 UNF data and analysis tool, formerly known as UNF-ST&DARDS, is being developed as a foundational resource to assist in the management of UNF data. It has the key capability to model UNF throughout the entire back end of the fuel cycle. STANDARDS also includes several compatible analysis tools for the time-dependent characterization of UNF and related systems by interfacing with the SCALE code system for nuclear analysis and COBRA-SFS for thermal analysis. Also, within the data and tools area is the Next Generation System Analysis Model (NGSAM), which is an agent-based simulation software tool expressly designed to be capable of modeling the waste management system, including the transportation of UNF to and from a FSF. NGSAM has been developed to enable informed decision-making by providing the capability to analyze various potential system options for the management of UNF and high-level radioactive waste. Finally, in the systems engineering execution area, the team has begun to apply a disciplined systems engineering approach at the system level along with supporting analysis to guide the development of the FSF project requirements (including associated transportation infrastructure). Systems engineering principles and practices and their adaptation/application to design and development activities will ensure that the waste management system is effectively implemented as work proceeds. Other activities include investigating the implications of changes in various assumptions and parameters related to waste management systems, such as UNF acceptance rates, receipt logic, facility capacities and capabilities, use of standardized canisters, and different assumed facility operation start dates. Keywords: federal staging facility (FSF), used nuclear fuel (UNF), integrated waste management (IWM) system, Next Generation System Analysis Model (NGSAM), STANDARDS, systems engineering

Joseph, Robert↗

Bibliometric review and recent advances in total scattering pair distribution function analysis: 21 years in retrospect

Global research activities have been driven by the quest to develop and characterize novel materials for technological advancements. The total scattering pair distribution function (TSPDF) is a powerful and versatile characterization technique for examining the structural details of diverse complex materials including liquid, amorphous, disordered crystalline, and nanostructured materials. Thus, it is critical to keep track of research progress, identify research gaps, and future research directions of the application of the TSPDF technique in materials development and discovery. In this work, a bibliometric analysis of literature regarding the TSPDF technique between 2000 and 2021 was conducted using datasets retrieved from the Web of Science database. The research trends based on publication outputs, research subject distribution, co-authorships among institutions, countries/regions, co-citation of referenced sources, and keyword co-occurrence are evaluated and discussed herein. The impact of the TSPDF technique is projected to increase due to its importance in probing emerging functional materials, and the advances in specialized facilities and instrumentation among the scientific communities engaged with it. Finally, current and emerging research hotspots related to TSPDF technique such as catalysis, computer modeling and simulation, pharmaceutics, machine learning, hydrogen storage, battery materials, and layered structured materials are also identified and discussed.

36 MATERIALS SCIENCE↗

Mapping the structural, magnetic and electronic behavior of (Eu 1-x Ca x ) 2 Ir 2 O 7 across a metal-insulator transition

In this study, we employ bulk electronic properties characterization and x-ray scattering/spectroscopy techniques to map the structural, magnetic and electronic properties of (Eu 1-x Ca x ) 2 Ir 2 O 7 as a function of Ca-doping. As expected, the metal-insulator transition temperature, T-MIT, decreases with Ca-doping until a metallic state is realized down to 2 K. In contrast, T-AFM becomes decoupled from the MIT and (likely short-range) AFM order persists into the metallic regime. This decoupling is understood as a result of the onset of an electronically phase separated state, the occurrence of which seemingly depends on both synthesis method and rare earth site magnetism. PDF analysis suggests that electronic phase separation occurs without accompanying chemical phase segregation or changes in the short-range crystallographic symmetry while synchrotron x-ray diffraction confirms that there is no change in the long-range crystallographic symmetry. X-ray absorption measurements confirm the $J_{eff}$ = 1/2 character of (Eu 1-x Ca x ) 2 Ir 2 O 7 . Surprisingly these measurements also indicate a net electron doping, rather than the expected hole doping, indicating a compensatory mechanism. Lastly, XMCD measurements show a weak Ir magnetic polarization that is largely unaffected by Ca-doping. Keywords: term, term, term.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases

RNAcentral is a comprehensive database of non-coding RNA (ncRNA) sequences that provides a single access point to 44 RNA resources and >18 million ncRNA sequences from a wide range of organisms and RNA types. RNAcentral now also includes secondary (2D) structure information for >13 million sequences, making RNAcentral the world’s largest RNA 2D structure database. The 2D diagrams are displayed using R2DT, a new 2D structure visualization method that uses consistent, reproducible and recognizable layouts for related RNAs. The sequence similarity search has been updated with a faster interface featuring facets for filtering search results by RNA type, organism, source database or any keyword. This sequence search tool is available as a reusable web component, and has been integrated into several RNAcentral member databases, including Rfam, miRBase and snoDB. To allow for a more fine-grained assignment of RNA types and subtypes, all RNAcentral sequences have been annotated with Sequence Ontology terms. The RNAcentral database continues to grow and provide a central data resource for the RNA community. RNAcentral is freely available at https://rnacentral.org.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing Sub-Cohorts via Data Normalization and Representation Learning

The process of identifying a cohort of interest is a very challenging task. It requires manually inspecting many patient records of complex structure that might include medical coding errors and missing data. This paper presents a computational pipeline for refining the process of cohort selection based on medical concepts recorded in the electronic health records (EHRs). The pipeline extracts EHR data for a given cohort and normalizes this data using standard vocabularies. Then a stacked denoising autoencoder is used to embed the normalized patient vectors in a low dimensional space, where the patients are subsequently clustered into sub-cohorts. The goal is to represent the cohort in a standard format and abstract variants of sub-populations. As a use-case, we applied the pipeline to 1.8 million Veterans diagnosed with major depressive disorder (MDD), and identified four meaningful sub-cohorts using the features learned by the autoencoder. Then, each sub-cohort was explored using a set of keywords for interpretation.

Rush III, Everett↗

ORGANIC RANKINE CYCLE TURBINE AND HEAT EXCHANGER SIZING FOR LIQUID AIR COMBINED CYCLE

Cryogenic energy storage offers several opportunities to design turbomachinery and other equipment for novel cycles. This paper presents the design and analysis of turbomachinery and heat exchangers for an Organic Rankine Cycle (ORC) subsystem for a hybrid energy storage concept. The Liquid Air Combined Cycle is an energy storage system that stores air at cryogenic conditions at times with high variable renewable energy to be dispatched along with a gas turbine to recover the exhaust heat. In order to re-vaporize the air, the liquid air is coupled with an ORC as an additional bottoming cycle. The ORC turbine is expected to expand the fluid with a pressure ratio of nearly 30 and a flow rate of approximately 45 kg/s. Sizing calculations for both a radial and axial turbine solution were performed over a range of speeds and stages to determine the optimal design point. The results show that either an axial (8- or 9-stage) or radial (four stages at two shaft speeds) turbine are capable of handling the pressure ratios. Further trades of the two configurations would be required to determine the best option. The ORC system also incorporates five heat exchangers to distribute heat, vaporize the liquid air, or recover exhaust heat from the gas turbine. Three heat exchangers were analyzed to understand the size of heat exchangers and pressure drop for the overall system. Different types of heat exchangers were explored for the different purposes, including plate-fin heat exchangers, gasketed plate heat exchangers and shell-in-tube heat exchangers. It was determined that the ORC recuperator, liquid-air vaporizer, and vaporized air pre-heater would be counter-flow heat exchangers using a gasketed plate design. Keywords: Energy Storage, Liquid Air Energy Storage, Organic Rankine Cycle

Pryor, Owen↗

Evaluation of OpenAI Codex for HPC Parallel Programming Models Kernel Generation

We evaluate AI-assisted generative capabilities on fundamental numerical kernels in high-performance computing (HPC), including AXPY, GEMV, GEMM, SpMV, Jacobi Stencil, and CG. We test the generated kernel codes for a variety of language-supported programming models, including (1) C++ (e.g., OpenMP [including offload], OpenACC, Kokkos, SyCL, CUDA, and HIP), (2) Fortran (e.g., OpenMP [including offload] and OpenACC), (3) Python (e.g., numpy, Numba, cuPy, and pyCUDA), and (4) Julia (e.g., Threads, CUDA.jl, AMDGPU.jl, and KernelAbstractions.jl). We use the GitHub Copilot capabilities powered by the GPT-based OpenAI Codex available in Visual Studio Code as of April 2023 to generate a vast amount of implementations given simple + + prompt variants. To quantify and compare the results, we propose a proficiency metric around the initial 10 suggestions given for each prompt. Results suggest that the OpenAI Codex outputs for C++ correlate with the adoption and maturity of programming models. For example, OpenMP and CUDA score really high, whereas HIP is still lacking. We found that prompts from either a targeted language such as Fortran or the more general purpose Python can benefit from adding code keywords, while Julia prompts perform acceptably well for its mature programming models (e.g., Threads and CUDA.jl). We expect for these benchmarks to provide a point of reference for each programming model's community. Overall, understanding the convergence of large language models, AI, and HPC is crucial due to its rapidly evolving nature and how it is redefining human-computer interactions.

Godoy, William↗

Web of Registries Search (WoRS) v1.0.0

The Web of Registries Search (WoRs) is a web based software application that enables users to search for publicly available biological parts using keywords or sequence fragments. For the initial version (1.0.0) of the application, WoRS targets 10 sources of biological part data: the GenBank NIH genetic sequence database (https://www.ncbi.nlm.nih.gov/genbank/), the iGem parts registry (parts.igem.org), the Addgene plasmid repository (https://www.addgene.org/), and 7 Inventory of Composable Elements (ACS Synbio, JGI, JBEI, JBEI Public, ABF, SynBerc, ABF Public) registry instances. WoRs has built-in automated web scrapers which extract data from sources that do not have a public or well-defined application programming interface (API). They extract as much public data as they can find and create a searchable index to speed up searches. Included in the indexed information is the source of the information.

Plahar, Hector↗