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At least 235 records · Page 13

Machine learning models for rat multigeneration reproductive toxicity prediction

Reproductive toxicity is one of the prominent endpoints in the risk assessment of environmental and industrial chemicals. Due to the complexity of the reproductive system, traditional reproductive toxicity testing in animals, especially guideline multigeneration reproductive toxicity studies, take a long time and are expensive. Therefore, machine learning, as a promising alternative approach, should be considered when evaluating the reproductive toxicity of chemicals. We curated rat multigeneration reproductive toxicity testing data of 275 chemicals from ToxRefDB (Toxicity Reference Database) and developed predictive models using seven machine learning algorithms (decision tree, decision forest, random forest, k-nearest neighbors, support vector machine, linear discriminant analysis, and logistic regression). A consensus model was built based on the seven individual models. An external validation set was curated from the COSMOS database and the literature. The performances of individual and consensus models were evaluated using 500 iterations of 5-fold cross-validations and the external validation data set. The balanced accuracy of the models ranged from 58% to 65% in the 5-fold cross-validations and 45%–61% in the external validations. Prediction confidence analysis was conducted to provide additional information for more appropriate applications of the developed models. The impact of our findings is in increasing confidence in machine learning models. We demonstrate the importance of using consensus models for harnessing the benefits of multiple machine learning models (i.e., using redundant systems to check validity of outcomes). While we continue to build upon the models to better characterize weak toxicants, there is current utility in saving resources by being able to screen out strong reproductive toxicants before investing in vivo testing. The modeling approach (machine learning models) is offered for assessing the rat multigeneration reproductive toxicity of chemicals. Our results suggest that machine learning may be a promising alternative approach to evaluate the potential reproductive toxicity of chemicals.

consensus model↗

A Step-Down Test Procedure for Wavelet Shrinkage Using Bootstrapping

Wavelet thresholding (or shrinkage) attempts to remove the noises existing in the signals while preserving inherent pattern characteristics in the reconstruction of true signals. For data-denoising purpose, we present a new wavelet thresholding procedure which employs the step-down testing idea of identifying active contrasts in unreplicated fractional factorial experiments. The proposed method employs bootstrapping methods to a step-down test for thresholding wavelet coefficients. By introducing the concept of a false discovery error rate in testing wavelet coefficients, we shrink the wavelet coefficients with p -values higher than the error rate. The error rate controls the expected proportion of wrongly accepted coefficients among chosen wavelet coefficients. Bootstrap samples are used to approximate the p -value for computational efficiency. We also present some guidelines for selecting the values of hyper-parameters which affect the performance in the step-down thresholding procedure. Based on some common testing signals and an air-conditioner sounds example, the comparison of our proposed procedure with other thresholding methods in the literature is performed. The analytical results show that the proposed procedure has a potential in data-denoising and data-reduction in a variety of signal reconstruction applications.

42 ENGINEERING↗

The Cell Utilized Partitioning Model as a Predictive Tool for Optimizing Counter-Current Chromatography Processes

Counter-current chromatography (CCC) is capable of unique elution modes that isolate analytes using the movement of the stationary phase in addition to moving the mobile phase. These modes include elution-extrusion CCC (EECCC) and dual-mode CCC (DM CCC) that are not possible in traditional solid-liquid chromatography systems. Although EECCC and DM CCC are widely used to recover highly retained components, to our knowledge, optimizing the elution process in these modes with predictive models has not been reported. To address this gap, we developed a predictive model for CCC dubbed the Cell Utilized Partitioning (CUP) model. The CUP model accurately predicts the effluents of multicomponent separations in EECCC and DM CCC modes when compared to experimental data. Furthermore, CUP model simulations were extended to investigate the influence of operating and intrinsic parameters on the yield and productivity, and to compare the separation performances of EECCC and DM CCC in various conditions. The results demonstrate that low distribution constants, usually a KD less than 1, and a selectivity > 1.3, under specific flowrate ranges, increase both productivity and yield. From these results, generalized optimization and scaleup guidelines are proposed that can apply to research settings and to industrial processes to maximize preparative CCC performance.

BIOMASS FUELS,INORGANIC, ORGANIC, PHYSICAL, AND AN↗

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

We need to effectively combine the knowledge from surging literature with complex datasets to propose mechanistic models of SARS-CoV-2 infection, improving data interpretation and predicting key targets of intervention. Here, we describe a large-scale community effort to build an open access, interoperable and computable repository of COVID-19 molecular mechanisms. The COVID-19 Disease Map (C19DMap) is a graphical, interactive representation of disease-relevant molecular mechanisms linking many knowledge sources. Notably, it is a computational resource for graph-based analyses and disease modelling. To this end, we established a framework of tools, platforms and guidelines necessary for a multifaceted community of biocurators, domain experts, bioinformaticians and computational biologists. The diagrams of the C19DMap, curated from the literature, are integrated with relevant interaction and text mining databases. We demonstrate the application of network analysis and modelling approaches by concrete examples to highlight new testable hypotheses. This framework helps to find signatures of SARS-CoV-2 predisposition, treatment response or prioritisation of drug candidates. Such an approach may help deal with new waves of COVID-19 or similar pandemics in the long-term perspective.

59 BASIC BIOLOGICAL SCIENCES↗

Applying the FAIR Principles to computational workflows

Recent trends within computational and data sciences show an increasing recognition and adoption of computational workflows as tools for productivity and reproducibility that also democratize access to platforms and processing know-how. As digital objects to be shared, discovered, and reused, computational workflows benefit from the FAIR principles, which stand for Findable, Accessible, Interoperable, and Reusable. The Workflows Community Initiative’s FAIR Workflows Working Group (WCI-FW), a global and open community of researchers and developers working with computational workflows across disciplines and domains, has systematically addressed the application of both FAIR data and software principles to computational workflows. We present recommendations with commentary that reflects our discussions and justifies our choices and adaptations. These are offered to workflow users and authors, workflow management system developers, and providers of workflow services as guidelines for adoption and fodder for discussion. The FAIR recommendations for workflows that we propose in this paper will maximize their value as research assets and facilitate their adoption by the wider community.

97 MATHEMATICS AND COMPUTING↗

Radiometric Testing of Germicidal UV Products, Round 1: UV-C Towers and Whole-Room Luminaires (CALiPER Summary Report)

This summary report analyzes the independently tested performance of 13 germicidal ultraviolet (GUV) products purchased between February and July 2022. A companion full report (DOE 2023) provides additional information and discussion of the tested products, test methods, and results. The products were of three different types: • Seven portable, consumer-oriented GUV towers designed to be placed on the floor or a desk of an unoccupied room to disinfect air and surfaces. Five of these products used LED sources and two products had low-pressure mercury (LPM) sources. • One GUV whole-room luminaire designed to be installed on a ceiling to disinfect air when a room is occupied. This product had LED sources. • Five GUV troffer or high-bay style whole-room luminaires designed to be installed in or suspended from a ceiling to disinfect air and surfaces when a room is unoccupied. All five had LPM sources. Product testing covered radiometric and electrical performance for all 13 products as well as photobiological safety evaluation if product documentation included testable claims. Measurement results enable comparison between products and against manufacturer or vendor claims. Testing identified numerous issues related to the accuracy of claimed GUV product performance. Claims were often untestable, contradictory, ambiguous, or used incorrect units and/or terminology. When claims were testable, they often did not match test results. For example, three LED products that claimed to emit UV-C emitted only UV-A. Product claim issues were more common among consumer-oriented tower products, but all product types exhibited problems with accurate performance claims. The UV-C radiant efficiency (calculated as UV-C output power divided by electrical input power) of the products varied widely, even among similar products using the same source technologies. For example, the UV-C radiant efficiency of LPM products varied by greater than a factor of three for the same product type, indicating a large potential energy savings opportunity for products that are better designed for efficiency. LED products had orders-of-magnitude lower UV-C radiant efficiency than LPM products. This study also identified several testing challenges and limitations. Most significant among these is the capability to accurately test and report the performance of larger GUV products. Whereas integrating spheres are used to quickly measure total radiant flux (i.e., output power) and spectral distribution, goniometers are used to measure radiant intensity distribution (from which radiant flux can be calculated). Integrating spheres require a specialized and costly coating to test UV, and the testing laboratory for this round of products had only a 20-inch diameter hemisphere with this capability. The integrating sphere accommodated just 2 of the 10 UV-C emitting products. Goniometer testing had a different size limitation in that mirrors typically used to increase goniometer test distance to the far field reflect little to no UV. As a result, the study evaluated only 6 of 13 products in the far field. Electronic files of UV-C intensity data for the other 7 products, which would typically be imported into design software for designing GUV applications, may not be reliable for predicting irradiance at arbitrary far-field distances (IES 2022a; CIE 2020). Specifiers and buyers of GUV products need accurate performance claims and data to deploy GUV technology safely and effectively. This CALiPER GUV Round 1 report demonstrates the significant education and training manufacturers and vendors still require to accurately test and report the performance of their GUV products. Further industry standards and guidelines may address testing limitations and improve test methods, product performance, and the accuracy of performance claims.

42 ENGINEERING↗

Radiometric Testing of Germicidal UV Products, Round 1: UV-C Towers and Whole-Room Luminaires (CALiPER Full Report)

This report analyzes the independently tested performance of 13 germicidal ultraviolet (GUV) products purchased between February and July 2022. The products were of three different types: • Seven portable, consumer-oriented GUV towers designed to be placed on the floor or a desk of an unoccupied room to disinfect air and surfaces. Five of these products used LED sources and two products had low-pressure mercury (LPM) sources. • One GUV whole-room luminaire designed to be installed on a ceiling to disinfect air when a room is occupied. This product had LED sources. • Five GUV troffer or high-bay style whole-room luminaires designed to be installed in or suspended from a ceiling to disinfect air and surfaces when a room is unoccupied. All five had LPM sources. Product testing covered radiometric and electrical performance for all 13 products as well as photobiological safety evaluation if product documentation included testable claims. Measurement results enable comparison between products and against manufacturer or vendor claims. Testing identified numerous issues related to the accuracy of claimed GUV product performance. Claims were often untestable, contradictory, ambiguous, or used incorrect units and/or terminology. When claims were testable, they often did not match test results. For example, three LED products that claimed to emit UV-C emitted only UV-A. Product claim issues were more common among consumer-oriented tower products, but all product types exhibited problems with accurate performance claims. The UV-C radiant efficiency (calculated as UV-C output power divided by electrical input power) of the products varied widely, even among similar products using the same source technologies. For example, the UV-C radiant efficiency of LPM products varied by greater than a factor of three for the same product type, indicating a large potential energy savings opportunity for products that are better designed for efficiency. LED products had orders-of-magnitude lower UV-C radiant efficiency than LPM products. This study also identified several testing challenges and limitations. Most significant among these is the capability to accurately test and report the performance of larger GUV products. Whereas integrating spheres are used to quickly measure total radiant flux (i.e., output power) and spectral distribution, goniometers are used to measure radiant intensity distribution (from which radiant flux can be calculated). Integrating spheres require a specialized and costly coating to test UV, and the testing laboratory for this round of products had only a 20-inch diameter hemisphere with this capability. The integrating sphere accommodated just 2 of the 10 UV-C emitting products. Goniometer testing had a different size limitation in that mirrors typically used to increase goniometer test distance to the far field reflect little to no UV. As a result, the study evaluated only 6 of 13 products in the far field. Electronic files of UV-C intensity data for the other 7 products, which would typically be imported into design software for designing GUV applications, may not be reliable for predicting irradiance at arbitrary far-field distances (IES 2022a; CIE 2020). Specifiers and buyers of GUV products need accurate performance claims and data to deploy GUV technology safely and effectively. This CALiPER GUV Round 1 report demonstrates the significant education and training manufacturers and vendors still require to accurately test and report the performance of their GUV products. Further industry standards and guidelines may address testing limitations and improve test methods, product performance, and the accuracy of performance claims.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Improving the prediction of daily reservoir releases over the CONUS using conditioned LSTM

Reservoirs play a vital role in regulating streamflow timing and variability for hydroelectricity, flood control, water supply, irrigation, and recreation. Despite their importance, many reservoirs lack comprehensive operational guidelines, making their management complex due to conflicting operational objectives. Hence traditional policy-based reservoir models often fail to capture real-world conditions accurately and they depend on perfect streamflow predictions, which are not always available. In contrast, data-driven models like Long Short-Term Memory (LSTM) networks offer a robust alternative. This study introduces an approach that integrates reservoir characteristics—such as main use, climate, and maximum capacity—into the LSTM model to enhance reservoir release predictions. Using data from nearly 200 reservoirs in the contiguous United States (CONUS), our conditioned LSTM model (LSTM_cond) was compared with both the vanila LSTM and a traditional policy-based approach. Furthermore, our results show that while both LSTM_cond and LSTM perfoms better than the policy-based approach, LSTM_cond consistently outperforms LSTM for hydroelectric, water supply, irrigation, and recreation reservoirs. The KGE median values for LSTM_cond for out-sample reservoirs are 0.764, 0.565, 0.821, and 0.779, respectively, for the aforementioned reservoir types, which are consistently higher that the corresponding KGE values of 0.737, 0.413, 0.775, and 0.713 of LSTM, demonstrating its advantages in improving generalizability.

CONUS↗

Uncovering I/O demands on HPC platforms: Peeking under the hood of Santos Dumont

High-Performance Computing (HPC) platforms are required to solve the most diverse large-scale scientific problems in various research areas, such as biology, chemistry, physics, and health sciences. Researchers use a multitude of scientific softwares, which have different requirements. These include input and output operations, which directly impact performance due to the existing difference in processing and data access speeds. Thus, supercomputers must efficiently handle mixed workload when storing data from the applications. Understanding the set of applications and their performance running in a supercomputer is paramount to understanding the storage system's usage, pinpointing possible bottlenecks, and guiding optimization techniques. This research proposes a methodology and visualization tool to evaluate a supercomputer's data storage infrastructure's performance, taking into account the diverse workload and demands of the system over a long period of operation. As a study case, we focus on the Santos Dumont supercomputer, identifying inefficient usage, problematic performance factors, and providing guidelines on how to tackle those issues.

97 MATHEMATICS AND COMPUTING↗

Entropy removal of medical diagnostics

Shannon entropy is a core concept in machine learning and information theory, particularly in decision tree modeling. To date, no studies have extensively and quantitatively applied Shannon entropy in a systematic way to quantify the entropy of clinical situations using diagnostic variables (true and false positives and negatives, respectively). Decision tree representations of medical decision-making tools can be generated using diagnostic variables found in literature and entropy removal can be calculated for these tools. This concept of clinical entropy removal has significant potential for further use to bring forth healthcare innovation, such as quantifying the impact of clinical guidelines and value of care and applications to Emergency Medicine scenarios where diagnostic accuracy in a limited time window is paramount. This analysis was done for 623 diagnostic tools and provided unique insights into their utility. For studies that provided detailed data on medical decision-making algorithms, bootstrapped datasets were generated from source data to perform comprehensive machine learning analysis on these algorithms and their constituent steps, which revealed a novel and thorough evaluation of medical diagnostic algorithms.

97 MATHEMATICS AND COMPUTING↗

π-Extended Ligands in Two-Coordinate Coinage Metal Complexes

Two-coordinate carbene-M I -amide (cMa, M I = Cu, Ag, Au) complexes have emerged as highly efficient luminescent materials for use in a variety of photonic applications, due to their extremely fast radiative rates via thermally activated delayed fluorescence (TADF) from an interligand charge transfer (ICT) process. A series of cMa derivatives were prepared to examine the variables which affect the radiative rate with the goal of understanding the parameters that control the radiative TADF process in these materials. We find that blue emissive complexes with high photoluminescence efficiency (Φ PL > 0.95) and fast radiative rates (k r = 4 x 10 6 s -1 ) can be achieved by selectively extending the π-system of the carbene and amide ligands. Of note is the role played by increasing the separation between the hole and electron in the ICT excited state. Analysis of temperature dependent luminescence data along with theoretical calculations indicate that the hole-electron separation alters the energy gap between the lowest energy singlet and triplet states (ΔE ST ) while keeping the radiative rate for the singlet state unchanged. As a result, this interpretation provides guidelines for the design of new cMa derivatives with even faster radiative rates as well as those with slower radiative rates and thus extended excited state lifetimes.

14 SOLAR ENERGY↗

Inverse Lieb materials: altermagnetism and more

The Lieb lattice, originally proposed for cuprate superconductors, has gained new attention in the emerging field of altermagnetism as a minimal analytical model for the latter. While the inverse Lieb lattice (ILL) was once considered purely theoretical, several materials with this motif have recently been discovered. Its unique geometry supports complex magnetic orders driven by geometric frustration, offering high tunability. In this work, we provide comprehensive insights into ILL magnetic phases and establish guidelines for identifying altermagnets. Using a Heisenberg model, we first construct phase diagrams to elucidate the mechanisms underlying experimental magnetic phases. We then bridge theory and experiment via density functional theory (DFT) calculations on existing ILL compounds, finding results consistent with experimental data. Notably, we identified a trend linking d-shell filling to magnetic order, where d x (x≤5) configurations show a propensity for altermagnetism. We also highlight Sr 2 CrO 2 Cr 2 OAs 2 as a promising metallic altermagnet with highly anisotropic J 2 exchange and a high Néel temperature (~600 K). Finally, our magnon spectra calculations confirm that chiral splittings correlate directly with anisotropies between inequivalent J 2 interactions.

36 MATERIALS SCIENCE↗

Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.

59 BASIC BIOLOGICAL SCIENCES↗

Greenhouse Rhizobox Experiment with Plant Characteristics, Porewater, Gas Flux, and Soil Biogeochemistry data, Seward Peninsula, Alaska, 2024

Data collected from a greenhouse rhizobox experiment (2024) using soils and plants collected at Council, AK (64°51’35.0”N 163°41’59.1”W) during a summer campaign in 2023. Water data consists of soil porewater collected by porewater samplers (rhizons). Gas data consists of CO2 and CH4 surface soil fluxes measured with an FTIR (Fourier-transformed infrared red) analyzer. Plant and root data consists of biomass, root length. This study is a part of 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).This dataset was generated to broadly address the following research question: how will climate change (i.e., thawing permafrost, landscape change) alter the ecosystem flux (sink versus source) of important greenhouse gases such as CO2 and CH4?Description of the contents of this data package: Rhizobox2024_Data.csv: This dataset contains plant, water and gas data. No software is needed to utilize them.nga535_flmd.csv: The file contains file level metadatanga535.dd.csv: This file contains the data dictionaryMethods.pdf: This file contains the data collection methods

54 ENVIRONMENTAL SCIENCES↗

KBase Educators Handbook

The KBase Educators Handbook is a community resource for educators teaching biology, computational biology, and bioinformatics using KBase. The Handbook includes supporting documentation on how to join and access community-developed resources for teaching with KBase, best practices, and guidelines on how to contribute to the KBase Educators Community.

59 BASIC BIOLOGICAL SCIENCES↗

FAIR Data and Interpretable AI Framework for Architectured Metamaterials

Our interdisciplinary effort successfully generated FAIR (Findable, Accessible, Interoperable, and Reusable) benchmark datasets for mechanical metamaterials while introducing a novel Artificial Intelligence (AI) framework known as Learning Refined Compositional Rules (LRCR). This framework was specifically designed to bridge the gap across varying computational length scales and extract the underlying physical mechanisms that connect a material's structural geometry to its bulk acoustic properties. Historically, the discovery of such structured materials relied heavily on human intuition or opaque, black-box optimization algorithms that were difficult to generalize. By combining interpretable machine learning techniques with rigorous experimental validation, this project established clear, generalizable design guidelines for tuning wave dispersion and controlling vibrations. Ultimately, the public availability of these structured datasets and algorithms will significantly reduce computational costs and accelerate the design of advanced multi-functional acoustic devices, offering broad societal impacts across fields like aerospace engineering, telecommunications, and biomedical implant design.

36 MATERIALS SCIENCE↗

Tuning the Intermolecular Electrostatic Interaction toward High-Efficiency and Low-Cost Organic Solar Cells

Organic solar cells (OSCs) have achieved much progress with rapidly increasing power conversion efficiencies (PCEs). It should be noted that the top-performance OSCs are generally consisted of active materials with complex chemical structures, resulting in high costs. Here, combining the material design and morphology control, high-efficiency OSCs are fabricated by a low-cost donor: acceptor blend. A completely non-fused electron acceptor named Tz is designed and synthesized via introducing thiazole units on both sides of a bithiophene core, which shows an outstanding PCE of 13.3% with a typical polythiophene donor. More importantly, optimization guidelines are presented to get excellent morphology for low-cost donor:acceptor systems. Three polythiophenes are selected, poly(3-hexylthiophene) and its two derivatives with electron-withdrawing substitutions (PDCBT and PDCBT-2F), as donors to fabricate the cell devices. The computational and experimental data reveal that decreasing the electrostatic interaction between polythiophene and Tz is the key to getting a suppressed miscibility and thus a high phase purity. Finally, this study provides insight into the molecular design and donor:acceptor matching requirements for high-efficiency and low-cost OSCs.

14 SOLAR ENERGY↗

Thermohydraulic experiments on a supercritical carbon dioxide–air microtube heat exchanger

Heat exchangers are critical components in supercritical CO 2 Brayton cycles and provide necessary heat input, recovery, and dissipation. Tubular heat exchangers with unconventionally small tube sizes (tube diameters less than 5 mm) are promising components for supercritical CO 2 cycles and potentially provide excellent structural stability with wide scope of application. This paper provides essential design and fabrication guidelines for a compact shell-and-tube heat exchanger with microtubes (with an inner diameter equal to 1.75 mm). A heat exchanger test rig is used to evaluate the thermohydraulic performance of this heat exchanger with supercritical CO 2 and air as working fluids. Thermohydraulic data are reported for more than forty sets of experiments with varying Reynolds numbers for shell and tube flows. Critical performance metrics are calculated from the data and compared with predictions from a previously described numerical model. The average deviations between the experimental and model results fall within 10% for all critical metrics. This excellent agreement validates the numerical model for supercritical CO 2 heat exchanger optimization and scale-up.

42 ENGINEERING↗