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At least 1,531 records · Page 85

Improving precision and accuracy of genetic mapping with genotyping‐by‐sequencing data in outcrossing species

Abstract Genotyping‐by‐sequencing (GBS) is a widely used strategy for obtaining large numbers of genetic markers in model and non‐model organisms. In crop plants, GBS‐derived marker datasets are frequently used to perform quantitative trait locus (QTL) mapping. In some plant species, however, high heterozygosity and complex genome structure mean that researchers must use care in handling GBS data to conduct QTL mapping most effectively. Such outbred crops include most of the perennial grass and tree species used for bioenergy. To identify strategies for increasing accuracy and precision of QTL mapping using GBS data in outbred crops, we conducted an empirical study of SNP‐calling and genetic map‐building pipeline parameters in a Miscanthus sinensis population, and a complementary simulation study to estimate the relationship between genome‐wide error rate, read depth, and marker number. The bioenergy grass Miscanthus is an obligate outcrossing species with a recent (diploidized) whole‐genome duplication. For the study of empirical M. sinensis data, we compared two SNP‐calling methods (one non‐reference‐based and one reference‐based), a series of depth filters (12×, 20×, 30×, and 40×) and two map‐construction methods (i.e., marker ordering: linkage‐only and order‐corrected based on a reference genome). We found that correcting the order of markers on a linkage map by using a high‐quality reference genome improved QTL precision (shorter confidence intervals). For typical GBS datasets of between 1000 and 5000 markers to build a genetic map for biparental populations, a depth filter set at 30× to 40× applied to outbred populations provided a genome‐wide genotype‐calling error rate of less than 1%, improved accuracy of QTL point estimates and minimized type I errors for identifying QTL. Based on these results, we recommend using a reference genome to correct the marker order of genetic maps and a robust genotype depth filter to improve QTL mapping for outbred crops.

59 BASIC BIOLOGICAL SCIENCES↗

Better bang for your buck? Comparing savings realization from ESPCs and direct-funded projects

Energy savings performance contracts (ESPCs) offer an opportunity to tremendously scale decarbonization projects, given their paid-from-savings premise. However, prospective customers still question whether ESPC is worth the effort and expense. This study evaluates the savings realization rates of ESPCs compared to direct-funded projects using ENERGY STAR Portfolio Manager (ESPM) benchmarking data. It compares normalized EUIs from ESPM before and after energy conservation projects implemented via ESPC or direct funding in roughly 450 federal buildings. This documented change, ideally a savings, can then be compared to the estimated savings from the energy conservation initiative in order to generate a rough realization rate. Preliminary results indicate a notably greater savings realization rate for the ESPC buildings (median = 105% of estimated savings) than those that underwent direct-funded projects (median = 46%). Because of a shortage of good quality data and the wide range in results, the difference is only significant at the p < 0.20 level. However, the higher savings realization of ESPCs corroborates the authors’ 2014 findings using a different comparison method. With continued soft government funding and regulatory impediments for climate change mitigation in the U.S., financed, paid-from-savings project models (e.g., ESPC, PACE, EaaS and others) certainly merit more attention. This study’s results are particularly compelling (and encouraging) given the country’s likely reliance on these vehicles to address existing building retrofits.

Earni, Shankar↗

Analog-to-digital converter based on voltage-controlled superconducting devices

The increasing demand for cryogenic electronics in superconducting and quantum computing systems calls for ultra-energy-efficient data conversion architectures that remain functional at deep cryogenic temperatures. Here, in this work, we present the first design of a voltage-controlled superconducting flash analog-to-digital converter (ADC) based on a voltage-controlled quantum-enhanced Josephson junction field-effect transistor (JJFET). Exploiting its strong gate tunability and transistor-like behavior, the JJFET offers a scalable alternative to conventional current-controlled superconducting devices while aligning naturally with CMOS-style design methodologies. Building on our previously developed Verilog-A compact model calibrated to experimental data, we design and simulate a three-bit JJFET-based flash ADC targeted for integration within cryogenic control and readout circuitry in quantum computing. The core comparator block is realized through careful bias current selection and augmented with a three-terminal nanocryotron to precisely define reference voltages. Cascaded JJFET comparators ensure robust voltage gain, cascadability, and logic-level restoration across stages. Simulation results demonstrate accurate quantization behavior with ultra-low power dissipation, underscoring the feasibility of voltage-driven superconducting mixed-signal circuits. This work establishes a critical step toward unifying superconducting logic and data conversion, paving the way for scalable cryogenic architectures in quantum–classical co-processors, low-power artificial intelligence accelerators, and next-generation energy-constrained computing platforms.

Analog-to-digital converter↗

NCBI’s Virus Discovery Codeathon: Building “FIVE” —The Federated Index of Viral Experiments API Index

Viruses represent important test cases for data federation due to their genome size and the rapid increase in sequence data in publicly available databases. However, some consequences of previously decentralized (unfederated) data are lack of consensus or comparisons between feature annotations. Unifying or displaying alternative annotations should be a priority both for communities with robust entry representation and for nascent communities with burgeoning data sources. To this end, during this three-day continuation of the Virus Hunting Toolkit codeathon series (VHT-2), a new integrated and federated viral index was elaborated. This Federated Index of Viral Experiments (FIVE) integrates pre-existing and novel functional and taxonomy annotations and virus–host pairings. Variability in the context of viral genomic diversity is often overlooked in virus databases. As a proof-of-concept, FIVE was the first attempt to include viral genome variation for HIV, the most well-studied human pathogen, through viral genome diversity graphs. As per the publication of this manuscript, FIVE is the first implementation of a virus-specific federated index of such scope. FIVE is coded in BigQuery for optimal access of large quantities of data and is publicly accessible. Many projects of database or index federation fail to provide easier alternatives to access or query information. To this end, a Python API query system was developed to enhance the accessibility of FIVE.

59 BASIC BIOLOGICAL SCIENCES↗

Data-driven recovery of hidden physics in reduced order modeling of fluid flows

In this article, we introduce a modular hybrid analysis and modeling (HAM) approach to account for hidden physics in reduced order modeling (ROM) of parameterized systems relevant to fluid dynamics. The hybrid ROM framework is based on using first principles to model the known physics in conjunction with utilizing the data-driven machine learning tools to model the remaining residual that is hidden in data. This framework employs proper orthogonal decomposition as a compression tool to construct orthonormal bases and Galerkin projection (GP) as a model to build the dynamical core of the system. Our proposed methodology hence compensates structural or epistemic uncertainties in models and utilizes the observed data snapshots to compute true modal coefficients spanned by these bases. The GP model is then corrected at every time step with a data-driven rectification using a long short-term memory (LSTM) neural network architecture to incorporate hidden physics. A Grassmannian manifold approach is also adopted for interpolating basis functions to unseen parametric conditions. The control parameter governing the system's behavior is thus implicitly considered through true modal coefficients as input features to the LSTM network. The effectiveness of the HAM approach is then discussed through illustrative examples that are generated synthetically to take hidden physics into account. Furthermore, our approach thus provides insights addressing a fundamental limitation of the physics-based models when the governing equations are incomplete to represent underlying physical processes.

42 ENGINEERING↗

An Investigation of Chemo-Mechanical Phenomena and Li Metal Penetration in All-Solid-State Lithium Metal Batteries Using In Situ Optical Curvature Measurements

Solid-electrolytes (SEs) can provide a pathway to increase energy-density in lithium metal batteries. However, lithium metal penetration through garnet based LLZO solid electrolytes has been identified as a critical failure process. This phenomenon is related to chemo-mechanical processes which are difficult to probe. In particular, characterizing the dynamic mechanical deformations that occur in electrode-SE structures is very challenging. Here study reports in situ curvature measurements that are thus designed to probe chemo-mechanical phenomena that occur during lithium plating. The novel experimental cell configuration created for this work shows that pressure builds up in the Li metal during plating, up until the point where short circuits occur. The resulting data are analyzed with a detailed finite element model (FEM) to quantitatively evaluate stress evolution. The results show that Li metal plating within a surface flaw can produce stress build-up prior to short-circuiting. The combined results from both the experiments and the FEM suggest that it is critical to minimize surface defects and flaws during the manufacturing processes.

25 ENERGY STORAGE↗

lumicap v0.1

Automated HDR luminance imaging system designed for daylighting research and building science. It controls a fisheye-lens camera to capture time-lapse bracket sequences, merges them into calibrated HDR images, and runs a full post-processing pipeline — all unattended. Features: - Scheduled LDR bracket capture via gphoto2 - HDR merging with vignetting, ND filter, and fisheye projection corrections - Illuminance and luminance meter integration (Konica Minolta T-10A, LS-100/150) - Daylight glare probability (DGP) and solar position computation - Automated false-color rendering, JPEG thumbnails, and daily time-lapse video - CSV data logging per timestep Uses: - Long-term monitoring of daylight conditions in buildings - Glare analysis for occupant comfort research - Solar irradiance and sky luminance studies Advantages: - End-to-end automation — capture, calibration, analysis, and archiving run without manual intervention - Built on the proven Radiance toolchain, ensuring photometrically accurate HDR output - Hardware-agnostic meter support via serial auto-detection - Lightweight — no GUI overhead, deployable on a headless Raspberry Pi or similar embedded system

Wang, Taoning [Lawrence Berkeley National Laborato↗

Data-Driven Understanding of Low-to-Moderate Income Customers’ Adoption and Financial Qualification in Community Solar

Through this project, we sought to gather a body of customer data that either proved or disproved our assumption that metrics other than FICO can and should be used to qualify customers for community solar. Using customer data on income, FICO scores, and utility/rent/cell phone repayment history, we developed an alternative metric in order to test in the market at a small scale whether new qualifying metrics could open the shared solar market up to millions of additional households. We demonstrate that the EnergyScore is both more accurate in qualifying customers that will not default, and more inclusive in qualifying low to moderate income households. We are now in the process of utilizing the EnergyScore in a number of pilot projects, building a robust dataset of customer churn and default, and subsequently disseminating this data to more traditional and larger scale financiers and solar developer partners to change the way potential customers are qualified.

14 SOLAR ENERGY↗

Long-run Marginal Emission Rates for Electricity - Workbooks for 2023 Cambium Data

These workbooks contain modeled estimates of long-run marginal emission rates (LRMER) for the contiguous United States' electric sector. A LRMER is an estimate of the rate of emissions that would be either induced or avoided by a change in electric demand, taking into account how the change could influence both the operation as well as the structure of the grid (i.e., the building and retiring of capital assets, such as generators and transmission lines). These workbooks provide data for 18 GEA regions covering the contiguous United States. Mappings of these regions to ZIP codes and counties is given in this workbook in the corresponding tabs. For more data underlying these emissions factors, see the Cambium 2023 project at https://scenarioviewer.nrel.gov/. For more details on input assumptions and methodology see the associated report (Cambium 2023 Scenario Descriptions and Documentation, https://www.nrel.gov/docs/fy24osti/88507.pdf). Users are advised to review section 4 of the report, which discusses limitations and caveats of the data. This data is planned to be updated annually. Information on the latest versions can be found at https://www.nrel.gov/analysis/cambium.html.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Burleyson et al. 2020 Energy

Raw and processed data associated with the Burleyson et al. 2020 paper in Energy. The data needed to reproduce all figures in the paper is also included.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Designing a Magnetic Measurement Data Acquisition and Control System With Reuse in Mind: A Rotating Coil System Example

Accelerator magnet test facilities frequently need to measure different magnets on differently equipped test stands and with different instrumentation. Designing a modular and highly reusable system that combines flexibility built-in at the architectural level as well as on the component level addresses this need. Specification of the backbone of the system, with the interfaces and dataflow for software components and core hardware modules, serves as a basis for building such a system. The design process and implementation of an extensible magnetic measurement data acquisition and control system are described, including techniques for maximizing the reuse of software. The discussion is supported by showing the application of this methodology to constructing two dissimilar systems for rotating coil measurements, both based on the same architecture and sharing core hardware modules and many software components. The first system is for production testing 10 m long cryo-assemblies containing two MQXFA quadrupole magnets for the high-luminosity upgrade of the Large Hadron Collider and the second for testing IQC conventional quadrupole magnets in support of the accelerator system at Fermilab.

43 PARTICLE ACCELERATORS↗

Comparative life cycle assessment of a modular cross-laminated timber residential building designed for disassembly and reuse versus traditional wood frame construction

There is a need for affordable housing across the U.S., with high-performance modular and prefabricated buildings providing a logical avenue for meeting some of this demand. However, there is a need to balance high performance construction – including low emissions – with affordability. To provide a proof-of-concept in meeting these goals, the Circular Home is a cross-laminated timber (CLT)-based deconstructible and reconfigurable single-family residence that meets high performance targets in moisture, energy, design, economics, and life cycle assessment (LCA). This study focuses on the LCA, presenting a cradle-to-cradle whole-building life cycle assessment (WBLCA) for the Circular Home and a functionally equivalent Baseline Home constructed with traditional materials and methods. The functional unit is 1 m 2 of gross floor area across 60 years. Revit building information models (BIM) provided material quantities and Tally LCA was utilized for impact data (inclusive of biogenic carbon sequestration), supplemented with manufacturer environmental product declarations (EPDs). The Circular Home outperforms the baseline residence in most measured impact categories, including global warming potential (GWP), producing −2.73 kgCO 2 eq/m 2 in embodied emissions, whereas the modeled baseline has an embodied GWP of 428 kgCO 2 eq/m 2 . The careful material selection and advanced building design optimizes performance, with the Circular Home containing only −0.006 times the embodied emissions and −0.02 times the operational emissions of its traditional counterpart. Finally, the unique contribution of this work is in the environmental impact comparison of a high-performance modular CLT structure that can be affordably scaled and mass produced in a U.S. market, compared to typical single family home construction.

Circularity↗

Direct prediction of inelastic neutron scattering spectra from the crystal structure*

Abstract Inelastic neutron scattering (INS) is a powerful technique to study vibrational dynamics of materials with several unique advantages. However, analysis and interpretation of INS spectra often require advanced modeling that needs specialized computing resources and relevant expertise. This difficulty is compounded by the limited experimental resources available to perform INS measurements. In this work, we develop a machine-learning based predictive framework which is capable of directly predicting both one-dimensional INS spectra and two-dimensional INS spectra with additional momentum resolution. By integrating symmetry-aware neural networks with autoencoders, and using a large scale synthetic INS database, high-dimensional spectral data are compressed into a latent-space representation, and a high-quality spectra prediction is achieved by using only atomic coordinates as input. Our work offers an efficient approach to predict complex multi-dimensional neutron spectra directly from simple input; it allows for improved efficiency in using the limited INS measurement resources, and sheds light on building structure-property relationships in a variety of on-the-fly experimental data analysis scenarios.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Online data-enabled predictive control

We develop an online data-enabled predictive (ODeePC) control method for optimal control of unknown systems, building on the recently proposed DeePC (Coulson et al., 2019). Our proposed ODeePC method leverages a primal-dual algorithm with real-time measurement feedback to iteratively compute the corresponding real-time optimal control policy as system conditions change. The proposed ODeePC conceptual-wise resembles standard adaptive system identification and model predictive control (MPC), but it provides a new alternative for the standard methods. ODeePC is enabled by computationally efficient methods that exploit the special structure of the Hankel matrices in the context of DeePC with Fast Fourier Transform (FFT) and primal-dual algorithm We provide theoretical guarantees regarding the asymptotic behavior of ODeePC, and we demonstrate its performance through numerical examples.

97 MATHEMATICS AND COMPUTING↗

Engaging a Diverse Workforce in the Building Sciences Through the JUMP Into STEM Program: Impact Study; Preprint

Ensuring inclusivity in building science professions requires engaging people from underrepresented demographics; unfortunately, many races, ethnicities, and genders continue to be underrepresented. The JUMP into STEM program works to rectify this, encouraging creative ideation and highlighting the unique perspectives of a diverse array of students. The top students are awarded internships that provide opportunities to work in building science research with close supervision from mentors in the field. In the research presented here, we investigate the impact of participation in JUMP into STEM on students' careers, including the impact on students from diverse backgrounds. Furthermore, we research students' awareness of career opportunities in building science, students' perception of their ability to meaningfully contribute to this field, and the career building opportunities that JUMP into STEM provides for students. Through participant interviews and data analysis, we measure program diversity, inclusion, and effectiveness at achieving goals. We find that among the hundreds of students who have participated in this program, more than 25 different majors and/or educational degree programs are represented and more than 45% of students attend minority serving institutions or historically black colleges and universities. The JUMP into STEM experience had a significant effect on career choices or career development for more than 80% of participants. Our results also indicate that the JUMP into STEM program is effective at promoting diversity in the building sciences and is successfully contributing to the larger effort within the building science industry to promote and ensure equity in technological progress and innovation.

building energy science↗

Prescreening-Based Subset Selection for Improving Predictions of Earth System Models With Application to Regional Prediction of Red Tide

We present the ensemble method of prescreening-based subset selection to improve ensemble predictions of Earth system models (ESMs). In the prescreening step, the independent ensemble members are categorized based on their ability to reproduce physically-interpretable features of interest that are regional and problem-specific. The ensemble size is then updated by selecting the subsets that improve the performance of the ensemble prediction using decision relevant metrics. We apply the method to improve the prediction of red tide along the West Florida Shelf in the Gulf of Mexico, which affects coastal water quality and has substantial environmental and socioeconomic impacts on the State of Florida. Red tide is a common name for harmful algal blooms that occur worldwide, which result from large concentrations of aquatic microorganisms, such as dinoflagellate Karenia brevis, a toxic single celled protist. We present ensemble method for improving red tide prediction using the high resolution ESMs of the Coupled Model Intercomparison Project Phase 6 (CMIP6) and reanalysis data. The study results highlight the importance of prescreening-based subset selection with decision relevant metrics in identifying non-representative models, understanding their impact on ensemble prediction, and improving the ensemble prediction. These findings are pertinent to other regional environmental management applications and climate services. Additionally, our analysis follows the FAIR Guiding Principles for scientific data management and stewardship such that data and analysis tools are findable, accessible, interoperable, and reusable. As such, the interactive Colab notebooks developed for data analysis are annotated in the paper. This allows for efficient and transparent testing of the results’ sensitivity to different modeling assumptions. Moreover, this research serves as a starting point to build upon for red tide management, using the publicly available CMIP, Coordinated Regional Downscaling Experiment (CORDEX), and reanalysis data.

54 ENVIRONMENTAL SCIENCES↗

An open-source framework for simulation-based testing of buildings control strategies

Here this paper presents a simulation framework for evaluating building control strategies (BCSs), developed with VOLTTRON, an opensource platform that integrates data, devices, and systems for sensing and control applications, and is based on co-simulation interfaces. It realizes an integrated environment for both testing and deploying BCSs, thereby eliminating the need for having a dedicated implementation of BCS for testing. For the first time, this framework provides critical functionalities, including scalable communication management and time-drive simulation advance, i.e., advancing the simulation based on clock time. We applied this framework to evaluating two BCSs from ASHRAE Guideline 36-2008 and ASHRAE Standard 90.1-2019. The evaluation results show that those BCSs primarily benefit the heating operation by reducing gas usage but yield insignificant savings in electricity consumption. The results also emphasize the importance of tuning the parameters of the BCSs to achieve better performances.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

PRODeepSyn: predicting anticancer synergistic drug combinations by embedding cell lines with protein–protein interaction network

Abstract Although drug combinations in cancer treatment appear to be a promising therapeutic strategy with respect to monotherapy, it is arduous to discover new synergistic drug combinations due to the combinatorial explosion. Deep learning technology holds immense promise for better prediction of in vitro synergistic drug combinations for certain cell lines. In methods applying such technology, omics data are widely adopted to construct cell line features. However, biological network data are rarely considered yet, which is worthy of in-depth study. In this study, we propose a novel deep learning method, termed PRODeepSyn, for predicting anticancer synergistic drug combinations. By leveraging the Graph Convolutional Network, PRODeepSyn integrates the protein–protein interaction (PPI) network with omics data to construct low-dimensional dense embeddings for cell lines. PRODeepSyn then builds a deep neural network with the Batch Normalization mechanism to predict synergy scores using the cell line embeddings and drug features. PRODeepSyn achieves the lowest root mean square error of 15.08 and the highest Pearson correlation coefficient of 0.75, outperforming two deep learning methods and four machine learning methods. On the classification task, PRODeepSyn achieves an area under the receiver operator characteristics curve of 0.90, an area under the precision–recall curve of 0.63 and a Cohen’s Kappa of 0.53. In the ablation study, we find that using the multi-omics data and the integrated PPI network’s information both can improve the prediction results. Additionally, the case study demonstrates the consistency between PRODeepSyn and previous studies.

Wang, Xiaowen↗