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At least 307 records · Page 17

Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC

The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.

59 BASIC BIOLOGICAL SCIENCES↗

The OCEAN ICE mooring compilation: a standardised, pan-Antarctic database of ocean hydrography and current time series

Continuous moored time series of temperature, salinity, pressure and current speed and direction are of great importance for understanding the continental shelf and under-ice-shelf dynamics and thermodynamics that govern water mass transformations and ice melting in and around Antarctic marginal seas. In these regions, icebergs and sea ice make ship-based mooring deployment and recovery challenging. Nevertheless, over decades, expeditions around the fringe of Antarctica sporadically deployed and recovered hundreds of moored instruments, including those facilitated through ice shelves boreholes. These datasets tend to be archived in a wide range of data centres, with, to our knowledge, no clear format standardisation. As a result, systematic analysis of historical mooring time series in the marginal seas is often challenging. Here we present the first version of a standardised pan-Antarctic moored hydrography and current time series compilation, with broad international contributions from data centres, research institutes and individual data owners. The mooring records in this compilation span over five decades, from the 1970s to the 2020s, providing an opportunity for a systematic study of the pan-Antarctic water mass transport and shelf connectivity. As a demonstration of the utility of this compilation, we present spectral analysis of the compiled current velocity time series, which unsurprisingly shows the dominating presence of tidal variability within most records. This component of the variability is fitted using multi-linear regression to tidal frequencies, and the tidal fit is removed from the original time series to leave de-tided variability. Given the limited record durations to months to years, de-tided variability is dominated by synoptic (3–10 d period), intraseasonal (10–80 d) and seasonal (∼6 months–1 year) signals. The spatial distribution of the kinetic energy integrated within frequency bands is presented and discussed within respective regional contexts, and future avenues of research are proposed. This data compilation is assembled under the endorsement of Ocean-Cryosphere Exchanges in ANtarctica: Impacts on Climate and the Earth System (OCEAN ICE) project (https://ocean-ice.eu/, last access: 23 October 2025) funded by the European Commission and UK Research and Innovation. It is available and regularly updated in NetCDF format with the SEANOE database at https://doi.org/10.17882/99922 (Zhou et al., 2024a).

54 ENVIRONMENTAL SCIENCES↗

Experimental protocol for phase 1 of the APARC QUOCA (QUasibiennial oscillation and Ozone Chemistry interactions in the Atmosphere) working group

The quasi-biennial oscillation (QBO) is the main mode of variability in the tropical stratosphere, influencing the predictability of other regions in the atmosphere through its teleconnections to the stratospheric polar vortices and coupling to surface tropical and extratropical variability. However, climate and forecasting models consistently underestimate QBO amplitudes in the lower stratosphere, likely contributing to their failure to simulate these teleconnections. One underexplored contributor to model biases is missing representation of ozone-radiative feedbacks, which enhance temperature variability in the lower stratosphere, particularly at periods at and greater than the QBO (>28 months). While previous studies suggest that ozone-radiative feedbacks can impact QBO periods, amplitudes and the associated secondary circulation in the lower stratosphere, the reported impacts differ widely among models and are hard to interpret due to differences in methodology. To this end, here we propose a coordinated experimental protocol – held joint between the Atmospheric Processes and their Role in Climate (APARC) Quasi-Biennial Oscillation Initiative (QBOi) and Chemistry Climate Modeling Initiative (CCMI) activities – which is aimed at assessing the coupling between stratospheric ozone, temperature and the circulation. We use the proposed experiments to define the ozone feedback on the QBO in both present-day and idealized (abrupt quadrupling of carbon dioxide) climates. While primary focus is on the QBO, the proposed protocol also enables analysis of other aspects of ozone-radiative-dynamical coupling in the atmosphere, including impacts on the Brewer-Dobson Circulation and tropospheric eddy-driven jet responses to future climate change. Here we document the scientific rationale and design of the QUOCA Phase 1 experiments, summarize the data request, and give a brief overview of participating models. Preliminary results using the NASA Goddard Institute for Space Studies E2-2 climate model are used to illustrate sensitivities to certain methodological choices.

Environmental sciences↗

Benchmark for two-dimensional large scale coherent structures in partially magnetized E × B plasmas—community collaboration & lessons learned

Low-temperature plasmas (LTPs) are essential to both fundamental scientific research and critical industrial applications. As in many areas of science, numerical simulations have become a vital tool for uncovering new physical phenomena and guiding technological development. Code benchmarking remains crucial for verifying implementations and evaluating performance. This work continues the Landmark benchmark initiative, a series specifically designed to support the verification of LTP codes. In this study, seventeen simulation codes from a collaborative community of nineteen international institutions modeled a partially magnetized E × B Penning discharge. The emergence of large scale coherent structures, or rotating plasma spokes, endows this configuration with an enormous range of time scales, making it particularly challenging to simulate. The codes showed excellent agreement on the rotation frequency of the spoke as well as key plasma properties, including time-averaged ion density, plasma potential, and electron temperature profiles. Achieving this level of agreement came with challenges, and we share lessons learned on how to conduct future benchmarking campaigns. Comparing code implementations, computational hardware, and simulation runtimes also revealed interesting trends, which are summarized with the aim of guiding future plasma simulation software development.

benchmarking↗

An Integrated Computer-Aided Design and Manufacturing Workflow for Synthetic Biology

Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Additionally, each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.

59 BASIC BIOLOGICAL SCIENCES↗

Privacy-Preserving Knowledge Transfer with Bootstrap Aggregation of Teacher Ensembles

There is a need to transfer knowledge among institutions and organizations to save effort in annotation and labeling or in enhancing task performance. However, knowledge transfer is difficult because of restrictions that are in place to ensure data security and privacy. Institutions are not allowed to exchange data or perform any activity that may expose personal information. With the leverage of a differential privacy algorithm in a high-performance computing environment, we propose a new training protocol, Bootstrap Aggregation of Teacher Ensembles (BATE), which is applicable to various types of machine learning models. The BATE algorithm is based on and provides enhancements to the PATE algorithm, maintaining competitive task performance scores on complex datasets with underrepresented class labels.We conducted a proof-of-the-concept study of the information extraction from cancer pathology report data from four cancer registries and performed comparisons between four scenarios: no collaboration, no privacy-preserving collaboration, the PATE algorithm, and the proposed BATE algorithm. The results showed that the BATE algorithm maintained competitive macro-averaged F1 scores, demonstrating that the suggested algorithm is an effective yet privacy-preserving method for machine learning and deep learning solutions.

Yoon, Hong-Jun↗

Nuclear Forces for Precision Nuclear Physics: A Collection of Perspectives

This is a collection of perspective pieces contributed by the participants of the Institute for Nuclear Theory’s Program on Nuclear Physics for Precision Nuclear Physics which was held virtually from April 19 to May 7, 2021. The collection represents the reflections of a vibrant and engaged community of researchers on the status of theoretical research in low-energy nuclear physics, the challenges ahead, and new ideas and strategies to make progress in nuclear structure and reaction physics, effective field theory, lattice QCD, quantum information, and quantum computing. Please note the contributed pieces solely reflect the perspectives of the respective authors and do not represent the viewpoints of the Institute for Nuclear theory or the organizers of the program.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Cultural Shifts in High Energy Physics Collaboration from the Cold War to the Present: A Historical and Philosophical Perspective

Here, this article employs empirical history and the philosophy of science to study cultural convergences and divergences in international collaborations in high energy physics. We examine two cases: (1) E-36, an experiment on small angle proton-proton scattering conducted during the Cold War at the National Accelerator Laboratory (NAL) in the USA by Soviet and US scientists and (2) an ongoing collaborative experiment, NICA, at the Joint Institute for Nuclear Research (JINR, Dubna), which is a project devoted to heavy-ion physics. The JINR, particularly its Laboratory of High Energy Physics (formerly the “Laboratory of High Energies”) is the main mediating actor between these two cases (i.e., E-36 and NICA), as the majority of Soviet participants in E-36 were representatives of the Institute. Using empirical data collected through archival searches, field observations conducted at JINR in 2018–2019, and in-depth interviews, we tell a story of cultural differences in high energy physics by applying the concepts of ‘trading zones’ (P. Galison) and the translation of interests in actor-networks (B. Latour, M. Callon and others). We analyze three types of cultural diversity (specialization, nationality, and generational) in light of the implications of temporal context and the dichotomy between East and West, showing the roles cultural diversity plays in scientific collaboration (which is an integral part of as well as obstacle to scientific research that can nevertheless provide learning opportunities). Our study aims to demonstrate how disunity and diversity may function in scientific research and how high energy physics collaborations can remain productive despite sometimes deep divergences, including those between East and West.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Total thermal neutron cross section measurements of hydrogen dense polymers from 0.0005–20 eV

Hydrogen dense polymers, specifically polyethylene, polystyrene, and Plexiglas, have served as neutron moderator and reflector materials in hundreds of separate critical benchmark experiments because of their low cost and abundance of hydrogen. In order to accurately model and simulate these critical benchmarks, the thermal scattering law (TSL) evaluation that governs how neutrons will thermalize must be well understood and rigorously validated. To support this validation, researchers at Rensselaer Polytechnic Institute performed total neutron cross section measurements for high-density polyethylene & polystyrene over the energy range 0.0005–20 eV and for Plexiglas G & Plexiglas G-UVT over the energy range 0.0005–3 eV. Comparisons were made between the measured cross section and that predicted by the ENDF/B-VIII.0 and Oak Ridge National Laboratory/European Spallation Source/Rensselaer Polytechnic Institute TSL evaluations for polyethylene, Plexiglas, and polystyrene, as available. These experiments represent the first total neutron cross section measurements for polystyrene.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Can we have clean energy and grow our crops too? Solar siting on agricultural land in the United States

We report a record amount of large-scale solar development is proposed and under construction in the US Midwest, much of it on agricultural land. This article contributes to the social science literature on renewable energy and public acceptance by addressing stakeholder perspectives on developing utility-scale solar power on agricultural land and complex institutional dynamics that shape these siting decisions. How do stakeholders’ interactions coproduce solar siting decisions? How are the existing complex contexts of energy and agricultural systems affecting solar siting? Who are the stakeholders involved in agricultural solar siting, and how do their epistemic paradigms about using agricultural land, especially prime farmland, differ? To answer these questions, interviews were conducted and analyzed across energy, agriculture, government, and expert stakeholder groups, focusing on Michigan, with comparison to other states. The results provide a conceptual map of stakeholder interaction related to solar development on farmland and characterize the main epistemic paradigms shaping stakeholder conflict. Issues shaping agricultural community perceptions include identity and farmland, the decisions of local farmland renters and non-operating landlords, prime versus lower quality farmland, farm financial viability, and farmland as private property or a public good. Some scientists and engineers seek to alleviate conflicts and drawbacks of agricultural land conversion for solar use by combining farming and solar energy generation: a practice called agrivoltaics. We argue that agrivoltaics are currently treated as a technological fix by not accounting for stakeholder interaction in complex policy, community, and scientific institutions. We conclude by identifying interdisciplinary research priorities to develop socially robust designs.

14 SOLAR ENERGY↗

Overcoming Barriers to Radiopharmaceutical Therapy (RPT): An Overview From the NRG-NCI Working Group on Dosimetry of Radiopharmaceutical Therapy

Radiopharmaceutical therapy (RPT) continues to demonstrate tremendous potential in improving the therapeutic gains in radiation therapy by specifically delivering radiation to tumors that can be well assessed in terms of dosimetry and imaging. Dosimetry in external beam radiation therapy is standard practice. This is not the case, however, in RPT. This NRG (acronym formed from the first letter of the 3 original groups: National Surgical Adjuvant Breast and Bowel Project, the Radiation Therapy Oncology Group, and the Gynecologic Oncology Group)-National Cancer Institute Working Group review describes some of the challenges to improving RPT. The main priorities for advancing the field include (1) developing and adopting best practice guidelines for incorporating patient-specific dosimetry for RPT that can be used at both large clinics with substantial resources and more modest clinics that have limited resources, (2) establishing and improving strategies for introducing new radiopharmaceuticals for clinical investigation, (3) developing approaches to address the radiophobia that is associated with the administration of radioactivity for cancer therapy, and (4) solving the financial and logistical issues of expertise and training in the developing field of RPT.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Fostering Radiation Oncology Physician Scientist Trainees Within a Diverse Workforce: The Radiation Oncology Research Scholar Track

There is a need to foster future generations of radiation oncology physician scientists, but the number of radiation oncologists with sufficient education, training, and funding to make transformative discoveries is relatively small. A large number of MD/PhD graduates have entered he field of radiation oncology over the past 2 decades, but this has not led to a significant cohort of externally funded physician scientists. Because radiation oncologists leading independent research labs have the potential to make transformative discoveries that advance our field and positively affect patients with cancer, we created the Duke Radiation Oncology Research Scholar (RORS) Program. In crafting this program, we sought to eliminate barriers preventing radiation oncology trainees from becoming independent physician scientists. The RORS program integrates the existing American Board of Radiology Holman Pathway with a 2-year post-graduate medical education instructor position with 80% research effort at the same institution. We use a separate match for RORS and traditional residency pathways, which we hope will increase the diversity of our residency program. Since the inception of the RORS program, we have matched 2 trainees into our program. We encourage other radiation oncology residency programs at peer institutions to consider this training pathway as a means to foster the development of independent physician scientists and a diverse workforce in radiation oncology.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Screening and Validation of Molecular Targeted Radiosensitizers

The development of molecular targeted drugs with radiation and chemotherapy is critically important for improving the outcomes of patients with hard-to-treat, potentially curable cancers. However, too many preclinical studies have not translated into successful radiation oncology trials. Major contributing factors to this insufficiency include poor reproducibility of preclinical data, inadequate preclinical modeling of intertumoral genomic heterogeneity that influences treatment sensitivity in the clinic, and a reliance on tumor growth delay instead of local control (TCD50) endpoints. There exists an urgent need to overcome these barriers to facilitate successful clinical translation of targeted radiosensitizers. To this end, we have used 3-dimensional (3D) cell culture assays to better model tumor behavior in vivo. Examples of successful prediction of in vivo effects with these 3D assays include radiosensitization of head and neck cancers by inhibiting epidermal growth factor receptor or focal adhesion kinase signaling, and radioresistance associated with oncogenic mutation of KRAS. To address the issue of tumor heterogeneity, we leveraged institutional resources that allow high-throughput 3D screening of radiation combinations with small-molecule inhibitors across genomically characterized cell lines from lung, head and neck, and pancreatic cancers. This high-throughput screen is expected to uncover genomic biomarkers that will inform the successful clinical translation of targeted agents from the National Cancer Institute Cancer Therapy Evaluation Program portfolio and other sources. Screening “hits” need to be subjected to refinement studies that include clonogenic assays, addition of disease-specific chemotherapeutics, target/biomarker validation, and integration of patient-derived tumor models. The chemoradiosensitizing activities of the most promising drugs should be confirmed in TCD50 assays in xenograft models with or without relevant biomarker and using clinically relevant radiation fractionation. We predict that appropriately validated and biomarker-directed targeted therapies will have a higher likelihood than past efforts of being successfully incorporated into the standard management of hard-to-treat tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Test and extraction methods for the QC parameters of silicon strip sensors for ATLAS upgrade tracker

The Quality Control (QC) of pre-production strip sensors for the Inner Tracker (ITk) of the ATLAS Inner Detector upgrade has finished, and the collaboration has embarked on the QC test programme for production sensors. This programme will last more than 3 years and comprises the evaluation of approximately 22000 sensors. 8 Types of sensors, 2 barrel and 6 endcap, will be measured at many different collaborating institutes. The sustained throughput requirement of the combined QC processes is around 500 sensors per month in total. Measurement protocols have been established and acceptance criteria have been defined in accordance with the terms agreed with the supplier. For effective monitoring of test results, common data file formats have been agreed upon across the collaboration. To enable evaluation of test results produced by many different test setups at the various collaboration institutes, common algorithms have been developed to collate, evaluate, plot and upload measurement data. This allows for objective application of pass/fail criteria and compilation of corresponding yield data. These scripts have been used to process the data of more than 3000 sensors so far, and have been instrumental for identification of faulty sensors and monitoring of QC testing progress.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

252 Cf yield calibration method for nuclear material accountancy and safeguards practitioners

Californium-252 is an isotope commonly encapsulated as a physically small but strong spontaneous fission neutron source for applications in industry, academia, and research. Within the nuclear safeguards community, a well-characterized 252 Cf source is often used as an accessible alternative for plutonium in calibrations measurements, which require the absolute source strength. Current methods of source strength quantification can provide an accurate estimate, approximately 1% uncertainty under optimal conditions, but are typically costly and time consuming. An alternative method was developed to determine 252 Cf source strength using passive neutron correlation counting (PNCC). The PNCC method enables institutions and facilities to perform 252 Cf source calibration measurements in-house using detection systems that are common within the nuclear safeguards community. This novel method was previously successfully demonstrated using neutron multiplicity well counters. However, the previous evaluation utilized detection systems with high neutron detection efficiencies, greater than 60%. The purpose of the current study is to extend the previous evaluation and demonstrate the feasibility of the PNCC 252 Cf calibration method for suite of coincidence counters with lower neutron detection efficiencies, between 15% and 35%, which are more commonly encountered in the field, as well as to provide a step-by-step guide to using the method. The neutron source used in this evaluation was previously certified by the National Institutes of Science and Technology (NIST), which provides a reference for the accuracy of the PNCC method. In conclusion, the present source yield calculations demonstrate excellent agreement with a NIST calibration technique and achieve a standard uncertainty below the target 1%.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Depletion benchmark for a high-assay low-enriched uranium fuel experiment in the advanced test reactor

Reactor physics depletion benchmarks for high-assay low-enriched uranium (HALEU) fuel are limited in number. In particular, there is limited data for HALEU benchmarks for U-10Mo (uranium-10% molybdenum) plate fuel that is being developed for use in the United States’ high performance research reactors including the Advanced Test Reactor (ATR), Advanced Test Reactor Critical Facility (ATR-C), High Flux Isotope Reactor (HFIR), Massachusetts Institute of Technology Reactor (MITR), University of Missouri Research Reactor (MURR), National Bureau of Standards Reactor (NBSR). These six reactors currently operate with highly enriched uranium dispersed fuel in an aluminum matrix. In support of conversion to a HALEU fuel, qualification of U-10Mo formed into a monolithic foil is being performed. Fuel qualification involves irradiating fuel specimens in the ATR. The irradiation tests provide an opportunity to benchmark depletion capabilities of reactor physics codes in support of the ATR operation, as well as develop benchmarks that can be used by other institutions to benchmark other reactor physics codes. This paper documents the development of a benchmark model of the irradiation of the ATR Full-size plate In center flux trap Position 7 (AFIP-7) experiment using the depletion codes MC21 and Advanced Dimensional Depletion for Engineering of Reactors (ADDER).

Nielsen, Joseph W. [Idaho National Laboratory (INL↗

Reducing Surface Recombination Velocity of Methylammonium-Free Mixed-Cation Mixed-Halide Perovskites via Surface Passivation

We control surface recombination in the mixed-cation, mixed-halide perovskite, FA0.83Cs0.17Pb(I0.85Br0.15)3, by passivating nonradiative defects with the polymerizable Lewis base (3-aminopropyl)trimethoxysilane (APTMS). We demonstrate average minority carrier lifetimes >4 µs, nearly single exponential monomolecular photoluminescence decays, and high external photoluminescence quantum efficiencies (>20%, corresponding to ~97% of the maximum theoretical quasi-Fermi-level splitting) at low excitation fluence. We confirm both the composition and valence band edge position of the FA0.83Cs0.17Pb(I0.85Br0.15)3 perovskite using multi-institutional, cross-validated, X-ray photoelectron spectroscopy and UV photoelectron spectroscopy measurements. We extend the APTMS surface passivation to higher bandgap double-cation (FA and Cs) compositions (1.7, 1.75, and 1.8 eV) as well as the widely used triple-cation (FA, MA, and Cs) composition. Finally, we demonstrate that the average surface recombination velocity decreases from ~1000 to ~10 cm/s post APTMS passivation for FA0.83Cs0.17Pb(I0.85Br0.15)3. Our results demonstrate that surface-mediated recombination is the primary nonradiative loss pathway in many methylammonium (MA)-free mixed-cation mixed-halide films with a range of different bandgaps, which is a problem observed for a wide range of perovskite active layers and reactive electrical contacts. Our study also provides insights to develop passivating molecules that help reduce surface recombination in MA-free mixed-cation mixed-halide films and indicates that surface passivation and contact engineering will enable near-theoretical device efficiencies with these materials.

14 SOLAR ENERGY↗

The Value of Reversible Carbon Storage in a Zero-Emissions World

Atmospheric carbon dioxide removal (CDR) is required to stabilize global temperature. CDR can be achieved via ecosystem-based approaches that are cost-effective but reversible (e.g., soil and forest management) or by more durable but expensive approaches (e.g., direct air capture coupled with geologic storage). Here, we examine trade-offs between these approaches, focusing on timing, climate impacts, and cost. We simulated reversible carbon accrual for a range of CDR contract structures using a general minimalist model of ecosystem carbon cycling, and parameterized it to simulate US agricultural soil management─specifically cover cropping─as a case study. We then quantified the resulting impact on atmospheric carbon and global temperature using a climate model emulator. We find that maintaining a patchwork of reversible CDR projects by replacing lapsed projects with new projects can reduce warming by 22–195 μ°C in 2100 and that the magnitude of this cooling effect depends on how effectively the patchwork is maintained. Long-term maintenance of reversible CDR projects requires institutional stability that cannot be guaranteed over multiple decades. Consequently, effective CDR ultimately requires replacing reversible projects with durable projects. To address this problem, we modeled the cost of replacing reversible agricultural soil CDR with geologic CDR. We found that using reversible CDR as a bridge to durable CDR is potentially more cost-effective as a global cooling strategy (0.20–0.81 billion USD per μ°C avoided) than perpetual maintenance of reversible CDR (0.32–1.31 billion USD per μ°C avoided) or an immediate transition to durable CDR (1.37–2.19 billion USD per μ°C avoided). However, we emphasize that institutional commitments to maintain reversible CDR projects cannot be guaranteed. Reliance on reversible CDR as a bridge to durable CDR therefore carries an unknown amount of risk and will only function if efforts to maintain reversible CDR are robust.

carbon capture and storage↗