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At least 1,099 records · Page 61

Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases

Replication-initiating HUH endonucleases (Reps) are sequence-specific nucleases that cleave and rejoin single-stranded DNA (ssDNA) during rolling-circle replication. These functions are mediated by covalent linkage of the Rep to its substrate post cleavage. Here, we describe the structures of the endonuclease domain from the Muscovy duck circovirus Rep in complex with its cognate ssDNA 10-mer with and without manganese in the active site. Structural and functional analyses demonstrate that divalent cations play both catalytic and structural roles in Reps by polarizing and positioning their substrate. Further structural comparisons highlight the importance of an intramolecular substrate Watson-Crick (WC) base pairing between the -4 and +1 positions. Subsequent kinetic and functional analyses demonstrate a functional dependency on WC base pairing between these positions regardless of the pair’s identity (i.e., A·T, T·A, G·C, or C·G), highlighting a structural specificity for substrate interaction. Finally, considering how well WC swaps were tolerated in vitro, we sought to determine to what extent the canonical -4T·+1A pairing is conserved in circular Rep-encoding single-stranded DNA viruses and found evidence of noncanonical pairings in a minority of these genomes. Altogether, our data suggest that substrate intramolecular WC base pairing is a universal requirement for separation and reunion of ssDNA in Reps.

59 BASIC BIOLOGICAL SCIENCES↗

The proton charge radius extracted from the initial-state radiation experiment at MAMI

Abstract We report on a comprehensive reinterpretation of the existing cross-section data for elastic electron-proton scattering obtained by the initial-state radiation technique, resulting in a significantly improved accuracy of the extracted proton charge radius. By refining the external energy corrections we have achieved an outstanding description of the radiative tail, essential for a detailed investigation of the proton finite-size effects on the measured cross sections. This development, together with a novel framework for determining the radius, based on a regression analysis of the cross sections employing a polynomial model for the form factor, led us to a new value for the charge radius, which is $$(0.878 \pm 0.011_\mathrm {stat.}\pm 0.031_\mathrm {sys.}\pm 0.002_\mathrm {mod.})\,\mathrm {fm}$$ ( 0.878 ± 0 . 011 stat . ± 0 . 031 sys . ± 0 . 002 mod . ) fm

Physics↗

sf-23-021 SONICC (SCALE-DEPENDENT OMEGA FOR NEUTRINO INITIAL CONDITION CODES)

SONICC computes density and velocity transfer functions for use in the initial conditions of massive neutrino cosmological simulations. The transfer functions are backscaled using a scale-dependent growth function that produces self-consistent evolution for all three matter species (cold dark matter, baryons, massive neutrinos) in the Newtonian forward model of cosmological simulations.

EMBERSON, JEFFREYD↗

Inhibition of the eukaryotic initiation factor-2α kinase PERK decreases risk of autoimmune diabetes in mice

Preventing the onset of autoimmune type 1 diabetes (T1D) is feasible through pharmacological interventions that target molecular stress–responsive mechanisms. Cellular stresses, such as nutrient deficiency, viral infection, or unfolded proteins, trigger the integrated stress response (ISR), which curtails protein synthesis by phosphorylating eukaryotic translation initiation factor-2α (eIF2α). In T1D, maladaptive unfolded protein response (UPR) in insulin-producing β cells renders these cells susceptible to autoimmunity. We found that inhibition of the eIF2α kinase PKR-like ER kinase (PERK), a common component of the UPR and ISR, reversed the mRNA translation block in stressed human islets and delayed the onset of diabetes, reduced islet inflammation, and preserved β cell mass in T1D-susceptible mice. Single-cell RNA-Seq of islets from PERK-inhibited mice showed reductions in the UPR and PERK signaling pathways and alterations in antigen-processing and presentation pathways in β cells. Spatial proteomics of islets from these mice showed an increase in the immune checkpoint protein programmed death-ligand 1 (PD-L1) in β cells. Golgi membrane protein 1, whose levels increased following PERK inhibition in human islets and EndoC-βH1 human β cells, interacted with and stabilized PD-L1. Collectively, our studies show that PERK activity enhances β cell immunogenicity and that inhibition of PERK may offer a strategy for preventing or delaying the development of T1D.

Research & Experimental Medicine↗

The UCAR Africa Initiative: Recent insights, challenges, and opportunities to foster collaborative research for environmental sustainability

Africa is increasingly being exposed to the negative impacts of climate and environmental change, while having less capacity to respond compared to other continents. The vulnerability partially results from unprecedented demographic growth, urbanization, and industrialization. However, the continent has still largely been underserved by the broader Earth System Science (ESS) community, as evidenced by the limited amount of ESS data and research that cover Africa compared to other areas of the world. Here we present the recent University Corporation for Atmospheric Research (UCAR) Africa Initiative that aims to enhance environmental sustainability in Africa by fostering international collaborative research partnerships co-led by African scientists. Specifically, we outline urgent challenges and opportunities identified through an international workshop in six areas of ESS namely (1) air quality and health, (2) weather, (3) climate, (4) land and water, (5) social science perspectives, and (6) developing equitable collaboration and sustainable infrastructure. We highlight examples of successful partnerships and conclude with recommendations to advance collaborative, actionable ESS research that addresses Africa’s critical environmental challenges.

African weather and land variability↗

Environmental controls on simulated deep moist convection initiation occurring during RELAMPAGO-CACTI

This study synthesizes the results of 13 high-resolution simulations of deep convective updrafts forming over idealized terrain using environments observed during the RELAMPAGO and CACTI field projects. Using composite soundings from multiple observed cases, and variations upon them, we explore the sensitivity of updraft properties (e.g., size, buoyancy, and vertical pressure gradient forces) to influences of environmental relative humidity, wind shear, and mesoscale orographic forcing that support or suppress deep convection initiation (CI). Emphasis is placed on differentiating physical processes affecting the development of updrafts (e.g., entrainment-driven dilution of updrafts) in environments typifying observed successful and null (i.e., no CI despite affirmative operational forecasts) CI events. Thermally-induced mesoscale orographic lift favors the production of deep updrafts originating from ~1–2-km-wide boundary layer thermals. Simulations without terrain forcing required much larger ( ~5-km-wide) thermals to yield precipitating convection. CI outcome was quite sensitive to environmental relative humidity; updrafts with increased buoyancy, depth, and intensity thrived in otherwise inhospitable environments by simply increasing the free tropospheric relative humidity. This implicates the entrainment of free-tropospheric air into updrafts as a prominent governor of CI, consistent with previous studies. Sensitivity of CI to the environmental wind is manifested by: 1) low-level flow affecting the strength and depth of mesoscale convergence along the terrain, and 2) clouds encountering updraft-suppressing pressure gradient forces while interacting with vertical wind shear in the free-troposphere. Among the ensemble of thermals occurring in each simulation, the widest deep updrafts in each simulation were the most sensitive to environmental influences.

54 ENVIRONMENTAL SCIENCES↗

Deep Convection Initiation, Growth, and Environments in the Complex Terrain of Central Argentina during CACTI

This study characterizes the wide range of deep convective cloud life cycles and their relationships with ambient environments observed during the Cloud, Aerosol, and Complex Terrain Interactions (CACTI) field campaign near the Sierras de Córdoba (SDC) range in central Argentina. We develop a novel convective cell tracking database for the entire field campaign using C-band polarimetric radar observations. The cell tracking database includes timing, location, area, depth, merge/split information, microphysical properties, collocated satellite-retrieved cloud properties, and sounding-derived environmental conditions. Results show that the SDC exerts a strong control on convection initiation (CI) and growth. CI preferentially occurs east of the SDC ridge during the afternoon, and cells often undergo upscale growth through the evening as they travel eastward toward the plains. Larger and more intense cells tend to occur in more unstable and humid low-level environments, and surface-based cells are stronger than elevated cells. Midtropospheric relative humidity and vertical wind shear also jointly affect the size and depth of the cells. Rapid cell area growth rates exhibit dependence on both large environmental wind shear and low-level moisture. Evolution of convective cell macro- and microphysical properties are strongly influenced by convective available potential energy and low-level humidity, as well as the presence of other cells in their vicinity. This cell tracking database demonstrates a framework that ties measurements from various platforms centering around convective life cycles to facilitate process understanding of factors that control convective evolution.

54 ENVIRONMENTAL SCIENCES↗

Near-Cloud Atmospheric Ingredients for Deep Convection Initiation

A lack of routine environmental observations located near deepening cumulus congestus clouds limits verification of important theorized and simulated updraft–environment interaction processes occurring during deep convection initiation (CI). We analyze radiosonde profiles collected during several hundred CI events near a mountain range in central Argentina during the CACTI field campaign. Statistical analyses illustrate environmental conditions supporting radar-observed CI outcomes that span a spectrum of convective cell depths, widths, and durations, as well as events lacking precipitating convection. Tested environmental factors include a large variety of sounding-derived measurements of CAPE, CIN, moisture, terrain-relative winds, vertical shear, and lifted parcel properties, with supplemental model reanalysis of background larger-scale vertical motion. CAPE and CIN metrics do not consistently differentiate CI success from failure. Only a few environmental factors contain consistent monotonic relationships among the spectrum of cloud depths achieved during CI: (i) the depth and strength of background ascent, and (ii) the component of low-level flow oriented parallel to the ridgeline. These metrics suggest that the ability of the surrounding flow to lift parcels to their LFC and terrain-modified flow are consistently relevant processes for CI. Low- to midlevel relative humidity strongly discriminated between CI and non-CI events, likely reflecting entrainment-driven dilution processes. However, we could not confidently conclude that relative humidity similarly discriminated robust from marginal CI events. Circumstantial evidence was found linking cell width, an important cloud property governing the probability of CI, to LCL height, boundary layer depth, depth and magnitude of the CIN layer, and ambient wind shear.

Storm environments↗

SARS-CoV2 Protein-Ligand Simulation Dataset: Layer 1 (Simulation Initial Conditions and Parameters)

A set of 24 protein structures/complexes from the SARS CoV-2 proteome and inputs prepared for simulation using the CHARMM36m forcefield in PDB and gromacs formats. Each system contains a pdb and gromacs top and related input files necessary for running a temperature replica-exchange simulation. In addition, we also include: charmm PSF files (generated from the gromacs topology), a list of temperatures at which replica-exchange simulations were done (tempRamp), example gromacs run input mdp files, and initial minimized structures where available (minimized.pdb).

60 APPLIED LIFE SCIENCES↗

AbacusSummit: Cosmological N-body Halos, Light Cones, Particles, Merger Trees, Initial Conditions, and Power Spectra

This is the primary data release of the AbacusSummit, a suite of large, high-accuracy cosmological N-body simulations. Documentation describing the suite and code, including links to refereed publications and instructions for manipulating the data contained in this release, may be found at the following URL: https://abacussummit.readthedocs.io/ The primary data products presented in this release are halo catalogs, light cones, and particle data. Several supplemental products are also presented: power spectra, initial conditions, and merger trees. Cleaned halo catalogs are also provided for the subset of simulations that were used in refereed publications at the time of this DOI. This release also contains several large scale-free and high-redshift simulations run as part of the same allocation used to produce AbacusSummit.

79 ASTRONOMY AND ASTROPHYSICS↗

Evaluating the X2 initial core zero power physics tests with Serpent-Ants

The validation of the Ants nodal neutronics code for VVER applications is started by modelling the zero power physics tests for the initial core of the Khmelnitsky 2 nuclear power plant as described in the X2 benchmark using the Serpent-Ants two step neutronics calculation chain. The Ants prediction compare favorably against an earlier continuous energy Monte-Carlo reference solution as well as the measured data, except for discrepancies in the SCRAM worth between predicted and measured values. Similar discrepancies have been previously reported for VVER-1000 reactors, and the Ants predicted SCRAM worths match well with the Serpent results. Additionally, the assembly power distribution and axial power distribution predicted by Ants for the critical HZP state of the reactor are also compared to a reference Serpent solution with very good results. Lastly, an investigation into the effects of the few-group structure used in the nodal calculations and the use or lack of leakage correction for group constants on the results shows that the best accuracy is reached with seven or eight energy groups without leakage correction, although a reasonable accuracy can also be obtained with two or three energy groups using fundamental mode leakage correction. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Initial study on cross-section generation requirements for a PBR equilibrium core

A Serpent model of the equilibrium core HTR-PM small modular nuclear reactor in China, was developed for use in cross-section preparation studies in order to guide methods development for the Griffin reactor multiphysics application. The model includes detailed isotopics for 10 distinct pebble burnup groups in 126 core zones with unique fuel and moderator temperatures obtained from a coupled neutronics-thermal-fluids equilibrium core calculation using Griffin-Pronghorn. A sensitivity study of the fuel and moderator temperatures for various core regions was performed with the MOOSE stochastic tools. The results show that the uncertainties are, not unexpectedly, dominated by the value of the fluid temperature and that the power level, heat transfer coefficient and effective conduction to neighboring pebbles and fluid constitute, at best, second order effects. The temperature uncertainty range varies from 28 K to 57 K between the core entry and exit planes, respectively, but these values are probably higher. We still have to quantify the significance of these uncertainties in the preparation of cross-sections in future work. In addition, we verified that the effective pebble approximation used in the PEBBED and V.S.O.P. computer codes works well for the preparation of region averaged cross-sections. Nevertheless, there are some discrepancies in the cross-sections when compared to the multi-pebble model, which could affect the prediction of peak values and the depletion calculation. We conclude that is highly desirable for future studies with Griffin to be able to handle both the 'effective' pebble approximation and the multi-pebble approach for various pebble burnup groups. This enables Griffin users with the flexibility to perform higher-fidelity studies. Finally, we initiated the preparation of cross-sections for various core regions from the full core Serpent reference model. We quantified the differences in 26 group cross-sections from infinite domain models versus the full core approach. These reference cross-sections will serve to verify the double heterogeneity, self-shielding, and spectrum-correction methods in Griffin. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Gen IV Education and Training Working Group Webinars’ Initiative

Collaboration and support among national laboratories, industry, universities, and research and development organizations are vital to not only maintain a skilled and competent nuclear workforce but also to avert the risk of human resource shortages. As stated in a recent IAEA paper [1], the world nuclear electrical generating capacity is projected to increase to 554 GW(e) by 2030 and up to 874 GW(e) by 2050 (Fig. 1). This represents a 42% increase over current levels by 2030 and a doubling of the current capacity by 2050. To promote Education and Training (E&T) on Gen IV reactor systems and other nuclear related topics of interest, the Gen IV Education and Training Working Group (ETWG) identifies and advertises training courses; engages collaboration with other international education and training organizations; delivers webinars dedicated to Gen IV systems; and maintains a modern social medium platform to exchange information and ideas on Gen IV R&D topics, as well as on related GIF education and training activities. At the end of June 2020, the GIF ETWG has produced, podcasted and posted forty-one webinars covering the six Gen IV systems and various subjects addressing e.g. the economics of the nuclear fuel cycle, sustainability aspects of Gen IV systems, nuclear fuels and materials challenges, the thorium fuel cycle, energy conversion systems, and lessons learned for knowledge management and preservation. This paper describes the development of these webinars from the initial concept to its full realization, with future webinars planned in 2021, addressing topics such as materials and fuels performance for advanced reactors, small modular reactor.

Paviet, Patricia D.↗

Initial Efforts Organizing WPNCS SG-8: Preservation of Expert Knowledge and Judgement Applied to Criticality Benchmarks

The Working Party on Nuclear Criticality Safety (WPNCS) under the guidance of the Organization for Economic Co-operation and Development (OECD) Nuclear Energy Agency (NEA) has over 20 years of experience addressing concerns related to static and transient configurations encountered within the nuclear fuel cycle: fuel fabrication, transportation, reprocessing, storage, and geological disposal. One of the cornerstone activities of the WPNCS is the International Criticality Safety Benchmark Evaluation Project (ICSBEP), which was established to identify a comprehensive set of criticality benchmark data, evaluate the data, including quantification of overall uncertainties; compile the data into a standardized format, perform sample calculations utilizing modern nuclear data sets and codes utilized in nuclear criticality safety, and formally document the work into a single source of verified benchmark data. Annually, members of the ICSBEP Technical Review Group (TRG) contribute evaluated benchmark data that undergoes comprehensive technical review prior to publication in the ICSBEP Handbook. In the years since the ICSBEP was established, there has been much work to prepare benchmark data to support validation activities in nuclear criticality safety. The 2020 edition of the ICSBEP Handbook contains acceptable benchmark specifications for 5,053 critical, subcritical, or near-critical configurations in 582 benchmark evaluations. Modern benchmark development benefits from decades of experienced international participants, a well-established handbook format, supplementary guides to deal with uncertainty quantification, and a comprehensive review process based upon independent reviews from international experts. The ICSBEP Handbook also contains 838 configurations deemed unacceptable to support criticality safety efforts. They are recorded, with the reasoning for their rejection, to preserve the experimental data, prevent reevaluation of data that are incomplete or contain known errors, and/or to potentially allow future reevaluation of the experiment pending the identification of sufficient data to resolve identified inconsistencies and errors. Users of the ICSBEP Handbook today might notice that the rigor and quality of modern criticality safety benchmarks is much greater than those prepared within the initial decade of the project. Benchmarks with 1s uncertainties in k eff greater than 1% were traditionally rejected unless they were identified as unique experiment types that encompassed materials, fuels, or designs not available from other benchmark experiments. However, benchmarks developed using modern experimental techniques and practices typically have uncertainties on the order of a few tenths of a percent. There have been ongoing efforts to improve the overall quality of previously published benchmark evaluations. Seventy-eight evaluations, containing approximately 600 configurations, have been revised just within the past decade. An additional eleven benchmarks are under revision for updated release in the 2020 edition of the ICSBEP Handbook. If some of the historic benchmarks were resubmitted in their current form to the TRG today, they would be rejected due to lack of data, missing components in the uncertainty analysis, or incomplete benchmark model development. The use of historic criticality safety benchmarks that underestimate the total uncertainty, lack properly quantified biases, or provide inadequate benchmark specifications do not sufficiently support modern criticality safety and nuclear data efforts. Although the ICSBEP Handbook is recognized by regulating bodies to support criticality safety, users are required to justify their reasons to ignore historic benchmark data and include additional safety margins within their designs. Discussions were held at the WPNCS 23rd Annual Meeting in September 2019 regarding the aforementioned issues. The resultant decision was to establish Subgroup 8 (SG-8): Preservation of Expert Knowledge and Judgement Applied to Criticality Benchmarks. The current activities of SG-8 are discussed herein.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A guide to the BRAIN Initiative Cell Census Network data ecosystem

Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipulate cell types in controlled ways and to understand their variation and vulnerability in brain disorders. The BRAIN Initiative Cell Census Network (BICCN) is an integrated network of data-generating centers, data archives, and data standards developers, with the goal of systematic multimodal brain cell type profiling and characterization. Emphasis of the BICCN is on the whole mouse brain with demonstration of prototype feasibility for human and nonhuman primate (NHP) brains. Here, we provide a guide to the cellular and spatial approaches employed by the BICCN, and to accessing and using these data and extensive resources, including the BRAIN Cell Data Center (BCDC), which serves to manage and integrate data across the ecosystem. We illustrate the power of the BICCN data ecosystem through vignettes highlighting several BICCN analysis and visualization tools. Finally, we present emerging standards that have been developed or adopted toward Findable, Accessible, Interoperable, and Reusable (FAIR) neuroscience. The combined BICCN ecosystem provides a comprehensive resource for the exploration and analysis of cell types in the brain.

59 BASIC BIOLOGICAL SCIENCES↗

The Global Spectra-Trait Initiative: A database of paired leaf spectroscopy and functional traits associated with leaf photosynthetic capacity (v1.0.0)

The Global Spectra-Trait Initiative (GSTI) aims to generate generalizable spectra trait models using reflectance data to predict leaf traits associated with the photosynthesis capacity of leaves. It comprises a synthesized dataset of leaf trait data, input datasets and code. Leaf traits include the maximum carboxylation rate of rubisco (Vcmax), the maximum electron transport rate (Jmax), the dark respiration, as well as the prediction of leaf nitrogen, leaf mass per area (LMA), and leaf water content (LWC). The dataset comprises >7500 paired observations from around 400 species from a broad range of biomes. This dataset comprises a zip file of the GSTI GitHub repository (https://github.com/plantphys/gsti), the synthesized database (.csv) and database metadata files. This dataset was updated on 2025-12-12 with minor edits to mirror the accepted manuscript version and GitHub release (Version 1.0.0 (ESSD accepted version)). Edits included minor changes to the project documentation on GitHub and removal of 12 duplicate entries from the database.

54 ENVIRONMENTAL SCIENCES↗

Realizing the potentials of density functional theory (DFT) and of the materials genome initiative (MGI)

Abstract From 1964 and 1965 to present, the wide spread utilization of an incomplete density functional theory (DFT) has led to mixed results: The second theorem of the theory asserts that the energy functional reaches its minimum if the calculation employs the ground state charge density—without providing a mechanism for finding this density. Calculations purporting to employ DFT have mostly assumed that results obtained with a judiciously selected basis set, following self-consistent iterations, are those of the ground state. The state obtained with a single basis set is a stationary one, among an infinite number of such states, with no proven relation to the actual ground state of the material. Most failures or limitations of the incomplete DFT can be traced to this error. We present results from calculations using the completed DFT. They are in excellent agreement with experiment and portend the realization of the Materials Genome Initiative.

Bagayoko, Diola↗

Initial dynamic photoactive materials testing of an atmospheric chamber intended for radioactive and hazardous gases

Radioisotopes and hazardous gases can have undetermined environmental pathways. Researchers at Pacific Northwest National Laboratory constructed a chamber that complies with the requirements needed for an atmospheric reaction platform and the safety principles of interacting with hazardous dispersible sources to enable the environmental testing of these gases. Initial dynamic testing showed inter-chamber mixing completed from minutes to 1.5 hours. The photooxidation of butyl iodine showed the presence of signals from reaction products, and intermediaries for up to 50 hours. Current detection limits of the chamber and analytical collection and testing approach were shown to be in the single-digit parts per billion levels. In conclusion, the comparisons between the measured oxidation trends and literature show the utility of performing laboratory experiments to validate the results of modeling for larger-scale scenarios.

54 ENVIRONMENTAL SCIENCES↗