R-Matrix Theory from the Green-Bloch Perspective
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73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
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Results for “PERSPECTIVE”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Research at the Jupiter Laser Facility - A discussion on Photonics from an Open-Access Government Perspective
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Physics - Plasma physics↗
A standards perspective on genomic data reusability and reproducibility
Genomic and metagenomic sequence data provides an unprecedented ability to re-examine findings, offering a transformative potential for advancing research, developing computational tools, enhancing clinical applications, and fostering scientific collaboration. However, effective and ethical reuse of genomics data is hampered by numerous technical and social challenges. The International Microbiome and Multi’Omics Standards Alliance (IMMSA, https://www.microbialstandards.org/) and the Genomic Standards Consortium (GSC, https://gensc.org) hosted a 5-part seminar series “A Year of Data Reuse” in 2024 to explore challenges and opportunities of data reuse and reproducibility across disparate domains of the genomic sciences. Addressing these challenges will require a multifaceted approach, including common metadata reporting, clear communication, standardized protocols, improved data management infrastructure, ethical guidelines, and collaborative policies that prioritize transparency and accessibility. We offer strategies to enable responsible and technically feasible data reuse, recognition of data reproducibility challenges, and emphasizing the importance of cross-disciplinary efforts in the pursuit of open science and data-driven innovation.
59 BASIC BIOLOGICAL SCIENCES↗
Quantification of heterogeneity in human CD8 + T cell responses to vaccine antigens: an HLA-guided perspective
Vaccines have historically played a pivotal role in controlling epidemics. Effective vaccines for viruses causing significant human disease, e.g., Ebola, Lassa fever, or Crimean Congo hemorrhagic fever virus, would be invaluable to public health strategies and counter-measure development missions. Here, we propose coverage metrics to quantify vaccine-induced CD8 + T cell-mediated immune protection, as well as metrics to characterize immuno-dominant epitopes, in light of human genetic heterogeneity and viral evolution. Proof-of-principle of our approach and methods are demonstrated for Ebola virus, SARS-CoV-2, and Burkholderia pseudomallei (vaccine) proteins.
60 APPLIED LIFE SCIENCES↗
Discovering novel therapeutic V H Hs for emerging viruses: perspectives from VEEV selection strategies
Introduction: Evolution or emergence of a new viral variant is a significant public health concern. Alphaviruses, such as Venezuelan equine encephalitis virus (VEEV), are mosquito-borne viruses which are becoming more prevalent due to expansion of vector habitats. Despite this, there are currently no antiviral therapies or FDA-approved vaccines available to treat or prevent VEEV infection. The increased prevalence of such viruses provides opportunities for novel variants to evolve. Key therapeutic molecules that could be developed against viral pathogens are recombinant antibodies or antibody fragments, such as the variable heavy domain of heavy chain antibodies (V H Hs). Methods: In vitro selections offer a promising pathway for identification of therapeutic antibodies, here we explored isolation of V H Hs using phage and yeast display methodology with three antigen formats 1) recombinant E2, 2) linear peptides of E2, selected based on molecular dynamics analysis, and 3) UV inactivated virus. Results: Here we report four novel “human” V H Hs which bind to the VEEV E2 protein selected using different strategies that include both computational and biochemical design of suitable antigens and whole virus selections. These V H Hs have distinct complementarity-determining regions (CDRs). Multiple VHHs bind to the VEEV viral particles in ELISAs, and we report the peptide epitope recognized by these V H Hs. Discussion: Though non-neutralizing, these V H Hs bind to and sequester VEEV viral particles preventing infection, demonstrating the potential of these V H Hs to perform viral “sponging” which represents a novel therapeutic approach. The selection strategies we report may have applications to further antibody developments against other viruses.
59 BASIC BIOLOGICAL SCIENCES↗
Multidimensional perspectives of geo-epidemiology: from interdisciplinary learning and research to cost–benefit oriented decision-making
Research typically promotes two types of outcomes (inventions and discoveries), which induce a virtuous cycle: something suspected or desired (not previously demonstrated) may become known or feasible once a new tool or procedure is invented and, later, the use of this invention may discover new knowledge. Research also promotes the opposite sequence—from new knowledge to new inventions. This bidirectional process is observed in geo-referenced epidemiology—a field that relates to but may also differ from spatial epidemiology. Geo-epidemiology encompasses several theories and technologies that promote inter/transdisciplinary knowledge integration, education, and research in population health. Based on visual examples derived from geo-referenced studies on epidemics and epizootics, this report demonstrates that this field may extract more (geographically related) information than simple spatial analyses, which then supports more effective and/or less costly interventions. Actual (not simulated) bio-geo-temporal interactions (never captured before the emergence of technologies that analyze geo-referenced data, such as geographical information systems) can now address research questions that relate to several fields, such as Network Theory. Thus, a new opportunity arises before us, which exceeds research: it also demands knowledge integration across disciplines as well as novel educational programs which, to be biomedically and socially justified, should demonstrate cost-effectiveness. Grounded on many bio-temporal-georeferenced examples, this report reviews the literature that supports this hypothesis: novel educational programs that focus on geo-referenced epidemic data may help generate cost-effective policies that prevent or control disease dissemination.
59 BASIC BIOLOGICAL SCIENCES↗
Enhancing segmentation fairness through curriculum learning and progressive loss: a centralized and federated perspective on radiograph analysis
Bias in medical image segmentation can lead to unequal performance across demographic subgroups, raising concerns about fairness and reliability in clinical AI systems. While deep learning models have achieved high segmentation accuracy, ensuring equitable performance across race and gender remains a significant challenge, particularly in privacy-sensitive healthcare environments. This study investigates fairness-aware medical image segmentation for hip and knee radiographs using deep learning models evaluated in both centralized and Federated Learning (FL) settings. We introduce Curriculum Learning (CL) strategies and Progressive Loss (PL) functions to regulate sample difficulty during training. In addition, we propose two novel fairness-oriented federated learning algorithms, Federated Intersection over Union (FedIoU) and Federated Intersection over Union with Outlier Analysis (FedIoUoutlier). Experiments are conducted using multiple segmentation backbones and simulated multi-site data partitions derived from the Osteoarthritis Initiative dataset. Model performance is evaluated using Intersection over Union (IoU), IoU standard deviation, Skewed Error Ratio (SER), and Min-Max Disparity across race and gender subgroups. Statistical significance was verified using paired t-tests to compare per-sample IoU performance against baseline configurations. Across both hip and knee segmentation tasks, curriculum learning and progressive loss strategies consistently improved segmentation accuracy and reduced demographic performance disparities in centralized training. In federated settings, fairness-aware aggregation further enhanced performance. Notably, FedIoUoutlier combined with balanced curriculum learning and tiered progressive loss achieved the highest mean IoU while yielding the lowest SER and Min-Max Disparity, indicating improved fairness without sacrificing accuracy. In several configurations, federated models matched or exceeded the performance of optimized centralized models, with statistically significant improvements in per-sample IoU over baseline configurations. The results demonstrate that structured training strategies and fairness-aware federated aggregation can jointly improve accuracy, stability, and demographic fairness in medical image segmentation. By integrating curriculum learning, progressive loss, and novel FL algorithms, this work provides a practical pathway toward equitable and privacy-preserving AI systems for medical imaging.
97 MATHEMATICS AND COMPUTING↗
Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective
Stoichiometric genome-scale metabolic models (generally abbreviated GSM, GSMM, or GEM) have had many applications in exploring phenotypes and guiding metabolic engineering interventions. Nevertheless, these models and predictions thereof can become limited as they do not directly account for protein cost, enzyme kinetics, and cell surface or volume proteome limitations. Lack of such mechanistic detail could lead to overly optimistic predictions and engineered strains. Initial efforts to correct these deficiencies were by the application of precursor tools for GSMs, such as flux balance analysis with molecular crowding. In the past decade, several frameworks have been introduced to incorporate proteome-related limitations using a genome-scale stoichiometric model as the reconstruction basis, which herein are called resource allocation models (RAMs). This review provides a broad overview of representative or commonly used existing RAM frameworks. This review discusses increasingly complex models, beginning with stoichiometric models to precursor to RAM frameworks to existing RAM frameworks. RAM frameworks are broadly divided into two categories: coarse-grained and fine-grained, with different strengths and challenges. Discussion includes pinpointing their utility, data needs, highlighting framework strengths and limitations, and appropriateness to various research endeavors, largely through contrasting their mathematical frameworks. Finally, promising future applications of RAMs are discussed.
59 BASIC BIOLOGICAL SCIENCES↗
Driving Electron Transfer in Photosystem I Using Far-Red Light: Overall Perspectives
Photosystem I (PSI) is a photosynthetic protein–pigment complex that, upon photoexcitation, transfers electrons to ferredoxin, facilitating the production of NADPH. Isolated PSI reaction centers (RCs) have also been used in hybrid systems to reduce protons and produce ‘biohydrogen’. This review article examines how various cyanobacteria with similar photosynthetic machinery utilize different wavelengths of light to execute photosynthetic electron transport through PSI. Key factors, such as, the structure of the electron transfer cofactors, the protein environment surrounding the primary donor pigments and hydrogen-bonding interactions with the surrounding protein matrix are analyzed to understand their roles in maintaining efficient electron transfer when it is driven using photons of different energies. We compare PSI complexes with known atomic structures from four species of cyanobacteria, Thermosynechococcus elongatus, Acaryochloris marina, Halomicronema hongdechloris, and Fischerella thermalis. T. elongatus is typical of most oxygenic photosynthetic organisms in that it requires visible light and uses only chlorophyll a (Chl a ) in PSI. In contrast, H. hongdechloris and F. thermalis are photoacclimating species capable of producing Chl f and Chl d that use red light when little visible light is available. A. marina , on the other hand, is adapted to red light conditions and consistently utilizes Chl d as its primary photosynthetic pigment, maintaining a stable pigment composition. Here, we explore the structural and functional differences between the PSI RCs of these organisms and the impact of these differences on electron transport. The structural differences in the cofactors influence both the absorption wavelengths of the cofactors and the energy levels of the intermediate states of electron transfer. An analysis of the surrounding protein shows how it has been adapted and underscores the interplay between the pigment structure, protein environment, and hydrogen bonding networks in tuning the efficiency and adaptability of photosynthetic mechanisms across different species of cyanobacteria.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Woody Plant Transformation: Current Status, Challenges, and Future Perspectives
Woody plants, comprising forest and fruit tree species, provide essential ecological and economic benefits to society. Their genetic improvement is challenging due to long generation intervals and high heterozygosity. Genetic transformation, which combines targeted DNA delivery with plant regeneration from transformed cells, offers a powerful alternative to accelerating their domestication and improvement. Agrobacterium tumefaciens, Rhizobium rhizogenes, and particle bombardment have been widely used for DNA delivery into a wide variety of explants, including leaves, stems, hypocotyls, roots, and embryos, with regeneration occurring via direct organogenesis, callus-mediated organogenesis, somatic embryogenesis, or hairy root formation. Despite successes, conventional approaches are hampered by low efficiency, genotype dependency, and a reliance on challenging tissue culture. This review provides a critical analysis of the current landscape in woody plant transformation, moving beyond a simple summary of techniques to evaluate the co-evolution of established platforms with disruptive technologies. Key advances among these include the use of developmental regulators to engineer regeneration, the rise in in planta systems to bypass tissue culture, and the imperative for DNA-free genome editing to meet regulatory and public expectations. By examining species-specific breakthroughs in key genera, including Populus, Malus, Citrus, and Pinus, this review highlights a paradigm shift from empirical optimization towards rational, predictable engineering of woody plants for a sustainable future.
Agrobacterium tumefaciens↗
Perspectives and Challenges in Bolide Infrasound Processing and Interpretation: A Focused Review with Case Studies
Infrasound sensing plays a critical role in the detection and analysis of bolides, offering passive, cost-effective global monitoring capabilities. Key objectives include determining the timing, location, and yield of these events. Achieving these goals requires a robust approach to detect, analyze, and interpret rapidly moving elevated sources such as bolides (also re-entry). In light of advancements in infrasonic methodologies, there is a need for a comprehensive overview of the characteristics that distinguish bolides from other infrasound sources and methodologies for bolide infrasound analysis. This paper provides a focused review of key considerations and presents a unified framework to enhance infrasound processing approaches specifically tailored for bolides. Three representative case studies are presented to demonstrate the practical application of infrasound processing methodologies and deriving source parameters while exploring challenges associated with bolide-generated infrasound. These case studies underscore the effectiveness of infrasound in determining source parameters and highlight interpretative challenges, such as variations in signal period measurements across different studies. Future research should place emphasis on improving geolocation and yield accuracy. This can be achieved through rigorous and systematic analyses of large, statistically significant samples of such events, aiming to resolve interpretative inconsistencies and explore the causes for variability in signal periods and back azimuths. The topic described here is also relevant to space exploration involving planetary bodies with atmospheres, such as Venus, Mars, and Titan.
79 ASTRONOMY AND ASTROPHYSICS↗
Towards Advancing Research with Workflows: A perspective from the Workflows Community Summit -- Amsterdam, 2025
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Bonati, Irene [SURF Cooperation, Innovation Team, ↗
2025 EIC-France Workshop: Physics Highlights and Perspectives
This document presents a synthesis of the theory contributions and discussions from the 2nd EIC-France Workshop, held at IJCLab (Orsay) on 1-3 December 2025. The workshop brought together members of the French hadron-physics community to review recent theoretical developments relevant to the future Electron-Ion Collider (EIC) and to coordinate national efforts in preparation for its early physics program. The report first summarizes the collider's initial running conditions and luminosity performance, as outlined in the EIC Early Science Matrix. It then provides concise overviews of the theoretical presentations on inclusive, semi-inclusive, exclusive, heavy-flavor, and small-x physics. Based on these discussions, two measurements emerged as especially well suited for early EIC operation and strongly aligned with areas of established French expertise: inclusive diffraction and inclusive quarkonium production. These channels offer clean signatures, robust theoretical interpretability, and direct sensitivity to fundamental QCD phenomena such as gluon saturation, heavy-quark dynamics, and the small-x structure of hadrons and nuclei. In addition, the workshop identified longer-term physics opportunities that will benefit from the full capabilities of the EIC after its ramp-up phase. These include accessing the three-dimensional structure of the pion through the Sullivan process and a broader program of exclusive three-body final states, both of which represent high-impact avenues for exploring hadronic structure and non-perturbative QCD. Together, the elements summarized in this report provide a coherent overview of the strategic priorities and scientific ambitions shaping the French community's contribution to the EIC physics program.
FOS: Physical sciences↗
Aerosol hygroscopicity over the southeast Atlantic Ocean during the biomass burning season – Part 1: From the perspective of scattering enhancement
Aerosol hygroscopicity plays a vital role in aerosol radiative forcing. One key parameter describing hygroscopicity is the scattering enhancement factor, f(RH), defined as the ratio of the scattering coefficient at humidified relative humidity (RH) to its dry value. Here, we utilize the f(80 %) from ORACLES (ObseRvations of Aerosols above CLouds and their intEractionS) 2016 and 2018 airborne measurements to investigate the hygroscopicity of aerosols, its vertical distribution, its relationship with chemical composition, and its sensitivity to organic aerosol (OA) hygroscopicity over the southeast Atlantic (SEA) Ocean during the biomass burning (BB) season. We found that aerosol hygroscopicity remains steady above 2 km, with a mean f(80 %) of 1.40 ± 0.17. Below 2 km, aerosol hygroscopicity increases with decreasing altitude, with a mean f(80 %) of 1.51 ± 0.22, consistent with higher values of BB aerosol hygroscopicity found in the literature. The hygroscopicity parameter of OA (κ OA ) is retrieved from the Mie model with a mean value of 0.11 ± 0.08, which is in the middle to upper range compared to the literature. Higher OA hygroscopicity is related to aerosols that are more aged, oxidized, and present at lower altitudes. The enhanced biomass burning aerosol (BBA) hygroscopicity at lower altitudes is mainly due to a lower OA fraction, increased sulfate fraction, and greater κ OA at lower altitudes. We propose a parameterization that quantifies f(RH) with chemical composition and κOA based on Mie simulation of internally mixed OA–(NH 4 ) 2 SO 4 –BC mixtures. The good agreement between the predictions and the ORACLES measurements implies that the aerosols in the SEA during the BB season can be largely represented by the OA–(NH 4 ) 2 SO 4 –BC internal mixture with respect to the f(RH) prediction. The sensitivity of f(RH) to κ OA indicates that applying a constant κ OA is only suitable when the OA fraction is low and κ OA shows limited variation. However, in situations deviating these two criteria, κ OA can notably impact scattering coefficients and aerosol radiative effect; therefore, accounting for κ OA variability is recommended.
54 ENVIRONMENTAL SCIENCES↗
Ideas and perspectives: Using meta-omics to unravel biogeochemical changes from cell to planetary scales
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Biological and medical sciences↗
Evaluating an Earth system model from a water manager perspective
Abstract. The large spatial scale of global Earth system models (ESMs) is often cited as an obstacle to using the output by water resource managers in localized decisions. Recent advances in computing have improved the fidelity of hydrological responses in ESMs through increased connectivity between model components. However, the models are seldom evaluated for their ability to reproduce metrics that are important for and resonate with practitioners or that allow practitioners to situate higher-resolution model outputs within a cascade of uncertainty stemming from different models and scenarios. We draw on the combined experience of the author team and water manager workshop participants to identify salient water management metrics and evaluate whether they are credibly reproduced over the conterminous USA by the Community Earth System Model v2 (CESM2) Large Ensemble. We find that, while the exact values may not match the observations, aspects such as interannual variability can be reproduced by CESM2 for the mean wet day precipitation and length of dry spells. CESM2 also captures the proportion of total annual precipitation that derives from the heaviest rain days in watersheds that are not snow-dominated. Aggregating the 7 d mean daily runoff to two-digit Hydrological Unit Code (HUC2) watersheds also shows that rain-dominated regions capture the timing and interannual variability of annual maximum and minimum flows. We conclude that there is potential for far greater use of large-ensemble ESMs, such as CESM2, in long-range water management decisions to supplement high-resolution regional projections.
Tye, Mari R. (ORCID:0000000324911020)↗
Perspective Chapter: Safe Disposal and Storage of Nuclear Waste
The use of nuclear energy inevitably generates nuclear waste as the byproduct of fission reactions. Depending on the initial composition of the fuel that goes into the reactor and the subsequent burn-up level, the chemistry of the resulting nuclear waste can vary substantially. This waste typically exhibits a broad spectrum of radioactivity and half-lives, making effective management one of the most critical challenges for global nuclear energy. This chapter provides a comprehensive overview of the origin and classification of nuclear waste and various strategies for its safe immobilization and disposal. The short- and long-term storage of waste with varying radioactivity is addressed. The significant technical and political complexities involving primarily long-term disposal are also discussed. To ensure the safe and permanent disposal of hazardous waste with extremely long half-lives, future efforts should focus on both technical innovation and public engagement.
36 MATERIALS SCIENCE↗
Embracing Uncertainty and Perseverance. A Brief Perspective on Conducting On-Site NDT Research
Dr. Judi E. See, a Systems Analyst and Human Factors Engineer at Sandia National Laboratories, reflects on her experience conducting NDT research in a male-dominated environment. She emphasizes the importance of persistence, flexibility, and persuasive skills in overcoming challenges, ranging from gaining access to test sites and equipment to building trust with inspectors. She shares her personal experience of navigating professional situations where gender disparities were evident, highlighting the need for women to adapt and overcome obstacles in traditionally male-dominated settings. See's journey demonstrates that perseverance and ingenuity can lead to significant contributions, process improvements, and recognition in the NDT field.
42 ENGINEERING↗