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We report the draft genomes of two morphologically distinct variants of Bacillus subtilis ATCC 6051 [NCBI3610]. The two isolates exhibit differences in not only morphology but also their genetics, despite identical 16S rRNA sequences. Investigating the genetic differences of colony morphology variation in this model organism can provide valuable insights.
A draft metagenome-assembled genome (MAG) of a Salinarimonas species was obtained from a sequenced metagenome of Chlorella sp. SLA-04, an alkaliphilic green alga.
Increasing the genomic resources of emerging aquaculture crop targets can expedite breeding processes as seen in molecular breeding advances in agriculture. High quality annotated reference genomes are essential to implement this relatively new molecular breeding scheme and benefit research areas such as population genetics, gene discovery, and gene mechanics by providing a tool for standard comparison. The brown macroalga Saccharina latissima (sugar kelp) is an ecologically and economically important kelp that is found in both the northern Pacific and Atlantic Oceans. Cultivation of Saccharina latissima for human consumption has increased significantly this century in both North America and Europe, and its single blade morphology allows for dense seeding practices used in the cultivation of its Asian sister species, Saccharina japonica. While Saccharina latissima has potential as a human food crop, insufficient information from genetic resources has limited molecular breeding in sugar kelp aquaculture. We present scaffolded and annotated Saccharina latissima nuclear and organelle genomes from a female gametophyte collected from Black Ledge, Groton, Connecticut. This Saccharina latissima genome compares well with other published kelp genomes and contains 218 scaffolds with a scaffold N50 of 1.35 Mb, a GC content of 49.84%, and 25,012 predicted genes. We also validated this genome by comparing the synteny and completeness of this Saccharina latissima genome to other kelp genomes. Our team has successfully performed initial genomic selection trials with sugar kelp using a draft version of this genome. This Saccharina latissima genome expands the genetic toolkit for the economically and ecologically important sugar kelp and will be a fundamental resource for future foundational science, breeding, and conservation efforts.
Large language models (LLMs) are evolving from chatbots with limited tool-using capabilities to agentic AI systems that can perform deep research, assist in proposing hypotheses, help design experiments, automate data analysis, and draft scientific reports. However, there are currently two bottlenecks limiting LLMs' real-world impact on the broader scientific research community beyond academic demonstrations: lack of interoperability (repetitive manual tool-integration is required across scenarios) and the need for scalable coordination (unstructured communication and memory become brittle as the number of agents grows). In this Perspective, we argue that the next phase of agentic scientific discovery requires the development of an ecosystem of protocol-native agents and tools organized through hierarchies inspired by human society, beyond the current paradigm of a single monolithic “AI scientist”. We use Model Context Protocol (MCP) as a concrete example of an emerging interoperability layer for scientific tool and context exchange, and we propose three complementary pathways to increase the scaling capabilities of an MCP-native scientific ecosystem by addressing the composability issues: (1) MCP servers for high-value scientific tools maintained by domain experts, (2) automated transformation of existing code repositories into MCP services, and (3) autonomous invention and evolution of new agents and workflows. Finally, we provide a practical roadmap for scaling AI-driven scientific discovery by expanding tool supply and coordination in MCP-native scientific ecosystems.
Aspergillus terreus has attracted interest due to its application in industrial biotechnology, particularly for the production of itaconic acid and bioactive secondary metabolites. As related species also seem to possess a prosperous secondary metabolism, they are of high interest for genome mining and exploitation. Here, we present draft genome sequences for six species from Aspergillus section Terrei and one species from Aspergillus section Nidulantes. Whole-genome phylogeny confirmed that section Terrei is monophyletic. Genome analyses identified between 70 and 108 key secondary metabolism genes in each of the genomes of section Terrei, the highest rate found in the genus Aspergillus so far. The respective enzymes fall into 167 distinct families with most of them corresponding to potentially unique compounds or compound families. Moreover, 53% of the families were only found in a single species, which supports the suitability of species from section Terrei for further genome mining. Intriguingly, this analysis, combined with heterologous gene expression and metabolite identification, suggested that species from section Terrei use a strategy for UV protection different to other species from the genus Aspergillus. Section Terrei contains a complete plant polysaccharide degrading potential and an even higher cellulolytic potential than other Aspergilli, possibly facilitating additional applications for these species in biotechnology.
In this document drafted by the Neutrino Scattering Theory Experiment Collaboration (NuSTEC), we provide input on the synergies between theoretical and experimental efforts that can provide critical input to the prediction accuracy needed for the forthcoming high-precision neutrino measurements. These efforts involve a wide range of energies and interaction processes, as well as target nuclei and interaction probes. The challenges discussed will be overcome only through the active support of integrated collaboration across strong and electroweak physics from both the nuclear and high energy physics communities.
This report outlines the history of the CLFV puzzle, gives an overview of the Mu2e Experiment, and details the results of the DOE (Department of Energy)-funded SULI (Science Undergraduate Laboratory Internship) research completed over the summer 2024 on site at Fermilab. The project focused on the otsdaq software responsible for data acquisition. The project included drafting updated documentation for new users, including new procedures relevant for the Alma- Linux 9 operating system update, and the UPS package managing system replacement with Spack (scientific software package manager). A new art module (ReadTriggerCounts) to track trigger rates was created, with compatibility to be displayed via a Grafana server. The author also assisted in calorimeter cable installation in the detector hall.
The Generation-IV Forum (GIF) Very-High-Temperature Reactor-Computational Methods Validation and Benchmark (VHTR-CMVB) initiative, involving organizations from Korea Atomic Energy Research Institute (KAERI) (South Korea), Institute of Nuclear and New Energy Technology of Tsinghua University (INET) (China), U.S. Department of Energy (DOE) (U.S.), Joint Research Centre (JRC) (Europe), and Japan Atomic Energy Agency (JAEA) (Japan), is dedicated to the verification and validation of tools for High-Temperature Gas-Cooled Reactors (HTGRs) analysis, using data shared by Computational Methods Validation and Benchmark (CMVB) signatories. For FY24, the US DOE CMVB has committed to several critical activities. Under WP1, led by the US, the integration of the High Temperature Gas Cooled Reactor - Pebble-Bed Module (HTR-PM) Phenomena Identification and Ranking Table (PIRT) into the comparative PIRT is progressing, with a new draft of the comparison tables issued earlier this year and currently being utilized by INET for their contribution. Neutronic validation efforts under WP3 include the preparation of the burnup analysis benchmark, preliminary calculations, and the development of reference models and results. In WP2, a validation exercise for hot gas mixing in the lower plenum of HTR-PM is in progress, using experimental data from INET (China) to validate modeling approaches. A model of the experimental facility has been developed using StarCCM+, with initial calculations slated for presentation at the GIF CMVB meeting this fall. Another WP2 activity focuses on validating numerical models for air-cooled Reactor Cavity Cooling System (RCCS) with experimental data from the Wisconsin Madison RCCS facility. A high-fidelity model, developed using NEK-RS, is currently being validated with available data from a low power forced convection test. These efforts are aimed at enhancing and confirming the accuracy of HTGR analysis tools, ensuring their alignment with experimental data and regulatory requirements.
The aim of this document is to lay out a first draft of the specifications for the MEDUSAL database (Machine-readable Experimental Data User App & Library) that is being described by OECD/NEA/WPEC SG-50. The EXFOR database (Otuka et al., 2014) has a format that is based on code-value pairs, and a significant portion of the information in the EXFOR entry is contained in free text sections. Several high-level requirements for the MEDUSAL database, as laid out in the Use Cases and Requirements Working Paper (citation), relate to the definition of the specifications
Final draft of my PhD dissertation to be submitted to the Texas Tech University graduate school.
Draft of paper for the Journal of Dynamic Behavior of Materials
Is there a quantum utility in establishing the masses of hadrons? Here we show that the best response is that of Farrés, Capó, and Davis: perhaps, perhaps, perhaps. This is interesting given the general case that particle physics demands quantum computers. For stable hadrons, classical LQCD has achieved sub-percent precision with no sign problem, and quantum computers offer no advantage. For resonances, the Maiani-Testa theorem is an obstruction that quantum simulation is immune to. For nuclei, Wick contractions and signal-to-noise are genuine classical barriers. Underlying these cases is a unified picture connecting the sign problem to Wigner negativity and T gate cost. This manuscript was drafted from extensive interaction with \textsc{Claude}.
The Molten Chloride Reactor Experiment (MCRE) will be the first reactor featuring a fast-spectrum molten chloride circulating nuclear fuel system in the world. Planning for equipment removal and disposal (ERD) of MCRE has identified several technology gaps due to the unique environment of this nuclear experiment. Some of the gaps arise from the application of existing disassembly and/or sizing methods to novel material forms or in novel configurations. Others arise from unknown material behavior. This paper summarizes proposed test plans for ERD validation experiments to address these complicated or unknown equipment removal procedures. At the Waste Management Symposia in 2024, the Idaho National Laboratory (INL) MCRE ERD team presented the challenges associated with hosting multiple nuclear experiments in series with only brief transition periods between systems. Such difficulties include higher dose rates, the presence of radioisotopes infrequently encountered in reactor decommissioning and radioactive waste management, lack of intrinsic remote-operations infrastructure in the test bed, space constraints in the test bed, and contamination minimization requirements. To address these challenges, remote or semi-remote technologies are planned to be implemented in a non-hot cell environment with limited space availability. The team also discussed how a systems engineering approach is being used for conceptual development and design of equipment removal systems to address these challenges. For example, to reduce constraints for the removal of more difficult components, non-activated, noncontaminated elements are planned to be taken out first where possible. Still, there are complexities associated with the remaining components. In this work, the operational framework for MCRE ERD was reviewed for technical gaps and open questions, and test plans were drafted to address these areas. The tests plans were written for the following categories: vision systems, pipe cutting, drill/grout/filler, flush salt, and miscellaneous, with the miscellaneous group consisting of tests like techniques for removing bearings and reflector bricks. The test plans explore material, infrastructure, and staffing requirements needed for test execution. The test plans additionally focus on the evaluation of success. Determining the outcome of a test is imperative - as these explorative actions have the potential to rearrange or re-scope planned ERD activities. Success criteria identified thus far include required tool output, required area(s), debris production and mitigation, and repeatability. Test plans are an essential aspect of the systems engineering approach to MCRE ERD. They are used as the beginning steps in defining use cases for the ERD system. Performance of the validation tests is expected to begin in the summer of 2025 and will take approximately 9 to 12 months to complete. Execution of these plans will be expedited by specifying test needs ahead of time, facilitating efficient interactions with any subcontractors tasked with running the requested tests. Evaluating the outcomes of these tests will inform MCRE ERD procedures and timing and will also identify additional technical constraints for the MCRE ERD System. This upfront process optimization effort will help the project save time and resources at the end of the experiment.
Powerpoint presentation. Background information provided on power plant uprates. Discussion of the current and proposed approaches to power plant uprates. Explanation of what data is used to draft a LAR. Methods such as retrieval augmented generation (RAG) and fine-tuning are discussed. Use case analysis is performed. Different failure types are examined. Conclusions are drawn from the analysis. Future work is proposed.
New abstract from the final version being submitted now: This paper discusses the evolution and enhanced usability of the ŠKODA VPVR/M cask for the transport of irradiated fuel assemblies, particularly within the context of the demand for the delivery of newly appearing irradiated HEU fuel types for which the cask did not yet have a license to transport. Over time, the cask’s internal basket construction has demonstrated notable adaptability to accommodate various exotic HEU fuel types from research reactors of differing origins. The paper outlines sever-al custom internal baskets developed for specific fuel types, including those from Belarus and Serbia, as well as from Georgia, Uzbekistan, and MNSR cores, as well as a recently designed basket for MTR and TRIGA assemblies. The findings high-light the high flexibility and adaptability of the cask, supported by successful rede-signs and licensing efforts, underscoring its value for the safe and secure transport of nuclear material. Old abstract from the draft version that was already approved: The Russian Research Reactor Fuel Return (RRRFR) program, since its inception, has continuously used the ŠKODA VPVR/M Cask fleet designed for the repatriation of irradiated highly enriched uranium (HEU) fuel. As the program progressed (from shut-down and a quasi-abandoned reactor, and/or as it began to include fuels of Chinese and US origin), new challenges emerged for the transport Cask. These were fuel types that had not yet been licensed for the Cask. Although these requirements did not arise during the design of the basic ŠKODA VPVR/M Cask, as revealed by the retrospective analyses, the Internal Basket of the ŠKODA VPVR/M Cask gives a high degree of flexibility to accommodate additional fuel types. This paper provides a brief overview of the ŠKODA VPVR/M Cask, which holds a B(U) type license, and introduces the different types of Internal Baskets that have already been licensed to transport so-called exotic irradiated HEU fuel types, in addition to the original license. The paper presents a new Internal Basket design for accommodating MTR-type and TRIGA-type irradiated HEU fuel assemblies. This includes a detailed presentation of the design basis and the new MTR-TRIGA Internal Basket, as well as the licensing matters of the package under the name ŠKODA MTR-TRIGA Cask, and the conformity test (dry- and wet-run) operations made to verify compliance with the new Internal Basket. Then, as a summary, the usage record for the Cask fleet is presented, and finally, the paper concludes with the consolidated experiences gained during the utilization of the ŠKODA VPVR/M Cask fleet, emphasizing the high degree of Cask flexibility ensured by the Internal Basket’s construction.
The physiochemical interactions between organic contaminants, minerals, and polymer additives in grout/cementitious materials are being identified. This research supports a proposed Resource Conservation and Recovery Act (RCRA) treatment variance relevant to the Land Disposal Restriction (LDR) organics present in Hanford tank waste. It provides the technical basis to address the aspects documented by the Environmental Protection Agency in a draft memo necessary to establish that organics can be immobilized/stabilized in a cementitious matrix. The organic species may interact with cementitious minerals, including slag, fly ash, cement, and other components/dopants like activated carbon. A list of 132 reasonably expected LDR organics associated with Hanford tank waste (RPP-RPT-63493, Rev 1a) was screened by functional groups, octanol-water partitioning coefficients, and detection frequency in Hanford tank waste samples. A subset of 15 compounds spanning the identified properties was tested using sorption and leachate tests. These compounds were subjected to traditional batch sorption tests and leaching tests on/from Cast Stone cementitious material with and without activated carbon (a potential organic adsorption additive). The interactions between organic compounds were observed in traditional batch sorption and modified TCLP leachate tests for surrogate Cast Stone material with and without activated carbon addition. Specifically, phthalic acid (negatively charged) and 4-chloroaniline (polar) sorbed strongly to unmodified Cast Stone, while a group of three phenolic compounds (2,4,6-Trichlorophenol, Pentachlorophenol, o-Cresol) sorbed to and were retained by Cast Stone with a 1% activated carbon amendment. Mixtures of these compounds demonstrated visible retention of the organics within the matrix with a quantifiable affinity of the organics to the cement. This novel testing supports the notion that organics within Hanford tank waste would be retained onto the cement phase with the addition of simple materials easily added to the formulation as part of the treatment process. To further provide additional support to this claim, models employing Flory-Huggins theory in conjunction with macromolecular and organic molecule solubility parameters and species activity coefficients are being utilized to better understand these interactions. Within this context, Van Krevelen (VK) and Hansen organic and polymer solubility parameters were used to inform the Flory-Huggins interaction parameter, allowing for a quantifiable method of evaluating polymer-solvent compatibility and, by extension, interactions with proposed binding additives (e.g., activated carbon). These models and measurement should test the hypothesis for our systems understanding and applicability of Flory-Huggins theory, and whether the prediction of organics in the polymer phase versus the aqueous phase can be confidently made using this strategy. The estimation of the organic molecular activity coefficient in these high salt-saturated aqueous systems is another factor that will be assessed. This project aims to predict and understand complicated organic interactions in these heterogenous systems, guiding optimal treatment and stabilization methodologies.
Neutrinos and other light relics leave characteristic imprints in the cosmic microwave background anisotropies, making their observation a sensitive probe of the particle content and thermal history of the early universe. The energy density in these relativistic species is parameterized by their effective number $N_\mathrm{eff}$. Measuring this parameter at the percent level, which is a long-standing science goal of CMB-S4 and other experiments, would test a wide range of well-motivated physics within and beyond the Standard Model of particle physics. In this paper, we present Fisher-matrix forecasts of the projected sensitivity to $N_\mathrm{eff}$ of several CMB-S4 survey configurations considered during its extensive design phase. The conceptual design reaches $σ(N_\mathrm{eff}) < 0.03$ over its seven-year observing period, while the revised configuration achieves the same precision over a longer timescale. We complement these results with a cosmic-variance-limited survey over the same multipole range to quantify the room for improvement accessible with additional instrumental, observational, and theoretical efforts. Finally, we discuss the broad implications of precise $N_\mathrm{eff}$ measurements for the radiation sector, big bang nucleosynthesis, light thermal relics, and other early-universe physics. The forecasts presented in this work are performed with the publicly released DRAFT (Dark Radiation Anisotropy Flowdown Team) tool. It provides an end-to-end pipeline from simulated foreground maps and component separation to delensing and projected sensitivities for any cosmological parameter, and it can be directly applied to other cosmic microwave background survey designs.
The OSCC Coupling Shaft Handling Fixture, known as the "Puppy Dog Tool," was originally designed by hand in 1976. The initial design was difficult to read and replicate, lacking 3D modeling for simulations and testing. To modernize the tool, the original drawings were reviewed and recreated in Autodesk Inventor with increased spacing for clarity. Key improvements included adding a hook, modifying the top plate and main body connection, and introducing a guiding wall for the clamp. These changes enhanced durability and usability, preventing bending and facilitating easier assembly. The updated design preserved the tool's functionality while making it more robust and user-friendly for high-precision operations.