Towards engineering phages for modulation of Bacteroides thetaiotaomicron and the human gut.
Draft version of conference poster
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Draft version of conference poster
Presentation for Reliability and Maintainability Symposium in January 2026. This is a ROUGH DRAFT that will be blind peer reviewed.
The intended purpose of this project was to bring alternative heat and ventilation options to rural communities off the road system in Northwestern Alaska. Most of the residents of these communities are reliant upon kerosene or other fossil fuels to provide heat to their homes. Our intention was to offer an alternative to using those sources by providing heat pumps to 45 homes in the communities of Elim and Koyuk. When projecting energy use for these units based on the fuel prices at the time, it was discovered that energy costs for heat pumps would equal or slightly exceed the costs of existing kerosene units. Secondly, as part of our E&l grant we installed 45 energy recovery ventilators (ERV’s) in those same homes. This was important given our experience over the years with moisture and comfort issues in most homes within this region. Exhaust-only systems are rarely used due to the high heating costs. Additionally, exhaust-only systems have a potential risk of back drafting due to tight building construction. Balanced systems like this eliminate that risk while improving indoor air quality. Another benefit to these types of systems is the fact that they help transfer heat from a single heat source equally throughout the building. Our overall goal was to offer new technology options to improve these structures and the families that reside in them where, given their location and extreme seasonal temperature swings, they have historically never been offered.
AutoSAC is an automated python program to conduct sample activation calculation immediately after neutron scattering experiment on VULCAN. AutoSAC takes account of sample dimensions, compositions, forms, sample environments, neutron beam configurations, neutron scattering history, and proton charged resolved beam power etc., and uses a simplified method to rapidly estimate the radioactivity at end of beam or after. It generates a draft report per sample and repository of radioactivity per measurement and provides feedback of current radioactivity and decay time back to a neutron proposal Slack channel to inform users immediately on sample handling. It also utilizes either the sample note field in EPICS or sample composition or thickness correction and takes slack prompt or command to conduct post-beam SAC by demand. The program can be shared to be used in other beamlines at spallation neutron source with modified instrument configurations including instrument specific characteristic beam fluxes.
[This is a 90% discussion draft.] This is the third Synthesis Memorandum funded by the U.S. Army Corps of Engineers and developed for the Columbia Estuary Ecosystem Restoration Program (CEERP) on the topic of habitat restoration in the Columbia River Estuary (CRE) from Bonneville Dam to the river mouth. While the first two were developed by PNNL and NOAA without the benefit of stakeholder participation, for the current memo, two key activities were initiated: (1) review, by the Expert Regional Technical Group (ERTG), of status and trends monitoring and action effectiveness monitoring funded by CEERP, and (2) a workshop including representatives of the Bonneville Power Administration and the U.S. Army Corps of Engineers (the action agencies [AAs]), the National Oceanic and Atmospheric Administration (NOAA), major research agencies contributing to CEERP, and sponsors who implement CEERP restoration actions. A systematic literature review was conducted using ClarivateTM Web of ScienceTM database. The topics of interest for CRE relevant research included salmon ecology, physical processes, and wetland habitats, and therefore required the use of broad search terms. Our final search criteria included a combination of Boolean operators and an approach to combine different sets of search terms. The final search result yielded 669 records. The records were classified by groups and assigned to the relevant disciplinary expert for review. The review identified substantive advances in understanding the provision of salmon habitat functions through spatiotemporally dynamic physical and ecological processes, and the use of CRE habitats by numerous stocks of juvenile salmon. It also uncovered heretofore unincorporated historical documentation of riparian habitats across the CRE. The characterization of the structural components of floodplain habitat including plant associations and channel networks has advanced considerably, together with the understanding of seasonal changes and long-term trends. The relative influence of salmon-habitat location in the CRE as compared with temporal factors, mainly season, has been well described, which affects the prioritization of restoration. Stressors on the ecosystem and fish, and the drivers of these stressors, have been more carefully elucidated and predictive models are in various stages of development. The vision, aims, and design of restoration projects have advanced together with methods of data collection, analysis, and modeling that have seen substantial improvements. Experiments intended to inform the design of restoration projects are underway or have been completed. An important outstanding area of research that has lagged behind the advances in fundamental understanding of the ecosystem and salmon habitat functions remains the peer-reviewed documentation of the outcomes of restoration for both habitats and fish functions.
Advanced high-temperature nuclear reactors rely on structural components that will operate for decades under combined mechanical, thermal, and environmental loading. Materials surveillance programs are a promising strategy for managing the resulting uncertainty in long-term structural integrity by monitoring degradation in service using passively actuated mechanical test articles. Previous reports have developed a simplified, spreadsheetimplementable framework for sizing these test articles and for inferring accumulated creep damage and remaining life from ex-situ test data. This report advances that work toward practical deployment by providing a sample-problem book: a collection of worked, end-toend examples in which the ASME Section III, Division 5 design analysis of a representative high-temperature reactor component is carried through to a sized surveillance article, verified with detailed finite-element analysis, and concluded with a remaining-life assessment based on an assumed ex-situ creep-rate measurement on the retrieved specimen. The report also summarizes ongoing ANL engagement with ASTM Committee E10 on Nuclear Technology and Applications toward drafting a standard covering surveillance procedures for advanced reactors.
Luteolibacter sp. strain Populi is bacterium from the phylum Verrucomicrobiota, isolated from the rhizosphere of a black cottonwood tree, Populus trichocarpa, from the Cascade mountains in Washington. Its 6.6 Mb chromosome was completely sequenced using Oxford Nanopore long-reads and is predicted to encode 5301 proteins and 60 RNAs. The bacteria was isolated from the rhizosphere of a mature Populus trichocarpa from the Tieton riverwatershed of Washington state, USA (Lat: 46°42’9” N, Lon: 120°25 39’36” W). A rhizosphere sample (fine roots and adhering soil) was used to obtain a microbial fraction by centrifugation on Histodenz (12) and stained with 5µM Syto59 (Thermo Fisher Scientific Inc). A Cytopeia Influx cell sorter (BD, Franklin Lakes, NJ) was used to sort and array single cells (100 per plate) based on forward-side scatter and fluorescence intensity on asparagine-glucose nutrient agar (ATCC medium 184). The Luteolibacter sp. Populi genome sequence has been deposited in GenBank under the accession number CP161812. A draft genome annotated with Prokka and DRAM is available in this Narrative as Luteolibacter_sp_Prokka.240711.
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.
Slide rule-type color chart determines the final reproduced gray tones in the production of briefing charts that are photographed in black and white. The chart shows both the color by drafting paint manufacturers name and mixture number, and the gray tone resulting from black and white photographic reproduction.
Investigations on the fundamental space shuttle propulsion systems program are reported, with emphasis on in-depth reviews of preliminary drafts of the guidelines. The guidelines will be used to incorporate the onboard checkout and monitoring function into the basic design of the propulsion systems and associated interfacing systems. The analysis of checkout and monitoring requirements of the Titan 3 L expandable booster propulsion systems was completed, and the techniques for accomplishing the checkout and monitoring functions were determined. Updating results of the basic study of propulsion system checkout and monitoring is continuing.
The features of two aircraft designs were selected to be included in the single RSRA configuration. A study was conducted for further preliminary design and a more detailed analysis of development plans and costs. An analysis was also made of foreseeable technical problems and risks, identification of parallel research which would reduce risks and/or add to the basic capability of the aircraft, and a draft aircraft specification.
Task assignments in support of the Nike-Tomahawk vehicles, which were completed from May, 1970 through November 1972 are reported. The services reported include: analytical, design and drafting, fabrication and modification, and field engineering.
Plots of the Mariner 5 and Venera 4, 5, and 6 pressure vs temperature show that the Venera profiles are essentially congruent with the Mariner 5 day and night profiles, but are displaced 28 percent higher in pressure. Data suggest a variability in the atmospheric water vapor content in the region from 30 to 50 km. The Venera 7 measurements are interpreted as evidence for updrafts, down-drafts, horizontal wind layers, and nonaqueous precipitation. The previously observed band of retrograde winds which circle the equator with an average speed of 110 m/s is found to extend downward to the one atmosphere level at the equatorial morning terminator. The possibility of a low altitude equator-to-pole circulation with warm gas rising at the poles is inferred. Venera 7 temperature data used with radar topography and microwaves interferometer measurements suggest that the variation of surface temperature with altitude in a band about the equator is less than 5 K/km. The available data are used to calculate a model of the structure of the Venus atmosphere for the first 75 km above the equatorial region.