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X-ray characterization of catalyst materials using synchrotron radiation has become more widely available to the scientific community in recent decades.
The vision of the National Microbiome Data Collaborative (NMDC) centers on the concept of connecting data, people, and ideas to advance microbiome innovation and discovery. Building data infrastructure, while key to NMDC’s ability to execute on our vision, can only go so far in creating scientific impact. By fostering strong community partnerships and developing a set of robust community outreach and training programs, we are able to turn our products – the Submission Portal, NMDC EDGE, and the Data Portal – into tools that empower the scientific community. Our multi-pronged community building approach spans individual researchers, research teams, consortia and scientific societies, and institutions and federal agencies. To foster a collaborative and inclusive community-centered environment, we have identified three strategic objectives to promote an inclusive and connected community: (1) recognize and support the diverse research needs and perspectives of the microbiome research community; (2) promote best practices across the microbiome community, from researchers to funders, through community-driven practices (FAIR, CARE, and TRUST); and (3) build a microbiome ecosystem that enables scientific discovery and innovation across stakeholders. These strategic objectives allow our team to focus on impact across a diverse range of activities, from launching the American Society for Microbiology (ASM) Microbiome Data Prize to supporting the Ambassador and Champions programs fostering learning and building a collaborative network. We broadly communicate our work through social media (X/Twitter, LinkedIn, and Instagram), The Microbiome Standard (our quarterly newsletter), and Annual Reports. All our work is underpinned by a strong commitment to diversity, equity, and inclusion as articulated in our Action Plan that tracks progress towards key metrics. A core component of our engagement strategy is user research. User research ensures the Submission Portal, NMDC EDGE, Data Portal, and the new Field Notes mobile app are designed with and for the scientific community. Our user research efforts consist of asking researchers exploratory questions to collect information on researcher priorities, methodologies, and perceptions to ensure that we are aware of the current state of microbiome research. Our usability testing provides researchers with prototypes or test environments of the NMDC products, and we capture valuable information on how users interact with the products to make improvements. Given the diverse nature of microbiome work, we acknowledge that we are not aware of all pressing data challenges and thus rely on the research community to help us identify the most important issues to prioritize. To date, we have conducted 24 interviews and one beta-testing call with 10 participants across all NMDC products, which have generated 321 insights and 120 action items. Herein, we describe the ways we engage with the microbiome research community to advance the NMDC mission.
This data package contains phospholipid fatty acid and branched glycerol dialkyl glycerol tetraethers data used for the paper: “Whole-soil warming decreases abundance and modifies the community structure of microorganisms in the subsoil but not in surface soil”. SOIL, https://doi.org/10.5194/soil-2021-14.On April 2018 (after 4.5 years of warming), we collected soil cores down to 90 cm depth from the whole soil profile warming experiment at the University of California Blodgett Forest Research Station, in the Sierra Nevada foothills near Georgetown, CA at 1370 m above sea level. Cores were collected from 6 experimental plots (three replicated blocks); samples were collected in 10 cm increments from 0 to 90 cm depth.This data package includes a file in .csv format and a file in .xlsx format, which can be accessed and processed using MS Excel or R. Phospholipid fatty acid and branched glycerol dialkyl glycerol tetraethers concentrations are provided as processed data files.
In early 2021, the National Association for State Community Services Programs (NASCSP) and its Workforce Development Working Group provided turnkey survey tools to the Weatherization Assistance Program (WAP) network on compensation rates for six core WAP positions. From February to April 2021 wage surveys were voluntarily conducted by 27 states, with 286 Subgrantees self-reporting hourly wage data. For context, a $1/hour increase in wages = $2,080/year increase in salary.
Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput. Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software ( https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using 18 O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were several Bacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics. Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
Core-collapse supernovae are vital phenomena for understanding the extreme physics of stellar evolution, nuclear interactions, and the origins of elements in the universe. This project developed high-resolution 3D simulations and innovative 1D turbulence models to study the explosion mechanisms, yielding critical insights into the role of turbulence, magnetohydrodynamics, and neutrino physics. The outcomes include enhanced sensitivity analyses connecting nuclear physics inputs to observable supernovae characteristics, tools for the broader research community, and substantial contributions to the training of future scientists.
The HFIR, RHF, and FRM II reactors represent a particular class of Research and Test Reactors that provide some of the most intense and continuous neutron fluxes for science, industry, and medical applications. These high-performance reactors have achieved compact cores by operating with Highly Enriched Uranium fuel (HEU, 235U/U ≥ 20 wt. %) and utilizing fuel plates curved as an involute. Due to the proliferation risks, the international community aims to reduce or eliminate, when possible, the use of HEU fuel in civilian facilities by converting them to a Low-Enriched Uranium fuel (LEU, 235U/U < 20 wt. %). Conversion of these reactors without significantly compromising their performance or safety is a challenging endeavor that can tremendously benefit from advanced computational tools and thus, eliminate unnecessary conservatism to ensure sufficient thermal margins. Therefore, models are being developed using modern Computational Fluid Dynamics (CFD) and Computational Structural Mechanics (CSM) software to evaluate the steady-state safety margins of various LEU designs instead of being reliant on the more traditional, conservative methods. To gain the confidence and acceptance of high-fidelity modeling by the nuclear regulators, Argonne National Laboratory (ANL) and the involute reactors have formed an informal scientific group, the Involute Working Group (IWG). The IWG facilitates inter-organizational collaboration on experimental benchmarking, code-to-code comparisons, and Verification and Validation (V&V). This paper describes some of the recent IWG efforts in validating software against the existing experimental data, as well as code-to-code comparisons of different software used by the IWG members.
Among multimessenger observations of the next Galactic core-collapse supernova, Super-Kamiokande (SK) plays a critical role in detecting the emitted supernova neutrinos, determining the direction to the supernova (SN), and notifying the astronomical community of these observations in advance of the optical signal. In 2022, SK has increased the gadolinium dissolved in its water target (SK-Gd) and has achieved a Gd concentration of 0.033%, resulting in enhanced neutron detection capability, which in turn enables more accurate determination of the supernova direction. Accordingly, SK-Gd’s real-time supernova monitoring system has been upgraded. SK_SN Notice, a warning system that works together with this monitoring system, was released on 2021 December 13, and is available through GCN Notices. When the monitoring system detects an SN-like burst of events, SK_SN Notice will automatically distribute an alarm with the reconstructed direction to the supernova candidate within a few minutes. In this paper, we present a systematic study of SK-Gd’s response to a simulated Galactic SN. Assuming a supernova situated at 10 kpc, neutrino fluxes from six supernova models are used to characterize SK-Gd’s pointing accuracy using the same tools as the online monitoring system. The pointing accuracy is found to vary from 3° to 7° depending on the models. However, if the supernova is closer than 10 kpc, SK_SN Notice can issue an alarm with three-degree accuracy, which will benefit follow-up observations by optical telescopes with large fields of view.
Brookhaven National Laboratory (BNL) was awarded a pilot project in FY22 under the U.S. Department of Energy (DOE) Office of Science Biopreparedness Research Virtual Environment (BRaVE) initiative, to define research priorities, needs, and requirements for a national virtual center devoted to the biosecurity of bioenergy crops. The mission of the proposed center, referred to as the National Virtual Biosecurity for Bioenergy Crop Center (NVBBCC), would be to provide the scientific basis and tools to detect, characterize, model, and mitigate biothreats to bioenergy crops. This function will be essential to ensure the projected increased US reliance over the next few decades on key plant-based energy products, such as biojet fuel. The NVBBCC is envisioned as a distributed, virtual center with multiple national laboratories at its core to maximize the use of existing unique facilities and expertise across the DOE complex. A major goal of the pilot project was to develop a roadmap for establishing NVBBCC through a series of meetings to gather community input. A total of about 150 individuals, drawn from DOE laboratories, the USDA, academia, NIH, DHS and the private sector participated in six planning meetings held in FY23. Four of the meetings were focused on specific research topics (disease detection, dispersion and disease propagation, biomolecular characterization of plant-pathogen interaction, and mitigation strategies). These four meetings were followed by a meeting that focused on computational needs to support collaborative, data-intensive research within a distributed center as well as workforce development. A final meeting focused on establishing and maintaining preparedness within NVBBCC to respond to an emerging disease within bioenergy crops and how it would collaborate and coordinate with USDA and DHS.
Rapid compression machines (RCMs) have been extensively used to quantify fuel autoignition chemistry and validate chemical kinetic models at high-pressure conditions. Historically, the analyses of experimental and modeling RCM autoignition data have been conducted based on the adiabatic core hypothesis with ideal gas assumption, where real-fluid behavior has been completely overlooked, though this might be significant at common RCM test conditions. Here, this work presents a first-of-its-kind study that addresses two significant but overlooked questions for autoignition studies within RCMs in the fundamental combustion community: (i) experiment-wise, can unaccounted-for real-fluid behavior in RCMs affect the interpretation and analysis of RCM experimental data? and (ii) simulation-wise, can unaccounted-for real-fluid behavior in RCMs affect RCM autoignition modeling and the validation of chemical kinetic models? To this end, theories for real-fluid isentropic change are newly proposed and derived based on high-order Virial EoS, and are further incorporated into an effective-volume real-fluid autoignition modeling framework newly developed for RCMs. With detailed analyses, the strong real-fluid behavior in representative RCM tests is confirmed, which can greatly influence the interpretation of RCM autoignition experiments, particularly the determination of end-of-compression temperature and evolution of the adiabatic core in the reaction chamber. Furthermore, real-fluid RCM modeling results reveal that considerable error can be introduced into simulating RCM autoignition experiments when following the community-wide accepted effective-volume approach by assuming ideal-gas behavior, which can be as high as 64% in the simulated ignition delay time at compressed pressure of 125 bar and lead to contradictory validation results of chemical kinetic models. Therefore, we recommend the community to adopt frameworks with real-fluid behavior fully accounted for (e.g., the one developed in this study) to analyze and simulate past and future RCM experiments, so as to avoid misinterpretation of RCM autoignition experiments and eliminate the potential errors that can be introduced into the simulation results with the existing RCM modeling frameworks.
Abstract Dynamic (temporal) graphs are a convenient mathematical abstraction for many practical complex systems including social contacts, business transactions, and computer communications. Community discovery is an extensively used graph analysis kernel with rich literature for static graphs. However, community discovery in a dynamic setting is challenging for two specific reasons. Firstly, the notion of temporal community lacks a widely accepted formalization, and only limited work exists on understanding how communities emerge over time. Secondly, the added temporal dimension along with the sheer size of modern graph data necessitates new scalable algorithms. In this paper, we investigate how communities evolve over time based on several graph metrics under a temporal formalization. We compare six different algorithmic approaches for dynamic community detection for their quality and runtime. We identify that a vertex-centric (local) optimization method works as efficiently as the classical modularity-based methods. To its advantage, such local computation allows for the efficient design of parallel algorithms without incurring a significant parallel overhead. Based on this insight, we design a shared-memory parallel algorithm DyComPar , which demonstrates between 4 and 18 fold speed-up on a multi-core machine with 20 threads, for several real-world and synthetic graphs from different domains.
Module-OT is a bump- in- the- wire solution acting as a secure conduit for data between devices or systems across a network. Using the latest in open-source cryptographic libraries, all defined communications undergo authentication, authorization, and encryption. The core system can be easily installed through industry standard processes, and the use of popular open-source packages allows for it to be customizable customized by the developer community or deployed in unique embedded environments.
E-bikes have been quickly growing in popularity in recent years. Access to e-bikes poses an opportunity to improve mobility options as a comparatively inexpensive yet similarly convenient alternative to car ownership. This study focuses on the outcomes of the CanBikeCO program developed by the Colorado Energy Office (CEO) that provided e-bikes to low-income users in sites across Colorado. This is the first large-scale, longitudinal evaluation of how privately-owned e-bikes are used, revealing energy, emissions, and behavior implications. The evaluation indicates that e-bikes primarily replaced driving alone. They were primarily used to access employment opportunities, although their use spanned the spectrum of mobility needs. They were popular among low-income, disadvantaged participants, with the greatest usage in the < $25,000 income bracket and by those who did not have access to a household vehicle. They have similar proportions to driving alone and shared rides for trips under 5 miles, so are a viable alternative for the majority of trips in the United States. Finally, they are competitive with cars in the number of destinations that can be reached in a given time, especially in urban cores and areas with good bicycling infrastructure. Analysis of the CanBikeCO pilot program revealed that e-bikes are a viable alternative to larger motorized modes, particularly for disadvantaged communities who may not have a variety of other mobility options. With supporting land use and infrastructure, their high energy efficiency can support substantial energy and emissions impacts due to mode shift, even in smaller communities. We will expand on these themes in a comprehensive paper to be released later this year.
Full text of publication follows. With about 200 reactors in operation, civilian Research and Test Reactors (RTRs) represent approximately a third of the global nuclear fleet. RTRs make use of core designs that are drastically different from commercial power plants to perform a wide variety of non-power applications that greatly benefit society. Because they often rely on high neutron fluxes, RTRs are designed with relatively compact cores and as a result, prior to the 1980's, were often deployed using Highly Enriched Uranium fuel (HEU, {sup 235}U/U = 20 wt. %). Due to proliferation concerns, the international community aims at eliminating the use of HEU in civilian facilities and favor instead the use of Low Enriched Uranium fuel (LEU, {sup 235}U/U < 20 wt. %). A program to support conversion of the world's RTRs to LEU fuel has been initiated in 1978 by the U.S. Department of Energy (DOE). This program is still alive today and has achieved more than 103 conversion metrics. Today, the program focuses heavily on the conversion of so-called high-performance RTRs, which are far more challenging than previous conversions as they require new fuel element designs and the use of new, higher density LEU fuel forms. Development and qualification of new LEU fuel elements is ongoing and requires extensive engineering analysis and testing. Both activities require the development and validation of codes and methods for reactor physics, thermal-hydraulics, and multi-physics, which in turn rely on experiments performed in RTRs or other experimental facilities. This talk will present the collection of RTR experimental data and benchmark analyses from the international conversion program that contribute to the validation of computer codes and methods.
River corridor metabolomes reflect organic matter (OM) processing that drives aquatic biogeochemical cycles. Recent work highlights the power of ultrahigh-resolution mass spectrometry for understanding metabolome composition and river corridor metabolism. However, there have been no studies on the global chemogeography of surface water and sediment metabolomes using ultrahigh-resolution techniques. Here, we describe a community science effort from the Worldwide Hydrobiogeochemistry Observation Network for Dynamic River Systems (WHONDRS) consortium to characterize global metabolomes in surface water and sediment that span multiple stream orders and biomes. We describe the distribution of key aspects of metabolomes including elemental groups, chemical classes, indices, and inferred biochemical transformations. We show that metabolomes significantly differ across surface water and sediment and that surface water metabolomes are more rich and variable. We also use inferred biochemical transformations to identify core metabolic processes shared among surface water and sediment. Finally, we observe significant spatial variation in sediment metabolites between rivers in the eastern and western portions of the contiguous United States. Our work not only provides a basis for understanding global patterns in river corridor biogeochemical cycles but also demonstrates that community science endeavors can enable global research projects that are unfeasible with traditional research models.
Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water–rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.
Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken in 2019 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) near the Meander C/Pumphouse floodplain sites of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (30-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (70-80 cm depth below surface). Sediments were homogenized from the 10 cm core for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0141020. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 436 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.
Microorganisms play a key role in cycling nutrients and contaminants in the terrestrial environment depending on their genetic potential. Here, we present metagenome-assembled genomes (MAGs) for the bacterial and archaeal community in floodplain sediment samples taken in 2017 in June (flooded conditions) and September (drained conditions) at two locations (MCB1 and MCB3) in an active meander (Meander C) of the East River. Sediment cores were collected from 2 depths, a near-surface, generally unsaturated depth (15-40 centimeter (cm) depth below surface) and a deeper depth influenced by flooding with redoximorphic features (50-88 cm depth below surface). Sediments were homogenized from the ~10 cm cores for microbial analyses. A total of 24 metagenomes were sequenced through the Joint genome institute (JGI) corresponding to 8 samples sequenced in triplicate. These metagenomes can be found under Genomes Online Database (GOLD) sequencing project: Gs0151851. Metagenomes were assembled, binned, and refined using metawrap to generate MAGs (>50% complete and < 10% contamination based on checkM scores). This dataset includes a zip file of 405 MAG fasta files and a csv file with quality, taxonomic classification (Genome Taxonomy Database Release RS220), and metagenome accessions for MAGs. This dataset also includes a file-level metadata (flmd.csv) file that lists each file contained in the dataset with associated metadata and a data dictionary (dd.csv) file that contains column/row headers used throughout the files along with a definition, units, and data type.This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Part of this work was performed at SLAC Accelerator Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-76SF00515.