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At least 73 records · Page 4

STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. In conclusion, STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

59 BASIC BIOLOGICAL SCIENCES↗

Human RNome Project draft human RNome sequence of GM12878, B-cell line, obtained by mass-spectrometry sequencing, long-read sequencing and short-read sequencing.

Here we report the first draft of the human RNome sequence, a reference map of RNA chemical modifications in a human B-cell line. RNA carries a diverse repertoire of chemical modifications that regulate gene expression, cellular function, and responses to physiological and pathological cues. Yet, unlike the genome, no reference map of RNA modifications is available for any human cell. To generate this resource, the Human RNome Project Consortium analyzed a shared RNA preparation from the well-characterized GM12878 B-cell line using short-read sequencing, long-read direct RNA sequencing, and mass spectrometry, generating more than 7.1 billion sequencing reads spanning approximately 1.2 trillion nucleotides. The resulting maps of the human RNome reveal that RNA modifications are organized according to function, transcript architecture, and cellular identity. Modifications concentrate at functional centers of ribosomal and transfer RNAs, follow the canonical topology of N6-methyladenosine in coding transcripts, and form coordinated hotspots in immune regulatory genes. This first reference human RNome provides a foundation for understanding how RNA chemistry shapes cellular identity, human disease, and the development of RNA-based therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗

Waveform modelling for the Laser Interferometer Space Antenna

LISA, the Laser Interferometer Space Antenna, will usher in a new era in gravitational-wave astronomy. As the first anticipated space-based gravitational-wave detector, it will expand our view to the millihertz gravitational-wave sky, where a spectacular variety of interesting new sources abound: from millions of ultra-compact binaries in our Galaxy, to mergers of massive black holes at cosmological distances; from the early inspirals of stellar-mass black holes that will ultimately venture into the ground-based detectors’ view to the death spiral of compact objects into massive black holes, and many sources in between. Central to realising LISA’s discovery potential are waveform models, the theoretical and phenomenological predictions of the pattern of gravitational waves that these sources emit. This White Paper is presented on behalf of the Waveform Working Group for the LISA Consortium. It provides a review of the current state of waveform models for LISA sources, and describes the significant challenges that must yet be overcome.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

A Novel Integrated Fermentation Process with Engineered Microbial Consortia for Butanol Production from Lignocellulose Sugars without CO 2 Emission

The goal of this project was to develop a synthetic microbial consortium consisting of a lactic acid bacterium, a carboxydotrophic acetogen, and a solventogenic clostridia for the production of n butanol, an advanced biofuel and industrial chemical, from lignocellulose sugars (mainly glucose and xylose) and formate (produced from CO 2 by electrochemical reduction) in an integrated bioprocess (biorefinery), which can provide an effective solution to the technical challenges in developing energy and carbon optimized synthesis for the bioeconomy and achieve the program objectives of ARPA-E. The project focused on the design, modeling and construction of synthetic microbial consortia consisting of three bacterial species to maximize carbon conversion and butanol production with a 100% theoretical product yield from glucose and zero or negative CO 2 emission.

09 BIOMASS FUELS↗

Recommendations for Minimum Required Diagnostics Information for Electric Vehicle Charging Infrastructure

The rapid growth of electrified transportation, including light- and medium-duty electric vehicles (EVs) as a mobility solution requires a reliable EV charging infrastructure. To advance charging reliability, the ChargeX Consortium reports “Recommendations for Minimum Required Error Codes for Electric Vehicle Charging Infrastructure” and “Implementation Guide for Minimum Required Error Codes in Electric Vehicle Charging Infrastructure” have provided recommendations for a set of minimum required error codes (MRECs), their functional and responsibility classifications, and a guide for their implementation using OCPP versions 1.6J and 2.0.1. These reports outline a recommended practice for consistent error reporting and interpretation, which is essential for communicating issues uniformly across the complex and diverse EV charging ecosystem. However, MRECs are just one part of diagnosing issues, another critical part is obtaining enough information about the current state and performance of the various charging components to identify root causes for each of the error codes. This additional diagnostics data can be used by technicians or automated systems to understand the context around an issue, allowing for timely resolution, decreased maintenance costs, and increased charging reliability. During everyday operations, data is regularly collected and analyzed across the ecosystem. Although sharing of all that available data would be great for diagnostics, concerns on data ownership, privacy, and OEM intellectual property pose a challenge. To overcome this obstacle, this report proposes a set of Minimum Required Diagnostic Information (MRDI) and recommends that the industry implement these uniformly across the North American EV charging ecosystem. MRDI provides a means to exchange only data deemed necessary for root cause determination.

32 - ENERGY CONSERVATION, CONSUMPTION, AND UTILIZA↗

Roadmap to Advance Heliostat Technologies for High Temperature Solar-Thermal Systems

Since its establishment, the Heliostat Consortium (HelioCon) has made substantial progress toward closing many of the gaps in concentrating solar power (CSP) research. Numerous techno-economic studies have been performed, investigating topics ranging from the trade-off between size and temperature for industrial process heat applications to optimization of the heliostat design itself for various applications. Significant improvements have been made in optical metrology techniques, with first steps toward in situ measurement of heliostat fields. Several standards have been, and continue to be, developed with the coordination of an international group of CSP industry participants. Training programs have been developed, with universities including CSP in their engineering curricula, and many public webinars have been held to provide broad access to the latest CSP research. Improved CSP components such as mirror facets and wireless communication systems have been developed, and the solar tower at Sandia National Laboratories has been upgraded with a testbed for closed-loop controls research and development. Field deployment challenges involving heliostat foundations and sensitive wildlife habitats have been explored, with progress made toward methods for streamlining project development and permitting. Additional knowledge has been added to the body of work on wind behavior of heliostats and arrays of heliostats, with progress made toward a holistic understanding of wind design methods. Finally, techniques have been developed and demonstrated for assessing soiling conditions at a proposed project site, with predictive models for the soiling rate showing good results. Taking these results together, HelioCon has contributed greatly to the global CSP research and development effort over the past several years.

14 SOLAR ENERGY↗

Durability of Pt-Alloy Catalyst for Heavy-Duty Polymer Electrolyte Fuel Cell Applications under Realistic Conditions

As an emerging technology, polymer electrolyte fuel cells (PEFCs) powered by clean hydrogen can be a great source of renewable power generation with flexible utilization because of high gravimetric energy density of hydrogen. To be used in real-life applications, PEFCs need to maintain their performance for long-term use under a wide range of conditions. Therefore, it's important to understand the degradation of the PEFC under protocols that are closely related to the catalyst lifetime. Alloying Pt with transitional metal improves catalyst activity. It is also crucial to understand Pt alloys degradation mechanisms to improve their durability. To study durability of Pt alloys, accelerated stress tests (ASTs) are performed on Pt-Co catalyst supported on two types of carbon. Two different AST protocols were being studied: Membrane Electrolyte Assembly (MEA) AST based on the protocol introduced by the Million Mile Fuel Cell Truck consortium in 2023 and Catalyst AST, adopted from the U.S. Department of Energy (DoE).

25 ENERGY STORAGE↗

The first ensemble of kilometer-scale simulations of a hydrological year over the third pole

An accurate understanding of the current and future water cycle over the Third Pole is of great societal importance, given the role this region plays as a water tower for densely populated areas downstream. An emerging and promising approach for skillful climate assessments over regions of complex terrain is kilometer-scale climate modeling. As a foundational step towards such simulations over the Third Pole, we present a multi-model and multi-physics ensemble of kilometer-scale regional simulations for the hydrological year of October 2019 to September 2020. The ensemble consists of 13 simulations performed by an international consortium of 10 research groups, configured with a horizontal grid spacing ranging from 2.2 to 4 km covering all of the Third Pole region. These simulations are driven by ERA5 and are part of a Coordinated Regional Climate Downscaling EXperiment Flagship Pilot Study on Convection-Permitting Third Pole. The simulations are compared against available gridded and in-situ observations and remote-sensing data, to assess the performance and spread of the model ensemble compared to the driving reanalysis during the cold and warm seasons. Although ensemble evaluation is hindered by large differences between the gridded precipitation datasets used as a reference over this region, we show that the ensemble improves on many warm-season precipitation metrics compared with ERA5, including most wet-day and hour statistics, and also adds value in the representation of wet spells in both seasons. As such, the ensemble will provide an invaluable resource for future improvements in the process understanding of the hydroclimate of this remote but important region.

54 ENVIRONMENTAL SCIENCES↗

Evaluation of IrO 2 catalysts doped with Ti and Nb at industrially relevant electrolyzer conditions: A comprehensive study

A series of commercial Oxygen Evolution Reaction (OER) IrO 2 -based materials doped with acid-stable titanium and niobium species were comprehensively characterized by Brunauer-Emmett-Teller (BET), X-ray diffraction analysis (XRD), X-ray photoelectron spectroscopy (XPS), transmission electron microscopy (TEM) with energy dispersive spectroscopy (EDS), and X-ray Scattering. Electrocatalysts were integrated into Membrane Electrode Assembly (MEA) using a fabrication method developed under the US DOE H2NEW consortium. An electrolysis performance in a commercial setup as well as a laboratory screening system was performed at conditions relevant to industrial application. According to the comprehensive characterizations, the studied materials are closer to doped iridium oxides rather than core–shell structures. In an electrolysis cell, the IrO 2 /TiO x catalyst slightly outperforms the IrO 2 /NbO x based on the activity. It was demonstrated that the operation of electrolysis cells at elevated temperatures and the implementation of thinner Nafion-type membranes allows for substantially increased performance, which is consistent with the literature report. Finally, this work provides valuable baselines including characterization and performance for guiding future research in this direction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Temporal multi-omic analysis uncovers sex-biased molecular programs underlying skeletal muscle adaptation to endurance training

Background. Exercise training is known to benefit health and reduce disease risk. While adaptations in skeletal muscles are fundamental to many of the health benefits of exercise training, the common and sex-specific molecular regulators that mediate these adaptations remain to be fully elucidated. Methods. To this end, we leveraged skeletal muscle multi-omics data generated by the Molecular Transducers of Physical Activity Consortium (MoTrPAC), where 6 month-old male and female rats endurance trained for 1, 2, 4, or 8 weeks. Our objective was to identify shared and sex-specific multi-omic molecular responses to endurance training in skeletal muscle, and relate them to phenotypic adaptations. Results. We identified largely sexually-conserved transcriptomic and proteomic enrichments in the gastrocnemius, which correlated with skeletal muscle responses from a published exercise study in humans. We uncovered sex-consistent post-translational modifications, including decreased oxidation of MYH2 and deacetylation of the ß-oxidation enzyme HADHA. Pathway enrichment analyses revealed sex-specific remodeling across the acetylome, redox proteome, and phosphoproteome; females decreased mitochondrial protein oxidation and increased mitochondrial cristae proteins, indicative of enhanced redox buffering and mitochondrial efficiency. Despite observed decreases in the oxidation of key mitochondrial proteins, females displayed increases in the oxidation of proteins involved in glucose catabolism relative to males after 8 weeks of training, suggestive of sex-biased subcellular reactive oxygen species generation. Conclusions. This work shows a large portion of the adaptive response to endurance training in skeletal muscle is shared between females and males, while there are distinct and nuanced sex-specific adaptations that are evident, particularly at the level of post-translational regulation.

Many, Gina M.↗

A real-time energy and cost efficient vehicle route assignment neural recommender system

Here, this paper presents a neural network recommender system algorithm for assigning vehicles to routes based on energy and cost criteria. In this work, we applied this new approach to efficiently identify the most cost-effective medium and heavy duty truck (MDHDT) powertrain technology, from a total cost of ownership (TCO) perspective, for given trips. We employ a machine learning based approach to efficiently estimate the energy consumption of various candidate vehicles over given routes, defined as sequences of links (road segments), with little information known about internal dynamics, i.e. using high level macroscopic route information. A complete recommendation logic is then developed to allow for real-time optimum assignment for each route, subject to the operational constraints of the fleet. We show how this framework can be used to (1) efficiently provide a single trip recommendation with a top-k vehicles star ranking system, and (2) engage in more general assignment problems where n vehicles need to be deployed over m (m ≤ n) trips. This new assignment system has been deployed and integrated into the POLARIS. Transportation System Simulation Tool for use in research conducted by the Department of Energy's Systems and Modeling for Accelerated Research in Transportation (SMART) Mobility Consortium (SMART, 2024).

Energy consumption↗

The role of quantum computing in advancing scientific high-performance computing: A perspective from the ADAC institute

Quantum computing (QC) has gained significant attention over the past two decades due to its potential for speeding up classically demanding tasks. This transition from an academic focus to a thriving commercial sector is reflected in substantial global investments. While advancements in qubit counts and functionalities continue at a rapid pace, current quantum systems still lack the scalability for practical applications, facing challenges such as too high error rates and limited coherence times. Here, this perspective paper examines the relationship between QC and high-performance computing (HPC), highlighting their complementary roles in enhancing computational efficiency. It is widely acknowledged that even fully error-corrected QC will not be suited for all computational tasks. Rather, future compute infrastructures are anticipated to employ quantum acceleration within hybrid systems that integrate HPC and QC. While QC can enhance classical computing, traditional HPC remains essential for maximizing quantum acceleration. This integration is a priority for supercomputing centers and companies, sparking innovation to address the challenges of merging these technologies. The novelty of this work lies in its unique perspective, reflecting the collective insights of the Accelerated Data Analytics and Computing (ADAC) Institute, a global consortium of over 20 leading HPC centers. Recognizing the growing importance of QC, ADAC established a Quantum Computing Working Group in 2023 to foster collaboration and knowledge-sharing among its members. This paper synthesizes insights from the group’s collaborative efforts and incorporates findings from a member survey that captures shared experiences, ongoing projects, and strategic directions. By outlining the current landscape and challenges of QC integration into HPC ecosystems, this work offers HPC specialists practical and forward-looking guidance on the opportunities and implications of QC in computationally intensive endeavors.

Accelerated Data Analytics and↗

A compendium of human gene functions derived from evolutionary modelling

A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this goal by generating a structured body of information about gene functions, which now includes experimental findings reported in more than 175,000 publications for human genes and genes in experimentally tractable model organisms 1,2 . Here, we describe the results of a large, international effort to integrate all of these findings to create a representation of human gene functions that is as complete and accurate as possible. Specifically, we apply an expert-curated, explicit evolutionary modelling approach to all human protein-coding genes. This approach integrates available experimental information across families of related genes into models that reconstruct the gain and loss of functional characteristics over evolutionary time. The models and the resulting set of 68,667 integrated gene functions cover approximately 82% of human protein-coding genes. The functional repertoire reveals a marked preponderance of molecular regulatory functions, and the models provide insights into the evolutionary origins of human gene functions. We show that our set of descriptions of functions can improve the widely used genomic technique of Gene Ontology enrichment analysis. The experimental evidence for each functional characteristic is recorded, thereby enabling the scientific community to help review and improve the resource, which we have made publicly available.

59 BASIC BIOLOGICAL SCIENCES↗

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗

Editorial for the Collection "Preparatory Work for the American Wake Experiment (AWAKEN)"

The American WAKE experimeNt (AWAKEN) is a large field campaign focused on gathering observations for improved understanding of atmospheric and wind power plant flow physics, one of the outstanding needs for the wind energy community as described in the Science paper by Veers et al.1 "Grand challenges in wind energy." AWAKEN was planned over several years with an international consortium of numerous stakeholders, including national laboratories, academic researchers, wind turbine manufacturers, and wind farm operators. A highlight of the AWAKEN campaign is the extensive use of remote sensing instrumentation to characterize the atmosphere and its interactions with wind power plants, enabled by recent developments in lidar, radar, and thermodynamic profiling technology. Advanced modeling techniques like mesoscale and large-eddy simulations (LES) also played an important role in the preparation of the experiment and the interpretation of the experimental data collected. This special-topic issue for the Journal of Renewable and Sustainable Energy presents a collection of 12 papers that describe the preparatory work and some initial analyses from the AWAKEN campaign. An overview of the contents of the various papers in this special issue is provided in Sec. II.

17 WIND ENERGY↗

Developing a Process for Collaboration-Based Siting of a Federal Consolidated Interim Storage Facility in the United States: Learning from Communities Living with Legacy Waste

In June of 2023, the U.S. Department of Energy (DOE), Office of Nuclear Energy (NE) announced the selection of its Collaboration-Based Siting (CBS) Consortia, a group of 12 awardees, including the Consortium for Risk Evaluation with Stakeholder Participation (CRESP) (led by Vanderbilt University) to assist DOE-NE with the development of its process for siting a federal consolidated interim storage facility (FCISF) for spent nuclear fuel (SNF) storage. At this time, DOE NE is not soliciting interested host communities, rather the CBS Consortia are tasked with in-depth engagement, mutual learning, and capacity building to provide DOE NE with feedback on the CBS process. CRESP’s objective is to engage communities in two regions (the Pacific Northwest and the Southeast) with sites currently storing defense- and research-related SNF to foster learning concerning the best and worst practices in community participation in risk-informed decision making. This includes learning from existing structures for public input in radioactive waste management decision making [e.g. citizen advisory boards (CABs)] and other local parties about how to build and sustain trust among the parties. CRESP has been working to engage stakeholders and Tribes surrounding two DOE sites historically differing in receptiveness to engaging with DOE and trusting in DOE to accomplish its missions. CRESP’s approach to date has consisted of (1) engaging voluntarily members and former members of the DOE Office of Environmental Management’s CABs to develop a mutual understanding of their perspectives, values, and experiences related to risk and participatory decision making; (2) engaging members of those communities that would likely be part of any radioactive waste management discussions and who may provide valuable feedback for the development of the CBS process; and in the longer term, (3) engaging communities to foster knowledge sharing on understanding and definitions of risk and how risk is factored into community decision making. Our emphasis is to identify opportunities for improving risk communication frameworks, strategies, and decision making. The selection of a future FCISF site is likely to result in the creation of a structure similar to a CAB composed of members of the local community. We anticipate that these insights can help DOE NE learn from existing participatory risk communication structures in place at sites storing defenseor research-related SNF to understand best practices for fostering enduring and participatory relationships with future CABs. Within this paper, we (1) describe CRESP’s overall approach to assisting DOE NE with maturing the CBS process; (2) present a summary of preliminary phase 1 project results, including the development of a body of knowledge (describing available resources to support community engagement, risk communica tion, and participatory decision making) and community ecosystem information (leveraging demographic, social, economic, and environmental attribute mapping and advanced sentiment analysis of social media data); and (3) based on these results, provide observations for future research opportunities to support the development of CBS processes for radioactive waste management facilities, generally.

collaboration-based siting↗

Helium plasma operations on ASDEX Upgrade and JET in support of the non-nuclear phases of ITER

For its initial operational phase, ITER has until recently considered using non-nuclear hydrogen (H) or helium (He) plasmas to keep nuclear activation at low levels. To this end, the Tokamak Exploitation Task Force of the EUROfusion Consortium carried out dedicated experimental campaigns in He on the ASDEX Upgrade (AUG) and JET tokamaks in 2022, with particular emphasis put on the ELMy H-mode operation and plasma-wall interaction processes as well as comparison to H or deuterium (D) plasmas. Both in pure He and mixed He + H plasmas, H-mode operation could be reached but more effort was needed to obtain a stable plasma scenario than in H or D. Even if the power threshold for the LH transition was lower in He, entering the type-I ELMy regime appeared to require equally much or even more heating power than in H. Suppression of ELMs by resonant magnetic perturbations was studied on AUG but was only possible in plasmas with a He content below 19%; the reason for this unexpected behaviour remains still unclear and various theoretical approaches are being pursued to properly understand the physics behind ELM suppression. The erosion rates of tungsten (W) plasma-facing components were an order of magnitude larger than what has been reported in hydrogenic plasmas, which can be attributed to the prominent role of He 2+ ions in the plasma. For the first time, the formation of nanoscale structures (W fuzz) was unambiguously demonstrated in H-mode He plasmas on AUG. However, no direct evidence of fuzz creation on JET was obtained despite the main conditions for its occurrence being met. The reason could be a delicate balance between W erosion by ELMs, competition between the growth and annealing of the fuzz, and coverage of the surface with co-deposits.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Continental-Scale Controls on Hyporheic Respiration Revealed by Knowledge-Guided Machine Learning

Hyporheic zone sediments regulate organic matter turnover and in-stream respiration, yet controls on sediment respiration remain poorly constrained across heterogeneous river networks, limiting prediction of stream metabolism and carbon processing at continental scales. Here, we integrate observations from ~90 river corridors across the United States in the WHONDRS consortium with a knowledge-guided machine learning (KGML) framework that couples thermodynamic rate theory with machine learning to identify dominant controls on hyporheic respiration. Diagnostic analyses show that organic matter concentration and thermodynamic favorability define an upper bound on respiration potential, whereas biological catalytic capacity and physical accessibility jointly govern realized respiration rates through interaction effects. To represent unmeasurable accessibility constraints, we use the mechanistic model as a scaffold for KGML, allowing machine learning to target residual structure not explained by process theory. This hybrid framework improves predictive skill relative to both the mechanistic model alone and fully data-driven models while preserving interpretability. These results indicate that variability in hyporheic respiration is largely mechanistically structured and demonstrate how integrating process theory with explainable AI enhances predictive performance while enabling scalable synthesis of river corridor observations.

Zheng, Jianqiu↗