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At least 505 records · Page 28

Prediction of histone post-translational modifications using deep learning

Abstract Motivation Histone post-translational modifications (PTMs) are involved in a variety of essential regulatory processes in the cell, including transcription control. Recent studies have shown that histone PTMs can be accurately predicted from the knowledge of transcription factor binding or DNase hypersensitivity data. Similarly, it has been shown that one can predict PTMs from the underlying DNA primary sequence. Results In this study, we introduce a deep learning architecture called DeepPTM for predicting histone PTMs from transcription factor binding data and the primary DNA sequence. Extensive experimental results show that our deep learning model outperforms the prediction accuracy of the model proposed in Benveniste et al. (PNAS 2014) and DeepHistone (BMC Genomics 2019). The competitive advantage of our framework lies in the synergistic use of deep learning combined with an effective pre-processing step. Our classification framework has also enabled the discovery that the knowledge of a small subset of transcription factors (which are histone-PTM and cell-type-specific) can provide almost the same prediction accuracy that can be obtained using all the transcription factors data. Availabilityand implementation https://github.com/dDipankar/DeepPTM. Supplementary information Supplementary data are available at Bioinformatics online.

Baisya, Dipankar Ranjan (ORCID:0000000267847359)↗

EARLY-STAGE DESIGN AND EVALUATION FOR NUCLEAR POWER PLANT CONTROL ROOM UPGRADES

As control rooms are modernized with new digital systems at nuclear power plants, it is necessary to evaluate operator performance with these systems as part of a verification and validation process. While there is regulatory and industry guidance for some modernization activities, there are no well defined standard processes or predefined metrics available for assessing what is satisfactory operator interaction with new systems, especially during the early design stages. This paper proposes a framework defining the design process and metrics for evaluating human system interfaces as part of control room modernization. The process and metrics are generalizable to other applications and serve as a guiding template for utilities undertaking their own control room modernization activities.

99 GENERAL AND MISCELLANEOUS↗

Managing time-substitutable electricity usage using dynamic controls

A predictive-control approach allows an electricity provider to monitor and proactively manage peak and off-peak residential intra-day electricity usage in an emerging smart energy grid using time-dependent dynamic pricing incentives. The daily load is modeled as time-shifted, but cost-differentiated and substitutable, copies of the continuously-consumed electricity resource, and a consumer-choice prediction model is constructed to forecast the corresponding intra-day shares of total daily load according to this model. This is embedded within an optimization framework for managing the daily electricity usage. A series of transformations are employed, including the reformulation-linearization technique (RLT) to obtain a Mixed-Integer Programming (MIP) model representation of the resulting nonlinear optimization problem. In addition, various regulatory and pricing constraints are incorporated in conjunction with the specified profit and capacity utilization objectives.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Managing time-substitutable electricity usage using dynamic controls

A predictive-control approach allows an electricity provider to monitor and proactively manage peak and off-peak residential intra-day electricity usage in an emerging smart energy grid using time-dependent dynamic pricing incentives. The daily load is modeled as time-shifted, but cost-differentiated and substitutable, copies of the continuously-consumed electricity resource, and a consumer-choice prediction model is constructed to forecast the corresponding intra-day shares of total daily load according to this model. This is embedded within an optimization framework for managing the daily electricity usage. A series of transformations are employed, including the reformulation-linearization technique (RLT) to obtain a Mixed-Integer Programming (MIP) model representation of the resulting nonlinear optimization problem. In addition, various regulatory and pricing constraints are incorporated in conjunction with the specified profit and capacity utilization objectives.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Managing time-substitutable electricity usage using dynamic controls

A predictive-control approach allows an electricity provider to monitor and proactively manage peak and off-peak residential intra-day electricity usage in an emerging smart energy grid using time-dependent dynamic pricing incentives. The daily load is modeled as time-shifted, but cost-differentiated and substitutable, copies of the continuously-consumed electricity resource, and a consumer-choice prediction model is constructed to forecast the corresponding intra-day shares of total daily load according to this model. This is embedded within an optimization framework for managing the daily electricity usage. A series of transformations are employed, including the reformulation-linearization technique (RLT) to obtain a Mixed-Integer Programming (MIP) model representation of the resulting nonlinear optimization problem. In addition, various regulatory and pricing constraints are incorporated in conjunction with the specified profit and capacity utilization objectives.

Ghosh, Soumyadip↗

The Renewable Fuel Standard May Limit Overall Greenhouse Gas Savings by Corn Stover-Based Cellulosic Biofuels in the U.S. Midwest: Effects of the Regulatory Approach on Projected Emissions

The Renewable Fuel Standard (RFS) program specifies a greenhouse gas (GHG) reduction threshold for cellulosic biofuels, while the Low Carbon Fuel Standard (LCFS) program in California does not. Here, we investigate the effects of the GHG threshold under the RFS on projected GHG savings from two corn stover-based biofuel supply chain systems in the United States Midwest. The analysis is based on a techno-economic framework that minimizes ethanol selling price. The GHG threshold lowers the lifecycle GHG of ethanol: 34.39 +/- 4.92 gCO(2) MJ(-1) in the RFS-compliant system and 46.30 +/- 10.05 gCO(2) MJ1 in the non RFS-compliant system. However, hypothetical biorefinery systems complying with the RFS will not process the more GHG-intensive corn stover, and thus much less biofuel will be produced compared to the non RFS-compliant system. Thus, taken as a whole, the non RFS-compliant system would achieve more GHG savings than an RFS-compliant system: 10.7 TgCO(2) year(-1) in the non RFS-compliant system compared with 4.4 TgCO(2) year1 in the RFS-compliant system. These results suggest that the current RFS GHG reduction threshold may not be the most efficient way to carry out the purposes of the Energy Security and Independence Act in the corn stover-based biofuel system: relaxing the threshold could actually increase the overall GHG savings from corn stover-based biofuels. Therefore, the LCFS-type regulatory approach is recommended for the corn stover-based cellulosic biofuel system under the RFS program. In addition, our calculation of the GHG balance for stover-based biofuel accounts for SOC losses, while the current RFS estimates do not include effects on SOC.

CARBON, BIOMASS, VOLUME↗

Assessment of coated cladding impact on large-break LOCA with TRACE-DAKOTA

Since 2011, the U.S. Department of Energy has launched new research and development (R&D) programs for developing new accident tolerant fuels (ATFs). These new fuel concepts are expected to bring several advancements in terms of plant safety. However, development, licensing, as well as deployment of ATF require a substantial investment among fuel vendors, operating utilities, and regulatory authorities. For ATF to be economically feasible, credited safety benefits may be necessary to provide an economic incentive for transition of nuclear power plants from Zr/UO2-based fuel technologies to ATFs. As a result, it is essential to evaluate the economic viability of ATF by conducting a comprehensive safety benefits study informed by R&D and demonstration studies. In the present work, based on the best estimate plus uncertainty methodology, sensitivity analysis and uncertainty quantification for key safety quantities under LB-LOCA are performed for the Peach Bottom boiling water reactor (BWR) with GE14 nuclear fuel design adopting the ATF concepts. A coupled TRACE-DAKOTA analysis framework is adopted to perform the uncertainty quantification. Based on the computational results and obtained statistics, the coping time increase, fuel performance improvement as well as the most dominating phenomena during the accident for Cr-coated cladding are investigated in detail. Overall, the results obtained are useful for subsequent plant PRA study and support a move to more modernized performance-based regulatory requirements to realize plant economic benefits.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

A Framework for Building Security into the Design Process

This report presents guidance to support the implementation of security objectives during the design process for nuclear facilities using an organization’s quality management system. The guidance in this document is intended for design vendors and operators of nuclear power facilities. Additionally, this guidance document can be beneficial to regulatory bodies, industry partners, customers, and other stakeholders within the nuclear power market. This report aims to ensure security consequences are identified before designs are completed, which may lead to reduced costs and higher security effectiveness and efficiency.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Framework for Building Security into the Design Process

This report presents guidance to support the implementation of security objectives during the design process for nuclear facilities using an organization’s quality management system. The guidance in this document is intended for design vendors and operators of nuclear power facilities. Additionally, this guidance document can be beneficial to regulatory bodies, industry partners, customers, and other stakeholders within the nuclear power market. This report aims to ensure security consequences are identified before designs are completed, which may lead to reduced costs and higher security effectiveness and efficiency.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Revolutionizing thermal Management in Next-Generation AI data centers: Challenges and breakthrough innovations

Data centers (DCs) serve as critical infrastructure for powering the growth and evolution of AI. Next-generation AI DCs present unique challenges in thermal management driven by unprecedented computational demands. This paper provides a comprehensive summary of key stakeholder perspectives on technology gaps, infrastructure requirements, test bed needs, emerging opportunities, and preliminary solutions related to thermal management for AI DCs. It establishes six strategic pillars of thermal management for next generation AI DC: reliability, deployability, efficiency, resilience, measurability, and valorization. The discussion spans a range of critical topics, including advanced cooling technologies, thermal strategies for emerging modular and edge DCs, system-level optimization and control frameworks, infrastructure planning and grid integration designs, benchmarking approaches, and pathways for waste heat recovery and reuse. The proposed research, development, and demonstration efforts are aimed at accelerating the deployment of AI DCs while ensuring energy efficiency, reliability, safety, and regulatory compliance.

Wang, Pengtao [ORNL] (ORCID:0000000214713429)↗

A systems genetics approach to deciphering the effect of dosage variation on leaf morphology in Populus

Abstract Gene copy number variation is frequent in plant genomes of various species, but the impact of such gene dosage variation on morphological traits is poorly understood. We used a large population of Populus carrying genomically characterized insertions and deletions across the genome to systematically assay the effect of gene dosage variation on a suite of leaf morphology traits. A systems genetics approach was used to integrate insertion and deletion locations, leaf morphology phenotypes, gene expression, and transcriptional network data, to provide an overview of how gene dosage influences morphology. Dosage-sensitive genomic regions were identified that influenced individual or pleiotropic morphological traits. We also identified cis-expression quantitative trait loci (QTL) within these dosage QTL regions, a subset of which modulated trans-expression QTL as well. Integration of data types within a gene co-expression framework identified co-expressed gene modules that are dosage sensitive, enriched for dosage expression QTL, and associated with morphological traits. Functional description of these modules linked dosage-sensitive morphological variation to specific cellular processes, as well as candidate regulatory genes. Together, these results show that gene dosage variation can influence morphological variation through complex changes in gene expression, and suggest that frequently occurring gene dosage variation has the potential to likewise influence quantitative traits in nature.

Biochemistry & Molecular Biology↗

NDE Reliability Issues for the Examination of CASS Components

The relatively low cost and corrosion resistance of cast austenitic stainless steel (CASS) materials resulted in their extensive use for piping systems in nuclear power plants (NPPs). However, CASS component welds are among the most challenging volumetric examinations required to be performed for detection of potential service degradation. Effective and reliable inspection methods for CASS materials are essential to achieving the objectives of defense-in-depth. A complicating issue is the presence of thermal aging embrittlement, a known degradation mechanism that occurs in CASS NPP materials. Further, while not as yet reported in CASS, many unforeseen instances of cracking in safety-related piping system welds have been experienced in other austenitic materials. Currently, a performance-based method to qualify NDE in CASS is not available. Pacific Northwest National Laboratory (PNNL) has performed nondestructive examination (NDE) research under the sponsorship of the U.S. Nuclear Regulatory Commission (NRC) for over four decades. A primary objective of the research has been to assess the effectiveness and reliability of conventional and advanced NDE methods for the inspection of light-water reactor components. One of the tasks being performed within this framework is to evaluate state-of-the-art technical approaches for examining safety-related nuclear reactor components that pose significant challenges to traditional NDE methods. A specific area of research in this regard is the volumetric examination of coarse-grained weldments and base materials. This report summarizes, compiles, and assesses relevant investigations performed by PNNL and other domestic and international organizations for welds adjacent to CASS components to provide a comprehensive evaluation on this subject. The primary objectives of the report are to assess the overall feasibility for advanced NDE methods to reliably and effectively examine field CASS piping components and to determine if techniques similar to those described in existing standards could be applied to develop performance demonstration requirements for CASS piping components. This report discusses improving the reliability of CASS examinations through the use of advanced low-frequency phased-array techniques, coupled with other “best practice” examination parameters, and makes recommendations for consideration by NRC Staff regarding the development of effective performance-based qualifications for CASS weldments. In addition to the PNNL research documented here, over 230 historical and more recent publications have been reviewed in the development of this document. The report is expected to be a useful resource for engineers and scientists involved in NDE of CASS for purposes of inservice inspection on existing plants during current and extended periods of operation. Finally, researchers and NDE practitioners conducting future investigations to advance the state-of-the-art should find the information contained in this report to be beneficial.

36 MATERIALS SCIENCE↗

Quality Assurance Framework Implementation Guide for Isolated Community Power Systems

This implementation guide is a companion document to the 'Quality Assurance Framework for Mini-Grids' technical report. This document is intended to be used by one of the many stakeholder groups that take part in the implementation of isolated power systems. Although the QAF could be applied to a single system, it was designed primarily to be used within the context of a larger national or regional rural electrification program in which many individual systems are being installed. This guide includes a detailed overview of the Quality Assurance Framework and provides guidance focused on the implementation of the Framework from the perspective of the different stakeholders that are commonly involved in expanding energy development within specific communities or regions. For the successful long-term implementation of a specific rural electrification program using mini-grid systems, six key stakeholders have been identified that are typically engaged, each with a different set of priorities 1. Regulatory agency 2. Governmental ministry 3. System developers 4. Mini-utility 5. Investors 6. Customers/consumers. This document is broken into two distinct sections. The first focuses on the administrative processes in the development and operation of community-based mini-grid programs, while the second focuses on the process around the installation of the mini-grid project itself.

24 POWER TRANSMISSION AND DISTRIBUTION↗

An allosteric photoredox catalyst inspired by photosynthetic machinery

Biological photosynthetic machinery allosterically regulate light harvesting via conformational and electronic changes at the antenna protein complexes as a response to specific chemical inputs. Fundamental limitations in current approaches to regulating inorganic light-harvesting mimics prevent their use in catalysis. Here we show that a light-harvesting antenna/reaction centre mimic can be regulated by utilizing a coordination framework incorporating antenna hemilabile ligands and assembled via a high-yielding, modular approach. As in nature, allosteric regulation is afforded by coupling the conformational changes to the disruptions in the electrochemical landscape of the framework upon recognition of specific coordinating analytes. The hemilabile ligands enable switching using remarkably mild and redox-inactive inputs, allowing one to regulate the photoredox catalytic activity of the photosynthetic mimic reversibly and in situ . Furthermore, we demonstrate that bioinspired regulatory mechanisms can be applied to inorganic light-harvesting arrays displaying switchable catalytic properties and with potential uses in solar energy conversion and photonic devices.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

How to implement security controls for an information security program at CBRN facilities

This document was prepared by PNNL within the framework of Project 19 of the European Union Chemical Biological Radiological and Nuclear Risk Mitigation Centres of Excellence Initiative entitled, ''Development of procedures and guidelines to create and improve secure information management systems and data exchange mechanisms for CBRN materials under regulatory control.'' It provides management and workers at CBRN facilities, parent organization managers responsible for those facilities, and regulatory agencies (governmental and nongovernmental) with guidance on the best practices for protecting information security. The security mitigation approaches presented in this document were chosen because they present generally accepted guidance in an easy-to-understand manner, making it easier for facility personnel to grasp key concepts and envision how security controls could be implemented by the facility. This guidance is presented from a risk management perspective.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

MELCOR Computer Code Manuals Volume 1: Primer and Users' Guide

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications.

97 MATHEMATICS AND COMPUTING↗

MELCOR Computer Code Manuals

MELCOR is a fully integrated, engineering-level computer code that models the progression of severe accidents in light water reactor nuclear power plants. MELCOR is being developed at Sandia National Laboratories for the U.S. Nuclear Regulatory Commission as a second-generation plant risk assessment tool and the successor to the Source Term Code Package. A broad spectrum of severe accident phenomena in both boiling and pressurized water reactors is treated in MELCOR in a unified framework. These include thermal-hydraulic response in the reactor coolant system, reactor cavity, containment, and confinement buildings; core heatup, degradation, and relocation; core-concrete attack; hydrogen production, transport, and combustion; fission product release and transport behavior. Current uses of MELCOR include estimation of severe accident source terms and their sensitivities and uncertainties in a variety of applications.

97 MATHEMATICS AND COMPUTING↗

Come Hell or High-Water: Challenges for Adapting Pacific Northwest Water Law

The Pacific Northwest region of the United States has been recognized as a leader in crafting water laws that work to balance human needs and ecological considerations. However, this region is experiencing changing dynamics that test the strength of existing water policies and laws. Such dynamics include increasing populations, new and exempt uses, quantification of tribal treaty rights, species protection, renegotiation of the Columbia River Treaty, and the impacts of a changing climate. Together, these dynamics are stressing the legal framework, which remains vital to ensuring sustainable water supplies now and into the future. Here, the history behind water resources management in Oregon, Washington, Idaho, and Montana provides the foundation for the laws in place today. Although all four states share regulatory features, nuances specific to each state have tremendously affected their governance structures and ability to adapt to changing dynamics. Although a challenge to meet these changing dynamics, collaborative efforts offer creative opportunities for meeting current and future needs.

99 GENERAL AND MISCELLANEOUS↗