Results for “data citations” — Page 3

DOE OSTI2024

Towards a RAG-based summarization for the Electron Ion Collider

Abstract The complexity and sheer volume of information — encompassing documents, papers, data, and other resources — from large-scale experiments demand significant time and effort to navigate, making the task of accessing and utilizing these varied forms of information daunting, particularly for new collaborators and early-career scientists.To tackle this issue, a Retrieval Augmented Generation (RAG)-based Summarization AI for EIC (RAGS4EIC) is under development. This AI-Agent not only condenses information but also effectively references relevant responses, offering substantial advantages for collaborators. Our project involves a two-step approach: first, querying a comprehensive vector database containing all pertinent experiment information; second, utilizing a Large Language Model (LLM) to generate concise summaries enriched with citations based on user queries and retrieved data. We describe the evaluation methods that use RAG assessments (RAGAs) scoring mechanisms to assess the effectiveness of responses. Furthermore, we describe the concept of prompt template based instruction-tuning which provides flexibility and accuracy in summarization. Importantly, the implementation relies on LangChain [1], which serves as the foundation of our entire workflow. This integration ensures efficiency and scalability, facilitating smooth deployment and accessibility for various user groups within the Electron Ion Collider (EIC) community. This innovative AI-driven framework not only simplifies the understanding of vast datasets but also encourages collaborative participation, thereby empowering researchers. As a demonstration, a web application has been developed to explain each stage of the RAG Agent development in detail. The application can be accessed athttps://rags4eic-ai4eic.streamlit.app.[A tagged version of the source code can be found inhttps://github.com/ai4eic/EIC-RAG-Project/releases/tag/AI4EIC2023_PROCEEDING.]

Instruments & Instrumentation↗

DOE OSTI2016

An Introduction to the FCRD Transmutation Fuels Handbook 2015

Transmutation of minor actinides such as Np, Am, and Cm in spent nuclear fuel is of international interest because of its potential for reducing the long-term health and safety hazards caused by the radioactivity of the spent fuel. For this reason, the DOE Fuel Cycle Research and Development (FCRD) Advanced Fuels Campaign (AFC) has been performing research on nuclear fuel technologies that could be used in conjunction with a future actinide transmutation mission. One important approach to transmutation involves incorporating the minor actinides into U-Pu-Zr alloys, which can be used as fuel in fast reactors. It is, therefore, important to understand the properties of U-Pu-Zr alloys. The Idaho National Laboratory has recently published a handbook intended to summarize key properties of these alloys for researchers. This handbook focuses on phases and key thermophysical properties of elements and alloys in the U-Pu-Zr system. It is envisioned as the first of a series, which will serve as a summary of current knowledge about important properties of transmutation fuels. Future volumes will include information about properties and materials not covered in the first edition, as well as updates to information in this edition of the handbook. The handbook is intended to serve two audiences. One audience is researchers, who may find it useful to know what has been measured, where it has been published, and what kinds of information are needed. A second audience is modelers, who need a concise summary of information about specific properties and the accuracy with which they are known. The two audiences have different needs, and the handbook is a compromise intended to be useful to both. Therefore, it includes summaries of research results and needs, but generally does not present the original data. It also includes numerous graphs and, where available, equations that provide convenient approximations to materials properties for modelers. It is important to understand that most of the equations provided in this handbook are derived by fitting polynomials to data and have no physical basis; while they can be used with caution for design studies, fuel modelers will probably want to use the original experimental data to develop or validate their own equations and/or models. Although the handbook includes some citations to research involving development of models, its primary focus is experimental data. Many of the measurements of the U-Pu-Zr system were made before 1980. Where possible, the handbook relies on previous reviews of experimental data rather than presenting new interpretations of the old information. It is expected that researchers will refer to the original literature for details that are not presented in the handbook. Metals and alloys in the U-Pu-Zr system are uniquely difficult to study for a number of reasons. Experimental designs may need to be modified to allow researchers to work with these hazardous materials safely. Kinetics of phase transformations are commonly sluggish, and it is highly unlikely that all of the samples in previous research had equilibrium phases and microstructures. Thermal cycling effects (changes in sample characteristics that are not fully reversed during cooling) are commonly reported and may be significant. Careful control of impurities (particularly oxygen) during sample fabrication and data collection is both crucial and difficult, and concentrations below 100 ppm in samples may significantly affect thermophysical properties. For all of these reasons, differences between measured values for similar alloys are commonly far larger than the estimated errors for individual measurements. Further research on well-characterized materials with careful control of impurities is needed for all of the alloys discussed here. The 2015 FCRD Handbook summarizes currently available information about U, Pu, Zr, and their binary and ternary alloys. It contains information about phase diagrams and related information (including phases and phase transformations); heat capacity, entropy, and enthalpy; thermal expansion; and thermal conductivity and diffusivity. In addition to presenting information about materials properties, it attempts to provide information about how well the property is known and how much variation exists between measurements. Although the handbook includes some references to publications about modeling, its primary focus is experimental data. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2022

A meta-analysis of semantic classification of citations

The aim of this literature review is to examine the current state of the art in the area of citation classification. In particular, we investigate the approaches for characterizing citations based on their semantic type. We conduct this literature review as a meta-analysis covering 60 scholarly articles in this domain. Although we included some of the manual pioneering works in this review, more emphasis is placed on the later automated methods, which use Machine Learning and Natural Language Processing (NLP) for analyzing the fine-grained linguistic features in the surrounding text of citations. The sections are organized based on the steps involved in the pipeline for citation classification. Specifically, we explore the existing classification schemes, data sets, pre-processing methods, extraction of contextual and non-contextual features, and the different types of classifiers and evaluation approaches. The review highlights the importance of identifying the citation types for research evaluation, the challenges faced by the researchers in the process, and the existing research gaps in this field.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2024

Ten simple rules for recognizing data and software contributions in hiring, promotion, and tenure

Not Available

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

KBase Credit Metadata Schema

As part of KBase’s commitment to promote open science, we offer users the ability to obtain a DOI (Digital Object Identifier) for their work, which can then be cited in an associated science publication. To further support the community-wide shift towards FAIR (Findable, Accessible, Interoperable, Reusable) data, KBase is expanding our data descriptors so that KBase DOIs have comprehensive citations for datasets, in addition to referencing publications or software used in the workflow. This helps encourage a culture of giving attribution for all research inputs and outputs; standard practice for literature, but still relatively new for software products or datasets. It also promotes open science by building trust that contributors get credit for their work, and accelerates knowledge discovery by supporting and incentivizing the release of data.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

DOE OSTI2022

U.S. Wind Siting Regulation and Zoning Ordinances

A machine readable collection of documented wind siting ordinances at the state and local (e.g., county, township) level throughout the United States. The data were compiled from several sources including, DOE's Wind Exchange Ordinance Database (Linked in the submission), National Conference of State and Legislatures Wind Energy Siting (also linked in the submission), and scholarly legal articles. The citations for each ordinance are included in the spreadsheet. This data is an updated to a previously developed database of wind ordinances found in OEDI Submission 1932: "U.S. Wind Siting Regulation and Zoning Ordinances"

analysis↗

DOE OSTI2024

Carbon Transport and Storage Planning and Viability Support Tools

The EDX disCO2ver Carbon Transport and Storage Planning and Viability Support Tools are made up of the Carbon Storage Planning Inquiry Tool (CS PlanIT, Justman et al. 2024) and the Carbon Storage Technical Viability Approach Support Tool (CS TVA). Together, these tools support data access to support understanding data availability to support planning efforts for carbon transport and storage. The Carbon Storage Planning Inquiry Tool (CS PlanIT) is an online web mapping application designed to help users explore, query, and evaluate multiple data layers to support and accelerate carbon storage resource and feasibility assessments and planning efforts. CS PlanIT currently contains a range of datasets associated with geologic, technical, and infrastructure factors. The data sets can be filtered geographically for an area of interest to update statistics and charts within the dashboard. The dashboard is divided into different sections called widgets, relating to different steps in the carbon storage planning process. The resources in this submission include a link to PlanIT, as well as a data catalog and link to user documentation. The original citation for the CS PlanIT tool, which has now been integrated into the toolset here, was: - Devin Justman, Scott Pantaleone, Maneesh Sharma, Lucy Romeo, Paige Morkner, CS PlanIT (Carbon Storage Planning Inquiry Tool) , 6/28/2024, https://edx.netl.doe.gov/dataset/cs-planit-carbon-storage-planning-inquiry-tool, DOI: 10.18141/2377953 The Carbon Storage Technical Viability Approach Support (CS TVA) Tool displays spatial data availability for the many components of Geologic Carbon Storage (GCS) technical viability assessment (Creason al 2025). Identifying sites suitable for GCS requires evaluating the intersection of myriad factors, including reservoir conditions, subsurface and surface hazards, infrastructure requirements, and energy community metrics. The technical viability of a site can only be confirmed for instances where all these factors have data available, and where those data support viability. Additional Resources related to the Technical Viability Assessment Tool: - Julia Mulhern, Casey White, Araceli Lara, Neyda Cordero Rodriguez, Zachary Jackson, Jacob Shay, Gabriel Creason, MacKenzie Mark-Moser, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Database, 3/26/2025, https://edx.netl.doe.gov/dataset/edx4ccs-carbon-storage-technical-viability-approach-database , DOI:10.18141/1984655 - Julia Mulhern, MacKenzie Mark-Moser, Gabriel Creason, Casey White, Araceli Lara, Neyda Cordero Rodriguez, Zach Jackson, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Matrix, 3/27/2025, https://edx.netl.doe.gov/dataset/carbon-storage-technical-viability-approach-cs-tva-matrix , DOI: 10.18141/2539979 - Gabriel Creason, Zach Jackson, Neyda Cordero Rodriguez, Julia Mulhern, Casey White, Araceli Lara, MacKenzie Mark-Moser, Paige Morkner, Kelly Rose, Carbon Storage Technical Viability Approach (CS TVA) Data Availability Results Database, 3/27/2025, https://edx.netl.doe.gov/dataset/carbon-storage-technical-viability-approach-cs-tva-data-availability-results-database, DOI:10.18141/2538557

Carbon storage↗

DOE OSTI2016

TH-C-204-00: Medical Physics Workshop: An Update On the Journal’s Improvement Activities and Guidance On Writing and Reviewing Papers

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-C-204-01: Vision for Medical Physics and Status of Current Initiatives

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-C-204-02: Improving Manuscript Quality Via Structured Reviews, Enhanced Scientific Category Taxonomy, and Outreach

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

TH-C-204-03: Writing Good Scientific Papers and Responding to Critiques

In this presentation, the Editors will outline our vision for the future of Medical Physics and review recent work-in-progress initiatives to implement this vision. Finally, we will close with guidance to authors on how to write a good Medical Physics paper. A major focus will be the transition to a new publisher in 2017 following a more than 40-year association with American Institute of Physics Publishing (AIPP). Vision for Medical Physics and status of current initiatives: Jeff Williamson, Editor-in-Chief The broad vision of Medical Physics is “to continue the Journal’s tradition of publishing the very best science that propels our discipline forward and improves our contribution to patient care.” More concretely, the Journal should be the preeminent forum for exchange of cutting edge medical physics science. We seek to identify the best contributions in (a) high impact clinical physics innovations; (b) clinical translation and validation of basic science innovations; and (c) cutting edge basic science developments with potential for patient care improvements. Among the challenges and opportunities, we face are: electronic-only and open access publishing; competition from new radiological science journals; trends towards more interactive, social-media based scientific communities; and diversification of the medical physics research, authorship, and readership domains, including clinical applications quite foreign to core ABR clinical competencies. Recently implemented and ongoing initiatives include: Revised Table of Contents (TOC) and more contemporary topical submission categories Structured review template in HTML format Comprehensive hierarchical taxonomy for identifying reviewer expertise Formal process for soliciting high quality and impact Review and Vision 20/20 Articles We have recruited four Review Article Co-editors: John Rowlands and Ingrid Reiser (imaging physics) and Joao Seco and Tim Zhu (therapy physics). The Co-Editors will identify timely topics and solicit high profile authors to submit review manuscripts. To submit an article, authors will need to work with an assigned Co-Editor to develop a mutually acceptable outline and abstract. 5) A new and exciting class of articles: Medical Physics Dataset Articles (MPDAs) MPDAs describe scientifically or clinically valuable open-access datasets with high potential for contributing to the research of medical physicists working on related problems. In contrast to Research Articles, MPDAs should not include hypothesis testing; or data analyses supporting generalizable conclusions. The publically accessible dataset must be permanently archived before the MPDA can be published. This initiative is being led by Joe Deasy. Update on new publisher transition: The transition of AAPM scientific publishing operations to a major publishing house is a major opportunity to expand Medical Physics readership and its scholarly impact. The advantages include: (a) common manuscript management and web hosting platforms for Medical Physics and its sister journal, JACMP; (b) greater than 4-fold expansion of subscribing institutions; and (c) resources to mount data-driven, highly targeted marketing campaigns to enhance citation and download rates. A transition update of this epochal development, which has only begun as of this writing (3/31/16), will be given. Improving manuscript quality via structured reviews, enhanced scientific category taxonomy, and outreach: Shiva Das, Therapy Physics Editor Medical Physics is committed to continuous improvement with the ultimate goal of improving the potential impact of accepted manuscripts. In order to do so, Medical Physics must be able to tap into important/emerging areas and be able to select high quality contributions consistently via discerning reviews. Improving the quality of reviews is crucial to selecting high quality manuscripts and also to improving manuscript impact via feedback in the review process. With this in mind, Medical Physics is in the process of: (a) fostering outreach to important areas that are currently underrepresented in Medical Physics; (b) implementing a structured template review form; and (c) implementing a comprehensive scientific category taxonomy to identify reviewers who are best suited to an article. Outreach efforts have begun to various scientific areas. Strategies to increase submissions from these areas will be discussed. As a consequence of this effort, a special issue on particle therapy is under development. A review template was implemented in late 2014 on a limited test basis. Based on reviewer feedback, the template was restructured and shortened to capture essential review elements. The restructured template is due to be released shortly. The new scientific category taxonomy is in the process of being deployed to reviewers and associate editors. Salient aspects of the structured review template and scientific category taxonomy will be discussed in this talk. Writing good scientific papers and responding to critiques: Mitch Goodsitt, Imaging Physics Editor The essential components of the abstract, introduction, methods, discussion and conclusion sections of manuscripts, as well as the desired writing style and style of the figures and tables will be reviewed. Publishable Medical Physics manuscripts must include clear and concise statements of the novelty and clinical and/or scientific importance of the authors’ work. Examples of novelty include: new technical solution to an important clinical problem; new generalizable knowledge; and first demonstration that an existing engineering solution solves a clinical problem. Please note that we encourage authors of recently published conference proceedings (e.g., SPIE, IEEE) papers on novel medical physics related work to submit more substantial versions of that work to our journal. All submissions must include: sufficient background information and rationale; enough detail for others to reproduce the authors’ work; sufficient statistical analysis to refute or validate the authors’ hypotheses; a description of how the present work compares to, is distinct from, and improves upon others’ work; and sections devoted to the limitations of the study and future directions. Writing should be polished. Poor wording, grammar and composition frustrate the review process. Our journal does not have copyeditors for revising manuscripts. When authors receive critiques from the referees and associate editor, the authors should provide a detailed point-by-point response to each comment. The authors’ rebuttal should include the text of the original criticism, the authors’ response, and a pasted copy of the modified text along with the line numbers in the revised article. The new text should be highlighted in a different font color in the revised submission. Following these recommendations will improve submissions and facilitate the review process.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2024

Data and scripts associated with a manuscript on a meta-analysis synthesizing stream biogeochemical response to wildfires across space and time (v2)

This data package is associated with the publication “Catchment characteristics modulate the influence of wildfires on nitrate and dissolved organic carbon in lotic systems across space and time: A meta-analysis” submitted to Global Biogeochemical Cycles (Cavaiani et al. 2025). This study uses meta-analytical techniques to evaluate the effect of wildfire on in-stream responses in burned and unburned watersheds. The study aims to provide additional insight into the range of responses and net influences that wildfires have on hydro-biogeochemistry across broad spatial scales, burn extents, and the persistence of water-quality change. This study compiles data and metadata from 18 total publications that includes 1) surface water geochemistry data (dissolved organic carbon; nitrate), 2) climate classifications, 3) year of the wildfire, 4) the time lag between when the fire occurred and when the sampling occurred, and 5) study design of the publication. In total, this meta-analysis draws data that spans 8 climate guilds, 3 biomes, 62 watersheds, and 20 unique wildfires. See Sites_meta_data.csv for citations of the papers used in this meta-analysis. All R scripts and the associated data can also be found on GitHub at This data package was originally published in March 2024. It was updated in April 2025 (v2; new and modified files). See the change history section in the readme for more details. This data package contains five primary folders that include the following: (1) inputs; (2) output for analysis; (3) initial plots; (4) R scripts; and (5) GIS data. The data package also contains a data dictionary (dd) that provides column header definitions and a file-level metadata (flmd) file that describes every file. The “inputs” folder contains a list of all publications identified during the formal web search and an indication of whether each publication was included in the final analysis. Additionally, it includes site-level metadata, catchment characteristics, and GIS data for all publications included in the final analysis. The “Output_for_analysis” folder contains all data frames and figures generated from each R script used for additional data analysis. The “initial_plots” folder includes all exploratory figures that will be included in a supplemental and figures that will be submitted with the manuscript for publication. The “R_scripts” folder contains the scripts that perform all the data manipulations, statistical analyses, and plots. The “gis_data” folder includes shape files for each fire included in this meta-analysis. This data package contains the following file types: csv, pdf, jpeg, cpg, dbf, prj, shp, shp.ea.iso.xml, shp.iso.xml, shx.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2019

A novel approach for characterizing the variability in mass–dimension relationships: results from MC3E

Abstract. Mass–dimension (m–D) relationships determining bulkmicrophysical properties such as total water content (TWC) and radarreflectivity factor (Z) from particle size distributions are used in bothnumerical models and remote sensing retrievals. The a and b coefficientsrepresenting m=aD b relationships, however, can vary significantlydepending on meteorological conditions, particle habits, the definition ofparticle maximum dimension, the probes used to obtain the data, techniquesused to process the cloud probe data, and other unknown reasons. Thus,considering a range of a,b coefficients may be more applicable for use innumerical models and remote sensing retrievals. Microphysical data collectedby two-dimensional optical array probes (OAPs) installed on the University ofNorth Dakota (UND) Citation aircraft during the Mid-latitude Continental ConvectiveClouds Experiment (MC3E) were used in conjunction with TWC data from aNevzorov probe and ground-based S-band radar data to determine a and busing a technique that minimizes the chi-square difference between the TWC andZ derived from the OAPs and those directly measured by a TWC probe andradar. All a and b values within a specified tolerance were regarded as equallyplausible solutions. Of the 16 near-constant-temperature flight legs analyzedduring the 25 April, 20 May, and 23 May 2011 events, the derived surfaces ofsolutions on the first 2 days where the aircraft-sampled stratiform cloudhad a larger range in a and b for lower temperature environments thatcorrespond to less variability in N(D), TWC, and Z for a flight leg.Because different regions of the storm were sampled on 23 May, differences inthe variability in N(D), TWC, and Z influenced the distribution ofchi-square values in the (a,b) phase space and the specified tolerance in away that yielded 2.8 times fewer plausible solutions compared to the flightlegs on the other dates. These findings show the importance of representingthe variability in a,b coefficients for numerical modeling and remotesensing studies, rather than assuming fixed values, as well as the need tofurther explore how these surfaces depend on environmental conditions inclouds containing ice hydrometeors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Temperature, Humidity, and Time-Lapse Video Data from the East River Watershed, Water Year 2024

A new version of this dataset is available at doi:10.15485/3001338 and is the first citation in the 'Related References' section. It is expands on this dataset by appending another water year of data collection and additional logger sites.This dataset contains time-lapse imagery and distributed measurements of air temperature, relative humidity, dew point, and soil temperature across the East River basin from 3 October 2023 to 12 August 2024. Instruments were deployed at 14 sites as part of the DOE Grant: Seasonal Cycles Unravel Mysteries of Missing Mountain Water organized by Jessica Lundquist (University of Washington), Rosemary Carroll (Desert Research Institute), and Ethan Gutmann (National Center for Atmospheric Research). The data are published to support studies of surface climate or hydrologic processes in complex terrain. Measurements were collected with low-cost data loggers installed 2 m high on evergreen trees or buried just below the soil surface. Time-lapse cameras were deployed at three sites. Imagery from sites AP BONUS and AP5 provides insight into large-scale seasonal snow cover variability. Imagery from site EL2 shows smaller-scale snow patterns across a nearby meadow.Dataset files are organized by site and variable (air measurements, ground measurements, or time-lapse video). Air and ground measurements are packaged in LoggerData.zip, and time-lapse imagery is compiled into short videos stored in TimelapseVideos.zip. File-level metadata contains details for each file included in the dataset. A data dictionary provides units and descriptions for column or row names in all files. The locations metadata file describes site characteristics, locations, and associated GPS methods.Dataset update 2025-03-03: Resolved header and datetime formatting inconsistencies within LoggerData.zip files KP1_Air, KP3_Air, KP3_Ground, KP6_Ground, AP3_Ground, AP4_Air, and AP6_Air.Dataset update 2025-11-18: Modified abstract and related references sections to include new version of dataset.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Deep-learning methods for contrast enhancement and artifact reduction in cryo-electron tomography: a systematic analysis of the state of the art and proposed improvements

Cryo-electron tomography (cryo-ET) has emerged as the preferred technique for visualizing the organization of macromolecular complexes in situ and resolving their structures at subnanometre resolution [Tegunov et al. (2021)View full citation, Nat. Methods, 18, 186–193]. Despite improvements in data quality as a result of advances in detector technology, microscope stability and stage precision, the analysis and interpretation of tomograms remains challenging due to a low signal-to-noise ratio and reconstruction artifacts stemming from experimental constraints in specimen tilt during data collection resulting in a missing wedge in the Fourier space. Recently, self-supervised deep-learning methods have been proposed for contrast enhancement and reduction of resolution anisotropy in reconstructed tomograms. Here, we evaluate several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions, with a focus on their performance on downstream tasks of template matching, subtomogram averaging and segmentation. We propose new training architectures and a loss function based on Fourier shell correlation that show improved performance over the standard U-Net with L1/L2 losses. We demonstrate our analysis on four diverse experimental datasets: purified 80S ribosomes, in situ Chlamydomonas reinhardtii, immature HIV-1 virus-like particles and INS-1E cells.

contrast enhancement↗

DOE OSTI2021

Pantropical Tree Sapwood Area Data, 1977 - 2015

This data package containsata synthesis of pantropical sapwood area as a function of tree size (height or DBH) for trees ranging in sizes 1 - 140 cm DBH and 6 - 44 m tall. Data span both natural tropical forests and plantations and rainfall gradients from deciduous dry tropical forests to everwet tropical forests, and come from the following countries: Queensland, Australia; Costa Rica; Panama; Sulawesi, Indonesia; Venezuela; Ecuador; Brazil; French Guiana; Bolivia. Three CSV files are included: SA_headers.csv: description of variables in the two files below SA.csv: tree size (DBH or height) sapwood area SA_references.csv: citation, bibliographic reference, and DOI for the published references from which data were extracted

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2012

Comparative analysis of LWR and FBR spent fuels for nuclear forensics evaluation

Some interesting issues are attributed to nuclide compositions of spent fuels from thermal reactors as well as fast reactors such as a potential to reuse as recycled fuel, and a possible capability to be manage as a fuel for destructive devices. In addition, analysis on nuclear forensics which is related to spent fuel compositions becomes one of the interesting topics to evaluate the origin and the composition of spent fuels from the spent fuel foot-prints. Spent fuel compositions of different fuel types give some typical spent fuel foot prints and can be estimated the origin of source of those spent fuel compositions. Some technics or methods have been developing based on some science and technological capability including experimental and modeling or theoretical aspects of analyses. Some foot-print of nuclear forensics will identify the typical information of spent fuel compositions such as enrichment information, burnup or irradiation time, reactor types as well as the cooling time which is related to the age of spent fuels. This paper intends to evaluate the typical spent fuel compositions of light water (LWR) and fast breeder reactors (FBR) from the view point of some foot prints of nuclear forensics. An established depletion code of ORIGEN is adopted to analyze LWR spent fuel (SF) for several burnup constants and decay times. For analyzing some spent fuel compositions of FBR, some coupling codes such as SLAROM code, JOINT and CITATION codes including JFS-3-J-3.2R as nuclear data library have been adopted. Enriched U-235 fuel composition of oxide type is used for fresh fuel of LWR and a mixed oxide fuel (MOX) for FBR fresh fuel. Those MOX fuels of FBR come from the spent fuels of LWR. Some typical spent fuels from both LWR and FBR will be compared to distinguish some typical foot-prints of SF based on nuclear forensic analysis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2021

ESS-DIVE guidelines for archiving terrestrial model data

This dataset contains supporting documents and images for ESS-DIVE terrestrial model data archiving guidelines.Terrestrial models are broadly defined as numerical models that couple both land dynamics and energy, water, carbon, or nutrient fluxes. We created these guidelines based on input from the U.S. Department of Energy’s Biological and Environmental Research land modeling community. The guidelines are intended to help modelers determine which components of their terrestrial model data associated with publication should be archived. Based on input from the land modeling community, the guidelines recommend archiving both model input and testing data, as well as code, script, and metadata. The guidelines also recommend archiving model data output, depending on the limitations set by data repositories. Lastly, we provide recommendations for bundling data files for publication as well as a discussion about tools that can facilitate model data archiving and reuse.This dataset is an archive of the associated GitHub repository for our model archiving guidelines (https://github.com/ess-dive-community/essdive-model-data-archiving-guidelines). The ‘README.pdf’ file gives a general introduction to the guidelines, and the ‘instructions.pdf’ file provides more detailed steps for following the guidelines. We also provide 2 figures in this data package: 1) a decision tree (model_data_guidelines_decision_tree.png) that can help users determine which components of their model data to archive. and 2) the ‘model_data_guidelines_flmd.png’ file depicts the different files that can be archived in addition to the model data itself. Lastly, we include 3 digitized tables from our associated manuscript and 3 CSV files with anonymized input from DOE scientists about the importance of different aspects of model data archiving from which we developed the guidelines.Dataset updates for v1.1.0: We updated this data package on 2021-11-22 in response to review comments on our related manuscript. In this update we removed one figure so that the model archiving guidelines are conveyed in text rather than an image. We updated the file-level metadata (FLMD) figure to be in accord with the most recent FLMD recommendations. We made minor edits to the README file to update the recommended citation and added two co-authors. We also added 6 new data files (3 are anonymized input from DOE scientists that helped to inform guidelines, and 3 are digitized tables from our manuscript.

54 ENVIRONMENTAL SCIENCES↗