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At least 595 records · Page 33

Report on the AAPM grand challenge on deep generative modeling for learning medical image statistics

Abstract Background The findings of the 2023 AAPM Grand Challenge on Deep Generative Modeling for Learning Medical Image Statistics are reported in this Special Report. Purpose The goal of this challenge was to promote the development of deep generative models for medical imaging and to emphasize the need for their domain‐relevant assessments via the analysis of relevant image statistics. Methods As part of this Grand Challenge, a common training dataset and an evaluation procedure was developed for benchmarking deep generative models for medical image synthesis. To create the training dataset, an established 3D virtual breast phantom was adapted. The resulting dataset comprised about 108 000 images of size 512 512. For the evaluation of submissions to the Challenge, an ensemble of 10 000 DGM‐generated images from each submission was employed. The evaluation procedure consisted of two stages. In the first stage, a preliminary check for memorization and image quality (via the Fréchet Inception Distance [FID]) was performed. Submissions that passed the first stage were then evaluated for the reproducibility of image statistics corresponding to several feature families including texture, morphology, image moments, fractal statistics, and skeleton statistics. A summary measure in this feature space was employed to rank the submissions. Additional analyses of submissions was performed to assess DGM performance specific to individual feature families, the four classes in the training data, and also to identify various artifacts. Results Fifty‐eight submissions from 12 unique users were received for this Challenge. Out of these 12 submissions, 9 submissions passed the first stage of evaluation and were eligible for ranking. The top‐ranked submission employed a conditional latent diffusion model, whereas the joint runners‐up employed a generative adversarial network, followed by another network for image superresolution. In general, we observed that the overall ranking of the top 9 submissions according to our evaluation method (i) did not match the FID‐based ranking, and (ii) differed with respect to individual feature families. Another important finding from our additional analyses was that different DGMs demonstrated similar kinds of artifacts. Conclusions This Grand Challenge highlighted the need for domain‐specific evaluation to further DGM design as well as deployment. It also demonstrated that the specification of a DGM may differ depending on its intended use.

Radiology, Nuclear Medicine & Medical Imaging↗

Regulatory utility of physiologically based pharmacokinetic modeling for assessing food impact in bioequivalence studies: A workshop summary report

This workshop report summarizes the presentations and panel discussion related to the use of physiologically based pharmacokinetic (PBPK) modeling approaches for food effect assessment, collected from Session 2 of Day 2 of the workshop titled “Regulatory Utility of Mechanistic Modeling to Support Alternative Bioequivalence Approaches.” The US Food and Drug Administration in collaboration with the Center for Research on Complex Generics organized this workshop where this particular session titled “Oral PBPK for Evaluating the Impact of Food on BE” presented successful cases of PBPK modeling approaches for food effect assessment. Recently, PBPK modeling has started to gain popularity among academia, industries, and regulatory agencies for its potential utility during bioavailability (BA) and/or bioequivalence (BE) studies of new and generic drug products to assess the impact of food on BA/BE. Considering the promises of PBPK modeling in generic drug development, the aim of this workshop session was to facilitate knowledge sharing among academia, industries, and regulatory agencies to understand the knowledge gap and guide the path forward. This report collects and summarizes the information presented and discussed during this session to disseminate the information into a broader audience for further advancement in this area.

60 APPLIED LIFE SCIENCES↗

A practical approach to using the Genomic Standards Consortium MIxS reporting standard for comparative genomics and metagenomics

Comparative analysis of (meta)genomes necessitates aggregation, integration, and synthesis of well-annotated data using standards. The Genomic Standards Consortium (GSC) collaborates with the research community to develop and maintain the Minimal Information about any (x) Sequence (MIxS) reporting standard for genomic data. To facilitate use of the GSC’s MIxS reporting standard, we provide a description of the structure and terminology, how to navigate ontologies for required terms in MIxS, and demonstrate practical usage through a soil metagenome example.

standards, metadata, genome, metagenome, schema, v↗

Patient-Reported Outcomes in the Acute Phase of the Randomized Hypofractionated Irradiation for Prostate Cancer (HYPRO) Trial

Many patients experience bowel and bladder toxicity during the acute phase of radiation therapy for prostate cancer. Recent literature indicates that hypofractionation (HF) might increase this acute response but little is known on patient-reported outcome during this phase with HF. We evaluated the course of patient-reported acute symptoms during HF versus standard fractionated (SF) radiation therapy within the hypofractionated irradiation for prostate cancer (HYPRO) trial.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Association of Short-term Patient-reported Outcomes With Long-term Oncologic Outcomes in Localized Prostate Cancer Patients Treated With Radiation Therapy and Androgen Deprivation Therapy in a Randomized Controlled Trial

Both oncologic outcomes and patient-reported outcomes are pivotal in prostate cancer (PCa). However, it remains unknown if there is any association between these 2 outcomes. In this secondary analysis of a randomized controlled trial, we investigated the association of short-term changes in patient-reported outcome with long-term event-free survival (EFS) and metastasis-free survival (MFS) in localized PCa.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Recommendations to standardize reporting, execution and interpretation of STEM/TEM measurements

In July of 2022, a National Science Foundation (NSF)- and US Department of Energy (DOE)-sponsored workshop was held on the topic of rigor and reproducibility (R&R) in thermal, heterogeneous catalysis. A report has been published entitled “Addressing Rigor and Reproducibility in Thermal, Heterogeneous Catalysis” as a result of the workshop [1]. This manuscript attempts to summarize one section of the report entitled Recommendations for catalyst characterization by transmission electron microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Science Requirements and Detector Concepts for the Electron-Ion Collider: EIC Yellow Report

Here, this report describes the physics case, the resulting detector requirements, and the evolving detector concepts for the experimental program at the Electron-Ion Collider (EIC). The EIC will be a powerful new high-luminosity facility in the United States with the capability to collide high-energy electron beams with high-energy proton and ion beams, providing access to those regions in the nucleon and nuclei where their structure is dominated by gluons. Moreover, polarized beams in the EIC will give unprecedented access to the spatial and spin structure of the proton, neutron, and light ions. The studies leading to this document were commissioned and organized by the EIC User Group with the objective of advancing the state and detail of the physics program and developing detector concepts that meet the emerging requirements in preparation for the realization of the EIC. The effort aims to provide the basis for further development of concepts for experimental equipment best suited for the science needs, including the importance of two complementary detectors and interaction regions. This report consists of three volumes. Volume I is an executive summary of our findings and developed concepts. In Volume II we describe studies of a wide range of physics measurements and the emerging requirements on detector acceptance and performance. Volume III discusses general-purpose detector concepts and the underlying technologies to meet the physics requirements. These considerations will form the basis for a world-class experimental program that aims to increase our understanding of the fundamental structure of all visible matter.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Fluorescence-Enabled Self-Reporting for Redox Flow Batteries

Monitoring battery health is challenging. Self-reporting enables the rapid health assessment of redox flow batteries (RFBs) and provides insight into degradation mechanisms of electrochemically active molecules (redoxmers). In this study, we introduce fluorescence as an orthogonal property to probe this chemistry in situ. An established anolyte redoxmer, 2,1,3-benzothiadiazole, is rendered an efficient blue-green fluorophore through minimalistic derivatization. One of the derivatives is electrochemically reversible with a long lifetime and cycling stability in the charged state. Spectroscopic measurements on this new redoxmer reveal strong effects of the electrolyte cation on the fluorescence that are useful for probing the solvent microenvironment. Using this probe, we demonstrate proof-of-concept in situ crossover sensing and characterize the effects of electrolyte composition on this crossover. In this way, real-time tracing of redoxmers in a flow cell is demonstrated, paving the way to include still more self-reporting functions into the redoxmers.

25 ENERGY STORAGE↗

A Guide to Using GitHub for Developing and Versioning Data Standards and Reporting Formats

Abstract Data standardization combined with descriptive metadata facilitate data reuse, which is the ultimate goal of the Findable, Accessible, Interoperable, and Reusable (FAIR) principles. Community data or metadata standards are increasingly created through an approach that emphasizes collaboration between various stakeholders. Such an approach requires platforms for collaboration on the development process that centers on sharing information and receiving feedback. Our objective in this study was to conduct a systematic review to identify data standards and reporting formats that use version control for developing data standards and to summarize common practices, particularly in earth and environmental sciences. Out of 108 data standards and reporting formats identified in our review, 32 used GitHub as the version control platform, and no other platforms were used. We found no universally accepted methodology for developing and publishing data standards. Many GitHub repositories did not use key features that could help developers to gather user feedback, or to create and revise standards that build on previous work. We provide guidance for community‐driven standard development and associated documentation on GitHub based on a systematic review of existing practices.

54 ENVIRONMENTAL SCIENCES↗

Comparative Analysis of Report-Back of Research Results Strategies for Personal Chemical Exposure Data

Background. Report-back of research results (RBRR) is ethically supported and highly requested by participants yet lacks broadly transferable guidelines for RBRR. Effective RBRR must be responsive to target audience needs and may not be addressed by a ‘one-size-fits-all’ approach. Objective. Within a subset of our 19 studies on RBRR, we had the unique opportunity to carry out a comparative analysis of RBRR strategies across cohorts with similar development and evaluation methods, yet distinct in life stage, geography, number and type of chemicals assessed, and community contexts. Methods. We highlight key outcomes from three environmental health studies: an ongoing New York, NY cohort (Fair Start; n=486) and a Detroit, MI cohort (CLEAR; n=34) assessing exposure to ambient urban pollution during pregnancy, and a longitudinal cohort in Houston, TX (Houston-3H) following Hurricane Harvey (n=312). Focus group and survey data were analyzed to identify lessons learned and explore how RBRR supports understanding of environmental health. Results. Commonalities emerged in RBRR development, design, organization, and data visualization, as well as in how RBRR can contribute to an understanding of health-environment connections. Differences included preferences for individual versus community level findings, as well as distinguishable contextual considerations. For pregnancy cohorts, messaging was framed with cultural sensitivity, and to avoid unintended consequences of parental guilt due to prenatal exposures. In the post-disaster Houston-3H study, participants requested additional transparency regarding sampling design and study rationale. Significance. All RBRR case studies reported chemicals without known regulatory or health guidelines, so results were contextualized within the study population. Participants across cohorts requested multi-study comparisons to better understand their results beyond their communities. While foundational RBRR elements (e.g. plain language, graphic organizers) may supersede cohort-specific differences, RBRR should be personalized to encompass perceptions of health across different life-stage, cultural, and environmental contexts.

Vogel, Taylor J.↗

Expanding the application of a UV-visible reporter for transient gene expression and stable transformation in plants

Abstract Green fluorescent protein (GFP) has been widely used for monitoring gene expression and protein localization in diverse organisms. However, highly sensitive imaging equipment, like fluorescence microscope, is usually required for the visualization of GFP, limitings its application to fixed locations in samples. A reporter that can be visualized in real-time regardless the shape, size and location of the target samples will increase the flexibility and efficiency of research work. Here, we report the application of a GFP-like protein, called eYGFPuv, in both transient expression and stable transformation, in two herbaceous plant species ( Arabidopsis and tobacco) and two woody plant species (poplar and citrus). We observed bright fluorescence under UV light in all of the four plant species without any effects on plant growth or development. eYGFPuv was shown to be effective for imaging transient expression in leaf and root tissues. With a focus on in vitro transformation, we demonstrated that the transgenic events expressing 1x eYGFPuv could be easily identified visually during the callus stage and the shoot stage, enabling early and efficient selection of transformants. Furthermore, whole-plant level visualization of eYGFPuv revealed its ubiquitous stability in transgenic plants. In addition, our transformation experiments showed that eYGFPuv can also be used to select transgenic plants without antibiotics. This work demonstrates the feasibility of utilizing 1x eYGFPuv in studies of gene expression and plant transformation in diverse plants.

59 BASIC BIOLOGICAL SCIENCES↗

Curation of a list of chemicals in biosolids from EPA National Sewage Sludge Surveys & Biennial Review Reports

Section 405(d) of the Clean Water Act requires the US Environmental Protection Agency to review sewage sludge regulations every two years to identify any additional pollutants that may occur in biosolids and to set regulations for pollutants identified in biosolids if sufficient scientific evidence shows they may harm human health or the environment. To date, EPA has conducted eight biennial reviews to identify chemical and microbial pollutants and three national sewage sludge surveys to identify pollutants and obtain concentration data for chemicals found in biosolids. Prior to 2021, there was inconsistent reporting of chemicals identified and EPA did not cumulatively track chemicals in biosolids. Through the efforts presented here, EPA produced a list of 726 chemicals and structure-based classes found in biosolids based on biennial reviews and national sewage sludge surveys. Summary statistics of concentration data are also reported for the 484 chemicals found in the three national sewage sludge surveys. The creation of the Biosolids List supports EPA in assessing the potential risk of chemical pollutants found in biosolids.

54 ENVIRONMENTAL SCIENCES↗

Summary report from the mini-conference on workforce development through research-based, plasma-focused activities

This report is a summary of the mini-conference on Workforce Development Through Research-Based, Plasma-Focused Science Education and Public Engagement held during the 2022 American Physical Society Division of Plasma Physics annual meeting. The motivation for organizing this mini-conference originates from recent studies and community-based reports highlighting important issues with the current state of the plasma workforce. Here, we summarize the main findings presented in the two speaker sessions of the mini-conference, the challenges, and recommendations identified in the discussion sessions and the results from a post-conference survey. Here, we further provide information on initiatives and studies presented at the mini-conference, along with references to further resources.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Volume III. DUNE far detector technical coordination

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay -- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. The Deep Underground Neutrino Experiment (DUNE) is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. Volume III of this TDR describes how the activities required to design, construct, fabricate, install, and commission the DUNE far detector modules are organized and managed. This volume details the organizational structures that will carry out and/or oversee the planned far detector activities safely, successfully, on time, and on budget. It presents overviews of the facilities, supporting infrastructure, and detectors for context, and it outlines the project-related functions and methodologies used by the DUNE technical coordination organization, focusing on the areas of integration engineering, technical reviews, quality assurance and control, and safety oversight. Because of its more advanced stage of development, functional examples presented in this volume focus primarily on the single-phase (SP) detector module.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Volume IV. The DUNE far detector single-phase technology

The preponderance of matter over antimatter in the early universe, the dynamics of the supernovae that produced the heavy elements necessary for life, and whether protons eventually decay -- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our universe, its current state, and its eventual fate. DUNE is an international world-class experiment dedicated to addressing these questions as it searches for leptonic charge-parity symmetry violation, stands ready to capture supernova neutrino bursts, and seeks to observe nucleon decay as a signature of a grand unified theory underlying the standard model. Central to achieving DUNE's physics program is a far detector that combines the many tens-of-kiloton fiducial mass necessary for rare event searches with sub-centimeter spatial resolution in its ability to image those events, allowing identification of the physics signatures among the numerous backgrounds. In the single-phase liquid argon time-projection chamber (LArTPC) technology, ionization charges drift horizontally in the liquid argon under the influence of an electric field towards a vertical anode, where they are read out with fine granularity. A photon detection system supplements the TPC, directly enhancing physics capabilities for all three DUNE physics drivers and opening up prospects for further physics explorations. The DUNE far detector technical design report (TDR) describes the DUNE physics program and the technical designs of the single- and dual-phase DUNE liquid argon TPC far detector modules. Volume IV presents an overview of the basic operating principles of a single-phase LArTPC, followed by a description of the DUNE implementation. Each of the subsystems is described in detail, connecting the high-level design requirements and decisions to the overriding physics goals of DUNE.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Evaluating algorithmic bias on biomarker classification of breast cancer pathology reports

Objectives: This work evaluated algorithmic bias in biomarkers classification using electronic pathology reports from female breast cancer cases. Bias was assessed across 5 subgroups: cancer registry, race, Hispanic ethnicity, age at diagnosis, and socioeconomic status. Materials and Methods: We utilized 594 875 electronic pathology reports from 178 121 tumors diagnosed in Kentucky, Louisiana, New Jersey, New Mexico, Seattle, and Utah to train 2 deep-learning algorithms to classify breast cancer patients using their biomarkers test results. We used balanced error rate (BER), demographic parity (DP), equalized odds (EOD), and equal opportunity (EOP) to assess bias. Results: We found differences in predictive accuracy between registries, with the highest accuracy in the registry that contributed the most data (Seattle Registry, BER ratios for all registries >1.25). BER showed no significant algorithmic bias in extracting biomarkers (estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2) for race, Hispanic ethnicity, age at diagnosis, or socioeconomic subgroups (BER ratio <1.25). DP, EOD, and EOP all showed insignificant results. Discussion: We observed significant differences in BER by registry, but no significant bias using the DP, EOD, and EOP metrics for socio-demographic or racial categories. This highlights the importance of employing a diverse set of metrics for a comprehensive evaluation of model fairness. Conclusion: A thorough evaluation of algorithmic biases that may affect equality in clinical care is a critical step before deploying algorithms in the real world. We found little evidence of algorithmic bias in our biomarker classification tool. Artificial intelligence tools to expedite information extraction from clinical records could accelerate clinical trial matching and improve care.

60 APPLIED LIFE SCIENCES↗

Critical assessment of the recent report on the gigaparsec-scale correlation of the orientations of large quasar groups

ABSTRACT Recently, it was reported that large quasar groups (LQGs) identified from the Sloan Digital Sky Survey (SDSS) data release seven catalogue are not randomly oriented but preferentially aligned or orthogonal over scales 1–2 Gpc. To confirm this claim, I reproduced the same LQG sample and performed Sobolev tests of uniformity on the LQG orientation axes in the redshift space. Contrary to the original report based on the bimodal distribution of the LQG position angles in the sky, I found no departure from uniformity in the distribution of the LQG orientation axes. I also examined whether the LQGs are physical structures using a statistically more reliable data set constructed from the SDSS data release 16 (DR16) large-scale structure (LSS) quasar catalogue. Considering the Gaussian primordial density fluctuations and shot noise, I estimated the mass density contrasts of the LQGs from the number counts of the DR16 LSS quasars and found that most of the LQGs do not trace statistically significant high-density regions. I conclude that the LQG sample is a collection of unphysical chance associations and should not be used for any cosmological studies.

Fujii, Hirokazu (ORCID:0000000161473512)↗

Scalable and Secure Power Outage Data Reporting: A Hexagonal Geospatial Approach

Power outages disrupt critical infrastructure and cause billions of dollars in economic losses annually in the United States. Accurate and granular outage reporting is vital for effective restoration and mitigation. This paper examines the integration of the Hexagonal Hierarchical Geospatial Indexing System (H3) to enhance power outage reporting, leveraging its uniform grid structure, scalable resolutions, and support for privacy-preserving analysis. Using high-resolution LandScan Global population data and K-anonymization techniques, this work achieves a balance between data granularity and privacy. Results show that lower privacy thresholds (e.g., K-anonymity = 2) enable higher resolution, while stricter thresholds (e.g., >15 people per hex) reduce granularity, potentially affecting localized responses. State-and county-level resolution case studies demonstrate H3’s adaptability and the trade-offs between precision and privacy. The proposed H3-based framework offers a scalable and efficient solution for geospatial data integration within the energy sector, such as outage data, aiding utilities and regulators in improving resilience and response efforts, particularly in disaster-prone regions.

Ahmad, Nasir [ORNL] (ORCID:0000000150677368)↗