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At least 19 records

Online Interactive Platform for COVID-19 Literature Visual Analytics: Platform Development Study

Background Papers on COVID-19 are being published at a high rate and concern many different topics. Innovative tools are needed to aid researchers to find patterns in this vast amount of literature to identify subsets of interest in an automated fashion. Objective We present a new online software resource with a friendly user interface that allows users to query and interact with visual representations of relationships between publications. Methods We publicly released an application called PLATIPUS (Publication Literature Analysis and Text Interaction Platform for User Studies) that allows researchers to interact with literature supplied by COVIDScholar via a visual analytics platform. This tool contains standard filtering capabilities based on authors, journals, high-level categories, and various research-specific details via natural language processing and dozens of customizable visualizations that dynamically update from a researcher’s query. Results PLATIPUS is available online and currently links to over 100,000 publications and is still growing. This application has the potential to transform how COVID-19 researchers use public literature to enable their research. Conclusions The PLATIPUS application provides the end user with a variety of ways to search, filter, and visualize over 100,00 COVID-19 publications.</:p>

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

MaTableGPT: GPT‐Based Table Data Extractor from Materials Science Literature

Abstract Efficiently extracting data from tables in the scientific literature is pivotal for building large‐scale databases. However, the tables reported in materials science papers exist in highly diverse forms; thus, rule‐based extractions are an ineffective approach. To overcome this challenge, the study presents MaTableGPT, which is a GPT‐based table data extractor from the materials science literature. MaTableGPT features key strategies of table data representation and table splitting for better GPT comprehension and filtering hallucinated information through follow‐up questions. When applied to a vast volume of water splitting catalysis literature, MaTableGPT achieves an extraction accuracy (total F1 score) of up to 96.8%. Through comprehensive evaluations of the GPT usage cost, labeling cost, and extraction accuracy for the learning methods of zero‐shot, few‐shot, and fine‐tuning, the study presents a Pareto‐front mapping where the few‐shot learning method is found to be the most balanced solution owing to both its high extraction accuracy (total F1 score >95%) and low cost (GPT usage cost of 5.97 US dollars and labeling cost of 10 I/O paired examples). The statistical analyses conducted on the database generated by MaTableGPT revealed valuable insights into the distribution of the overpotential and elemental utilization across the reported catalysts in the water splitting literature.

Yi, Gyeong Hoon [Computational Science Research Ce↗

Emerging Pathways to Upgrade the US Housing Stock: A Review of the Home Energy Upgrade Literature

The residential buildings sector is responsible for about 20% of total US energy use. In order to achieve climate goals, we need ways to reduce carbon emissions and energy use in this sector. In addition, resiliency, electric grid stability, emergency survivability and other energy and building-related issues are becoming increasingly important challenges. New homes in most of the US meet various energy codes and are reasonably energy efficient. However, the vast majority of energy use is from existing homes that were not required to conform to energy performance requirements. It is becoming imperative to reach as many of these existing homes as possible and find ways to improve their energy-related performance. This must be done in such a way that it meets the needs and desires of homeowners and building occupants, as well as those of the contractors and design professionals engaged in doing the upgrades themselves. Energy retrofits of homes started in the 1970’s in response to the energy crisis, however, these retrofits were very limited in scope and relatively few homes were upgraded. Those homes that have been upgraded generally still have much scope for improvement. A huge effort is needed to get to scale to address the energy use in housing. The target population is effectively every home in the country, whether a large suburban single-family home, or a small downtown apartment. In order to provide a framework for analysis and the basis for plans to get to large-scale retrofits of homes, this literature review summarizes the state-of-the art in the US buildings industry. It identifies where more research, engineering, or technology is needed, as well as relevant industry trends, such as electrification, one-stop shop program design and others. It also examines other key topics, such as availability of financing, minimizing household disruption, and engaging home owners and occupants. This literature review builds on a similar review from several years ago (Less and Walker, 2014). The current review focuses on efforts in the intervening years. This literature review is part of a larger DOE study of deep energy upgrades that includes industry surveys and development of cost-stack analyses. For this review, we gathered data not just from the published literature, but also from practitioners in conjunction with other aspects of the larger DOE study. In some cases, we refer to comments from specific individuals or companies, or refer to specific products by name. This is not intended as an endorsement, but rather to provide clarity on sources of information and examples of relevant technologies.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Ultraviolet Germicidal Irradiation for Heating, Ventilation, and Air Conditioning: Literature Review

Ultraviolet germicidal irradiation (UVGI) remains the only ASHRAE-recognized technology for the effective disinfection of air and surfaces, yet the technology still faces barriers to adoption. Even so, there is a growing body of literature on the subject, somewhat due the possibilities that a technology that can disinfect from a distance presents but also because the technology has been known for some time. Recent interest in the technology has been driven by the COVID-19 pandemic, increasing the rate of growth of the literature. This document attempts to provide an overview of the technology and map out the various important parts of the literature, including potential sources of literature.

60 APPLIED LIFE SCIENCES↗

Gulf of Mexico Offshore Wind Transmission - Literature Review and Gaps Analysis: Environmental Considerations, Community Readiness, and Infrastructure

The ability to effectively and efficiently connect offshore wind energy resources to end users in the Gulf of Mexico, requires coordinated transmission planning to ensure that electric transmission facilities can adequately support future offshore development. The Gulf of Mexico has substantial wind resources in both shallow shelf waters and deeper waters off the shelf where fixed bottom and floating wind technologies would be most appropriate. Most interest in offshore wind development to date has been in the central and western portions of the Gulf of Mexico (Louisiana and Texas) in federal and state waters. As a companion study to other federal activities in the offshore wind transmission space, including the Atlantic Offshore Wind Transmission Literature Review and Gaps Analysis, the Atlantic Offshore Wind Transmission Study, the West Coast Offshore Wind Transmission Literature Review and Gaps Analysis, the West Coast Offshore Wind Transmission Study, and the Advancing Offshore Wind Energy in the United States: U. S. Department of Energy Strategic Contributions Toward 30 Gigawatts and Beyond Report, this literature review and gaps analysis for offshore wind transmission in the Gulf of Mexico builds off previous literature reviews and supports the role of federal leadership to facilitate offshore wind energy. The overarching goal of this document is to identify gaps and lay the groundwork to inform coordinated transmission planning, ocean co-use, existing energy infrastructure, and siting associated with offshore wind energy development in the Gulf of Mexico. There are unique regional considerations for offshore wind transmission, which are summarized herein based on a review and assessment of publicly available information.

08 HYDROGEN↗

Towards a machine-readable literature: finding relevant papers based on an uploaded powder diffraction pattern

A prototype application for machine-readable literature is investigated. The program is called pyDataRecognition and serves as an example of a data-driven literature search, where the literature search query is an experimental data set provided by the user. The user uploads a powder pattern together with the radiation wavelength. The program compares the user data to a database of existing powder patterns associated with published papers and produces a rank ordered according to their similarity score. The program returns the digital object identifier and full reference of top-ranked papers together with a stack plot of the user data alongside the top-five database entries. The paper describes the approach and explores successes and challenges.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DancePartner: Python Package to Mine Multiomics Relationship Networks from Literature and Databases

A goal of multi-omics experiments is to understand how mechanistic molecular biology is altered between conditions, typically a control group and experimental groups. Oftentimes this involves studying changes in biomolecule relationships (e.g. interactions, metabolic relationships) of several types of biomolecules (e.g. proteins, lipids, metabolites). Though several databases contain relationships between biomolecules, understudied species may have little to no relationship information in databases and thus must be mined from literature. There are several challenges to literature mining, including automated full-text extraction, duplicate biomolecule term collapsing, and implementing complex machine learning tools. To make relationship extraction more accessible to the community, a python package called DancePartner was developed to allow for the extraction of relationships from literature and databases, with functions to map biomolecule synonyms to standardized identifiers and visualize and characterize the resulting multi-omics network. Here, in this study, an example dataset involving Caenorhabditis elegans is presented, where relationships are mined from 1443 publications using DancePartner. These relationships are combined with relationships from KEGG, WikiPathways, UniProt, and LipidMaps, and visualized.

BERT↗

Literature Data on Foam Fracturing Fluid

At the beginning of this project, the Temple team spent significant effort to collect data relevant to foam fracturing. More than 40 articles/reports were found in the open literature that reported the properties of aqueous foams under various testing conditions. The foam properties included viscosity and stability in terms of half-life, while were influenced by the foam quality, shear rate, temperature, pressure, as well as surfactants and additives used in making the foam base solutions. As a result, more than 1100 data points were collected, which are included in a master worksheet named "Literature data on Foam Fracturing Fluid". These data points are organized based on following parameters: 1. Literature source, including authors and publication year 2. Gaseous phase (e.g. CO2, N2) 3. Liquid phase (e.g. tap water, DI water, salt water) 4. Surfactants and their concentrations 6. Additives 7. Foam quality 8. Pressure 9. Temperature 10. Viscosity 11. Foam stability, which was characterized by its half-life: Half-life Foam study data base with data analysis was completed and a webpage is designed hosted on public server at https://surfactant-dashboard.herokuapp.com

15 GEOTHERMAL ENERGY↗

Deep learning of electrochemical CO 2 conversion literature reveals research trends and directions

Large-scale and openly available material science databases are mainly composed of computer simulation results rather than experimental data. Some examples include the Materials Project, Open Quantum Materials Database, and Open Catalyst 2022. Unfortunately, building large-scale experimental databases remains challenging due to the difficulties in consolidating locally distributed datasets. In this work, focusing on the catalysis literature of CO 2 reduction reactions (CO 2 RRs), we present a machine learning (ML)-based protocol for selecting highly relevant papers and extracting important experimental data. First, we report a document embedding method (Doc2Vec) for collecting papers of greatest relevance to the specific target domain, which yielded 3154 CO 2 RR-related papers from six publishers. Next, we developed named entity recognition (NER) models to extract twelve entities related to material names (catalyst, electrolyte, etc.) and catalytic performance (Faradaic efficiency, current density, etc.). Further, among several tested models, the MatBERT-based approach achieved the highest accuracy, with an average F1-score of 90.4% and an F1-score of 95.2% in a boundary relaxation evaluation scheme. The accurate and accelerated NER-based data extraction from a large volume of catalysis literature enables temporal trend analyses of the CO 2 RR catalysts, products, and performances, revealing the potentially effective material space in CO 2 RRs. While this work demonstrates the effectiveness of our ML-based text mining methods for specifically CO 2 RR literature, the methods and approach are applicable to and may be used to accelerate the development of other catalytic chemical reactions.

36 MATERIALS SCIENCE↗

Copy number variation in pituitary stalk interruption syndrome: A large case series of sporadic non‐syndromic patients and literature review

Abstract Abnormal hypothalamic/posterior pituitary development appears to be a major determinant of pituitary stalk interruption syndrome (PSIS). The observation of familial cases and associated congenital abnormalities suggests a genetic basis. Single‐gene mutations explain less than 5% of the cases, and whole exome sequencing has shown heterogeneous results. The present study aimed to assess copy number variation (CNV) using array‐based comparative genomic hybridization (aCGH) in patients with non‐syndromic PSIS and comprehensively review data from the literature on CNV analysis in congenital hypopituitarism (CH) patients. Twenty‐one patients with sporadic CH from our outpatient clinics presented with ectopic posterior pituitary (EPP) and no central nervous system abnormalities on magnetic resonance image (MRI) or any other malformations on physical examination at presentation were enrolled in the study. aCGH using a whole‐genome customized 400K oligonucleotide platform was performed in our patients. For the literature review, we searched for case reports of patients with CH and CNV detected by either karyotype or aCGH reported in PubMed up to November 2021. Thirty‐five distinct rare CNVs were observed in 18 patients (86%) and two of them (6%) were classified as pathogenic: one deletion of 1.8 Mb in chromosome 17 (17q12) and one deletion of 15 Mb in chromosome 18 (18p11.32p11.21), each one in a distinct patient. In the literature review, 67 pathogenic CNVs were published in 83 patients with CH, including the present study. Most of these patients had EPP (78% out of the 45 evaluated by sellar MRI) and were syndromic (70%). The most frequently affected chromosomes were X, 18, 20 and 1. Our study has found that CNV can be a mechanism of genetic abnormality in non‐syndromic patients with CH and EPP. In future studies, one or more genes in those CNVs, both pathogenic and variant of uncertain significance, may be considered as good candidate genes.

Correa‐Silva, Silvia R.↗

Literature Review and Experimental Observations of the Effects of Salinity, Hardness, Lithology, and ATBS Content on HPAM Polymer Retention for the Milne Point Polymer Flood

Summary At the Milne Point polymer flood (North Slope of Alaska), polymer retention is dominated by the clay, illite. Illite, and kaolinite cause no delay in polymer propagation in Milne Point core material, but they reduce the effective polymer concentration and viscosity by a significant amount (e.g., 30%), thus reducing the efficiency of oil displacement until the full injected polymer concentration is regained [which requires several pore volumes (PVs) of throughput]. This work demonstrates that polymer retention on illite is not sensitive to monovalent ion concentration, but it increases significantly with increased divalent cation concentration. The incorporation of a small percentage of acrylamido tertiary butyl sulfonic acid (ATBS) monomers into hydrolyzed polyacrylamide (HPAM) polymers is shown to dramatically reduce retention. The results are discussed in context with previous literature reports. Bridging adsorption was proposed as a viable mechanism to explain our results. Interestingly, an extensive literature review reveals that polymer retention (on sands and sandstones) is typically only modestly sensitive to the presence of oil. Extensive examination of the literature on inaccessible pore volume (IAPV) suggests the parameter was commonly substantially overestimated, especially in rock/sand more permeable than 500 md (which comprises the vast majority of existing field polymer floods).

Engineering↗

Understanding the TiH (2-x) /TiO y System at Elevated Temperature: A Literature Review

Titanium hydride of varying TiH stoichiometry is used in pyrotechnic compositions. In order to yield consistent performance, manufacturing processes must be developed to ensure precise and reproducible material properties, including composition and morphology. Legacy synthesis protocols are not comprehensive nor are the required apparatuses still available. To guide the development of novel production procedures, this report reviews literature on relevant chemical reactions and diffusion events occurring at elevated temperature in the TiH (2-x) /TiO y system. Titanium hydride exposed to air spontaneously forms a passivating oxide layer. Upon heating, significant hydrogen release, which is accompanied by changes to the surface oxide layer, is noted by 375–400°C. At higher temperatures (above about 500°C) the oxide layer is reported to be essentially nonexistent as a result of oxide-layer dissolution processes and, potentially, oxide-layer reduction due to water formation. Based on the reviewed literature, we hypothesize that, by 500°C, the surface layer consists of an oxyhydride phase, which is a solid solution of oxygen in titanium hydride. We believe that hydrogen release from titanium hydride is controlled by the kinetics of molecular hydrogen desorption on the oxyhydride surface. No literature data is available for corresponding activation energies of the dynamic desorption process, and the equilibrium phase diagram of this three-component system remains largely unexplored as well. These gaps in knowledge might be addressed through coordinated computational modeling and experimental efforts.

36 MATERIALS SCIENCE↗

Research on Remote and Hybrid Scientific Work: A Literature Review

This literature review is divided into two parts. The first part looks at new developments and emerging research specifically related to remote work since the start of the COVID-19 pandemic. This encompasses research and reporting on the impacts of COVID-19 on the workplace, more speculative writing on the possible future of remote and hybrid work, and impacts of remote work during COVID-19 for diversity, equity, and inclusion. The second part focuses on more fundamental research done on remote collaboration and remote work tools prior to COVID-19, which addresses in more detail how different types, aspects, or stages of work can best be supported using virtual collaboration tools. In both sections, we review literature that directly focuses on remote scientific collaboration, which is somewhat limited, as well as the broader literature on remote and hybrid work, which is relevant to a wide variety of workplaces, including scientific ones.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Literature Review of Electromagnetic Pulse (EMP) and Geomagnetic Disturbance (GMD) Effects on Oil and Gas Pipeline Systems

This document summarizes the findings of a review of published literature regarding the potential impacts of electromagnetic pulse (EMP) and geomagnetic disturbance (GMD) phenomena on oil and gas pipeline systems. The impacts of telluric currents on pipelines and their associated cathodic protection systems has been well studied. The existing literature describes implications for corrosion protection system design and monitoring to mitigate these impacts. Effects of an EMP on pipelines is not a thoroughly explored subject. Most directly related articles only present theoretical models and approaches rather than specific analyses and in-field testing. Literature on SCADA components and EMP is similarly sparse and the existing articles show a variety of impacts to control system components that range from upset and damage to no effect. The limited research and the range of observed impacts for the research that has been published suggests the need for additional work on GMD and EMP and natural gas SCADA components.

02 PETROLEUM↗

A Computed Tomography Automation Architecture Developed from a Comprehensive Literature Review

This paper presents a literature review on techniques related to the computed tomography procedure that incorporate automation elements in their research investigations or industrial applications. Computed tomography (CT) is a non-destructive testing (NDT) technique in that the imaging and inspection are performed without damaging the sample, allowing for additional or repeated analysis if necessary. The reviewed literature is organized based on the steps associated with a general NDT task in order to define an end-to-end computed tomography automation architecture. The process steps include activities prior to image collection, during the scan, and after the data are collected. It further reviews efforts related to repeating this process based on a previous scan result. By analyzing the multiple existing but disparate efforts found in the literature, we present a framework for fully automating NDT procedures and discuss the remaining technical gaps in the developed framework.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Thermal Storage Integrated into Air-Source Heat Pumps to Leverage Building Electrification: A Systematic Literature Review

Air-source heat pumps (ASHPs) can support a decarbonized economy by replacing combustion appliances in homes and electrifying heating systems in buildings. However, ASHPs have not seen significant adoption primarily due to deteriorated performance under cold conditions - at very low temperatures they require auxiliary resistance heating to meet the heating demand and defrost the evaporator. The additional heat lowers the system efficiency. Thermal energy storage (TES) is a candidate technology to help overcome some of these issues. This paper presents a systematic literature review to map the existing research on the integration of TES into ASHPs. Our review of 59 publications indicates that thermal storage increases the ASHP coefficient of performance by 27% on average, albeit with higher initial cost compared to conventional fossil-fueled heating systems. Phase change materials may be ideal to be integrated with ASHPs due to their high energy density and compact design, but only a few publications address TES sizing and design. First and Second Laws of Thermodynamics are widely used to create metrics to assess ASHP-TES integration, and only recently have cost and environmental impact been explored. This literature review suggests that more comprehensive metrics are needed to evaluate the potential benefits of ASHP-TES systems.

air source heat pump↗

Adaptive anomaly detection for identifying attacks in cyber-physical systems: A systematic literature review

Modern cyberattacks in cyber-physical systems (CPS) rapidly evolve and cannot be deterred effectively with most current methods, which focus on characterizing past threats. Adaptive anomaly detection (AAD) is among the most promising techniques to detect evolving cyberattacks, with an emphasis on fast data processing and model adaptation. AAD has been researched extensively; however, to the best of our knowledge, our work is the first systematic literature review (SLR) on current research in this field. We present a comprehensive SLR, gathering 397 relevant papers and systematically analyzing 65 of them (47 research and 18 survey papers) on AAD in CPS from 2013 to November 2023. We introduce a novel taxonomy considering attack types, CPS application, learning paradigm, data management, and algorithms. Our findings show that most studies addressed either model adaptation or data processing, but rarely both simultaneously. This indicates a research gap in fully adaptive solutions. We also categorize algorithms, datasets, and attack characteristics, and summarize strengths and weaknesses across the literature. Our review provides a structured and accessible reference for researchers and practitioners, offering insights into key trends and highlighting limitations in current approaches. Finally, we outline several future research directions, including the need for integrated real-time processing and adaptive learning, explainability, and uncertainty quantification in AAD for CPS.

Adaptation↗

Challenges and Advances in Information Extraction from Scientific Literature: a Review

Scientific articles have long been the primary means of disseminating scientific discoveries. Over the centuries, valuable data and potentially groundbreaking insights have been collected and buried deep in the mountain of publications. In materials engineering, such data are spread across technical handbooks specification sheets, journal articles, and laboratory notebooks in myriad formats. Extracting information from papers on a large scale has been a tedious and time-consuming job to which few researchers have wanted to devote their limited time and effort, yet is an activity that is essential for modern data-driven design practices. However, in recent years, significant progress has been made by the computer science community on techniques for automated information extraction from free text. Yet, transformative application of these techniques to scientific literature remains elusive-due not to a lack of interest or effort but to technical and logistical challenges. Using the challenges in the materials science literature as a driving motivation, we review the gaps between state-of-the-art information extraction methods and the practical application of such methods to scientific texts, and offer a comprehensive overview of work that can be undertaken to close these gaps.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗