bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII
Authors: Leaman Robert , Islamaj Rezarta , Adams Virginia , Alliheedi Mohammed A , Almeida João Rafael , Antunes Rui , Bevan Robert , Chang Yung-Chun , Erdengasileng Arslan , Hodgskiss Matthew , Ida Ryuki , Kim Hyunjae , Li Keqiao , Mercer Robert E , Mertová Lukrécia , Mobasher Ghadeer , Shin Hoo-Chang , Sung Mujeen , Tsujimura Tomoki , Yeh Wen-Chao , Lu Zhiyong 
Published: March 2023

AbstractThe BioCreative National Library of Medicine (NLM)-Chem track calls for a community effort to fine-tune automated recognition of chemical names in the biomedical literature. Chemicals are one of the most searched biomedical entities in PubMed, and—as highlighted during the coronavirus disease 2019 pandemic—their identification may significantly advance research in multiple biomedical subfields. While previous community challenges focused on identifying chemical names mentioned in titles and abstracts, the full text contains valuable additional detail. We, therefore, organized the BioCreative NLM-Chem track as a community effort to address automated chemical entity recognition in full-text articles. The track consisted of two tasks: (i) chemical identification and (ii) chemical indexing. The chemical identification task required predicting all chemicals mentioned in recently published full-text articles, both span [i.e. named entity recognition (NER)] and normalization (i.e. entity linking), using Medical Subject Headings (MeSH). The chemical indexing task required identifying which chemicals reflect topics for each article and should therefore appear in the listing of MeSH terms for the document in the MEDLINE article indexing. This manuscript summarizes the BioCreative NLM-Chem track and post-challenge experiments. We received a total of 85 submissions from 17 teams worldwide. The highest performance achieved for the chemical identification task was 0.8672 F-score (0.8759 precision and 0.8587 recall) for strict NER performance and 0.8136 F-score (0.8621 precision and 0.7702 recall) for strict normalization performance. The highest performance achieved for the chemical indexing task was 0.6073 F-score (0.7417 precision and 0.5141 recall). This community challenge demonstrated that (i) the current substantial achievements in deep learning technologies can be utilized to improve automated prediction accuracy further and (ii) the chemical indexing task is substantially more challenging. We look forward to further developing biomedical text–mining methods to respond to the rapid growth of biomedical literature. The NLM-Chem track dataset and other challenge materials are publicly available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BC7-NLM-Chem-track/.Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/BC7-NLM-Chem-track/
The 2021 emergence of Brood X periodical cicadas Magicicada spp. (Hemiptera: Cicadidae) in Georgia, United States of America
Authors: Lampert Evan C , Perez Gaby , Reyes Alejo Daleana , Jones Sydney Marie , Ignatius Amber 
Published: March 2023

Abstract
The US state of Georgia includes the range of several periodical cicada broods and is the southernmost state in which Brood X periodical cicadas emerge; however, no research has focused on this brood in this state. We used reports of sightings on social media, communication with the public, and our own searches to determine the geographic range in Georgia and timing of biological events. Both adults and exuviae were identified to species to determine the species makeup at those locations. The first Brood X adult was photographed on April 26 in Lumpkin County, and Magicicada septendecim L. was the most common species. Online records and site visits led to distribution records in nine counties, including six that provided no records in the 2004 emergence. Driving surveys revealed patchy distributions of chorusing adults and species distribution modeling further predicted locations where Brood X can be found in future surveys. We observed cicada oviposition scars at two locations and found no effect of host plant on presence or density of scars. Lastly, collections of dead adults showed female remains were less common and more likely to be dismembered. Further investigations of the periodical cicadas in Georgia are recommended to better understand the phenology, evolution, and ecology of these remarkable insects.
Dual antiplatelet therapy de-escalation in acute coronary syndrome: an individual patient meta-analysis
Authors: Kang Jeehoon , Rizas Konstantinos D , Park Kyung Woo , Chung Jaewook , van den Broek Wout , Claassens Daniel M F , Choo Eun ho , Aradi Dániel , Massberg Steffen , Hwang Doyeon , Han Jung-Kyu , Yang Han-Mo , Kang Hyun-Jae , Chang Kiyuk , ten Berg Jur M , Sibbing Dirk , Koo Bon-Kwon , Kim Hyo-Soo 
Published: March 2023

Abstract

Aims
Dual-antiplatelet therapy (DAPT) with aspirin and a potent P2Y12 inhibitor is the standard treatment for patients with acute coronary syndrome (ACS) undergoing percutaneous coronary intervention (PCI). De-escalation of the potent P2Y12 inhibtor is an appealing concept to balance the ischaemic and bleeding risks after PCI. An individual patient data meta-analysis was performed to compare de-escalation versus standard DAPT in patients with ACS.

Methods and results
Electronic databases, including PubMed, Embase, and the Cochrane database, were searched to identify randomised clinical trials (RCTs) comparing the de-escalation strategy with the standard DAPT after PCI in patients with ACS. Individual patient-level data were collected from the relevant trials. The co-primary endpoints of interest were the ischaemic composite endpoint (a composite of cardiac death, myocardial infarction, and cerebrovascular events) and bleeding endpoint (any bleeding) at 1-year post-PCI. Four RCTs (the TROPICAL-ACS, POPular Genetics, HOST-REDUCE-POLYTECH-ACS, and TALOS-AMI trials) including 10 133 patients were analysed. The ischaemic endpoint was significantly lower in the patients assigned to the de-escalation strategy than in those assigned to the standard strategy (2.3% vs. 3.0%, hazard ratio [HR] 0.761, 95% confidence interval [CI] 0.597-0.972, log rank P = 0.029). Bleeding was also significantly lower in the de-escalation strategy group (6.5% vs. 9.1%, HR 0.701, 95% CI 0.606-0.811, log rank P &lt; 0.001). No significant intergroup differences were observed in terms of all-cause death and major bleeding events. Subgroup analyses revealed that compared to guided de-escalation, unguided de-escalation had a significantly larger impact on bleeding endpoint reduction (P for interaction = 0.007); no intergroup differences were observed for the ischaemic endpoints.

Conclusion
In this individual patient data meta-analysis, DAPT-based de-escalation was associated with both decreased ischaemic and bleeding endpoints. Reduction in bleeding endpoints was more prominent for the unguided than the guided de-escalation strategy.

Study registration number
This study was registered in the PROSPERO (ID: CRD42021245477).
Bacterial virulence regulation through soluble peptidoglycan fragments sensing and response: knowledge gaps and therapeutic potential
Authors: Escobar-Salom María , Barceló Isabel María , Jordana-Lluch Elena , Torrens Gabriel , Oliver Antonio , Juan Carlos 
Published: March 2023

AbstractGiven the growing clinical–epidemiological threat posed by the phenomenon of antibiotic resistance, new therapeutic options are urgently needed, especially against top nosocomial pathogens such as those within the ESKAPE group. In this scenario, research is pushed to explore therapeutic alternatives and, among these, those oriented toward reducing bacterial pathogenic power could pose encouraging options. However, the first step in developing these antivirulence weapons is to find weak points in the bacterial biology to be attacked with the goal of dampening pathogenesis. In this regard, during the last decades some studies have directly/indirectly suggested that certain soluble peptidoglycan-derived fragments display virulence-regulatory capacities, likely through similar mechanisms to those followed to regulate the production of several β-lactamases: binding to specific transcriptional regulators and/or sensing/activation of two-component systems. These data suggest the existence of intra- and also intercellular peptidoglycan-derived signaling capable of impacting bacterial behavior, and hence likely exploitable from the therapeutic perspective. Using the well-known phenomenon of peptidoglycan metabolism-linked β-lactamase regulation as a starting point, we gather and integrate the studies connecting soluble peptidoglycan sensing with fitness/virulence regulation in Gram-negatives, dissecting the gaps in current knowledge that need filling to enable potential therapeutic strategy development, a topic which is also finally discussed.
Split-marker-mediated genome editing improves homologous recombination frequency in the CTG clade yeastCandida intermedia
Authors: Peri Kameshwara V R , Faria-Oliveira Fábio , Larsson Adam , Plovie Alexander , Papon Nicolas , Geijer Cecilia 
Published: March 2023

AbstractGenome-editing toolboxes are essential for the exploration and exploitation of nonconventional yeast species as cell factories, as they facilitate both genome studies and metabolic engineering. The nonconventional yeast Candida intermedia is a biotechnologically interesting species due to its capacity to convert a wide range of carbon sources, including xylose and lactose found in forestry and dairy industry waste and side-streams, into added-value products. However, possibilities of genetic manipulation have so far been limited due to lack of molecular tools for this species. We describe here the development of a genome editing method for C. intermedia, based on electroporation and gene deletion cassettes containing the Candida albicans NAT1 dominant selection marker flanked by 1000 base pair sequences homologous to the target loci. Linear deletion cassettes targeting the ADE2 gene originally resulted in &lt;1% targeting efficiencies, suggesting that C. intermedia mainly uses nonhomologous end joining for integration of foreign DNA fragments. By developing a split-marker based deletion technique for C. intermedia, we successfully improved the homologous recombination rates, achieving targeting efficiencies up to 70%. For marker-less deletions, we also employed the split-marker cassette in combination with a recombinase system, which enabled the construction of double deletion mutants via marker recycling. Overall, the split-marker technique proved to be a quick and reliable method for generating gene deletions in C. intermedia, which opens the possibility to uncover and enhance its cell factory potential.
Health literacy and COVID-19-related beliefs and behaviors: a longitudinal study of the Japanese general population
Authors: Ishikawa Hirono , Kato Mio 
Published: March 2023

SummarySince the outbreak of novel coronavirus disease-2019 (COVID-19), health communication has played a critical role in the process of disease prevention. Based on the concepts of health literacy and protection motivation theory, this study longitudinally examined the relationship between general health literacy measured immediately before the COVID-19 outbreak, and COVID-19–related information utilization, health literacy, beliefs and protective behaviors during the subsequent year in the Japanese general population. The participants were 767 Japanese residents who completed self-administered questionnaire surveys in January 2020 and February 2021. Based on the hypotheses, we constructed and tested a path model to predict the adoption of protective behaviors. Higher health literacy in 2020 was significantly related to higher COVID-19-related health literacy in 2021, which, in turn, was related to the adoption of recommended protective behaviors both directly and indirectly through threat and coping appraisal. Coping appraisal, but not threat appraisal, significantly differed by health literacy level. Generic health literacy skills for accessing, understanding and applying health information may enable people to better adapt to specific health risks. Our findings provide guidance for future health literacy education and health risk communication in populations with different health literacy levels.
El Tribunal de Cuentas de la Unión brasilero: una institución muy peculiar
Authors: Jordão Eduardo , Palma Juliana 
Published: March 2023

Abstract
Created in 1890, the Tribunal de Contas da União (TCU) is today one of the most relevant institutions in the Brazilian State. This article explains how the TCU became this very particular institution, from its historical origins as a simple court of accounts to its efforts to differentiate itself from this model and gain other (many) powers, reshaping itself. In the end, we present a synthesis of the current debates on the institutional model of the TCU in Brazil.
Lithium-ion battery equalization circuit and control strategy for photovoltaic energy storage applications
Authors: Yao Haiyan , Thinzar Aung 
Published: March 2023

Abstract
Solar photovoltaic (PV) is considered a very promising technology, and PV-lithium-ion battery energy storage is widely used to obtain smoother power output. In this paper, we propose a battery equalization circuit and control strategy to improve the performance of lithium-ion batteries. In the equalization circuit, the passive equalization and active equalization circuits are combined, and the active equalization circuit used is simple and has high performance, whereas in the equalization strategy, because the system works 24 h a day, the equalization speed is sacrificed to obtain a smaller temperature rise by adjusting the duty cycle of the passive equalization metal-oxide-semiconductor field-effect transistors and by calculating the state of charge instead of the voltage to obtain better performance. The proposed circuit and strategy can not only achieve the goal of battery equalization, while turning on four batteries at the same time and the temperature rise of passive equalization is only 1°C for ~1.5 h. Compared with the traditional equalization control strategy with 8 mV voltage error, the proposed strategy is only 3 mV, which has better performance.
Gepotidacin: a novel, oral, ‘first-in-class’ triazaacenaphthylene antibiotic for the treatment of uncomplicated urinary tract infections and urogenital gonorrhoea
Authors: Watkins Richard R , Thapaliya Dipendra , Lemonovich Tracy L , Bonomo Robert A 
Published: March 2023

Abstract
The ongoing spread of antimicrobial resistance has made the treatment of uncomplicated urinary tract infections (UTIs) and urogenital gonorrhoea increasingly difficult. New oral treatment options are urgently needed. Gepotidacin (previously GSK2140944) is a novel, bactericidal, oral, ‘first-in-class’ triazaacenaphthylene antibiotic that inhibits bacterial DNA replication by blocking two essential topoisomerase enzymes. Mutations in both enzymes would likely be necessary for resistance to occur, thus raising hopes that the drug will be able to maintain long-term effectiveness. Data from Phase II clinical trials of gepotidacin in UTIs and urogenital gonorrhoea appear promising, and Phase III trials are underway. In this review we summarize the development of gepotidacin and discuss its potential role in clinical practice. If approved, gepotidacin will be the first new oral antibiotic for UTIs in more than 20 years.
Feasibility and utility of Point-of-Care electronic clinical data capture in Uganda’s healthcare system: a qualitative study
Authors: Nabukenya Josephine , Egwar Andrew Alunyu , Drumright Lydia , Semwanga Agnes Rwashana , Kasasa Simon 
Published: March 2023

Abstract

Objective
This study aimed to assess Uganda’s readiness for implementing a national Point-of-Care (PoC) electronic clinical data capture platform that can function in near real-time.

Methods
A qualitative, cross-sectional design was adopted to obtain a snapshot of Uganda’s eHealth system landscape with an aim to assess the readiness for implementing PoC platform. A purposive sampling strategy was used to select the study districts per region, health facilities per district, and participants per facility or district.

Results
Nine facilitators were identified, including health worker motivation to serve the community, affirmative action on eHealth financing, improved integrating information and communication technology (ICT) infrastructure, Internet and electricity power connectivity, improved human resource skills and knowledge, the culture of sensitizing and training of stakeholders on eHealth interventions, the perceived value of the platform, health workers’ motivation to improve health data quality, interest to improve data use, and continuous improvement in the eHealth regulatory environment. Other suggestions entailed several requirements that must be met, including infrastructure, eHealth governance, human resources, as well as functional and data requirements.

Discussion
Uganda, like other low-income countries, has adopted ICT to help solve some of its health system challenges. Although several challenges face eHealth implementations in Uganda, this study revealed facilitators that can be leveraged and requirements that, if met, would facilitate the successful implementation of a near real-time data capture platform capable of improving the country’s health outcomes.

Conclusion
Other countries with eHealth implementations similar to those faced in Uganda can also leverage identified facilitators and address the stakeholders’ requirements.
An Overall Validation Approach Based on β-Content, γ-Confidence Tolerance Interval, and Uncertainty Profile: Application to LC–MS/MS Quantification of Carbendazim in Drinking Water
Authors: Aaziz Hicham , Saffaj Taoufiq , Saffaj Nabil , Mamouni Rachid , Ihssane Bouchaib 
Published: March 2023

Abstract

Background
Carbendazim is a fungicide which can seep into the water supply, presenting a public health risk, and therefore the accurate trace determination of this substance is very important.

Objective
The purpose of the study is to take a top-down analytical validation approach in order to determine the amount of carbendazim in drinking water by using an SPE–LC–MS/MS technique.

Methods
Quantification of carbendazim using solid-phase extraction coupled with LC–MS/MS was used in order to ensure the accuracy of the analytical method and to control the risk of its routine application. An overall validation methodology based on two-sided tolerance interval type β-content, γ-confidence has been applied for the validation and estimation of uncertainty by building a decision graphical tool called the “uncertainty profile” by using the statistical process known as the Satterthwaite approximation with no recourse to additional data by satisfying intermediate precision condition for each concentration level within the acceptance limits fixed in advance.

Results
The process of validation is based on the selection of a linear weighted 1/X model enabling validation of the carbendazim dosage using LC–MS/MS in the range of working concentrations as the βγ-CCTI fell inside acceptable limits of ±10%, and the relative expanded uncertainty did not surpass 7% regardless of the β values (66.7, 80, and 90%) and the 1− γ = risk (10 and 5%).

Conclusion
The application of the uncertainty profile approach for full validation of a SPE–LC–MS/MS assay for the quantification of carbendazim has been successfully achieved.

Highlights
Implementation of a full validation strategy based on validation and measurement uncertainty with no additional effort using data from analytical validation under intermediate precision conditions at each level of concentration for carbendazim quantification in drinking water using SPE–LC–MS/MS. So we have shown the flexibility of this approach for carbendazim assay by LC–MS/MS. Indeed, It provides an efficient decision-making tool that allows selection and modification of β-content and γ-confidence values.
Development of building information modeling-based automation assessment process for universal design of public buildings
Authors: Yu Eunsang , Choi Jungsik 
Published: March 2023

AbstractThe aging population is growing drastically all over the world. With the advent of the global era, universal design is garnering considerable interest, as the number of multicultural families is increasing, and various user classes are being created. In addition, with the advances in construction technology, architectural design is becoming more diverse, and convenience facilities are also getting distributed in various ways. As a result, more buildings need to apply universal design, indicating that various architectural information and universal design for the user class are required. Various data are needed for universal design evaluation, but there is a limit to evaluating with two-dimensional (2D) drawings. However, the limitations of 2D drawings can be overcome via building information modeling (BIM) combined with architectural data, which remarkably simplifies the universal design evaluation. This study was conducted with the aim to analyze architectural information by extracting architectural elements necessary for universal design evaluation from BIM data. It was confirmed that the calculations for universal design evaluation can be performed by 3D shape or attribute analysis using BIM data and computer programming. In order to create an automated evaluation algorithm for universal design, the evaluation methods were classified according to the universal design evaluation guide, based on building users and user diversity. In addition, even if the evaluation methods were the same by location, different points were classified by location, and evaluation items and information necessary for the evaluation were organized by category for each facility. Through this classification, we created an algorithm with seven types of methods for extracting the BIM data and comparing them by evaluation method for an automated analysis. In addition, an analysis was performed directly on the BIM design sample model using an automated evaluation algorithm. Although there were various architectural objects in the design data, evaluation was possible using algorithms. By applying the universal design evaluation and BIM data evaluation methods, we could confirm that the BIM-based universal design automation evaluation method prevents human error and is thus superior to the existing evaluation methods. Further, the automation evaluation method can contribute to BIM activation as the BIM data can be used in various studies such as design certification evaluation and automation analysis.