bluuebunny/crossref_metadata_2025_split huggingface dataset:
Durga: an R package for effect size estimation and visualization
Authors: Khan Md Kawsar , McLean Donald James 
Published: June 2024

Abstract
Statistical analysis and data visualization are integral parts of science communication. One of the major issues in current data analysis practice is an overdependency on—and misuse of—p-values. Researchers have been advocating for the estimation and reporting of effect sizes for quantitative research to enhance the clarity and effectiveness of data analysis. Reporting effect sizes in scientific publications has until now been mainly limited to numeric tables, even though effect size plotting is a more effective means of communicating results. We have developed the Durga R package for estimating and plotting effect sizes for paired and unpaired group comparisons. Durga allows users to estimate unstandardized and standardized effect sizes and bootstrapped confidence intervals of the effect sizes. The central functionality of Durga is to combine effect size visualizations with traditional plotting methods. Durga is a powerful statistical and data visualization package that is easy to use, providing the flexibility to estimate effect sizes of paired and unpaired data using different statistical methods. Durga provides a plethora of options for plotting effect size, which allows users to plot data in the most informative and aesthetic way. Here, we introduce the package and its various functions. We further describe a workflow for estimating and plotting effect sizes using example data sets.
The function of prolonged copulations in Enchenopa treehoppers (Hemiptera: Membracidae)
Authors: Cirino Lauren A , Rodríguez Ariel N , DeLong Sage A , Rodríguez Rafael L 
Published: June 2024

Abstract
Copulations are very brief in many species, sometimes taking only seconds, but in other species, they can be quite prolonged. Potential explanations for prolonged copulations include time requirements for the transfer of sperm and/or other ejaculate substances. Ejaculate substances could function to regulate female receptivity to subsequent matings, provide nutritional nuptial gifts, or hasten egg oviposition at a potential survival cost to the female. We investigated prolonged copulation in a member of the Enchenopa binotata complex of treehoppers (Hemiptera: Membracidae), in which females rarely remate and copulation can last several hours. We assigned females to treatments in which we interrupted copulation at different times. We also included a control where copulation was not interrupted. We found that females that experienced shorter copulations were more likely to be subsequently receptive to an attractive male. We also found that few females produced offspring when they engaged in short copulations compared to those with longer copulations. We did not find any differences in female survival. Our results support the sperm transfer and receptivity regulation hypotheses. We discuss potential reasons for why these processes should take so long in a species with low female remating.
Logging Business Challenges in the US South and Lake States
Authors: Conrad Joseph L , Blinn Charles R 
Published: June 2024

Abstract
Logging businesses are the critical link between forest management and the forest products industry. Through analysis of data from logging business owner surveys, contacts with trade associations, and personal contacts, six challenges facing logging businesses in the US South and the Lake States were identified: logging business consolidation, demographics and labor availability, changing markets, rising costs, timber transportation, and impacts from COVID-19. The impact of each challenge was summarized using data from peer-reviewed journal articles, trade publications, and federal databases. Although loggers are accustomed to fluctuations in their business environment, overcoming all of these challenges may have a profound impact on the logging sector and thus the wood supply chain. Owners may not be able to address all of these challenges without support from forest industry as well as logging and forestry trade associations who may be positioned to develop programs and advocate for the sector as a whole.
Study Implications: A vibrant logging sector is essential to ensure forest management prescriptions are implemented and forest products mills, important economic drivers in rural areas, receive a consistent supply of raw material. In the short term, it is essential for logging business owners and procurement foresters to better understand logging costs and be quicker to negotiate adjustments when costs rise rapidly, as they did during 2020–2023. In the long term, individual logging businesses, forestry and logging trade associations, and forest industry should collaborate to address labor challenges and advocate for any needed policy changes.
Knowledge domains and emerging trends in radiotherapy in oesophageal cancer from 2004 to 2023: a bibliometric analysis and visualization study
Authors: Feng Yue , Lv Minghe , Zeng Su , Zeng Hongwei , Yu Jingping 
Published: June 2024

Abstract
Esophageal cancer (EC) is a malignant tumour with high morbidity and mortality rates. Recent studies have shown that much progress has been made in the research of radiotherapy in EC. This study aims to provide a comprehensive overview of the knowledge structure and research hotspots of radiotherapy in EC through bibliometrics. Publications related to radiotherapy in EC from 2014 to 2023 were searched on the web of science core collection database. VOSviewers, CiteSpace and R package ‘bibliometrix’ were used to conduct this bibliometric analysis. In total, 4258 articles from 76 countries led by China and the USA were included. The Chinese Academy of Medical Sciences—Peking Union Medical College has the highest number of publications. International Journal of Radiation Oncology Biology Physics is the most popular journal and also the most co-cited journal in this field. These publications come from 21 972 authors among which Liao Zhongxing had published the most papers and Cooper JS was co-cited most often. Neoadjuvant chemoradiotherapy and strategies based on it are the main topics in this research field. ‘IMRT’ and ‘immunotherapy’ are the primary keywords of emerging research hotspots. This is a bibliometric study that comprehensively summarizes the research trends and developments of radiotherapy in EC. This information identifies recent research frontiers and hot directions, which will provide a reference for scholars studying radiotherapy in EC.
Cross-linguistic authorship attribution and gender profiling. Machine translation as a method for bridging the language gap
Authors: Mikros George , Boumparis Dimitris 
Published: June 2024

Abstract
This study explores the feasibility of cross-linguistic authorship attribution and the author’s gender identification using Machine Translation (MT). Computational stylistics experiments were conducted on a Greek blog corpus translated into English using Google’s Neural MT. A Random Forest algorithm was employed for authorship and gender profiling, using different feature groups [Author’s Multilevel N-gram Profiles, quantitative linguistics (QL), and cross-lingual word embeddings (CLWE)] in both original and translated texts. Results indicate that MT is a viable method for converting a multilingual corpus into one language for authorship attribution and gender profiling research, with considerable accuracy when training and testing datasets use identical language. In the pure cross-linguistic scenario, higher accuracies than the baselines were obtained using CLWE and QL features.
Fecal miRNA profiles in colorectal cancers with mucinous morphology
Authors: Naccarati Alessio , Dragomir Mihnea P , Tarallo Sonia , Gagliardi Amedeo , Alberini Virginia , Buchler Tomas , Liska Vaclav , Gallo Gaetano , Vymetalkova Veronika , Vodickova Ludmila , Vodicka Pavel , Pardini Barbara , Ferrero Giulio 
Published: June 2024

Abstract
The diagnostic performance of molecular markers in surrogate tissues like stool may be affected by colorectal cancer (CRC) morphological heterogeneity. The mucinous histotype represents a subgroup of CRC with a peculiar molecular program and unfavorable disease progression. However, the percentage of mucinous morphology necessary to define this subtype is still a matter of debate. In this study, we investigated whether stool miRNA profiles of CRC patients differ in patients with mucinous histopathological subtypes compared to non-mucinous cancers. In this respect, we also explored how the stool miRNA signature reported in our previous multicentric study behaves in this histotype. Small-RNA sequencing was performed in fecal and tissue samples of an Italian cohort (n = 172), including 27 CRC with mucinous morphology (mucinous cancers with ≥ 50% mucinous morphology and those with mucinous component ≥ 5% but &lt; 50%), 58 non-mucinous CRC, and 87 colonoscopy-negative controls. Results were compared with fecal miRNA profiles of a cohort from the Czech Republic (n = 98). Most of the differentially expressed (DE) stool miRNAs (n = 324) were in common between CRC with mucinous morphology and non-mucinous histopathological subtypes in comparison with healthy controls. Interestingly, the altered levels of 25 fecal miRNAs previously identified distinguishing CRC cases from controls in both cohorts were also confirmed after stratification for mucinous morphology. Forty-nine miRNAs were DE exclusively in CRC with mucinous morphology and 61 in non-mucinous CRC. Mucinous cancers and those with mucinous component showed fairly similar profiles that were comparable in the Czech cohort. Among the stool DE miRNAs observed in CRC with mucinous morphology, 20 were also altered in the comparison between tumor and adjacent mucosa tissue. This study highlights miRNAs specifically altered in CRC with mucinous morphology. Nevertheless, the performance of our stool miRNA signature in accurately distinguishing CRC cases from controls was not significantly affected by this histological subtype. This aspect further supports the use of stool miRNAs for noninvasive diagnosis and screening strategies.
Detecting co-selection through excess linkage disequilibrium in bacterial genomes
Authors: Mallawaarachchi Sudaraka , Tonkin-Hill Gerry , Pöntinen Anna K , Calland Jessica K , Gladstone Rebecca A , Arredondo-Alonso Sergio , MacAlasdair Neil , Thorpe Harry A , Top Janetta , Sheppard Samuel K , Balding David , Croucher Nicholas J , Corander Jukka 
Published: June 2024

Abstract
Population genomics has revolutionized our ability to study bacterial evolution by enabling data-driven discovery of the genetic architecture of trait variation. Genome-wide association studies (GWAS) have more recently become accompanied by genome-wide epistasis and co-selection (GWES) analysis, which offers a phenotype-free approach to generating hypotheses about selective processes that simultaneously impact multiple loci across the genome. However, existing GWES methods only consider associations between distant pairs of loci within the genome due to the strong impact of linkage-disequilibrium (LD) over short distances. Based on the general functional organisation of genomes it is nevertheless expected that majority of co-selection and epistasis will act within relatively short genomic proximity, on co-variation occurring within genes and their promoter regions, and within operons. Here, we introduce LDWeaver, which enables an exhaustive GWES across both short- and long-range LD, to disentangle likely neutral co-variation from selection. We demonstrate the ability of LDWeaver to efficiently generate hypotheses about co-selection using large genomic surveys of multiple major human bacterial pathogen species and validate several findings using functional annotation and phenotypic measurements. Our approach will facilitate the study of bacterial evolution in the light of rapidly expanding population genomic data.
NFixDB (Nitrogen Fixation DataBase)—a comprehensive integrated database for robust ‘omics analysis of diazotrophs
Authors: Bellanger Madeline , Figueroa Jose L , Tiemann Lisa , Friesen Maren L , III Richard Allen White 
Published: June 2024

Abstract
Biological nitrogen fixation is a fundamental biogeochemical process that transforms molecular nitrogen into biologically available nitrogen via diazotrophic microbes. Diazotrophs anaerobically fix nitrogen using the nitrogenase enzyme which is arranged in three different gene clusters: (i) molybdenum nitrogenase (nifHDK) is the most abundant, followed by it's alternatives, (ii) vanadium nitrogenase (vnfHDK) and (iii) iron nitrogenase (anfHDK). Multiple databases have been constructed as resources for diazotrophic ‘omics analysis; however, an integrated database based on whole genome references does not exist. Here, we present NFixDB (Nitrogen Fixation DataBase), a comprehensive integrated whole genome based database for diazotrophs, which includes all nitrogenases (nifHDK, vnfHDK, anfHDK) and nitrogenase-like enzymes (e.g. nflHD) linked to ribosomal RNA operons (16S–5S–23S). NFixDB was computed using Hidden Markov Models (HMMs) against the entire whole genome based Genome Taxonomy Database (GTDB R214), providing searchable reference HMMs for all nitrogenase and nitrogenase-like genes, complete ribosomal RNA operons, both GTDB and NCBI/RefSeq taxonomy, and an SQL database for querying matches. We compared NFixDB to nifH databases from Buckley, Zehr, Mise and FunGene finding extensive evidence of nifH, in addition to vnfH and nflH. NFixDB contains &gt;4000 verified nifHDK sequences contained on 50 unique phyla of bacteria and archaea. NFixDB provides the first comprehensive nitrogenase database available to researchers unlocking diazotrophic microbial potential.
Characterization of trans-spliced chimeric RNAs: insights into the mechanism of trans-splicing
Authors: Yokomori Rui , Kusakabe Takehiro G , Nakai Kenta 
Published: June 2024

Abstract
Trans-splicing is a post-transcriptional processing event that joins exons from separate RNAs to produce a chimeric RNA. However, the detailed mechanism of trans-splicing remains poorly understood. Here, we characterize trans-spliced genes and provide insights into the mechanism of trans-splicing in the tunicate Ciona. Tunicates are the closest invertebrates to humans, and their genes frequently undergo trans-splicing. Our analysis revealed that, in genes that give rise to both trans-spliced and non-trans-spliced messenger RNAs, trans-splice acceptor sites were preferentially located at the first functional acceptor site, and their paired donor sites were weak in both Ciona and humans. Additionally, we found that Ciona trans-spliced genes had GU- and AU-rich 5′ transcribed regions. Our data and findings not only are useful for Ciona research community, but may also aid in a better understanding of the trans-splicing mechanism, potentially advancing the development of gene therapy based on trans-splicing.
Multiscale Bayesian simulations reveal functional chromatin condensation of gene loci
Authors: Brandani Giovanni B , Gu Chenyang , Gopi Soundhararajan , Takada Shoji 
Published: June 2024

Abstract
Chromatin, the complex assembly of DNA and associated proteins, plays a pivotal role in orchestrating various genomic functions. To aid our understanding of the principles underlying chromatin organization, we introduce Hi-C metainference, a Bayesian approach that integrates Hi-C contact frequencies into multiscale prior models of chromatin. This approach combines both bottom-up (the physics-based prior) and top-down (the data-driven posterior) strategies to characterize the 3D organization of a target genomic locus. We first demonstrate the capability of this method to accurately reconstruct the structural ensemble and the dynamics of a system from contact information. We then apply the approach to investigate the Sox2, Pou5f1, and Nanog loci of mouse embryonic stem cells using a bottom-up chromatin model at 1 kb resolution. We observe that the studied loci are conformationally heterogeneous and organized as crumpled globules, favoring contacts between distant enhancers and promoters. Using nucleosome-resolution simulations, we then reveal how the Nanog gene is functionally organized across the multiple scales of chromatin. At the local level, we identify diverse tetranucleosome folding motifs with a characteristic distribution along the genome, predominantly open at cis-regulatory elements and compact in between. At the larger scale, we find that enhancer–promoter contacts are driven by the transient condensation of chromatin into compact domains stabilized by extensive internucleosome interactions. Overall, this work highlights the condensed, but dynamic nature of chromatin in vivo, contributing to a deeper understanding of gene structure–function relationships.
ChatGPT prompts for generating multiple-choice questions in medical education and evidence on their validity: a literature review
Authors: Kıyak Yavuz Selim , Emekli Emre 
Published: June 2024

Abstract
ChatGPT’s role in creating multiple-choice questions (MCQs) is growing but the validity of these artificial-intelligence-generated questions is unclear. This literature review was conducted to address the urgent need for understanding the application of ChatGPT in generating MCQs for medical education. Following the database search and screening of 1920 studies, we found 23 relevant studies. We extracted the prompts for MCQ generation and assessed the validity evidence of MCQs. The findings showed that prompts varied, including referencing specific exam styles and adopting specific personas, which align with recommended prompt engineering tactics. The validity evidence covered various domains, showing mixed accuracy rates, with some studies indicating comparable quality to human-written questions, and others highlighting differences in difficulty and discrimination levels, alongside a significant reduction in question creation time. Despite its efficiency, we highlight the necessity of careful review and suggest a need for further research to optimize the use of ChatGPT in question generation.
Main messages Ensure high-quality outputs by utilizing well-designed prompts; medical educators should prioritize the use of detailed, clear ChatGPT prompts when generating MCQs. Avoid using ChatGPT-generated MCQs directly in examinations without thorough review to prevent inaccuracies and ensure relevance. Leverage ChatGPT’s potential to streamline the test development process, enhancing efficiency without compromising quality.
Survival analysis of adult visceral leishmaniasis patients admitted to Metema Hospital, Metema, Ethiopia: a hospital-based cross-sectional study
Authors: Wudu Habitamu , Alemu Chekol 
Published: June 2024

Abstract

Background
Visceral leishmaniasis (VL) is a neglected tropical disease that mostly affects the working class and impoverished segments of society, having a significant negative effect on the economic development of the affected nation. While anti-leishmanial medications lower mortality among VL patients, patients may still die or require more time to recover while receiving treatment. In this regard, there are limited studies in Ethiopia. This study aims to determine the time to recovery and its associated predictors among adult VL patients at Metema Hospital, Metema, Ethiopia.

Methods
A hospital-based cross-sectional study was employed and the data were collected from patient's charts from September 2017 to September 2021. Data were entered and analysed using EpiData version 3.1, Stata version 14.2 and R version 3.4.0 statistical software. Kaplan–Meier survival curves and logrank tests were used to compare the survival time. The Cox proportional hazards model assumption and model fitness were checked and used to identify statistical association predictors in VL patients.

Results
The Cox proportional hazards model was fitted. The overall medium recovery time was 7 d (minimum 4, maximum 14). The variables of nasal bleeding (adjusted hazard ratio [aHR] 0.44 [95% confidence interval {CI} 0.19 to 0.89]), no comorbidity (aHR 2.29 [95% CI 1.27 to 4.11]), relapse of VL (aHR 0.33 [95% CI 0.15 to 0.75]), low parasite load (aHR 2.58 [95% CI 1.48 to 4.51]) and ambulatory (aHR 3.26 [95% CI 2.45 to 6.53]) were significantly associated with time to recovery in VL patients.

Conclusions
Patients with comorbidities, nasal bleeding, relapse of VL, bedridden and high parasite load should be treated and monitored carefully to recover quickly from their illness.
Sugammadex and oral contraceptives
Authors: Devoy Tamblyn , Smith Natalie 
Published: June 2024

Purpose of review
This review article explores the evidence regarding sugammadex (MSD Australia) and its potential interaction with hormonal contraceptives. The impact of recent clinical trials and review articles is examined.

Recent findings
Recent clinical data suggest that the interaction between sugammadex and estrogen and progesterone concentrations may not be clinically significant and may confer some protection against ovulation. There are no clinical trials reporting interactions between sugammadex and the exogenous hormonal compounds found in oral contraceptive pills. The method of contraception is an important consideration, as sugammadex theoretically affects oral and nonoral, and combined versus single agent methods differently. Two large retrospective database studies have reported two cases of pregnancy postoperatively in patients on hormonal contraceptives whose anesthetic included sugammadex.

Summary
Strong clinical evidence to support or refute claims of a significant impact of sugammadex on contraceptive efficacy in women on contraception is lacking. The existing evidence does not suggest a basis for concern regarding the impact of sugammadex on contraception in the perioperative setting.
Racial Disparities in Newborn Drug Testing After Implementation of Question-Based Screening for Prenatal Substance Use
Authors: Soos Alexandra , Plegue Melissa , Darwiche Adam , Oshman Lauren , Frank Christopher J. 
Published: June 2024

OBJECTIVE:
To examine the association of universal question-based screening for prenatal substance use on racial inequities in prenatal and newborn drug testing.

METHODS:
We conducted a retrospective cohort study of 32,802 live births of patients receiving prenatal care at an academic medical center in the midwestern United States from 2014 to 2022, before and after implementation of question-based screening in 2018. Primary outcomes included prenatal and newborn drug test orders. Logistic regression models using a generalized estimating equation framework assessed associations with question-based screening and results, birthing parent age, race, ethnicity, marital status, and insurance type. Charts of patients who indicated difficulties stopping substance use were audited for guideline-directed care.

RESULTS:
A total of 12,725 of 14,992 pregnant people (85.3%) received question-based screening. Implementation of question-based screening was associated with a decrease in prenatal urine test orders (5.0% [95% CI, 4.6–5.3%] before implementation, 3.1% [95% CI, 2.8–3.4%] after implementation; P<.001), with Black birthing parents having the largest reduction in prenatal urine drug testing (10.3% [95% CI, 9.0–11.7%] before implementation, 4.9% [95% CI, 3.9–5.9%] after implementation). However, rates of newborn drug testing did not change (4.7% [95% CI, 4.4–5.0%] before implementation, 4.5% [95% CI, 4.2–4.8%] after implementation; P=.46), and clinicians continued to order significantly more newborn drug tests for newborns of Black birthing parents compared with other race and ethnicity groups.

CONCLUSION:
Implementation of question-based screening for substance use in pregnancy was associated with decreased prenatal urine drug testing but no change in overall newborn drug testing or racial inequities in newborn drug testing for Black birthing people. Further policy efforts are warranted to improve substance use treatment and to eliminate racial inequities in punitive policies such as newborn drug testing and subsequent child protective services reporting.