bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing AI efficacy in medical knowledge tests: A study using Taiwan's internal medicine exam questions from 2020 to 2023
Authors: Lin Shih-Yi , Hsu Ying-Yu , Ju Shu-Woei , Yeh Pei-Chun , Hsu Wu-Huei , Kao Chia-Hung 
Published: October 2024

Background The aim of this study is to evaluate the ability of generative artificial intelligence (AI) models to handle specialized medical knowledge and problem-solving in a formal examination context. Methods This research utilized internal medicine exam questions provided by the Taiwan Internal Medicine Society from 2020 to 2023, testing three AI models: GPT-4o, Claude_3.5 Sonnet, and Gemini Advanced models. Rejected queries for Gemini Advanced were translated into French for resubmission. Performance was assessed using IBM SPSS Statistics 26, with accuracy percentages calculated and statistical analyses such as Pearson correlation and analysis of variance (ANOVA) performed to gauge AI efficacy. Results GPT-4o’s top annual score was 86.25 in 2022, with an average of 81.97. Claude_3.5 Sonnet reached a peak score of 88.13 in 2021 and 2022, averaging 84.85, while Gemini Advanced lagged with an average score of 69.84. In specific specialties, Claude_3.5 Sonnet scored highest in Psychiatry (100%) and Nephrology (97.26%), with GPT-4o performing similarly well in Hematology & oncology (97.10%) and Nephrology (94.52%). Gemini's best scores were in Psychiatry (86.96%) and Hematology & Oncology (82.76%). Gemini Advanced models struggled with Neurology, scoring below 60%. Additionally, all models performed better on text-based questions than on image-based ones, without significant differences. Claude 3 Opus scored highest on COVID-19-related questions at 89.29%, followed by GPT-4o at 75.00% and Gemini Advanced at 67.86%. Conclusions AI models showed varied proficiency across medical specialties and question types. GPT-4o demonstrated higher image-based correction rates. Claude_3.5 Sonnet generally and consistently outperformed others, highlighting significant potential for AI in assisting medical education.
Clinical Outcomes and Tendon Structure at 3- to 4-Year Follow-up After Exercise-Based Treatment of Patellar Tendinopathy: A Prospective Study
Authors: Agergaard Anne-Sofie , Svensson Rene B. , Malmgaard-Clausen Nikolaj M. , Magnusson S. Peter 
Published: October 2024

Background: The long-term recovery (in years) of patellar tendinopathy treated with loading-based rehabilitation remains largely unknown. Purpose: To examine the clinical outcome and tendon structure years after exercise-based treatment of chronic patellar tendinopathy. Study Design: Case series; Level of evidence, 4. Methods: This was a 3- to 4-year follow-up evaluation of participants (N = 28) from a previous randomized clinical trial by the author group. All participants received loading-based rehabilitation for 12 weeks with either moderate-slow resistance (55% of 1 repetition maximum) or heavy-slow resistance (up to 90% of 1 repetition maximum). Both groups showed similar improvements after 3 and 12 months and were therefore collapsed in the present analysis. Function and symptoms (the Victorian Institute of Sport Assessment–Patella [VISA-P] questionnaire), tendon pain (numeric rating scale [NRS] during activity and during a single-leg decline squat test), and tendon structure (tendon vascularization and thickness on ultrasound) were assessed. Results: The mean follow-up was 3.6 ± 0.4 years after the baseline assessment in the original clinical trial. The VISA-P score was 83.9 ± 11.9 (95% CI, 79.3-88.5) at the latest follow-up and did not differ from the 1-year follow-up score ( P = .54). Similarly, NRS score during preferred sport (1.6 ± 1.7; 95% CI, 0.9-2.2) and single-leg decline squat (1.0 ± 1.8; 95% CI, 0.3-1.7) did not differ from the 1-year values and remained elevated. Power Doppler area and tendon thickness decreased significantly from 1 year to latest follow-up ( P < .0001 and P = .02, respectively), but power Doppler area >1 mm2 was still present in 43% of the participants after 3 to 4 years, and the tendon thickness was still mildly elevated (6.4 ± 1.8 mm; 95% CI, 5.7-7.1 mm). Sports participation after 3 to 4 years (3.9 ± 2.7 h/wk; 95% CI, 2.9-7.1 h/wk) was significantly lower compared with preinjury levels ( P < .0001). Conclusion: Clinical symptoms remained even years after loading-based treatment for patellar tendinopathy, whereas some but not all tendon structures normalized in this longer term follow-up.
Defining, Measuring, and Increasing “Rootedness” in the High Migration Context of Honduras
Authors: Hare Tom , Rivero Fuentes María Estela , Waitkuweit Kevin Hans 
Published: October 2024

Executive Summary The notion of “rootedness” in the sociology and migration literature is not well defined despite its increasing use by academics and, especially, practitioners. Defining and measuring rootedness has been problematic given that it is often operationalized as, but is not fully captured by, a concept related to social capital, community attachment, and participation. Rootedness is also often thought of as solely the absence of the desire to migrate. However, we argue that an individual’s desire to stay can be just as important as the well-documented “root causes” of migration; that is, economic poverty, insecurity, and strong migration networks. We propose a working definition of the concept of rootedness based on an empirical analysis of data from a nationally representative survey in the high migration context of Honduras. We find that rootedness can both be defined as and measured by an individual’s agreement with the idea that where they live is their “true home” and that they “see a good future” in that location. We further find that rootedness can be increased via a strong sense of security (not only the absence of victimization) and active community support for youth. Programs and policies should therefore promote security that goes beyond just preventing crime and fosters a general sense of wellbeing. In particular, programs should promote efforts to ensure that youth are supported by incorporating them in community decision-making, listening to what youth propose, promoting youth participation, and supporting youth leadership. Importantly, income is not strongly associated with this definition of rootedness. This finding highlights the important role of non-economic factors in migration decisions. Even when income increases, it does not necessarily increase the aspiration to stay. To be rooted, as we conceive of it, means more than having sufficient income. In summary, the paper examines and offers a new understanding of the concept of “rootedness,” which speaks to why some members of a community want to migrate and others desire to remain in their home communities. Fleshing out our understanding of rootedness as a way to talk about and measure the desire to remain is therefore crucial to realizing the “right” or “freedom” to stay at home.
The Impact of the COVID-19 Pandemic on Recovery From Substance Use Disorder: Findings From a Qualitative Study
Authors: Hassett-Walker Connie 
Published: October 2024

Background: This study considers how the COVID-19 pandemic impacted individuals recovering from a substance use disorder (SUD). Method: Fifty individuals recovering from SUD in Vermont, a rural New England state (U.S.), were recruited for an interview from 12-step recovery meetings (Alcoholics Anonymous, Narcotics Anonymous) as well as via word-of-mouth. Interviews were transcribed and coded, and qualitative analyses were performed. Results: Many of the participants who were in recovery prior to the pandemic starting remained substance-free and in recovery throughout the pandemic period. Some individuals used substances during the pandemic period, although not typically in the context of a relapse caused by negative emotions (eg, distress over a loved one contracting COVID-19). The majority of those individuals indicated that the risk of catching COVID-19 did not alter their substance use. Conclusions: Many individuals already in SUD recovery before COVID-19 remained in recovery despite the challenges of pandemic era. The role of peer support in recovering individuals managing negative emotions caused by COVID-19 is considered.
Interstitial lung diseases in collagen vascular diseases
Authors: Lamblin C. , Bergoin C. , Saelens T. , Wallaert B. 
Published: October 2024

In this review, a clinical update is presented of the most important collagen vascular diseases (CVDs) and the different types of interstitial lung disease (ILD) encountered in these CVDs. These CVDs represent a heterogenous group of immunologically mediated inflammatory disorders with a large variety of affected organs besides the lungs.The frequency, clinical presentation, prognosis and response to therapy vary depending on the histological pattern (usual interstitial pneumonia, desquamative interstitial pneumonia, organising pneumonia, diffuse alveolar damage, nodular lesions,etc.), as well as on the underlying CVD (scleroderma, rheumatoid arthritis, systemic lupus erythematosus, dermatopolymyositis, Sjögren's syndrome or mixed connective tissue disease).The diagnosis of most of these CVDs is based on a number of criteria; in several of these, however, lung involvement is not part of the diagnostic criteria. In addition, there may be overlaps between several of these CVDs.Optimal treatment varies depending on the type of collagen vascular disease and the presence of interstitial lung disease, although in many cases, a combination of corticosteroids and cytostatic drugs are given.
Oral supplementation of choline attenuates the development of alcohol-related liver disease (ALD)
Authors: Sánchez Victor , Baumann Anja , Kromm Franziska , Yergaliyev Timur , Brandt Annette , Scholda Julia , Kopp Florian , Camarinha-Silva Amélia , Bergheim Ina 
Published: October 2024

Abstract
Background
Chronic alcohol intake is associated with alterations of choline metabolism in various tissues. Here, we assessed if an oral choline supplementation attenuated the development of alcohol-related liver disease (ALD) in mice.

Methods
Female C57BL/6 J mice (n = 8/group) were either pair-fed a liquid control diet, or a Lieber DeCarli liquid diet (5% ethanol) ± 2.7 g choline/kg diet for 29 days. Liver damage, markers of intestinal permeability and intestinal microbiota composition were determined. Moreover, the effects of choline on ethanol-induced intestinal permeability were assessed in an ex vivo model.

Results
ALD development as determined by liver histology and assessing markers of inflammation (e.g., nitric oxide, interleukin 6 and 4-hydroxynonenal protein adducts) was attenuated by the supplementation of choline. Intestinal permeability in small intestine being significantly higher in ethanol-fed mice was at the level of controls in ethanol-fed mice receiving choline. In contrast, no effects of the choline supplementation were found on intestinal microbiota composition. Choline also significantly attenuated the ethanol-induced intestinal barrier dysfunction in small intestinal tissue ex vivo, an effect almost entirely abolished by the choline oxidase inhibitor dimbunol.

Conclusion
Our results suggest that an oral choline supplementation attenuates the development of ALD in mice and is related to a protection from intestinal barrier dysfunction.
mulea: An R package for enrichment analysis using multiple ontologies and empirical false discovery rate
Authors: Turek Cezary , Ölbei Márton , Stirling Tamás , Fekete Gergely , Tasnádi Ervin , Gul Leila , Bohár Balázs , Papp Balázs , Jurkowski Wiktor , Ari Eszter 
Published: October 2024

AbstractTraditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. mulea is distributed as a CRAN R package downloadable from https://cran.r-project.org/web/packages/mulea/ and https://github.com/ELTEbioinformatics/mulea. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.
Biomedical relation extraction method based on ensemble learning and attention mechanism
Authors: Jia Yaxun , Wang Haoyang , Yuan Zhu , Zhu Lian , Xiang Zuo-lin 
Published: October 2024

Abstract
Background
Relation extraction (RE) plays a crucial role in biomedical research as it is essential for uncovering complex semantic relationships between entities in textual data. Given the significance of RE in biomedical informatics and the increasing volume of literature, there is an urgent need for advanced computational models capable of accurately and efficiently extracting these relationships on a large scale.

Results
This paper proposes a novel approach, SARE, combining ensemble learning Stacking and attention mechanisms to enhance the performance of biomedical relation extraction. By leveraging multiple pre-trained models, SARE demonstrates improved adaptability and robustness across diverse domains. The attention mechanisms enable the model to capture and utilize key information in the text more accurately. SARE achieved performance improvements of 4.8, 8.7, and 0.8 percentage points on the PPI, DDI, and ChemProt datasets, respectively, compared to the original BERT variant and the domain-specific PubMedBERT model.

Conclusions
SARE offers a promising solution for improving the accuracy and efficiency of relation extraction tasks in biomedical research, facilitating advancements in biomedical informatics. The results suggest that combining ensemble learning with attention mechanisms is effective for extracting complex relationships from biomedical texts. Our code and data are publicly available at: https://github.com/GS233/Biomedical.
Complementing aculiferan mitogenomics: comparative characterization of mitochondrial genomes of Solenogastres (Mollusca, Aplacophora)
Authors: Bergmeier Franziska S. , Brachmann Andreas , Kocot Kevin M. , Leasi Francesca , Poustka Albert J. , Schrödl Michael , Sevigny Joseph L. , Thomas W. Kelley , Todt Christiane , Jörger Katharina M. 
Published: October 2024

Abstract
Background
With the advances in high-throughput sequencing and bioinformatic pipelines, mitochondrial genomes have become increasingly popular for phylogenetic analyses across different clades of invertebrates. Despite the vast rise in available mitogenomic datasets of molluscs, one class of aplacophoran molluscs – Solenogastres (or Neomeniomorpha) – is still neglected.

Results
Here, we present six new mitochondrial genomes from five families of Solenogastres (Amphimeniidae, Gymnomeniidae, Proneomeniidae, Pruvotinidae, Simrothiellidae), including the first complete mitogenomes, thereby now representing three of the four traditional orders. Solenogaster mitogenomes are variable in size (ranging from approximately 15,000 bp to over 17,000 bp). The gene order of the 13 protein coding genes and two rRNA genes is conserved in three blocks, but considerable variation occurs in the order of the 22 tRNA genes. Based on phylogenetic analyses and reconstruction of ancestral mitochondrial genomes of Aculifera, the position of (1) trnD gene between atp8 and atp6, (2) trnT and P genes between atp6 and nad5, and (3) trnL1 gene between G and E, resulting in a ‘MCYWQGL1E’-block of tRNA genes, are all three considered synapomorphies for Solenogastres. The tRNA gene block ‘KARNI’ present in Polyplacophora and several conchiferan taxa is dissolved in Solenogastres.

Conclusion
Our study shows that mitogenomes are suitable to resolve the phylogenetic relationships among Aculifera and within Solenogastres, thus presenting a cost and time efficient compromise to approach evolutionary history in these clades.
Does time matter? Intraspecific diversity of ribosomal RNA genes in lineages of the allopolyploid model grass Brachypodium hybridum with different evolutionary ages
Authors: Trunova Dana , Borowska-Zuchowska Natalia , Mykhailyk Serhii , Xia Kai , Zhu Yuanbin , Sancho Ruben , Rojek-Jelonek Magdalena , Garcia Sònia , Wang Kai , Catalan Pilar , Kovarik Ales , Hasterok Robert , Kolano Bozena 
Published: October 2024

Abstract
Background
Polyploidisation often results in genome rearrangements that may involve changes in both the single-copy sequences and the repetitive genome fraction. In this study, we performed a comprehensive comparative analysis of repetitive DNA, with a particular focus on ribosomal DNA (rDNA), in Brachypodium hybridum (2n = 4x = 30, subgenome composition DDSS), an allotetraploid resulting from a natural cross between two diploid species that resemble the modern B. distachyon (2n = 10; DD) and B. stacei (2n = 20; SS). Taking advantage of the recurrent origin of B. hybridum, we investigated two genotypes, Bhyb26 and ABR113, differing markedly in their evolutionary age (1.4 and 0.14 Mya, respectively) and which resulted from opposite cross directions. To identify the origin of rDNA loci we employed cytogenetic and molecular methods (FISH, gCAPS and Southern hybridisation), phylogenetic and genomic approaches.

Results
Unlike the general maintenance of doubled gene dosage in B. hybridum, the rRNA genes showed a remarkable tendency towards diploidisation at both locus and unit levels. While the partial elimination of 35S rDNA units occurred in the younger ABR113 lineage, unidirectional elimination of the entire locus was observed in the older Bhyb26 lineage. Additionally, a novel 5S rDNA family was amplified in Bhyb26 replacing the parental units. The 35S and 5S rDNA units were preferentially eliminated from the S- and D-subgenome, respectively. Thus, in the more ancient B. hybridum lineage, Bhyb26, 5S and 35S rRNA genes are likely expressed from different subgenomes, highlighting the complexity of polyploid regulatory networks.

Conclusion
Comparative analyses between two B. hybridum lineages of distinct evolutionary ages revealed that although the recent lineage ABR113 exhibited an additive pattern of rDNA loci distribution, the ancient lineage Bhyb26 demonstrated a pronounced tendency toward diploidisation manifested by the reduction in the number of both 35S and 5S loci. In conclusion, the age of the allopolyploid appears to be a decisive factor in rDNA turnover in B. hybridum.
Meta-analysis accelerator: a comprehensive tool for statistical data conversion in systematic reviews with meta-analysis
Authors: Abbas Abdallah , Hefnawy Mahmoud Tarek , Negida Ahmed 
Published: October 2024

Abstract
Background
Systematic review with meta-analysis integrates findings from multiple studies, offering robust conclusions on treatment effects and guiding evidence-based medicine. However, the process is often hampered by challenges such as inconsistent data reporting, complex calculations, and time constraints. Researchers must convert various statistical measures into a common format, which can be error-prone and labor-intensive without the right tools.

Implementation
Meta-Analysis Accelerator was developed to address these challenges. The tool offers 21 different statistical conversions, including median & interquartile range (IQR) to mean & standard deviation (SD), standard error of the mean (SEM) to SD, and confidence interval (CI) to SD for one and two groups, among others. It is designed with an intuitive interface, ensuring that users can navigate the tool easily and perform conversions accurately and efficiently. The website structure includes a home page, conversion page, request a conversion feature, about page, articles page, and privacy policy page. This comprehensive design supports the tool’s primary goal of simplifying the meta-analysis process.

Results
Since its initial release in October 2023 as Meta Converter and subsequent renaming to Meta-Analysis Accelerator, the tool has gained widespread use globally. From March 2024 to May 2024, it received 12,236 visits from countries such as Egypt, France, Indonesia, and the USA, indicating its international appeal and utility. Approximately 46% of the visits were direct, reflecting its popularity and trust among users.

Conclusions
Meta-Analysis Accelerator significantly enhances the efficiency and accuracy of meta-analysis of systematic reviews by providing a reliable platform for statistical data conversion. Its comprehensive variety of conversions, user-friendly interface, and continuous improvements make it an indispensable resource for researchers. The tool’s ability to streamline data transformation ensures that researchers can focus more on data interpretation and less on manual calculations, thus advancing the quality and ease of conducting systematic reviews and meta-analyses.
Distribution and antifungal susceptibility profiles of Candida species isolated from candidemia patients admitted to Egyptian tertiary hospitals: a cross-sectional study
Authors: Aziz Heba Sherif Abdel , Ismail Dalia Kadry , Mohammed Nessma Sayed Ahmed , Elgendy Marwa O. , Bassiouny Dina M. 
Published: October 2024

Abstract
Background
Candidemia is a widespread threat that can lead to significant complications in healthcare settings.

Objectives
Our study aimed to identify isolates of Candida isolated from blood culture bottles of patients with candidemia and assess their antifungal susceptibility profiles.

Methods
We conducted a cross-sectional study at Cairo University tertiary care hospitals over 16 months including 90 patients. Candida isolates were collected from blood culture bottles, and identified using MALDI-TOF MS technology of VITEK MS PRIME (bioMérieux) with the corresponding database VITEK IVD Database 3.2. followed by antifungal susceptibility testing using VITEK 2 Compact system.

Results
Candida albicans was the most common species isolated from both pediatric and adult patients with percentages of 47.3% and 36.4% respectively, followed by Candida parapsilosis with percentages of 32.6% and 25.0% respectively. Voriconazole showed the highest antifungal activity at 90.9% of isolates in adults and 95.7% in pediatrics, followed by caspofungin and micafungin. The mean hospital stays for adults ranged from 8 to 30 days and from 10 to 42 days in the pediatric group.

Conclusions
C. albicans remains the predominant species isolated from both pediatric and adult candidemia patients, despite a notable increase in other species. C. tropicalis and C. parapsilosis are considered the most common non-albicans Candida (NAC) species. The rise in Candida species other than albicans highlights the urgent need for effective antifungal stewardship programs. Voriconazole exhibited the higher antifungal activity followed by caspofungin and micafungin.