bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hospital-Acquired Complications in Critically Ill Children and PICU Length of Stay, Duration of Respiratory Support, and Economics: Propensity Score Matching in a Single-Center Cohort, 2015–2020
Authors: Schults Jessica A. , Hall Lisa , Charles Karina R. , Rickard Claire M. , Le Marsney Renate , Ergetu Endrias , Gregg Alex , Byrnes Joshua , Rahiman Sarfaraz , Long Debbie , Lake Anna , Gibbons Kristen 
Published: December 2024

Objectives:
To identify the health and economic costs of hospital-acquired complications (HACs) in children who require PICU admission.

Design:
Propensity score matched cohort study analyzing routinely collected medical and costing data collected by the health service over 6 years (2015–2020).

Setting:
Tertiary referral PICU in Queensland, Australia.

Patients:
All children admitted to the PICU were included.

Interventions:
None.

Measurements and Main Results:
We assessed ventilator- and respiratory support-free days at 30 days post-PICU admission, length of PICU stay, prevalence of individual HACs, and attributable healthcare costs. A total of 8437 admissions, representing 6054 unique patients were included in the analysis. Median (interquartile range) for cohort age was 2.1 years (0.4–7.7 yr), 56% were male. Healthcare-associated infections contributed the largest proportion of HACs (incidence rate per 100 bed days, 46.5; 95% CI, 29.5–47.9). In the propensity score matched analyses (total 3852; 1306 HAC and 1371 no HAC), HAC events were associated with reduced ventilator- (adjusted subhazard ratio [aSHR], 0.88 [95% CI, 0.82–0.94]) and respiratory support-free days (aSHR, 0.74 [95% CI, 0.69–0.79]) and increased PICU length of stay (aSHR, 0.63 [95% CI, 0.58–0.68]). Healthcare costs for children who developed a HAC were higher compared with children with no HAC, with mean additional cost ranging from Australian dollar (A$) 77,825 (one HAC [95% CI, $57,501–98,150]) to $310,877 (≥ 4 HACs [95% CI, $214,572–407,181]; in 2022, the average conversion of A$ to U.S. dollar was 0.74).

Conclusions:
In our PICU (2015–2020), the burden of HAC for critically ill children was highest for healthcare-associated infections. Further high-quality evidence regarding HAC prevention and prospective risk assessment could lead to improved patient outcomes and reduced costs.
A randomized trial for combination nicotine replacement therapy for smoking cessation among people with HIV in a low-resourced setting
Authors: Elf Jessica L. , Lebina Limakatso , Motlhaoleng Katlego , Chon Sandy , Niaura Raymond , Abrams David , Variava Ebrahim , Gupte Nikhil , Martinson Neil , Golub Jonathan E. 
Published: December 2024

Objective:
The purpose of this study was to evaluate the efficacy of combination nicotine replacement therapy (c-NRT) for smoking cessation among people with HIV (PWH) in South Africa.

Design:
We conducted an open label, individually randomized clinical trial.

Methods:
Using a two-armed approach, PWH who smoke were randomized to receive either 1) intensive anti-smoking behavioral counseling (BC) or 2) intensive anti-smoking BC plus c-NRT (nicotine patches augmented by nicotine gum). Self-reported smoking abstinence was biochemically validated with exhaled breath carbon monoxide (CO) and urine cotinine at six months. Recruitment, provision of trial interventions, and follow-up of participants took place March 2014 through June 2016.

Results:
We randomly assigned 280 participants to the BC arm and 281 participants to the BC + c-NRT arm. 438 (78%) participants were male and 123 (22%) were female. For our primary outcome of biochemically verified abstinence at six months, 41 (15%) were quit in the BC + c-NRT arm versus 28 (10%) in the BC arm, resulting in a 5% (95% CI -1%, 10%) absolute difference in relative risk and an adjusted odd ratio of 1.47 (95% CI: 0.86, 2.52) comparing the BC + c-NRT to the BC arm.

Conclusions:
Although our results did not reach statistical significance, we found augmentation of BC with c-NRT to increase smoking abstinence at six months, which is consistent with performance in the general population. PWH in low-resource settings may benefit from the addition of c-NRT to existing tobacco cessation interventions.
Accessory Posterior Cerebral Artery—The Hyperplastic Anterior Choroidal Artery Variant
Authors: Triantafyllou George , Papadopoulos-Manolarakis Panagiotis , Piagkou Maria 
Published: December 2024

Variants of the cerebral arterial circle, both common and rare, are frequently documented. The authors present a distinct case involving a 54-year-old male patient who underwent a computed tomography angiogram (CTA), which was analyzed using planar slices and 3-dimensional reconstruction. In this case, the left posterior cerebral artery (PCA) received the posterior communicating artery (PComA) 7 mm distal to its origin from the basilar artery (BA). In addition, an accessory vessel originated 4.2 mm distal from the PComA origin, branching from the left internal carotid artery (ICA). This vessel was identified as an accessory posterior cerebral artery (APCA), corresponding to a hyperplastic anterior choroidal artery (AChA). This case illustrates a rare variant in the posterior circulation of the brain, in which the territory of the PCA is supplied by both the internal carotid and vertebrobasilar systems.
Perioperative Opioid Use in Urogynecologic Mesh Removal
Authors: Artsen Amanda M. , Gichuru Roseanne , Bonidie Michael , Giugale Lauren , Moalli Pamela A. 
Published: December 2024

Importance
Forty percent of patients with urogynecologic mesh pain complications are taking narcotics.

Objectives
We aimed to compare comorbidities and pain scores between patients with and without narcotic use and assess postoperative narcotic use rates.

Study Design
This was a secondary analysis of a prospective cohort study of patients undergoing urogynecologic mesh removal. Patients with mesh removal for pain within 7 years were included due to data availability. Narcotic prescriptions were verified using the Pennsylvania Prescription Drug Monitoring Program. Pain scores were assessed at baseline and 6–24 months postoperatively.

Results
Of 139 patients, 30 (21.6%) filled narcotic prescriptions within 3 months preceding surgery. These patients were younger and more likely to have a chronic pain condition. Narcotic use did not differ by sling versus prolapse mesh, or presence of exposure. Patients taking preoperative narcotics had a 27-point higher median baseline visual analog scale pelvic pain score (P = 0.01). Patients with pain comorbidities had 6 times odds of using preoperative narcotics. Younger patients had less improvement in pelvic pain after removal. Only 8 (27%) of those taking narcotics discontinued use postoperatively with no significant predictors of prolonged (≥3 months) use. Eighty-seven percent of patients with prolonged postoperative use had a prior pain diagnosis, commonly joint and back pain.

Conclusions
In patients with mesh-related pain, those with chronic pain conditions had much higher odds of taking preoperative narcotics, and in most, mesh removal did not eliminate narcotic use. Counseling is warranted in patients with chronic pain conditions that pain and narcotic use are likely to persist after removal.
A comprehensive workflow for allele-specific immune gene quantification and expression analysis in single-cell RNA-seq data
Authors: Al Ajami Ahmad , Schuck Jonas , Marini Federico , Imkeller Katharina 
Published: December 2024

ABSTRACTMotivationImmune molecules such as B and T cell receptors, human leukocyte antigens (HLAs), or killer Ig-like receptors (KIRs) are encoded in the most genetically diverse loci of the human genome. Many of these immune genes exhibit remarkable allelic diversity across populations. While computational methods for HLA typing from bulk RNA sequencing data have emerged, streamlined solutions for allele-specific quantification in single-cell RNA sequencing (scRNA-seq) are lacking. Moreover, no standardized data structure or analytical framework has been established to handle allele-specific immune gene expression data at single-cell level.ResultsWe present a comprehensive workflow to (1) automate allele-typing and allele-specific expression quantification of HLA transcripts in scRNA-seq data using a Snakemake workflow,scIGD(single-cell ImmunoGenomic Diversity), and (2) represent and interactively explore immune gene expression at different annotation levels using a multi-layer data structure implemented as an R/Bioconductor software package,SingleCellAlleleExperiment. We validated our approach on a diverse spectrum of scRNA-seq datasets, and found that it performs consistently across different sequencing platforms and experimental setups. We illustrate how our method can be utilized to study loss of HLA expression in tumor cells or discover differential HLA allele expression in specific immune cell subtypes. By capturing such allele-specific expression patterns and their variation, our workflow offers novel insights into human immunogenomic diversity.Availability and implementationscIGDis available under the MIT license at:https://github.com/AGImkeller/scIGD.SingleCellAlleleExperimentis available under the MIT license at:https://bioconductor.org/packages/SingleCellAlleleExperiment.scaeDataprovides validation datasets and is available under the MIT license at:https://bioconductor.org/packages/scaeData.Data processed withscIGDare available at:https://doi.org/10.5281/zenodo.14033960.ContactKatharina Imkeller. E-mail:imkeller@rz.uni-frankfurt.de.Supplementary informationSupplementary data are available within the same submission.
Gasdermin D mediates a fast transient release of ATP after NLRP3 inflammasome activation before ninjurin 1–induced lytic cell death
Authors: Schachter Julieta , Guijarro Adriana , Angosto-Bazarra Diego , Pinilla Miriam , Hurtado-Navarro Laura , Meunier Etienne , Pérez-Oliva Ana B. , Schwarzbaum Pablo J , Pelegrin Pablo 
Published: December 2024

SummaryPyroptosis is a lytic cell death triggered by the cleavage of gasdermin (GSDM) proteins and subsequent pore formation by the N-terminal domain oligomerization in the plasma membrane. GSDMD is cleaved by caspase-1/-4/-5/-11 upon inflammasome activation and mediates IL-1β and IL-18 release. GSDMD pores favors ninjurin-1 (NINJ1) induced plasma membrane rupture and cell death. Here, we demonstrate that GSDMD mediates early ATP release upon NLRP3 inflammasome activation independently of NINJ1, occurring before IL-1β release and cell death and constituting an early danger signal. The release of ATP is a transient signal terminated before the cells continue to permeabilize and die. The different N-terminal of GSDMA to E are also able to release ATP and induce monocyte migration towards pyroptotic cells. This study reveals ATP release as an early, and transient danger signal depending on GSDMD plasma membrane permeabilization, independently of the late stages of lytic cell death.
An artificial intelligence-based model for prediction of Clonal Hematopoiesis mutants in cell-free DNA samples
Authors: Arango-Argoty Gustavo , Haghighi Marzieh , Sun Gerald J. , Markovets Aleksandra , Barrett J. Carl , Lai Zhongwu , Jacob Etai 
Published: December 2024

AbstractCirculating tumor DNA is a critical biomarker in cancer diagnostics, but its accurate interpretation requires careful consideration of clonal hematopoiesis (CH), which can contribute to variants in cell-free DNA and potentially obscure true tumor-derived signals. Accurate detection of somatic variants of CH origin in plasma samples remains challenging in the absence of matched white blood cells sequencing. Here we present an open-source machine learning framework (MetaCHIP) which classifies variants in cfDNA from plasma-only samples as CH or tumor origin, surpassing state-of-the-art classification rates.
Mapping cell-cell fusion at single-cell resolution
Authors: Gardner Andrea L. , Zheng Lan , Howland Kennedy , Saunders Andrew , Ramirez Andrea , Parker Patrik , Iloegbunam Chisom , Morgan Daylin , Jost Tyler A. , Brock Amy 
Published: December 2024

AbstractCell-cell fusion is a tightly controlled process in the human body known to be involved in fertilization, placental development, muscle growth, bone remodeling, and viral response. Fusion between cancer cells results first in a whole-genome doubled state, which may be followed by the generation of aneuploidies; these genomic alterations are known drivers of tumor evolution. The role of cell-cell fusion in cancer progression and treatment response has been understudied due to limited experimental systems for tracking and analyzing individual fusion events. To meet this need, we developed a molecular toolkit to map the origins and outcomes of individual cell fusion events within a tumor cell population. This platform, ClonMapper Duo (‘CMDuo’), identifies cells that have undergone cell-cell fusion through a combination of reporter expression and engineered fluorescence-associated index sequences paired to randomly generated nucleotide barcodes. scRNA-seq of the indexed barcodes enables the mapping of each set of parental cells and fusion progeny throughout the cell population. In triple-negative breast cancer cells CMDuo uncovered subclonal transcriptomic hybridization and unveiled distinct cell-states which arise in direct consequence of homotypic cell-cell fusion. CMDuo is a platform that enables mapping of cell-cell fusion events in high-throughput single cell data and enables the study of cell fusion in disease progression and therapeutic response.
Error reduction in leukemia machine learning classification with conformal prediction
Authors: Lysenkova Wiklander Mariya , Zachariah Dave , Krali Olga , Nordlund Jessica 
Published: December 2024

ABSTRACTPurposeRecent advances in machine learning (ML) have led to the development of classifiers that predict molecular subtypes of acute lymphoblastic leukemia (ALL) using RNA sequencing (RNA-seq) data. While these models have shown promising results, they often lack robust performance guarantees. The aim of this study was three-fold: to quantify the uncertainty of these classifiers; to provide prediction sets that control the false negative rate (FNR); and to perform implicit reduction by transforming incorrect predictions into uncertain predictions.MethodsConformal prediction is a distribution-agnostic framework for generating statistically calibrated prediction sets whose size reflects model uncertainty. In this study, we applied an extension called conformal risk control to ALLIUM, an RNA-seq ALL subtype classifier. Leveraging RNA-seq data from 1042 patient samples taken at diagnosis, we developed a multi-class conformal predictor, ALLCoP, which generates statistically guaranteed FNR-controlled prediction sets.ResultsALLCoP was able to create prediction sets with specified FNR tolerances ranging from 7.5-30%. In a validation cohort, ALLCoP successfully reduced the FNR of the ALLIUM classifier from 8.95% to 3.5%. For cases whose subtype was not previously known, the use of ALLCoP was able to reduce the occurrence of empty predictions from 37% to 17%. Notably, up to 34% of the multiple-class prediction sets included the PAX5alt subtype, suggesting that increased prediction set size may reflect secondary aberrations and biological complexity, contributing to classifier uncertainty. Finally, ALLCoP was validated on two additional RNA-seq ALL subtype classifiers, ALLSorts and ALLCatchR.ConclusionOur results highlight the potential of conformal prediction in enhancing the use of oncological RNA-seq subtyping classifiers and also in uncovering additional molecular aberrations of potential clinical importance.
PARP inhibitor counteracts Temozolomide Resistance in Glioblastoma Multiforme
Authors: Samarut Edouard , Gaston Tabourel , Joséphine Briand , Yuna Landais , Catherine Gratas , Pierre-François Cartron , François Vallette , Lisa Oliver , Aurélien Sérandour A. 
Published: December 2024

AbstractGlioblastoma multiforme (GBM), a highly aggressive brain tumor, frequently develops resistance to temozolomide (TMZ), the current standard chemotherapy. Our study investigates the potential of combining TMZ with the poly (ADP-ribose) polymerase inhibitor Olaparib (OLA) to overcome TMZ resistance. Usingin vitromodels, including U251 cell lines and patient-derived GBM primary cultures, we demonstrate that OLA enhances TMZ efficacy by disrupting base excision repair and potentiating DNA damage-induced cytotoxicity. A CRISPR knockout screen identified DNA mismatch repair (MMR) gene deficiencies as key drivers of TMZ resistance, which OLA effectively counteracts. Co-treatment with TMZ and OLA significantly reduced tumor cell viability, even in MMR-deficient and MGMT-expressing contexts, suggesting a synergistic mechanism. Gene expression analysis revealed that the combination therapy impacts cell cycle regulation, stress responses, and extracellular matrix integrity, leading to mitotic catastrophe and apoptosis. These findings propose the TMZ-OLA combination as a promising therapeutic strategy for overcoming chemoresistance in GBM.
From boardroom to sustainability reporting: stakeholder-RBV insights into ESG disclosures among Malaysian banks
Authors: Lui Tze Kiat , Zainuldin Mohd Haniff 
Published: December 2024

Purpose
Strengthening ESG strategies in Malaysian banks is necessary as they continue to face difficulties integrating ESG into their strategies and disclosure despite existing government frameworks. This study aims to use stakeholder-resource-based view (RBV) concept to explore how board characteristics and ownership concentration influence ESG disclosure practices in Malaysian banks.

Design/methodology/approach
The study analysed annual, environmental, social and governance (ESG) and integrated reports of Malaysian banks from 2010 to 2022 to examine the effects of board characteristics on ESG disclosures. Using content analysis and 481 balanced data sets, ordinary least squares (OLS) and robust regressions were applied, with interaction terms testing the moderating effects of ownership concentration.

Findings
Board independence negatively impacts ESG disclosure in Malaysian banks, suggesting that independent directors may not prioritise sustainability. Board size, diversity and sustainability committees positively influence ESG practices. Ownership concentration interactions reinforce these findings, but board independence remains negatively significant.

Research limitations/implications
Future research should expand the sample to other emerging markets, explore a wider range of bank board attributes and use advanced econometric methods to increase the generalisability of the results.

Practical implications
The study impacts theory, financial institutions and policy, redefining ESG practices in Malaysian banking. It highlights the role of board characteristics and the importance of ownership concentration. Several practical recommendations are provided.

Social implications
The study impacts theory, financial institutions and policy by redefining ESG practices within Malaysian banking. It highlights the significance of board characteristics and ownership concentration, offering several practical recommendations.

Originality/value
The study fills gaps in the literature by examining the impact of board characteristics on ESG disclosures through content and statistical analyses. It integrates stakeholder theory with RBV to provide novel insights into ESG reporting in Malaysian banks, highlighting the role of high ownership concentration in emerging markets.
The text mining approach to investigate active areas of library and information science and discover emerging topics
Authors: Nemati-Anaraki Leila , Dehghan Sogand , Asadzandi Shadi , Malgard Shiva 
Published: December 2024

Purpose
This study aims to adopt text mining to discover emerging topics in librarianship and information science research in the last decade. Based on the number of citations obtained during the previous 10 years, the authors selected emerging topics in this study and evaluated the strength of their presence. Additionally, the authors determined if the trend was substantial over time and identified the active topics in library and information science (LIS) through the past 10 years.

Design/methodology/approach
All library and medical information studies were retrieved by the WC = “Information Science & Library Science” tag in the Web of Science. Python programming was used for data analysis. The topics were identified by combining the unsupervised deep learning algorithms TOP2VEC and the term frequency-inverse document frequency and also the Mann–Kendall trend test is used to determine whether the trend was significant over time.

Findings
Following text mining, the total data from 2012 to 2021 was 63,712. Eleven main topics were also extracted: academic education of LIS, acquisition and collection development, publishing articles, cataloging and classification, journalism, knowledge management, infometrics, social media, university ranking, information and communication technologies and information storage and retrieval. Knowledge management has experienced the greatest growth over the past 10 years.

Originality/value
This analysis reveals which fields are prioritized and which are neglected by the LIS. The findings of this study can help researchers discover newer topics, focus on less-seen subjects and prevent repetitive research in one area.
Educators and students in entrepreneurship education are challenging the “think entrepreneur–think male” paradigm
Authors: Stoker Saskia , Wakkee Ingrid , Khapova Svetlana 
Published: December 2024

PurposeThe paradigm “think entrepreneur–think male” continues to prevail in entrepreneurship education (EE). Aiming to explore how EE educators and EE students engage with this paradigm, this paper examines how students’ beliefs about entrepreneurship are shaped within the classroom.Design/methodology/approachThis study is based on a single case comprising 32 interviews with EE students and educators from a variety of higher education institutions in the Netherlands. Observations were conducted in a learning environment where undergraduate students from a range of EE minors (general, social and tech entrepreneurship) collaborated on projects under the guidance of entrepreneurship educators.FindingsOur findings reveal that gendered constructs are deeply embedded in EE, shaping perceptions of entrepreneurship. However, these constructs are changing and challenging the “think entrepreneur–think male”.Originality/valueThis study contributes to gender and entrepreneurship literature by challenging the existence of the prevailing paradigm “think entrepreneur–think male” in EE. We emphasise the importance of acknowledging individual entrepreneurial motivations while recognising gendered constructs in entrepreneurial support and resource access.