bluuebunny/crossref_metadata_2025_split huggingface dataset:
Project Victoria: A pragmatic data model to automate RWE generation from the national French claims database
Authors: Ouazzani Kevin , Ansolabehere Xavier , Journeau Florence , Vidal Alexandre , Jaubourg Nicolas , Doublet Maxime , Thollot Raphael , Fabre Arnaud , Glatt Nicolas 
Published: February 2025

Objective: This paper describes Victoria, an empirically built data pipeline for SNDS to: - Build an automated, scalable pipeline supporting changes to the data model inherent to the use of large databases, - Deliver a documented pipeline with clear processes, enabling scientific, epidemiological researches, - Ease access to SNDS data in compliance with regulatory requirements. Methods: This paper describes the 2-steps process of the Victoria pipeline and its final output. The initial cleaning step consists in formatting, deleting empty, error or duplicate records and renaming variables without changing their values, accordingly with the official SNDS documentation. The second step consists in creating 2 linearised data models: every line of each table is an event, and each table is indexed with a unique patient identifier, without the need for a central patient or identifier table. These 2 models are: - the epidemiological model, used for answering most of the research questions requiring population phenotyping (demography, diagnosis, procedures characteristics). - the medico-economic model is used for costs and healthcare consumption analyses. It contains more complex information about reimbursements rates and the data quality assessment is focused on costs rather than medico-administrative information. Results: The pipeline was executed on 2 different datasets representing ∼85 000 and ∼870 000 beneficiaries with the following configuration: one master with 4 cores and 16Go of RAM and respectively 4 and 6 workers. The total execution time for the smaller dataset was 25 h and 96 h for the larger one. The longest part of those times is represented by the format conversion to parquet. The cleaning step took only 4 h in both cases. The epidemiological model took 344 min for the smaller dataset and 1934 min for the larger one. The medico-economic model took the longest time with 704 min and 2145 min, respectively. Conclusion: Victoria pipeline is a successfully implemented SNDS pipeline. Compared to previous pipelines, reviewability is part of its design as unit tests and quality assessments can natively be developed to ensure data and analysis quality. The pipeline has been used for 2 published studies. The recent work toward OMOP conversion will be integrated in upcoming versions and, as Victoria is set to run on a CD platform, the potential evolution if SNDS format can be considered.
Investigating the Role of the Physical Environment on Communication Patterns in Emergency Departments During Caregiving for Pediatric Mental and Behavioral Health Patients
Authors: Jiang Yueci , Joseph Anjali , Gripko Monica , Mihandoust Sahar , Zinzow Heidi , Easler Lucinda , Dietrich Ann ,   RIPCHD.PED Study Group
Published: February 2025

Objective This study investigates how the physical environment influences communication dynamics among staff members, pediatric mental and behavioral health (MBH) patients, and their families in the emergency department (ED). Background The United States faces a public health challenge as MBH conditions in school-age children contribute to an increasing number of ED visits. Effective communication plays a pivotal role in pediatric MBH caregiving, where challenges often arise due to the sensitive nature of these conditions. Methods This qualitative study involved observations and semistructured interviews with 55 care providers across four hospital-based EDs in the southeastern United States. Results Qualitative thematic analysis of the interviews identified physical environment impacts on communication at three scales: unit, staff workstation, and patient care space. This study identified aspects of the physical environment, such as proximity, visibility, crowding, and privacy as influential factors in communication patterns for the MBH care process in ED. Conclusions The physical environment has an essential impact on communication patterns and care delivery for the increasing number of pediatric MBH patients in the ED.
Exploring Men’s Experiences of Engagement With General Practice: A Qualitative Study
Authors: Mursa Ruth , Patterson Christopher , McErlean Gemma , Halcomb Elizabeth 
Published: February 2025

Introduction: As males are less engaged with healthcare than females, they often present when a condition is more advanced, reducing the potential for early intervention. Little is known about why men are less engaged and what influences them to be more proactive. This study sought to explore men’s experiences of engagement with general practice. Methods: A qualitative descriptive study was nested within a sequential mixed-methods project. Semi-structured interviews were undertaken with 17 male staff and volunteers of the New South Wales Rural Fire Service about their experiences, attitudes, and preferences for general practice engagement. Thematic analysis was used to analyze data. Results: Five sub-themes emerged about men’s engagement with general practice. “Reasons for engagement” revealed motivations for seeking healthcare. “Seeking validation” explained how social influences impacted engagement. The “importance of relationships” highlighted the value men place on trust with the healthcare provider/team, and how this impacts engagement. “Interpersonal communication” addressed preferences for direct and authentic communication. Finally, “barriers to engagement” revealed the challenges in accessing care. Conclusions: Awareness of the barriers and facilitators to men’s engagement with general practice can inform strategies to improve care. This study suggests that health professionals play a crucial role in building therapeutic relationships with men and partnering with them in their healthcare journey to improve engagement and health outcomes.
Effects of Transverse Process Hook Fixation for Preventing Proximal Junctional Kyphosis/Failure in Adult Spinal Deformity Surgery: A Multiple Regression Analysis Adjusting for Confounding Factors
Authors: Park Se-Jun , Park Jin-Sung , Kang Dong-Ho , Kang Minwook , Jung Kyunghun , Lee Chong-Suh 
Published: February 2025

Study design Retrospective study. Objectives To investigate the effects of transverse process hook (TPH) at the uppermost instrumented vertebra (UIV) + 1 on the prevention of proximal junctional kyphosis/failure (PJK/F) following adult spinal deformity (ASD) surgery. Methods We included patients who underwent fusion of the lower thoracic spine (T8–T11) to the sacrum for ASD. The patients were divided into the non-TPH and TPH groups. PJK and PJF were defined as proximal junctional angle >20° and any cases requiring revision surgery. Multiple regression analysis was performed, including surgical techniques (non-use of TPH vs TPH) and confounding variables. Results Altogether, 153 patients were included in the study (women, 91.5%; mean age, 69.2 years; total levels fused, 8.5). The non-TPH and TPH groups comprised 88 and 65 patients. Unadjusted bivariate analysis showed that the TPH did not significantly affect the risk of PJK and PJF. However, multiple regression analysis revealed that the non-use of TPH was associated with an increased risk of developing PJK and PJF (odds ratio [OR] = 3.079, P = 0.029 for PJK; OR = 6.363, P = 0.049 for PJF). In patients who underwent TPH fixation, confounder-adjusted regression analysis showed that two-level TPH fixation did not further decrease the risk of PJK/F. Conclusions The preventive effect of TPH against PJK/F development was not significant in the unadjusted bivariate analysis. However, multiple regression analysis adjusted for the confounding factors demonstrated that TPH fixation at the UIV +1 significantly decreased the risk of PJK and PJF.
A foundation systematic review of natural language processing applied to gastroenterology & hepatology
Authors: Stammers Matthew , Ramgopal Balasubramanian , Owusu Nimako Abigail , Vyas Anand , Nouraei Reza , Metcalf Cheryl , Batchelor James , Shepherd Jonathan , Gwiggner Markus 
Published: February 2025

Abstract

Objective
This review assesses the progress of NLP in gastroenterology to date, grades the robustness of the methodology, exposes the field to a new generation of authors, and highlights opportunities for future research.

Design
Seven scholarly databases (ACM Digital Library, Arxiv, Embase, IEEE Explore, Pubmed, Scopus and Google Scholar) were searched for studies published between 2015 and 2023 that met the inclusion criteria. Studies lacking a description of appropriate validation or NLP methods were excluded, as were studies ufinavailable in English, those focused on non-gastrointestinal diseases and those that were duplicates. Two independent reviewers extracted study information, clinical/algorithm details, and relevant outcome data. Methodological quality and bias risks were appraised using a checklist of quality indicators for NLP studies.

Results
Fifty-three studies were identified utilising NLP in endoscopy, inflammatory bowel disease, gastrointestinal bleeding, liver and pancreatic disease. Colonoscopy was the focus of 21 (38.9%) studies; 13 (24.1%) focused on liver disease, 7 (13.0%) on inflammatory bowel disease, 4 (7.4%) on gastroscopy, 4 (7.4%) on pancreatic disease and 2 (3.7%) on endoscopic sedation/ERCP and gastrointestinal bleeding. Only 30 (56.6%) of the studies reported patient demographics, and only 13 (24.5%) had a low risk of validation bias. Thirty-five (66%) studies mentioned generalisability, but only 5 (9.4%) mentioned explainability or shared code/models.

Conclusion
NLP can unlock substantial clinical information from free-text notes stored in EPRs and is already being used, particularly to interpret colonoscopy and radiology reports. However, the models we have thus far lack transparency, leading to duplication, bias, and doubts about generalisability. Therefore, greater clinical engagement, collaboration, and open sharing of appropriate datasets and code are needed.
Anti-inflammatory treatment using alpha melanocyte stimulating hormone (α-MSH) does not alter osteoblasts differentiation and fracture healing
Authors: Graue Johanna , Timmen Melanie , Schmitz Katharina , Kronenberg Daniel , Böhm Markus , Sivaraj Kishor K. , Bixel M. Gabriele , Stange Richard 
Published: February 2025

Abstract

Background
Alpha-melanocyte-stimulating-hormone (α-MSH) has been identified as a new anti-inflammatory treatment compound in rheumatoid arthritis (RA) and other inflammatory diseases. However, its direct effect on bone cell differentiation or on bone regeneration, which is an inflammatory process, too, has not been investigated, yet. Bone tissue is significantly affected in inflammatory joint diseases. Additionally, inflammatory signaling is essential -in bone regeneration during fracture healing. Therefore, we evaluated the impact of α-MSH-treatment on bone forming cells in an inflammatory setting in vitro and as a treatment approach in a murine fracture healing model in vivo.

Methods
The influence of α-MSH treatment and melanocortin-receptor expression patterns was investigated in vitro in the presence of either IL-1β or/and TNF-α as an inflammatory stimulus. Osteoblast cell function was evaluated by analyzing proliferation and mineralisation capacities. Using quantitative real time PCR, we analyzed mRNA expression of receptors. To explore the impact of α-MSH on bone regeneration in vivo, treatment with α-MSH or NaCl (control) was performed in a murine fracture-healing model using a closed femur fracture stabilized with an intramedullary implant (female, n = 6–8 mice per group).

Results
α-MSH-treatment did not impair either proliferation nor mineralisation of osteoblastic cells under native or inflammatory conditions (no significant differences found). All four melanocortin receptor-molecules were expressed in murine osteoblastic cells but in very limited amounts and this did not change upon treatment with inflammatory cytokines or α-MSH or both at the same time. Callus formation in fractured femurs of α-MSH-treated mice was slightly delayed at day 14 post fracture with regard to less cartilage formation (NaCl: 19.9%; α-MSH: 13.5%) and soft tissue remodeling (NaCl: 15.2%; α-MSH: 19.5%) but these results were not significantly different and fracture healing overall occurred in a regular way.

Conclusion
α-MSH has no negative impact on bone or bone-forming cells in native, inflammatory, or regenerative contexts. We can conclude from our results, that treatment of inflammatory diseases using α-MSH does not interfere significantly with bone regeneration in a murine fracture model and therefore treatment with α-MSH could be continued without negative effects on bone formation and bone regeneration in patients.

Clinical trial number
Not applicable.
Introducing 3D printed models of fractures in osteology learning improves clinical reasoning skills among first-year medical students: a pilot study
Authors: Agarwal Abhishek , D Souza Anne , Jyostna B. , Shetty Ashwija , Bhat Nandini 
Published: February 2025

Abstract

Background
The human bone anatomy is commonly taught using normal adult bones. However, students often face difficulties comprehending the clinical correlations related to fractures, as they only rely on text content or diagrams without three-dimensional visual aids. Therefore, this study aims to evaluate the effectiveness of using 3D-printed models of limb bone fractures in routine osteology classes to enhance the clinical reasoning skills of first-year medical undergraduate students.

Methodology
In this experimental study, 105 first-year medical undergraduate students were divided into intervention and control groups based on their pre-assigned serial numbers. The control group was taught using dry adult human bones, with the teacher explaining clinical correlations verbally. Meanwhile, in two sessions, the intervention group was taught using 3D-printed models of fractures in addition to real bones. At the end of the second session, students were evaluated for their clinical reasoning ability using a case-based MCQ test (maximum score 5). The scores were compared between the two groups using an unpaired t-test. Students of the intervention group were asked to rate their learning experience using a 10-point Likert Scale questionnaire.

Results
The intervention group scored significantly higher (2.54 ± 1.15) than the control group (2.04 ± 0.94) (p = 0.015). The maximum score for both groups was five, and the minimum was one. Most students agreed that the 3D-printed models helped them understand the fractures’ clinical relevance and provided better orientation to the bones, joints, and structures involved in fractures (92%, n = 46). The students expressed a desire for more similar types of sessions.

Conclusion
Incorporating 3D-printed models of fractures was a novel approach to help students comprehend the clinical correlations. This strategy improved students’ clinical reasoning skills in the intervention group, as evidenced by their higher scores and feedback. Therefore, 3D-printed models are a valuable addition to the traditional teaching methods of learning osteology.
Clinical characteristics and prognosis of amyopathic dermatomyositis patients with interstitial lung disease: insights from a retrospective cohort
Authors: Ying Yanan , Wu Tingting , Wang Long , Zhang Yun , Yu Yiming , Deng Zaichun , Ding Qunli 
Published: February 2025

Abstract

Introduction
The diagnosis of amyopathic dermatomyositis with interstitial lung disease (ADM-ILD) is challenging due to the lack of typical skin features and overlapping syndromes. We aimed to determine the characteristics and prognosis of patients with ADM-ILD to further guide their clinical management.

Methods
A retrospective cohort study comprising 190 Chinese patients diagnosed with interstitial lung disease (ILD) was conducted. Patients were stratified into four groups using the Sontheimer criteria and predominant high-resolution computed tomography (HRCT) patterns. Demographic features, clinical presentation, laboratory parameters, duration of ILD, and follow-up data were analysed.

Results
There were significant differences in the clinical parameters among the 190 patients with ILD in the amyopathic dermatomyositis (ADM, n = 69) and control (n = 121) groups. The ADM with nonspecific interstitial pneumonia (NSIP) group (n = 46) presented increased haemoglobin (125.93 ± 12.91 g/L, p = 0.005), creatine kinase-MB (15.19 ± 8.58 U/L, p < 0.001), and partial pressure of oxygen (93.08 ± 26.20 mmHg, p = 0.003) levels and decreased β2-microglobulin (2.61 ± 1.21 mg/L, p = 0.039) levels compared to the control-NSIP group (n = 92). The ADM with organizing pneumonia (OP) group (n = 23) had a greater percentage of females (7/16, p = 0.023) and higher alanine aminotransferase (30.30 ± 20.67 U/L, p = 0.039) and aspartate aminotransferase (53.35 ± 65.86 U/L, p = 0.003) levels than the control-OP group (n = 29). Both the ADM-NSIP and OP groups presented elevated lactate dehydrogenase (LDH) levels (290.61 ± 86.49 U/L, p = 0.009; 317.35 ± 181.32 U/L, p = 0.003, respectively) and increased anti-nuclear antibody (ANA) positivity rates (82.61%, p = 0.01; 73.91%, p < 0.001, respectively). Notably, 81.26% of patients with ADM-NSIP/OP had LDH levels above normal. The serum LDH levels could be used to distinguish patients with ADM-NSIP/OP (sensitivity: 73.91%, specificity: 82.64%). Survival was shorter among patients with ADM-OP than among control patients (p = 0.002). Cox multivariate analysis revealed that age (p = 0.002), smoking status (p = 0.011), anti-melanoma differentiation-associated gene 5 (MDA5) antibody (p = 0.017), and white blood cell count (p = 0.004) were independent predictors of shorter survival.

Conclusions
Elevated serum LDH levels in patients predominantly presenting with NSIP or OP patterns may indicate the presence of ADM-ILD. The identified prognostic factors underscore the importance of early detection and personalized management strategies for optimizing outcomes in patients with ADM-ILD.
TGF-β induces cholesterol accumulation to regulate the secretion of tumor-derived extracellular vesicles
Authors: Rodrigues-Junior Dorival Mendes , Tsirigoti Chrysoula , Psatha Konstantina , Kletsas Dimitris , Aivaliotis Michalis , Heldin Carl-Henrik , Moustakas Aristidis 
Published: February 2025

Abstract

Background
Cancer cells are avid extracellular vesicle (EV) producers. EVs transport transforming growth factor-β (TGF-β), which is commonly activated under late stages of cancer progression. Nevertheless, whether TGF-β signaling coordinates EV biogenesis is a relevant topic that remains minimally explored.

Method
We sought after specific TGF-β pathway mediators that could regulate EV release. To this end, we used a large number of cancer cell models, coupled to EV cell biological assays, unbiased proteomic and transcriptomic screens, followed by signaling and cancer biology analyses, including drug resistance assays.

Results
We report that TGF-β, by activating its type I receptor and MEK-ERK1/2 signaling, increased the numbers of EVs released by human cancer cells. Upon examining cholesterol as a mediator of EV biogenesis, we delineated a pathway whereby ERK1/2 acted by phosphorylating sterol regulatory element-binding protein-2 that transcriptionally induced 7-dehydrocholesterol reductase expression, thus raising cholesterol abundance at both cellular and EV levels. Notably, inhibition of MEK or cholesterol synthesis, which impaired TGF-β-induced EV secretion, sensitized cancer cells to chemotherapeutic drugs. Furthermore, proteomic profiling of two distinct EV populations revealed that EVs secreted by TGF-β-stimulated cells were either depleted or enriched for different sets of cargo proteins. Among these, latent-TGF-β1 present in the EVs was not affected by TGF-β signaling, while TGF-β pathway-related molecules (e.g., matrix metalloproteinases, including MMP9) were either uniquely enriched on EVs or strongly enhanced after TGF-β stimulation. EV-associated latent-TGF-β1 activated SMAD signaling, even when EV uptake was blocked by heparin, indicating competent signaling capacity from target cell surface receptors. MMP inhibitor or proteinase treatment blocked EV-mediated SMAD signaling, suggesting that EVs require MMP activity to release the active TGF-β from its latent complex, a function also linked to the EV-mediated transfer of pro-migratory potential and ability of cancer cells to survive in the presence of cytotoxic drugs.

Conclusion
Hence, we delineated a novel signaling cascade that leads to high rates of EV generation by cancer cells in response to TGF-β, with cholesterol being a key intermediate step in this mechanism.

Graphical Abstract

• TGF-β increases EV release by activating a MEK-ERK1/2-SREBP2-DHCR7 signaling and transcriptional pathway.

• TGF-β-induced DHCR7 expression raises cholesterol abundance that promotes EV release.

• EVs carry surface latent TGF-β and MMP9 that can activate TGF-β receptor signaling on the surface of recipient cells.
Public health significance of the white-tailed deer (Odocoileus virginianus) and its role in the eco-epidemiology of tick- and mosquito-borne diseases in North America
Authors: Rochlin Ilia , Kenney Joan , Little Eliza , Molaei Goudarz 
Published: February 2025

Abstract
White-tailed deer (Odocoileus virginianus) are a ubiquitous species in North America. Their high reproductive potential leads to rapid population growth, and they exhibit a wide range of biological adaptations that influence their interactions with vectors and pathogens. This review aims to characterize the intricate interplay between white-tailed deer and the transmission cycles of various tick- and mosquito-borne pathogens across their range in the eastern United States and southeastern Canada. The first part offers insights into the biological characteristics of white-tailed deer, their population dynamics, and the consequential impacts on both the environment and public health. This contextual backdrop sets the stage for the two subsequent sections, which delve into specific examples of pathogen transmission involving white-tailed deer categorized by tick and mosquito vectors into tick-borne and mosquito-borne diseases. This classification is essential, as ticks and mosquitoes serve as pivotal elements in the eco-epidemiology of vector-borne diseases, intricately linking hosts, the environment, and pathogens. Through elucidating these associations, this paper highlights the crucial role of white-tailed deer in the transmission dynamics of tick- and mosquito-borne diseases. Understanding the interactions between white-tailed deer, vectors, and pathogens is essential for effective disease management and public health interventions.

Graphical Abstract