bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innateness transcriptome gradients characterize mouse T lymphocyte populations
Authors: Ascui Gabriel , Cedillo-Castelan Viankail , Mendis Alba , Phung Eleni , Liu Hsin-Yu , Verstichel Greet , Chandra Shilpi , Murray Mallory Paynich , Luna Cindy , Cheroutre Hilde , Kronenberg Mitchell 
Published: February 2025

Abstract
A fundamental dichotomy in lymphocytes separates adaptive T and B lymphocytes, with clonally expressed antigen receptors, from innate lymphocytes, which carry out more rapid responses. Some T cell populations, however, are intermediates between these 2 poles, with the capacity to respond rapidly through T cell receptor activation or by cytokine stimulation. Here, using publicly available datasets, we constructed linear mixed models that not only define a gradient of innate gene expression in common for mouse innate-like T cells, but also are applicable to other mouse T lymphoid populations. A similar gradient could be identified for chromatin landscape based on ATAC-seq (assay for transposase-accessible chromatin using sequencing) data. The gradient included increased transcripts related to many traits of innate immune responses, with increased scores related to evidence for antigen experience. While including genes typical for T helper 1 (Th1) responses, the innateness gene program could be separated from Th1, Th2, and Th17 responses. Lymphocyte populations with higher innateness scores correlated with lower calcium-dependent T cell receptor–mediated cell activation, with some downstream signaling proteins dependent on calcium or affecting metabolism prephosphorylation. Therefore, as a group, different mouse innate-like T cell populations had related gene expression programs and activation pathways that are different from naive CD4 and CD8 T cells.
Arts of the Tea Ceremony
Authors: Corbett Rebecca 
Published: February 2025

Chanoyu (literally “hot water for tea”), alternately known as Sadō/Chadō (“The Way of Tea”), often described as “tea ceremony” in English, is an art of social interaction based around the preparation and consumption of matcha (powdered green tea). Considered an art form in its own right, since its development in the sixteenth century, tea culture has provided an important context for the creation, consumption, and display of art forms such as calligraphy, painting, ceramics, lacquerware, and metalwork, to name but a few. Scholarship on chanoyu began in the early twentieth century and burgeoned in the postwar period. Much of the scholarship is dominated by authors associated with the Urasenke School of Tea which has become the largest school both within Japan and internationally in the postwar period and has its own publishing arm, Tankōsha. There is therefore a bias in existing scholarship toward this school, its style of practice and history, however, this has begun to be corrected in recent years. There has been a trend away from focusing on a linear narrative of the development of chanoyu with a focus on the three so–called “founders” of chanoyu: Murata Jukō (Shukō) (b. 1422/3–d. 1502); Takeno Joo (b. 1502–d. 1555); and Sen no Rikyū (b. 1522–d. 1591). More attention is given to developments after the formative period in which they lived, as well as more nuanced approaches to the contributions of these leading figures. The material culture of tea has become an increasingly fruitful area of study, with attention being given not only to the objects themselves but to patterns of consumption, the role of tea practitioners as producers of tea utensils and patrons of craftsman, and the function of tea utensils in gift exchange, identity construction, and for cultivating political capital. Another burgeoning area of study is the role of women in both historical and contemporary tea practice, and what the study of tea brings to women’s lives. This is correcting the male-centered narratives of earlier scholarship. Much tea scholarship is historical but there is a growing interest in bringing academic perspectives to bear on contemporary practice. Recent English-language scholarship has moved away from the term “tea ceremony” because it is not a translation of any existing Japanese term, nor does it capture the breadth of the practice. The term “tea culture” or even simply “tea” is now preferred as it is more encompassing of the various art forms included within chanoyu.
Asiatic acid improves the damage of HaCaT cells induced by nitrogen mustard through inhibiting endoplasmic reticulum stress
Authors: Liu Haoyin , Cheng Jin , Ye Feng , Dong Xunhu , Ge Wei , Wang Xiaogang , Zhao Yuanpeng , Dan Guorong , Chen Mingliang , Sai Yan 
Published: February 2025

Abstract
Nitrogen mustard (NM) belongs to vesicant agents. Blisters are one of the important characteristics of NM skin damage. It is urgent to further elucidate the mechanism and develop effective countermeasures for the skin damage induced by NM. The endoplasmic reticulum (ER) is an important intracellular organelle, playing an important role in maintaining cellular homeostasis. In this study, we explored the role of endoplasmic reticulum stress (ERS) and the protective effect of asiatic acid (AA) in the HaCaT cells induced by NM. It was found that the key regulatory proteins of ERS, such as glucose regulated protein 78 (GRP78), X-box binding protein 1 (XBP1), inositol requiring enzyme 1 (IRE1), Phospho-IRE1 (pIRE1), and TNF receptor associated factor 2 (TRAF2) were increased respectively in HaCaT cells exposed to NM compared with those of the control group, showing an increasing trend with the increase of NM exposure concentration and exposure time. Additionally, the protein expression of Caspase-3 and the Cleaved-Caspase-3 was also increased by NM in HaCaT cells, resulting in the apoptosis of HaCaT cells. Meanwhile, the content of tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL-6) was also increased in HaCaT cells exposed to NM. Further study showed that AA pretreatment could decrease the protein expression of GRP78, XBP1 and IRE1, pIRE1, TRAF2, Caspase-3, and Cleaved-Caspase-3. And moreover, AA also could reduce the content of TNF-α and IL-6. Overall, the present study showed that AA played an important protective effect in HaCaT cells exposed to NM through the inhibition of the ERS-induced apoptosis and inflammatory response.
A Novel Competency-Based, Time-Variable Mid-Career Fellowship Program in Hospice and Palliative Medicine
Authors: Heath Janae K. , Devlin Shannon , Leiter Richard E. , Lindenberger Elizabeth , Shameklis Jaclyn , Dingfield Laura 
Published: February 2025

Abstract

Problem
The field of hospice and palliative medicine (HPM) is grappling with a significant workforce shortage. An untapped source of growth for the HPM specialist workforce is mid-career physicians interested in specialist training and certification. This study describes a pilot competency-based, time-variable (CBTV) fellowship program for mid-career physicians interested in HPM, called the Mid-Career Fellowship.

Approach
The pilot program was approved by the Accreditation Council for Graduate Medical Education (ACGME) Advancing Innovation in Residency Education program in consultation with certification boards. The Mid-Career Fellowship enrolled 2 mid-career fellows in July 2019 at the University of Pennsylvania, ultimately expanding in July 2020 and July 2021 to 7 participating sites. Clinical training in the fellowship was scheduled on an interrupted, part-time basis, with full- or partial-week clinical HPM rotations scheduled to accommodate fellows’ other professional and academic responsibilities. Mid-career fellows’ progression on HPM competencies was assessed through direct observation during HPM clinical rotations using validated assessments and the ACGME HPM milestones framework. Participants and traditional HPM fellows were surveyed for their perceptions of the program.

Outcomes
From July 2019-June 2024, the Mid-Career Fellowship had enrolled 22 individuals and produced 14 graduates across the 7 participating sites. As of June 2024, 12 of 14 (86%) graduates had entered full- or part-time practice in an HPM specialty. Two mid-career fellows have passed the biannual HPM board certification, with additional fellows being eligible to sit for the certification exam in fall 2024.

Next Steps
Aspects of the program could be adapted by other specialties facing workforce shortages. Future work is needed to determine the long-term impact of this training and the role of similar programs in other specialties. The authors’ next steps will be to conduct qualitative analyses of such programs’ impact on professional development for participants.
Increased Risks of Major Cardiac Adverse Events in Stimulant Use Disorder as Compared With Other Substance Use Disorders: A Propensity-score Matching Cohort Study
Authors: Garel Nicolas , Greenway Kyle T. , Lavin Paola , Pike C. William , Hyde Rebecca , Jutras-Aswad Didier , Tate Steven D. , Lembke Anna 
Published: February 2025

Objectives:
Individuals with stimulant use disorders (StSUDs) present an elevated risk of cardiovascular complications compared with the general population. However, it remains unclear whether, within the subpopulation of individuals with substance use disorders (SUDs), those specifically affected by StSUDs face even higher cardiovascular complications.

Methods:
We conducted a retrospective cohort study using the EVERSANA databank, spanning from January 2015 to December 2023. The EVERSANA data set comprises deidentified electronic health record data aggregated and standardized across the United States. Participants included patients diagnosed with SUDs, encompassing alcohol, cannabis, opioids, stimulants, tobacco, hallucinogens, sedative-hypnotics, or inhalants. We employed the International Classification of Disease 10th (ICD-10) version codes to define the presence of StSUD and SUD. Major adverse cardiac events (MACE) were assessed, and Cox proportional hazard ratios were adjusted using high-dimensional propensity score (hdPS) matching to account for potential confounders.

Results:
Among 137,106 patients with SUD, 7706 (5.6%) had StSUD. The cohort was 50.2% female, 53.0% non-White, with a mean age of 49.1 years (SD±15). After adjustment, stimulant users exhibited significantly higher MACE rates (HR=1.37, 95% CI: 1.22–1.53, P<0.001), including an elevated risk of death (HR=1.23, 95% CI: 1.02–1.47, P=0.026).

Conclusion:
Individuals with StSUD face increased MACE compared with those with nonstimulant SUDs.
Patterns of Perspectives on Oncology Healthcare Needs Among Women With Gynecologic Cancer
Authors: Yu Shu-Chuan , Guo Jong-Long , Sun Chia-Hui , Chang Ching-Hao , Chen Shu-Fen , Huang Chiu-Mieh 
Published: February 2025

Background
Gynecologic cancer significantly impacts women’s healthcare needs; however, these needs are often underexplored from the patients’ perspectives.

Objective
To identify and describe the patterns of perspectives on the oncology healthcare needs of women with gynecologic cancer.

Methods
This Q-methodology study was conducted between January and October 2023 using 60 female patients with gynecologic cancer. Thirty-six Q statements were constructed based on the guidelines of the Cancer Diagnosis and Treatment Quality Assurance Measures, and 10 gynecological nursing staff members were interviewed to explore their experiences with current clinical practices in hospitals. The study adhered to SQUIRE 2.0 (Standards for QUality Improvement Reporting Excellence). PQ Method 2.35 software was used to identify different patterns of patients’ perspectives.

Results
The final model retained 4 factors, explaining 59% of the variance. These factors emphasized (1) family-centered communication over palliative care information, (2) patient-centered communication over rehabilitation information, (3) psychological and physiological adaptation over receiving information in advance, and (4) treatment and side effect information over palliative care information.

Conclusions
Clustering patients by perspectives can assist healthcare providers in understanding patient expectations. The emerging perspectives highlight the patients’ expectations of communication regarding their treatment plans. Palliative care was the least evident healthcare need across the 4 groups of patients.

Implication for Practice
The findings capture 4 unique perspectives of patients’ expectations with healthcare needs. These insights can inform researchers and practitioners in developing needs-matched healthcare for women with gynecologic cancer.
Changing Intimate Partner Violence Screening and Intervention: Focus Group Perspectives
Authors: Galambos Colleen , Jerofke-Owen Teresa , Paquette Heidi , Piacentine Linda , Schubert Erin , Vang Mychoua , Arrington Erica , Lodh Nil , Gecsi Kimberly S. 
Published: February 2025

Background:
Many survivors of intimate partner violence (IPV) remain unconnected to professional help. Screenings in health settings may improve connections to support services.

Purpose:
The purpose of this study was to gather data to help inform an IPV screening intervention in an obstetrics/gynecology health clinic.

Methods:
A qualitative analysis was employed using a summative content analysis approach of the transcripts of 2 focus groups consisting of health care providers, advocates, and survivors of IPV.

Results:
Four thematic categories and additional subcategories emerged from the analysis, including (1) current process (what is done); (2) need (what is not done); (3) concerns (roadblocks); and (4) suggestions (next steps).

Conclusions:
Information obtained from this analysis was used to inform our intervention. Specifically, all clinic providers and staff received training on IPV, screening for IPV was done on all patients using an IPV screening tool, and patients were privately screened.
Moving Beyond CT Body Composition Analysis
Authors: Haubold Johannes , Pollok Olivia Barbara , Holtkamp Mathias , Salhöfer Luca , Schmidt Cynthia Sabrina , Bojahr Christian , Straus Jannis , Schaarschmidt Benedikt Michael , Borys Katarzyna , Kohnke Judith , Wen Yutong , Opitz Marcel , Umutlu Lale , Forsting Michael , Friedrich Christoph M. , Nensa Felix , Hosch René 
Published: February 2025

Objectives
Deep learning for body composition analysis (BCA) is gaining traction in clinical research, offering rapid and automated ways to measure body features like muscle or fat volume. However, most current methods prioritize computed tomography (CT) over magnetic resonance imaging (MRI). This study presents a deep learning approach for automatic BCA using MR T2-weighted sequences.

Methods
Initial BCA segmentations (10 body regions and 4 body parts) were generated by mapping CT segmentations from body and organ analysis (BOA) model to synthetic MR images created using an in-house trained CycleGAN. In total, 30 synthetic data pairs were used to train an initial nnU-Net V2 in 3D, and this preliminary model was then applied to segment 120 real T2-weighted MRI sequences from 120 patients (46% female) with a median age of 56 (interquartile range, 17.75), generating early segmentation proposals. These proposals were refined by human annotators, and nnU-Net V2 2D and 3D models were trained using 5-fold cross-validation on this optimized dataset of real MR images. Performance was evaluated using Sørensen-Dice, Surface Dice, and Hausdorff Distance metrics including 95% confidence intervals for cross-validation and ensemble models.

Results
The 3D ensemble segmentation model achieved the highest Dice scores for the body region classes: bone 0.926 (95% confidence interval [CI], 0.914–0.937), muscle 0.968 (95% CI, 0.961–0.975), subcutaneous fat 0.98 (95% CI, 0.971–0.986), nervous system 0.973 (95% CI, 0.965–0.98), thoracic cavity 0.978 (95% CI, 0.969–0.984), abdominal cavity 0.989 (95% CI, 0.986–0.991), mediastinum 0.92 (95% CI, 0.901–0.936), pericardium 0.945 (95% CI, 0.924–0.96), brain 0.966 (95% CI, 0.927–0.989), and glands 0.905 (95% CI, 0.886–0.921). Furthermore, body part 2D ensemble model reached the highest Dice scores for all labels: arms 0.952 (95% CI, 0.937–0.965), head + neck 0.965 (95% CI, 0.953–0.976), legs 0.978 (95% CI, 0.968–0.988), and torso 0.99 (95% CI, 0.988–0.991). The overall average Dice across body parts (2D = 0.971, 3D = 0.969, P = ns) and body regions (2D = 0.935, 3D = 0.955, P < 0.001) ensemble models indicates stable performance across all classes.

Conclusions
The presented approach facilitates efficient and automated extraction of BCA parameters from T2-weighted MRI sequences, providing precise and detailed body composition information across various regions and body parts.
Recurrent Giant Subcutaneous Tumor in Juvenile Hyaline Fibromatosis
Authors: Wang Xinyao , Wei Jia , Wang Xiaoqiang 
Published: February 2025

This case report presents a 5-year-old boy diagnosed with juvenile hyaline fibromatosis (JHF), an extremely rare autosomal recessive disorder characterized by the abnormal accumulation of collagen. The patient exhibited a recurrent giant subcutaneous tumor measuring 20 cm in diameter, along with multiple tumors in the oral cavity, gingiva, and joints, leading to significant facial deformity and functional impairments. Previous surgeries at ages 1 and 2 for tumor removal resulted in recurrence. Surgical intervention was performed to excise the large tumor and alleviate symptoms. Pathologic analysis confirmed the diagnosis of JHF. This case highlights the challenges in managing JHF and the need for multidisciplinary approaches in treatment.
Application of Anterolateral Thigh Chimeric Flap in Reconstruction of Orbitomaxillary Defects
Authors: Li Wen-Wen , Zhou Xiao-Long , Chen Lei , Yu Zi-Li , Jia Jun 
Published: February 2025

Objective:
This study aimed to investigate the feasibility and applicability of anterolateral thigh chimeric flap in the reconstruction of orbitomaxillary defects.

Methods:
This retrospective study involved 3 patients with orbitomaxillary defects due to maxillary or maxillary sinus tumors invading the orbit, who underwent anterolateral thigh chimeric flap reconstruction from November 2013 to February 2023.

Results:
All 3 patients were males, with maxillary sinus or maxillary tumors invading the orbit, and all underwent extended maxillectomy and orbital exenteration. Anterolateral thigh chimeric flaps were used to repair the postoperative defects. The size of flaps ranged from 12 cm×6 cm to 13 cm×10 cm. There were no postoperative complications and the patients recovered well.

Conclusion:
Anterolateral thigh chimeric flap is safe and reliable for the reconstruction of orbitomaxillary complex defects caused by maxillary tumor surgery.
Intraoperative nerve imaging with sodium fluorescein
Authors: Park Roy K. , Arús Bernardo A. , Lee Jennifer Y. , Weitzenberg Merle M. , Lee Melissa C. , Nyaeme Mark S. , Barthel Julia , Balsamo Giuseppe , Baik Fred M. , Speirs Katie , Blume Berit , Heller-Algazi Metar , Chmyrov Andriy , Plettenburg Oliver , Megwalu Uchechukwu C. , Weitz Jürgen , Distler Marius , Bruns Oliver T. , Valdez Tulio A. 
Published: February 2025

AbstractNerve damage during surgery is a common and serious complication, often leading to chronic pain, functional impairments, and diminished quality of life. However, existing methods for intraoperative nerve identification remain insufficient, especially for detecting small or hidden nerve branches. Here we present a new application of a clinically approved fluorescent agent, sodium fluorescein, to enhance nerve visualization during surgery. Utilizing both clinical and customized imaging systems, fluorescein remarkably improved nerve contrast, revealing structures undetectable with white light, including small branches embedded within tissues. With its established safety profile, low cost, and immediate clinical applicability, sodium fluorescein offers the potential to revolutionize surgical practice by minimizing nerve injuries and improving patient outcomes. Clinical Trial Registration:NCT06054178.Graphical abstract
Finding the Clinical Traces of Cognitive Impairment in Patients with Heart Failure: A Natural Language Processing Study of Clinical Letters from Routine Care
Authors: Overmars L. Malin , van Es Bram , Tan Sander C. , Vonk Jet M. J. , Muller Majon , De Groot Mark C. H. , Biessels Geert Jan , Van der Meer M.G. , van Solinge Wouter W. , Haitjema Saskia , Bots Michiel L. , Exalto Lieza G. 
Published: February 2025

AbstractCognitive impairment is common in patients with heart failure, but to which extent cognitive complaints are evaluated and listed in clinical practice is unknown. Therefore, this study aims to identify whether cognitive complaints are listed in clinical notes of patients with heart failure, consistent with listed complaints in clinical notes of patients attending memory clinics, by using natural language processing (NLP) techniques. Patients with heart failure and patients attending a memory outpatient clinic were identified by using echocardiography reports and presence of memory outpatient clinic codes stored in the Utrecht Individual-Oriented Database (UPOD) from 2011 to 2023. Named Entity Detection and Linking (NER+L) strategies MedCAT and MedCATTrainer were used to extract listed complaints in clinical notes by patient group, and it was assessed whether cognitive complaints were listed in clinical notes of patients with heart failure. Among 5803 patients with heart failure, dyspnea (57.1%), chest pain (48.4%), and oedema (43.6%) were the most listed complaints. In 967 patients attending memory clinics, memory problem (80.9%), getting lost (24.1%), and being morose (22.5%) were the most listed complaints. Notably, in patients with heart failure, the reporting of memory problems was low at 2.6%. This study shows a low reporting frequency of cognitive complaints in clinical notes of patients with heart failure, even though both conditions often co-occur according to cross-sectional studies. This points towards a potential underrecognition of cognitive complaints in patients with heart failure during clinical practice.
SoEM-Web: a user-friendly platform for the analysis and visualization of small-organelle-enriched metagenomics data
Authors: Oh Jooseong , Kim Hanjin , Park Chungoo 
Published: February 2025

AbstractBackgroundMarine microeukaryotes play a crucial role in global biogeochemical cycles and ecosystem functioning. However, their diversity and distribution patterns remain poorly understood. To improve the biodiversity assessment of environmental samples, we recently developed a PCR-free, small-organelle-enriched metagenomics (SoEM) method, accompanied by a bioinformatics workflow for analyzing SoEM metagenomic data. However, the complexity of these analyses typically requires extensive bioinformatics expertise, potentially limiting their broader adoption.MethodsTo address this challenge, we present SoEM-Web, a user-friendly web application for the interactive analysis, classification, and visualization of SoEM metagenomic data. SoEM-Web integrates all necessary procedures, including raw sequencing data preprocessing, paired-end read merging, automated taxonomic identification, and diversity visualization, into a streamlined workflow accessible through an intuitive interface. This application is designed to facilitate SoEM data analysis for researchers who may not have advanced bioinformatics skills.ResultsWe demonstrated the capabilities of SoEM-Web by reanalyzing previously published datasets. This reanalysis not only confirmed the utility of the platform but also revealed additional taxa, emphasizing the value of updated reference datasets. The application successfully simplifies complex bioinformatics processes, enhancing accessibility and reproducibility in marine microeukaryote diversity research. SoEM-Web aims to enhance accessibility and reproducibility in marine microeukaryote diversity research. The web server is freely available athttp://compsysbio.re.kr/soem-web/.