bluuebunny/crossref_metadata_2025_split huggingface dataset:
Minimally invasive thoracoscopic resection of a micronodular thymoma with lymphoid stroma via a subxiphoid single-incision approach: A case report
Authors: Wu Qiang , Qiao Kun , Zhang Xiaoming , Zhou Zizi 
Published: November 2024

Rationale:
This study aims to present a novel surgical approach for the resection of anterior mediastinal tumors, specifically focusing on micronodular thymoma with lymphoid stroma (MNT), a rare and distinct variant of thymoma. The single subxiphoid incision technique, although reported in limited cases, offers a minimally invasive option with potential benefits. We report the case of a 76-year-old male who underwent this innovative procedure and was diagnosed with MNT, providing insight into the management and outcomes of this rare pathology.

Patient concerns:
The patient presented for the excision of an anterior mediastinal tumor, with the surgery facilitated by sternal hooks to improve visualization. The rarity of MNT and its unclear prognosis underscore the need for enhanced diagnostic accuracy and tailored treatment strategies.

Diagnoses:
Initially diagnosed preoperatively with a thymic cyst, the patient’s final diagnosis was revised to MNT following surgery, highlighting the diagnostic challenges associated with this rare tumor.

Interventions:
The tumor was successfully removed using minimally invasive thoracoscopic surgery through a subxiphoid single-incision, demonstrating the feasibility and potential advantages of this approach.

Outcomes:
The patient had a favorable postoperative course, with a swift recovery and no complications, and remained in good health without signs of relapse at the 9-month follow-up.

Lessons:
This case underscores the importance of recognizing the unique pathological features of MNT and the need for a cautious diagnostic approach to differentiate it from other cystic lesions. Additionally, the successful use of single-port thoracoscopy under the xiphoid process for the removal of thymic tumors suggests its potential as an effective surgical method for these challenging cases.
Awareness and preparedness of health systems and emergency medicine systems to the climate change challenges and threats: an international survey
Authors: Petrino Roberta , Garcia-Castrillo Luis , Uccheddu Graziano , Meucci Letizia , Codecà Roberta 
Published: November 2024

Background and importance
Climate change is widely recognised as a critical public health challenge.

Objective
The objective of this study was to assess the awareness, preparedness and mitigation plans for climate change threats.

Design, settings and participants
A cross-sectional observational study targeting emergency medical societies in different countries was conducted between 15 February and 15 March 2024.

Intervention or exposure
The survey featured 16 closed questions on climate change awareness, preparedness and risks. Focus groups of 4–6 members were organised by country. Results were correlated to income levels, United Nations (UN) regional classification and the World Risk Index.

Outcome measure and analysis
The questions were ranked using a Likert-like scale from 0 to 9 (9 being the highest). Descriptive statistics used central tendency estimators, and inferential analysis used chi-square and Kruskal–Wallis tests, with the significance level set at P < 0.05.

Results
Forty-two focus groups responded, representing 36 countries: 21 (50%) high-income, seven (16.7%) low-income, five (11.9%) lower middle-income and nine (21.4%) upper middle-income countries, representing 31 of the 22 UN regions. According to the World Risk Index, the respondent countries belonged to the different categories as follows: very low risk, 6 (14%); low risk, 8 (19%); medium risk, 5 (12%); high risk, 8 (19%) and very high risk, 14 (34%). The estimated impact of climate change on national health systems had a mean score of 6.75 (SD = 2.16), while on Emergency Medical Systems was 6.96 (SD = 2.05). Overall, assessment and preparedness measures were reported by just 21.4 and 37.6% of respondents, respectively. Analysis by income did not show significant differences, with the exception of food supply. The main differences in the analysis by region were the risks of extreme weather events, vector-borne diseases and wildfires, whereas the World Risk Index was food and chain of supplies. Education and integration of health services were indicated by all as the main mitigation actions.

Conclusion
Geographical position and country risk index influence risk perception among focus groups more than income economy, with vector-borne diseases, extreme weather events and food shortages being the threats with the most variability. The most important actions identified to mitigate Climate Change effects are educational and strategic plans.
Surgical resection of a rare scalp arteriovenous malformation: a case report
Authors: Haq Khitamul , Waqas Muhammad A. , Akhter Saleem , Cardona Juan J. , Scalia Gianluca , Umana Giuseppe E. , Chaurasia Bipin 
Published: November 2024

Introduction and importance:
Scalp arteriovenous malformations (AVMs) are intricate vascular anomalies with abnormal connections between arteries and veins in the scalp, leading to serious complications and cosmetic concerns. Managing scalp AVMs is particularly complex in young female patients, where both functional and aesthetic outcomes are crucial. This case report highlights the successful treatment of a young woman with a scalp AVM, emphasizing the importance of early diagnosis and a multidisciplinary approach.

Case presentation:
A 30-year-old female presented with a pulsatile scalp mass and significant cosmetic concerns. Diagnostic imaging, including ultrasonography, brain CT scan, MRI, and carotid CT angiogram, confirmed a scalp AVM. The patient underwent a comprehensive treatment plan beginning with endovascular embolization to reduce blood flow to the AVM, followed by surgical resection to remove the lesion. Postoperative follow-up showed a marked reduction in symptoms and lesion volume, with no complications observed.

Clinical discussion:
Scalp AVMs, though rare, require prompt diagnosis due to the risk of severe complications such as hemorrhage and cosmetic impact. In this case, a combination of ultrasonography, CT, and MRI provided a detailed assessment of the AVM. A multidisciplinary approach, involving interventional radiology and surgical expertise, was crucial for success. Endovascular embolization minimized intraoperative bleeding and simplified surgical resection, leading to significant symptom and cosmetic improvements. Continuous monitoring is essential for long-term success and early detection of recurrences.

Conclusion:
This case underscores the effectiveness of a multidisciplinary approach in managing scalp AVMs in young female patients. Early diagnosis through advanced imaging techniques enables timely and targeted intervention. The combined use of endovascular embolization and surgical resection led to significant symptom resolution and aesthetic enhancement. Collaboration among specialists is vital for optimizing outcomes, and ongoing research will further refine treatment strategies, improving the quality of life for patients with scalp AVMs.
The effect of therapeutic education program on hypertensive Tunisian patients’ knowledge: a randomized controlled trial
Authors: Turki Fatma , Turki Imen , Jedidi Jihen , Said Houyem 
Published: November 2024

Background:
Hypertension is a prevalent non-communicable disease and unequivocally one of the most serious health threats of the twenty-first century. The prevention of both immediate and long-term consequences depends on ongoing therapeutic education.

Aims:
To assess Tunisian hypertensive patients’ knowledge of hypertension and then evaluate the impact of an educational program on knowledge among this population.

Methods:
A randomized controlled trial was carried out among 639 hypertensive patients in Tunisia. The control group received only basic medical care, while the experimental group acquired additionally an educational program. The data collection tool was a questionnaire that included an information sheet and the Hypertension Knowledge Level Scale (HK-LS).

Results:
Before to the implementation of the program, only 12.1% of the participants had a good level of knowledge about hypertension (12.8% for the experimental group, vs. 10.5% for the control group, P=0.57). Following the program’s deployment, the rate of good level of knowledge became 63.6% for the experimental group vs. 11.4% for the control group, P<0.001). The results revealed that the experimental group showed a significant amelioration in the total score of the HK-LS: from 58.49 to 76.94%, P<0.0001. In contrast, no significant amelioration was noted in the control group. Concerning the six dimensions of the scale, the amelioration in the experimental group was observed in all dimensions, except the treatment dimension.

Conclusion:
Overall, the findings indicated low levels of knowledge about hypertension. This kind of approach proved an effective improvement in disease-related knowledge and may be essential for hypertension management.
The Importance of 18F-FDG PET/CT in a Rare Case of Multiple Myeloma Presenting With Nasal Plasmacytoma
Authors: Erol Fenercioğlu Özge , Çermik Tevfik Fikret 
Published: November 2024

Abstract
Nasopharyngeal plasmacytoma is a rare presentation of multiple myeloma. We emphasize the importance of imaging by presenting the 18F-FDG PET/CT findings of a patient with nasopharyngeal plasmacytoma and lytic hypermetabolic bone lesions.
PRECISE EXOME ANALYSIS OF BLASTOCYST BIOPSY SCALE SAMPLES USING PRIMARY TEMPLATE-DIRECTED AMPLIFICATION
Authors: Samitova Alina , Belova Vera , Vasiliadis Iuliia , Repinskaia Zhanna , Gorodnicheva Tatiana , Romanov Evgeny , Pogosyan Mariam , Gaysin Emil , Nazarenko Tatyana , Rebrikov Denis , Korostin Dmitriy 
Published: November 2024

AbstractThis study evaluates primary template-directed amplification (PTA) for whole exome sequencing (WES) on small fibroblast cell groups, mimicking the limited cell quantities typical of trophectoderm embryo biopsies. PTA’s consistent amplification reduces allelic dropout (ADO) and impoves uniform coverage, overcoming challenges associated with conventional methods such as multiple displacement amplification (MDA). Using fibroblast samples alongside well-characterised genomic references (E701, NA12878), we benchmarked PTA-WES, achieving 97.5% target region coverage at 10x, meeting American College of Medical Genetics and Genomics (ACMG) standards. Preliminary results from embryo biopsies sequenced with PTA-WES showed a median coverage of 102x, significantly improving upon the variability and coverage gaps observed in MDA-WES. The findings support PTA’s potential to enhance the clinical applicability of WES for preimplantation genetic testing for monogenic disorders (PGT-M), expanding capabilities to detect inherited and de novo mutations in embryos. Further optimisation and variant detection analyses are planned to evaluate PTA’s robustness for routine clinical use.
Single-nucleus transcriptome-wide association study of human brain disorders
Authors: Venkatesh Sanan , Wu Zhenyi , Anyfantakis Marios , Dillard Christian , Prashant N.M. , Burstein David , Mathur Deepika , Kosoy Roman , Chatzinakos Chris , Ajanaku Bukola , Tsetsos Fotis , Zeng Biao , Hong Aram , Casey Clara , Alvia Marcela , Shao Zhiping , Argyriou Stathis , Therrien Karen ,   VA Million Veteran Program,   PsychAD Consortium, Bigdeli Tim , Auluck Pavan , Bennett David A. , Marenco Stefano , Haroutunian Vahram , Girdhar Kiran , Bendl Jaroslav , Lee Donghoon , Fullard John F. , Hoffman Gabriel E. , Voloudakis Georgios , Roussos Panos 
Published: November 2024

AbstractNeuropsychiatric and neurodegenerative disorders exhibit cell-type-specific characteristics1–8, yet most transcriptome-wide association studies have been constrained by the use of homogenate brain tissue9–11, limiting their resolution and power. Here, we present a single-nucleus transcriptome-wide association study (snTWAS) leveraging single-nucleus RNA sequencing of over 6 million nuclei from the dorsolateral prefrontal cortex of 1,494 donors across three ancestries—European, African, and Admixed American. We constructed ancestry-specific single-nucleus-derived transcriptomic imputation models (snTIMs) including up to 27 non-overlapping cellular populations, enhancing the resolution of genetically regulated gene expression (GReX) in the brain and uncovering novel gene-trait associations across 12 neuropsychiatric and neurodegenerative traits. Our snTWAS framework revealed cell-type-specific dysregulation of GReX, identifying over 4,000 novel gene-trait associations not detected by bulk tissue approaches. By applying these snTIMs to the Million Veteran Program, we validated major findings and explored the pleiotropy of cell-type-specific GReX, revealing cross-ancestry concordance and fine-mapping causal genes. This approach enhances the discovery of biologically relevant pathways and gene targets, highlighting the importance of cell-type resolution and ancestry-specific models in understanding the genetic architecture of complex brain disorders.
Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion
Authors: Yang Xinrun , Yang Tianjie , Zhang Ziru , Zhang Yaozhong , Mei Xinlan , Gao Yang , Wang Ningqi , Jiang Gaofei , Xu Yangchun , Shen Qirong , Medema Marnix H. , Wei Zhong , Jousset Alexandre 
Published: November 2024

AbstractUnderstanding how microbiomes resist pathogen invasion remains a key challenge in natural ecosystems. Here, we combined genome-scale metabolic models with synthetic community experiments to unravel the mechanisms driving pathogen suppression. We developed curated genome-scale models for each strain, incorporating 48 common resource utilization profiles to fully capture their metabolic capacities. Trophic interactions inferred from models accurately predicted pathogen invasion outcomes, achieving an F1 score of 96% across 620 invasion tests involving diverse microbial communities and nutrient environments. Importantly, considering both substrate and metabolite features provided a more holistic understanding of pathogen suppression. In particular, cross-feeding metabolites within the native community emerged as crucial yet often overlooked predictors of community resistance, disproportionally favoring native species over invaders. This study lays the foundation for designing disease-resistant microbiomes, with broad implications for mitigating pathogen exposure in diverse environments.
Evolutionarily recent transcription factors partake in human cell cycle regulation
Authors: Pulver Cyril , Forey Romain , Lederer Alex R. , Begnis Martina , Rosspopoff Olga , Carlevaro-Fita Joana , Martins Filipe , Planet Evarist , Duc Julien , Raclot Charlène , Offner Sandra , Coudray Alexandre , Dorschel Arianna , Trono Didier 
Published: November 2024

AbstractThe cell cycle is a fundamental process in eukaryotic biology and is accordingly controlled by a highly conserved core signaling cascade. However, whether recently evolved proteins also influence this process is unclear. Here, we systematically map the influence of evolutionarily recent transcription factors (TFs) on human cell cycle progression. We find that the genomic targets of select young TFs, many of which belong to the rapidly evolving Krüppel-associated box (KRAB) zinc-finger proteins (KZFP) family, exhibit synchronized cell cycle expression. Systematic perturbation studies reveal that silencing recent TFs disrupts normal cell cycle progression, which we experimentally confirm for ZNF519, a simian-restricted KZFP. Further, we show that the therian-specific KZFP ZNF274 sets the cell cycle expression and replication timing of hundreds of clustered genes. These findings highlight an underappreciated level of lineage specificity in cell cycle regulation.
Geometrically balanced model of cell growth
Authors: Vazquez Alexei , Gedeon Tomáš 
Published: November 2024

AbstractThe proteome balance constraint in metabolic flux balance analysis asserts that the proteome is constructed by ribosomes, which themselves contain many proteins. This leads to a fundamental question of optimal allocation of limited proteome among different pools of enzymes, which include ribosomes themselves. However, recent work points to additional constraints imposed by the cell geometry. In this paper we deduce theproteogeometric constraint, whereπA,πPandπLare the proteomic fractions allocated to the cell surface area, protein synthesis and cell membrane phospholipids synthesis andandθare constants imposed by geometry of the cell. We illustrate the relevance of this constraint using a reduced model of cell metabolism, illuminating the interplay between cell metabolism and cell geometry.
Diverse ancestral representation improves genetic intolerance metrics
Authors: Han Alexander L. , Sands Chloe F. , Matelska Dorota , Butts Jessica C. , Ravanmehr Vida , Hu Fengyuan , Gonzalez Esmeralda Villavicencio , Katsanis Nicholas , Bustamante Carlos D. , Wang Quanli , Petrovski Slavé , Vitsios Dimitrios , Dhindsa Ryan S. 
Published: November 2024

SummaryRapidly expanding genomic databases have enabled the identification of regions in the human genome intolerant to variation and thus likely relevant to human disease. However, despite their unprecedented scale, these datasets remain constrained by limited ancestral diversity. Here, we systematically evaluate how genetic diversity impacts gene- and sub-genic intolerance metrics by analyzing whole-exome sequencing data from 460,551 UK Biobank participants and 125,748 gnomAD participants across diverse ancestral backgrounds. Through comprehensive analysis of randomly sampled datasets with varying ancestral compositions, we demonstrate that genetic diversity, rather than sample size alone, drives the performance of intolerance metrics in identifying functionally critical genes and genic sub-regions. Notably, scores trained on variation observed in African and Admixed American ancestral groups showed superior resolution in detecting neurodevelopmental disease risk genes and haploinsufficient genes compared to scores trained on variation observed in European ancestry cohorts. Most strikingly, the Missense Tolerance Ratio (MTR) trained on 43,000 multi-ancestry exomes demonstrated greater predictive power than when trained on a nearly 10-fold larger dataset of 440,000 non-Finnish European exomes, indicating that European ancestry-based scores are approaching saturation. These findings establish ancestral diversity as the fundamental determinant for advancing intolerance metrics and underscore the urgent scientific and ethical imperative for enhanced population representation in genomic resources to fully realize the potential of precision medicine and drug discovery.
PPD-H1Improves Stress Resistance and Energy Metabolism to Boost Spike Fertility under High Ambient Temperatures
Authors: Lan Tianyu , Walla Agatha , Çolpan Karışan Kumsal Ecem , Buchmann Gabriele , Wewer Vera , Metzger Sabine , Vardanega Isaia , Haraldsson Einar Baldvin , Helmsorig Gesa , Thirulogachandar Venkatasubbu , Simon Rüdiger , von Korff Maria 
Published: November 2024

AbstractHigh ambient temperature (HT) impairs reproductive development and grain yield in temperate crops. To ensure reproductive success under HT, plants must maintain developmental stability. However, the mechanisms integrating plant development and temperature resilience are largely unknown. Here, we demonstrate thatPHOTOPERIOD 1(PPD-H1), homologous toPSEUDO RESPONSE REGULATORgenes of the Arabidopsis circadian clock, controls developmental stability in response to HT in barley. We analyzed HT responses in independent introgression lines with either the ancestral wild-typePpd-H1allele or the naturalppd-h1variant, selected in spring varieties to delay flowering and enhance yield under favourable conditions. HT delayed inflorescence development and reduced grain number inppd-h1mutant lines, while the wild-typePpd-H1genotypes accelerated reproductive development and showed a stable grain set under HT. Using a CRISPR/Cas9-inducedppd-h1mutant, we confirmed that the CCT domain ofPpd-H1controls developmental stability, but not clock gene expression. Transcriptome and phytohormone analyses in developing leaves and inflorescences revealed increased stress gene expression and abscisic acid levels in the leaf and inflorescence of the natural and induced mutantppd-h1lines. Furthermore, the mutantppd-h1lines downregulated photosynthesis-and energy metabolism-related genes, and reduced auxin and cytokinin levels in the inflorescence, which impaired anther and pollen development. By contrast, in the wild-typePpd-H1plants, the transcriptome and phytohormone levels and anther and pollen development remained stable under HT. Our findings suggest thatPpd-H1enhances stress resistance and energy metabolism, thereby stabilizing reproductive development, floret fertility and grain set under HT.
Sulfide-responsive transcription control inEscherichia coli
Authors: Hori Koichi , Balasubramanian Rajalakshmi , Masuda Shinji 
Published: November 2024

AbstractTo elucidate the mechanism of large-scale transcriptional changes dependent on sulfide inEscherichia coli, a large scale RNA-sequencing analysis was performed on wild-type and sulfide-responsive transcription factor YgaV deletion mutants grown under three conditions: aerobic, semi-aerobic, and semi-aerobic with sulfide. The resulting dataset from these six conditions was subjected to principal component analysis, which categorized the data into five principal components. Estimation of the typical gene expression regulatory mechanisms in each category suggested the presence of mechanisms that are dependent on sulfide but independent of YgaV, as well as those that depend on YgaV but not on sulfide. In YgaV-dependent transcriptional regulation, YgaV was found to function as both a repressor and an activator. These results support the previous hypothesis that YgaV acts as a global regulator responsible for redox homeostasis.
Structure of Blm10:13S proteasome intermediate reveals parallel assembly pathways for the proteasome core particle
Authors: Kaur Mandeep , Chen Xiang , Lee Stella Y. , Weaver Tyler M. , Freudenthal Bret D. , Walters Kylie J. , Roelofs Jeroen 
Published: November 2024

AbstractProteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory particles (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, and is thought to be replaced by Blm10 to form Blm10:CP, which promotes ATP-independent degradation of disordered proteins. Here, we present evidence of distinct parallel assembly pathways for CP by solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model of Blm10 and Pba1/Pba2 sequential activity in a single assembly pathway, as we find their CP binding is mutually exclusive and both are present on early and late assembly intermediates. CP affinity for Pba1/Pba2 is reduced during maturation, promoting Pba1/Pba2 release. We find Blm10 undergoes no such affinity switch, suggesting this pathway predominantly yields mature Blm10-bound CP. Altogether, our findings conflict with the current paradigm of sequential CP binding to instead indicate parallel assembly pathways by Pba1/Pba2 and Blm10.