bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel metabolomic predictors of incident colorectal cancer in men and women
Authors: Downie Jonathan M , Joshi Amit D , Geraghty Connor M , Guercio Brendan J , Zeleznik Oana A , Song Mingyang , Bever Alaina M , Drew David A , Tabung Fred K , Zhang Xuehong , Jin Lina , Eliassen A Heather , Willett Walter C , Wu Kana , Kraft Peter , Tamimi Rulla , Clish Clary , Fuchs Charles S , Giovannucci Edward , Meyerhardt Jeffrey A , Chan Andrew T 
Published: October 2024

Abstract

Background
Metabolomic profiles may influence colorectal cancer (CRC) development. Few studies have performed prediagnostic metabolome-wide analyses with CRC risk.

Methods
We conducted a nested case-control study among women (Nurses’ Health Study) and men (Health Professionals Follow-Up Study) who provided blood between 1989 and 1995. Over 22.9 years, 684 (409 Nurses’ Health Study, 275 Health Professionals Follow-Up Study) individuals developed CRC and were matched 1:1 to unaffected participants. Liquid chromatography-mass spectrometry identified 255 plasma metabolites after quality control. Cohort-specific and combined metabolite association analyses were performed using conditional logistic regression. Metabolite set enrichment analysis was used to identify differential abundance in metabolite classes. The R Weighted Correlation Network Analysis package provided modules of covarying metabolites, which were tested for CRC association.

Results
Metabolite set enrichment analysis identified specific acylcarnitines associated with higher CRC risk and triacylglycerols with lower CRC risk among women and men. Further, phosphatidylcholines were associated with a higher risk of CRC among men. In an analysis restricted to CRC diagnosed 2 years after blood draw, myristoleic acid (odds ratio = 1.37 [95% CI = 1.15 to 1.62]; false discovery rate = 0.072) and C60:12 triacylglycerol (odds ratio = 0.75 [95% CI = 0.64 to 0.88]; false discovery rate = 0.072) were associated with CRC risk in women. Weighted correlation network analysis identified amino acids associated with CRC in men, fatty acid esters (carnitines) with distal CRC in men, and triradylcglycerols inversely associated with CRC in women.

Conclusions
We identified prediagnostic CRC-associated metabolites with distinct sex-specific profiles. These results provide insight into CRC etiopathogenesis and have implications for risk prediction strategies.
Unraveling the influence of essential climatic factors on the number of tones through an extensive database of languages in China
Authors: Wang Shuai , Liang Yuzhu , Wang Tianheng , Huang Wei , Xu Ke , Mitkov Aleksandr , Yuan Shuting , Ding Jun , Wang Lining , Zhou Yongdao , Xia Quansheng , Ran Qibin 
Published: October 2024

Abstract
Recent research has provided supportive evidence for the role of humidity in the evolution of tones. However, there remain numerous challenges in delving deeper into the intricate relationship between the tone system and climatic factors: precisely tracking and identifying potentially relevant climate factors at appropriate temporal and spatial scales, while effectively controlling the potential interference caused by geographical proximity and language inheritance. Based on a substantial database of 1,525 language varieties in China and 41 years of monthly climate data, this study has delved into the correlation between multiple climate factors and number of tones, examined the mediating role of voice quality in this process, and further analyzed the interrelationship between climate factors and pitch variations. The findings reveal that climate factors influencing voice quality and the number of tones are diverse, with specific humidity, precipitation, and average temperature playing pivotal roles. After controlling the influence of language inheritance and geographical proximity, the chain of climate → voice quality → number of tones remains significant in China. Specifically, people living in a humid and warm environment tend to exhibit better voice quality. Meanwhile, regions with higher specific humidity and precipitation tend to have a richer and more diverse range of tone types. These findings enrich the theoretical framework of the interaction between language and the environment and provide robust empirical support for understanding the natural mechanisms of language evolution.
Pilot study of a parent-based intervention for functional somatic symptoms in children
Authors: Etkin Rebecca G , Winograd Sara M , Calhoun Amanda J , Silverman Wendy K , Lebowitz Eli R , Shapiro Eugene D 
Published: October 2024

Abstract

Objective
Functional somatic symptoms are associated with significant distress and impairment for children and their families. Despite the central role that families play in their children’s care, there is little clinical research to guide how parents can support their children with functional somatic symptoms and promote better functioning. To address this gap, we developed a parent-based intervention for functional somatic symptoms in children and obtained preliminary data on acceptability, feasibility, treatment satisfaction, and clinical outcomes.

Method
The intervention was adapted from SPACE (Supportive Parenting for Anxious Childhood Emotions), an evidence-based treatment for anxiety and related disorders in children. The intervention, SPACE-Somatic, was delivered to parents of 16 children (Mage = 14.50 years; 75% girls) with a range of functional somatic symptoms. Parents participated in seven weekly group sessions conducted via telehealth.

Results
We found that SPACE-Somatic was acceptable, feasible, and satisfactory to parents. There were significant improvements in several clinical outcomes from baseline to posttreatment, including children’s level of functional impairment, with some gains maintained at 3-month follow-up. Parents also reported improvements in their own stress and their accommodation of children’s symptoms.

Conclusion
This pilot study provides preliminary evidence that a parent-based intervention is viable and beneficial to children with functional somatic symptoms and their parents.
Determining the prior mean in Bayesian logistic regression with sparse data: a nonarbitrary approach
Authors: Gosho Masahiko , Ishii Ryota , Nagashima Kengo , Noma Hisashi , Maruo Kazushi 
Published: October 2024

Abstract
Logistic regression models lead to a bias of the odds ratio (OR) as estimated using the maximum-likelihood (ML) method, when there are few study participants at the binary outcome and factor levels. Although Bayesian methods are frequently applied to reduce this sparse data bias, the specification of the prior distribution for regression coefficients is the most controversial feature. We propose a nonarbitrary and empirical method to determine the prior mean for regression coefficients in Bayesian logistic regression analysis for sparse data. The proposed prior mean is calculated as the difference between the observed log OR and the quasi-expectation of log OR, and is interpreted as a shrinkage statistic of the ML estimate. Further, for easy and fast inference, the proposed method applies to Bayesian logistic regression with the normal prior and the log-F prior via data augmentation. Simulation results indicate that the OR bias based on the proposed method is consistently smaller than that based on the ML method. The OR bias estimated using the proposed method is generally smaller than that based on the mean prior of zero for the regression coefficient. We apply the proposed methods to 2 real data sets.
Postoperative chylothorax following video-assisted mediastinoscopic lymphadenectomy (VAMLA) for early-stage non-small cell lung carcinoma
Authors: van Dam Kayleigh A M , Vissers Yvonne L J , Hulsewé Karel W E , de Loos Erik R 
Published: October 2024

Abstract
Chylothorax is a rare condition in which chylous fluid accumulates in the pleural cavity, most often due to iatrogenic injury of the thoracic duct. This paper reports a case of a woman in her 50s presenting with chyle leakage after a video-assisted mediastinoscopic lymphadenectomy (VAMLA) for staging of a nodule suspected of non-small cell lung carcinoma. After the VAMLA, a Uniportal Video Assisted Thoracoscopic Surgery lobectomy was scheduled during which the chylothorax was observed. The chyle was evacuated and the planned resection was conducted. The chest drain could be removed after 6 days while the patient followed a medium-chain triglyceride diet for 4 weeks. The purpose of this case report is to raise awareness for this very rare complication after VAMLA and discuss treatment options.
Identification of genes associated with sex expression and sex determination in hemp (Cannabis sativa L.)
Authors: Shi Jiaqi , Toscani Matteo , Dowling Caroline A , Schilling Susanne , Melzer Rainer 
Published: October 2024

Abstract
Dioecy in flowering plants has evolved independently many times, and thus the genetic mechanisms underlying sex determination are diverse. In hemp (Cannabis sativa), sex is controlled by a pair of sex chromosomes (XX for females and XY for males). In an attempt to understand the molecular mechanism responsible for sex expression in hemp plants, we carried out RNA sequencing of male and female plants at different developmental stages. Using a pipeline involving differential gene expression analysis and weighted gene co-expression network analysis, we identified genes important for male and female flower development. We also demonstrate that sex-biased expression is already established at very early vegetative stages, before the onset of reproductive development, and identify several genes encoding transcription factors of the REM, bZIP, and MADS families as candidate sex-determination genes in hemp. Our findings demonstrate that the gene regulatory networks governing male and female development in hemp diverge at a very early stage, leading to profound morphological differences between male and female hemp plants.
Juvenile Spring Eruption: A Report on an Outbreak and 2 Sporadic Cases in French Military Personnel
Authors: Lachaux Jordan , Vuillemin Quentin , Savatier Emilie , Duval Maxime , Colléony Thomas , Schwartzbrod Pierre-Éric 
Published: October 2024

ABSTRACT
Juvenile spring eruption is a sun-related skin eruption primarily affecting boys or young adult males. The pathophysiology is unknown, but there appears to be a link with sun exposure in cold weather. It can cause small outbreaks, particularly in groups of children or young adults. The primary lesions can be pruritic erythema, with or without associated papules, vesicles, or bullae. They are notable for almost exclusively affecting the ears. Spontaneous healing occurs within a few days without leaving scars. We report an outbreak and 2 sporadic cases that occurred at the Valdahon military camp in France between 2021 and 2024 among military personnel.
Psychological Distress and Quality of Life Among Military Trauma Patients
Authors: Al-Ghabeesh Suhair Hussni , Al-Taamraha Gusoon , Abualruz Hasan 
Published: October 2024

ABSTRACT

Introduction
Military trauma has a significant impact on soldiers, affecting many aspects of their lives, with the highest impact on their quality of life and psychological wellness. This study aimed to measure psychological distress and its relationship with the quality of life among Jordanian military trauma patients.

Materials and Methods
A descriptive cross-sectional study was conducted in The Hashemite Protection Departments for military causalities in Amman, Irbid, and Al-Karuk. The authors used the WHO Quality of Life Scale-Brief and Trauma Symptoms Checklist-40 scales for assessing the quality of life and psychological distress among Jordanian military trauma patients. A total of 145 trauma survivors participated in the study and responded to all questionnaires out of 173 distributed. The study was approved by the institutional review board of Al-Zaytoonah University.

Results
The result of this study revealed that military trauma survivors had high levels of psychological distress with a mean of 85.66 (SD = 19.418). The subscale of “Dissociation symptoms” had the highest rating (M = 19.92, SD = 5.096), while the “sleep disorders” subscale had the lowest rating (M = 10.000, SD = 3.501). On the quality of life scale, a moderate level of quality of life resulted among the participants with a mean of 61.620 (SD = 17.190). The “general health” subscale scored the highest among the other domains (M = 18.241, SD = 5.434), while the “physical health” domain scored the lowest (M = 4.910, SD = 2.078). Furthermore, a statistically significant negative relationship between psychological distress and quality of life was reported (r =−0.178, P &lt; .05).

Conclusion
Jordanian injured military persons had a moderate quality of life level and high level of psychological distress. A structured follow-up program is required to be developed to improve those patients’ health and quality of life. Furthermore, additional research is needed to investigate the impact of military trauma and services on soldiers in Jordan and the Middle East.
Dental Emergency Rates at an Expeditionary Medical Facility Supporting Operation Inherent Resolve
Authors: Struthers Michael W , Kosaraju Amar , Vandewalle Kraig S 
Published: October 2024

ABSTRACT

Introduction
A core objective of U.S. medical services is to ensure the medical and dental readiness of military personnel. Oral diseases, resulting in pain, infection, or functional impairment, greatly affect the operational effectiveness of military personnel. This study aimed to compare the current causes of dental emergencies and the rates of dental disease nonbattle injuries in a deployed setting with those documented in previous research. Additionally, the study sought to determine if these rates have decreased because of preventive measures or potential improvements in overall oral health.

Methods
Each soldier reporting to the health facility for dental care was screened by a dentist to determine the presence of a dental emergency. The reason for seeking care was classified into 1 of 7 categories and the rate of dental emergencies per 1,000 military members per calendar year was calculated.

Results
The majority of emergencies (38.60%) were due to tooth fractures and/or caries. The second most common reason for visiting the dental clinic was pain from a tooth requiring endodontic therapy (16.81%). This was followed by musculoskeletal or nonendodontic tooth pain (16.10%), most often associated with stress. Periodontal issues accounted for 14.33% of emergencies. Teeth requiring extraction made up 7.16% of all emergencies, prosthodontic bonding complications accounted for 5.16%, and orthodontic bonding complications affected 1.84% of individuals. The dental disease nonbattle injuries rates determined from the current study were 154 emergencies per 1,000 personnel per year for Air Force members and 264 emergencies per 1,000 personnel per year for Army members, which align with previous research findings.

Conclusions
The results of this study confirm that dental emergencies continue to be a threat to overall readiness in deployed environments. The primary etiologic factor in the current study was as a result of tooth fracture and/or caries.
LnCeCell 2.0: an updated resource for lncRNA-associated ceRNA networks and web tools based on single-cell and spatial transcriptomics sequencing data
Authors: Guo Qiuyan , Liu Qian , He Danni , Xin Mengyu , Dai Yifan , Sun Rui , Li Houxing , Zhang Yujie , Li Jiatong , Kong Congcong , Gao Yue , Zhi Hui , Li Feng , Ning Shangwei , Wang Peng 
Published: October 2024

Abstract
We describe LnCeCell 2.0 (http://bio-bigdata.hrbmu.edu.cn/LnCeCell), an updated resource for lncRNA-associated competing endogenous RNA (ceRNA) networks and web tools based on single-cell and spatial transcriptomics sequencing (stRNA-seq) data. We have updated the LnCeCell 2.0 database with significantly expanded data and improved features, including (i) 257 single-cell RNA sequencing and stRNA-seq datasets across 86 diseases/phenotypes and 80 human normal tissues, (ii) 836 581 cell-specific and spatial spot-specific ceRNA interactions and functional networks for 1 002 988 cells and 367 971 spatial spots, (iii) 15 489 experimentally supported lncRNA biomarkers related to disease pathology, diagnosis and treatment, (iv) detailed annotation of cell type, cell state, subcellular and extracellular locations of ceRNAs through manual curation and (v) ceRNA expression profiles and follow-up clinical information of 20 326 cancer patients. Further, a panel of 24 flexible tools (including 8 comprehensive and 16 mini-analysis tools) was developed to investigate ceRNA-regulated mechanisms at single-cell/spot resolution. The CeCellTraject tool, for example, illustrates the detailed ceRNA distribution of different cell populations and explores the dynamic change of the ceRNA network along the developmental trajectory. LnCeCell 2.0 will facilitate the study of fine-tuned lncRNA-ceRNA networks with single-cell and spatial spot resolution, helping us to understand the regulatory mechanisms behind complex microbial ecosystems.
VDGE: a data repository of variation database for gene-edited animals across multiple species
Authors: Shi Wenwen , Jin Enhui , Fang Lu , Sun Yanling , Fan Zhuojing , Zhu Junwei , Liang Chengzhi , Zhang Ya-Ping , Zhang Yong Q , Wang Guo-Dong , Zhao Wenming 
Published: October 2024

Abstract
Gene-edited animals are crucial for addressing fundamental questions in biology and medicine and hold promise for practical applications. In light of the rapid advancement of gene editing technologies over the past decade, a dramatically increased number of gene-edited animals have been generated. Genome editing at off-target sites can, however, introduce genomic variations, potentially leading to unintended functional consequences in these animals. So, there is an urgent need to systematically collect and collate these variations in gene-edited animals to aid data mining and integrative in-depth analyses. However, existing databases are currently insufficient to meet this need. Here, we present the Variation Database of Gene-Edited animals (VDGE, https://ngdc.cncb.ac.cn/vdge), the first open-access repository to present genomic variations and annotations in gene-edited animals, with a particular focus on larger animals such as monkeys. At present, VDGE houses 151 on-target mutations from 210 samples, and 115,710 variations identified from 107 gene-edited and wild-type animal trios through unified and standardized analysis and concurrently provides comprehensive annotation details for each variation, thus facilitating the assessment of their functional consequences and promoting mechanistic studies and practical applications for gene-edited animals.
HSCGD: a comprehensive database of single-cell whole-genome data and metadata
Authors: Fu Jiye , He Shiyang , Yang Yixuan , Chen Zitong , Qiao Yi , Lu Na , Lu Zuhong , Tu Jing 
Published: October 2024

Abstract
Single-cell whole-genome sequencing is a powerful tool for uncovering mutations in individual cells. In recent times, the generation of vast amounts of data has significantly advanced our understanding of key biological processes, including cell development and tumor progression. This rapid accumulation of data underscores the urgent need for a comprehensive resource platform to manage and utilize this information effectively. To address this need, we introduce HSCGD, the first open-access and comprehensive database dedicated to the collection, integration, analysis, and visualization of single-cell whole-genome data and metadata. The current release of HSCGD includes processed single-cell whole-genome sequencing data and curated metadata of 74 154 human cells derived from 63 public single-cell datasets, involving 23 cell types and 17 major single-cell whole-genome amplification methods. HSCGD is designed to help researchers interested in cellular heterogeneity explore and utilize whole genome data at the single-cell level by providing browsing, searching, visualization, downloading and online tools. The database can be accessed from the following URL: http://www.hscgd.com.
Imaging PD-L1 in the brain—Journey from the lab to the clinic
Authors: Dar Dawoud , Rodak Magdalena , Da Pieve Chiara , Gorczewska Izabela , Sharma Gitanjali , Chmielik Ewa , Niedbala Marcin , Bzowski Pawel , d’Amico Andrea , Bobek-Billewicz Barbara , Nowicka Elzbieta , Tarnawski Rafal , Kaspera Wojciech , Kramer-Marek Gabriela 
Published: October 2024

Abstract

Background
Immune checkpoint inhibitors (ICPIs) have proven to restore adaptive anti-tumor immunity in many cancers; however, no noteworthy therapeutic schedule has been established for patients with glioblastoma (GBM). High programmed death-ligand 1 (PD-L1) expression is associated with immunosuppressive and aggressive phenotypes in GBM. Presently, there is no standardized protocol for assessing PD-L1 expression levels to select patients and monitor their response to ICPI therapy. The aim of this study was to investigate the use of 89Zr-DFO-Atezolizumab to image the spatio-temporal distribution of PD-L1 in preclinical mouse models and in patients with newly diagnosed GBM treated with/without neoadjuvant Pembrolizumab.

Methods
The immunoreactivity, binding affinity, and specificity of 89Zr-DFO-Atezolizumab were confirmed in vitro. Mice-bearing orthotopic GBM tumors or patients with newly diagnosed GBM treated with/without Pembrolizumab were intravenously injected with 89Zr-DFO-Atezolizumab, and PET/CT images were acquired 24, 48, and 72 hours in mice and at 48 and 72 post-injection in patients. Radioconjugate uptake was quantified in the tumor and healthy tissues. Ex vivo immunohistochemistry (IHC) and immunophenotyping were performed on mouse tumor samples or resected human tumors.

Results
89Zr-DFO-Atezolizumab was prepared with high radiochemical purity (RCP &gt; 99%). In vitro cell-associated radioactivity of 89Zr-DFO-Atezolizumab corroborated cell line PD-L1 expression. PD-L1 in mouse GBM tumors was detected with high specificity using 89Zr-DFO-Atezolizumab and radioconjugate uptake correlated with IHC. Patients experienced no 89Zr-DFO-Atezolizumab-related side effects. High 89Zr-DFO-Atezolizumab uptake was observed in patient tumors at 48 hours post-injection, however, the uptake varied between patients treated with/without Pembrolizumab.

Conclusions
89Zr-DFO-Atezolizumab can visualize distinct PD-L1 expression levels with high specificity in preclinical mouse models and in patients with GBM, whilst complementing ex vivo analysis.