bluuebunny/crossref_metadata_2025_split huggingface dataset:
Trends in depression in the European population aged 50 years and older by geographic region
Authors: Núñez-Cortés Rodrigo , Calatayud Joaquín , Andersen Lars Louis , Villafañe Jorge Hugo , Suso-Martí Luis , López-Bueno Rubén 
Published: February 2025

Abstract
This study assesses the prevalence and trends of depression in the European population aged 50 years and older between 2004 and 2022 in different geographical regions. We retrieved and pooled data from waves 1,2,4,5,6,7,8, and 9 of the Survey of Health, Ageing and Retirement in Europe (SHARE) conducted between 2004 and 2022. The 12-item EURO-D scale was used as a continuous marker of depression risk. Twenty-eight countries were classified into five geographical regions (Eastern, Western, Southern and Northern Europe, and Israel) as defined by the United Nations. A total of 375 693 observations corresponding to 146 888 participants (weighted mean age 65.8 years [SE=0.2], 54.2% women) were included in the study. In 2022, the overall prevalence of self-reported depression in Europe was 28.3% (95% CI: 27.0-29.7). From 2004 to 2022, the prevalence of self-reported depression in Europe decreased significantly by 5.9% (95% CI= -8.1 to -3.8). In particular, in Southern Europe, the prevalence of depression decreased significantly by 8.8% (95% CI= -12.3 to -5.2). No significant differences were observed in the other geographic regions. These findings highlight the need to develop depression screening and prevention strategies focused on countries with higher prevalence and identified associated factors.
CRIBAR: a fast and flexible sgRNA design tool for CRISPR imaging
Authors: Chen Xiaoli , Rahaman Md Mahfuzur , Naseri Ardalan , Zhang Shaojie 
Published: February 2025

Abstract

Motivation
CRISPR imaging enables the real-time tracking of nucleic acids. Using guide RNAs (gRNAs) to direct fluorescent tags to target regions allows for precise nucleic acid monitoring via microscopy. The design of gRNAs largely affects the efficacy of CRISPR imaging. Currently, available gRNA design tools are developed primarily for gene editing, often producing individual gRNAs that target genes or regulatory elements.

Results
In this study, we introduce CRIBAR, a computational tool developed to systematically design single-guide RNAs (sgRNAs) for CRISPR imaging applications. CRIBAR first generates sgRNA sets optimized to maximize the number of on-target binding sites and then evaluates the potential off-target effect. The results of the in silico experiment show that CRIBAR enables CRISPR imaging in non-repetitive regions.

Availability and implementation
CRIBAR is available as a software package at https://github.com/ucfcbb/CRIBAR and as a web server at http://genome.ucf.edu/CRIBAR.
Prediction of molecular subtypes for endometrial cancer based on hierarchical foundation model
Authors: Cui Haoyu , Guo Qinhao , Xu Jun , Wu Xiaohua , Cai Chengfei , Jiao Yiping , Ming Wenlong , Wen Hao , Wang Xiangxue 
Published: February 2025

Abstract

Motivation
Endometrial cancer is a prevalent gynecological malignancy that requires accurate identification of its molecular subtypes for effective diagnosis and treatment. Four molecular subtypes with different clinical outcomes have been identified: POLE mutation, mismatch repair deficient, p53 abnormal, and no specific molecular profile. However, determining these subtypes typically relies on expensive gene sequencing. To overcome this limitation, we propose a novel method that utilizes hematoxylin and eosin-stained whole slide images to predict endometrial cancer molecular subtypes.

Results
Our approach leverages a hierarchical foundation model as a backbone, fine-tuned from the UNI computational pathology foundation model, to extract tissue embedding from different scales. We have achieved promising results through extensive experimentation on the Fudan University Shanghai Cancer Center cohort (N = 364). Our model demonstrates a macro-average AUROC of 0.879 (95% CI, 0.853–0.904) in a 5-fold cross-validation. Compared to the current state-of-the-art molecular subtypes prediction for endometrial cancer, our method outperforms in terms of predictive accuracy and computational efficiency. Moreover, our method is highly reproducible, allowing for ease of implementation and widespread adoption. This study aims to address the cost and time constraints associated with traditional gene sequencing techniques. By providing a reliable and accessible alternative to gene sequencing, our method has the potential to revolutionize the field of endometrial cancer diagnosis and improve patient outcomes.

Availability
The codes and data used for generating results in this study are available at https://github.com/HaoyuCui/hi-UNI for GitHub and https://doi.org/10.5281/zenodo.14627478 for Zenodo.

Supplementary information
Supplementary data are available at Bioinformatics online.
Effectiveness and safety of methods to prevent bloodstream and other infections and noninfectious complications associated with peripherally inserted central catheters: A systematic review and meta-analysis
Authors: Dobrescu Andreea , Constantin Alexandru Marian , Pinte Larisa , Chapman Andrea , Ratajczak Piotr , Klerings Irma , Emprechtinger Robert , Allegranzi Benedetta , Grayson Michael Lindsay , Toledo Joao Paulo , Gartlehner Gerald , Nussbaumer-Streit Barbara 
Published: February 2025

Abstract

Background
Peripherally inserted central catheters (PICCs) have a 29% complication rate. This systematic review assessed 25 interventions to prevent PICC-associated infectious and noninfectious complications in participants of all ages.

Methods
We searched electronic databases (MEDLINE, Embase, Cochrane Library, WHO Global Index Medicus, CINAHL) and reference lists for randomized (RCTs) and nonrandomized studies published from January 1, 1980–May 8, 2024. We dually selected studies, assessed risk of bias, extracted data, and rated certainty of evidence (COE). We included both single interventions of interest and combinations of at least two (bundle/multimodal). If three or more RCTs existed, we conducted Bayesian random-effects meta-analyses.

Results
Seventy-four studies met our eligibility criteria (60 on individual interventions, 14 on bundle/multimodal), addressing 13 of 25 research questions. The majority were conducted in high-income countries; 36 focused on neonates. Evidence was very uncertain for 11 of the 13 research questions. Evidence with a stronger COE showed that ultrasound-guided catheter insertion reduced phlebitis/thrombophlebitis in adults compared to non-ultrasound-guided insertion (five RCTs; risk ratio [RR] 0.19, 95% credible interval 0.08–0.50); silicone catheters increased phlebitis/thrombophlebitis compared to nonsilicone (one RCT, RR 2.00, 95% confidence interval [95%CI] 1.26–3.17). Bundle interventions decreased local infections (one RCT, RR 0.47, 95%CI 0.31–0.72) and phlebitis/thrombophlebitis in adults (one RCT, RR 0.35, 95%CI 0.22–0.56) compared to routine care.

Conclusions
Ultrasound-guided catheter insertion and nonsilicone catheters effectively prevented PICC complications. The evidence for other comparisons was too uncertain to draw conclusions, highlighting the urgent need for additional studies on prevention and control interventions.
Floral scent emission of Epiphyllum oxypetalum: discovery of its cytosol-localized geraniol biosynthesis
Authors: Zhang Yiyang , Zhang Yuhan , Zhang Andong , Tian Qiurui , Yang Bin , Wei Likun , Wu Wei , Zhu Ting , Zhou Zhiwei , Wang Jiaqi , Liu Zhibin , Tang Wei , Xiao Haijun , Liu Mingchun , Li Tao , Sun Qun 
Published: February 2025

Abstract
Epiphyllum oxypetalum, a renowned ornamental species in Cactaceae, releases attractive fragrance during its infrequent, transient and nocturnal blooms. However, the floral fragrance composition and biosynthesis remain largely unexplored. Employing volatilomics, transcriptomics and biochemistry, we systematically characterized the composition, emission dynamics and biosynthesis of the floral scent of E. oxypetalum. The floral scent composition of E. oxypetalum was highly dynamic. Starting after 20:00 local time, volatile emission increased 200-fold within six hours. At full bloom, geraniol accounted for 72.54% of the total emission, followed by benzyl alcohol (12.96%) and methyl salicylate (3.75%). These scents predominantly originated from petals and sepals. Transcriptomic analysis and inhibition assays using pathway-specific inhibitors revealed that the mevalonate pathway was the precursor source for geraniol biosynthesis. Functionally characterized cytosol localizing geraniol synthase EoTPSa1 was the key enzyme responsible for geraniol biosynthesis. Together, these findings pinpointed a cytosolic biosynthetic route for the major scent volatile geraniol in E. oxypetalum. Our study provides new insights into the emission dynamics and biosynthesis of E. oxypetalum floral scents. In particular, we demonstrated a distinctive mevalonate pathway-based geraniol biosynthetic pathway, which may hold potential for the development of novel perfume products.
Characteristics of Lateral Clavicle Fractures Treated With Coracoclavicular Ligament Repair or Reconstruction in a Military Population
Authors: Panarello Nicholas M , O’Hara Matthew M , Harrington Colin J , Feeley Scott M , McCarthy Conor F , Colantonio Donald F , Dickens Jonathan F , Kilcoyne Kelly G 
Published: February 2025

ABSTRACT

Introduction
Lateral clavicle fractures comprise a minority of all clavicle fractures and are associated with high rates of nonunion when managed nonoperatively. Various fixation methods have been described, including augmentation with coracoclavicular (CC) ligament repair or reconstruction. Outcomes following the surgical treatment of lateral clavicle fractures are limited to small case series and systematic reviews, and the literature within physically demanding populations remains sparse. We sought to describe the characteristics and complications of operative lateral clavicle fractures treated with CC ligament repair or reconstruction within the Military Health System.

Materials and Methods
We queried the U.S. Military Health System Data Repository for patients with a lateral clavicle fracture treated with CC ligament repair or reconstruction between October 2013 and March 2020. We reviewed electronic health records, including patient demographics, radiographs, operative reports, and clinical notes, to assess injury characteristics, surgical constructs, postoperative complications, and functional outcomes.

Results
A total of 40 patients underwent CC ligament repair (n = 20, 50%) or reconstruction (n = 20, 50%) for treatment of lateral clavicle fractures during the study period. Twenty-two (55%) patients underwent surgery within 6 weeks of injury, and 40% (n = 18) required concomitant open reduction and internal fixation. Complications included adhesive capsulitis (n = 3, 7.5%), unplanned return to the operating room (n = 4, 10%), and loss of CC reduction (n = 10, 25%). Twenty-six (65%) patients achieved a full, pain-free range of motion. There was a statistically significant association between postoperative complications and shoulder pain or diminished range of motion (P = .026). Seven of 32 (21.9%) active-duty service members required medical separation from military service. Female sex (P = .04) and distal clavicle plate fixation increase the risk of unplanned return to the operating room (P = .01). Nicotine use was predictive of eventual military separation (P = .004).

Conclusions
In this case, a series of lateral clavicle fractures treated with CC ligament repair or reconstruction, all patients achieved fracture union and the majority of patients regained full, pain-free range of motion. Complications were common and portended a poor functional outcome. At the conclusion of their fracture care, 1 in 5 active-duty patients necessitated medical separation from military service.
Human Single-Cell RNA-Sequencing Data Supports the Hypothesis of X Chromosome Insensitivity but Is Ineffective in Testing the Dosage Compensation Model
Authors: Chen Jiabi , Chen Xiaoshu 
Published: February 2025

Abstract
A controversy in evolutionary genetics is whether active dosage compensation is necessary to resolve the gene dosage imbalance between the X chromosome and autosomes. ScRNA-seq data could provide insight into this issue. However, it's crucial to carefully evaluate whether inherent characteristics of scRNA-seq, such as the sparsity of detected genes, might bias the X:AA expression ratio in mammals. This study evaluated two common strategies for selecting genes in the calculation of X:AA, namely, filter-by-expression and filter-by-fraction, with simulated scRNA-seq and bulk RNA-seq datasets. We found that both strategies produce an inflated X:AA, thus artifactually supporting dosage compensation. Analyzing empirical human Smart-seq2 data, results from the filter-by-expression strategy suggested that X-linked genes were more highly expressed than autosomal genes, a pattern that is neither predicted by dosage compensation nor explained by genes escaping X chromosome inactivation. However, the results of the filter-by-fraction strategy are consistent with the simulation. Furthermore, despite biasing for mean expression levels, we found that scRNA-seq data could be used to detect X-to-autosome expression noise differences as small as 10%, which enabled investigation into the distribution of genes that are more likely insensitive to gene dosage changes. Analysis of the empirical Smart-seq2 data revealed a 10% to 15% increase in expression noise for X chromosomes compared with autosomes and a significant depletion of dosage-sensitive genes on X chromosomes. Overall, these results highlight the need to be cautious when interpreting scRNA-seq data, particularly when comparing the expression of different genes, and provide additional evidence for the hypothesis of X chromosome insensitivity.
Hepatitis E virus Infection in Vietnamese Pregnant Women with Hepatitis B: Prevalence and Clinical Outcomes
Authors: Thi Hong Van Le , Van Tong Hoang , Thanh Thuyet Bui , Lan Anh Bui , Chi Cao Le , Thu Trang Do , Xuan Hoan Nghiem , Xuan Huy Trinh , Thu Hang Ngo , Van Mao Can , Thi Thanh Huyen Tran , Linh Toan Nguyen , Huu Song Le , Bock C -Thomas , Wedemeyer Heiner , Velavan Thirumalaisamy P , Tien Sy Bui 
Published: February 2025

Abstract

Background
Hepatitis E virus (HEV) infection during pregnancy is associated with obstetric complications and adverse maternal and neonatal outcomes. This study aimed to determine the seroprevalence of HEV and RNA positivity in both healthy pregnant women and women co-infected with hepatitis B virus (HBV).

Methods
A cross-sectional study was conducted involving 528 pregnant women (278 with and 250 without HBsAg) in their third trimester. Anti-HEV specific IgG and IgM antibodies were tested using ELISA, while HEV-RNA was detected by nested PCR. The status of anti-HEV antibodies was analysed regarding pregnancy outcomes and the risks of obstetric complications.

Results
The results indicated that 24% (127/528) of participants tested positive for anti-HEV IgG, while 2.5% (13/528) showed detectable anti-HEV IgM. Among HBV-positive women, 26% (55/250) had anti-HEV IgG, comparable to 22% (61/278) in HBV-negative controls. Notably, 28% (140/501) of cord blood samples were positive for anti-HEV IgG. No cases of HEV-RNA were detected. The prevalence of anti-HEV IgG increased with maternal age and was associated with higher infant birth weights. Anti-HEV IgM positivity was associated with an increased risk of neonatal infections (OR=20.6; p=0.05). Among HBsAg-positive women, those with anti-HEV IgG (26%) had higher gestational age at delivery, infant birth weights, but lower platelet counts and prothrombin times (p&lt;0.05).

Conclusions
These findings highlight the endemic nature of HEV in Vietnam and underscore the potential risks of co-infection with HBV during pregnancy, which may lead to adverse obstetric outcomes.
Assessment of immune modulation strategies to enhance survival and integration of human neural progenitor cells in rodent models of spinal cord injury
Authors: Lou Zijian , Post Alex , Nagoshi Narihito , Hong James , Hejrati Nader , Chio Jonathon Chon Teng , Khazaei Mohamad , Fehlings Michael G 
Published: February 2025

Abstract
Regenerative therapies are currently lacking for spinal cord injury (SCI). Neural progenitor cells (NPCs) have emerged as a promising therapeutic approach. To facilitate translation of NPCs into the clinic, studying human NPCs in rodent models is required. The preclinical study of human NPCs in rodent models of SCI necessitates an optimal selection of immunomodulatory strategies, requiring a balance between modulating the immune system and preserving its functionality.
Network expression analysis identifies and experimentally validates the involvement of Fosb in acute kidney injury
Authors: Tang Xiaoyan , Shen Changqiong , Liu Chunqiu , Gao Jianya 
Published: February 2025

AbstractAcute kidney injury (AKI) is a complex clinical syndrome associated with increased incidence and mortality rates among critically ill patients, often leading to multiple organ dysfunction, which underscores the need to better understand its molecular mechanisms. In this study, common differentially expressed genes (DEGs) between various AKI models and control groups were extracted using the Gene Expression Omnibus (GEO) database, followed by an exploration of potential signaling pathways involved in AKI. Key genes in the development of AKI were identified through Weighted Gene Co‐expression Network Analysis (WGCNA) and protein–protein interaction (PPI) networks, and the expression of hub genes was validated using quantitative PCR (qPCR), Western blotting, immunohistochemistry (IHC) and flow cytometry. A total of 1265 DEGs significantly associated with AKI were identified, with GO and KEGG analyses revealing significant enrichment in pathways related to kidney development, muscle regulation, and amino acid biosynthesis. WGCNA further screened AKI‐related modules, identifying 290 DEGs significantly linked to the disease state. PPI network analysis revealed Fosb as a significantly upregulated hub gene in AKI, with experimental validation demonstrating its substantial upregulation in patients with acute tubular necrosis (ATN), HR‐induced HK‐2 cells injury and ischemia–reperfusion injury (IRI) mice. Inhibition of Fosb alleviated hypoxia‐reoxygenation (HR)‐induced apoptosis and inflammation in HK‐2 cells by suppressing the AP‐1 complex (Fosb/C‐Jun) signaling pathway. Therefore, Fosb is significantly upregulated in AKI and associated with inflammation mediated by the AP‐1 signaling pathway, suggesting its potential as a diagnostic biomarker and therapeutic target for AKI.
Prussian blue nanoparticles prevent RANKL‐induced osteoclastogenesis by scavenging ROS and inactivating NF‐κB/MAPK signaling pathways
Authors: Yang Jiancheng , Tang Qinghua , Li Siyu , Yang Lei , Yang Ming , Li Qingmei , Feng Yan , Pan Mingming , Zeng Yuhong 
Published: February 2025

AbstractThe accumulation of intracellular reactive oxygen species (ROS) is widely recognized to stimulate the development of osteoclasts, a crucial factor in the onset of osteoporosis. The ROS scavenging capability of Prussian blue nanoparticles (PBNPs) is exceptional, and they possess excellent biocompatibility. However, the effects of PBNPs on osteoporosis remain unknown. Present study aimed to investigate whether PBNPs could inhibit osteoclast differentiation and prevent ovariectomy (OVX)‐induced bone loss by suppressing ROS. In vitro experiments demonstrated that PBNPs attenuated osteoclastogenesis and downregulated the expression of osteoclast‐related genes. Mechanistically, PBNPs reduce cellular ROS by blocking RANKL‐induced ROS generation and increasing the expression of ROS scavenging enzymes, which in turn block the NF‐κB, ERK, JNK, and p38 pathways, thereby reducing NFATc1 signaling. According to in vivo experimental results, OVX caused a significant rise in ROS in the bone marrow, an increase in osteoclastic number on the bone surface, and substantial bone loss; however, PBNPs significantly reduced ROS and successfully protected OVX‐induced bone damages. In conclusion, this study showed for the first time that PBNPs prevented OVX‐induced bone loss and attenuate osteoclastogenesis, indicating that PBNPs may be a viable alternative therapy for the management of osteoclast‐associated bone disorders.
Intraoperative Cholangiogram Interpretation for Laparoscopic Transcystic Bile Duct Exploration: Is Concurrence Possible?
Authors: Turco Jennifer , Pugliese Matthew , Trivedi Anand , Aldridge Oscar , Webber Laurence , Ballal Mohammed 
Published: February 2025

Background:
Laparoscopic transcystic bile duct exploration (LTCBDE) represents a secure and efficacious approach for managing common bile duct (CBD) stones, particularly in patients concurrently undergoing laparoscopic cholecystectomy (LC). The decision to proceed with LTCBDE hinges on real-time assessment of the intraoperative cholangiogram (IOC), which is highly operator-dependent and poorly interpreted. No established criteria exist to guide the evaluation of IOCs for LTCBDE. This study aims to ascertain the concordance among surgeons, experienced in LTCBDE, on critical aspects of IOC interpretation.

Methods:
A retrospective collection of IOC images of 40 patients who underwent LC, IOC, and LTCBDE at a tertiary university hospital between 2017 and 2018 was undertaken. Two hepato-pancreato-biliary (HPB) and 2 acute care surgery (ACS) specialists independently reviewed the images. They were tasked with assessing IOC features hypothesized to influence duct exploration and stone extraction complexity, along with overall suitability for LTCBDE based exclusively on the IOC images. Agreement percentages were calculated and Kappa inter-rater reliability statistics were assessed.

Results:
The overall agreement percentages concerning IOC features ranged between 52.5% and 82.5% with agreements surpassing 75% deemed robust. Maximum agreement was achieved in the interpretation of cystic duct morphology, whether straight or characterized by spiral valves. The concurrence for amenability of LTCBDE also demonstrated substantial accord among surgeons (ACS: 92.5%, HPB: 95%, total: 87.5%). Consistently high agreement was evident within specialty groups.

Conclusions:
Anatomical attributes displayed superior agreement levels, as opposed to variables necessitating measurements. We recommend the development of a structured approach for the interpretation of IOC to facilitate surgical education in LTCBDE.