bluuebunny/crossref_metadata_2025_split huggingface dataset:
Double edged roles of endogenous PRDX6 in ventilator-induced lung injury via modulating oxidative stress and macrophages activation
Authors: Cheng Gao , Zhou Leiying , Tang Weijie , Li Wei , Lv Changming , Wang Chunhui , Shen Qiying 
Published: March 2024

Abstract

PRDX6 is highly expressed in lung tissues and shows an important biological significance. However, its specific roles in ventilator-induced lung injury (VILI) have not been clearly explored. The present study investigated the roles of endogenous PRDX6 in VILI, focusing on its overall and the iPLA2 function on lung injury, oxidative stress (OS), macrophages activation and polarization. Broncho-alveolar lavage fluid (BALF) from patients with mechanical ventilation was acquired. Both wild-type (WT) Sprague-Dawley rats and PRDX6 gene-knock out (PRDX6-/-) rats were used to set up VILI model. Biological and histopathological analyses were performed. Our results showed that OS and PRDX6 expression were up-regulated after mechanical ventilation. PRDX6 deficiency led to lung inflammation and VILI aggravation, and the OS was further elevated and the activation and M1 polarization of lung macrophages were obviously increased in PRDX6-/- rats. The iPLA2 inhibitor MJ33 alleviated VILI in rats and reversed the increased OS and M1 macrophages activation and polarization. The present study showed the double-edged roles of endogenous PRDX6 in VILI, including its overall protective role and the role of promoting VILI via iPLA2 by producing the excessive OS and subsequent increase of M1 macrophages polarization.
No Genetic Causal Association between Iron Status and Intervertebral Disc Degeneration: A Two-Sample Mendelian Randomization Study
Authors: Li Hewen , Su Chen’guang , Yu Rongbo , Wan Chao , Xiang Yiliu , Dou Haoduan , Ma Guiyun , Chen Bin 
Published: March 2024

Abstract

Many clinical and basic studies have shown an association between iron status and intervertebral disc degeneration (IVDD). However, their causal relationship is still unclear. The aim of this study was to explore the genetic causality between iron status and IVDD using Mendelian randomization. Random effects inverse variance weighted (IVW) meta-analysis was the primary method of analysis, with MR‒Egger, weighted median, simple modal, and weighted modal methods as secondary methods. Subsequently, we used IVW, MR‒Egger, MR-PRESSO, and leave-one-out analyses to test for heterogeneity and horizontal pleiotropy. Finally, we used the maximum likelihood, penalized weighted median and IVW (fixed effects) methods to further verify the reliability of the results. Random-effects IVW and IVW meta-analyses revealed that transferrin, total iron binding capacity (TIBC), ferritin, iron, and transferrin saturation (TSAT) were not genetically causally related to IVDD, and removal of outliers detected by MR-PRESSO resulted in broad consistency. Our study revealed that there is no genetic causal relationship between iron status and IVDD, but it cannot be excluded that there is a correlation between the two at a level other than genetics.
Variations in microbiota populations in chronic periodontits patients compared to healthy controls
Authors: Abujamel Turki S. , Alhazmi Shaima , Assas Motaz B. , Assas Mushref B. , Moubayed Nadine , BinShabaib Munerah S. , ALHarthi Shatha Subhi , Aabed Kawther 
Published: March 2024

Abstract
Background Periodontitis is a common gum disease that affects the soft tissue surrounding teeth and may lead to the deterioration of the bone that supports the teeth. The composition of saliva microbiota plays a significant role in the development and progression of periodontitis. Nonetheless, there is a lack of information relating to saliva microbiota composition in adults and its correlation with periodontitis.Methods Saliva samples were collected from healthy adults and patients with chronic periodontitis. Saliva microbiota was comprehensively characterized by sequencing the V3-V4 region of the 16S rRNA gene and analyzed using established bioinformatics pipeline and statistical analysis. Finally, the metagenome of the saliva microbiota was predicted using the PICRUSt algorithm and compared between the groups.Results A significant increase in biodiversity of the saliva microbiota associated with periodontitis patients was detected. In our study, the composition of saliva microbiota revealed a significant abundance of Streptococcus, Moryella, Granulicatella, Osenella, Prevotella nanceiensis, and Neisseria oralis in the healthy group. In contrast, periodontitis patients’ saliva was enriched with Leptotrichia, Filifactor, Selenomonas, Acholeplasma, Prevotella intermedia, Porphyromonas endodontalis, and Rothia dentocariosa. The predicted metagenome showed higher abundance of carbohydrate metabolism and transcription factors in healthy individuals, while cofactors, vitamins metabolism, and glycan biosynthesis were enriched in the periodontitis group.Conclusion Our study revealed a distinctive dysbiosis in the saliva microbiota of adults with periodontitis. These findings present a significant step in understanding the microbial aspects of this disease and have the potential to understand further the intrinsic co-factors in the onset of chronic periodontitis.
Combined scRNA-seq and bulk transcriptome analysis establishes a stromal signature for predicting prognosis and therapeutic sensitivity in gastric cancer
Authors: Yu Fei , Tan Yuanfei 
Published: March 2024

Abstract

Gastric cancer (GC) is a major disease threatening human health. Tumor stroma component, mainly including fibroblasts, pericytes and endothelial cells (ECs), play a prominent role in tumor progression. This study wanted to establish a stromal prognostic signature for GC patients. Published single-cell RNA sequencing (scRNA-seq) and bulk gene expression data were obtained from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA). 572 stromal marker genes were identified from scRNA-seq analysis. We performed univariate cox regression and LASSO algorithm on TCGA training cohort (n=297) to construct stromal prognostic model, which were verified in validation cohorts of GSE15459 (n=182), GSE62254 (n=297) and GSE84437 (n=431). pRRophetic and Tumor Immune Dysfunction and Exclusion (TIDE) method was applied to predict chemosensitivity and immunotherapy response. Microenvironment Cell Populations-counter (MCP-counter) method was used to assess stromal and immune cell infiltration from bulk gene expression data. ScRNA-seq analysis and Immumohistochemical staining image derived from Human Protein Atlas (HPA) database was to explore gene expression location in GC tissue. We established a seven-gene prognostic signature from training cohort, which was further verified in other three validation cohorts. The seven genes (SERPINE1, SLCO2A1, GJA1, SDC2, BEX3, PLOD2, MARCKS) had different expression in GC stroma. The stromal signature could be a robust prognostic factor in GC, which provided evidence for patient stratification and stroma-targeted immunotherapeutic strategy.
Improving Adult Inpatient Eating Disorder Treatment: Perspectives of a Sample of Canadians with Lived Experience
Authors: Armour Catherine Q. , Feicht Becky , Gahagan Jacqueline 
Published: March 2024

Abstract

Background
Eating disorders (EDs) are common, affecting over one million Canadians. Canadian adults (i.e., age 18+) requiring medical stabilization for their eating disorder (ED) may be referred to adult inpatient (IP) ED treatment for care. Recent Canadian publications have brought attention to the need for improved approaches to Canadian ED treatment; urging researchers to seek perspectives of people with lived experience to determine how to best do so. This study explored the perspectives of Canadians with lived experience to identify recommendations for improvement of adult IP ED treatment programs and processes.
Methods
Employing a transformative philosophical view and feminist standpoint theory, this study utilizes a qualitative hermeneutic phenomenological approach to fulfill the objectives. Eleven participants with lived adult IP ED treatment experiences from across Canada were interviewed individually, to discuss their experiences and recommendations regarding referral, transitions into and out of care, and treatment itselfusing an online video conference platform. Data were analyzed using interpretative phenomenological analysis. A comprehensive list of recommendations was drafted and brought back to participants for feedback. The feedback was implemented to create the final list of recommendations.
Results
Several limitations of referral, transitions, and treatment, facilitated and exacerbated by stigma at individual and societal levels, were identified by participants. These included guilt and shame upon referral, lack of respect and trust from healthcare providers during transitions, and lack of consideration of social determinants of health during treatment. Participant-informed recommendations, which can be categorized as interim support, individualized care, dignified treatment, resources, and stigma, were identified to ameliorate the experiences of Canadians with EDs while also combatting stigma.
Conclusions
Adult IP ED treatment in Canada is in urgent need of significant change to meet the needs of those requiring care and to address harmful stigma. Implementing participant-informed recommendations may aid in achieving this goal. The meaningful inclusion of those with lived experience, particularly marginalized populations, will be paramount to the development of an approach to adult IP ED treatment that properly serves Canadians who need it.
Are We In or Out of Conservation Units in Brazil? A Gap Analysis for the Conservation of Bats in Brazil
Authors: Rodrigues Felipe Baia , Alexandre Rafaela Jemely Rodrigues , Pena Simone Almeida , Correia Letícia Lima , Vieira Thiago Bernardi 
Published: March 2024

Abstract

With approximately 1,400 known species, 184 of which are found in Brazil, the order Chiroptera is the second most diverse among mammals, and this taxon is relevant in terms of the ecosystem services it provides to humans. However, disturbances caused by anthropogenic factors amplify processes of extinction, changes in geographic distributions, and phenological alterations in species, despite efforts to protect biodiversity and its resources through the creation and establishment of Conservation Units, in addition to Indigenous Lands. Nevertheless, taxonomic knowledge gaps or geographical distribution challenges pose obstacles to the effective implementation of conservation strategies in areas designated for biodiversity protection. Therefore, this study evaluates the contribution of Brazilian Conservation Units (Full Protection Units and Sustainable Use Units) and Indigenous Lands to the protection of bat species and ecosystem services in Brazil. It also presents maps of richness by trophic guilds and threat classification according to IUCN, including species classified as Data Deficient. The results indicated low percentages of areas within Conservation Units and Indigenous Lands with the potential distribution of bats, especially for insectivorous, nectarivorous, and frugivorous guilds in the Cerrado, classified as Near Threatened. Additionally, higher bat richness was observed in the Amazon and Atlantic Forest.
Mechanical, Morphological and Thermal Properties of Thermoplastic Copolyester Elastomer Composites Filled with Calcite
Authors: Sucu Yunus Emre , Doganci Merve Dandan 
Published: March 2024

Abstract
In this study, the effects of different concentrations of stearic acid-coated calcite (CaCO3) on the mechanical, thermal, and morphological properties of thermoplastic polyester elastomers (COPE or TPE-E) were investigated. Moreover, COPEs, which consist of process wastes that are qualified as postindustrial recycled (PIR), were physically recycled. Recycled polymer composites (100%) were obtained by blending the physically recycled COPE polymer with stearic acid-coated calcite at different concentrations. COPE composites (virgin and PIR) containing different concentrations of calcite (5 to 30 wt%) were prepared by melt compounding. It has been determined that mechanical properties such as flexural strength and modulus increase with calcite concentration, while tensile strength decreases at higher concentrations owing to the stronger interfacial relationships between the polymer matrix and stearic acid-coated calcite. The thermal properties of the composite increased with increasing calcite filler concentration. Morphological studies revealed good dispersion of calcite fillers at lower concentrations in the polymer matrix.
Systematic review of methods used in prediction models with recurrent event data
Authors: Watson Victoria , Smith Catrin Tudur , Bonnett Laura J 
Published: March 2024

Abstract

Background
Patients who suffer from chronic conditions or diseases are susceptible to experiencing repeated events of the same type (e.g. seizures), termed ‘recurrent events’. Prediction models can be used to predict the risk of recurrence so that intervention or management can be tailored accordingly, but statistical methodology can vary.
The objective of this systematic review was to identify and describe statistical approaches that have been applied for the development and validation of multivariable prediction models with recurrent event data. A secondary objective was to informally assess the characteristics and quality of analysis approaches used in the development and validation of prediction models of recurrent event data.
Methods
Searches were run in MEDLINE using a search strategy which included index terms and phrases related to recurrent events and prediction models. For studies to be included in the review they must have developed or validated a multivariable clinical prediction model for recurrent event outcome data, specifically modelling the recurrent events and the timing between them.
The statistical analysis methods used to analyse the recurrent event data in the clinical prediction model were extracted to answer the primary aim of the systematic review. In addition, items such as the event rate as well as any discrimination and calibration statistics that were used to assess the model performance were extracted for the secondary aim of the review.
Results
A total of 855 publications were identified using the developed search strategy and 301 of these are included in our systematic review. The Andersen-Gill method was identified as the most commonly applied method in the analysis of recurrent events, which was used in 152 (50.50%)studies. This was closely followed by frailty models which were used in 116 (38.54%) included studies. Of the 301 included studies, only 75 (24.9%) internally validated their model(s) and three (1.0%) validated their model(s) in an external dataset.
Conclusions
This review identified a variety of methods which are used in practice when developing or validating prediction models for recurrent events. Further work is required to ensure publications report all required information and use robust statistical methods for model development and validation.
PROPSERO Registration Number: CRD42019116031.
Epidemiology of maxillofacial trauma in elderly patients receiving oral anticoagulant or antithrombotic medication; a Swiss retrospective study
Authors: Bettschen David , Tsichlaki Dimitra , Chatzimichail Eleftherios , Klukowska-Rötzler Jolanta , Müller Martin , Sauter Thomas C. , Burkhard John-Patrik , Exadaktylos Aristomenis K , Ziaka Mairi , Doulberis Michael 
Published: March 2024

Abstract

Background:The percentage of elderly trauma patients under anticoagulation and antiplatelet agents has been rising lately. With time, newer agents have been introduced with certain advantages and precautions. We aimed to investigate the demographic data, causes, and type of maxillofacial trauma, concomitant injuries, hospitalization time, haemorrhagic complications, and total costs of emergency department (ED) care in elderly patients admitted to the ED with maxillofacial trauma while receiving anticoagulation (AC) or antiplatelet therapy (APT).Methods:Data were gathered from the ED of Bern University Hospital. In this retrospective analysis, patients older than 65 years with maxillofacial trauma presenting to our ED between 2013 and 2019 with therapeutic AC/APT were included.Results: A total of 196 patients were included. The median age was 81 years (interquartile range [IQR]: 74-87), and 111 (56.6%) were men. 54.1% (n=106) were 80 years or older. One hundred thirty-seven of the patients (69.9%) suffered from a cardiovascular disease. Previous thromboembolic events (n=82, 41.8%) and atrial fibrillation (n=50, 25.5%) were the most reported indications for oral anticoagulation or antithrombotic therapy intake. Falls (n=162, 82.7%) were the leading cause of facial injury, followed by road traffic injuries (n=26, 13.2%). The most reported primary injuries were orbital fracture (n=46, 23,5%) along with a fracture of the zygomatic bone (n=38, 19,4%) and fracture of the midface (Le Fort I, II, III) (n=35, 17,9%) followed by zygomatic bone fracture (n=38, 19.4%) and mandible fracture (n=20, 10.2%). Epistaxis was noted in 23 cases (11.7%) and oral bleeding in 10 (5.1%). In 120 patients (61.2%), haematomas involved the middle third of the face, which were operated on most frequently in absolute terms. Fourteen patients suffered an intracerebral haemorrhage (n=14, 7.1%), whereas retrobulbar bleeding was observed in 20 patients (10.2%). The overall in-hospital mortality rate was 2.6% (n=5).Conclusions:This study reaffirms the link between falls and the prevalence of maxillofacial trauma in older individuals. Additionally, it underscores the substantial occurrence of mid-face haematomas in geriatric patients undergoing AC/APT. Considering the increasing growth of the geriatric population, enhancing prevention strategies and refining safety guidelines are urgently necessary.
Insights into tumor microenvironment and HPV integrations in cervical cancer pathogenesis revealed by single-cell transcriptome data
Authors: Peng Fang , Zeng Xi , Wang Ziying , Sha Ying , Leung Ross Ka-Kit , LAI Koon Chi Christopher , Li Guoliang , Huang Xiaoyuan , Lin Shitong 
Published: March 2024

Abstract
Background HPV infection is prevalent among women, and can lead to severe diseases. This study leverages single-cell RNA-sequencing (scRNA-seq), a cutting-edge technology that allows for cellular-level exploration, to investigate the relationship between cellular heterogeneity and HPV integrations in cervical histopathology.Methods We applied scRNA-seq to examine heterogeneity across normal and three disease stages patients with normal, high-grade squamous intraepithelial lesions (HSIL), microinvasive carcinoma (MIC), and cervical squamous epithelium carcinoma cancer (CSCC) tissues. A pipeline was developed to detect the HPV integration events from scRNA-seq data in this study.Results Our findings revealed an increase in the proportion of squamous epithelial cells and a decrease in the proportion of columnar epithelial cells in the disease progress from normal to CSCC. We identified HPV genes expressed differentially across normal and three disease stages. Notably, we observed HPV integration events occurring more frequently in squamous epithelial cells at single-cell level. An increasing trend in the ratio of HPV-integrated cells was observed in the disease progress from normal tissue to CSCC, which eventually plateaued. We identified several genes, including EGR1, S100A11, S100A8, KRT5, RPL34, ATP1B1, RPS4X and EEF2 that were frequently integrated by HPV across patients. In contrast, genes such as PAN3, BABAM2, SPEN, TCIM-SIRLNT, TEX41-PABPC1P2 and KCNV1-LINC01608 showed frequent integration events across cells. Some of these genes exhibited significant expression differences between tumor and normal squamous epithelial cells. KRT5, ATP1B1, RPS4X, PAN3 and SPEN were novel recurrent HPV-integrated genes we observed at the patient or cell level in this study. Furthermore, we found that HPV genes from various HPV types demonstrated integration preferences in different samples and disease stages.Conclusions These findings uncovered the intricate heterogeneity across normal and three disease stages caused by varying degrees of HPV infection, offering a valuable single-cell perspective on the mechanism of HPV-induced cervical cancer and its clinical relevance.
Identifications of genes involved in ABA and MAPK signaling pathways positively regulating cold tolerance in rice
Authors: Ding Guohua , Cao Liangzi , Iqbal Zubair , Zhao Minghui , Cui Zhibo , Zhou Jinsong , Lei Lei , Luo Yu , Bai Liangming , Yang Guang , Wang Tongtong , Wang Xueyang , Wang Rongsheng , Liu Kai , Li Zhugang , Qu Mingnan , Sun Shichen 
Published: March 2024

Abstract
Cold stress (CS) significantly impacts rice growth during seedling and heading stages. This study based on two-year field observations identified two rice lines, L9 (cold stress-sensitive) and LD18 (cold stress-tolerant) showing contrasting CS response. L9 exhibited 38% reduction in photosynthetic efficiency, whereas LD18 remained unchanged, correlating with seed rates. Transcriptome analysis identified differentially expressed genes (DEGs) with LD18 showing enriched pathways (carbon fixation, starch/sucrose metabolism, glutathione metabolism). LD18 displayed dramatically enhanced expression of MAPK-related genes (LOC4327351, LOC4352460, LOC4337850) and increased ABA signaling genes (LOC4333690, LOC4345611, LOC4335640) compared to L9 exposed to CS. Results from qPCR confirmed the enhanced expression of the three MAPK-related genes in LD18 while dramatic reduction in L9 under CS relative to that under CK. We also observed up to 66% reduction in expression levels of the three genes related to ABA signaling pathway in L9 relative to LD18 under CS. In consistent with results of photosynthetic efficiency, metabolic analysis suggests pyruvate metabolism, TCA cycle and carbon metabolism enrichment in LD18 under CS. The study reveals reprogramming of the carbon assimilation metabolic pathways, emphasizing the critical roles of the key DEGs involved in ABA and MAPK signaling pathways in positive regulation of LD18 response to CS, offering the foundation towards cold tolerance breeding through targeted gene editing.
Mechanism of Initiation and Regeneration Convective Cell in Bandung Basin, Indonesia
Authors: Firdaus Irfans Maulana , Trilaksono Nurjanna Joko , Yamazaki Takeshi 
Published: March 2024

Abstract

The mechanism of convective cell initiation and regeneration in the Bandung Basin (\(107.35^\circ \text{E}-107.95^\circ \text{E};6.75^\circ \text{S}-7.25^\circ \text{S}\)), Indonesia is investigated using a Weather Research and Forecasting model. Based on the cumulative distribution function and regeneration index, model simulations were conducted using case studies in February-March 2019. Upslope wind flows to the mountain peak in north and south of the basin due to solar heating, carrying water vapor from the bottom of the basin. Therefore, low-level convergence is formed due to the convergence of winds from the bottom of the basin and from outside the basin. The low-level convergence causes the developing updraft, makes atmosphere unstable, and generates convective initiation. The convective system will be developed in the mountains region, produced precipitation, and formed cold pools on the surface. The cold pool will fall down the slopes and convective activity from the mountains will continue to the bottom of the basin. The convective system’s outflow causes the cold pool to move in the west-east direction. The cold pool will collide with warmer air from the opposite direction, resulting in an updraft at the cold pool leading edge, and convection will be re-initiated (convective regeneration) in the Bandung Basin, with the new convective system tending to move eastward.