bluuebunny/crossref_metadata_2025_split huggingface dataset:
The implication of the vaginal microbiome in female infertility and assisted conception outcomes
Authors: chen xiuju , sui yanyu , gu jiayi , wang liang , Sun Ningxia 
Published: April 2024

Abstract

Background: Infertility rates are on the rise, presenting a complex array of causative factors. Recent advancements in human microbiome and associated techniques have shed light on the potential impact of vaginal microbiota disruptions on female fertility. Our study aims to investigate differences in vaginal microbiome between fertile women and those experiencing infertility. Additionally, we aim to investigate how microbial composition in infertile population may affect the success of assisted reproduction technology (ART).
Methods: We enrolled 194 women diagnosed with infertility at the Reproductive Medicine Center of Shanghai Changzheng Hospital between November 2018 and November 2021, along with 102 healthy women undergoing routine physical examinations at the hospital’s Physical Examination Center. Vaginal secretions were collected from both groups, and polymerase chain reaction (PCR) was used to amplify the bacterial 16S rRNA V4-V6 conserved region for microbial analysis. A machine learning model was built based on the genus abundances to predict infertility. Additionally, we employed the PICRUSt algorithm to predict the metabolic pathway activities, providing insights into potential molecular mechanisms underlying female infertility and ART outcomes.
Results: Women with infertility exhibited a significantly different vaginal microbial composition compared to healthy women, with the infertility group showing higher microbial diversity. Burkholderia, Pseudomonas, and Prevotella levels were significantly elevated in the vaginal microbiota of the infertility group, while Bifidobacterium and Lactobacillus abundances were reduced. Recurrent implantation failure (RIF) within the infertile population showed even higher diversity of vaginal microbiota, with specific genera such as Mobiluncus, Peptoniphilus, Prevotella, and Varibaculum being more abundant. Overgrowth of Mobiluncus and Varibaculum emerged as independent risk factors affecting ART outcomes. Eleven metabolic pathways were associated with both RIF and infertility, with Prevotella demonstrating stronger correlations.
Conclusions: The present study provides insights into the differences in vaginal mircobiome between healthy and infertile women, offering a new understanding of how vaginal microbiota may impact infertility and ART outcomes. Our findings underscore the significance of specific microbial taxa in women with recurrent implantation failure, suggesting avenues for targeted interventions to enhance embryo transplantation success rates.
Integrated transcriptomic and metabolomic analysis reveals the role of jasmoic acid biosynthesis in pollen development of CMS-D1 rice
Authors: Wang Jie , Ying Suping , Long Weixiong , Luo Lihua , Qian Mingjuan , Chen Wei , Luo Laiyang , Xu Weibiao , Li Yonghui , Cai Yaohui , Peng Xiaojue , Xie Hongwei 
Published: April 2024

Abstract
Background
Cytoplasmic male sterility (CMS) has greatly improved the utilization of heterosis in crops due to the absence of functional male gametophyte. The newly developed sporophytic D1 type CMS (CMS-D1) rice exhibits unique characteristics compared to the well-known sporophytic CMS-WA line, making it a valuable resource for rice breeding.
Results
In this research, a novel CMS-D1 line named Xingye A (XYA) was established, characterized by small, transparent, and shriveled anthers. Histological and terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) assays conducted on anthers from XYA and its maintainer line XYB revealed that male sterility in XYA is a result of delayed degradation of tapetal cells and abnormal programmed cell death (PCD) of microspores. Transcriptome analysis of young panicles revealed that differentially expressed genes (DEGs) in XYA, compared to XYB, were significantly enriched in processes related to chromatin structure and nucleosomes during the microspore mother cell (MMC) stage. Conversely, processes associated with sporopollenin biosynthesis, pollen exine formation, chitinase activity, and pollen wall assembly were enriched during the meiosis stage. Metabolome analysis identified 176 specific differentially accumulated metabolites (DAMs) during the meiosis stage, enriched in pathways such as α-linoleic acid metabolism, flavone and flavonol biosynthesis, and linolenic acid metabolism. Integration of transcriptomic and metabolomic data underscored the importance of the jasmonic acid (JA) biosynthesis pathway in XYA during the meiosis stage compared to XYB. Furthermore, levels of JA, MeJA, OPC4, OPDA, and JA-Ile were all higher in XYA than in XYB at the meiosis stage.
Conclusions
These results highlight the critical role of the JA biosynthetic pathway in pollen development of the CMS-D1 line and lay a foundation for further revealing the molecular mechanism of CMS-D1 sterility.
High-throughput proteo-genomic identification of functional endothelial cell microproteins encoded by non-canonical small open reading frames
Authors: Siragusa Mauro , Graumann Johannes , Kuenne Carsten , Günther Stefan , Jeratsch Sylvia , Güven Beyza , Raheja Manav , Süsser Sebastian , Talyan Sweta , Bezuneh Bethlehem , Cartura Matteo , Zhou Xiaozhu , Szymanski Witold , Cho Haaglim , Sachs Nadia , Maegdefessel Lars , Muller Oliver , Troidl Christian , Nef Holger , Looso Mario , Kaulich Manuel , Offermanns Stefan , Fleming Ingrid 
Published: April 2024

Abstract

Detecting microproteins (miPs) translated from small open reading frames (smORFs) by mass spectrometry poses major challenges. Here we report a high-throughput proteo-genomic pipeline that identified a large number of intracellular and extracellular endothelial cell miPs encoded by non-canonical smORFs. Vascular inflammation in vitro and in vivo profoundly altered smORF expression and miPs were identified in the serum of patients following cardiac tissue damage. The functional importance of 256 miPs for endothelial cell growth and viability was demonstrated by a high-throughput CRISPR/Cas9 screen. Moreover, the inflammation-induced expression of a non-canonical miP, miP-PSTPIP2, was validated in vivo and in carotid arteries from patients with atherosclerosis. Combining gain/loss-of-function with multi-omic approaches demonstrated the involvement of miP-PSTPIP2 in the regulation of gene expression, proliferation and viability through interaction with proteins in different subcellular compartments. Thus, the proteo-genomic approach implemented here enables the identification of large numbers of miPs. Non-canonical miPs play a fundamental role in the regulation of endothelial cell function and may become biomarkers or therapeutic targets in cardiovascular disease
Changes of bilateral tear film stability and corneal nerve in patients with unilateral neurotrophic keratitis
Authors: Wang Fan , Li Yue , Zhang Zhaowei , Lu Qiuchen , Shi Cancan , Yu Xiaofan , Hu Fen , Li Mingxin , Guo Jianxin , Wang He 
Published: April 2024

Abstract

Objective: To observe the stability of the tear film bilaterally in patients with unilateral neurotrophic keratitis and the changes in corneal nerve and immune cells under confocal microscopy.
Methods: Prospective cross-sectional study including 63 patients with confirmed neurotrophic keratitis (NK) and 40 normal controls of similar sex and age, the NK patients were divided into stage 1 and stage 2 according to the severity of the disease. The tear meniscus height (TMH), first non-invasive tear film break-up time (NIBUT-f), and corneal fluorescence staining were examined. Corneal sensitivity was accessed by Cochet Bonnet esthesiometer. The corneal subbasal plexus (SNP) and dendritic cells (DC) were scanned by in vivo confocal microscopy (IVCM), and SNP was analyzed using the fully automated corneal nerve analysis software “ACCmetric”.
Results: Eyes with NK stage 2 showed worse performance in TMH, NIBUT-f, corneal fluorescein staining score, cornealsensitivity examination, SNP parameters, and DC density compared to NK stage 1 (all P < 0.001). And contralateral eyes of NK patients had significantly shorter NIBUT-f and significantly increased dendritic cell density compared to controls (P< 0.001).
Conclusion: The contralateral eyes of NK patients are more prone to dry eye signs than normal subjects and should be attended to and treated promptly. Increased numbers of dendritic cells in the contralateral eyes of NK patients suggest bilateral immune alterations in unilateral disease.
Evaluating the moral courage of nurses and its relationship with their caring behaviors
Authors: Abbasi Fatemeh , Karampourian Arezou , Bonyad Sajjad Amiri , Shadi Yahya , Ashbeh Pouneh 
Published: April 2024

Abstract

Background and Aim: Nurses need ethical courage to make correct decisions in various clinical situations and to engage in proper care behaviors based on ethical principles. In this regard, the present study aimed to determine the relationship between ethical courage and care behaviors of nurses in the year 2023. Method In this cross-sectional study, 146 nurses employed in educational hospitals in the city of Hamadan were selected using stratified sampling method. Data collection instruments included: a checklist of demographic characteristics, Sekerka and colleagues' Ethical Courage Questionnaire, and the Caregiver Behavior Inventory (CDI-25) questionnaire. Data were analyzed using SPSS 24 software and descriptive statistics, Pearson correlation coefficient, t-test, and ANOVA. Findings: The results showed that the majority of participating nurses were female (67.1%) and had a bachelor's degree (89%). The mean ± standard deviation of ethical courage and nurses' care behaviors were 9.26 ± 3.15 and 13.254 ± 101.164, respectively. Also, there was a significant and positive correlation between ethical courage and nurses' care behaviors (P < 0.001, r = 0.264). Conclusion Considering the direct relationship between ethical courage and care behaviors, it is recommended that relevant managers strive to promote ethical courage among all nurses by supporting and encouraging those who demonstrate ethical courage, thus playing an influential role in achieving a higher level of desired care behaviors.
Assessment of Cardiotoxicity incidence in patients receiving HER-2-targeted therapies for breast cancer in Saudi Arabia
Authors: Shahbar Alaa , Alhifany Abdullah A. , Alatawi Yasser M. , Alnuhait Mohammed , Alshammari Abdullah , Alshamrani Majed , Kinsara Abdulhalim , AlQubbany Atif , Alharbi Mahasen , Alnatsheh Abdelmajid , Alfoheidi Meteb 
Published: April 2024

Abstract
Background:
Human Epidermal growth factor Receptor (HER2) targeting therapies may raise the risk of decreased left ventricular ejection fraction (LVEF), which might appear clinically as heart failure. Trastuzumab's incidence of cardiotoxicity in individuals with a history of anthracycline usage varies between 4% and 18.6%, with 0.4–4.1% of patients developing serious heart failure. The increasing number of breast cancer survivors as a consequence of HER2-targeted treatment has necessitated the long-term care of cardiotoxicity induced by iatrogenic chemotherapy.
Method:
This retrospective study included all HER-2-positive breast cancer patients aged 18 or older who received at least one dose of HER-2-targeting treatment between 2016 and 2020. The primary endpoint was to determine the incidence of cardiotoxicity induced by HER-2 targeted treatment, which was defined as LVEF < 50% with LVEF decline by 10%, LVEF drop by > 15%, or the onset of symptomatic heart failure. The secondary endpoints were the proportion of patients with LVEF between 50% and 55% at baseline who developed cardiotoxicity, the proportion of patients who temporarily or permanently discontinued HER-2 targeting therapy due to HF, the proportion of patients who developed HF and were treated with HF medications, and the proportion of patients who received HF medications for cardiotoxicity and continued their HER-2 targeting therapy. The development of a hospital protocol for monitoring and managing cardiotoxicity in patients receiving HER-2-targeted treatments was another secondary outcome.
Results:
A total of 212 patients were included in the research, with a median age of 56.5 years and an interquartile range of 43–58 years. 105 patients with early breast cancer (EBC), and 107 patients with metastatic breast cancer (MBC). Twenty-two patients (10.37%) suffered cardiotoxicity with HER-2-specific treatment. Thirteen of the 22 patients (6.13%) had asymptomatic heart failure with a decrease in LVEF from baseline of more than 10% to less than 50%. Five patients (2.35%) with LVEF less than 40% had asymptomatic heart failure, while four patients (1.88%) presented with symptomatic heart failure regardless the LVEF decline. HER-2 targeted treatment was discontinued temporarily in 3 (13.63%) patients and permanently in 4 (18.18%) patients due to cardiotoxicity. The remaining fifteen patients resumed their treatment without interruption. Only 13 out of 22 patients were referred to cardiologists and prescribed medicines for heart failure.
Conclusion:
Close monitoring of LVEF for patients receiving HER-2 targeting therapy can assist healthcare providers to initiate anti-heart failure medications to prevent deterioration of LVEF and maintain Her-2 targeting therapy.
Light water loss delays mechanical injury of Actinidia arguta by Inhibiting cell wall metabolism
Authors: YU Xin-yu , WANG Qing-xuan , WANG Jin-yan , WEI Bao-dong , ZHOU Qian , CHENG Shunchang , Yang SUN 
Published: April 2024

Abstract

This study aimed to investigate the effect of light water loss on the mechanical injury of Actinidia arguta fruit by regulating cell wall metabolism. By comparing the effect of water loss on mechanical injury of Actinidia argutafruit after simulated transport vibration, the changes in sensory quality and cell wall metabolism of treated Actinidia arguta fruit during storage were measured, compared with non-water-loss simulated transport vibration as the control. Light water loss slowed the growth rate of pectin and cellulose and decreased the activities of polygalacturonase, pectin methylesterase, pectinlyase, cellulase, β-glucosidase, and β-galactosidase. Electron and transmission microscopy imaging show that light water loss helps maintain cell wall structure and slows down cell wall degradation. The results indicate that light water loss alleviates post-harvest mechanical injury in Actinidia arguta by regulating cell wall metabolism and inhibiting cell wall degradation, thereby contributing to the maintenance of redox homeostasis and cell structural integrity to maintain fruit quality.
Investigation of acoustic events during shear loading of layered rock bridge; Particle flow code approach
Authors: Mohammadi Seyed Davoud , Mortezaei Rahim , Sarfarazi Vahab , Abharian Soheil 
Published: April 2024

Abstract
This research investigates acoustic emission (AE) phenomena during shear failure of layered rock bridges under different normal stresses using experimental punch tests and numerical simulation. Firstly, particle flow code (PFC) was calibrated by UCS and Brazilian experimental test results and then the shear behavior of the numerical model was verified by experimental punch test outputs. Finally, acoustic phenomena during shear failure of layered rock bridges were discussed. Rectangular specimens were utilized, incorporating a combination of different layers. These layers included a pairing of soft and hard materials, as well as variations such as a two-layered model comprising hard gypsum and soft gypsum. Furthermore, three-layered models were examined, featuring a soft interlayer in one case and a hard interlayer in another. Additionally, a four-layered model was employed for the investigation. In each model, two vertical edge fissures were introduced, with fissure lengths set at 20, 40, and 60 mm. The angle between bedding layers and shear loading direction was 90°. The results indicate that cracks initiate at the notch tip and propagate vertically until they meet the upper boundary. The frequency of significant Acoustic hits is tied to factors like crack initiation and material properties. Increasing the number of layers in the specimen leads to more Acoustic hits. The sequence of Acoustic hits between major hits is influenced by parameters such as bedding number and material properties. This correlation is attributed to different gypsum types on the shear surface. The findings from numerical bedding models mirror those from physical samples.
Clarification of the clinical significance of an intron variant in a case of Peutz–Jeghers syndrome with abnormal RNA splicing of STK11
Authors: Ishikawa Aki , Gotoh Masahiro , Ushiama Mineko , Sakamoto Hiromi , Tanabe Noriko , Watanabe Tomoko , Cho Hourin , Yamada Masayoshi , Sugano Kokichi , Shiraishi Kouya , Hirata Makoto , Yoshida Teruhiko , Sakurai Akihiro 
Published: April 2024

Abstract

Peutz–Jeghers syndrome is an autosomal dominant disease characterized by intestinal polyposis, mucocutaneous pigmentation, and an increased risk of various types of cancer. Germline mutations in STK11 (LKB1), which encodes serine/threonine kinase 11, have been identified as the major cause of Peutz–Jeghers syndrome. Here, we detected a rare variant of undetermined significance in intron 2 of STK11 using multi-gene panel analysis in a girl with clinically suspected Peutz–Jeghers syndrome based on family history and characteristic mucocutaneous pigmentation. We confirmed this variant caused abnormal splicing in exons 2 and 3 using reverse transcription-PCR and Sanger sequencing. To validate the predicted impact of this variant on splicing, we performed functional analysis using a minigene assay. The functional analysis experiments demonstrated that this variant suppressed normal splicing, and the clinical significance of the STK11 variant, which was initially thought to be a variant of “Uncertain Significance,” was determined to be “Likely Pathogenic.” Functional analysis and confirming the genetic diagnosis of cases with actionable hereditary diseases would be helpful for surveillance decisions and family diagnosis.
Transcriptome Analysis Reveals Key Genes and Pathways Associated with Heat Stress in Pleurotus pulmonarius
Authors: Wang Weike , Lu Na , Lin Jiayao , Lai Liqin , Chen Guanping 
Published: April 2024

Abstract
Pleurotus pulmonarius is a medium temperature edible mushroom, and its yield and quality are severely affected by high temperature. However, the molecular mechanism of Pleurotus pulmonarius response to heat stress remains unknown. In this study, transcriptome sequencing and analysis of Pleurotus pulmonarius mycelia under heat stress were performed, related differentially expressed genes (DEGs) were verified by fluorescence quantitative PCR (qPCR) and the reduced glutathione content was detected. 5906 DEGs, including 1086 upregulated and 4820 downregulated, were identified by RNA-seq. GO analysis revealed that DEGs were mainly enriched in the pathways of Aminoacyl-tRNA biosynthesis, pyrimidine metabolism, arginine and proline metabolism, fructose and mannose metabolism, and glutathione metabolism. qPCR analysis showed that the expression of ggt decreased after heat stress treatment, while gst2 and gst3 increased. The glutathione content in mycelia after heat stress was significantly higher than that in the control group. These results suggest that glutathione metabolism may play an important role in the response to heat stress. Our study will provide a molecular-level perspective on fungal response to heat stress and a basis for research on fungal environmental response and molecular breeding.
Quantitative Proteogenomic Characterization In MUC1 And MUC4 In Oral Squamous Cell Carcinoma, Oral Potentially Malignant Disorders, And Normal Oral Mucosa In Carcinogenesis
Authors: John Sharon , Sharma Kriti , Chandra Shaleen , Singh Priyanka , Singh Geeta , Gupta Shalini 
Published: April 2024

Abstract
Context: Mucins are glycoproteins with a significant molecular weight that have a diverse range of biological functions. MUC1 & MUC4 are transmembrane mucin family members that are expressed in airway epithelial cells and body fluids. It is expressed excessively in numerous carcinomas in addition to their altered expression. A thorough review of the literature reveals very limited research about MUC1 & 4 expressions in oral malignancies and oral premalignant disorders.
Aim: To assess the pattern and quantity of gene expression in MUC1 & MUC4 individually in various grades of oral squamous cell carcinoma (OSCC), oral premalignant disorders (OPMDs)- oral epithelial dysplasia (OED), oral submucous fibrosis (OSF), oral lichen planus (OLP), and compared with normal oral mucosa (NOM).
Materials and Methods: Immunohistochemistry and qRTPCR evaluation of MUC1 & 4 on sixty-three cases of OSCC, OPMD, and NOM was accomplished.
Statistical analysis: The one-way ANOVA test and Chi-square test were done for statistical analysis.
Results: The overall immunoexpression of MUC1 & 4 increased significantly from NOM to OPMDs to OSCC. In the subgrades of OSCC and OPMDs, the staining intensity varied. For MUC4, the intensity was strongest in well-differentiated grades and MUC1, exhibiting a higher expression in poorly differentiated grades of OSCC and OPMDs.
Conclusion: The study's results indicate that MUC1 & 4 individually are crucial for monitoring OSCC and OPMD pathogenesis as the former gives an idea of highly undifferentiated grades while the latter indicated more differentiated tumors and perhaps a better prognosis. Therefore, the two can be useful tumor markers for determining the severity and eliminating it in its early phases
Hospital-Based Violence Intervention Programs: An Analysis of Costs and Key Components
Authors: O'Toole Megan Joyce , Schnippel Kathryn , Larson Bruce 
Published: April 2024

Abstract
Firearm assaults contribute to nearly 18,000 deaths and at least twice as many injuries annually, with immense human and financial costs. Gun violence survivors especially face unique and long-term physical, mental, economic, and safety-related challenges. Hospital-based violence intervention programs (HVIPs) connect survivors with violence prevention professionals at their hospital bedsides, then provide them with wraparound services in the months to come. Promising research shows that HVIPs reduce risks of reinjury, retaliation, and recidivism. This report provides a cost analysis of HVIPs, to inform researchers and implementers of the budget and key resources necessary for the first three years of implementation. Researchers employ an ingredients-based costing approach and base-case assumptions for a hospital-linked HVIP situated in a mid-sized city emergency department, serving 100 participants annually. Results indicate that this base-case HVIP costs an estimated $1.1 million annually, or just under $10,800 per participant. Staffing accounts for the majority of HVIP budgets, followed by operations, crisis support, and finally transportation. Upfront costs are limited to technical assistance, first-time equipment, and accreditation courses, leaving annual costs relatively stable across the first three years of implementation. A customizable workbook is provided, through which users can adjust this study’s assumptions to reflect their own program’s specifications, which may vary. This research can inform future cost, benefit, and savings analyses, and empower more communities to implement lifesaving HVIPs.