bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of the VisionArray® Chip Assay for HPV DNA testing in Histology Specimens of Oropharyngeal Squamous Cell Carcinoma
Authors: Channir Hani Ibrahim , Bendtsen Simone Kloch , Melchior Linea Cecilie , Sandholm Pia Rovsing , Mordhorst Christine , Carlander Amanda-Louise Fenger , von Buchwald Christian , Kiss Katalin 
Published: January 2024

Abstract
Background: The detection of Human papillomavirus (HPV) has several implications in the diagnostic work-up and management of oropharyngeal squamous cell carcinoma (OPSCC). The choice of HPV detection assay and testing algorithms differs across institutions and vary in cost, detection targets, technical feasibility, and turn-around time. In this study we aimed to validate the VisionArray®HPV Chip for formalin-fixed and paraffin-embedded (FFPE) samples of OPSCC using the previously applied standard pan-HPV DNA PCR assay as a reference.
Methods: The validation cohort consisted of FFPE tissue samples from patients previously diagnosed with HPV-DNA positive OPSCC (n=80), HPV-DNA negative OPSCC (n=21), and a benign group of tumor samples consisting of Warthin’s tumors (n= 20) and branchial cleft cysts of the lateral neck (n=14). All samples were tested with p16 immunohistochemistry, pan-HPV DNA PCR and the VisionArray® HPV Chip.
Results: The overall sensitivity and specificity of the VisionArray® HPV Chip assay were 100% [95% CI, 95.5%;100.0 %] and 96.3% [95% CI, 87.3%;99.6%] and the positive predictive value and negative predictive value were 97.6% [95% CI, 91.5%;99.7%] and 100% [95% CI, 93.2%;100%], respectively.
Conclusions: The VisionArray® HPV Chip assay can be recommended for high-risk HPV-testing in FFPE tissue samples from OPSCC, providing both a fast and simultaneous genotyping for the most common 41 clinically relevant HPV types.
Treatment of ocular surface squamous neoplasia in an Indian rural facility: A study of 38 eyes
Authors: Agarwal Ayushi , Ghose Neha , Rathi Varsha , Khanna Rohit , Kaliki Swathi 
Published: January 2024

Abstract
Purpose
To report the demographic profile, clinical presentation, and management outcomes of ocular surface squamous neoplasia (OSSN) treated with primary topical chemotherapy in a limited resource secondary eye care facility in rural parts of South India.
Methods
Retrospective interventional study of 38 eyes of 37 patients with OSSN treated with topical 1% 5-Fluoro uracil (5-FU), over a period of two years.
Results
The median age at presentation with OSSN was 44 years (mean, 46 years; range 13 to 74 years). Majority (76%) were males. The most common morphological variant was placoid OSSN (18, 47%). Limbus was the most common epicenter (31, 82%). Corneal OSSN was the most initially misdiagnosed variant (n = 3). Of the 38 eyes receiving one week on and 3-weeks off cycles of 5-FU regimen, complete tumor resolution was achieved in 36 (95%) eyes. The median number of topical 5-FU cycles for tumor resolution was 2 (mean, 2; range, 1 to 4). Over a median follow-up period of 5 months (mean, 6 months; range, 1 to 27 months), tumor recurrence was noted in 3 eyes (8%), of which one case had xeroderma pigmentosum with bilateral multifocal recurrence. Complication rate was 5% (n = 2), which included transient conjunctival hyperemia (n = 1), and bacterial keratitis (n = 1) which resolved with fortified antibiotics.
Conclusion
Primary chemotherapy with topical 1% 5-FU is a safe and effective management modality for OSSN at limited resource settings in rural India.
Gut microbiota and venous thromboembolism: a two-sample Mendelian randomization study Gut microbiota and venous thromboembolism
Authors: Wang Jia , Fei Bojian , Wang Chao 
Published: January 2024

Abstract
Background
Recent studies have suggested an association between gut microbiota (GM) and venous thromboembolism (VTE). However, observational studies cannot indicate causality and population-level studies with a higher evidence level for causality are lacking. Therefore, our study aimed to explore the causal association of GM and VTE.
Methods
This study utilized the summary-level data of respective genome-wide association study for 196 gut microbial taxa and VTE. Two-sample Mendelian randomization (MR) design was deployed and comprehensively sensitive analyses were followed to validate the robustness of results. We used the inverse-variance weighted (IVW) method, the weighted median method, weighted mode method, simple mode method, MR-Egger regression, MR-Egger intercept test, Cochrane’s Q-test, outlier test, and leave-one-out analysis as the primary analysis.
Results
We identified suggestive associations between 17 bacterial traits and the risk of VTE. Porphyromonadaceae (IVW odds ratio (OR): 1.3729, p = 0.0035) and Cyanobacteria (IVW OR: 1.2151, p = 0.0048) were associated with increased risk of VTE. Three gut microbiota taxa (Eubacteriumrectalegroup (IVW OR: 1.0038, p = 0.0278), Coprococcus2 (IVW OR: 1.0041, p = 0.0063), and LachnospiraceaeUCG001 (IVW OR: 1.0041, p = 0.0009) were predicted to play a causal role in enhancing the risk of encompassing deep vein thrombosis. And three gut microbiota taxa (Christensenellaceae (IVW OR: 1.0023, p = 0.0497), Streptococcaceae (IVW OR: 1.0031, p = 0.0279), Victivallaceae (IVW OR: 1.0014, p = 0.0493) were positively associated with pulmonary embolism.
Conclusions
This study suggested the role of the specific GM on the risk for VTE, which may provide new ideas and a theoretical basis for the prevention and treatment of VTE in the future.
The relationship of the religious faith and practice of student youth and adults in southeastern Poland and western Ukraine with their health status and attitudes toward physical culture
Authors: Cynarski Wojciech J. , Dyndał Stanisław , Wąsik Jacek , Mosler Dariusz , Pavlova Iulia , Yu Jong-Hoon , Ambroży Tadeusz , Rydzik Łukasz , Kasicki Krzysztof 
Published: January 2024

Abstract
Background: Religious faith and practice are important aspects of human life and give meaning to human existence. The development of modernity and consumerism has significantly undermined the religious foundations of a present-day global society. The aim of this study is to determine the relationships of the religious faith and practice of student youth and adults in Poland (Podkarpacie and Lesser Poland regions) and in western Ukraine (Lviv region) with the self-rated health status and their attitudes toward physical culture. Participants included 1,458 people from southeastern Poland and western Ukraine. The diagnostic survey method was used, with a questionnaire including items about faith in God versus atheism, religious affiliation, and the extent to which religion is practiced. The questionnaire contained 16 items in its main part, along with 7 record-related questions.
Results: The component of health that was rated highest was physical health among believers and mental health among non-believers. The results of the analysis of variance showed significant differences between the individual variables depending on the declaration of faith in God.
Conclusion: While the faith of the inhabitants of southeastern Poland and western Ukraine is largely related to their regular religious practice, irregularity dominates this practice. Respondents combined ratings of their faith and/or practice with self-rated health status; more religious people had statistically lower levels of self-rated health.
Cardioprotective effect of eugenol against Cd-induced inflammation, oxidative stress and dyslipidemia in male rats: An invivo and molecular docking study
Authors: Kumar Abhishek , Sharma Bechan 
Published: January 2024

Abstract
Background
Cadmium, a highly toxic heavy metal, can cause severe damage to several vital organs including the kidney, liver and brain. Many of the natural compounds found in aromatic plants have beneficial pharmacological properties, Eugenol, is one such compound reported to have anti-inflammatory and antioxidant properties. This study aimed to examine the potential of eugenol in alleviating cardiac inflammation, oxidative stress and dyslipidemia caused by cadmium exposure.
Methods
Male albino rats were randomized into four groups with six animals in each group, to examine the role of eugenol in reversing cadmium toxicity. All groups received oral gavage treatment for 21 days. Afterwards, heart tissues were collected from the rats. Assessment of the cardiac antioxidant status was performed by analyzing the enzymatic activities of Catalase, SOD, GST and GPx. Levels of lipid peroxidation, reduced glutathione, protein carbonyl oxidation, and thiol levels were determined in heart tissue. To evaluate cardiac damage, marker enzymes such as LDH and CK-MB were measured. Cadmium-induced cardiac inflammation was assessed by measuring NO, TNF-α and IL-6 levels. Docking and molecular dynamics studies were conducted using autodock and GLIDE.
Results
Cadmium administration markedly enhanced the activities of LDH and CK-MB, prominent cardiac markers. Furthermore, cadmium treatment also demonstrated a significant decrease in the reduced glutathione levels and antioxidant enzyme activities. Significant elevation of the inflammatory markers was also observed in the cadmium-treated group. Eugenol treatment effectively ameliorates cadmium-induced biochemical changes.
Conclusion
This study highlights eugenol’s strong anti-inflammatory and antioxidant properties. Co-supplementation of eugenol with cadmium demonstrated its protective potential against cadmium-induced cardiotoxicity. Eugenol was able to restore the cellular redox system of cadmium-treated rats to normal control levels.
Helicobacter pylori and acne vulgaris: is there a relationship?
Authors: afify ahmed , Saleh Hanan Mohamed Ahmed , Farrag Abeer 
Published: January 2024

Abstract
Background: Helicobacter pylori (H. pylori) is a gastric Gram-negative, spiral-shaped microaerophilic pathogen. H. pylori may play a potential pathogenic role in extra-intestinal diseases such as hepatobiliary, respiratory, and dermatological disorders. The latter included chronic urticaria, psoriasis and rosacea. The first report in literature on the relationship between H. pylori and acne vulgaris (AV), found association between severe AV and H. pylori infection. There are very limited data in AV patients addressing the impact of H. pylori infection on various severities. In this context, the aim of the present work was to determine the association of H. Pylori infection among AV patients and correlate it with the disease severity.
Methods: This case-control study included 45 Patients with AV and 45 age and sex matched healthy volunteers as a control group. H. pylori antigen in stool and serum H. pylori antibody IgG using commercially available ELISA kits was tested in all included subjects.
Results: The percentage of participants with a positive H. pylori antigen in stool and positive H. pylori antibody in serum in the whole study population was 35/90 (38. 9%) and 41/90 (45. 6%). On comparing between the percentagesof positive H. pylori antigen in stool and positive H. pylori antibody in serum between the patients with AV and healthy controls, a highly statistically significant difference was found between the two groups (P<0.001, P=0.006). On comparing between the percentages of positive H. pylori antigen in stool and positive H. pylori antibody in serum in the patients with different grades of acne severity and healthy controls, the rate of positive H. pylori antigen in stool and positive H. pylori Ab in serum was significantly associated with severity of acne comparing with healthy controls (p<0. 001).
Conclusion: The rate of H. pylori infection in patients with AV is high so it may influence the pathogenesis of this skin disease. Patients with severe AV had higher rates of H. pylori antigen in stool and H. pylori antibody in serum as compared to the patients with mild AV and healthy controls.
A Variable Neighborhood Hybridizing for Better Ranking Models in Information Retrieval
Authors: Ibrahim Osman Ali Sadek 
Published: January 2024

Abstract
Variable Neighborhood Search (VNS) optimizes heuristic solutions for daily problems by adjusting neighboring solutions' systematic changes. This study uses two adaptations of VNS, utilizing four random probability distributions and tradition random number generator to fine-tune offspring solutions. The first generates solutions using a singular probability distribution, while the second perturbs each solution by randomly selecting a probability distribution for each mutation step size. The paper uses the two variants with the traditional variable neighborhood, combining variable neighborhood with gradient ascent and combining variable neighborhood with simulated annealing algorithms. From the obtained results, we can conclude that the second randomization method applied on combining variable neighborhood with a simulated annealing (VNARandom) method outperformed the other methods and recent research. In addition, this second randomization technique has a significant positive impact on the VNS methods for better evolving ranking models. Specifically, it has an improved impact on the recent GVN (combining Variable neighborhood with Gradient Ascent) method from the previous research studies. Although, it has a negative effectiveness impact on traditional VNS. This paper proposes novel VNS approaches as a contribution as well.
Nanobubble-Based Carbon Dioxide Massive Dissolution Using Friction Tubes and Real-Time Reaction
Authors: Yoo Taekeun , Yoo Young-Ho , Byun Suk-Joo , You A-Ram , Park Chang-Hee , Choi Dae-Hyun , Lee Woo-Seung 
Published: January 2024

Abstract
To prevent global warming, various technologies are being developed to suppress carbon dioxide emissions. Nanobubbles are useful in various industrial fields. Carbon dioxide capture technology was studied using the property of activating the reaction of nanobubbles. In this study, carbon dioxide capture was attempted using nanobubble generation tubes based on the friction principle. The world has paid attention to carbon capture, utilization, and storage (CCUS) to inhibit and reduce carbon dioxide emissions, which are known as the main cause of global warming. The problem is that the new process that utilizes carbon dioxide must consume less energy and resources than existing alternative processes. To address this problem, research was conducted on the possibility of dissolving carbon dioxide in large quantities at low power consumption using a nanobubble generation system and real-time chemical reactions in this study. In addition, a mass dissolution system was constructed, and real-time neutralization was verified through the reactions of nanobubble carbon dioxide with ammonia water (NH4OH) and calcium hydroxide (Ca(OH)2) solution.
Celastrol can inhibit the growth of SHH medulloblastoma: In vitro and in vivo studies
Authors: 王 薄鸿 , 徐 道 , 余 丽生 , 秋 陈杰 , 赵 香毛 , 徐 赵 , 徐 尚宇 , 盛 汉松 , 晒黑 冯 , 张 努 
Published: January 2024

Abstract
Celastrol is a naturally occurring compound with a range of pharmacological properties derived from the traditional Chinese herb Tripterygium wilfordii. To develop a new therapeutic strategy for medulloblastoma (MB), this study will investigate the inhibitory effect of celastrol on MB and its underlying signaling pathway. We evaluated the effects of celastrol on cell proliferation using the CCK-8 assay and colony formation assay. Scratch assays and transwell invasion assays were used to assess the effects of celastrol on metastasis. The flow cytometry method was used to detect apoptosis and reactive oxygen species (ROS) levels in the cells. The potential signaling pathways were detected by transcriptomics and quantitative PCR. To study the anticancer effect of celastrol on MB in vivo using a mouse xenograft model. Cell proliferation and metastasis of the SHH subgroup MB cell line can be inhibited by celastrol, and the effect of the drug on apoptosis is associated with its proliferation inhibition effect. Animal experiments showed that celastrol inhibited the growth of MB in vivo. In addition, the pro-apoptotic effect of celastrol on ONS-76 cells may be caused by ROS. Our findings indicate that celastrol inhibits the progression of MB both in vitro and in vivo, and this effect is associated with the induction of ROS in cells by celastrol in vitro studies.
Capsaicin pretreatment attenuates salt-sensitive hypertension by alleviating AMPK/Akt/Nrf2 pathway in hypothalamic paraventricular nucleus
Authors: Jia Xiu-Yue , Yang Yu , Jia Xiao-Tao , Jiang Da-Li , Fu Li-Yan , Tian Hua , Yang Xin-Yan , Zhao Xin-Yue , Liu Kai-Li , Kang Yu-Ming , Yu Xiao-Jing 
Published: January 2024

Abstract
Long term hypertension seriously affects target organ damage such as the brain, heart, and kidneys, and has become an increasingly serious public health problem worldwide. Capsaicin has been proven to improve blood pressure. However, whether capsaicin can reduce salt induced hypertension and the mechanism has yet to be elucidated. This study aimed to identify the AMPK/Akt/iNOS pathway in hypothalamic paraventricular nucleus (PVN) mediates capsaicin in improving the process of high salt induced hypertension. Dahl salt-sensitive (Dahl S) rats were uesed as the animal model for the present study. All rats were randomly divided into four groups based on their dietary regimen (0.3% salt diet and 8% salt diet) and treatment methods. Chronic administration capsaicin to the PVN during the process of blood pressure rise in rats. The entire process lasted for 6 weeks. Our results demonstrated that PVN pretreatment with capsaicin can slow down the blood pressure elevation and heart rate (HR) of Dahl S hypertensive rats. Interestingly, The cardiac hypertrophy was significantly improved. Furthermore, PVN pretreatment with capsaicin induced decrease in mRNA expression of NOX2, Inducible nitric oxide synthase (iNOS), NOX4 and proinfammatory cytokines and increase in positive cell level of Nrf2, p-IKKβ, iNOS and HO-1 in the PVN of Dahl S hypertensive rats. Additionally, the protein expressions of phosphorylated adenosine Monophosphate-activated protein kinase (p-AMPK), the phosphatidylinositol 3-kinase (p-PI3K) and phosphorylated protein kinase-B (p-AKT) were attenuated after PVN pretreatment with capsaicin. Capsaicin pretreatment attenuates salt-sensitive hypertension by alleviating AMPK/Akt/iNOS pathway in the PVN.
Predicting promoters in multiple prokaryotes with Prompt
Authors: Du Qimeng , Guo Yixue , Zhang Junpeng , Lu Fuping , Peng Chong , Zhou Chichun 
Published: January 2024

Abstract
Promoters are important cis-regulatory elements for the regulation of gene expression, and their accurate predictions are crucial for elucidating the biological functions and potential mechanisms of genes. Many previous prokaryotic promoter prediction methods are encouraging in terms of the prediction performance, but most of them focus on the recognition of promoters in only one or a few bacterial species. Moreover, due to ignoring the promoter sequence motifs, the interpretability of predictions with existing methods is limited. In this work, we present a generalized method Prompt (Promoters in multiple prokaryotes) to predict promoters in 16 prokaryotes and improve the interpretability of prediction results. Prompt integrates three methods including RSK (Regression based on Selected K-mer), CL (Contrastive Learning) and MLP (Multilayer Perception), and employs a voting strategy to divides the datasets into high-confidence and low-confidence categories. Results on the promoter prediction tasks in 16 prokaryotes show that the accuracy (Accuracy, Matthews correlation coefficient.) of Prompt is greater than 80% in highly credible datasets of 16 prokaryotes, and is greater than 90% in 12 prokaryotes, and Prompt performs the best compared with other existing methods. Moreover, by identifying promoter sequence motifs, Prompt can improve the interpretability of the predictions. Prompt is freely available at https://github.com/duqimeng/PromptPrompt, and will contribute to the research of promoters in prokaryote.
Motivation:Promoters are important cis-regulatory elements for the regulation of gene expression, and their accurate predictions are crucial for elucidating the biological functions and potential mechanisms of genes. Many previous prokaryotic promoter prediction methods are encouraging in terms of the prediction performance, but most of them focus on the recognition of promoters in only one or a few bacterial species. Moreover, due to ignoring the promoter sequence motifs, the interpretability of predictions with existing methods is limited.
Results: Results on the promoter prediction tasks in 16 prokaryotes show that the accuracy (Accuracy, Matthews correlation coefficient.) of Prompt is greater than 80% in highly credible datasets of 16 prokaryotes, and isgreater than 90% in 12 prokaryotes, and PromptPrompt performs the best compared with other existing methods.
Availability:Moreover, by identifying promoter sequence motifs, PromptPrompt can improve the interpretability of the predictions. Prompt is freely available at https://github.com/duqimeng/PromptPrompt, and will contribute to the research of promoters in prokaryote.
Supplementary information: Supplementary data are available at Bioinformaticsonline.
miR-595/Cldnd1 axis: a potential risk factor for bone loss in postmenopausal women with hip osteoporotic fracture
Authors: Jingyue Sun , Peixin Liu , Xiao Wang 
Published: January 2024

Abstract
Background Recently researches have reported that miRNA and its target genes are associated with osteoporosis. MiRNAs/mRNA axis might be an potential diagnostic marker for osteoporosis.
Purposes The aim of this study is to explore the potential miRNA and mRNA markers by bioinformatics method and clinical analysis.
Patients and Methods The miRNA expression profiles were obtained from GSE74209, GSE64433 and GSE115773 in Gene expression Omnibus (GEO). The mRNA expression profiles were obtained from GSE100609. Wayne intersection were used to explore the different expressed miRNAs (DE-miRs). Select the miRNA with the highest Fold Change for subsequent research. Screening of miRNA target genes using TargetScan and miRDB tools. GO and KEGG analyses of target genes (TGs) function were performed. Validate the selected TGs in the GSE100609. We collected female patients with femural intertrochanteric fractures from July 1, 2023 to October 31, 2023. Patient's bone marrow and clinical data were collected. MiRNA and the target mRNA differentially expressed in bone marrow were verified through RT-qPCR. All data were subjected to Shapiro-Wilk test. Using Pearson or Spearman test to detect the correlation between various indicators, and then incorporating indicators related to bone density into multiple linear regression equations. Partial correlation analysis was used to analyze the correlation between the final indicators and bone density.
Results A total of 140 DE-miRs were identified between high bone density and low bone density women. Set the fold change to “>1” and ultimately include 5 miRNAs. Using miR-595 (highest |log2 FC|) as the subject of subsequent research. 3542 targeted mRNAs were predicted from TargetScan and 362 were from miRDB. 337 TGs were intersected, which were mainly enriched in nucleus. Only Cldnd1 were identified using the GSE100609 dataset. We found that miR-595 was highly expressed in patients with high bone mass, while its target gene Cldnd1 was downregulated. There was a strong collinearity between miR-595 and Cldnd1. Further multiple linear regression analysis showed a high correlation between miR-595 and bone density.
Conclusions These data suggest that Cldnd1 might be a downstream factor of miR-595. miR-595/Cldnd1 axis might be an independent risk factor for decreased bone mass.