bluuebunny/crossref_metadata_2025_split huggingface dataset:
High C1QTNF1 expression mediated by potential ncRNAs is associated with poor prognosis and tumor immunity in kidney renal clear cell carcinoma
Authors: Qiu Jiechuan , Wang Zicheng , Zhao Leizuo , Zhang Peizhi , Xu Yingkun , Xia Qinghua 
Published: July 2023

Background: Kidney renal clear cell carcinoma (KIRC) originates from proximal tubular cells and is the most common subtype of renal cell carcinoma. KIRC is characterized by changes in lipid metabolism, and obesity is a risk factor for it. C1q And TNF Related 1 (C1QTNF1), a novel adipokine and member of the C1q and TNF-related protein (CTRP) family, has been shown to affect the progression of various cancers. However, the role of C1QTNF1 in KIRC has not been studied.Methods: The Wilcoxon rank sum test was used to analyze the expression of C1QTNF1 in KIRC tissues and normal tissues. The relationship between clinicopathological features and C1QTNF1 levels was also examined by logistic regression and the Wilcoxon rank sum test. In addition, the effect of C1QTNF1 on the prognosis of KIRC patients was analyzed by Kaplan-Meier (KM). The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the potential signaling pathways and biological functions of differential genes. A nomogram was constructed to predict the prognosis of KIRC patients. Spearman correlation analysis was performed to determine the association between C1QTNF1 expression and immune cell infiltration and immune checkpoint genes. The upstream miRNAs and lncRNAs of C1QTNF1 were predicted by the ENCORI online tool. Finally, we examined the proliferation, invasion, and migration abilities of KIRC cells after C1QTNF1 knockdown.Results: The expression of C1QTNF1 in KIRC tissues was significantly higher than in normal renal tissues. Patients with higher C1QTNF1 expression had a poor prognosis, a finding supported by Kaplan-Meier survival analysis. C1QTNF1 expression was significantly correlated with TNM and pathologic stages, age, and gender (p &lt; 0.05). The C1QTNF1 expression level was significantly correlated with immune cell infiltration and immune checkpoint genes in KIRC. Additionally, high C1QTNF1 expression was associated with poor prognosis in stage I and II, T1 and T2, T3 and T4, N0, and M0 patients (HR &gt; 1, p &lt; 0.05). The calibration diagram shows that the C1QTNF1 model has effective predictive performance for the survival of KIRC patients. Knockdown of C1QTNF1 inhibited KIRC cell proliferation, cell migration, and cell invasion. In addition, CYTOR and AC040970.1/hsa-miR-27b-3p axis were identified as the most likely upstream ncRNA-related pathways of C1QTNF1 in KIRC.Conclusion: In conclusion, our study suggests that high expression of C1QTNF1 is associated with KIRC progression and immune infiltration. The increased expression of C1QTNF1 suggests a poor prognosis in KIRC patients.
2′-fucosyllactose alone or combined with resistant starch increases circulating short-chain fatty acids in lean men and men with prediabetes and obesity
Authors: Canfora Emanuel E. , Vliex Lars M. M. , Wang Taojun , Nauta Arjen , Bouwman Freek G. , Holst Jens J. , Venema Koen , Zoetendal Erwin G. , Blaak Ellen E. 
Published: July 2023

BackgroundInfusion of short-chain fatty acids (SCFA) to the distal colon beneficially affects human substrate and energy metabolism. Here, we hypothesized that the combination of 2′-fucosyllactose (2′-FL) with resistant starch (RS) increases distal colonic SCFA production and improves metabolic parameters.MethodsIn this randomized, crossover study, 10 lean (BMI 20–24.9 kg/m2) and nine men with prediabetes and overweight/obesity (BMI 25–35 kg/m2) were supplemented with either 2′-FL, 2′-FL+RS, or placebo one day before a clinical investigation day (CID). During the CID, blood samples were collected after a overnight fast and after intake of a liquid high-fat mixed meal to determine plasma SCFA (primary outcomes). Secondary outcomes were fasting and postprandial plasma insulin, glucose, free fatty acid (FFA), glucagon-like peptide-1, and peptide YY concentrations. In addition, fecal SCFA and microbiota composition, energy expenditure and substrate oxidation (indirect calorimetry), and breath hydrogen excretion were determined.ResultsIn lean men, supplementation with 2′-FL increased postprandial plasma acetate (P = 0.017) and fasting H2 excretion (P = 0.041) compared to placebo. Postprandial plasma butyrate concentration increased after 2′-FL and 2′-FL+RS as compared to placebo (P &lt; 0.05) in lean men and men with prediabetes and overweight/obesity. Additionally, 2′-FL+RS decreased fasting and postprandial plasma FFA concentrations compared to placebo (P &lt; 0.05) in lean men.ConclusionSupplementation of 2′-FL with/without RS the day before investigation increased systemic butyrate concentrations in lean men as well as in men with prediabetes and obesity, while acetate only increased in lean men. The combination of 2′-FL with RS showed a putatively beneficial metabolic effect by lowering plasma FFA in lean men, indicating a phenotype-specific effect.Clinical trial registrationnr. NCT04795804.
Association of bone mineralization markers with dietary nutrient intake in adolescents with and without biochemical osteomalacia
Authors: Al-Daghri Nasser M. , Sabico Shaun , Wani Kaiser , Hussain Syed Danish , Yakout Sobhy , Aljohani Naji , Uday Suma , Högler Wolfgang 
Published: July 2023

BackgroundDietary intake is widely known to play a crucial role in achieving peak bone mass among children and adolescents. Unfortunately, this information is lacking among Arab adolescents, an understudied demographic that has recently been observed to have a high prevalence of abnormal mineralization markers [low serum 25(OH)D, high serum alkaline phosphatase (ALP), low calcium (Ca) and/or inorganic phosphate (Pi)] suggestive of biochemical osteomalacia (OM, defined as any 2 of the 4 parameters). In order to fill this gap, we aimed to evaluate the associations of serum markers of biochemical OM with dietary intake of macronutrients, vitamins and trace minerals.MethodsSaudi adolescents (N = 2,938, 57.8% girls), aged 12–17 years from 60 different schools in Riyadh, Saudi Arabia were included. Dietary intake of nutrients was calculated following a semi-quantitative 24 h dietary recall over 3 weekdays and 1 weekend-day using a validated food frequency questionnaire. Compliance to reference daily intake (RDI) of macronutrients, vitamins and trace minerals were calculated. Fasting blood samples were collected and circulating levels of 25(OH)D, ALP, Ca, and Pi were analyzed.ResultsA total of 1819 (1,083 girls and 736 boys) adolescents provided the dietary recall data. Biochemical OM was identified in 175 (9.6%) participants (13.5% in girls, 3.9% in boys, p &lt; 0.01) while the rest served as controls (N = 1,644). All participants had serum 25(OH)D levels &lt;50 nmoL/L. Most participants had very low dietary intakes of Ca (median ~ 290 mg) and vitamin D (median ~ 4 μg) which are far below the RDI of 1,300 mg/day and 20 μg/day, respectively. In contrast, excess dietary intakes of Pi, Na, K, and Fe were observed in all participants. In the biochemical OM group, thiamine and protein intake were significant predictors of serum 25(OH)D, explaining 4.3% of the variance perceived (r = 0.23, adjusted r2 = 4.3%, p = 0.01). Among controls, dietary vitamin C and vitamin D explained 0.6% of the total variation in serum 25(OH)D (r = 0.09, adjusted r2 = 0.6%, p = 0.004).ConclusionArab adolescents do not meet the RDI for dietary Ca and vitamin D, and none have sufficient vitamin D status (25(OH)D levels &gt;50 nmol/L) but they exceed the RDI for dietary Pi. Interpreting these data in the light of the increased prevalence of rickets in Arab countries, food fortification to optimise vitamin D and Ca intake in Saudi adolescents should be considered.
Characteristics of glioblastomas and immune microenvironment in a Chinese family with Lynch syndrome and concurrent porokeratosis
Authors: Yao Zhi-Gang , Hua Fang , Yin Zuo-Hua , Xue Ying-Jie , Hou Yang-Hao , Nie Yi-Cong , Zheng Zhi-Ming , Zhao Miao-Qing , Guo Xiao-Hong , Ma Chao , Li Xiao-Kang , Wang Zhou , Liu Guang-Cun , Zhang Gui-Hui 
Published: July 2023

BackgroundLynch syndrome (LS)-associated glioblastoma (GBM) is rare in clinical practice, and simultaneous occurrence with cutaneous porokeratosis is even rarer. In this study, we analyzed the clinicopathological and genetic characteristics of LS-associated GBMs and concurrent porokeratosis, as well as evaluated the tumor immune microenvironment (TIME) of LS-associated GBMs.MethodsImmunohistochemical staining was used to confirm the histopathological diagnosis, assess MMR and PD-1/PD-L1 status, and identify immune cell subsets. FISH was used to detect amplification of EGFR and PDGFRA, and deletion of 1p/19q and CDKN2A. Targeted NGS assay analyzed somatic variants, MSI, and TMB status, while whole-exome sequencing and Sanger sequencing were carried out to analyze the germline mutations.ResultsIn the LS family, three members (I:1, II:1 and II:4) were affected by GBM. GBMs with loss of MSH2 and MSH6 expression displayed giant and multinucleated bizarre cells, along with mutations in ARID1A, TP53, ATM, and NF1 genes. All GBMs had TMB-H but not MSI-H. CD8+ T cells and CD163+ macrophages were abundant in each GBM tissue. The primary and recurrent GBMs of II:1 showed mesenchymal characteristics with high PD-L1 expression. The family members harbored a novel heterozygous germline mutation in MSH2 and FDPS genes, confirming the diagnosis of LS and disseminated superficial actinic porokeratosis.ConclusionLS-associated GBM exhibits heterogeneity in clinicopathologic and molecular genetic features, as well as a suppressive TIME. The presence of MMR deficiency and TMB-H may serve as predictive factors for the response to immune checkpoint inhibitor therapy in GBMs. The identification of LS-associated GBM can provide significant benefits to both patients and their family members, including accurate diagnosis, genetic counseling, and appropriate screening or surveillance protocols. Our study serves as a reminder to clinicians and pathologists to consider the possibility of concurrent genetic syndromes in individuals or families.
Human precision-cut cystic duct and gallbladder slices: a novel method for studying cholangiopathies
Authors: Fridrichs Jeske , Hamel Bart , Kelder Wendy , van den Hoed Ewoud , van den Heuvel Marius C. , Hulscher Jan B. F. , Olinga Peter 
Published: July 2023

Background and aimsPrecision-cut tissue slices (PCTS) are widely used as an ex vivo culture tissue culture technique to study pathogeneses of diseases and drug activities in organs in vitro. A novel application of the PCTS model may be in the field of translational research into cholangiopathies such as biliary atresia. Therefore, the aim of this study was to apply the precision-cut slice technique to human bile duct and gallbladder tissue.MethodsCystic duct and gallbladder tissue derived from patients undergoing a cholecystectomy were collected, preserved and used for preparation of precision-cut cystic duct slices (PCCDS) and precision-cut gallbladder slices (PCGS). The PCCDS and PCGS were prepared using a mechanical tissue slicer and subsequently incubated for 24 and 48 h respectively in William's Medium E (WME) culture medium. Viability was assessed based on ATP/protein content and tissue morphology [hematoxylin and eosin (H&amp;E) staining].ResultsIt was shown that viability, assessed by the ATP/protein content and morphology, of the PCCDS (n = 8) and PCGS (n = 8) could be maintained over the 24 and 48 h incubation period respectively. ATP/protein content of the PCCDS increased significantly from 0.58 ± 0.13 pmol/µg at 0 h to 2.4 ± 0.29 pmol/µg after 24 h incubation (P = .0003). A similar significant increase from 0.94 ± 0.22 pmol/µg at 0 h to 3.7 ± 0.41 pmol/µg after 24 h (P = .0005) and 4.2 ± 0.47 pmol/µg after 48 h (P = .0002) was observed in the PCGS. Morphological assessment of the PCCDS and PCGS showed viable tissue at 0 h and after 24 and 48 h incubation respectively.ConclusionThis study is the first to report on the use of the PCTS model for human gallbladder and cystic duct tissue. PCCDS and PCGS remain viable for an incubation period of at least 24 h, which makes them suitable for research purposes in the field of cholangiopathies, including biliary atresia.
Use of Trichoderma culture filtrates as a sustainable approach to mitigate early blight disease of tomato and their influence on plant biomarkers and antioxidants production
Authors: Imran Muhammad , Abo-Elyousr Kamal A. M. , Mousa Magdi A. A. , Saad Maged M. 
Published: July 2023

IntroductionAlternaria solani is a challenging pathogen in the tomato crop globally. Chemical control is a rapid approach, but emerging fungicide resistance has become a severe threat. The present study investigates the use of culture filtrates (CFs) of three species of Trichoderma spp. to control this disease.MethodsHighly virulent A. solani strain and three Trichoderma fungal strains viz., T. harzianum (Accession No: MW590687), T. atroviride (Accession No: MW590689) and T. longibrachiatum (Accession No: MW590688) previously isolated by authors were used in this study. The efficacy of culture filtrates (CFs) to mitigate early blight disease were tested under greenhouse and field conditions, experiments were conducted in different seasons of 2020 using a tomato variety “doucen”.Results and discussionThe CFs of T. harzianum, T. longibrachiatum, and T. atroviride significantly inhibited the in vitro mycelial growth of A. solani (62.5%, 48.73%, and 57.82%, respectively, followed by control 100%). In the GC–MS analysis of Trichoderma CF volatile compounds viz., harzianic acid (61.86%) in T. harzianum, linoleic acid (70.02%) in T. atroviride, and hydroxymethylfurfural (68.08%) in the CFs of T. longibrachiatum, were abundantly present. Foliar application of CFs in the greenhouse considerably reduced the disease severity (%) in all treatments, viz., T. harzianum (18.03%), T. longibrachiatum (31.91%), and T. atroviride (23.33%), followed by infected control (86.91%), and positively affected the plant biomarkers. In the greenhouse, the plants treated with CFs demonstrated higher flavonoids after 6 days of inoculation, whereas phenolic compounds increased after 2 days. The CF-treated plants demonstrated higher antioxidant enzymes, i.e., phenylalanine ammonia-lyase (PAL) and peroxidase (POD), after 4 days, whereas polyphenol oxidase (PPO) was higher after 6 days of inoculation, followed by healthy and infected controls. In open field conditions, disease severity in CF-treated plants was reduced in both seasons as compared to naturally infected plants, whereas CF-treated plants exhibited a higher fruit yield than controls. The present results conclude that CFs can be a potential biocontrol candidate and a promising alternative to the early blight pathogen for sustainable production.
Mental health trajectories in university students across the COVID-19 pandemic: findings from the Student Wellbeing at Northern England Universities prospective cohort study
Authors: Paton Lewis W. , Tiffin Paul A. , Barkham Michael , Bewick Bridgette M. , Broglia Emma , Edwards Lisa , Knowles Louise , McMillan Dean , Heron Paul N. 
Published: July 2023

IntroductionPsychological wellbeing in university students is receiving increased focus. However, to date, few longitudinal studies in this population have been conducted. As such, in 2019, we established the Student Wellbeing At Northern England Universities (SWANS) cohort at the University of York, United Kingdom aiming to measure student mental health and wellbeing every six months. Furthermore, the study period included the COVID-19 pandemic, giving an opportunity to track student wellbeing over time, including over the pandemic.MethodsEligible participants were invited to participate via email. Data were collected, using Qualtrics, from September 2019 to April 2021, across five waves (W1 to W5). In total, n = 4,622 students participated in at least one wave of the survey. Data collection included sociodemographic, educational, personality measures, and mental health and wellbeing. Latent profile analyses were performed, exploring trajectories of student wellbeing over the study period for those who had completed at least three of the five waves of the survey (n = 765), as measured by the Warwick-Edinburgh Mental Wellbeing Scale (WEMWBS).ResultsFive latent profile trajectories of student wellbeing were identified. Of these, the two latent classes with initially higher wellbeing scores had broadly stable wellbeing across time (total n = 505, 66%). Two classes had lower initial scores, which lowered further across time (total n = 227, 30%). Additionally, a fifth class of students was identified who improved substantially over the study period, from a mean WEMWBS of 30.4 at W1, to 49.4 at W5 (n = 33, 4%). Risk factors for having less favourable wellbeing trajectories generally included identifying as LGBT+, self-declaring a disability, or previously being diagnosed with a mental health condition.ConclusionOur findings suggest a mixed picture of the effect of the COVID-19 pandemic on student wellbeing, with a majority showing broadly consistent levels of wellbeing across time, a smaller but still substantial group showing a worsening of wellbeing, and a small group that showed a very marked improvement in wellbeing. Those from groups traditionally underrepresented in higher education were most at risk of poorer wellbeing. This raises questions as to whether future support for wellbeing should target specific student subpopulations.
COVID-19 vaccine acceptance among pregnant women: a hospital-based cross-sectional study in Sudan
Authors: Omar Saeed M. , Osman Osama S. , Khalil Rehana , Al-Wutayd Osama , Adam Ishag 
Published: July 2023

IntroductionPregnancy increases the risk of developing a severe illness due to COVID-19 infection. To the best of our knowledge, no previous study has been conducted on COVID-19 vaccine acceptance among pregnant women in Sudan. Hence, this study aimed to determine COVID-19 vaccination acceptance and its predictors among pregnant women.MethodsA cross-sectional study was conducted among 623 pregnant women attending Gadarif maternity hospital in eastern Sudan through a structured questionnaire. Data were obtained on sociodemographic characteristics, obstetric and health-related characteristics, COVID-19 infection, and vaccination-related information, as well as beliefs about and acceptance of COVID-19 vaccination.ResultsCOVID-19 vaccine acceptance among the pregnant women was 2.7%. The vaccine acceptance was higher if their husband’s education was secondary school or higher [adjusted odds ratio [AOR] 4.30, 95% confidence interval (CI) 1.11–16.65, p = 0.035] and discussion of COVID-19 vaccine with the pregnant women by a health care professional in the hospital (AOR 5.46, 95% CI 1.94–15.35, p &lt; 0.001). The most common reasons for resistance to the vaccine were concerns about the side effects of the vaccine for the mother and her baby.ConclusionAcceptance of the COVID-19 vaccination among the pregnant women was very low. Discussions with pregnant women and their husbands by health care professionals regarding the safety of COVID-19 vaccine for the mother and her baby are highly recommended.
Identifying the role of vision transformer for skin cancer—A scoping review
Authors: Khan Sulaiman , Ali Hazrat , Shah Zubair 
Published: July 2023

IntroductionDetecting and accurately diagnosing early melanocytic lesions is challenging due to extensive intra- and inter-observer variabilities. Dermoscopy images are widely used to identify and study skin cancer, but the blurred boundaries between lesions and besieging tissues can lead to incorrect identification. Artificial Intelligence (AI) models, including vision transformers, have been proposed as a solution, but variations in symptoms and underlying effects hinder their performance.ObjectiveThis scoping review synthesizes and analyzes the literature that uses vision transformers for skin lesion detection.MethodsThe review follows the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Revise) guidelines. The review searched online repositories such as IEEE Xplore, Scopus, Google Scholar, and PubMed to retrieve relevant articles. After screening and pre-processing, 28 studies that fulfilled the inclusion criteria were included.Results and discussionsThe review found that the use of vision transformers for skin cancer detection has rapidly increased from 2020 to 2022 and has shown outstanding performance for skin cancer detection using dermoscopy images. Along with highlighting intrinsic visual ambiguities, irregular skin lesion shapes, and many other unwanted challenges, the review also discusses the key problems that obfuscate the trustworthiness of vision transformers in skin cancer diagnosis. This review provides new insights for practitioners and researchers to understand the current state of knowledge in this specialized research domain and outlines the best segmentation techniques to identify accurate lesion boundaries and perform melanoma diagnosis. These findings will ultimately assist practitioners and researchers in making more authentic decisions promptly.
Reduced immunomodulatory metabolite concentrations in peri-transplant fecal samples from heart allograft recipients
Authors: Dela Cruz Mark , Lin Huaiying , Han Jiho , Adler Emerald , Boissiere Jaye , Khalid Maryam , Sidebottom Ashley , Sundararajan Anitha , Lehmann Christopher , Moran Angelica , Odenwald Matthew , Stutz Matthew , Kim Gene , Pinney Sean , Jeevanandam Valluvan , Alegre Maria-Luisa , Pamer Eric , Nguyen Ann B. 
Published: July 2023

BackgroundEmerging evidence is revealing the impact of the gut microbiome on hematopoietic and solid organ transplantation. Prior studies postulate that this influence is mediated by bioactive metabolites produced by gut-dwelling commensal bacteria. However, gut microbial metabolite production has not previously been measured among heart transplant (HT) recipients.MethodsIn order to investigate the potential influence of the gut microbiome and its metabolites on HT, we analyzed the composition and metabolite production of the fecal microbiome among 48 HT recipients at the time of HT.ResultsCompared to 20 healthy donors, HT recipients have significantly reduced alpha, i.e. within-sample, microbiota diversity, with significantly lower abundances of key anaerobic commensal bacteria and higher abundances of potentially pathogenic taxa that have been correlated with adverse outcomes in other forms of transplantation. HT recipients have a wide range of microbiota-derived fecal metabolite concentrations, with significantly reduced levels of immune modulatory metabolites such as short chain fatty acids and secondary bile acids compared to healthy donors. These differences were likely due to disease severity and prior antibiotic exposures but were not explained by other demographic or clinical factors.ConclusionsKey potentially immune modulatory gut microbial metabolites are quantifiable and significantly reduced among HT recipients compared to healthy donors. Further study is needed to understand whether this wide range of gut microbial dysbiosis and metabolite alterations impact clinical outcomes and if they can be used as predictive biomarkers or manipulated to improve transplant outcomes.