bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insight into biological activities of chemically characterized extract from Marrubium vulgare L. in vitro, in vivo and in silico approaches
Authors: Gourich Aman Allah , Touijer Hanane , Drioiche Aziz , Asbabou Ayoub , Remok Firdaous , Saidi Soukaina , Siddique Farhan , Ailli Atika , Bourhia Mohammed , Salamatullah Ahmad Mohammad , Ouahmane Lahcen , Mouradi Aicha , Eto Bruno , Zair Touriya 
Published: August 2023

Aqueous extracts of Marrubium vulgare L. (M. vulgare) are widely used in traditional medicine for their therapeutic effects. Hence, this study aims to evaluate in vitro, in vivo, and in silico the biological activities of M. vulgare aqueous extract to further support their traditional use. Qualitative phytochemical tests of M. vulgare extracts showed the presence of primary and secondary metabolites, while quantitative analyses recorded revealed the contents of total phenols, flavonoids, and tannins, with values of 488.432 ± 7.825 mg/EAG gallic acid extract/g, 25.5326 ± 1.317 mg/EQ Quercetin extract/g and 23.966 ± 0.187 mg/EC catechin extract/g, respectively. Characterization of the phytochemical constituents of the extract revealed the presence of catechin and maleic acid as the most abundant while the evaluation of the antioxidant power revealed that the extract possesses significant antioxidant capacity, antimitotic potential, and antimicrobial properties against Streptococcus agalactiae and Staphylococcus epidermidis among many others. The antidiabetic activity of the extract showed a potent antihyperglycemic effect and a significant modulation of the pancreatic α-amylase activity as revealed by both in vitro and in vivo analysis, while an in silico evaluation showed that chemicals in the studied extract exhibited the aforementioned activities by targeting 1XO2 antimitotic protein, W93 antidiabetic protein and 1AJ6 antimicrobial protein, which revealed them as worthy of exploration in drug discovery odyssey. Conclusively, the result of this study demonstrates the numerous biological activities of M. vulgare and gives credence to their folkloric and traditional usage.
Antibacterial activity of the novel compound Sudapyridine (WX-081) against Mycobacterium abscessus
Authors: Nie Wenjuan , Gao Shan , Su Lei , Liu Lina , Geng Ruixue , You Yingxia , Chu Naihui 
Published: August 2023

ObjectiveThis study aimed to investigate sudapyridine (WX-081) antibacterial activity against Mycobacterium abscessus in vitro and its effect on in vivo bacterial growth and host survival using a zebrafish model of M. abscessus infection.MethodsWX-081 in vitro antibacterial activity was assessed based on growth inhibition of M. abscessus standard strain ATCC19977 and 36 clinical isolates. Maximum tolerated concentrations (MTCs) of WX-081, bedaquiline, and azithromycin and inhibition of M. abscessus growth were assessed in vivo after fluorescently labelled bacilli and drugs were injected into zebrafish. Bacterial counts were analysed using one-way ANOVA and fluorescence intensities of zebrafish tissues were analysed and expressed as the mean ± SE. Moreover, Kaplan-Meier survival analysis was conducted to assess intergroup differences in survival of M. abscessus-infected zebrafish treated with different drug concentrations using a log-rank test, with a p value &lt;0.05 indicating a difference was statistically significant.ResultsDrug sensitivity testing of M. abscessus standard strain ATCC19977 and 36 clinical isolates revealed MICs ranging from 0.12-0.96 µg/mL and MIC50 and MIC90 values of 0.48 µg/mL and 0.96 µg/mL, respectively. Fluorescence intensities of M. abscessus-infected zebrafish tissues was lower after treatment with the WX-081 MTC (62.5 µg/mL) than after treatment with the azithromycin MTC (62.5 µg/mL) and the bedaquiline MTC (15.6 µg/mL). When the concentration of WX-081 increased from 1.95µg/mL to 1/8 MTC(7.81µg/mL), the survival rate of zebrafish at 4-9 dpf decreased from 90.00% to 81.67%.ConclusionWX-081 effectively inhibited M. abscessus growth in vitro and in vivo and prolonged survival of M. abscessus-infected zebrafish, thus indicating that WX-081 holds promise as a clinical treatment for M. abscessus infection.
Lactobacillus reuteri in digestive system diseases: focus on clinical trials and mechanisms
Authors: Peng Yijing , Ma Yizhe , Luo Zichen , Jiang Yifan , Xu Zhimin , Yu Renqiang 
Published: August 2023

ObjectivesDigestive system diseases have evolved into a growing global burden without sufficient therapeutic measures. Lactobacillus reuteri (L. reuteri) is considered as a new potential economical therapy for its probiotic effects in the gastrointestinal system. We have provided an overview of the researches supporting various L. reuteri strains’ application in treating common digestive system diseases, including infantile colic, diarrhea, constipation, functional abdominal pain, Helicobacter pylori infection, inflammatory bowel disease, diverticulitis, colorectal cancer and liver diseases.MethodsThe summarized literature in this review was derived from databases including PubMed, Web of Science, and Google Scholar.ResultsThe therapeutic effects of L. reuteri in digestive system diseases may depend on various direct and indirect mechanisms, including metabolite production as well as modulation of the intestinal microbiome, preservation of the gut barrier function, and regulation of the host immune system. These actions are largely strain-specific and depend on the activation or inhibition of various certain signal pathways. It is well evidenced that L. reuteri can be effective both as a prophylactic measure and as a preferred therapy for infantile colic, and it can also be recommended as an adjuvant strategy to diarrhea, constipation, Helicobacter pylori infection in therapeutic settings. While preclinical studies have shown the probiotic potential of L. reuteri in the management of functional abdominal pain, inflammatory bowel disease, diverticulitis, colorectal cancer and liver diseases, its application in these disease settings still needs further study.ConclusionThis review focuses on the probiotic effects of L. reuteri on gut homeostasis via certain signaling pathways, and emphasizes the importance of these probiotics as a prospective treatment against several digestive system diseases.
Depressive and anxiety disorders and antidepressant prescriptions among insured children and young adults with congenital adrenal hyperplasia in the United States
Authors: Harasymiw Lauren A. , Grosse Scott D. , Cullen Kathryn R. , Bitsko Rebecca H. , Perou Ruth , Sarafoglou Kyriakie 
Published: August 2023

BackgroundDysfunction in the hypothalamic-pituitary-adrenal axis has been associated with depressive and anxiety disorders. Little is known about the risk for these disorders among individuals with congenital adrenal hyperplasia (CAH), a form of primary adrenal insufficiency.ObjectiveWe investigated the prevalence of depressive and anxiety disorders and antidepressant prescriptions in two large healthcare databases of insured children, adolescents, and young adults with CAH in the United States.MethodsWe conducted a retrospective cohort study using administrative data from October 2015 through December 2019 for individuals aged 4–25 years enrolled in employer-sponsored or Medicaid health plans.ResultsAdjusting for age, the prevalence of depressive disorders [adjusted prevalence ratio (aPR) = 1.7, 95% confidence interval (CI): 1.4-2.0, p&lt;0.001], anxiety disorders [aPR = 1.7, 95% CI: 1.4-1.9, p&lt;0.001], and filled antidepressant prescriptions [aPR = 1.7, 95% CI: 1.4-2.0, p&lt;0.001] was higher among privately insured youth with CAH as compared to their non-CAH peers. Prevalence estimates were also higher among publicly insured youth with CAH for depressive disorders [aPR = 2.3, 95% CI: 1.9-2.9, p&lt;0.001], anxiety disorders [aPR = 2.0, 95% CI: 1.6-2.5, p&lt;0.001], and filled antidepressant prescriptions [aPR = 2.5, 95% CI: 1.9-3.1, p&lt;0.001] as compared to their non-CAH peers.ConclusionsThe elevated prevalence of depressive and anxiety disorders and antidepressant prescriptions among youth with CAH suggests that screening for symptoms of depression and anxiety among this population might be warranted.
Obtaining SF-6D utilities from FACT-H&N in thyroid carcinoma patients: development and results from a mapping study
Authors: Yang Qing , Huang Deyu , Jiang Longlin , Tang Yuan , Zeng Dingfen 
Published: August 2023

ObjectiveThere is limited evidence for mapping clinical tools to preference-based generic tools in the Chinese thyroid cancer patient population. The current study aims to map the FACT-H&amp;N (Functional Assessment of Cancer Therapy-Head and Neck Cancer) to the SF-6D (Short Form Six-Dimension), which will inform future cost-utility analyses related to thyroid cancer treatment.MethodsA total of 1050 participants who completed the FACT-H&amp;N and SF-6D questionnaires were included in the analysis. Four methods of direct and indirect mapping were estimated: OLS regression, Tobit regression, ordered probit regression, and beta mixture regression. We evaluated the predictive performance in terms of root mean square error (RMSE), mean absolute error (MAE), concordance correlation coefficient (CCC), Akaike information criterion (AIC) and Bayesian information criterion (BIC) and the correlation between the observed and predicted SF-6D scores.ResultsThe mean value of SF-6D was 0.690 (SD = 0.128). The RMSE values for the fivefold cross-validation as well as the 30% random sample validation for multiple models in this study were 0.0833-0.0909, MAE values were 0.0676-0.0782, and CCC values were 0.6940-0.7161. SF-6D utility scores were best predicted by a regression model consisting of the total score of each dimension of the FACT-H&amp;N, the square of the total score of each dimension, and covariates including age and gender. We proposed to use direct mapping (OLS regression) and indirect mapping (ordered probit regression) to establish a mapping model of FACT-H&amp;N to SF-6D. The mean SF-6D and cumulative distribution functions simulated from the recommended mapping algorithm generally matched the observed ones.ConclusionsIn the absence of preference-based quality of life tools, obtaining the health status utility of thyroid cancer patients from directly mapped OLS regression and indirectly mapped ordered probit regression is an effective alternative.
Ferroptosis and its potential role in gestational diabetes mellitus: updated evidence from pathogenesis to therapy
Authors: Zhao Yan , Gao Qianqian , Li Baoxuan , Wang Yang , Wang Yue 
Published: August 2023

BackgroundStudies have demonstrated that high iron status is positively associated with gestational diabetes mellitus (GDM), implying that iron overload and ferroptosis play important roles in the development of GDM. The aim of this study was to explore effective therapeutic drugs from traditional Chinese medicine (TCM)formulas for the treatment of GDM based on ferroptosis.MethodsIn this study, the presence of ferroptosis in the placenta was verified through clinical and experimental data, and key genes were subsequently screened for association with ferroptosis in the development of GDM. The analysis was based on transcriptome sequencing of datasets combined with differentially expressed genes (DEGs) analysis and weighted gene correlation network analysis (WGCNA); functional enrichment analysis was also performed. A protein−protein interaction (PPI) network was constructed and pivotal genes were identified using Cytoscape. Finally, traditional Chinese medicine (TCM)formulas related to treating GDM were collected, then the proteins corresponding to the key genes were molecularly docked with the small molecular structures of clinically proven effective herbal tonics, and molecular dynamic simulations were performed to select the best candidates for pharmacological compounds.ResultsElevated ferritin levels in patients with GDM were verified using clinical data. The presence of ferroptosis in placental tissues of patients with GDM was confirmed using electron microscopy and western blotting. Ninety-nine key genes with the highest correlation with ferroptosis were identified from DEGs and weighted gene co-expression network analysis (WGCNA). Analysis using the Kyoto Encyclopedia of Genes and Genomes demonstrated that the DEGs were primarily involved in the oxidative phosphorylation pathway. The key genes were further screened by PPI; two key genes, SF3B14 and BABAM1, were identified by combining the gene corresponding to protein structure and function, followed by molecular docking and molecular dynamic simulation. Coptis chinensis was proposed as the best candidate for herbal treatment at the molecular level.ConclusionThis data revealed the presence of ferroptosis in patients with GDM and identified possible modulatory roles of ferroptosis-related genes involved in the molecular mechanisms of GDM, providing new insights into the pathogenesis of GDM, which also provided new directions for the systematic optimization of TCM formulas for the management and targeted treatment of GDM.
The association between non-alcoholic fatty liver disease and atopic dermatitis: a population-based cohort study
Authors: Gau Shuo-Yan , Huang Ching-Hua , Yang Yih , Tsai Tung-Han , Huang Kuang-Hua , Lee Chien-Ying 
Published: August 2023

BackgroundIn previous studies, it was reported that non-alcoholic fatty liver disease (NAFLD) incidence and prevalence increased in children with atopic dermatitis. Nevertheless, the actual association between the two diseases has not been fully proven in large-scale studies, and real-world evidence is missing. The objective of this nationwide, longitudinal cohort study was to evaluate the association between NAFLD and atopic dermatitis.MethodsThe National Health Insurance Research Database in Taiwan was utilized in this study. Patients with records of NAFLD diagnosis were recruited as the experimental group, and patients having less than three outpatient visits or one inpatient visiting record due to NAFLD were excluded from the study design. Non-NAFLD controls were matched based on a 1:4 propensity score matching. Potential confounders including age, gender, comorbidity, and medical utilization status were considered as covariates. The risk of future atopic dermatitis would be evaluated based on multivariate Cox proportional hazard regression.ResultsCompared with people without NAFLD, a decreased risk of atopic dermatitis in NALFD patients had been observed (aHR = 0.93, 95% CI 0.87–0.98). The trend was especially presented in young NAFLD patients. In patients younger than 40 years old, a 20% decreased risk of atopic dermatitis was reported (aHR = 0.80, 95% CI 0.70–0.92).ConclusionPeople with NAFLD were not associated with an increased risk of atopic dermatitis. Conversely, a 0.93-fold risk was noted in NAFLD patients, compared with NAFLD-free controls. Future studies are warranted to evaluate further the mechanism regarding the interplay between the inflammatory mechanisms of NAFLD and atopic dermatitis.
Allele-specific quantification of human leukocyte antigen transcript isoforms by nanopore sequencing
Authors: Hughes Andrew E. O. , Montgomery Maureen C. , Liu Chang , Weimer Eric T. 
Published: August 2023

IntroductionWhile tens of thousands of HLA alleles have been identified by DNA sequencing, the contribution of alternative splicing to HLA diversity is not well characterized. In this study, we sought to determine if long-read sequencing could be used to accurately quantify allele-specific HLA transcripts in primary human lymphocytes.MethodscDNA libraries were prepared from peripheral blood lymphocytes from 12 donors and sequenced by nanopore long-read sequencing. HLA reads were aligned to donor-specific reference sequences based on the known type of each donor. Allele-specific exon utilization was calculated as the proportion of reads aligning to each allele containing known exons, and transcript isoforms were quantified based on patterns of exon utilization within individual reads.ResultsSplice variants were rare among class I HLA genes (median exon retention rate 99%–100%), except for several HLA-C alleles with exon 5 spliced out of up to 15% of reads. Splice variants were also rare among class II HLA genes (median exon retention rate 98%–100%), except for HLA-DQB1. Consistent with previous work, exon 5 of HLA-DQB1 was spliced out in alleles with a mutated splice acceptor site at rs28688207. Surprisingly, a 28% loss of exon 5 was also observed in HLA-DQB1 alleles with an intact splice acceptor site at rs28688207.DiscussionWe describe a simple bioinformatic workflow to quantify allele-specific expression of HLA transcript isoforms. Further studies are warranted to characterize the repertoire of HLA transcripts expressed in different cell types and tissues across diverse populations.
Serum CHI3L1 as a biomarker of interstitial lung disease in rheumatoid arthritis
Authors: Yu Rui , Liu Xiaomin , Deng Xiaoyue , Li Siting , Wang Yifei , Zhang Yan , Ke Dan , Yan Rui , Wang Qian , Tian Xinping , Li Mengtao , Zeng Xiaofeng , Hu Chaojun 
Published: August 2023

BackgroundInterstitial lung disease (ILD) is a relatively prevalent extra-articular manifestation of rheumatoid arthritis (RA) and contributes to significant morbidity and mortality. This study aimed to analyze the association between chitinase-3 like-protein-1(CHI3L1) and the presence of RA-ILD.MethodsA total of 239 RA patients fulfilling the American Rheumatism Association (ACR) 1987 revised criteria were enrolled and subclassified as RA-ILD and RA-nILD based on the results of high-resolution computed tomography scans (HRCT) of the chest. The disease activity of RA was assessed by Disease Activity Score for 28 joints (DAS28) and categorized as high, moderate, low, and remission. Chemiluminescence immunoassays were applied to determine the serum levels of CHI3L1. Univariate analysis was performed and the receiver operating characteristics (ROC) curves were plotted to evaluate the correlation between RA-ILD and CHI3L1.ResultsAmong the eligible RA patients studied, 60 (25.1%) patients were diagnosed with RA-ILD. Compared with RA-nILD, RA patients with ILD had significantly higher median age (median [IQR], 68.00 [62.00-71.75] vs 53.00 [40.00-63.00], p&lt;0.001) and a higher proportion of males (21 (35.0%) vs 30 (16.8%), p=0.003). Notably, differences in DAS28 scores between the two groups were not observed. The serum level of CHI3L1 was significantly higher in RA-ILD patients (median [IQR], 69.69 [44.51-128.66] ng/ml vs 32.19 [21.63-56.99] ng/ml, p&lt;0.001). Furthermore, the areas under the curve (AUC) of CHI3L1 attained 0.74 (95% confidence interval [CI], 0.68-0.81, p&lt;0.001) in terms of identifying patients with RA-ILD from those without ILD. Similar trends were seen across the spectrum of disease activity based on DAS28-ESR.ConclusionOur findings of elevated serum CHI3L1 levels in RA-ILD patients suggest its possible role as a biomarker to detect RA-ILD noninvasively.
The impact of immunoglobulin G N-glycosylation level on COVID-19 outcome: evidence from a Mendelian randomization study
Authors: Long Feiwu , Xiao Chenghan , Cui Huijie , Wang Wei , Jiang Zongze , Tang Mingshuang , Zhang Wenqiang , Liu Yunjie , Xiang Rong , Zhang Li , Zhao Xunying , Yang Chao , Yan Peijing , Wu Xueyao , Wang Yutong , Zhou Yanqiu , Lu Ran , Chen Yulin , Li Jiayuan , Jiang Xia , Fan Chuanwen , Zhang Ben 
Published: August 2023

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic has exerted a profound influence on humans. Increasing evidence shows that immune response is crucial in influencing the risk of infection and disease severity. Observational studies suggest an association between COVID‐19 and immunoglobulin G (IgG) N-glycosylation traits, but the causal relevance of these traits in COVID-19 susceptibility and severity remains controversial.MethodsWe conducted a two-sample Mendelian randomization (MR) analysis to explore the causal association between 77 IgG N-glycosylation traits and COVID-19 susceptibility, hospitalization, and severity using summary-level data from genome-wide association studies (GWAS) and applying multiple methods including inverse-variance weighting (IVW), MR Egger, and weighted median. We also used Cochran’s Q statistic and leave-one-out analysis to detect heterogeneity across each single nucleotide polymorphism (SNP). Additionally, we used the MR-Egger intercept test, MR-PRESSO global test, and PhenoScanner tool to detect and remove SNPs with horizontal pleiotropy and to ensure the reliability of our results.ResultsWe found significant causal associations between genetically predicted IgG N-glycosylation traits and COVID-19 susceptibility, hospitalization, and severity. Specifically, we observed reduced risk of COVID-19 with the genetically predicted increased IgG N-glycan trait IGP45 (OR = 0.95, 95% CI = 0.92–0.98; FDR = 0.019). IGP22 and IGP30 were associated with a higher risk of COVID-19 hospitalization and severity. Two (IGP2 and IGP77) and five (IGP10, IGP14, IGP34, IGP36, and IGP50) IgG N-glycosylation traits were causally associated with a decreased risk of COVID-19 hospitalization and severity, respectively. Sensitivity analyses did not identify any horizontal pleiotropy.ConclusionsOur study provides evidence that genetically elevated IgG N-glycosylation traits may have a causal effect on diverse COVID-19 outcomes. Our findings have potential implications for developing targeted interventions to improve COVID-19 outcomes by modulating IgG N-glycosylation levels.
The immune checkpoint VISTA is associated with prognosis in patients with malignant uveal melanoma
Authors: Issam Salah Nour el Imane , Marnissi Farida , Lakhdar Abdelhakim , Karkouri Mehdi , ElBelhadji Mohamed , Badou Abdallah 
Published: August 2023

IntroductionUveal melanoma (UM) is a rare yet deadly tumor. It is known for its high metastatic potential, which makes it one of the most aggressive and lethal cancers. Recently, immune checkpoints such as Programmed cell Death protein-1 (PD1) and Cytotoxic T-Lymphocyte-Associated significantly increasing patient survival in multiple human cancers, especially cutaneous melanoma. However, patients with UMs were excluded from these studies because of their molecular characteristics, which tend to be widely different from those of cutaneous melanoma. This study aimed to analyze the expression of V domain Ig Suppressor T-cell Activation (VISTA), a novel immune checkpoint, to evaluate its prognosis significance and its correlation with PD1 and CTLA-4.MethodsEvaluation of VISTA, CTLA-4, and PD1 expression was performed through TCGA database analysis and immunohistochemistry using two independent cohorts with primary malignant UM.Results and discussionOur results showed that VISTA expression was associated with tumor aggressiveness, T cell exhaustion, and the shortest median overall survival among patients. Surprisingly, PD1 protein expression was negative in all patients, whereas CTLA-4 expression was high in patients with advanced stages. Our findings suggest that VISTA may be a prognostic marker and an attractive treatment strategy for immunotherapy in patients with UM. Exploring its expression profile may predict response to immunotherapy and may lead to the improvement of precision therapy in malignant uveal melanoma patients.