bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal relationships between gut microbiota and programmed cell death protein 1/programmed cell death-ligand 1: A bidirectional Mendelian randomization study
Authors: Huang Yu-Feng , Zhang Wei-Ming , Wei Zhi-Song , Huang Huan , Mo Qi-Yan , Shi Dan-Li , Han Lu , Han Yu-Yuan , Nong Si-Kai , Lin Guo-Xiang 
Published: March 2023

BackgroundMultiple clinical studies have indicated that the gut microbiota influences the effects of immune checkpoint blockade (ICB) therapy comprising PD-1/PD-L1 inhibitors, but the causal relationship is unclear. Because of numerous confounders, many microbes related to PD-1/PD-L1 have not been identified. This study aimed to determine the causal relationship between the microbiota and PD-1/PD-L1 and identify possible biomarkers for ICB therapy.MethodWe used bidirectional two-sample Mendelian randomization with two different thresholds to explore the potential causal relationship between the microbiota and PD-1/PD-L1 and species-level microbiota GWAS to verify the result.ResultIn the primary forward analysis, genus_Holdemanella showed a negative correlation with PD-1 [βIVW = -0.25; 95% CI (-0.43 to -0.07); PFDR = 0.028] and genus_Prevotella9 showed a positive correlation with PD-1 [βIVW = 0.2; 95% CI (0.1 to 0.4); PFDR = 0.027]; order_Rhodospirillales [βIVW = 0.2; 95% CI (0.1 to 0.4); PFDR = 0.044], family_Rhodospirillaceae [βIVW = 0.2; 95% CI (0 to 0.4); PFDR = 0.032], genus_Ruminococcaceae_UCG005 [βIVW = 0.29; 95% CI (0.08 to 0.5); PFDR = 0.028], genus_Ruminococcus_gnavus_group [βIVW = 0.22; 95% CI (0.05 to 0.4); PFDR = 0.029], and genus_Coprococcus_2 [βIVW = 0.4; 95% CI (0.1 to 0.6); PFDR = 0.018] were positively correlated with PD-L1; and phylum_Firmicutes [βIVW = -0.3; 95% CI (-0.4 to -0.1); PFDR = 0.031], family_ClostridialesvadinBB60group [βIVW = -0.31; 95% CI (-0.5 to -0.11), PFDR = 0.008], family_Ruminococcaceae [βIVW = -0.33; 95% CI (-0.58 to -0.07); PFDR = 0.049], and genus_Ruminococcaceae_UCG014 [βIVW = -0.35; 95% CI (-0.57 to -0.13); PFDR = 0.006] were negatively correlated with PD-L1. The one significant species in further analysis was species_Parabacteroides_unclassified [βIVW = 0.2; 95% CI (0-0.4); PFDR = 0.029]. Heterogeneity (P &gt; 0.05) and pleiotropy (P &gt; 0.05) analyses confirmed the robustness of the MR results.
Dietary supplementation of coated sodium butyrate improves growth performance of laying ducks by regulating intestinal health and immunological performance
Authors: Zeng Tao , Sun Hanxue , Huang Manman , Guo Rongbing , Gu Tiantian , Cao Yongqing , Li Chengfeng , Tian Yong , Chen Li , Li Guoqin , Lu Lizhi 
Published: March 2023

IntroductionThis study was conducted to assess the effects of dietary supplementation of coated sodium butyrate (CSB) on the growth performance, serum antioxidant, immune performance, and intestinal microbiota of laying ducks.MethodsA total of 120 48-week-old laying ducks were randomly divided into 2 treatment groups: the control group (group C fed a basal diet) and the CSB-treated group (group CSB fed the basal diet + 250 g/t of CSB). Each treatment consisted of 6 replicates, with 10 ducks per replicate, and the trial was conducted for 60 days.ResultsCompared with the group C, the group CSB showed a significant increase in the laying rate (p&lt;0.05) of the 53-56 week-old ducks. Additionally, the serum total antioxidant capacity, superoxide dismutase activity and immunoglobulin G level were significantly higher (p&lt;0.05), while the serum malondialdehyde content and tumor necrosis factor (TNF)-a level were significantly lower (p&lt;0.05) in the serum of the group CSB compared to the group C. Moreover, the expression of IL-1b and TNF-a in the spleen of the group CSB was significantly lower (p&lt;0.05) compared to that of the group C. In addition, compared with the group C, the expression of Occludin in the ileum and the villus height in the jejunum were significantly higher in the group CSB (p&lt;0.05). Furthermore, Chao1, Shannon, and Pielou-e indices were higher in the group CSB compared to the group C (p&lt;0.05). The abundance of Bacteroidetes in the group CSB was lower than that in the group C (p&lt;0.05), while the abundances of Firmicutes and Actinobacteria were higher in the group CSB compared to the group C (p&lt;0.05).ConclusionsOur results suggest that the dietary supplementation of CSB can alleviate egg-laying stress in laying ducks by enhancing immunity and maintaining the intestinal health of the ducks.
Constructing a prediction model of inflammatory bowel disease recurrence based on factors affecting the quality of life
Authors: Li Maojuan , Tao Yan , Sun Yang , Wu Jing , Zhang Fengrui , Wen Yunling , Gong Min , Yan Jingxian , Liang Hao , Bai Xinyu , Niu Junkun , Miao Yinglei 
Published: March 2023

AimThis study aimed to determine the factors affecting the quality of life of patients with inflammatory bowel disease (IBD) and to construct a disease recurrence prediction model based on these influencing factors.MethodsA prospective, single-center study in China was conducted between October 2020 and March 2021. The quality of life of patients was assessed using the Inflammatory Bowel Disease Questionnaire (IBDQ). Multiple stepwise regression analysis was used to analyze the factors influencing the quality of life of patients with IBD. The chi-square test and the point-biserial correlation analysis were performed to identify factors associated with clinical recurrence. A binary logistic regression model was constructed to predict the recurrence. The receiver operating characteristic curve was used to evaluate the prediction model. Patients with IBD from April 2021 to June 2021 were randomly included for model verification to evaluate the disease recurrence prediction model.ResultsThe average IBDQ score of patients with IBD was 172.2 ± 35.0 (decreased by 23.2%). The scores of all dimensions of the IBDQ were decreased, especially emotional function and systemic symptoms. Disease activity, age, extraintestinal manifestations (EIMs), and annual household income were important factors influencing the IBDQ scores of patients with ulcerative colitis, and these accounted for ~57.0% of the factors affecting the quality of life. Disease activity, EIMs, and occupational stress were important factors influencing the IBDQ scores of patients with Crohn's disease, and they accounted for approximately 75.1% of the factors affecting the quality of life. Annual household income, occupational stress, and IBDQ scores were independent risk factors for recurrence. The area under the curve of the recurrence prediction model was 81.1%. The sensitivity and specificity were 81.7 and 71.7%, respectively. The Youden index of the model was 0.534. The established recurrence prediction model has good discriminant validity in the validation cohort.ConclusionThe quality of life of patients with IBD was generally poor. The use of factors affecting the quality of life to predict disease recurrence has high predictive value and can support the management of IBD by selecting patients at a higher risk for relapse.
Niche-mediated bacterial community composition in continental glacier alluvial valleys under cold and arid environments
Authors: Chen Xianke , Qi Xiangning , Ren Ge , Chang Ruiying , Qin Xiang , Liu Guohua , Zhuang Guoqiang , Ma Anzhou 
Published: March 2023

IntroductionBacteria are an essential component of glacier-fed ecosystems and play a dominant role in driving elemental cycling in the hydrosphere and pedosphere. However, studies of bacterial community composition mechanisms and their potential ecological functions from the alluvial valley of mountain glaciers are extremely scarce under cold and arid environments.MethodsHere, we analyzed the effects of major physicochemical parameters related to soil on the bacterial community compositions in an alluvial valley of the Laohugou Glacier No. 12 from the perspective of core, other, and unique taxa and explored their functional composition characteristics.Results and discussionThe different characteristics of core, other, and unique taxa highlighted the conservation and difference in bacterial community composition. The bacterial community structure of the glacial alluvial valley was mainly affected by the above sea level, soil organic carbon, and water holding capacity. In addition, the most common and active carbon metabolic pathways and their spatial distribution patterns along the glacial alluvial valley were revealed by FAPTOTAX. Collectively, this study provides new insights into the comprehensive assessment of glacier-fed ecosystems in glacial meltwater ceasing or glacier disappearance.
Study on the removal characteristics and degradation pathways of highly toxic and refractory organic pollutants in real pharmaceutical factory wastewater treated by a pilot-scale integrated process
Authors: Dai Wei , Pang Ji-Wei , Ding Jie , Wang Yu-Qian , Zhang Lu-Yan , Ren Nan-Qi , Yang Shan-Shan 
Published: March 2023

IntroductionPharmaceutical wastewater frequently contains high levels of toxic pollutants. If they are discharged untreated, they pose a threat to the environment. The traditional activated sludge process and the advanced oxidation process do not sufficiently remove toxic and conventional pollutants from pharmaceutical wastewater treatment plants (PWWTPs).MethodsWe designed a pilot-scale reaction system to reduce toxic organic pollutants and conventional pollutants from pharmaceutical wastewater during the biochemical reaction stage. This system included a continuous stirred tank reactor (CSTR), microbial electrolysis cells (MECs), an expanded sludge bed reactor (EGSB), and a moving bed biofilm reactor (MBBR). We used this system to further investigate the benzothiazole degradation pathway.Results and discussionThe system effectively degraded the toxic pollutants (benzothiazole, pyridine, indole, and quinoline) and the conventional chemicals (COD, NH4+-N, TN). During the stable operation of the pilot-scale plant, the total removal rates of benzothiazole, indole, pyridine, and quinoline were 97.66, 94.13, 79.69, and 81.34%, respectively. The CSTR and MECs contributed the most to the removal of toxic pollutants, while the EGSB and MBBR contributed less to the removal of the four toxic pollutants. Benzothiazoles can be degraded via two pathways: the benzene ring-opening reaction and the heterocyclic ring-opening reaction. The heterocyclic ring-opening reaction was more important in degrading the benzothiazoles in this study.ConclusionThis study provides feasible design alternatives for PWWTPs to remove both toxic and conventional pollutants at the same time.
Transcriptome analysis of auxin transcription factor OsARF17-mediated rice stripe mosaic virus response in rice
Authors: Ma Qiang , Wang Fengmin , Song Weiqi , Huang Chaorui , Xie Kaili , Wei Zhongyan , Li Yanjun , Chen Jianping , Zhang Hehong , Sun Zongtao 
Published: March 2023

IntroductionPlant auxin response factors (ARFs) play an irreplaceable role in regulating the expression of auxin response genes. Our previous studies have indicated that auxin response factor OsARF17 plays a crucial role in plant defense against diverse rice viruses.MethodsUtilizing a comparative transcriptome analysis of Rice stripe mosaic virus (RSMV)-inoculated OsARF17 mutant rice plants, to further elucidate the molecular mechanism of OsARF17 in antiviral defense pathway.ResultsKEGG enrichment analyses showed that the down-regulated differentially expressed genes (DEGs) belonged to plant-pathogen interaction and plant hormone signal transduction pathways were markedly enriched in OsARF17 mutants under RSMV inoculation. Furthermore, Gene ontology (GO) analyses revealed that these genes were enriched in a variety of hormone biosynthetic process, including jasmonic acid (JA), auxin, and abscisic acid (ABA). RT-qPCR assays showed that the induction of plant defense-related genes, such as WRKY transcription factors, OsAHT2 and OsDR8, and JA-related genes, were significantly suppressed in OsARF17 mutants in response to RSMV.DiscussionOur study reveals that OsARF17-mediated antiviral immunity may be achieved through affecting the interaction between different phytohormones and regulating defense gene expression in rice. This study provides new insights into the molecular mechanisms of auxin signaling in the rice-virus interaction.
Variation in synonymous evolutionary rates in the SARS-CoV-2 genome
Authors: Sun Qianru , Zeng Jinfeng , Tang Kang , Long Haoyu , Zhang Chi , Zhang Jie , Tang Jing , Xin Yuting , Zheng Jialu , Sun Litao , Liu Siyang , Du Xiangjun 
Published: March 2023

IntroductionCoronavirus disease 2019 is an infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Influential variants and mutants of this virus continue to emerge, and more effective virus-related information is urgently required for identifying and predicting new mutants. According to earlier reports, synonymous substitutions were considered phenotypically silent; thus, such mutations were frequently ignored in studies of viral mutations because they did not directly cause amino acid changes. However, recent studies have shown that synonymous substitutions are not completely silent, and their patterns and potential functional correlations should thus be delineated for better control of the pandemic.MethodsIn this study, we estimated the synonymous evolutionary rate (SER) across the SARS-CoV-2 genome and used it to infer the relationship between the viral RNA and host protein. We also assessed the patterns of characteristic mutations found in different viral lineages.ResultsWe found that the SER varies across the genome and that the variation is primarily influenced by codon-related factors. Moreover, the conserved motifs identified based on the SER were found to be related to host RNA transport and regulation. Importantly, the majority of the existing fixed-characteristic mutations for five important virus lineages (Alpha, Beta, Gamma, Delta, and Omicron) were significantly enriched in partially constrained regions.DiscussionTaken together, our results provide unique information on the evolutionary and functional dynamics of SARS-CoV-2 based on synonymous mutations and offer potentially useful information for better control of the SARS-CoV-2 pandemic.