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  1. Article ; Online: RSNET

    Xiaohan Jiang / Xiujun Zhang

    BMC Bioinformatics, Vol 23, Iss 1, Pp 1-

    inferring gene regulatory networks by a redundancy silencing and network enhancement technique

    2022  Volume 18

    Abstract: Abstract Background Current gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the predictions. Filtering out the indirect interactions from direct ones remains an important challenge in ... ...

    Abstract Abstract Background Current gene regulatory network (GRN) inference methods are notorious for a great number of indirect interactions hidden in the predictions. Filtering out the indirect interactions from direct ones remains an important challenge in the reconstruction of GRNs. To address this issue, we developed a redundancy silencing and network enhancement technique (RSNET) for inferring GRNs. Results To assess the performance of RSNET method, we implemented the experiments on several gold-standard networks by using simulation study, DREAM challenge dataset and Escherichia coli network. The results show that RSNET method performed better than the compared methods in sensitivity and accuracy. As a case of study, we used RSNET to construct functional GRN for apple fruit ripening from gene expression data. Conclusions In the proposed method, the redundant interactions including weak and indirect connections are silenced by recursive optimization adaptively, and the highly dependent nodes are constrained in the model to keep the real interactions. This study provides a useful tool for inferring clean networks.
    Keywords Gene regulatory network ; Indirect interaction ; Network inference ; Network enhancement ; Redundancy silencing ; Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 006
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: QSPR Analysis of Drugs for Treatment of Schizophrenia Using Topological Indices

    Xiujun Zhang / Muhammad Jawwad Saif / Nazeran Idrees / Salma Kanwal / Saima Parveen / Fatima Saeed

    ACS Omega, Vol 8, Iss 44, Pp 41417-

    2023  Volume 41426

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2023-10-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Effect of Arabinoxylan and Xylo-Oligosaccharide on Growth Performance and Intestinal Barrier Function in Weaned Piglets

    Feize Sun / Huahui Li / Zhiqiang Sun / Ling Liu / Xiujun Zhang / Jinbiao Zhao

    Animals, Vol 13, Iss 964, p

    2023  Volume 964

    Abstract: The purpose of this study was to explore the effects of xylose with different polymerizations on growth performance, intestinal barrier function, and gut microbial composition in weaned piglets. A total of 144 weaned piglets were assigned to 3 dietary ... ...

    Abstract The purpose of this study was to explore the effects of xylose with different polymerizations on growth performance, intestinal barrier function, and gut microbial composition in weaned piglets. A total of 144 weaned piglets were assigned to 3 dietary treatments in a completely randomized design according to their body weight and sex. Dietary treatments included a corn-soybean meal basal diet (CON) and 2 additional diets formulated with 1% arabinoxylan (AX) and 1% xylo-oligosaccharide (XOS), respectively. Results showed that dietary supplementation of XOS or AX reduced diarrhea incidence of weaned piglets compared with the CON group ( p < 0.05). XOS or AX increased the ileal villus height and intestinal activity of antioxidases in weaned piglets compared with the CON group ( p < 0.05). XOS or AX reduced the ileal and colonic IL-6 content and increased the colonic sIgA and IL-10 concentrations in weaned piglets compared with the CON group ( p < 0.05). XOS or AX increased the total organic acids concentrations in the ileum and in vitro fermentation ( p < 0.05). XOS increased the abundance of Lactobacillus and Bifidobacterium in the ileal digesta ( p < 0.05), while AX increased the population of Lactobacillus in the ileal digesta and the abundance of Bifidobacterium in the colonic digesta of weaned piglets ( p < 0.05). In conclusion, both XOS and AX reduce diarrhea incidence and improve antioxidant capacity, immune function, and populations of beneficial bacteria, while microbial fermentation of XOS with a lower polymerization and molecular mass can produce more organic acids and an increased abundance of Lactobacillus and Bifidobacterium in the upper gut of weaned pigs compared with AX.
    Keywords xylo-oligosaccharides ; arabinoxylans ; weaned piglets ; gut microbiota ; intestinal barrier ; Veterinary medicine ; SF600-1100 ; Zoology ; QL1-991
    Subject code 610
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Study of Hardness of Superhard Crystals by Topological Indices

    Xiujun Zhang / Muhammad Naeem / Abdul Qudair Baig / Manzoor Ahmad Zahid

    Journal of Chemistry, Vol

    2021  Volume 2021

    Abstract: Topological indices give immense information about a molecular structure or chemical structure. The hardness of materials for the indentation can be defined microscopically as the total resistance and effect of chemical bonds in the respective materials. ...

    Abstract Topological indices give immense information about a molecular structure or chemical structure. The hardness of materials for the indentation can be defined microscopically as the total resistance and effect of chemical bonds in the respective materials. The aim of this paper is to study the hardness of some superhard BCx crystals by means of topological indices, specifically Randić index and atom-bond connectivity index.
    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Association between PM 1 Exposure and Lung Function in Children and Adolescents

    Zhiqiang Zong / Mengjie Zhao / Mengyue Zhang / Kexin Xu / Yunquan Zhang / Xiujun Zhang / Chengyang Hu

    International Journal of Environmental Research and Public Health, Vol 19, Iss 15888, p

    A Systematic Review and Meta-Analysis

    2022  Volume 15888

    Abstract: The detrimental effects of PM 2.5 and PM 10 (particulate matter less than 2.5 or 10 μm) on human respiratory system, including lung function, have been widely assessed. However, the associations between PM 1 (particulate matter of less than 1 μm) and ... ...

    Abstract The detrimental effects of PM 2.5 and PM 10 (particulate matter less than 2.5 or 10 μm) on human respiratory system, including lung function, have been widely assessed. However, the associations between PM 1 (particulate matter of less than 1 μm) and lung function in children and adolescents are less explored, and current evidence is inconsistent. We conducted a meta-analysis of the literature on the association between PM 1 and lung function in children and adolescents to fill this gap. With no date or language constraints, we used a combination of MeSH (Medical Subject Headings) terms and free text to search PubMed, EMBASE and Web of Science databases through, 1 October 2022 for “PM 1 exposure” and “lung function”. A total of 6420 relevant studies were identified through our initial search, and seven studies were included in our study. In this meta-analysis, the fixed effect and random effects statistical models were used to estimate the synthesized effects of the seven included studies. For every 10 μg/m 3 increase in short-term PM 1 exposure, forced vital capacity (FVC), forced expiratory volume in the first second (FEV 1 ), peak expiratory flow (PEF) and maximal mid-expiratory flow (MMEF) decreased by 31.82 mL (95% CI: 20.18, 43.45), 32.28 mL (95% CI: 16.73, 48.91), 36.85 mL/s (95% CI: 15.33, 58.38) and 34.51 mL/s (95% CI: 19.61, 49.41), respectively. For each 10 μg/m 3 increase in long-term PM 1 exposure, FVC, FEV 1 , PEF and MMEF decreased by 102.34 mL (95% CI: 49.30, 155.38), 75.17 mL (95% CI: 39.61, 110.73), 119.01 mL/s (95% CI: 72.14, 165.88) and 44.94 mL/s (95% CI: 4.70, 85.18), respectively. Our study provides further scientific evidence for the harmful effects of PM 1 exposure on lung function in children and adolescents, indicating that exposure to PM 1 is detrimental to pulmonary health. To reduce the adverse health effects of air pollution on children and adolescents, effective preventive measures should be taken.
    Keywords PM 1 ; lung function ; air pollution ; cohort study ; children ; adolescents ; Medicine ; R
    Subject code 333
    Language English
    Publishing date 2022-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Multiplicative Zagreb Indices of Molecular Graphs

    Xiujun Zhang / H. M. Awais / M. Javaid / Muhammad Kamran Siddiqui

    Journal of Chemistry, Vol

    2019  Volume 2019

    Abstract: Mathematical modeling with the help of numerical coding of graphs has been used in the different fields of science, especially in chemistry for the studies of the molecular structures. It also plays a vital role in the study of the quantitative structure ...

    Abstract Mathematical modeling with the help of numerical coding of graphs has been used in the different fields of science, especially in chemistry for the studies of the molecular structures. It also plays a vital role in the study of the quantitative structure activities relationship (QSAR) and quantitative structure properties relationship (QSPR) models. Todeshine et al. (2010) and Eliasi et al. (2012) defined two different versions of the 1st multiplicative Zagreb index as ∏Γ=∏p∈VΓdΓp2 and ∏1Γ=∏pq∈EΓdΓp+dΓq, respectively. In the same paper of Todeshine, they also defined the 2nd multiplicative Zagreb index as ∏2Γ=∏pq∈EΓdΓp×dΓq. Recently, Liu et al. [IEEE Access; 7(2019); 105479–-105488] defined the generalized subdivision-related operations of graphs and obtained the generalized F-sum graphs using these operations. They also computed the first and second Zagreb indices of the newly defined generalized F-sum graphs. In this paper, we extend this study and compute the upper bonds of the first multiplicative Zagreb and second multiplicative Zagreb indices of the generalized F-sum graphs. At the end, some particular results as applications of the obtained results for alkane are also included.
    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Fixed cutaneous sporotrichosis in a patient with numerous fungal elements

    Ankang Gu / Xiujun Zhang / Faku Ma / Zhenhua Nie / G. Sybren de Hoog / Yu Zhang

    Medical Mycology Case Reports, Vol 29, Iss , Pp 32-

    2020  Volume 34

    Abstract: Sporotrichosis generally shows no or a small number of fungal cells in tissue. Numerous fungal elements are usually associated with suppression of cellular immunity, either acquired or innate. The present case demonstrates that also topical ... ...

    Abstract Sporotrichosis generally shows no or a small number of fungal cells in tissue. Numerous fungal elements are usually associated with suppression of cellular immunity, either acquired or innate. The present case demonstrates that also topical immunosuppression can lead to increased fungal load at the affected site.
    Keywords Sporotrichosis ; Sporothrix globosa ; Fungal burden ; Medicine (General) ; R5-920 ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2020-09-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: A bottom-up model of functional outcome in schizophrenia

    Hongge Luo / Yanli Zhao / Fengmei Fan / Hongzhen Fan / Yunhui Wang / Wei Qu / Zhiren Wang / Yunlong Tan / Xiujun Zhang / Shuping Tan

    Scientific Reports, Vol 11, Iss 1, Pp 1-

    2021  Volume 10

    Abstract: Abstract Schizophrenia results in poor functional outcomes owing to numerous factors. This study provides the first test of a bottom-up causal model of functional outcome in schizophrenia, using neurocognition, vocal emotional cognition, alexithymia, and ...

    Abstract Abstract Schizophrenia results in poor functional outcomes owing to numerous factors. This study provides the first test of a bottom-up causal model of functional outcome in schizophrenia, using neurocognition, vocal emotional cognition, alexithymia, and negative symptoms as predictors of functional outcome. We investigated a cross-sectional sample of 135 individuals with schizophrenia and 78 controls. Using a series of structural equation modelling analyses, a single pathway was generated among scores from the MATRICS Consensus Cognitive Battery (MCCB), vocal emotion recognition test, Toronto Alexithymia Scale (TAS), Brief Negative Symptom Scale, and the Personal and Social Performance Scale. The scores for each dimension of the MCCB in the schizophrenia group were significantly lower than that in the control group. The recognition accuracy for different emotions (anger, disgust, fear, sadness, surprise, and satire, but not calm was significantly lower in the schizophrenia group than in the control group. Moreover, the scores on the three dimensions of TAS were significantly higher in the schizophrenia group than in the control group. On path analysis modelling, the proposed bottom-up causal model showed a strong fit with the data and formed a single pathway, from neurocognition to vocal emotional cognition, to alexithymia, to negative symptoms, and to poor functional outcomes. The study results strongly support the proposed bottom-up causal model of functional outcome in schizophrenia. The model could be used to better understand the causal factors related to the functional outcome, as well as for the development of intervention strategies to improve functional outcomes in schizophrenia.
    Keywords Medicine ; R ; Science ; Q
    Subject code 150
    Language English
    Publishing date 2021-04-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Functional Amino Acids and Autophagy

    Chunchen Liu / Linbao Ji / Jinhua Hu / Ying Zhao / Lee J. Johnston / Xiujun Zhang / Xi Ma

    International Journal of Molecular Sciences, Vol 22, Iss 11427, p

    Diverse Signal Transduction and Application

    2021  Volume 11427

    Abstract: Functional amino acids provide great potential for treating autophagy-related diseases by regulating autophagy. The purpose of the autophagy process is to remove unwanted cellular contents and to recycle nutrients, which is controlled by many factors. ... ...

    Abstract Functional amino acids provide great potential for treating autophagy-related diseases by regulating autophagy. The purpose of the autophagy process is to remove unwanted cellular contents and to recycle nutrients, which is controlled by many factors. Disordered autophagy has been reported to be associated with various diseases, such as cancer, neurodegeneration, aging, and obesity. Autophagy cannot be directly controlled and dynamic amino acid levels are sufficient to regulate autophagy. To date, arginine, leucine, glutamine, and methionine are widely reported functional amino acids that regulate autophagy. As a signal relay station, mammalian target of rapamycin complex 1 (mTORC1) turns various amino acid signals into autophagy signaling pathways for functional amino acids. Deficiency or supplementation of functional amino acids can immediately regulate autophagy and is associated with autophagy-related disease. This review summarizes the mechanisms currently involved in autophagy and amino acid sensing, diverse signal transduction among functional amino acids and autophagy, and the therapeutic appeal of amino acids to autophagy-related diseases. We aim to provide a comprehensive overview of the mechanisms of amino acid regulation of autophagy and the role of functional amino acids in clinical autophagy-related diseases and to further convert these mechanisms into feasible therapeutic applications.
    Keywords autophagy ; autophagy-related diseases ; functional amino acids ; mTORC1 ; signal transduction ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
    Language English
    Publishing date 2021-10-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: M-Polynomial and Topological Indices of Benzene Ring Embedded in P-Type Surface Network

    Hong Yang / A. Q. Baig / W. Khalid / Mohammad Reza Farahani / Xiujun Zhang

    Journal of Chemistry, Vol

    2019  Volume 2019

    Abstract: The representation of chemical compounds and chemical networks with the M-polynomials is a new idea, and it gives nice and good results of the topological indices. These results are used to correlate the chemical compounds and chemical networks with ... ...

    Abstract The representation of chemical compounds and chemical networks with the M-polynomials is a new idea, and it gives nice and good results of the topological indices. These results are used to correlate the chemical compounds and chemical networks with their chemical properties and bioactivities. In this article, particular attention will be put on the derivation of M-polynomial for the benzene ring embedded in the P-type surface network in 2D. Furthermore, the topological indices based on the degrees are also derived by using the general form of M-polynomial of the benzene ring embedded in the P-type surface network BRm,n. In the end, the graphical representation and comparison of the M-polynomial and the topological indices of the benzene ring embedded in the P-type surface network in 2D are described.
    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher Hindawi Limited
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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