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International Journal of Biological Sciences

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https://www.readbyqxmd.com/read/29989106/special-issue-on-computational-resources-and-methods-in-biological-sciences
#1
EDITORIAL
Hao Lin, Shaoliang Peng, Jian Huang
This special issue covers a wide range of topics in computational biology, such as database construction, sequence analysis and function prediction with machine learning methods, disease-related diagnosis, drug-target and drug discovery, and electronic health record system construction.
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989105/an-inhibitor-of-casein-kinase-1%C3%AE%C2%B5-%C3%AE-pf670462-prevents-the-deterioration-of-dextran-sodium-sulfate-induced-ulcerative-colitis-caused-by-uvb-eye-irradiation
#2
Keiichi Hiramoto, Yurika Yamate, Emiko Kasahara, Eisuke F Sato
Although we previously reported the exacerbation of dextran sodium sulfate (DSS)-induced ulcerative colitis by ultraviolet (UV) B eye irradiation, we do not yet understand the mechanism behind this phenomenon. In this study, we examined the relationship between the deterioration of DSS-induced ulcerative colitis and clock genes. We induced a mouse model of ulcerative colitis by administering DSS for 5 days, and administered UVB eye irradiation on each day of the DSS treatment period. The DSS-induced ulcerative colitis was deteriorated by the UVB eye irradiation...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989104/classification-of-sputum-sounds-using-artificial-neural-network-and-wavelet-transform
#3
Yan Shi, Guoliang Wang, Jinglong Niu, Qimin Zhang, Maolin Cai, Baoqing Sun, Dandan Wang, Mei Xue, Xiaohua Douglas Zhang
Sputum sounds are biological signals used to evaluate the condition of sputum deposition in a respiratory system. To improve the efficiency of intensive care unit (ICU) staff and achieve timely clearance of secretion in patients with mechanical ventilation, we propose a method consisting of feature extraction of sputum sound signals using the wavelet transform and classification of sputum existence using artificial neural network (ANN). Sputum sound signals were decomposed into the frequency subbands using the wavelet transform...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989103/overexpression-of-toll-like-receptor-4-linked-mitogen-activated-protein-kinase-signaling-contributes-to-internalization-of-escherichia-coli-in-sheep
#4
Sutian Wang, Yang Cao, Shoulong Deng, Xiaojing Jiang, Jiahao Wang, Xiaosheng Zhang, Jinlong Zhang, Guoshi Liu, Zhengxing Lian
Escherichia coli is one of the most common causal pathogens of mastitis in milk-producing mammals. Toll-like receptor 4 (TLR4) is important for host recognition of this bacteria. Increased activation of TLR4 can markedly enhance the internalization of E. coli . In this study, the relationship between TLR4 and mitogen-activated protein kinase (MAPK) signaling pathways in mediating E. coli internalization was evaluated in sheep monocytes. Using a TLR4-overexpressing transgenic (Tg) sheep model, we explored the bacterial internalization mechanism in sheep...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989102/translational-bioinformatics-for-cholangiocarcinoma-opportunities-and-challenges
#5
REVIEW
Fuliang Qian, Junping Guo, Zhi Jiang, Bairong Shen
Translational bioinformatics is becoming a driven force and a new scientific paradigm for cancer research in the era of big data. To promote the cross-disciplinary communication and research, we take cholangiocarcinoma as an example to review the present status and the future perspectives of the bioinformatics models applied in cancer study. We first summarize the present application of computational methods to the study of cholangiocarcinoma ranged from pattern recognition of biological data, knowledge based data annotation to systems biological level modeling and clinical translation...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989101/computational-design-of-antiangiogenic-peptibody-by-fusing-human-igg1-fc-fragment-and-hrh-peptide-structural-modeling-energetic-analysis-and-dynamics-simulation-of-its-binding-potency-to-vegf-receptor
#6
Lin Ning, Zhongyan Li, Zhengya Bai, Shasha Hou, Bifang He, Jian Huang, Peng Zhou
Peptibodies represent a new class of biological therapeutics with combination of peptide activity and antibody-like properties. Previously, we discovered a novel peptide HRH that exhibited a dose-dependent angiogenesis-suppressing effect by targeting vascular endothelial growth factor receptors (VEGFRs). Here, we computationally designed an antiangiogenic peptibody, termed as PbHRH, by fusing the HRH peptide to human IgG1 Fc fragment using the first approved peptibody drug Romiplostim as template. The biologically active peptide of Romiplostim is similar with HRH peptide; both of them have close sequence lengths and can fold into a α-helical conformation in free state...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989100/zika-virus-envelope-protein-induces-g2-m-cell-cycle-arrest-and-apoptosis-via-an-intrinsic-cell-death-signaling-pathway-in-neuroendocrine-pc12-cells
#7
Jun Liu, Qingqing Li, Xiaoxin Li, Zhenzhen Qiu, Andrew Li, Wenhan Liang, Huangyao Chen, Xiangsheng Cai, Xinglu Chen, Xinyue Duan, Jingjing Li, Wangsheng Wu, Mingyu Xu, Yingying Mao, Huiying Chen, Jinlong Li, Weiwang Gu, Hongwei Li
Clinical evidence suggests that there exists a strong correlation between Zika virus (ZIKV) infection and abnormal development of the nervous system. However, the underlying mechanisms remain to be elusive. In this study, recombinant lentiviral vectors coding for ZIKV structural proteins and truncations (prM-Env, M-Env and Env) were transduced into PC12 cells. Envelope (Env) overexpression induced significant inhibition of proliferation and triggered G2/M cell cycle arrest and apoptosis in PC12 cells. Flow cytometry and western blot analysis showed that the apoptosis was associated with up-regulation of both p53 and p21Cip1/Waf1 and down-regulation of cyclin B1...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989099/non-coding-rna-linked-epigenetic-regulation-in-cardiac-hypertrophy
#8
REVIEW
Yanhan Dong, Sheng Xu, Jing Liu, Murugavel Ponnusamy, Yanfang Zhao, Yanhui Zhang, Qi Wang, Peifeng Li, Kun Wang
Cardiac hypertrophy is an adaptive enlargement of myocardium in response to pressure overload caused various pathological insults, which is accompanied by alteration of a complex cascade of signaling pathways. During the hypertrophy process, many changes occur at cellular level including gene reprogramming by turning off chromatin regulators. Studies from the past decade have demonstrated that the abnormal epigenetic modifications, such as DNA methylation, histone modification, and oxidative modification of nucleic acid, could lead to changes in chromosome structure and cardiac dysfunction...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989098/genome-wide-analyses-on-single-disease-samples-for-potential-biomarkers-and-biological-features-of-molecular-subtypes-a-case-study-in-gastric-cancer
#9
Wei Zeng, Nini Rao, Qian Li, Guangbin Wang, Dingyun Liu, Zhengwen Li, Yuntao Yang
Purpose: Based on the previous 3 well-defined subtypes of gastric adenocarcinoma (invasive, proliferative and metabolic), we aimed to find potential biomarkers and biological features of each subtype. Methods: The genome-wide co-expression network of each subtype of gastric cancer was firstly constructed. Then, the functional modules in each genome-wide co-expression network were divided. Next, the key genes were screened from each functional module. Finally, the enrichment analysis was performed on the key genes to mine the biological features of each subtype...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989096/ptm-ssmp-a-web-server-for-predicting-different-types-of-post-translational-modification-sites-using-novel-site-specific-modification-profile
#10
Yu Liu, Minghui Wang, Jianing Xi, Fenglin Luo, Ao Li
Protein post-translational modifications (PTMs) are chemical modifications of a protein after its translation. Owing to its play an important role in deep understanding of various biological processes and the development of effective drugs, PTM site prediction have become a hot topic in bioinformatics. Recently, many online tools are developed to prediction various types of PTM sites, most of which are based on local sequence and some biological information. However, few of existing tools consider the relations between different PTMs for their prediction task...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989095/microshare-privacy-preserved-medical-resource-sharing-through-microservice-architecture
#11
Yilong Yang, Quan Zu, Peng Liu, Defang Ouyang, Xiaoshan Li
This paper takes up the problem of medical resource sharing through MicroService architecture without compromising patient privacy. To achieve this goal, we suggest refactoring the legacy EHR systems into autonomous MicroServices communicating by the unified techniques such as RESTFul web service. This lets us handle clinical data queries directly and far more efficiently for both internal and external queries. The novelty of the proposed approach lies in avoiding the data de-identification process often used as a means of preserving patient privacy...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989093/an-investigation-of-the-distribution-and-location-of-mast-cells-affected-by-the-stiffness-of-substrates-as-a-mechanical-niche
#12
Hong-Wei Yang, Xin-Yue Liu, Zhou-Feng Shen, Wei Yao, Xiao-Bo Gong, Hua-Xiong Huang, Guang-Hong Ding
The distribution and location of mast cells are closely related to their physiological and pathological functions, such as allergic responses, immunity, and fibrosis, and are used in acupuncture. In this study, the distribution of mast cells in vivo was observed, and mechanical clues for understanding their distribution based on mechanical niches were explored. By toluidine blue staining and immunohistochemical staining, we examined the distribution and location of mast cells in rat skin and found that mast cells are distributed in a spatially nonuniform manner, preferring to locate at regions in the tissue and extracellular matrix with stiffness changes...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989092/ccl2-sqstm1-positive-feedback-loop-suppresses-autophagy-to-promote-chemoresistance-in-gastric-cancer
#13
Wenxia Xu, Qi Wei, Mengjiao Han, Bingluo Zhou, Hanying Wang, Jianbing Zhang, Qiang Wang, Jie Sun, Lifeng Feng, Shouyu Wang, Yang Ye, Xian Wang, Jianwei Zhou, Hongchuan Jin
Chemotherapy is one of the most important approaches for the treatment of various cancers. However, tumor cells often develop resistance to chemotherapeutic drugs. The tumor microenvironment reconstituted by various cytokines secreted from immune cells was recently found to play important roles in affecting therapeutic response of tumor cells. Herein, we reported that tumor cells can secrete autocrine cytokines to confer chemoresistance by inactivating proapoptotic autophagy. Through cytokine screening, we found that drug resistant cancer cells secreted more CCL2 than drug sensitive cells...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989091/ricyerdb-a-database-for-collecting-rice-yield-related-genes-with-biological-analysis
#14
Jing Jiang, Fei Xing, Xiangxiang Zeng, Quan Zou
The Rice Yield-related Database (RicyerDB) was created to complement with related research of influence rice (Oryza sativa L.) yield in multiple traits by manually curating the related databases and literature, and genomics and proteomics information that could be useful for comprehensive understanding of the rice biology. RicyerDB provides a more valuable resource in which to efficiently investigate, browse and analyze yield-related genes. The whole data set can be easily queried and downloaded through the webpage...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989090/a-comprehensive-review-of-web-based-resources-of-non-coding-rnas-for-plant-science-research
#15
REVIEW
Peiran Liao, Shipeng Li, Xiuming Cui, Yun Zheng
Non-coding RNAs (ncRNAs) are transcribed from genome but not translated into proteins. Many ncRNAs are key regulators of plants growth and development, metabolism and stress tolerance. In order to make the web-based ncRNA resources for plant science research be more easily accessible and understandable, we made a comprehensive review for 83 web-based resources of three types, including genome databases containing ncRNA data, microRNA (miRNA) databases and long non-coding RNA (lncRNA) databases. To facilitate effective usage of these resources, we also suggested some preferred resources of miRNAs and lncRNAs for performing meaningful analysis...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989089/research-on-folding-diversity-in-statistical-learning-methods-for-rna-secondary-structure-prediction
#16
Yu Zhu, ZhaoYang Xie, YiZhou Li, Min Zhu, Yi-Ping Phoebe Chen
How to improve the prediction accuracy of RNA secondary structure is currently a hot topic. The existing prediction methods for a single sequence do not fully consider the folding diversity which may occur among RNAs with different functions or sources. This paper explores the relationship between folding diversity and prediction accuracy, and puts forward a new method to improve the prediction accuracy of RNA secondary structure. Our research investigates the following: 1. The folding feature based on stochastic context-free grammar is proposed...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989088/identification-of-inhibitors-of-mmps-enzymes-via-a-novel-computational-approach
#17
Jian Song, Jijun Tang, Fei Guo
Matrix metalloproteases (MMPs) are a family of zinc-dependent proteinases that play complex and diverse roles in metabolism, which are vital for physiological development. In this paper, we present a novel method to identify peptide binding to seven matrix metalloproteases. First, we propose a novel sampling criteria for constructing a training set for each new peptide motif. Then, we select nine physicochemical properties of amino acids and compute their auto-cross covariance to effectively extract features for both natural and non-natural amino acids...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989085/hbpred-a-tool-to-identify-growth-hormone-binding-proteins
#18
Hua Tang, Ya-Wei Zhao, Ping Zou, Chun-Mei Zhang, Rong Chen, Po Huang, Hao Lin
Hormone-binding protein (HBP) is a kind of soluble carrier protein and can selectively and non-covalently interact with hormone. HBP plays an important role in life growth, but its function is still unclear. Correct recognition of HBPs is the first step to further study their function and understand their biological process. However, it is difficult to correctly recognize HBPs from more and more proteins through traditional biochemical experiments because of high experimental cost and long experimental period...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989084/integrated-multifactor-analysis-explores-core-dysfunctional-modules-in-autism-spectrum-disorder
#19
Yan Huang, Zhenghong Chang, Xiaodan Li, Shuang Liang, Ying Yi, Lijie Wu
Autism spectrum disorder (ASD) is a complex neurodevelopmental disease in early childhood, and growing up to be a major cause of disability in children. However, the underlying molecular mechanism of ASD remains elusive. Hence, we represented integrated multifactor analysis exploring dysfunctional modules based on RNA-Seq data from corpus callosum in 6 patients with ASD and 6 normal individuals. According to protein-protein interactions (PPIs) and WGCNA, we performed co-expression modules analysis for ASD-associated genes, and identified 25 modules with differentially expressed genes (DEGs), observing that genes in these modules were significantly involved in various biological processes in nervous system, sensory system, phylogenetic system and variety of signaling pathways...
2018: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29989083/irspot-pse6nc-identifying-recombination-spots-in-saccharomyces-cerevisiae-by-incorporating-hexamer-composition-into-general-pseknc
#20
Hui Yang, Wang-Ren Qiu, Guoqing Liu, Feng-Biao Guo, Wei Chen, Kuo-Chen Chou, Hao Lin
Meiotic recombination caused by meiotic double-strand DNA breaks. In some regions the frequency of DNA recombination is relatively higher, while in other regions the frequency is lower: the former is usually called "recombination hotspot", while the latter the "recombination coldspot". Information of the hot and cold spots may provide important clues for understanding the mechanism of genome revolution. Therefore, it is important to accurately predict these spots. In this study, we rebuilt the benchmark dataset by unifying its samples with a same length (131 bp)...
2018: International Journal of Biological Sciences
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