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Yimin Wang, Fang Ye, Chanyan Huang, Faling Xue, Yingyuan Li, Shaowei Gao, Zeting Qiu, Si Li, Qinchang Chen, Huaqiang Zhou, Yiyan Song, Wenqi Huang, Wulin Tan, Zhongxing Wang
BACKGROUND: Neuropathic pain is one of the common complications after spinal cord injury (SCI), affecting patients' life quality. The molecular mechanism for neuropathic pain after SCI is still unclear. We aimed to discover potential genes and MicroRNAs(miRNAs) related to neuropathic pain by bioinformatics method. METHODS: Microarray data of GSE69901 were obtained from Gene Expression Omnibus (GEO) database. Peripheral blood samples from patients with or without neuropathic pain after spinal cord injury (SCI) were collected...
March 15, 2018: Clinical Journal of Pain
Quan Zhou, Li Hong, Jing Wang
PURPOSE: The aim of this study was to elucidate the molecular mechanisms and to identify the key genes and pathways for pelvic organ prolapse (POP) using bioinformatics analysis. METHODS: The microarray data for GSE53868 included 12 POP and 12 non-POP anterior vaginal wall samples. Differentially expressed genes (DEGs) were identified by GEO2R online tool. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed using the DAVID database, and a DEG-associated protein-protein interaction (PPI) network was constructed using STRING and visualized in Cytoscape...
March 15, 2018: Archives of Gynecology and Obstetrics
Zhong Ni, Xiting Wang, Tianchen Zhang, Linlin Li, Jianxue Li
Small cell lung cancer (SCLC) is the subtype of lung cancer with the highest degree of malignancy and the lowest degree of differentiation. The purpose of this study was to investigate the molecular mechanisms of SCLC using bioinformatics analysis, and to provide new ideas for the early diagnosis and targeted therapy of SCLC. Microarray data were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) in SCLC were compared with the normal lung samples and identified. Gene Ontology (GO) function and pathway analysis of DEGs was performed through the DAVID database...
April 2018: Experimental and Therapeutic Medicine
Yan Zheng, Liwei Liu, Jifeng Ye
Type 1 diabetes is a prevalent autoimmune disease of which the underlying mechanisms remain to be elucidated. The aim of the study was to identify dysregulated modules of type 1 diabetes. After microarray data were preprocessed, 20,545 genes were obtained. By integrating gene expression data and protein-protein interactions (PPI) data, 48,778 new networks were obtained, including 7,953 genes. After simplifying networks, we obtained 24 target networks. By ranking networks with P-values, two modules with P<0...
April 2018: Experimental and Therapeutic Medicine
Javier Molina-Infante, Carolina Gutierrez-Junquera, Edoardo Savarino, Roberto Penagini, Ines Modolell, Ottavia Bartolo, Alicia Prieto-García, Aurelio Mauro, Javier Alcedo, Antonia Perelló, Carlos Guarner-Argente, Noelia Alcaide, Ana M Vegas, Patricia Barros-García, Marianette Murzi-Pulgar, Monica Perona, Javier P Gisbert, Alfredo J Lucendo
OBJECTIVES: Rising trends in eosinophilic esophagitis (EoE) have been repeatedly linked to declining Helicobacter pylori (H. pylori) infection, mostly in retrospective studies. We aimed to prospectively evaluate this inverse association. METHODS: Prospective case-control study conducted in 23 centers. Children and adults naïve to eradication therapy for H. pylori were included. Cases were EoE patients, whereas controls were defined by esophageal symptoms and <5 eos/HPF on esophageal biopsies...
March 15, 2018: American Journal of Gastroenterology
Igor Poltavsky, Robert A DiStasio, Alexandre Tkatchenko
Nuclear quantum effects (NQE), which include both zero-point motion and tunneling, exhibit quite an impressive range of influence over the equilibrium and dynamical properties of molecules and materials. In this work, we extend our recently proposed perturbed path-integral (PPI) approach for modeling NQE in molecular systems [I. Poltavsky and A. Tkatchenko, Chem. Sci. 7, 1368 (2016)], which successfully combines the advantages of thermodynamic perturbation theory with path-integral molecular dynamics (PIMD), in a number of important directions...
March 14, 2018: Journal of Chemical Physics
Bipin Balan, Ana M Ibáñez, Abhaya M Dandekar, Tiziano Caruso, Federico Martinelli
A bioinformatic analysis of previously published RNA-Seq studies on Huanglongbing (HLB) response and tolerance in leaf tissues was performed. The aim was to identify genes commonly modulated between studies and genes, pathways and gene set categories strongly associated with this devastating Citrus disease. Bioinformatic analysis of expression data of four datasets present in NCBI provided 46-68 million reads with an alignment percentage of 72.95-86.76%. Only 16 HLB-regulated genes were commonly identified between the three leaf datasets...
2018: Frontiers in Plant Science
Yan Xue, Xianghong Qin, Liya Zhou, Sanren Lin, Ling Wang, Haitang Hu, Jielai Xia
AIM AND BACKGROUND: Proton pump inhibitors (PPIs) are the main drugs for the treatment of reflux esophagitis. Phase II clinical trials showed that, compared with Esomeprazole, the new PPI Ilaparazole is great in terms of efficacy for reflux symptoms relief and curling for esophagitis. The aim of this study was to confirm suitable dose of Ilaparazole in the treatment of reflux esophagitis. METHODS: This study used a randomized, double-blind, parallel positive drug control, multi-center design...
March 11, 2018: Contemporary Clinical Trials
Mariette Andersson, Helle Turesson, Stéphanie Arrivault, Youjun Zhang, Ann-Sofie Fält, Alisdair R Fernie, Per Hofvander
The importance of a plastidial soluble inorganic pyrophosphatase (psPPase) and an ATP/ADP translocator (NTT) for starch composition and tuber formation in potato (Solanum tuberosum) was evaluated by individual and simultaneous down-regulation of the corresponding endogenous genes. Starch and amylose content of the transgenic lines were considerably lower, and granule size substantially smaller, with down-regulation of StpsPPase generating the most pronounced effects. Single-gene down-regulation of either StpsPPase or StNTT resulted in increased tuber numbers per plant and higher fresh weight yield...
March 10, 2018: Journal of Experimental Botany
Hongfang Li, Yuzhi Zhen, Yunshuang Geng, Junyan Feng, Jun Wang, Hongsong Zhang
BACKGROUND The aim of this study was to identify some key genes related to the pathogenesis of thoracic aortic aneurysm (TAA) and gain more insights to the molecular mechanism of TAA. MATERIAL AND METHODS The expression profile of GSE9106 was downloaded from the Gene Expression Omnibus (GEO) database. The data contained 58 TAA peripheral blood samples and 36 normal peripheral blood samples. The differently expressed genes (DEGs) between the TAA samples and the normal samples were identified via limma package of R...
March 14, 2018: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
Linda E Flinterman, Karin Hek, Joke C Korevaar, Liset van Dijk
Governments have several options to reduce the increasing costs of health care, including restrictions for the reimbursement of medicines. Next to the intended effect of reduced costs for medicines, reimbursement restriction can have unintended effects such as patients refraining from their treatment which may lead to health problems and increased use of health care. An example of a reimbursement restriction is the one for proton pump inhibitors (PPIs) that became effective in the Netherlands in January 2012...
2018: Frontiers in Public Health
Anupriya Razdan, Ramaswamy Viswanathan, Alan Tusher
Background: Proton pump inhibitors (PPIs) are frequently prescribed antiulcer agents in hospitals and are shown to be safer than H-2 blockers. We present a case report of PPI-induced delirium, regarding which not much has been written in the literature. Case Report: We present a case of a 93-year-old woman with no known past psychiatric history, who was hospitalized for syncope workup and who developed delirium after a double dose of pantoprazole. Discussion: Very few reports of PPI-induced delirium exist in the literature...
2018: Case Reports in Psychiatry
Y Wang, W Guo, H Xu, X Zhu, T Yu, Z Jiang, Q Jiang, X Gang
The study aimed to identify the pivotal genes and pathways involved in prostate cancer metastasis. Using the expression profile dataset GSE7930, downloaded from the Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) between primary and highly metastatic prostate cell samples were screened, followed by functional analysis and tumor associated genes (TAG) screening. Protein-protein interaction (PPI) network of DEGs was constructed and module analysis was performed. The expression of DEGs and pathway related genes were evaluated by PCR analysis and the migra- tion ability of prostate tumor cells was observed after FABP4-siRNA blocking...
2018: Neoplasma
F Wu, S Wu, X Gou
Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer in adults. The aim of this study is to identify the biomarkers and potential molecular mechanisms of ccRCC. Three gene expression profiles and two miRNA expression profiles were downloaded from GEO database. A total of 330 up-regulated differentially expressed genes (DEGs), 545 down-regulated DEGs, 26 up-regulated differentially expressed miRNAs (DEMs) and 11 down-regulated DEMs were identified by GEO2R. The gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed by KOBAS software...
2018: Neoplasma
Shoji Segami, Mariko Asaoka, Satoru Kinoshita, Mayu Fukuda, Yoichi Nakanishi, Masayoshi Maeshima
Proton-translocating inorganic pyrophosphatase (H+-PPase) actively translocates protons across membranes coupled with the hydrolysis of inorganic pyrophosphate (PPi). H+-PPase, which is composed of a single protein and uses a simple compound as a substrate, has been recognized as a new type of ion pump in addition to the P-, F-, and V-type ion translocating ATPases. H+- and Na+-PPases are distributed in various organisms including plants, parasitic protozoa, Archaebacteria, and bacteria, but are not present in animals or yeast...
March 9, 2018: Plant & Cell Physiology
Sayan Poddar, Devlina Chakravarty, Pinak Chakrabarti
Characterization and prediction of the DNA-biding regions in proteins are essential for our understanding of how proteins recognize/bind DNA. We analyze the unbound (U) and the bound (B) forms of proteins from the protein-DNA docking benchmark that contains 66 binary protein-DNA complexes along with their unbound counterparts. Proteins binding DNA undergo greater structural changes on complexation (in particular, those in the enzyme category) than those involved in protein-protein interactions (PPI). While interface atoms involved in PPI exhibit an increase in their solvent-accessible surface area (ASA) in the bound form in the majority of the cases compared to the unbound interface, protein-DNA interactions indicate increase and decrease in equal measure...
March 9, 2018: Nucleic Acids Research
Thomas Walther, Ganesh Manoharan, Axel Linke, Helge Möllmann, David Holzhey, Stephen G Worthley, Won-Keun Kim, Ulrich Schäfer
OBJECTIVES: To examine the incidence and timing of new-onset left bundle branch block (LBBB) and new permanent pacemaker implantation (PPI) in patients undergoing transcatheter aortic valve implantation (TAVI) using the repositionable, self-expanding Portico™ TAVI system (St. Jude Medical, St Paul, MN, USA). Clinical impact and periprocedural factors associated with new PPI were also assessed. METHODS: A total of 198 high-risk patients without pre-existing pacemaker [83...
March 9, 2018: European Journal of Cardio-thoracic Surgery
M Wolf, M Ao, M B Chavez, T N Kolli, V Thumbigere-Math, K Becker, E Y Chu, A Jäger, M J Somerman, B L Foster
Previous studies revealed that cementum formation is tightly regulated by inorganic pyrophosphate (PPi ), a mineralization inhibitor. Local PPi concentrations are determined by regulators, including ectonucleotide pyrophosphatase/phosphodiesterase 1 (ENPP1), which increases PPi concentrations by adenosine triphosphate hydrolysis. Orthodontic forces stimulate alveolar bone remodelling, leading to orthodontic tooth movement (OTM). To better understand how disturbed mineral metabolism and the resulting altered periodontal structures affect OTM, we employed Enpp1 mutant mice that feature reduced PPi and increased cervical cementum in a model of OTM induced by a stretched closed-coil spring ligated between the maxillary left first molar and maxillary incisors...
March 1, 2018: Journal of Dental Research
Lixin Cheng, Pengfei Liu, Kwong-Sak Leung
Computational clustering methods help identify functional modules in protein-protein interaction (PPI) network, in which proteins participate in the same biological pathways or specific functions. Subcellular localisation is crucial for proteins to implement biological functions and each compartment accommodates specific portions of the protein interaction structure. However, the importance of protein subcellular localisation is often neglected in the studies of module identification. In this study, the authors propose a novel procedure, subcellular module identification with localisation expansion (SMILE), to identify super modules that consist of several subcellular modules performing specific biological functions among cell compartments...
April 2018: IET Systems Biology
Guangming Liu, Bianfang Chai, Kuo Yang, Jian Yu, Xuezhong Zhou
A large amount of available protein-protein interaction (PPI) data has been generated by high-throughput experimental techniques. Uncovering functional modules from PPI networks will help us better understand the underlying mechanisms of cellular functions. Numerous computational algorithms have been designed to identify functional modules automatically in the past decades. However, most community detection methods (non-overlapping or overlapping types) are unsupervised models, which cannot incorporate the well-known protein complexes as a priori...
April 2018: IET Systems Biology
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