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Network analysis and COPD

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https://www.readbyqxmd.com/read/28438154/network-based-analysis-reveals-novel-gene-signatures-in-peripheral-blood-of-patients-with-chronic-obstructive-pulmonary-disease
#1
Ma'en Obeidat, Yunlong Nie, Virginia Chen, Casey P Shannon, Anand Kumar Andiappan, Bernett Lee, Olaf Rotzschke, Peter J Castaldi, Craig P Hersh, Nick Fishbane, Raymond T Ng, Bruce McManus, Bruce E Miller, Stephen Rennard, Peter D Paré, Don D Sin
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is currently the third leading cause of death and there is a huge unmet clinical need to identify disease biomarkers in peripheral blood. Compared to gene level differential expression approaches to identify gene signatures, network analyses provide a biologically intuitive approach which leverages the co-expression patterns in the transcriptome to identify modules of co-expressed genes. METHODS: A weighted gene co-expression network analysis (WGCNA) was applied to peripheral blood transcriptome from 238 COPD subjects to discover co-expressed gene modules...
April 24, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28396329/outcomes-of-patients-with-chronic-obstructive-pulmonary-disease-diagnosed-with-or-without-pulmonary-function-testing
#2
Andrea Gershon, Graham Mecredy, Ruth Croxford, Teresa To, Matthew B Stanbrook, Shawn D Aaron
BACKGROUND: A small number of people with chronic obstructive pulmonary disease (COPD) receive pulmonary function testing around the time of diagnosis. Because omitting testing increases misdiagnosis, we sought to determine whether health outcomes differed between patients whose COPD was diagnosed with or without pulmonary function testing. METHODS: We conducted a longitudinal population study of patients with physician-diagnosed COPD from 2005 to 2012 using health administrative data from Ontario, Canada...
April 10, 2017: CMAJ: Canadian Medical Association Journal, Journal de L'Association Medicale Canadienne
https://www.readbyqxmd.com/read/28334727/discovering-the-relative-efficacy-of-inhaled-medications-for-chronic-obstructive-pulmonary-disease-multiple-treatment-comparisons
#3
Ying Zhu, Tong Zhang, Haiyan Li, Yang Yang, Qiong Chen, Lei Kong, Bo Tai
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is managed by three major classes of inhaled medications: inhaled corticosteroids (ICS), long-acting Beta 2-agonist (LABA), long-acting muscarinic antagonist (LAMA). Single inhaled medication is usually replaced by combined inhaled medications for efficacy enhancement. However, this practice should be supported by clinical evidence for large-scale implementations. METHODS: The relative efficacy of inhaled medications is determined by three endpoints: changes in the trough forced expiratory volume in 1 second (tFEV1), changes in the St George's Respiratory Questionnaire (SGRQ) score and the proportion of SGRQ responders which represents a reduction in SGRQ total score at week 24 of ≥4...
March 27, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28287180/functional-interactors-of-three-genome-wide-association-study-genes-are-differentially-expressed-in-severe-chronic-obstructive-pulmonary-disease-lung-tissue
#4
Jarrett D Morrow, Xiaobo Zhou, Taotao Lao, Zhiqiang Jiang, Dawn L DeMeo, Michael H Cho, Weiliang Qiu, Suzanne Cloonan, Victor Pinto-Plata, Bartholome Celli, Nathaniel Marchetti, Gerard J Criner, Raphael Bueno, George R Washko, Kimberly Glass, John Quackenbush, Augustine M K Choi, Edwin K Silverman, Craig P Hersh
In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28271730/recent-mass-spectrometry-based-proteomics-for-biomarker-discovery-in-lung-cancer-copd-and-asthma
#5
Kiyonaga Fujii, Haruhiko Nakamura, Toshihide Nishimura
Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made it possible to analyze disease-relevant proteins expressed in clinical specimens by proteomic challenges. Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches...
March 17, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28206676/thoracic-ct-mri-co-registration-for-regional-pulmonary-structure-function-measurements-of-obstructive-lung-disease
#6
Fumin Guo, Sarah Svenningsen, Miranda Kirby, Dante P I Capaldi, Khadija Sheikh, Aaron Fenster, Grace Parraga
PURPOSE: Recent pulmonary imaging research has revealed that in patients with chronic obstructive pulmonary disease (COPD) and asthma, structural and functional abnormalities are spatially heterogeneous. This novel information may help optimize treatment in individual patients, monitor interventional efficacy and develop new treatments. Moreover, by automating the measurement of regional biomarkers for the 19 different anatomical lung segments, there is an opportunity to embed imaging biomarkers into clinically-acceptable clinical workflows and improve lung disease clinical care...
February 16, 2017: Medical Physics
https://www.readbyqxmd.com/read/28190672/-bibliometric-analysis-of-iberpoc-and-epi-scan-studies-contribution-of-the-smoking-variable-on-the-iberpoc-study
#7
J I de Granda-Orive, A Alonso-Arroyo, D López-Padilla, G Segrelles-Calvo, C A Jiménez-Ruiz, S Solano-Reina
OBJECTIVES: The aim of this study was to perform a bibliometric analysis of EPI-SCAN and IBERPOC studies using the Science Citation Index and Scopus databases, and to determine the overall impact with the impact of smoking on IBERPOC as a secondary objective. METHOD: A general searching was conducted in Science Citation Index-Expanded through the Web of Science (WoS) (Thomson Reuters) platform and Scopus on 23 March 2015. The search strategy included the terms "iberpoc" OR "episcan" was performed on 15 October 2015...
February 9, 2017: Semergen
https://www.readbyqxmd.com/read/28185567/from-comorbidities-of-chronic-obstructive-pulmonary-disease-to-identification-of-shared-molecular-mechanisms-by-data-integration
#8
David Gomez-Cabrero, Jörg Menche, Claudia Vargas, Isaac Cano, Dieter Maier, Albert-László Barabási, Jesper Tegnér, Josep Roca
BACKGROUND: Deep mining of healthcare data has provided maps of comorbidity relationships between diseases. In parallel, integrative multi-omics investigations have generated high-resolution molecular maps of putative relevance for understanding disease initiation and progression. Yet, it is unclear how to advance an observation of comorbidity relations (one disease to others) to a molecular understanding of the driver processes and associated biomarkers. RESULTS: Since Chronic Obstructive Pulmonary disease (COPD) has emerged as a central hub in temporal comorbidity networks, we developed a systematic integrative data-driven framework to identify shared disease-associated genes and pathways, as a proxy for the underlying generative mechanisms inducing comorbidity...
November 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28176892/comparative-efficacy-of-long-acting-%C3%AE-2-agonists-as-monotherapy-for-chronic-obstructive-pulmonary-disease-a-network-meta-analysis
#9
James F Donohue, Keith A Betts, Ella Xiaoyan Du, Pablo Altman, Pankaj Goyal, Dorothy L Keininger, Jean-Bernard Gruenberger, James E Signorovitch
PURPOSE: Long-acting β2-agonists (LABAs) have demonstrated efficacy in patients with COPD in clinical trials. The purpose of this study was to assess the comparative efficacy of all available dosages of all LABA monotherapies using a network meta-analysis. METHODS: A systematic literature review identified 33 randomized controlled trials of LABA monotherapies (salmeterol 50 μg twice daily [BID]; formoterol 12 μg BID; indacaterol 75, 150, and 300 μg once daily [OD]; olodaterol 5 and 10 μg OD, and vilanterol 25 μg OD)...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28166215/genetic-loci-associated-with-chronic-obstructive-pulmonary-disease-overlap-with-loci-for-lung-function-and-pulmonary-fibrosis
#10
Brian D Hobbs, Kim de Jong, Maxime Lamontagne, Yohan Bossé, Nick Shrine, María Soler Artigas, Louise V Wain, Ian P Hall, Victoria E Jackson, Annah B Wyss, Stephanie J London, Kari E North, Nora Franceschini, David P Strachan, Terri H Beaty, John E Hokanson, James D Crapo, Peter J Castaldi, Robert P Chase, Traci M Bartz, Susan R Heckbert, Bruce M Psaty, Sina A Gharib, Pieter Zanen, Jan W Lammers, Matthijs Oudkerk, H J Groen, Nicholas Locantore, Ruth Tal-Singer, Stephen I Rennard, Jørgen Vestbo, Wim Timens, Peter D Paré, Jeanne C Latourelle, Josée Dupuis, George T O'Connor, Jemma B Wilk, Woo Jin Kim, Mi Kyeong Lee, Yeon-Mok Oh, Judith M Vonk, Harry J de Koning, Shuguang Leng, Steven A Belinsky, Yohannes Tesfaigzi, Ani Manichaikul, Xin-Qun Wang, Stephen S Rich, R Graham Barr, David Sparrow, Augusto A Litonjua, Per Bakke, Amund Gulsvik, Lies Lahousse, Guy G Brusselle, Bruno H Stricker, André G Uitterlinden, Elizabeth J Ampleford, Eugene R Bleecker, Prescott G Woodruff, Deborah A Meyers, Dandi Qiao, David A Lomas, Jae-Joon Yim, Deog Kyeom Kim, Iwona Hawrylkiewicz, Pawel Sliwinski, Megan Hardin, Tasha E Fingerlin, David A Schwartz, Dirkje S Postma, William MacNee, Martin D Tobin, Edwin K Silverman, H Marike Boezen, Michael H Cho
Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10(-6)) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new...
March 2017: Nature Genetics
https://www.readbyqxmd.com/read/28123294/global-scientific-collaboration-in-copd-research
#11
Yanbing Su, Chao Long, Qi Yu, Juan Zhang, Daisy Wu, Zhiguang Duan
PURPOSE: This study aimed to investigate the multiple collaboration types, quantitatively evaluate the publication trends and review the performance of institutions or countries (regions) across the world in COPD research. MATERIALS AND METHODS: Scientometric methods and social network analysis were used to survey the development of publication trends and understand current collaboration in the field of COPD research based on the Web of Science publications during the past 18 years...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28096283/laba-lama-combination-in-copd-a-meta-analysis-on-the-duration-of-treatment
#12
REVIEW
Luigino Calzetta, Paola Rogliani, Josuel Ora, Ermanno Puxeddu, Mario Cazzola, Maria Gabriella Matera
When there are no randomised clinical trials directly comparing all relevant treatment options, an indirect treatment comparison via meta-analysis of the available clinical evidence is an acceptable alternative. However, meta-analyses may be very misleading if not adequately performed. Here, we propose and validate a simple and effective approach to meta-analysis for exploring the effectiveness of long-acting β2-agonist (LABA)/long-acting muscarinic antagonist (LAMA) fixed-dose combinations in chronic obstructive pulmonary disease...
January 2017: European Respiratory Review: An Official Journal of the European Respiratory Society
https://www.readbyqxmd.com/read/28057018/bioinformatic-analysis-of-microrna-and-mrna-regulation-in-peripheral-blood-mononuclear-cells-of-patients-with-chronic-obstructive-pulmonary-disease
#13
Xiaomin Dang, Xiaoyan Qu, Weijia Wang, Chongbing Liao, Ying Li, Xiaojin Zhang, Dan Xu, Carolyn J Baglole, Dong Shang, Ying Chang
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a progressive, irreversible chronic inflammatory disorder typified by increased recruitment of monocytes, lymphocytes and neutrophils. Because of this, as well as the convenience of peripheral blood nuclear cells (PBMCs) assessments, miRNA profiling of PBMCs has drawn increasing attention in recent years for various disease. Therefore, we analyzed miRNA and mRNA profiles to understand their regulatory network between COPD subjects versus smokers without airflow limitation...
January 5, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28026794/classification-of-exacerbation-frequency-in-the-copdgene-cohort-using-deep-learning-with-deep-belief-networks
#14
Jun Ying, Joyita Dutta, Ning Guo, Chenhui Hu, Dan Zhou, Arkadiusz Sitek, Quanzheng Li
This study aims to develop an automatic classifier based on deep learning for exacerbation frequency in patients with chronic obstructive pulmonary disease (COPD). A threelayer deep belief network (DBN) with two hidden layers and one visible layer was employed to develop classification models and the models' robustness to exacerbation was analyzed. Subjects from the COPDGene cohort were labeled with exacerbation frequency, defined as the number of exacerbation events per year. 10,300 subjects with 361 features each were included in the analysis...
December 21, 2016: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28025995/prediction-of-key-genes-and-mirnas-responsible-for-loss-of-muscle-force-in-patients-during-an-acute-exacerbation-of-chronic-obstructive-pulmonary-disease
#15
Yanhong Duan, Min Zhou, Jian Xiao, Chaomin Wu, Lei Zhou, Feng Zhou, Chunling Du, Yuanlin Song
The present study aimed to identify genes and microRNAs (miRNAs or miRs) that were abnormally expressed in the vastus lateralis muscle of patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD). The gene expression profile of GSE10828 was downloaded from the Gene Expression Omnibus database, and this dataset was comprised of 4 samples from patients with AECOPD and 5 samples from patients with stable COPD. Differentially expressed genes (DEGs) were screened using the Limma package in R...
November 2016: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/27994450/how-do-general-practitioners-implement-decision-making-regarding-copd-patients-with-exacerbations-an-international-focus-group-study
#16
Johanna Laue, Hasse Melbye, Peder A Halvorsen, Elena A Andreeva, Maciek Godycki-Cwirko, Anja Wollny, Nick A Francis, Mark Spigt, Kenny Kung, Mette Bech Risør
PURPOSE: To explore the decision-making of general practitioners (GPs) concerning treatment with antibiotics and/or oral corticosteroids and hospitalization for COPD patients with exacerbations. METHODS: Thematic analysis of seven focus groups with 53 GPs from urban and rural areas in Norway, Germany, Wales, Poland, Russia, the Netherlands, and Hong Kong. RESULTS: Four main themes were identified. 1) Dealing with medical uncertainty: the GPs aimed to make clear medical decisions and avoid unnecessary prescriptions and hospitalizations, yet this was challenged by uncertainty regarding the severity of the exacerbations and concerns about overlooking comorbidities...
2016: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/27835945/external-validation-of-multidimensional-prognostic-indices-ado-bodex-and-dose-in-a-primary-care-international-cohort-proepoc-copd-cohort
#17
Maite Espantoso-Romero, Miguel Román Rodríguez, Ana Duarte-Pérez, Jaime Gonzálvez-Rey, Pedro A Callejas-Cabanillas, Durdica Kasuba Lazic, Berta Anta-Agudo, Pere Torán Monserrat, Rosa Magallon-Botaya, Biljana Gerasimovska Kitanovska, Heidrun Lingner, Radost S Assenova, Claudia Iftode, Francisco Gude-Sampedro, Ana Clavería
BACKGROUND: Due to the heterogeneous and systemic nature of the chronic obstructive pulmonary disease (COPD), the new guidelines are oriented toward individualized attention. Multidimensional scales could facilitate its proper clinical and prognostic assessment, but not all of them were validated in an international primary care cohort, different from the original ones used for model development. Therefore, our main aim is to assess the prognostic capacity of the ADO, BODEx and DOSE indices in primary care for predicting mortality in COPD patients and to validate the models obtained in subgroups of patients, classified by revised Global Initiative for Chronic Obstructive Lung Disease (2011) and updated Spanish Guideline (2014)...
November 11, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27829448/the-bronchial-epithelial-cell-bacterial-microbiome-and-host-response-in-patients-infected-with-human-immunodeficiency-virus
#18
Marc A Sze, Stella Xu, Janice M Leung, Emily A Vucic, Tawimas Shaipanich, Aida Moghadam, Marianne Harris, Silvia Guillemi, Sunita Sinha, Corey Nislow, Darra Murphy, Cameron Hague, Jonathon Leipsic, Stephen Lam, Wan Lam, Julio S Montaner, Don D Sin, S F Paul Man
BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is an important comorbidity in patients living with human immunodeficiency virus (HIV). Previous bacterial microbiome studies have shown increased abundance of specific bacterium, like Tropheryma whipplei, and no overall community differences. However, the host response to the lung microbiome is unknown in patients infected with HIV. METHODS: Two bronchial brush samples were obtained from 21 HIV-infected patients...
November 9, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27814717/differential-dna-methylation-marks-and-gene-comethylation-of-copd-in-african-americans-with-copd-exacerbations
#19
Robert Busch, Weiliang Qiu, Jessica Lasky-Su, Jarrett Morrow, Gerard Criner, Dawn DeMeo
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort...
November 5, 2016: Respiratory Research
https://www.readbyqxmd.com/read/27809917/gene-expression-network-analyses-in-response-to-air-pollution-exposures-in-the-trucking-industry
#20
Jen-Hwa Chu, Jaime E Hart, Divya Chhabra, Eric Garshick, Benjamin A Raby, Francine Laden
BACKGROUND: Exposure to air pollution, including traffic-related pollutants, has been associated with a variety of adverse health outcomes, including increased cardiopulmonary morbidity and mortality, and increased lung cancer risk. METHODS: To better understand the cellular responses induced by air pollution exposures, we performed genome-wide gene expression microarray analysis using whole blood RNA sampled at three time-points across the work weeks of 63 non-smoking employees at 10 trucking terminals in the northeastern US...
November 3, 2016: Environmental Health: a Global Access Science Source
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