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Network analysis and COPD

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/27794560/molecular-mechanisms-underlying-copd-muscle-dysfunction-unveiled-through-a-systems-medicine-approach
#9
Igor Marín de Mas, Eric Fanchon, Balázs Papp, Susana Kalko, Josep Roca, Marta Cascante
MOTIVATION: Skeletal muscle dysfunction is a systemic effect in one-third of patients with chronic obstructive pulmonary disease (COPD), characterized by high reactive-oxygen-species (ROS) production and abnormal endurance training-induced adaptive changes. However, the role of ROS in COPD remains unclear, not least because of the lack of appropriate tools to study multifactorial diseases. RESULTS: We describe a discrete model-driven method combining mechanistic and probabilistic approaches to decipher the role of ROS on the activity state of skeletal muscle regulatory network, assessed before and after an 8-week endurance training program in COPD patients and healthy subjects...
January 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/27730185/recommendations-to-improve-smoking-cessation-outcomes-from-people-with-lung-conditions-who-smoke
#10
Sarah Masefield, Pippa Powell, Carlos Jiménez-Ruiz, Peter Hajek, Keir Lewis, Stefan Andreas, Philip Tønnesen, Onno van Schayck, Christina Gratziou, Bertrand Dautzenberg, Serena Tonstad, Thomas Hering, Stephano Nardini, Monica Fletcher
This study aimed to gain insight into the impact of lung conditions on smoking behaviour and smoking cessation, and identify recommendations for smoking cessation and professional-patient communications. The study was led by the European Lung Foundation in collaboration with the European Respiratory Society Task Force on "Statement on smoking cessation on COPD and other pulmonary diseases and in smokers with comorbidities who find it difficult to quit". A web-based observational cross-sectional questionnaire was developed from a patient-centered literature review...
April 2016: ERJ Open Research
https://www.readbyqxmd.com/read/27660429/inflammatory-biomarkers-in-asthma-copd-overlap-syndrome
#11
Seiichi Kobayashi, Masakazu Hanagama, Shinsuke Yamanda, Masatsugu Ishida, Masaru Yanai
BACKGROUND: The clinical phenotypes and underlying mechanisms of asthma-COPD overlap syndrome (ACOS) remain elusive. This study aimed to investigate a comparison of COPD patients with and without ACOS, focusing on inflammatory biomarkers, in an outpatient COPD cohort. METHODS: We conducted a cross-sectional study analyzing prospectively collected data from the Ishinomaki COPD Network registry. All participants were diagnosed with COPD, confirmed by using spirometry, and were aged 40-90 years and former smokers...
2016: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/27618581/bipartite-community-structure-of-eqtls
#12
John Platig, Peter J Castaldi, Dawn DeMeo, John Quackenbush
Genome Wide Association Studies (GWAS) and expression quantitative trait locus (eQTL) analyses have identified genetic associations with a wide range of human phenotypes. However, many of these variants have weak effects and understanding their combined effect remains a challenge. One hypothesis is that multiple SNPs interact in complex networks to influence functional processes that ultimately lead to complex phenotypes, including disease states. Here we present CONDOR, a method that represents both cis- and trans-acting SNPs and the genes with which they are associated as a bipartite graph and then uses the modular structure of that graph to place SNPs into a functional context...
September 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27585677/molecular-modeling-of-gly80-and-ser80-variants-of-human-group-iid-phospholipase-a2-and-their-receptor-complexes-potential-basis-for-weight-loss-in-chronic-obstructive-pulmonary-disease
#13
Mohd Imran Khan, Ashish Kumar Gupta, Domada Ratna Kumar, Manoj Kumar, Abdul Samarth Ethayathulla, Gururao Hariprasad
Weight loss is a well known systemic manifestation of chronic obstructive pulmonary disease (COPD). A Gly80Ser mutation on human group IID secretory phospholipase A2 (sPLA2) enhances expression of the cytokines that are responsible for weight loss. In this study, we seek to establish a structural correlation of wild type sPLA2 and the Gly80Ser mutation with function. sPLA2 with glycine and serine at the 80th positions and the M-type receptor were modelled. The enzymes were docked to the receptor and molecular dynamics was carried out to 70 ns...
September 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27508494/susceptibility-to-childhood-pneumonia-a-genome-wide-analysis
#14
Lystra P Hayden, Michael H Cho, Merry-Lynn N McDonald, James D Crapo, Terri H Beaty, Edwin K Silverman, Craig P Hersh
: Previous studies have indicated that in adult smokers, a history of childhood pneumonia is associated with reduced lung function and chronic obstructive pulmonary disease. There have been few previous investigations using genome-wide association studies to investigate genetic predisposition to pneumonia. This study aims to identify the genetic variants associated with the development of pneumonia during childhood and over the course of the lifetime. Study subjects included current and former smokers with and without chronic obstructive pulmonary disease participating in the COPDGene Study...
January 2017: American Journal of Respiratory Cell and Molecular Biology
https://www.readbyqxmd.com/read/27487959/proton-pump-inhibitors-are-associated-with-increased-risk-of-development-of-chronic-kidney-disease
#15
Pradeep Arora, Anu Gupta, Mojgan Golzy, Nilang Patel, Randolph L Carter, Kabir Jalal, James W Lohr
BACKGROUND: Acute interstitial nephritis secondary to proton pump inhibitors (PPIs) frequently goes undiagnosed due to its subacute clinical presentation, which may later present as chronic kidney disease (CKD). We investigated the association of PPI use with the development of CKD and death. METHODS: Two separate retrospective case-control study designs were employed with a prospective logistic regression analysis of data to evaluate the association of development of CKD and death with PPI use...
August 3, 2016: BMC Nephrology
https://www.readbyqxmd.com/read/27461979/integrative-proteomic-analysis-reveals-reprograming-tumor-necrosis-factor-signaling-in-epithelial-mesenchymal-transition
#16
Yingxin Zhao, Bing Tian, Rovshan G Sadygov, Yueqing Zhang, Allan R Brasier
UNLABELLED: The airway epithelium is a semi-impermeable barrier whose disruption by growth factor reprogramming is associated with chronic airway diseases of humans. Transforming growth factor beta (TGFβ)-induced epithelial mesenchymal transition (EMT) plays important roles in airway remodeling characteristic of idiopathic lung fibrosis, asthma and chronic obstructive pulmonary disease (COPD). Inflammation of the airways leads to airway injury and tumor necrosis factor alpha (TNFα) plays an important pro-inflammatory role...
October 4, 2016: Journal of Proteomics
https://www.readbyqxmd.com/read/27437639/evaluating-the-utility-of-binax-now-streptococcus-pneumoniae-urinary-antigen-test-in-adults-with-community-acquired-pneumonia-in-china
#17
Fei Zhou, Li Gu, Jiuxin Qu, Yingmei Liu, Bin Cao
INTRODUCTION: Binax NOW rapid immunochromatographic membrane test (ICT), a rapid method for detection of Streptococcus pneumoniae antigen, has been used widely in Europe and America, but rarely in China. OBJECTIVE: Our aim is to evaluate the utility of the ICT among adult patients with community acquired pneumonia (CAP) in China. METHODS: Adult patients with CAP were prospectively recruited from 12 general hospitals. ICT tests were done in all patients and clinical data were recorded...
July 20, 2016: Clinical Respiratory Journal
https://www.readbyqxmd.com/read/27364603/the-copd-assessment-test-can-it-discriminate-across-copd-subpopulations
#18
N Gupta, L Pinto, A Benedetti, P Z Li, W Tan, S Aaron, K R Chapman, J M FitzGerald, P Hernandez, D Marciniuk, F Maltais, D O'Donnell, D Sin, B Walker, J Bourbeau
BACKGROUND: The COPD Assessment Test (CAT) is a valid disease specific questionnaire measuring health status. However, knowledge concerning its use regarding patient and disease characteristics remains limited. Our main objective was to assess the degree to which the CAT score varies and can discriminate between specific patient population groups. METHODS: The Canadian Cohort Obstructive Lung Disease (CanCOLD) is a random-sampled population-based, multicenter prospective cohort that includes subjects with COPD: GOLD 1 to 3...
June 27, 2016: Chest
https://www.readbyqxmd.com/read/27196484/chinese-herbal-medicine-and-salmeterol-and-fluticasone-propionate-for-chronic-obstructive-pulmonary-disease-systematic-review-and-network-meta-analysis
#19
Vincent C H Chung, Xinyin Wu, Polly H X Ma, Robin S T Ho, Simon K Poon, David S Hui, Samuel Y S Wong, Justin C Y Wu
Among Chinese populations worldwide, Chinese herbal medicines (CHMs) are often used as an adjunct to pharmacotherapy in managing chronic obstructive pulmonary disease (COPD). However, the relative performance among different CHM is unknown.The aim of this study was to evaluate comparative effectiveness of different CHM when used with salmeterol and fluticasone propionate (SFP), compared with SFP alone.This study is a systematic review of randomized controlled trials (RCTs) with network meta-analyses (NMAs)...
May 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27109808/the-german-copd-cohort-cosyconet-aims-methods-and-descriptive-analysis-of-the-study-population-at-baseline
#20
Annika Karch, Claus Vogelmeier, Tobias Welte, Robert Bals, Hans-Ulrich Kauczor, Jürgen Biederer, Joachim Heinrich, Holger Schulz, Sven Gläser, Rolf Holle, Henrik Watz, Stephanie Korn, Nina Adaskina, Frank Biertz, Charlotte Vogel, Jørgen Vestbo, Emiel F M Wouters, Klaus Friedrich Rabe, Sandra Söhler, Armin Koch, Rudolf A Jörres
BACKGROUND: The German COPD cohort study COSYCONET ("COPD and SYstemic consequences-COmorbidities NETwork") investigates the interaction of lung disease, comorbidities and systemic inflammation. Recruitment took place from 2010 to 2013 in 31 study centers. In addition to the baseline visit, follow-up visits are scheduled at 6, 18, 36 and 54 months after baseline. The study also comprises a biobank, image bank, and includes health economic data. Here we describe the study design of COSYCONET and present baseline data of our COPD cohort...
May 2016: Respiratory Medicine
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