The role of bacteria in the pathogenesis and progression of idiopathic pulmonary fibrosis

Rationale:Idiopathic pulmonaryfibrosis (IPF)isa progressivelung disease of unknown cause that leads to respiratory failure and death within 5 years of diagnosis. Overt respiratory infection and immunosuppression carry a high morbidity and mortality, and polymorphisms in genes related to epithelial integrity and host defense predispose to IPF. Objectives: To investigate the role of bacteria in the pathogenesis and progression of IPF. Methods: We prospectively enrolled patients diagnosed with IPF according to international criteria together with healthy smokers, nonsmokers, and subjectswithmoderate chronic obstructive pulmonary disease as control subjects. Subjects underwent bronchoalveolar lavage (BAL), from which genomic DNA was isolated. The V3–V5 region of the bacterial 16S rRNA gene was amplified, allowing quantification of bacterial load and identification of communities by 16S rRNA quantitative polymerase chain reaction and pyrosequencing. Measurements and Main Results: Sixty-five patients with IPF had double the burden of bacteria in BAL fluid compared with 44 control subjects. Baseline bacterial burden predicted the rate of decline in lung volume and risk of death and associated independently with the rs35705950 polymorphism of the MUC5B mucin gene, a proven host susceptibilityfactorfor IPF. Sequencing yielded912,883 high-quality reads from all subjects.WeidentifiedHaemophilus, Streptococcus,Neisseria, and Veillonella spp. to be more abundant in cases than control subjects. Regression analyses indicated that these specific operational taxonomic units as well as bacterial burden associated independently with IPF. Conclusions: IPF is characterized by an increased bacterial burden in BAL that predicts decline in lung function and death. Trials of antimicrobial therapy are needed to determine if microbial burden is pathogenic in the disease

Fast Computing Betweenness Centrality with Virtual Nodes on Large Sparse Networks

Betweenness centrality is an essential index for analysis of complex networks. However, the calculation of betweenness centrality is quite time-consuming and the fastest known algorithm uses time and space for weighted networks, where and are the number of nodes and edges in the network, respectively. By inserting virtual nodes into the weighted edges and transforming the shortest path problem into a breadth-first search (BFS) problem, we propose an algorithm that can compute the betweenness centrality in time for integer-weighted networks, where is the average weight of edges and is the average degree in the network. Considerable time can be saved with the proposed algorithm when , indicating that it is suitable for lightly weighted large sparse networks. A similar concept of virtual node transformation can be used to calculate other shortest path based indices such as closeness centrality, graph centrality, stress centrality, and so on. Numerical simulations on various randomly generated networks reveal that it is feasible to use the proposed algorithm in large network analysis

Free-standing polyelectrolyte membranes made of chitosan and alginate

Free-standing films have increasing applications in the biomedical field as drug delivery systems for wound healing and tissue engineering. Here, we prepared free-standing membranes by the layer-by-layer assembly of chitosan and alginate, two widely used biomaterials. Our aim was to produce a thick membrane and to study the permeation of model drugs and the adhesion of muscle cells. We first defined the optimal growth conditions in terms of pH and alginate concentration. The membranes could be easily detached from polystyrene or polypropylene substrate without any postprocessing step. The dry thickness was varied over a large range from 4 to 35 μm. A 2-fold swelling was observed by confocal microscopy when they were immersed in PBS. In addition, we quantified the permeation of model drugs (fluorescent dextrans) through the free-standing membrane, which depended on the dextran molecular weight. Finally, we showed that myoblast cells exhibited a preferential adhesion on the alginate-ending membrane as compared to the chitosan-ending membrane or to the substrate side.This work was financially supported by Foundation for Science and Technology (FCT) through the Scholarship SFRH/BD/64601/2009 granted to S.G.C. C.M. is indebted to Grenoble INP for financial support via a postdoctoral fellowship. This work was supported by the European Commission (FP7 Program) via a European Research Council starting grant (BIOMIM, GA 259370 to C.P.). C.P. is also grateful to Institut Universitaire de France and to Grenoble Institute of Technology for financial support. We thank Isabelle Paintrand for her technical help with the confocal apparatus and Patrick Chaudouet for his help with SEM imaging

From system to organ to cell: oxygenation and perfusion measurement in anesthesia and critical care

Maintenance or restoration of adequate tissue oxygenation is a main goal of anesthesiologic and intensive care patient management. Pathophysiological disturbances which interfere with aerobic metabolism may occur at any stage in the oxygen cascade from atmospheric gas to the mitochondria, and there is no single monitoring modality that allows comprehensive determination of “the oxygenation”. To facilitate early detection of tissue hypoxia (or hyperoxia) and to allow a goal directed therapy targeted at the underlying problem, the anesthesiologist and intensive care physician require a thorough understanding of the numerous determinants that influence cellular oxygenation. This article reviews the basic physiology of oxygen uptake and delivery to tissues as well as the options to monitor determinants of oxygenation at different stages from the alveolus to the cell