PhysarumSpreader: A New Bio-Inspired Methodology for Identifying Influential Spreaders in Complex Networks

Identifying influential spreaders in networks, which contributes to optimizing the use of available resources and efficient spreading of information, is of great theoretical significance and practical value. A random-walk-based algorithm LeaderRank has been shown as an effective and efficient method in recognizing leaders in social network, which even outperforms the well-known PageRank method. As LeaderRank is initially developed for binary directed networks, further extensions should be studied in weighted networks. In this paper, a generalized algorithm PhysarumSpreader is proposed by combining LeaderRank with a positive feedback mechanism inspired from an amoeboid organism called Physarum Polycephalum. By taking edge weights into consideration and adding the positive feedback mechanism, PhysarumSpreader is applicable in both directed and undirected networks with weights. By taking two real networks for examples, the effectiveness of the proposed method is demonstrated by comparing with other standard centrality measures.     

Expression levels of 10 candidate genes in lung tissue of vaccinated and TB‐infected cynomolgus macaques

The expression of ten tuberculosis candidate genes in lung and lymph nodes of cynomologus macaques vaccinated and experimentally infected with Mycobacterium tuberculosis (Mtb) was quantified. The expression of TNFα, IL10, IL1β, TLR4, IL17, IL6, IL12, and iNOS in the lungs of vaccinated animals was higher than that of non‐vaccinated animals.     

A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins

Lipid modification of the N-terminal Cys residue (N-acyl-S-diacylglyceryl-Cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. Such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. Hence, being able to identify such proteins is of great value. To this end, we have created a comprehensive database of bacterial lipoproteins, called DOLOP, which contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. The website also features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include the following: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. The website, along with additional information on the biosynthetic pathway, statistics on predicted lipoproteins, and related figures, is available at http://www.mrc-lmb.cam.ac.uk/genomes/dolop/.     

Viral suppression and immune restoration in the gastrointestinal mucosa of human immunodeficiency virus type 1-infected patients initiating therapy during primary or chronic infection

Although the gut-associated lymphoid tissue (GALT) is an important early site for human immunodeficiency virus (HIV) replication and severe CD4+ T-cell depletion, our understanding is limited about the restoration of the gut mucosal immune system during highly active antiretroviral therapy (HAART). We evaluated the kinetics of viral suppression, CD4+ T-cell restoration, gene expression, and HIV-specific CD8+ T-cell responses in longitudinal gastrointestinal biopsy and peripheral blood samples from patients initiating HAART during primary HIV infection (PHI) or chronic HIV infection (CHI) using flow cytometry, real-time PCR, and DNA microarray analysis. Viral suppression was more effective in GALT of PHI patients than CHI patients during HAART. Mucosal CD4+ T-cell restoration was delayed compared to peripheral blood and independent of the time of HAART initiation. Immunophenotypic analysis showed that repopulating mucosal CD4+ T cells were predominantly of a memory phenotype and expressed CD11 alpha, alpha(E)beta 7, CCR5, and CXCR4. Incomplete suppression of viral replication in GALT during HAART correlated with increased HIV-specific CD8+ T-cell responses. DNA microarray analysis revealed that genes involved in inflammation and cell activation were up regulated in patients who did not replenish mucosal CD4+ T cells efficiently, while expression of genes involved in growth and repair was increased in patients with efficient mucosal CD4+ T-cell restoration. Our findings suggest that the discordance in CD4+ T-cell restoration between GALT and peripheral blood during therapy can be attributed to the incomplete viral suppression and increased immune activation and inflammation that may prevent restoration of CD4+ T cells and the gut microenvironment.     

The first nonradioactive fluorescence assay for phosphatidylglycerol:prolipoprotein diacylglyceryl transferase that initiates bacterial lipoprotein biosynthesis

The unique and physiologically vital bacterial enzyme, prolipoprotein diacylglyceryl transferase (Lgt), which catalyzes the committed first step in the posttranslational transfer of diacylglyceryl group from phosphatidylglycerol to the prospective N-terminal cysteine of prolipoproteins, remains to be characterized for want of a simpler but equally sensitive nonradioactive assay. We, for the first time, report a coupled enzymatic fluorescence assay for Lgt using the de novo synthetic peptide substrate MKATKSAVGSTLAGCSSHHHHHH. The assay is based on the conversion of the by-product, glycerol-1-phosphate, to dihydroxyacetone using an alkaline phosphatase-glycerol dehydrogenase combination and estimating the fluorescence of the coupled reduction of resazurin to resorufin. The minimum amount of glycerol-1-phosphate, and hence the modified peptide, detected by this method is approximately 20pmol, thereby making this assay a promising alternative to the radioactive assays. The assay is rapid, more convenient, less laborious, and suitable for purification and characterization of Lgt.     

Improving the quality of care for infants: a cluster randomized controlled trial

Background

We developed and tested a new method, called the Evidence-based Practice for Improving Quality method, for continuous quality improvement.

Methods

We used cluster randomization to assign 6 neonatal intensive care units (ICUs) to reduce nosocomial infection (infection group) and 6 ICUs to reduce bronchopulmonary dysplasia (pulmonary group). We included all infants born at 32 or fewer weeks gestation. We collected baseline data for 1 year. Practice change interventions were implemented using rapid-change cycles for 2 years.

Results

The difference in incidence trends (slopes of trend lines) between the ICUs in the infection and pulmonary groups was − 0.0020 (95% confidence interval [CI] − 0.0007 to 0.0004) for nosocomial infection and − 0.0006 (95% CI − 0.0011 to − 0.0001) for bronchopulmonary dysplasia.

Interpretation

The results suggest that the Evidence-based Practice for Improving Quality method reduced bronchopulmonary dysplasia in the neonatal ICU and that it may reduce nosocomial infection.Although methods for continuous quality improvement have been used to improve outcomes,^1–3 some, such as the National Institutes of Child Health and Human Development Quality Collaborative,⁴ have reported little or no effect in neonatal intensive care units (ICUs). These methods have been criticized for being based on intuition and anecdotes rather than on evidence.⁵ To address these concerns, researchers have developed methods aimed at improving the use of evidence in quality improvement. Tarnow-Mordi and colleagues,⁶ Sankaran and colleagues⁷ and others^8–10 have used benchmarking instruments^6,8,11 to show risk-adjusted variations in outcomes in neonatal ICUs. Synnes and colleagues¹² reported that variations in the rates of intraventricular hemorrhage could be attributed to practice differences. MacNab and colleagues¹³ showed how multilevel modelling methods can be used to identify practice differences associated with variations in outcomes for targeted interventions and to quantify their attributable risks.Building on these results, we developed the Evidence-based Practice for Improving Quality method for continuous quality improvement. This method is based on 3 pillars: the use of evidence from published literature; the use of data from participating hospitals to identify hospital-specific practices for targeted intervention; and the use of a national network to share expertise. By selectively targeting hospital-specific practices for intervention, this method reduces the reliance on intuition and anecdotes that are associated with existing quality-improvement methods.Our objective was to evaluate the efficacy of the Evidence-based Practice for Improving Quality method by conducting a prospective cluster randomized controlled trial to reduce nosocomial infection and bronchopulmonary dysplasia among infants born at 32 or fewer weeks’ gestation and admitted to 12 Canadian Neonatal Network hospitals¹⁴ over a 36-month period. We hypothesized that the incidence of nosocomial infection would be reduced among infants in ICUs randomized to reduce infection but not among those in ICUs randomized to reduce bronchopulmonary dysplasia. We also hypothesized that the incidence of bronchopulmonary dysplasia would be reduced among infants in the ICUs randomized to reduce this outcome but not among those in ICUs randomized to reduce infections.     

Structure of yeast regulatory subunit: a glimpse into the evolution of PKA signaling

The major cAMP receptors in eukaryotes are the regulatory (R) subunits of PKA, an allosteric enzyme conserved in fungi through mammals. While mammals have four R-subunit genes, Saccharomyces cerevisiae has only one, Bcy1. To achieve a molecular understanding of PKA activation in yeast and to explore the evolution of cyclic-nucleotide binding (CNB) domains, we solved the structure of cAMP-bound Bcy1(168-416). Surprisingly, the relative orientation of the two CNB domains in Bcy1 is very different from mammalian R-subunits. This quaternary structure is defined primarily by a fungi-specific sequence in the hinge between the αB/αC helices of the CNB-A domain. The unique interface between the two CNB domains in Bcy1 defines the allosteric mechanism for cooperative activation of PKA by cAMP. Some interface motifs are isoform-specific while others, although conserved, play surprisingly different roles in each R-subunit. Phylogenetic analysis shows that structural differences in Bcy1 are shared by fungi of the subphylum Saccharomycotina.     

Localization to the cortical cytoskeleton is necessary for Nf2/merlin-dependent epidermal growth factor receptor silencing

Merlin, the product of the NF2 tumor suppressor gene, is closely related to the ERM (ezrin, radixin, moesin) proteins, which provide anchorage between membrane proteins and the underlying cortical cytoskeleton; all four proteins are members of the band 4.1 superfamily. Despite their similarity, the subcellular distributions and functional properties of merlin and the ERM proteins are largely distinct. Upon cell-cell contact merlin prevents internalization of and signaling from the epidermal growth factor receptor (EGFR) by sequestering it into an insoluble membrane compartment. Here we show that the extreme amino (N) terminus directs merlin biochemically to an insoluble membrane compartment and physically to the cortical actin network, with a marked concentration along cell-cell boundaries. This insoluble-membrane distribution is required for the growth-suppressing function of merlin and for the functional association of merlin with EGFR and other membrane receptors. Our data support a model whereby locally activated merlin sequesters membrane receptors such as EGFR at the cortical network, contributing to the long-held observation that the cortical actin cytoskeleton can control the lateral mobility of and signaling from certain membrane receptors.