A re-appraisal of the reliability of the 20 m multi-stage shuttle run test

This is the author's PDF version of an article published in European journal of applied physiology in 2007. The original publication is available at www.springerlink.co

A systematic review of the use of an expertise-based randomised controlled trial design

Acknowledgements JAC held a Medical Research Council UK methodology (G1002292) fellowship, which supported this research. The Health Services Research Unit, Institute of Applied Health Sciences (University of Aberdeen), is core-funded by the Chief Scientist Office of the Scottish Government Health and Social Care Directorates. Views express are those of the authors and do not necessarily reflect the views of the funders.Peer reviewedPublisher PD

Clustering in surgical trials : database of intracluster correlations

PMID: 22217216 [PubMed - indexed for MEDLINE] PMCID: PMC3311136 Free PMC ArticlePeer reviewedPublisher PD

Nanopods: A New Bacterial Structure and Mechanism for Deployment of Outer Membrane Vesicles

Background: Bacterial outer membrane vesicles (OMV) are packets of periplasmic material that, via the proteins and other molecules they contain, project metabolic function into the environment. While OMV production is widespread in proteobacteria, they have been extensively studied only in pathogens, which inhabit fully hydrated environments. However, many (arguably most) bacterial habitats, such as soil, are only partially hydrated. In the latter, water is characteristically distributed as films on soil particles that are, on average thinner, than are typical OMV (ca. ≤10 nm water film vs. 20 to >200 nm OMV;). Methodology/Principal Findings: We have identified a new bacterial surface structure, termed a "nanopod", that is a conduit for projecting OMV significant distances (e.g., ≥6 µm) from the cell. Electron cryotomography was used to determine nanopod three-dimensional structure, which revealed chains of vesicles within an undulating, tubular element. By using immunoelectron microscopy, proteomics, heterologous expression and mutagenesis, the tubes were determined to be an assembly of a surface layer protein (NpdA), and the interior structures identified as OMV. Specific metabolic function(s) for nanopods produced by Delftia sp. Cs1-4 are not yet known. However, a connection with phenanthrene degradation is a possibility since nanopod formation was induced by growth on phenanthrene. Orthologs of NpdA were identified in three other genera of the Comamonadaceae family, and all were experimentally verified to form nanopods. Conclusions/Significance: Nanopods are new bacterial organelles, and establish a new paradigm in the mechanisms by which bacteria effect long-distance interactions with their environment. Specifically, they create a pathway through which cells can effectively deploy OMV, and the biological activity these transmit, in a diffusion-independent manner. Nanopods would thus allow environmental bacteria to expand their metabolic sphere of influence in a manner previously unknown for these organisms

Learning curves for pediatric laparoscopy: how many operations are enough? The Amsterdam experience with laparoscopic pyloromyotomy

Few studies on the surgical outcomes of open (OP) versus laparoscopic pyloromyotomy (LP) in the treatment of hypertrophic pyloric stenosis have been published. The question arises as to how many laparoscopic procedures are required for a surgeon to pass the learning curve and which technique is best in terms of postoperative complications. This study aimed to evaluate and quantify the learning curve for the laparoscopic technique at the authors' center. A second goal of this study was to evaluate the pre- and postoperative data of OP versus LP for infantile hypertrophic pyloric stenosis. A retrospective analysis was performed for 229 patients with infantile hypertrophic pyloric stenosis. Between January 2002 and September 2008, 158 infants underwent OP and 71 infants had LP. The median operating time between the OP (33 min) and LP (40 min) groups was significantly different. The median hospital stay after surgery was 3 days for the OP patients and 2 days for the LP patients (p = 0.002). The postoperative complication rates were not significantly different between the OP (21.5%) and LP (21.1%) groups (p = 0.947). Complications were experienced by 31.5% of the first 35 LP patients. This rate decreased to 11.4% during the next 35 LP procedures (p = 0.041). Two perforations and three conversions occurred in the first LP group, compared with one perforation in the second LP group. The number of complications decreased significantly between the first and second groups of the LP patients, with the second group of LP patients quantifying the learning curve. Not only was the complication rate lower in the second LP group, but severe complications also were decreased. This indicates that the learning curve for LP in the current series involved 35 procedure

An Infinite-Dimensional Family of Black-Hole Microstate Geometries

We construct the first explicit, smooth, horizonless black-hole microstate geometry whose moduli space is described by an arbitrary function of one variable and is thus infinite-dimensional. This is achieved by constructing the scalar Green function on a simple D6 anti-D6 background, and using this Green function to obtain the fully back-reacted solution for a supertube with varying charge density in this background. We show that this supertube can store parametrically more entropy than in flat space, confirming the entropy enhancement mechanism that was predicted using brane probes. We also show that all the local properties of the fully back-reacted solution can, in fact, be obtained using the DBI action of an appropriate brane probe. In particular, the supergravity and the DBI analysis yield identical functional bubble equations that govern the relative locations of the centers. This indicates that there is a non-renormalization theorem that protects these functional equations as one moves in moduli space. Our construction creates configurations that are beyond the scope of recent arguments that appear to put strong limits on the entropy that can be found in smooth supergravity solutions.Comment: 46 pages, 1 figure, LaTe

A database of microRNA expression patterns in Xenopus laevis

MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase

Environmental Controls on Tropical Sea Breeze Convection and Resulting Aerosol Redistribution

Sea breeze fronts propagate inland from the coastline, driving convective initiation and aerosol redistribution. Forecasting sea breezes is challenging due to uncertainties in the initial conditions, as well as the covariance and interaction of various meteorological and surface parameters. Using the Regional Atmospheric Modeling System coupled to an interactive land‐surface model, we conduct an ensemble of 130 idealized cloud‐resolving simulations by simultaneously perturbing six atmospheric and four surface parameters describing the initial conditions. To identify the key parameters impacting the inland characteristics and the intensity of the sea breeze convection in a tropical rainforest, we apply statistical emulation and variance‐based sensitivity analysis techniques. This study extends a previous study which explored the impacts of various parameters on sea breeze characteristics in arid environments devoid of moist convection. Wind speed is identified as the main contributor to the inland extent, similar to the arid environment study. However, the relative impacts of surface properties on the inland extent are less significant in the moist environment where land‐surface heating can be suppressed via moist convective processes and vegetation‐atmosphere interactions. Two sea breeze‐initiated convection regimes are also identified: shallow and deep. Over the shallow regime, where convective available potential energy is limited, the inversion layer strength is the primary control of the convective intensity. Over the deep regime, boundary layer temperature exerts a robust control over the convective available potential energy and hence the convective intensity. The potential vertical redistribution of aerosols is closely related to the convective intensity

The proangiogenic capacity of polymorphonuclear neutrophils delineated by microarray technique and by measurement of neovascularization in wounded skin of CD18-deficient mice

Growing evidence supports the concept that polymorphonuclear neutrophils (PMN) are critically involved in inflammation-mediated angiogenesis which is important for wound healing and repair. We employed an oligonucleotide microarray technique to gain further insight into the molecular mechanisms underlying the proangiogenic potential of human PMN. In addition to 18 known angiogenesis-relevant genes, we detected the expression of 10 novel genes, namely midkine, erb-B2, ets-1, transforming growth factor receptor-beta(2) and -beta(3), thrombospondin, tissue inhibitor of metalloproteinase 2, ephrin A2, ephrin B2 and restin in human PMN freshly isolated from the circulation. Gene expression was confi rmed by the RT-PCR technique. In vivo evidence for the role of PMN in neovascularization was provided by studying neovascularization in a skin model of wound healing using CD18-deficient mice which lack PMN infi ltration to sites of lesion. In CD18-deficient animals, neo- vascularization was found to be signifi cantly compromised when compared with wild- type control animals which showed profound neovascularization within the granulation tissue during the wound healing process. Thus, PMN infiltration seems to facilitate inflammation mediated angiogenesis which may be a consequence of the broad spectrum of proangiogenic factors expressed by these cells. Copyright (c) 2006 S. Karger AG, Basel

Combining best evidence: A novel method to calculate the alcohol-attributable fraction and its variance for injury mortality

<p>Abstract</p> <p>Background</p> <p>The alcohol-attributable fraction for injury mortality is defined as the proportion of fatal injury that would disappear if consumption went to zero. Estimating this fraction has previously been based on a simplistic view of drinking and associated risk. This paper develops a new way to calculate the alcohol-attributable fraction for injury based on different dimensions of drinking, mortality data, experimental data, survey research, new risk scenarios, and by incorporating different distributions of consumption within populations. For this analysis, the Canadian population in 2005 was used as the reference population.</p> <p>Methods</p> <p>Binge drinking and average daily consumption were modeled separately with respect to the calculation of the AAF. The acute consumption risk was calculated with a probability-based method that accounted for both the number of binge drinking occasions and the amount of alcohol consumed per occasion. The average daily consumption was computed based on the prevalence of daily drinking at various levels. These were both combined to get an overall estimate. 3 sensitivity analyses were performed using different alcohol consumption parameters to test the robustness of the model. Calculation of the variance to generate confidence limits around the point estimates was accomplished via Monte Carlo resampling methods on randomly generated AAFs that were based on the distribution and prevalence of drinking in the Canadian population.</p> <p>Results</p> <p>Overall, the AAFs decrease with age and are significantly lower for women than men across all ages. As binge drinking increases, the injury mortality AAF also increases. Motor vehicle collisions show the largest relative increases in AAF as alcohol consumption is increased, with over a 100% increase in AAF from the lowest to highest consumption category. Among non-motor vehicle collisions, the largest change in total AAF occurred both for homicide and other intentional injuries at about a 15% increase in the AAF from the lowest to the highest binge consumption scenarios.</p> <p>Conclusions</p> <p>This method combines the best available evidence to generate new alcohol-attributable fractions for alcohol-attributable injury mortality. Future research is needed to refine the risk function for non-motor vehicle injury types and to investigate potential interactions between binge drinking and average volume of alcohol consumption.</p