Large scale deployment of molecular docking application on computational grid infrastructures for combating malaria

PCSVInternational audienceComputational grids are solutions for several biological applications like virtual screening or molecular dynamics where large amounts of computing power and storage are required. The WISDOM project successfully deployed virtual screening at large scale on EGEE grid infrastructures in the summer 2005 and achieved 46 million dockings in 45 days, which is equivalent to 80 CPU years. WISDOM is one good example of a successful deployment of an embarrassingly parallel application. In this paper, we describe the improvements in our deployment. We screened ZINC database against four targets implicated in malaria. During more than 2 months and a half, we have achieved 140 million dockings, representing an average throughput of almost 80,000 dockings per hour. This was made possible by the availability of thousands of CPUs through different infrastructures worldwide. Through the acquired experience, the WISDOM production environment is evolving to enable an easy and fault-tolerant deployment of biological tool

Modelling growth and form of the scleractinian coral Pocillopora verrucosa and the influence of hydrodynamics

The growth of scleractinian corals is strongly influenced by the effect of water motion. Corals are known to have a high level of phenotypic variation and exhibit a diverse range of growth forms, which often contain a high level of geometric complexity. Due to their complex shape, simulation models represent an important option to complement experimental studies of growth and flow. In this work, we analyzed the impact of flow on coral's morphology by an accretive growth model coupled with advection-diffusion equations. We performed simulations under no-flow and uni-directional flow setup with the Reynolds number constant. The relevant importance of diffusion to advection was investigated by varying the diffusion coefficient, rather than the flow speed in Péclet number. The flow and transport equations were coupled and solved using COMSOL Multiphysics. We then compared the simulated morphologies with a series of Computed Tomography (CT) scans of scleractinian corals Pocillopora verrucosa exposed to various flow conditions in the in situ controlled flume setup. As a result, we found a similar trend associated with the increasing Péclet for both simulated forms and in situ corals; that is uni-directional current tends to facilitate asymmetrical growth response resulting in colonies with branches predominantly developed in the upstream direction. A closer look at the morphological traits yielded an interesting property about colony symmetry and plasticity induced by uni-directional flow. Both simulated and in situ corals exhibit a tendency where the degree of symmetry decreases and compactification increases in conjunction with the augmented Péclet thus indicates the significant importance of hydrodynamics

Contarinia gossypii Felt (Diptera: Cecido myiidae) nueva plaga del algodonero

En cultivos de algodonero del Sinú, de 80 días de edad, se presentó durante la cosecha 83-84 una malformación de botones y "capullos" que al ocasionar la caída de las estructuras del tercio superior pudo reducir Ia producción hasta en 700 Kg./ha, según estimativos preliminares. En muchos casos, Ia malformación estuvo seguida por una pudrición bacteria producida por Pseudomonas sin tener aCm claridad sobre la relación patógeno-insecto.Algodón-Gossypium herbaceu

Preoperative Predictors of Arthroscopic Partial Meniscectomy Outcomes: The APM Index Score

Problem Statement: - Arthroscopic partial meniscectomy (APM) has been shown to be the most common meniscal surgical treatment in the United States - Pre-op risk factors known to contribute to poor outcomes after APM: Symptom duration and radiographic OA at baseline - Factors with no conclusive effect on post-op outcomes: Baseline knee functional score, location of meniscal tear, BMI, activity level, age, sex, and chondral damage on MRI Project AIM: To create an index score using easily available preoperative risk factors such as Kellgren-Lawrence (KL) grade, age, duration of symptoms, BMI, activity level, and preoperative outcome scores to predict the likelihood of favorable outcomes after APM.https://jdc.jefferson.edu/aoa_research_symposium_posters/1003/thumbnail.jp

HER2 testing in breast cancer: Opportunities and challenges

Human epidermal growth factor receptor 2 (HER2) is overexpressed in 15-25% of breast cancers, usually as a result of HER2 gene amplification. Positive HER2 status is considered to be an adverse prognostic factor. Recognition of the role of HER2 in breast cancer growth has led to the development of anti-HER2 directed therapy, with the humanized monoclonal antibody trastuzumab (Herceptin (R)) having been approved for the therapy of HER2-positive metastatic breast cancer. Clinical studies have further suggested that HER2 status can provide important information regarding success or failure of certain hormonal therapies or chemotherapies. As a result of these developments, there has been increasing demand to perform HER2 testing on current and archived breast cancer specimens. This article reviews the molecular background of HER2 function, activation and inhibition as well as current opinions concerning its role in chemosensitivity and interaction with estrogen receptor biology. The different tissue-based assays used to detect HER2 amplification and overexpression are discussed with respect to their advantages and disadvantages, when to test (at initial diagnosis or pre-treatment), where to test (locally or centralized) and the need for quality assurance to ensure accurate and valid testing results

Neutrino Mass from R-parity Violation in Split Supersymmetry

We investigate how the observed neutrino data can be accommodated by R-parity violation in Split Supersymmetry. The atmospheric neutrino mass and mixing are explained by the bilinear parameters $\xi_i$ inducing the neutrino-neutralino mixing as in the usual low-energy supersymmetry. Among various one-loop corrections, only the quark-squark exchanging diagrams involving the order-one trilinear couplings $\lambda'_{i23,i32}$ can generate the solar neutrino mass and mixing if the scalar mass $m_S$ is not larger than $10^9$ GeV. This scheme requires an unpleasant hierarchical structure of the couplings, e.g., $\lambda_{i23,i32}\sim 1$, $\lambda'_{i33} \lesssim 10^{-4}$ and $\xi_i \lesssim 10^{-6}$. On the other hand, the model has a distinct collider signature of the lightest neutralino which can decay only to the final states, $l_i W^{(*)}$ and $\nu Z^{(*)}$, arising from the bilinear mixing. Thus, the measurement of the ratio; $\Gamma(e W^{(*)}) : \Gamma(\mu W^{(*)}) : \Gamma(\tau W^{(*)})$ would provide a clean probe of the small reactor and large atmospheric neutrino mixing angles as far as the neutralino mass is larger than 62 GeV.Comment: 10 pages, 3 figures, version submitted to JHE

Theta-13 as a Probe of Mu-Tau symmetry for Leptons

Many experiments are being planned to measure the neutrino mixing parameter $\theta_{13}$ using reactor as well as accelerator neutrino beams. In this note, the theoretical significance of a high precision measurement of this parameter is discussed. It is emphasized that it will provide crucial information about different ways to understand the origin of large atmospheric neutrino mixing and move us closer towards determining the neutrino mass matrix. For instance if exact $\mu\leftrightarrow \tau$ symmetry in the neutrino mass matrix is assumed to be the reason for maximal $\nu_\mu-\nu_\tau$ mixing, one gets $\theta_{13}=0$. Whether $\theta_{13}\simeq \sqrt{\Delta m^2_{\odot}/\Delta m^2_A}$ or $\theta_{13}\simeq \Delta m^2_{\odot}/\Delta m^2_A$ can provide information about the way the $\mu\leftrightarrow \tau$ symmetry breaking manifests in the case of normal hierarchy. We also discuss the same question for inverted hierarchy as well as possible gauge theories with this symmetry.Comment: 12 pages; no figures; latex; more exact expressions given for some parameters and minor typos corrected; paper accepted for publication in JHE

Statefinder Parameter for Varying G in Three Fluid System

In this work, we have considered variable G in flat FRW universe filled with the mixture of dark energy, dark matter and radiation. If there is no interaction between the three fluids, the deceleration parameter and statefinder parameters have been calculated in terms of dimensionless density parameters which can be fixed by observational data. Also the interaction between three fluids has been analyzed due to constant $G$. The statefinder parameters also calculated in two cases: pressure is constant and pressure is variable.Comment: 5 pages, Accepted for publication in "Astrophysics and Space Science

Ensemble prediction for nowcasting with a convection-permitting model—I: description of the system and the impact of radar-derived surface precipitation rates

A key strategy to improve the skill of quantitative predictions of precipitation, as well as hazardous weather such as severe thunderstorms and flash floods is to exploit the use of observations of convective activity (e.g. from radar). In this paper, a convection-permitting ensemble prediction system (EPS) aimed at addressing the problems of forecasting localized weather events with relatively short predictability time scale and based on a 1.5 km grid-length version of the Met Office Unified Model is presented. Particular attention is given to the impact of using predicted observations of radar-derived precipitation intensity in the ensemble transform Kalman filter (ETKF) used within the EPS. Our initial results based on the use of a 24-member ensemble of forecasts for two summer case studies show that the convective-scale EPS produces fairly reliable forecasts of temperature, horizontal winds and relative humidity at 1 h lead time, as evident from the inspection of rank histograms. On the other hand, the rank histograms seem also to show that the EPS generates too much spread for forecasts of (i) surface pressure and (ii) surface precipitation intensity. These may indicate that for (i) the value of surface pressure observation error standard deviation used to generate surface pressure rank histograms is too large and for (ii) may be the result of non-Gaussian precipitation observation errors. However, further investigations are needed to better understand these findings. Finally, the inclusion of predicted observations of precipitation from radar in the 24-member EPS considered in this paper does not seem to improve the 1-h lead time forecast skill