ViralZone: recent updates to the virus knowledge resource.

ViralZone (http://viralzone.expasy.org) is a knowledge repository that allows users to learn about viruses including their virion structure, replication cycle and host-virus interactions. The information is divided into viral fact sheets that describe virion shape, molecular biology and epidemiology for each viral genus, with links to the corresponding annotated proteomes of UniProtKB. Each viral genus page contains detailed illustrations, text and PubMed references. This new update provides a linked view of viral molecular biology through 133 new viral ontology pages that describe common steps of viral replication cycles shared by several viral genera. This viral cell-cycle ontology is also represented in UniProtKB in the form of annotated keywords. In this way, users can navigate from the description of a replication-cycle event, to the viral genus concerned, and the associated UniProtKB protein records.

Helicopter rescue involving the winching of a physician.

INTRODUCTION: We sought to study the operational and medical aspects of helicopter rescue missions involving the use of a winch.¦SETTING: A single helicopter-based medical service of a pre-alpine region of Switzerland.¦METHODS: We prospectively studied consecutive primary rescue interventions involving winching of a physician, from October 1, 1998 to October 1, 2002. Demographic, medical and operational aspects as well as outcome at 48 hours were analyzed.¦RESULTS: We included 133 patients. Most (74%) were male, with traumatic injuries (77%). The median scene time of the nine severely injured patients (Injury Severity Scale [ISS] > 15) was significantly longer compared with the other patients (54 vs 37 minutes; P < .05). The main medical procedures performed were orotracheal intubation (n = 5), fracture reductions (n = 5), major analgesia with sedation (n = 4), and intravenous fluid administration of more than 1,500 mL (n = 4). Fourteen (10%) patients suffering from minor injuries were triaged by the physician and not airlifted to the hospital. All 133 patients were alive at 48 hours. Sixty-nine (52%) were still hospitalized. No secondary interhospital transfer was required.¦CONCLUSION: Our study provides a better knowledge of injury profile, medical aspects, and outcomes of patients rescued necessitating a winching procedure.

Evolution of Coordination in Social Networks: A Numerical Study

Coordination games are important to explain efficient and desirable social behavior. Here we study these games by extensive numerical simulation on networked social structures using an evolutionary approach. We show that local network effects may promote selection of efficient equilibria in both pure and general coordination games and may explain social polarization. These results are put into perspective with respect to known theoretical results. The main insight we obtain is that clustering, and especially community structure in social networks has a positive role in promoting socially efficient outcomes.

Numerical procedure for estimating temperature in solarized soils

The objective of this work was to develop a simplified numerical procedure for the estimation of accumulated monthly hours of solarized soil temperatures. The proposed model requires monthly means of daily solar radiation and maximum air temperature as input data, and a daily pattern of temperature variation assumed to be sine-shaped. The procedure was verified using observations made during the years 1992 and 1993 in Jaguariúna, SP. The proposed procedure can predict monthly temperature hours at 10 cm depth in the solarized soil, with acceptable accuracy, in the region for which it was developed.

Direct numerical simulations of interface dynamics to link capillary pressure and total surface energy

The flow of two immiscible fluids through a porous medium depends on the complex interplay between gravity, capillarity, and viscous forces. The interaction between these forces and the geometry of the medium gives rise to a variety of complex flow regimes that are difficult to describe using continuum models. Although a number of pore-scale models have been employed, a careful investigation of the macroscopic effects of pore-scale processes requires methods based on conservation principles in order to reduce the number of modeling assumptions. In this work we perform direct numerical simulations of drainage by solving Navier-Stokes equations in the pore space and employing the Volume Of Fluid (VOF) method to track the evolution of the fluid-fluid interface. After demonstrating that the method is able to deal with large viscosity contrasts and model the transition from stable flow to viscous fingering, we focus on the macroscopic capillary pressure and we compare different definitions of this quantity under quasi-static and dynamic conditions. We show that the difference between the intrinsic phase-average pressures, which is commonly used as definition of Darcy-scale capillary pressure, is subject to several limitations and it is not accurate in presence of viscous effects or trapping. In contrast, a definition based on the variation of the total surface energy provides an accurate estimate of the macroscopic capillary pressure. This definition, which links the capillary pressure to its physical origin, allows a better separation of viscous effects and does not depend on the presence of trapped fluid clusters.

Insights into the Design and Characteristics of the Sedimentation Process at Multi-Barrel Culverts in Iowa, TR-596, 2010

The present study is an integral part of a broader study focused on the design and implementation of self-cleaning culverts, i.e., configurations that prevent the formation of sediment deposits after culvert construction or cleaning. Sediment deposition at culverts is influenced by many factors, including the size and characteristics of material of which the channel is composed, the hydraulic characteristics generated under different hydrology events, the culvert geometry design, channel transition design, and the vegetation around the channel. The multitude of combinations produced by this set of variables makes the investigation of practical situations a complex undertaking. In addition to the considerations above, the field and analytical observations have revealed flow complexities affecting the flow and sediment transport through culverts that further increase the dimensions of the investigation. The flow complexities investigated in this study entail: flow non-uniformity in the areas of transition to and from the culvert, flow unsteadiness due to the flood wave propagation through the channel, and the asynchronous correlation between the flow and sediment hydrographs resulting from storm events. To date, the literature contains no systematic studies on sediment transport through multi-box culverts or investigations on the adverse effects of sediment deposition at culverts. Moreover, there is limited knowledge about the non-uniform, unsteady sediment transport in channels of variable geometry. Furthermore, there are few readily useable (inexpensive and practical) numerical models that can reliably simulate flow and sediment transport in such complex situations. Given the current state of knowledge, the main goal of the present study is to investigate the above flow complexities in order to provide the needed insights for a series of ongoing culvert studies. The research was phased so that field observations were conducted first to understand the culvert behavior in Iowa landscape. Modeling through complementary hydraulic model and numerical experiments was subsequently carried out to gain the practical knowledge for the development of the self-cleaning culvert designs.

Rate of undesirable events at beginning of academic year: retrospective cohort study.

OBJECTIVE: To determine whether an increase in the rate of undesirable events occurs after care provided by trainees at the beginning of the academic year. DESIGN: Retrospective cohort study using administrative and patient record data. SETTING: University affiliated hospital in Melbourne, Australia. PARTICIPANTS: 19,560 patients having an anaesthetic procedure carried out by first to fifth year trainees starting work for the first time at the hospital over a period of five years (1995-2000). MAIN OUTCOME MEASURES: Absolute event rates, absolute rate reduction, and rate ratios of undesirable events. RESULTS: The rate of undesirable events was higher at the beginning of the academic year compared with the rest of the year (absolute event rate 137 v 107 per 1000 patient hours, relative rate reduction 28%, P<0.001). The overall adjusted rate ratio for undesirable events was 1.40, 95% confidence interval 1.24 to 1.58. This excess risk was seen for all residents, regardless of their level of seniority. The excess risk decreased progressively after the first month, and the trend disappeared fully after the fourth month of the year (rate ratio for fourth month 1.21, 0.93 to 1.57). The most important decreases were for central and peripheral nerve injuries (relative difference 82%), inadequate oxygenation of the patient (66%), vomiting/aspiration in theatre (53%), and technical failures of tracheal tube placement (49%). CONCLUSIONS: The rate of undesirable events was greater among trainees at the beginning of the academic year regardless of their level of clinical experience. This suggests that several additional factors, such as knowledge of the working environment, teamwork, and communication, may contribute to the increase.

Current knowledge on the Ralstonia solanacearum type III secretion system

R. solanacearum was ranked in a recent survey the second most important bacterial plant pathogen, following the widely used research model Pseudomonas syringae (Mansfield et al., 2012). The main reason is that bacterial wilt caused by R. solanacearum is the world"s most devastating bacterial plant disease (http://faostat.fao.org), threatening food safety in tropical and subtropical agriculture, especially in China, Bangladesh, Bolivia and Uganda (Martin and French, 1985). This is due to the unusually wide host range of the bacterium, its high persistence and because resistant crop varieties are unavailable. In addition, R. solanacearum has been established as a model bacterium for plant pathology thanks to pioneering molecular and genomic studies (Boucher et al., 1985; Cunnac et al., 2004b; Mukaihara et al., 2010; Occhialini et al., 2005; Salanoubat et al., 2002). As for many bacterial pathogens, the main virulence determinant in R. solanacearum is the type III secretion system (T3SS) (Boucher et al., 1994), which injects a number of effector proteins into plant cells causing disease in hosts or an hypersensitive response in resistant plants. In this article we discuss the current state in the study of the R. solanacearum T3SS, stressing the latest findings and future perspectives.

Trust region versus line search for computing the optical flow

We consider the numerical treatment of the optical flow problem by evaluating the performance of the trust region method versus the line search method. To the best of our knowledge, the trust region method is studied here for the first time for variational optical flow computation. Four different optical flow models are used to test the performance of the proposed algorithm combining linear and nonlinear data terms with quadratic and TV regularization. We show that trust region often performs better than line search; especially in the presence of non-linearity and non-convexity in the model.