OGSA first impressions: a case study re-engineering a scientific applicationwith the open grid services architecture

We present a case study of our experience re-engineeringa scientific application using the Open Grid Services Architecture(OGSA), a new specification for developing Gridapplications using web service technologies such as WSDLand SOAP. During the last decade, UCL?s Chemistry departmenthas developed a computational approach for predictingthe crystal structures of small molecules. However,each search involves running large iterations of computationallyexpensive calculations and currently takes a fewmonths to perform. Making use of early implementationsof the OGSA specification we have wrapped the Fortranbinaries into OGSI-compliant service interfaces to exposethe existing scientific application as a set of loosely coupledweb services. We show how the OGSA implementationfacilitates the distribution of such applications across alarge network, radically improving performance of the systemthrough parallel CPU capacity, coordinated resourcemanagement and automation of the computational process.We discuss the difficulties that we encountered turning Fortranexecutables into OGSA services and delivering a robust,scalable system. One unusual aspect of our approachis the way we transfer input and output data for the Fortrancodes. Instead of employing a file transfer service wetransform the XML encoded data in the SOAP message tonative file format, where possible using XSLT stylesheets.We also discuss a computational workflow service that enablesusers to distribute and manage parts of the computationalprocess across different clusters and administrativedomains. We examine how our experience re-engineeringthe polymorph prediction application led to this approachand to what extent our efforts have succeeded

Grid service orchestration using the Business Process Execution Language (BPEL)

Modern scientific applications often need to be distributed across grids. Increasingly applications rely on services, such as job submission, data transfer or data portal services. We refer to such services as grid services. While the invocation of grid services could be hard coded in theory, scientific users want to orchestrate service invocations more flexibly. In enterprise applications, the orchestration of web services is achieved using emerging orchestration standards, most notably the Business Process Execution Language (BPEL). We describe our experience in orchestrating scientific workflows using BPEL. We have gained this experience during an extensive case study that orchestrates grid services for the automation of a polymorph prediction application

The SHARC framework:utilizing personal dropbox accounts to provide a scalable solution to the storage and sharing of community generated locative media

The emergence of personal cloud storage services provides a new paradigm for storing and sharing data. In this paper we present the design of the SHARC framework and in particular focus on the utilization of personal Dropbox accounts to provide a scalable solution to the storage and sharing of community generated locative media relating to a community's Cultural Heritage. In addition to scalability issues, the utilization of personal Dropbox storage also supports 'sense of ownership' (relating to community media) which has arisen as an important requirement during our on-going 'research-in-the-wild' working with the rural village community of Wray and involving public display deployments to support the display and sharing of community photos and stories. While the framework presented here is currently being tested with a particular place-based community (Wray), it has been designed to provide a general solution that should support other place-based communities

Quantification of habitat fragmentation reveals extinction risk in terrestrial mammals

Although habitat fragmentation is often assumed to be a primary driver of extinction, global patterns of fragmentation and its relationship to extinction risk have not been consistently quantified for any major animal taxon. We developed high-resolution habitat fragmentation models and used phylogenetic comparative methods to quantify the effects of habitat fragmentation on the world's terrestrial mammals, including 4,018 species across 26 taxonomic Orders. Results demonstrate that species with more fragmentation are at greater risk of extinction, even after accounting for the effects of key macroecological predictors, such as body size and geographic range size. Species with higher fragmentation had smaller ranges and a lower proportion of high-suitability habitat within their range, andmost high-suitability habitat occurred outside of protected areas, further elevating extinction risk. Our models provide a quantitative evaluation of extinction risk assessments for species, allow for identification of emerging threats in species not classified as threatened, and provide maps of global hotspots of fragmentation for the world's terrestrial mammals. Quantification of habitat fragmentation will help guide threat assessment and strategic priorities for global mammal conservation

Epide·miology of non-fatal injuries due to external causes in Johannesburg-Soweto Part I. Methodology and materials

In this, the first of two articles examining the epidemiology of non-fatal trauma in Johannesburg-Soweto, we define case inclusion criteria, and discuss the methodology and materials used in this low-cost, hospital-based survey. The survey was conducted between 8 June 1989 and 24 August 1990. Sampling of both inpatient trauma cases and those seen in casualty departments took place in 6 state and 5 private hospitals located within or nearby the Johannesburg magisterial district. Demographic details about each patient, as well as information concerning spatial and temporal details of the incident, involvement of alcohol or drugs, diagnosis, severity of injury, and placement after casualty treatment, were collected by interviewing each patient. Data concerning the age, sex and racial composition of the background population were assembled from a number of sources. After discussing the internal limitations of this methodology, it is concluded that its findings may be of limited use for improving secondary interventions, but are of definite value for trauma prevention programmes

Epidemiology of non-fatal injuries due to external causes in Johannesburg-Soweto Part 11. Incidence and determinants

A total of 3535 trauma cases were enumerated in Johannesburg- Soweto between 1989 and 1990 in the course of 271 hospital ward rounds and 43 casualty watches. The overall trauma incidence was 2886 new cases per annum per 100000 population, rising to 19872 for coloured males aged 20 - 24 years and to 8761 for black males aged 20 - 24 years. Overall the malelfemale ratio was 2,9 rising to 6 or more in adolescence (15 - 19) for blacks andcoloureds. There were some 156 new resident cases of trauma daily; half these were victims of interpersonal violence, and coloureds constituted 22% of this group, although forming only 8% of the denominator population. Witluegards to cause, most trauma among blacks and coloureds arose from interpersonal violence and significantly less from transport accidents. Among blacks injured in transport accidents (the majority of which involved motor vehicles) most were pedestrians, whereas most whites injured in such accidents were occupants of vehicles. For all groups trauma was most likely to be incurred 'in the street' although for white and coloured women the home was most dangerous. The implications of these and related findings for treatment and prevention and briefly reviewed

Measurement of extravascular lung water to diagnose severe reperfusion lung injury following pulmonary endarterectomy: a prospective cohort clinical validation study

The measurement of extravascular lung water is a relatively new technology which has not yet been well validated as a clinically useful tool. We studied its utility in patients undergoing pulmonary endarterectomy as they frequently suffer reperfusion lung injury and associated oedematous lungs. Such patients are therefore ideal for evaluating this new monitor. We performed a prospective observational cohort study during which extravascular lung water index measurements were taken before and immediately after surgery and postoperatively in intensive care. Data were analysed for 57 patients; 21 patients (37%) experienced severe reperfusion lung injury. The first extravascular lung water index measurement after cardiopulmonary bypass failed to predict severe reperfusion lung injury, area under the receiver operating characteristic curve 0.59 (95%CI 0.44–0.74). On intensive care, extravascular lung water index correlated most strongly at 36 h, area under the receiver operating characteristic curve 0.90 (95%CI 0.80–1.00). Peri‐operative extravascular lung water index is not a useful measure to predict severe reperfusion lung injury after pulmonary endarterectomy, however, it does allow monitoring and measurement during the postoperative period. This study implies that extravascular lung water index can be used to directly assess pulmonary fluid overload and that monitoring patients by measuring extravascular lung water index during their intensive care stay is useful and correlates with their clinical course. This may allow directed, pre‐empted therapy to attenuate the effects and improve patient outcomes and should prompt further studies

Explanation in mathematical conversations:An empirical investigation

Analysis of online mathematics forums can help reveal how explanation is used by mathematicians; we contend that this use of explanation may help to provide an informal conceptualization of simplicity. We extracted six conjectures from recent philosophical work on the occurrence and characteristics of explanation in mathematics. We then tested these conjectures against a corpus derived from online mathematical discussions. To this end, we employed two techniques, one based on indicator terms, the other on a random sample of comments lacking such indicators. Our findings suggest that explanation is widespread in mathematical practice and that it occurs not only in proofs but also in other mathematical contexts. Our work also provides further evidence for the utility of empirical methods in addressing philosophical problems

Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa

Population trends play a large role in species risk assessments and conservation planning, and species are often considered threatened if their recent rate of decline meets certain thresholds, regardless how large the population is. But how reliable an indicator of extinction risk is a single estimate of population trend? Given the integral role this decline-based approach has played in setting conservation priorities, it is surprising that it has undergone little empirical scrutiny. We compile an extensive global dataset of time series of abundance data for over 1300 vertebrate populations to provide the first major test of the predictability of population growth rates in nature. We divided each time series into assessment and response periods and examined the correlation between growth rates in the two time periods. In birds, population declines tended to be followed by further declines, but mammals, salmon, and other bony fishes showed the opposite pattern: past declines were associated with subsequent population increases, and vice versa. Furthermore, in these taxa subsequent growth rates were higher when initial declines were more severe. These patterns agreed with data simulated under a null model for a dynamically stable population experiencing density dependence. However, this type of result could also occur if conservation actions positively affected the population following initial declines—a scenario that our data were too limited to rigorously evaluate. This ambiguity emphasizes the importance of understanding the underlying causes of population trajectories in drawing inferences about rates of decline in abundance