CamGrid: Experiences in constructing a university-wide, Condor-based grid at the University of Cambridge

Proceedings of the 2004 UK e-Science All Hands Meeting, 31st August - 3rd September, Nottingham UKIn this article we describe recent work done in building a university-wide grid at the University of Cambridge based on the Condor middleware [1]. Once the issues of stakeholder concerns (e.g. security policies) and technical problems (e.g. firewalls and private IP addresses) have been taken into account, a solution based on two separate Condor environments was decided on. The first of these is a single large pool administered centrally by the University Computing Service (UCS) and the second a federated service of flocked Condor pools belonging to various departments and run over a Virtual Private Network (VPN). We report on the current status of this ongoing work

Talactoferrin Immunotherapy in Metastatic Renal Cell Carcinoma: A Case Series of Four Long-Term Survivors

Talactoferrin alfa (also known as recombinant human lactoferrin, rhLF) is a novel immunomodulatory protein that has previously demonstrated anti-tumor properties in animal models. Following a successful phase I trial, it was administered orally to patients with metastatic renal cell carcinoma (RCC) in a phase II trial conducted at the Michael E. DeBakey Veterans Affairs Medical Center in Houston, Texas, among other sites. We report a case series of 4 patients treated at our institution with very encouraging progression-free survivals, all exceeding 30 months, in order to suggest that this agent merits further study. These four patients with radiographically progressive metastatic RCC received single-agent oral talactoferrin in daily doses of 9 grams, given in cycles of 2 weeks on/2 weeks off, until evidence of toxicity or disease progression. Given the small sample size and the heterogenous tumor biology of RCC, tumor growth rate was used as a primary endpoint so that each patient could serve as their own control. The agent's effectiveness was then determined through radiographic tracking of the tumors before, during, and after treatment, with use of the Response Evaluation Criteria in Solid Tumors (RECIST) protocol to follow target lesions. The results showed that the drug was well tolerated, with no occurrence of talactoferrin-related grade 3 or 4 adverse events or laboratory anomalies by NCI-CTEP criteria. The four patients described in the case series demonstrated very encouraging progression-free survivals, all exceeding 30 months. We conclude that decreased tumor growth rate may correlate with increased progression-free survival. Talactoferrin is a promising, well-tolerated agent whose clinical benefits should be evaluated in a randomized phase III study with a placebo control arm

Assessing the potential impacts of a changing climate on the distribution of a rabies virus vector

Common vampire bats (Desmodus rotundus) occur throughout much of South America to northern MeÂxico. Vampire bats have not been documented in recent history in the United States, but have been documented within about 50 km of the U.S. state of Texas. Vampire bats feed regularly on the blood of mammals and can transmit rabies virus to native species and livestock, causing impacts on the health of prey. Thus cattle producers, wildlife management agencies, and other stakeholders have expressed concerns about whether vampire bats might spread into the southern United States. On the other hand, concerns about vampire- borne rabies can also result in wanton destruction at bat roosts in areas occupied by vampire bats, but also in areas not known to be occupied by this species. This can in turn negatively affect some bat roosts, populations, and species that are of conservation concern, including vampire bats. To better understand the current and possible future distribution of vampire bats in North America and help mitigate future cattle management problems, we used 7,094 vampire bat occurrence records from North America and species distribution modeling (SDM) to map the potential distribution of vampire bats in North America under current and future climate change scenarios. We analysed and mapped the potential distribution of this species using 5 approaches to species distribution modeling: logistic regression, multivariate adaptive regression splines, boosted regression trees, random forest, and maximum entropy. We then projected these models into 17 ªworst-caseº future climate scenarios for year 2070 to generate hypotheses about how the vampire bat distribution in North America might change in the future. Of the variables used in this analysis, minimum temperature of the coldest month had the highest variable importance using all 5 SDM approaches. These results suggest two potential near-future routes of vampire bat dispersal into the U. S., one via southern Texas, and a second into southern Florida. Some of our SDM models support the hypothesis that suitable habitat for vampire bats may currently exist in parts of the Mexico-U.S. borderlands, including extreme southern portions of Texas, as well as in southern Florida. However, this analysis also suggests that extensive expansion into the south-eastern and south-western U.S. over the coming ~60 years appears unlikely

The inheritance of resistance to bacterial leaf spot of lettuce caused by Xanthomonas campestris pv. vitians in three lettuce cultivars.

Lettuce yields can be reduced by the disease bacterial leaf spot (BLS) caused by the pathogen Xanthomonas campestris pv. vitians (Xcv) and host resistance is the most feasible method to reduce disease losses. The cultivars La Brillante, Pavane and Little Gem express an incompatible host-pathogen interaction as a hypersensitive response (HR) to California strains of Xcv resulting in resistance. Little was known about the inheritance of resistance; however, resistance to other lettuce pathogens is often determined by resistance gene candidates (RGCs) encoding nucleotide-binding leucine-rich repeat (NB-LRR) proteins. Therefore, we determined the inheritance of BLS resistance in the cultivars La Brillante, Little Gem and Pavane and mapped it relative to RGCs. The reaction to Xcv was analyzed in nine F1, F2 and recombinant inbred line populations of lettuce from HR×compatible or HR×HR crosses. The HR in La Brillante, Pavane and Little Gem is conditioned by single dominant genes, which are either allelic or closely linked genes. The resistance gene in La Brillante was designated Xanthomonas resistance 1 (Xar1) and mapped to lettuce linkage group 2. Xar1 is present in a genomic region that contains numerous NB-LRR encoding RGCs and functional pathogen resistance loci in the RGC2 family. The Xar1 gene confers a high level of BLS resistance in the greenhouse and field that can be introgressed into commercial lettuce cultivars to reduce BLS losses using molecular markers

Distribution of Fish Species in Cedar Lake

With over 13,000 described species of freshwater fishes, diversity within aquatic systems can vary extensively. At the local scale small changes in the diversity of fish species within an ecosystem will modify processes within the ecosystem such as community decomposition and metabolism. Recent analyses indicate that actual species diversity within small, shallow ponds may be higher than previously thought. Fish species distribution will differ based on location within the aquatic system relative to the species’ position in the trophic web. We will measure both quantitative and qualitative differences among species at different locations within of Cedar Lake, expecting to find a decrease in both species diversity and total number of fish as the depth increases. We will count the number of fish species and the total number of fish at each depth and use t-test analysis to determine if depth influences fish diversity

A Comparison of Methods to Estimate Forest Canopy Structure in Cedarville, Ohio

Plant canopy architecture results from the relationships of species composition, historical land use, succession, and species competition. Each forest’s canopy architecture influences the plant and animal community that live below. Key variables used to quantify the canopy architecture are leaf area index (LAI, m2 leaf m-2 ground) and canopy openness. The objective of our study was to analyze the accuracy of several mobile phone applications in interpreting the varying light environments of a second-growth forest in Ohio as compared to the standard technique using hemispherical photography. For this pilot project we measured 30 randomly selected points throughout a 15 acre forest stand in Greene County, Ohio. Mean canopy openness (minimum - maximum) for the site was 14.7 (5.7 - 23.8) and 46.1 (20.0 - 77.4) for GLAMA and Canopeo, respectively. Additionally, we processed digital hemispherical photographs using Gap Light Analyzer (GLA v 2.0) and calculated a mean % openness of 20.6 (12.2 - 45.5) and LAI of 2.1. When compared to the standard method of hemispherical photographs Canopeo and GLAMA described 41 and 19% of the total variability in forest canopy openness as measured by GLA. Our data show that GLAMA consistently over estimated while Canopeo underestimated openness. The data from this study reveals how each application used image processing methods to calculate canopy openness. The various applications showed inadequacies regarding the typical methods used to calculate canopy openness; none of the applications proved to be more accurate at calculating canopy openness than the others