permGPU: Using graphics processing units in RNA microarray association studies.

BACKGROUND: Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed. RESULTS: We have developed a CUDA based implementation, permGPU, that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of permGPU within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using permGPU on an NVIDIA GTX 280 card compared to an optimized C/C++ solution running on a conventional Linux server. CONCLUSIONS: permGPU is available as an open-source stand-alone application and as an extension package for the R statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.

Developing the Cost of Large Carnivore Conflict Rapid Response Units - A Namibian Case Study

Namibia is home to half the world’s remaining wild cheetahs and - provides critical habitat for lions, leopards, spotted and brown hyena and African Wild Dogs. Despite such ecological importance, only 5% of cheetah's, <1% of African Wild Dogs', and similar percentages of remaining habitat for other large carnivores exists on officially protected lands. As a result, human/carnivore conflict is a large problem on private lands, where 60% of surveyed farmers will shoot any large carnivore on sight. This project explores building a carnivore rapid response team equipped to mitigate human/carnivore conflict through researching the financial costs of such an endeavor, with an eye on capitalizing potential benefits to all 6 Namibian large carnivore species.

Fluid resuscitation practice patterns in intensive care units of the USA: a cross-sectional survey of critical care physicians.

BACKGROUND: Fluid resuscitation is a cornerstone of intensive care treatment, yet there is a lack of agreement on how various types of fluids should be used in critically ill patients with different disease states. Therefore, our goal was to investigate the practice patterns of fluid utilization for resuscitation of adult patients in intensive care units (ICUs) within the USA. METHODS: We conducted a cross-sectional online survey of 502 physicians practicing in medical and surgical ICUs. Survey questions were designed to assess clinical decision-making processes for 3 types of patients who need volume expansion: (1) not bleeding and not septic, (2) bleeding but not septic, (3) requiring resuscitation for sepsis. First-choice fluid used in fluid boluses for these 3 patient types was requested from the respondents. Descriptive statistics were performed using a Kruskal-Wallis test to evaluate differences among the physician groups. Follow-up tests, including t tests, were conducted to evaluate differences between ICU types, hospital settings, and bolus volume. RESULTS: Fluid resuscitation varied with respect to preferences for the factors to determine volume status and preferences for fluid types. The 3 most frequently preferred volume indicators were blood pressure, urine output, and central venous pressure. Regardless of the patient type, the most preferred fluid type was crystalloid, followed by 5 % albumin and then 6 % hydroxyethyl starches (HES) 450/0.70 and 6 % HES 600/0.75. Surprisingly, up to 10 % of physicians still chose HES as the first choice of fluid for resuscitation in sepsis. The clinical specialty and the practice setting of the treating physicians also influenced fluid choices. CONCLUSIONS: Practice patterns of fluid resuscitation varied in the USA, depending on patient characteristics, clinical specialties, and practice settings of the treating physicians.