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.

Autobiographical memories of anxiety-related experiences.

Ninety-nine undergraduate students retrieved three memories associated with each of the five emotional experiences: panic, trauma, worry, social anxiety, and feeling content. Subsequently, they answered 24 questions assessing properties of each memory, including the vividness and perceived accuracy of the memories and sensory, emotional, and anxiety-related experiences during retrieval. Memories were coded for affective tone and specificity. Results indicated that panic-related and trauma-related memories were rated similarly as content memories, but that they generally were associated with more imagery and emotional experiencing than worry-related or social anxiety-related memories. Participants experienced panic and worry symptoms to the greatest degree when they retrieved panic-related and trauma-related memories. All anxiety-related memories were characterized by more negative tone than content memories. Panic-related and trauma-related memories were more specific than worry-related, social anxiety-related, and content memories. These findings can explain partially why individuals with some, but not all, anxiety disorders experience enhanced memory for threatening material.