Nonconscious priming of communication

This study investigated whether nonconscious priming can affect the communicative quality of narratives. In two experiments, narrators were primed with words associated with helpfulness or unhelpfulness, and then, in an apparently unrelated task, read and retold a short story to addressees. In Experiment 1, the narrator provided a spoken description, and we also manipulated whether the narrator retold the story to the addressee or to a microphone. In Experiment 2, the narrator provided a written description. In both experiments, narrators primed with helpful words took longer to read the story and provided retellings that were rated to be higher quality than narrators primed with unhelpful words. We propose that priming the concept of helpfulness influences the processes involved in message construction

High-performance epistasis detection in quantitative trait GWAS

epiSNP is a program for identifying pairwise single nucleotide polymorphism (SNP) interactions (epistasis) in quantitative-trait genome-wide association studies (GWAS). A parallel MPI version (EPISNPmpi) was created in 2008 to address this computationally expensive analysis on large data sets with many quantitative traits and SNP markers. However, the falling cost of genotyping has led to an explosion of large-scale GWAS data sets that challenge EPISNPmpi’s ability to compute results in a reasonable amount of time. Therefore, we optimized epiSNP for modern multi-core and highly parallel many-core processors to efficiently handle these large data sets. This paper describes the serial optimizations, dynamic load balancing using MPI-3 RMA operations, and shared-memory parallelization with OpenMP to further enhance load balancing and allow execution on the Intel Xeon Phi coprocessor (MIC). For a large GWAS data set, our optimizations provided a 38.43× speedup over EPISNPmpi on 126 nodes using 2 MICs on TACC’s Stampede Supercomputer. We also describe a Coarray Fortran (CAF) version that demonstrates the suitability of PGAS languages for problems with this computational pattern. We show that the Coarray version performs competitively with the MPI version on the NERSC Edison Cray XC30 supercomputer. Finally, the performance benefits of hyper-threading for this application on Edison (average 1.35× speedup) are demonstrated

Stability of mRNA/DNA and DNA/DNA Duplexes Affects mRNA Transcription

Nucleic acids, due to their structural and chemical properties, can form double-stranded secondary structures that assist the transfer of genetic information and can modulate gene expression. However, the nucleotide sequence alone is insufficient in explaining phenomena like intron-exon recognition during RNA processing. This raises the question whether nucleic acids are endowed with other attributes that can contribute to their biological functions. In this work, we present a calculation of thermodynamic stability of DNA/DNA and mRNA/DNA duplexes across the genomes of four species in the genus Saccharomyces by nearest-neighbor method. The results show that coding regions are more thermodynamically stable than introns, 3′-untranslated regions and intergenic sequences. Furthermore, open reading frames have more stable sense mRNA/DNA duplexes than the potential antisense duplexes, a property that can aid gene discovery. The lower stability of the DNA/DNA and mRNA/DNA duplexes of 3′-untranslated regions and the higher stability of genes correlates with increased mRNA level. These results suggest that the thermodynamic stability of DNA/DNA and mRNA/DNA duplexes affects mRNA transcription

Performance and Scalability of MPI on PC Clusters

Abstract. The purpose of this paper is to compare the communication performance and scalability of MPI communication routines on an NT cluster, a Myrinet Linux cluster, an Ethernet Linux cluster, a Cray T3E-600, and an SGI Origin 2000. All tests in this paper were run for the various numbers of processors and 2 message sizes. For most of the MPI tests used in this paper, the T3E-600 and Origin 2000 outperform the NT cluster, the Myrinet and Ethernet Linux clusters. In spite of the fact that the Cray T3E-600 is about 5 years old, it performs best of all machines for most of the tests. For mpi_bcast, mpi_allgather, andmpi_alltoall, the Myrinet Linux cluster outperforms the NT cluster. For all other MPI collective routines, the NT cluster outperforms the Myrinet Linux cluster. For all MPI collective routines, the Myrinet Linux cluster performs significantly better than the Ethernet Linux cluster.