Hierarchical Parallelization of Gene Differential Association Analysis

<p>Abstract</p> <p>Background</p> <p>Microarray gene differential expression analysis is a widely used technique that deals with high dimensional data and is computationally intensive for permutation-based procedures. Microarray gene differential association analysis is even more computationally demanding and must take advantage of multicore computing technology, which is the driving force behind increasing compute power in recent years. In this paper, we present a two-layer hierarchical parallel implementation of gene differential association analysis. It takes advantage of both fine- and coarse-grain (with granularity defined by the frequency of communication) parallelism in order to effectively leverage the non-uniform nature of parallel processing available in the cutting-edge systems of today.</p> <p>Results</p> <p>Our results show that this hierarchical strategy matches data sharing behavior to the properties of the underlying hardware, thereby reducing the memory and bandwidth needs of the application. The resulting improved efficiency reduces computation time and allows the gene differential association analysis code to scale its execution with the number of processors. The code and biological data used in this study are downloadable from <url>http://www.urmc.rochester.edu/biostat/people/faculty/hu.cfm.</url></p> <p>Conclusions</p> <p>The performance sweet spot occurs when using a number of threads per MPI process that allows the working sets of the corresponding MPI processes running on the multicore to fit within the machine cache. Hence, we suggest that practitioners follow this principle in selecting the appropriate number of MPI processes and threads within each MPI process for their cluster configurations. We believe that the principles of this hierarchical approach to parallelization can be utilized in the parallelization of other computationally demanding kernels.</p

Science, technology, engineering, and mathematics graduate teaching assistants teaching self-efficacy

The graduate experience is a critical time for development of academic faculty, but often there is little preparation for teaching during the graduate career. Teaching self-efficacy, an instructor’s belief in his or her ability to teach students in a specific context, can help to predict teaching behavior and student achievement, and can be used as a measure of graduate students’ development as instructors. An instrument measuring teaching self-efficacy of science, technology, engineering, and mathematics (STEM) graduate teaching assistants (GTAs) was developed from a general university faculty teaching instrument to the specific teaching context of STEM GTAs. Construct and face validity, measurement reliability, and factor structure of the instrument were determined from survey data of 253 STEM GTAs at six universities. STEM GTA teaching self-efficacy correlated to various measures of GTA professional development and teaching experience. Implications and applications for faculty involved in GTA professional development, supervision, and research are discussed

Inside co-production: ruling, resistance, and practice

It might be argued that a narrative of co-production has come to re-define contemporary social and public policy. Elinor Ostrom’s pioneering work on co-production, that started in the 1970s and was awards the Nobel prize for economics in 2009, offers a way to bridge the gap between the market and the state through involving citizens in the production of common goods (Ostrom et al. 1978; Ostrom 2015). This ‘disarmingly simple’ idea (Alford 2014) is now engrained within contemporary policy-making and public service delivery (Ansell and Gash 2008), symbolising a more humane and inclusive alternative to New Pubic Management (Newman 2005) and cornerstone to New Public Governance (Osborne et al. 2016)

A hafted halberd excavated at Trecastell, Powys: from undercurrent to uptake – the emergence and contextualisation of halberds in Wales and North-west Europe

Excavations at Trecastell, Powys, south Wales, in 2007 yielded a copper halberd complete with its haft-grip. This has major implications for the mode of hafting halberds, but the discovery has also prompted a reconsideration of insular halberds in their north-west European context. Understanding the relationships between different types of halberd and different regional groups continues to be hampered by the dearth of good dating evidence, but the creation of better classifications for British and Irish weapons and new radiocarbon dates on two examples, one being Trecastell, have allowed a new developmental scheme to be advanced.The emergence of metal-headed halberds is considered more generally. While it is acknowledged that halberd-like implements pre-existed in other materials in some parts of Europe, it is argued that the appearance of metal-headed halberds depended on the transmission of a particular set of metallurgical and related skills. A new model for the vigorous uptake of halberds on a regional basis helps explain the patchiness and anachronism of halberd hotspots.The Trecastell halberd adds to one of the significant concentrations of the weapon type in Britain and prompts a more general review of the earliest metalwork from Wales and the Marches. For the Chalcolithic, halberds are instrumental in identifying a major contrast in depositional behaviour; this contrast dissolves at the beginning of the Early Bronze Age when a ‘new deposition ground’ is established. The former is attributed to the existence of a regional group across much of the region for whom the halberd served as a cultural icon, while the latter may relate to the demise of this enshrined value for the halberd.</jats:p

Nurr1 dependent regulation of pro-inflammatory mediators in immortalised synovial fibroblasts

BACKGROUND: Nurr1 is an orphan member of the nuclear receptor superfamily; these orphan receptors are a group for which a ligand has yet to be identified. Nurr1 has been shown to regulate the expression of a small number of genes as a monomeric, constitutively active receptor. These Nurr1 regulated genes are primarily associated with dopamine cell maturation and survival. However, previous reports have shown an increased expression of Nurr1 in the synovium of patients with rheumatoid arthritis (RA) suggesting a pro-inflammatory role for Nurr1 in RA. In this study we investigate the potential pro-inflammatory role of Nurr1 by monitoring Nurr1 dependent gene expression in an immortalised synoviocyte cell line, K4IM. METHODS: We overexpressed the wild type and a dominant negative form of the orphan nuclear receptor Nurr1, in a model synoviocyte cell line. Using the Affymetrix HG-U133 Genechips we demonstrate the effects on the transcriptome by the receptor. Further evidence of gene expression change was demonstrated using quantitative RT-PCR and ELISA analysis. RESULTS: We show that Nurr1 regulates transcription of a small number of genes for pro-inflammatory modulators of which the most significant is interleukin-8 (IL-8). We also demonstrate increased synthesis and secretion of IL-8 further supporting a role for Nurr1 in inflammatory signalling pathways. CONCLUSION: Using microarray analysis we show that elevated levels of Nurr1 leads to increased gene expression of pro-inflammatory genes: IL-8, Amphiregulin and Kit ligand in a model cell line. This data provides further evidence for an additional role for Nurr1 in inflammation and may play a role in the pathogenesis of rheumatoid arthritis

Activity Substitutability and Degree of Specialization among Deer and Elk Hunters in Multiple States

This article examines relationships between hunter specialization and activity substitutability. Data were obtained from a mail survey of 6,983 deer hunters in eight states and 2,584 elk hunters in three states. Activity substitutability was measured by asking what activity would provide the same satisfaction as deer or elk hunting. Between 41% and 59% of deer hunters and 38% to 46% of elk hunters reported substitutes such as fishing and other big game hunting. Cluster analyses of hunter skill, centrality, equipment, and experience revealed four specialization groups (casual, intermediate, focused, veteran). Casual hunters were most likely to report a substitute followed by intermediates, focused, and veterans. This inverse relationship between concepts was consistent across states and species hunted. Veteran hunters were most likely to report other big game hunting as a substitute, whereas casual hunters in many states were most likely to consider fishing as a substitute.Keywords: wildlife, substitutability, hunting, recreation specializationKeywords: wildlife, substitutability, hunting, recreation specializatio

Science, Technology, Engineering, and Mathematics Graduate Teaching Assistants Teaching Self-Efficacy

The graduate experience is a critical time for development of academic faculty, but often there is little preparation for teaching during the graduate career.  Teaching self-efficacy, an instructor’s belief in his or her ability to teach students in a specific context, can help to predict teaching behavior and student achievement, and can be used as a measure of graduate students’ development as instructors.  An instrument measuring teaching self-efficacy of science, technology, engineering, and mathematics (STEM) graduate teaching assistants (GTAs) was developed from a general university faculty teaching instrument to the specific teaching context of STEM GTAs.  Construct and face validity, measurement reliability, and factor structure of the instrument were determined from survey data of 253 STEM GTAs at six universities.  STEM GTA teaching self-efficacy correlated to various measures of GTA professional development and teaching experience.  Implications and applications for faculty involved in GTA professional development, supervision, and research are discussed

A theory for the impact of a wave breaking onto a permeable barrier with jet generation

We model a water wave impact onto a porous breakwater. The breakwater surface is modelled as a thin barrier composed of solid matter pierced by channels through which water can flow freely. The water in the wave is modelled as a finite-length volume of inviscid, incompressible fluid in quasi-one-dimensional flow during its impact and flow through a typical hole in the barrier. The fluid volume moves at normal incidence to the barrier. After the initial impact the wave water starts to slow down as it passes through holes in the barrier. Each hole is the source of a free jet along whose length the fluid velocity and width vary in such a way as to conserve volume and momentum at zero pressure. We find there are two types of flow, depending on the porosity, ß , of the barrier. If ß : 0 = ß < 0.5774 then the barrier is a strong impediment to the flow, in that the fluid velocity tends to zero as time tends to infinity. But if ß : 0.5774 = ß = 1 then the barrier only temporarily holds up the flow, and the decelerating wave water passes through in a finite time. We report results for the velocity and impact pressure due to the incident wave water, and for the evolving shape of the jet, with examples from both types of impact. We account for the impulse on the barrier and the conserved kinetic energy of the flow. Consideration of small ß gives insight into the sudden changes in flow and the high pressures that occur when a wave impacts a nearly impermeable seawall