Dynamics and pragmatics for high performance concurrency

This thesis is concerned with support at all levels for building highly concurrent and dynamic parallel processing systems. The CSP model of concurrency, as (largely) embodied in the occam programming language is used due to its simplicity, expressiveness, architecture- independent nature, and potential for high performance. Additionally, occam provides guarantees regarding freedom from aliasing and race-hazard error. This thesis addresses one of the grand challenges of present day computer science: providing a software technology that offers the dynamic flexibility and performance of mainstream object oriented environments with the level of safety, formal analysis, modularity and lightweight concurrency offered by CSP/occam. Two approaches to this challenge are possible: do something to make the mainstream languages (e.g. Java, C++) safe, or make occam dynamic -- without compromising its existing good properties. This thesis follows the latter route. The first part of this thesis concentrates on enhancing the occam language and run-time system, on a commodity platform (IBM PC) running the freely available Linux operating system. After a brief introduction to the various components of the kroc occam system, additions and extensions to the occam programming language and supporting run-time system are examined. These provide a greater degree of programming flexibility in occam (for example, by adding support for dynamic allocation, mobile semantics and dynamic network construction), without compromising the safety of programs which use them. Benchmarks are reported that demonstrate significant improvements in performance (for example, channel communication in tens of nano-seconds). The second part concentrates on improving the level of interaction between occam programs and the OS environment. Providing easy access to sockets and networking, for example. This thesis concludes with a discussion of the work presented herein, with consideration given to parallels with object-oriented languages. Also described are details of ongoing and potential future research. The modified language grammar, details of new compiler generated code, and miscellany are provided in the appendices

Dynamics and pragmatics for high performance concurrency

This thesis is concerned with support at all levels for building highly concurrent and dynamic parallel processing systems. The CSP model of concurrency, as (largely) embodied in the occam programming language is used due to its simplicity, expressiveness, architecture- independent nature, and potential for high performance. Additionally, occam provides guarantees regarding freedom from aliasing and race-hazard error. This thesis addresses one of the grand challenges of present day computer science: providing a software technology that offers the dynamic flexibility and performance of mainstream object oriented environments with the level of safety, formal analysis, modularity and lightweight concurrency offered by CSP/occam. Two approaches to this challenge are possible: do something to make the mainstream languages (e.g. Java, C++) safe, or make occam dynamic -- without compromising its existing good properties. This thesis follows the latter route. The first part of this thesis concentrates on enhancing the occam language and run-time system, on a commodity platform (IBM PC) running the freely available Linux operating system. After a brief introduction to the various components of the kroc occam system, additions and extensions to the occam programming language and supporting run-time system are examined. These provide a greater degree of programming flexibility in occam (for example, by adding support for dynamic allocation, mobile semantics and dynamic network construction), without compromising the safety of programs which use them. Benchmarks are reported that demonstrate significant improvements in performance (for example, channel communication in tens of nano-seconds). The second part concentrates on improving the level of interaction between occam programs and the OS environment. Providing easy access to sockets and networking, for example. This thesis concludes with a discussion of the work presented herein, with consideration given to parallels with object-oriented languages. Also described are details of ongoing and potential future research. The modified language grammar, details of new compiler generated code, and miscellany are provided in the appendices.EThOS - Electronic Theses Online ServiceGBUnited Kingdo

An evaluation of Intel’s Restricted Transactional Memory for CPAs,

Abstract. With the release of their latest processor microarchitecture, codenamed Haswell, Intel added new Transactional Synchronization Extensions (TSX) to their processors' instruction set. These extensions include support for Restricted Transactional Memory (RTM), a programming model in which arbitrary sized units of memory can be read and written in an atomic manner. This paper describes the low-level RTM programming model, benchmarks the performance of its instructions and speculates on how it may be used to implement and enhance Communicating Process Architectures

The Ninth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the SDSS-III Baryon Oscillation Spectroscopic Survey

The Sloan Digital Sky Survey III (SDSS-III) presents the first spectroscopic data from the Baryon Oscillation Spectroscopic Survey (BOSS). This ninth data release (DR9) of the SDSS project includes 535,995 new galaxy spectra (median z=0.52), 102,100 new quasar spectra (median z=2.32), and 90,897 new stellar spectra, along with the data presented in previous data releases. These spectra were obtained with the new BOSS spectrograph and were taken between 2009 December and 2011 July. In addition, the stellar parameters pipeline, which determines radial velocities, surface temperatures, surface gravities, and metallicities of stars, has been updated and refined with improvements in temperature estimates for stars with T_eff<5000 K and in metallicity estimates for stars with [Fe/H]>-0.5. DR9 includes new stellar parameters for all stars presented in DR8, including stars from SDSS-I and II, as well as those observed as part of the SDSS-III Sloan Extension for Galactic Understanding and Exploration-2 (SEGUE-2). The astrometry error introduced in the DR8 imaging catalogs has been corrected in the DR9 data products. The next data release for SDSS-III will be in Summer 2013, which will present the first data from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) along with another year of data from BOSS, followed by the final SDSS-III data release in December 2014.Comment: 9 figures; 2 tables. Submitted to ApJS. DR9 is available at http://www.sdss3.org/dr

Analytical Processing of Binary Mixture Information by Olfactory Bulb Glomeruli

Odors are rarely composed of a single compound, but rather contain a large and complex variety of chemical components. Often, these mixtures are perceived as having unique qualities that can be quite different than the combination of their components. In many cases, a majority of the components of a mixture cannot be individually identified. This synthetic processing of odor information suggests that individual component representations of the mixture must interact somewhere along the olfactory pathway. The anatomical nature of sensory neuron input into segregated glomeruli with the bulb suggests that initial input of odor information into the bulb is analytic. However, a large network of interneurons within the olfactory bulb could allow for mixture interactions via mechanisms such as lateral inhibition. Currently in mammals, it is unclear if postsynaptic mitral/tufted cell glomerular mixture responses reflect the analytical mixture input, or provide the initial basis for synthetic processing with the olfactory system. To address this, olfactory bulb glomerular binary mixture representations were compared to representations of each component using transgenic mice expressing the calcium indicator G-CaMP2 in olfactory bulb mitral/tufted cells. Overall, dorsal surface mixture representations showed little mixture interaction and often appeared as a simple combination of the component representations. Based on this, it is concluded that dorsal surface glomerular mixture representations remain largely analytical with nearly all component information preserved

Going against the herd: psychological and cultural factors underlying the 'vaccination confidence gap'

By far the most common strategy used in the attempt to modify negative attitudes toward vaccination is to appeal to evidence-based reasoning. We argue, however, that focusing on science comprehension is inconsistent with one of the key facts of cognitive psychology: Humans are biased information processors and often engage in motivated reasoning. On this basis, we hypothesised that negative attitudes can be explained primarily by factors unrelated to the empirical evidence for vaccination; including some shared attitudes that also attract people to complementary and alternative medicine (CAM). In particular, we tested psychosocial factors associated with CAM endorsement in past research; including aspects of spirituality, intuitive (vs analytic) thinking styles, and the personality trait of openness to experience. These relationships were tested in a cross-sectional, stratified CATI survey (N = 1256, 624 Females). Whilst educational level and thinking style did not predict vaccination rejection, psychosocial factors including: preferring CAM to conventional medicine (OR .49, 95% CI .36 .83, 95% CI .71 to vaccination. Furthermore, for 9 of the 12 CAMs surveyed, utilisation in the last 12 months was associated with lower levels of vaccination endorsement. From this we suggest that vaccination scepticism appears to be the outcome of a particular cultural and psychological orientation leading to unwillingness to engage with the scientific evidence. Vaccination compliance might be increased either by building general confidence and understanding of evidence-based medicine, or by appealing to features usually associated with CAM, e.g.&ndash;.66), endorsement of spirituality as a source of knowledge (OR&ndash;.96), and openness (OR .86, 95% CI .74&ndash;.99), all predicted negative attitudes&lsquo;strengthening your natural resistance to disease&rsquo;

Optical Coherence Tomography in Parkinsonian Syndromes

BACKGROUND/OBJECTIVE: Parkinson's disease (PD) and the atypical parkinsonian syndromes multiple system atrophy (MSA), progressive supranuclear palsy (PSP) and corticobasal syndrome (CBS) are movement disorders associated with degeneration of the central nervous system. Degeneration of the retina has not been systematically compared in these diseases. METHODS: This cross-sectional study used spectral-domain optical coherence tomography with manual segmentation to measure the peripapillar nerve fiber layer, the macular thickness, and the thickness of all retinal layers in foveal scans of 40 patients with PD, 19 with MSA, 10 with CBS, 15 with PSP, and 35 age- and sex-matched controls. RESULTS: The mean paramacular thickness and volume were reduced in PSP while the mean RNFL did not differ significantly between groups. In PSP patients, the complex of retinal ganglion cell- and inner plexiform layer and the outer nuclear layer was reduced. In PD, the inner nuclear layer was thicker than in controls, MSA and PSP. Using the ratio between the outer nuclear layer and the outer plexiform layer with a cut-off at 3.1 and the additional constraint that the inner nuclear layer be under 46 µm, we were able to differentiate PSP from PD in our patient sample with a sensitivity of 96% and a specificity of 70%. CONCLUSION: Different parkinsonian syndromes are associated with distinct changes in retinal morphology. These findings may serve to facilitate the differential diagnosis of parkinsonian syndromes and give insight into the degenerative processes of patients with atypical parkinsonian syndromes

Proteasome inhibition for treatment of leishmaniasis, Chagas disease and sleeping sickness

Chagas disease, leishmaniasis and sleeping sickness affect 20 million people worldwide and lead to more than 50,000 deaths annually. The diseases are caused by infection with the kinetoplastid parasites Trypanosoma cruzi, Leishmania spp. and Trypanosoma brucei spp., respectively. These parasites have similar biology and genomic sequence, suggesting that all three diseases could be cured with drugs that modulate the activity of a conserved parasite target. However, no such molecular targets or broad spectrum drugs have been identified to date. Here we describe a selective inhibitor of the kinetoplastid proteasome (GNF6702) with unprecedented in vivo efficacy, which cleared parasites from mice in all three models of infection. GNF6702 inhibits the kinetoplastid proteasome through a non-competitive mechanism, does not inhibit the mammalian proteasome or growth of mammalian cells, and is well-tolerated in mice. Our data provide genetic and chemical validation of the parasite proteasome as a promising therapeutic target for treatment of kinetoplastid infections, and underscore the possibility of developing a single class of drugs for these neglected diseases