Compiling an Array Language to a Graphics Processor

Graphics processors are significantly faster than traditional processors, particularly for numerical code, and in recent years have become flexible enough to permit general-purpose use, rather than just graphics use. NVIDIA\u27s CUDA makes general-purpose graphics processor computing feasible, but it still requires significant programmer effort. My thesis is that array programming can be an effective way to program graphics processors, and that a restricted, functionally pure array language coupled with simple optimizations can have performance competitive with handwritten GPU programs. I support this thesis through the research language Barracuda, an array language embedded within Haskell that generates optimized CUDA code

Strain accumulation in the Santa Barbara Channel, 1971-1987

Geophysical evidence suggests a significant amount of north-south convergence occurs across the Santa Barbara Channel. Tectonic studies indicate a discrepancy between observed fault slip in California and the North American-Pacific plate motion. Newer plate motion models (NUVEL-1) yield a lower rate of convergence. Global Positioning System (GPS) data collected in the Santa Barbara Channel in 1987, when combined with 1971 trilateration measurements, should be sufficient to resolve the present-day convergence rate. In early 1987. from January 3 to 7, GPS data were collected at 14 sites in California and at 5 additional stations throughout North America. The data can be used to estimate the rate of crustal deformation (convergence) ocurring across the Santa Barbara Channel. The GPS baselines were computed with the Bernese 2nd generation software. A comparison was made between baseline lengths obtained with the Burnese and MIT softwares. Baseline changes from 1971 to January, 1987 (GPS-Bernese) across the Santa Barbara Channel were computed. A uniform strain model was calculated from the baseline changes. The present-day rate of convergence across the Santa Barbara Channel was determined to be 8 to 10 mm/yr. This conclusion is obtained from changes in the baseline length measured with a 1971 trilateration survey and a January, 1987, GPS survey. The rapid convergence rate, in addition to the history of large seismic events, suggests this region is a prime target for future geodetic and geophysical studies

Determination of convergence rates across the Ventura Basin, Southern California, using GPS and historical triangulation

Comparison of angles from historical triangulation observations dating as far back as 1932 with Global Positions System (GPS) measurements taken in 1987 indicates that rapid convergence may be taking place on decade timescales in the central and eastern part of the Ventura basin, an east-west trending trough bounded by thrust faults. Changes in angles over this time were analyzed using Prescott's modified Frank's method and in terms of a model which assumes that the regions to the north and south of the basin are rigid blocks undergoing relative motion. For the two block model, inversion of the observed angle changes over the last 28 years for the relative motion vector leads to north-south convergence across the basin of 30 + or - 5 mm/yr, with a left lateral component of 10 + or - 1 mm/yr in the Fillmore-Santa Paula area in the central part of the basin. The modified Frank's method yields strain rates of approximately 2 microrad/yr in both the east and central parts of the basin for measurements spanning the 1971 San Fernando earthquake. Assuming no east-west strain yeilds north-south compression of approximately 3.5 + or - .2 cm/yr. Comparison of triangulation data prior to the earthquake shows no strain outside the margin of error. The convergence rates determined by geodetic techniques are consistent with geologic observations in the area. Such large geodetic deformation rates, with no apparent near-surface creep on the major thrust, can be understood if these faults become subhorizontal at relatively shallow depths and if the subhorizontal portions of the faults are creeping. An alternative explanation of the large displacement rates might be that the pumping of oil in the vicinity of the benchmarks caused large horizontal motions, although it is unlikely that meter scale horizontal motions are due to oil withdrawal. These and other hypotheses are evaluated to better constrain the tectonics of this active region

Behavior change interventions: the potential of ontologies for advancing science and practice

A central goal of behavioral medicine is the creation of evidence-based interventions for promoting behavior change. Scientific knowledge about behavior change could be more effectively accumulated using "ontologies." In information science, an ontology is a systematic method for articulating a "controlled vocabulary" of agreed-upon terms and their inter-relationships. It involves three core elements: (1) a controlled vocabulary specifying and defining existing classes; (2) specification of the inter-relationships between classes; and (3) codification in a computer-readable format to enable knowledge generation, organization, reuse, integration, and analysis. This paper introduces ontologies, provides a review of current efforts to create ontologies related to behavior change interventions and suggests future work. This paper was written by behavioral medicine and information science experts and was developed in partnership between the Society of Behavioral Medicine's Technology Special Interest Group (SIG) and the Theories and Techniques of Behavior Change Interventions SIG. In recent years significant progress has been made in the foundational work needed to develop ontologies of behavior change. Ontologies of behavior change could facilitate a transformation of behavioral science from a field in which data from different experiments are siloed into one in which data across experiments could be compared and/or integrated. This could facilitate new approaches to hypothesis generation and knowledge discovery in behavioral science

Formation of the oxygen torus in the inner magnetosphere: Van Allen Probes observations

We study the formation process of an oxygen torus during the 12–15 November 2012 magnetic storm, using the magnetic field and plasma wave data obtained by Van Allen Probes. We estimate the local plasma mass density (ρL) and the local electron number density (neL) from the resonant frequencies of standing Alfvén waves and the upper hybrid resonance band. The average ion mass (M) can be calculated by M ∼ ρL/neL under the assumption of quasi-neutrality of plasma. During the storm recovery phase, both Probe A and Probe B observe the oxygen torus at L = 3.0–4.0 and L = 3.7–4.5, respectively, on the morning side. The oxygen torus has M = 4.5–8 amu and extends around the plasmapause that is identified at L∼3.2–3.9. We find that during the initial phase, M is 4–7 amu throughout the plasma trough and remains at ∼1 amu in the plasmasphere, implying that ionospheric O+ ions are supplied into the inner magnetosphere already in the initial phase of the magnetic storm. Numerical calculation under a decrease of the convection electric field reveals that some of thermal O+ ions distributed throughout the plasma trough are trapped within the expanded plasmasphere, whereas some of them drift around the plasmapause on the dawnside. This creates the oxygen torus spreading near the plasmapause, which is consistent with the Van Allen Probes observations. We conclude that the oxygen torus identified in this study favors the formation scenario of supplying O+ in the inner magnetosphere during the initial phase and subsequent drift during the recovery phase

Excitation of EMIC waves detected by the Van Allen Probes on 28 April 2013

Abstract We report the wave observations, associated plasma measurements, and linear theory testing of electromagnetic ion cyclotron (EMIC) wave events observed by the Van Allen Probes on 28 April 2013. The wave events are detected in their generation regions as three individual events in two consecutive orbits of Van Allen Probe-A, while the other spacecraft, B, does not detect any significant EMIC wave activity during this period. Three overlapping H+ populations are observed around the plasmapause when the waves are excited. The difference between the observational EMIC wave growth parameter (Eh) and the theoretical EMIC instability parameter (Sh) is significantly raised, on average, to 0.10 ± 0.01, 0.15 ± 0.02, and 0.07 ± 0.02 during the three wave events, respectively. On Van Allen Probe-B, this difference never exceeds 0. Compared to linear theory (Eh\u3eSh), the waves are only excited for elevated thresholds

A survey of fertility and sexual health following allogeneic haematopoietic stem cell transplantation in New South Wales, Australia

Four hundred and twenty-one adult allogeneic haematopoietic stem cell transplant (HSCT) survivors participated in a cross-sectional study to assess sexual dysfunction and infertility post-transplant. Survey instruments included the Sydney Post-Blood and Marrow Transplant (BMT) Survey, Functional Assessment of Cancer Treatment (FACT) – BMT, the Depression, Anxiety, Stress Scales (DASS 21), the Chronic Graft-versus-Host Disease (cGVHD) Activity Assessment- Patient Self Report (Form B), the Lee cGVHD Symptom Scale and The Post-Traumatic Growth Inventory. Most HSCT survivors reported sexual difficulties (51% of males; 66% of females). Men reported erectile dysfunction (79%) and decreased libido (61·6%) and women reported loss of libido (83%), painful intercourse (73%) and less enjoyment of sex (68%). Women also commonly reported vaginal dryness (73%), vaginal narrowing (34%) and vaginal irritation (26%). Woman had much higher rates of genital cGvHD than men (22% vs. 5%). Age and cGVHD were significantly associated with sexual dysfunction. Few survivors had children following transplant (3·3%). However, for those of reproductive age at HSCT, 22% reported trying to conceive, with 10·3% reporting success. This study is the largest to date exploring sexual function in survivors of allo-HSCT. This data provides the basis for health service reform to better meet the needs of HSCT survivors, including evidence to support counselling and education both pre- and post-transplant.Funded by New South Wales Agency for Clinical Innovation Blood and Marrow Transplant Networ

Mycobacterial 65-kD heat shock protein induces release of proinflammatory cytokines from human monocytic cells

Monocytes having phagocytosed mycobacteria are known to present the bacterial 65-kD heat shock protein (hsp) on their cell surface to ΑΒ and ΓΔ T lymphocytes. Cytotoxic CD4 + cells may then lyse monocytes expressing mycobacterial 65-kD hsp. However, it is not known whether 65-kD hsp directly stimulates monocyte functions other than antigen presentation. This study has demonstrated that following extraction of bacterial lipopolysaccharide, purified recombinant mycobacterial 65-kD hsp may directly activate THP-1 cells, a human monocytic line, to accumulate mRNA for and secrete tumour necrosis factor (TNF), a cytokine important in granuloma formation, the characteristic host immune response to mycobacterial infection. TNF gene expression and secretion following stimulation by hsp was dose-dependent and abolished by heat-induced proteolysis. Subsequently, THP-1 cells secreted IL-6 and IL-8, cytokines involved in recruitment and differentiation of T lymphocytes. The data indicate that secretion of proinflammatory cytokines from monocytes activated by mycobacterial 65-kD hsp may be important in the host immune response and in the development of antigen-specific T cell-mediated immunity.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72917/1/j.1365-2249.1993.tb03354.x.pd

The genome of the protozoan parasite Cystoisospora suis and a reverse vaccinology approach to identify vaccine candidates

Vaccine development targeting protozoan parasites remains challenging, partly due to the complex interactions between these eukaryotes and the host immune system. Reverse vaccinology is a promising approach for direct screening of genome sequence assemblies for new vaccine candidate proteins. Here, we applied this paradigm to Cystoisospora suis, an apicomplexan parasite that causes enteritis and diarrhea in suckling piglets and economic losses in pig production worldwide. Using Next Generation Sequencing we produced an ∼84 Mb sequence assembly for the C. suis genome, making it the first available reference for the genus Cystoisospora. Then, we derived a manually curated annotation of more than 11,000 protein-coding genes and applied the tool Vacceed to identify 1,168 vaccine candidates by screening the predicted C. suis proteome. To refine the set of candidates, we looked at proteins that are highly expressed in merozoites and specific to apicomplexans. The stringent set of candidates included 220 proteins, among which were 152 proteins with unknown function, 17 surface antigens of the SAG and SRS gene families, 12 proteins of the apicomplexan-specific secretory organelles including AMA1, MIC6, MIC13, ROP6, ROP12, ROP27, ROP32 and three proteins related to cell adhesion. Finally, we demonstrated in vitro the immunogenic potential of a C. suis-specific 42 kDa transmembrane protein, which might constitute an attractive candidate for further testing