Parallel computing : the story of the elves and the shoemaker : inaugural lecture delivered at Rhodes University

Inaugural lecture delivered at Rhodes UniversityRhodes University Libraries (Digitisation

Interrupt-generating active data objects

An investigation is presented into an interrupt-generating object model which is designed to reduce the effort of programming distributed memory multicomputer networks. The object model is aimed at the natural modelling of problem domains in which a number of concurrent entities interrupt one another as they lay claim to shared resources. The proposed computational model provides for the safe encapsulation of shared data, and incorporates inherent arbitration for simultaneous access to the data. It supplies a predicate triggering mechanism for use in conditional synchronization and as an alternative mechanism to polling. Linguistic support for the proposal requires a novel form of control structure which is able to interface sensibly with interrupt-generating active data objects. The thesis presents the proposal as an elemental language structure, with axiomatic guarantees which enforce safety properties and aid in program proving. The established theory of CSP is used to reason about the object model and its interface. An overview is presented of a programming language called HUL, whose semantics reflect the proposed computational model. Using the syntax of HUL, the application of the interrupt-generating active data object is illustrated. A range of standard concurrent problems is presented to demonstrate the properties of the interrupt-generating computational model. Furthermore, the thesis discusses implementation considerations which enable the model to be mapped precisely onto multicomputer networks, and which sustain the abstract programming level provided by the interrupt-generating active data object in the wider programming structures of HUL

Design automation of a machine-independent code generator

As both computer languages and architectures continue to proliferate, there is a continuing need for new compilers. Researchers have attempted to ease the work of producing compilers by developing methods to automate compiler writing. While much work has been done (and considerable success achieved) in writing parsers which can handle a variety of source languages (using mainly table-driven analysis methods), less progress has been made in formalizing the code generation end of the compiler. Nevertheless, some of the more recent publications in code generation stress portability or retargetability of the resulting compiler. A number of code generator synthesisers have been developed, some of which produce code that can be compared in quality with that produced by a conventional code generator. However, because of the complexity of generalizing the mapping from source language to target machine, and the need for efficiency of various kinds, code generator synthesisers are large, complicated programs. Consequently, the person who develops a code generator using one of these tools invariably needs to be a code generation specialist himself. Many compilers follow a pattern of having a front end which generates intermediate code, and a back end which converts intermediate code to machine code. The intermediate code is effectively machine independent, or can be designed that way. With these points in mind, we have set out to write a system of programs which -- 1. will allow the generation of such a back end in a reasonably short time, for a general intermediate code, and for a general machine code, and -- 2. can be used by anyone who has a sound knowledge of the target machine's architecture and associated assembler language, but is not necessarily a specialist compiler writer. The system consists of a series of friendly, interactive programs by means of which the user sets up tables defining the architecture and assembly level instructions for the target machine, and the code templates onto which intermediate codes produced by a parser have been mapped. A general notation has been developed to represent machine instructions using the same format as the target assembler. Thus the code generator writer is able to write code sequences to perform the effects of the intermediate codes, using assembly mnemonics familiar to him. The resultant table-driven code generator simply replaces a sequence of intermediate codes by their respective code templates, relocating them in memory and filling in addresses known only at code-generation time. This thesis describes the use and implementation details of this generalized code generation system. As an example, the implementation of a code generator for a CLANG [23] parser on an 8080 processor is described. The discussion also includes guide-lines on how to implement a loader and associated run-time routines for use in executing the object code. The results of a number of bench-marks have shown, as expected, that code produced by a code generator developed in this manner is larger and slower than that from a special purpose optimizing code generator, but is still several times faster than interpreting the intermediate code. The major benefit to be gained from using this system lies in the shorter development time by a less skilled person.KMBT_223Adobe Acrobat 9.53 Paper Capture Plug-i

Interrupt-generating active data objects

An investigation is presented into an interrupt-generating object model which is designed to reduce the effort of programming distributed memory multicomputer networks. The object model is aimed at the natural modelling of problem domains in which a number of concurrent entities interrupt one another as they lay claim to shared resources. The proposed computational model provides for the safe encapsulation of shared data, and incorporates inherent arbitration for simultaneous access to the data. It supplies a predicate triggering mechanism for use in conditional synchronization and as an alternative mechanism to polling. Linguistic support for the proposal requires a novel form of control structure which is able to interface sensibly with interrupt-generating active data objects. The thesis presents the proposal as an elemental language structure, with axiomatic guarantees which enforce safety properties and aid in program proving. The established theory of CSP is used to reason about the object model and its interface. An overview is presented of a programming language called HUL, whose semantics reflect the proposed computational model. Using the syntax of HUL, the application of the interrupt-generating active data object is illustrated. A range of standard concurrent problems is presented to demonstrate the properties of the interrupt-generating computational model. Furthermore, the thesis discusses implementation considerations which enable the model to be mapped precisely onto multicomputer networks, and which sustain the abstract programming level provided by the interrupt-generating active data object in the wider programming structures of HUL

Fascicles and the interfascicular matrix show decreased fatigue life with ageing in energy storing tendons

Tendon is composed of rope-like fascicles bound together by interfascicular matrix (IFM). The IFM is critical for the function of energy storing tendons, facilitating sliding between fascicles to allow these tendons to cyclically stretch and recoil. This capacity is required to a lesser degree in positional tendons. We have previously demonstrated that both fascicles and IFM in energy storing tendons have superior fatigue resistance compared with positional tendons, but the effect of ageing on the fatigue properties of these different tendon subunits has not been determined. Energy storing tendons become more injury-prone with ageing, indicating reduced fatigue resistance, hence we tested the hypothesis that the decline in fatigue life with ageing in energy storing tendons would be more pronounced in the IFM than in fascicles. We further hypothesised that tendon subunit fatigue resistance would not alter with ageing in positional tendons. Fascicles and IFM from young and old energy storing and positional tendons were subjected to cyclic fatigue testing until failure, and mechanical properties were calculated. The results show that both IFM and fascicles from the SDFT exhibit a similar magnitude of reduced fatigue life with ageing. By contrast, the fatigue life of positional tendon subunits was unaffected by ageing. The age-related decline in fatigue life of tendon subunits in energy storing tendons is likely to contribute to the increased risk of injury in aged tendons. Full understanding of the mechanisms resulting in this reduced fatigue life will aid in the development of treatments and interventions to prevent age-related tendinopathy

Oxygen and hydrogen isotope fractionation in serpentine–water and talc–water systems from 250 to 450°C, 50 MPa

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 73 (2009): 6789-6804, doi:10.1016/j.gca.2009.07.036.Oxygen and hydrogen isotope fractionation factors in the talc-water and serpentine-water systems have been determined by laboratory experiment from 250 to 450°C at 50 MPa using the partial exchange technique. Talc was synthesized from brucite + quartz, resulting in nearly 100% exchange during reaction at 350 and 450°C. For serpentine, D-H exchange was much more rapid than 18O-16O exchange when natural chrysotile fibers were employed in the initial charge. In experiments with lizardite as the starting charge, recrystallization to chrysotile enhanced the rate of 18O-16O exchange with the coexisting aqueous phase.This work was supported by NSF Grants OCE-9313980 to the Woods Hole Oceanographic Institution and OCE-9820287 to Bridgewater State College (BSC)

Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis

Regulation of cutaneous immunity is severely compromised in inflammatory skin disease. To investigate the molecular crosstalk underpinning tolerance versus inflammation in atopic dermatitis, we utilise a human in vivo allergen challenge study, exposing atopic dermatitis patients to house dust mite. Here we analyse transcriptional programmes at the population and single cell levels in parallel with immunophenotyping of cutaneous immunocytes revealed a distinct dichotomy in atopic dermatitis patient responsiveness to house dust mite challenge. Our study shows that reactivity to house dust mite was associated with high basal levels of TNF-expressing cutaneous Th17 T cells, and documents the presence of hub structures where Langerhans cells and T cells co-localised. Mechanistically, we identify expression of metallothioneins and transcriptional programmes encoding antioxidant defences across all skin cell types, that appear to protect against allergen-induced inflammation. Furthermore, single nucleotide polymorphisms in the MTIX gene are associated with patients who did not react to house dust mite, opening up possibilities for therapeutic interventions modulating metallothionein expression in atopic dermatitis

Explosive volcanism on the ultraslow-spreading Gakkel ridge, Arctic Ocean

Author Posting. © Nature Publishing Group, 2008. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 453 (2008): 1236-1238, doi:10.1038/nature07075.Roughly 60% of the Earth’s outer surface is comprised of oceanic crust formed by volcanic processes at mid-ocean ridges (MORs). Although only a small fraction of this vast volcanic terrain has been visually surveyed and/or sampled, the available evidence suggests that explosive eruptions are rare on MORs, particularly at depths below the critical point for steam (3000 m). A pyroclastic deposit has never been observed on the seafloor below 3000 m, presumably because the volatile content of mid-ocean ridge basalts is generally too low to produce the gas fractions required to fragment a magma at such high hydrostatic pressure. We employed new deep submergence technologies during an International Polar Year expedition to the Gakkel Ridge in the Arctic Basin at 85°E, to acquire the first-ever photographic images of ‘zero-age’ volcanic terrain on this remote, ice-covered MOR. Our imagery reveals that the axial valley at 4000 m water depth is blanketed with unconsolidated pyroclastic deposits, including bubble wall fragments (limu o Pele), covering a large area greater than 10 km2. At least 13.5 wt% CO2 is required to fragment magma at these depths, which is ~10x greater than the highest values measured to-date in a MOR basalt. These observations raise important questions regarding the accumulation and discharge of magmatic volatiles at ultra-slow spreading rates on the Gakkel Ridge (6- 14 mm yr-1, full-rate), and demonstrate that large-scale pyroclastic activity is possible along even the deepest portions of the global MOR volcanic system.This research was funded by the National Aeronautics and Space Administration, the National Science Foundation, and the Woods Hole Oceanographic Institution

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

Localization of type 1 diabetes susceptibility to the MHC class I genes HLA-B and HLA-A

The major histocompatibility complex (MHC) on chromosome 6 is associated with susceptibility to more common diseases than any other region of the human genome, including almost all disorders classified as autoimmune. In type 1 diabetes the major genetic susceptibility determinants have been mapped to the MHC class II genes HLA-DQB1 and HLA-DRB1 (refs 1-3), but these genes cannot completely explain the association between type 1 diabetes and the MHC region. Owing to the region's extreme gene density, the multiplicity of disease-associated alleles, strong associations between alleles, limited genotyping capability, and inadequate statistical approaches and sample sizes, which, and how many, loci within the MHC determine susceptibility remains unclear. Here, in several large type 1 diabetes data sets, we analyse a combined total of 1,729 polymorphisms, and apply statistical methods - recursive partitioning and regression - to pinpoint disease susceptibility to the MHC class I genes HLA-B and HLA-A (risk ratios >1.5; Pcombined = 2.01 × 10-19 and 2.35 × 10-13, respectively) in addition to the established associations of the MHC class II genes. Other loci with smaller and/or rarer effects might also be involved, but to find these, future searches must take into account both the HLA class II and class I genes and use even larger samples. Taken together with previous studies, we conclude that MHC-class-I-mediated events, principally involving HLA-B*39, contribute to the aetiology of type 1 diabetes. ©2007 Nature Publishing Group