A speculative execution approach to provide semantically aware contention management for concurrent systems

PhD ThesisMost modern platforms offer ample potention for parallel execution of concurrent programs yet concurrency control is required to exploit parallelism while maintaining program correctness. Pessimistic con- currency control featuring blocking synchronization and mutual ex- clusion, has given way to transactional memory, which allows the composition of concurrent code in a manner more intuitive for the application programmer. An important component in any transactional memory technique however is the policy for resolving conflicts on shared data, commonly referred to as the contention management policy. In this thesis, a Universal Construction is described which provides contention management for software transactional memory. The technique differs from existing approaches given that multiple execution paths are explored speculatively and in parallel. In the resolution of conflicts by state space exploration, we demonstrate that both concur- rent conflicts and semantic conflicts can be solved, promoting multi- threaded program progression. We de ne a model of computation called Many Systems, which defines the execution of concurrent threads as a state space management problem. An implementation is then presented based on concepts from the model, and we extend the implementation to incorporate nested transactions. Results are provided which compare the performance of our approach with an established contention management policy, under varying degrees of concurrent and semantic conflicts. Finally, we provide performance results from a number of search strategies, when nested transactions are introduced

Frobenius test exponents for parameter ideals in generalized Cohen-Macaulay local rings

This paper studies Frobenius powers of parameter ideals in a commutative Noetherian local ring R of prime characteristic p. For a given ideal a of R, there is a power Q of p, depending on a, such that the Qth Frobenius power of the Frobenius closure of a is equal to the Qth Frobenius power of a. The paper addresses the question as to whether there exists a uniform Q(0) which 'works' in this context for all parameter ideals of R simultaneously. In a recent paper, Katzman and Sharp proved that there does exists such a uniform Q(0) when R is Cohen-Macaulay. The purpose of this paper is to show that such a uniform Q(0) exists when R is a generalized Cohen-Macaulay local ring. A variety of concepts and techniques from commutative algebra are used, including unconditioned strong d-sequences, cohomological annihilators, modules of generalized fractions, and the Hartshome-Speiser-Lyubeznik Theorem employed by Katzman and Sharp in the Cohen-Macaulay case. (c) 2006 Elsevier Inc. All rights reserved

Bioactive scaffolds for potential bone regenerative medical applications

Fracture non-unions and bone defects represent a recalcitrant problem in the field of orthopaedic surgery. Although the current gold-standard treatment, autologous bone grafting, has a relatively high success rate, the technique is not without serious problems. The emerging field of regenerative medicine may have the potential to provide an alternative treatment. One promising strategy involves the delivery of both cells and multiple growth factors with different release profiles. A range of scaffolds was developed from Poly( -caprolactone) (PCL), Poly(lactideco- glycolide) (PLGA), and two blends of PCL (Mn 42,500) and PLGA. The scaffolds were manufactured utilising a novel modified fused deposition modelling system, using polymer/dichloromethane solutions. The scaffolds were found to have pore sizes suitable for bone regenerative medical applications (373±9.5 μm in the Ydirection and 460±13 μm in the X-direction). However, the scaffolds were found to be only 52±3 μm in height. This means that the two-layer scaffolds were relatively flat. This was undesirable, as direct control of the complete 3D geometry was the favoured strategy, though it may not be a necessary requirement. Five scaffold coatings were also developed from alginate, chitosan (crosslinked using sodium hydroxide or tripolyphosphate), Type-I collagen and Type-A gelatin. The scaffold coatings were screened in vitro for their cell-compatibility with human marrow stromal cells (hMSCs), human osteoblasts and MG63 cells. This was assessed using an assay for cell death, and assessing total cell counts. From these studies, Type-I collagen was found to be the optimum coating. For hMSCs, their death rates were found to be 19.1±6.3% for alginate, 5.3±3.6% and 2.9±1.4% for chitosan crosslinked with tripolyphosphate and sodium hydroxide respectively, compared to 0.11±0.07% for Type-I collagen, and 0.15±0.13% and 0.16±0.12% for 0.1% and 0.2% gelatin respectively. Type-I collagen was found to be the most cellcompatible coating, as it was consistently associated with higher cell counts than Type-A gelatin. Similarly, PCL scaffolds vacuum dried for 1 hr were found to be cell-compatible. No detectable clinically significant difference was found in either total cell counts, or the proportion of cell death in; hMSCs exposed to PCL scaffolds processed with dichloromethane, hMSCs either exposed to scaffolds known to be biocompatible, or hMSCs cultured in the absence of scaffolds. When cell morphology was compared, scaffolds vacuum dried for 1 hr or more were found to have a similar morphology to the cells cultured in the absence of scaffolds. It was therefore concluded that a vacuum drying time of 1 hr was sufficient for cell-compatibility. The scaffold materials were screened both for their encapsulation efficiencies and release characteristics using the model drug, methylene blue. The encapsulation efficiency was found to be both relatively high and consistent for both Mn 42,500 and 80,000 PCL as well as PCL:PLGA 66:33, at 71±6%, 71±5%, and 78±10% respectively, relative to the low efficiencies recorded for both PCL:PLGA 66:33 and PLGA: 57±5% and 38±10% respectively. The release rate of methylene blue from PCL (Mn 42,500), was found to be relatively slow, controlled, and consistent between batches (between 21±2% and 20±3% released in the first 24 hr). Despite the release rate being consistent for PCL (Mn 80,000), the release rate was thought to be too high, since between 29±3% and 39±5% of the test compound was released in the first 24 hr period. The release rate of methylene blue from the PCL/PLGA blends (between 17±2% – 30±7% and 18±4% – 31±6% in the first 24 hr) and PLGA (between 7.1±3.4% – 9.3±2.9% in the first 24 hr) were found to be inconsistent, and low in the case of PLGA, even taking the different loading efficiencies into account. Therefore, PCL (Mn 42,500) was selected as the favoured candidate scaffold material. The loading content and release profiles from methylene blue loaded collagen scaffold coatings were also evaluated. The drug loading capacity was found to be suitable for use as a drug delivery system (65±5 μg/g of methylene blue per unit scaffold mass). The release of methylene blue was observed to be rapid (between 54±10% – 70±17% in the first 24 hr), which was thought to be desirable for the coating delivery system. Recombinant human bone morphogenetic protein-7 (rhBMP-7) was used as a representative growth factor of interest for bone regenerative medical applications. It was loaded in collagen scaffold coatings (CoatBMP 1.25) and encapsulated within PCL (Mn 42,500) scaffolds (ScaffBMP 1.25). Control coatings and scaffolds were designated CoatPBS and ScaffPBS respectively. Both delivery systems were found to release detectable quantities of rhBMP-7 (releasing 2.8±0.2 μg/g and 87±7 ng/g respectively in the first 24 hr), even after 14 days. The release rate of the growth factor from the scaffold coating was higher than that from the encapsulating scaffolds. However, the cumulative release profiles were found to deviate from the desired ideal release profiles, and burst release was observed from both delivery systems. Although differences were observed for the two delivery systems, this difference may not be of clinical significance. Nevertheless, scaffolds with less than ideal delivery properties may still be of potential clinical use. The bioactivity of the rhBMP-7 released from the test scaffolds was therefore assessed by quantifying the area of normalised ALP staining of hMSCs. The release of rhBMP-7 from the collagen coating of the PCL (Mn 42,500) scaffolds (CoatBMP 1.25ScaffPBS) was capable of statistically significantly increasing hMSC normalised ALP expression, although the actual differences were often relatively small. Therefore, at least a proportion of the growth factor released is likely to have been bioactive. The release from scaffolds encapsulating rhBMP-7 (CoatPBSScaffBMP 1.25) did not have this effect on the hMSCs, indicating that either the concentration released was too low, or the growth factor released was no longer bioactive. However, when the cells were seeded directly onto the scaffolds, the activity of ALP, normalised by a DNA assay, was statistically significantly increased for the CoatPBSScaffBMP 1.25 scaffolds, in hMSCs from all three test patient donors (by 35±10% on the control). ALP activity was also significantly increased in hMSCs from two of the three patients seeded onto CoatBMP 1.25ScaffBMP 1.25 scaffolds (by 39±10% on the control). ALP activity was only statistically significantly increased for one of the hMSC patients when seeded onto CoatBMP 1.25ScaffPBS scaffolds (by 35±14% on the control). The functional osteoinductive capacity of Type-I collagen coated PCL (Mn 42,500) scaffolds loaded with rhBMP-7 was assessed using C2C12 cells seeded onto the scaffolds, and quantified using qRT-PCR. The genes of interest were; Type-I collagen (Col1), osteopontin (OP), ALP, osteocalcin (OC) and runt related transcription factor 2 (Runx2). The CoatBMP 1.25ScaffPBS scaffolds had an early osteoinductive effect on the C2C12 cells, as ALP, OC and Runx2 were elevated during the first 2 days only, compared to the control (e.g. by 44±12%, 128±42%, 60±25% and 46±25% respectively at the 24 hr mark). The CoatPBSScaffBMP 1.25 scaffolds also had an osteoinductive effect on the cells, which was more sustained than that observed for the CoatBMP 1.25ScaffPBS group. While OP, ALP and Runx2 were up-regulated in the first 24 hr compared to the control (by 38±10%, 208±82% and 72±31% respectively), statistically significant up-regulation of the late marker OC was delayed until the 48 hr mark (by 73±49%). The effect was found to be sustained until day 7, when OC and Runx2 were both statistically significantly up-regulated compared to the control (by 151±91% and 93±27% respectively). The CoatBMP 1.25ScaffBMP 1.25 scaffolds were found to combine the early effect of the CoatBMP 1.25ScaffPBS scaffolds, with the more sustained effect of the CoatPBSScaffBMP 1.25 scaffolds. ALP, OC and Runx2 were all up-regulated at the 24 hr mark (by 312±56%, 329±39% and 96±25% respectively). This osteoinductive effect was sustained until day 7 when Col1, ALP and Runx2 were still up-regulated compared to the control (by 174±78%, 72±24% and 178±78% respectively). These data suggest that the scaffolds containing rhBMP-7 have a weak osteoinductive effect on the cells seeded onto them. The different delivery systems were found to affect the cells differently. The clinical significance of this was not assessed in these studies. 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) was used as a model drug to assess the feasibility of releasing lipid-soluble active factors from the scaffolds. This was assessed by quantifying the area of normalised ALP staining of hMSCs. The release of 1,25(OH)2D3 from the loaded collagen scaffold coatings and the encapsulating scaffolds significantly increased ALP expression compared to the control scaffold groups (by 115±28% and 69±25% respectively). Furthermore, ALP expression was significantly increased when the two delivery systems were used together, when compared to either delivery system on its own. These data suggest that the delivery of lipid-soluble active factors is feasible from collagen coated PCL scaffolds, and that the coating and encapsulating delivery systems are mutually compatible

The pathology and immunology of some parasitic infestations in domestic animals

This thesis describes the development, from the early laboratory-test stage, of the first vaccine to be successfully used on a wide scale against a parasitic helminth. The process utilises X-irradiation to attenuate the infective larvae. The work is presented in four parts, followed by technical, bibliographical and tabular appendices. The first part ie a discussion on both parasitic immunity and the application of X-irradiation to holminths. The second part describes experiments designed to test a vaccine against Dityoeaulus viviparus. The third part is a quantitative and qualitative study of D. viviparus larvae under the respective effects of X-irradiation, antibody and diethyl-carbamazine. The fourth part concerns the testing of a vaccine against Haetaonchus contorfcus. Part I contains a general introduction to parasitic immunity, with a brief indication of the importance of parasitism in both animals and man. this is followed by a description of: (a) previous attempts by other workers to vaccinate against helminth diseases; (b) the background of work behind the present method of vaccination. Part I ends with a review of various applications of X-irradiation to helminths. Part II is introduced by a small experiment designed to test the longevity of both first and third stage larvae of D. viviparus under a wide range of laboratory conditions. A short description of the parasite is included. Then follow the four experiments which form the bulk of this part. These were designed to test the effectiveness of the D. viviparus vaccine in various combinations of dose against a challenge apectrum ranging from a large single dose of infective larvae to a natural famsapasture challenge. Approximately 1,250 calves were involved in these expariments. Part III is mainly concerned with histo-pathological and quantitative assess-monts on the distribution and fate of irradiated larvae in the normal host and of normal larvae in the immune host. This work was done to study the made of action of, and the hoist-reaction to, the vaccine against D. viviparous in calves. It was known that a dose of irradiated larvae did not: produce a population of adult worms in the bronchi, and this experiment showed whore the larvae wore ceasing to develop. The pathological basis of the transient clinical signs sometimes seen after vaccination is described, as well as the correlation of lesions and clinical signs observed in the immune animal under heavy challenge. The last experiment in this part is a histopathological study of the pulmonary lesions produced by treating calves, in the prepatent or patent stage of parasitic bronchitis, with diethylcarbamazine. This drug inactivates or kills the parasite, and the host-reaction to the drug-disabled worn is interestingly similar to the reactions of the normal calf lung to irradiated larvae and of the immune-calf lung to normal larvae, The lesions in the calves treated at patency were correlated with the clinical signs sometimes seen following such treatment. Part IV. The previous parts dealt with the successful application of the larval irradiation technique to a parasite with an extensive migratory cycle. It was thought that this method might be less effective in parasites which undergo only a limited histotrophic phase - such as some of the gastro-intestinal nematodes. The experiments in this part indicated that a servicable degree of immunity could be induced in sheep against Haemonchus contortus

Developing a spatial-statistical model and map of historical malaria prevalence in Botswana using a staged variable selection procedure

<p>Abstract</p> <p>Background</p> <p>Several malaria risk maps have been developed in recent years, many from the prevalence of infection data collated by the MARA (Mapping Malaria Risk in Africa) project, and using various environmental data sets as predictors. Variable selection is a major obstacle due to analytical problems caused by over-fitting, confounding and non-independence in the data. Testing and comparing every combination of explanatory variables in a Bayesian spatial framework remains unfeasible for most researchers. The aim of this study was to develop a malaria risk map using a systematic and practicable variable selection process for spatial analysis and mapping of historical malaria risk in Botswana.</p> <p>Results</p> <p>Of 50 potential explanatory variables from eight environmental data themes, 42 were significantly associated with malaria prevalence in univariate logistic regression and were ranked by the Akaike Information Criterion. Those correlated with higher-ranking relatives of the same environmental theme, were temporarily excluded. The remaining 14 candidates were ranked by selection frequency after running automated step-wise selection procedures on 1000 bootstrap samples drawn from the data. A non-spatial multiple-variable model was developed through step-wise inclusion in order of selection frequency. Previously excluded variables were then re-evaluated for inclusion, using further step-wise bootstrap procedures, resulting in the exclusion of another variable. Finally a Bayesian geo-statistical model using Markov Chain Monte Carlo simulation was fitted to the data, resulting in a final model of three predictor variables, namely summer rainfall, mean annual temperature and altitude. Each was independently and significantly associated with malaria prevalence after allowing for spatial correlation. This model was used to predict malaria prevalence at unobserved locations, producing a smooth risk map for the whole country.</p> <p>Conclusion</p> <p>We have produced a highly plausible and parsimonious model of historical malaria risk for Botswana from point-referenced data from a 1961/2 prevalence survey of malaria infection in 1–14 year old children. After starting with a list of 50 potential variables we ended with three highly plausible predictors, by applying a systematic and repeatable staged variable selection procedure that included a spatial analysis, which has application for other environmentally determined infectious diseases. All this was accomplished using general-purpose statistical software.</p

Pad-printed Prussian blue doped carbon ink for real-time peroxide sensing in cell culture

Hydrogen peroxide has important roles within cellular functions, as a prevalent form of Reactive Oxygen Species, detection within mammalian cells is of metabolic importance; typically requiring cell lysis or fluorescence-based methods to quantify. Herein, we explore the novel use of Prussian blue mediated, pad printed carbon electrodes to allow the indirect detection of cellular peroxides in bulk culture media, which facilitates non-invasive, real-time detection. Electrodes demonstrated capacity to detect H2O2 with a linear range of 1-200 μM in CMEM (R2 = 0.9988), enabling detection of peroxides found in culture media and lysate. Developed electrodes had a Limit of Detection (LOD) of 0.41 μM H2O2 in Britton-Robinson Buffer (BRB), 0.38 μM in Eagle's Minimum Essential Medium (EMEM) and 9.19 μM in Dulbecco's Modified Eagles Medium (DMEM). Electrodes were tested in a conventional 5% serum supplemented EMEM (CMEM) and demonstrated an LOD of 0.5 μM and LOQ of 0.9 μM. The results demonstrate proof of concept for monitoring H2O2 in complex culture media with potential long-term use and reusability using simple, pad printed Prussian Blue / Carbon electrodes. The lack of further modification, and cost-effectiveness of these disposable electrodes could offer great advancement to monitoring of peroxides in complex media

Genetic Risk, Muscle Strength, and Incident Stroke: Findings From the UK Biobank Study.

OBJECTIVE: To examine the associations of muscle strength and genetic risk for stroke with stroke incidence. PARTICIPANTS AND METHODS: We included 284,767 white British participants of UK Biobank without genetic relatedness and stroke or myocardial infarction at baseline between March 13, 2006, and October 1, 2010. Genetic risk was assessed with polygenic risk scores, calculated by summing the risk-increasing alleles, weighted by the effect estimates. Muscle strength was assessed through grip strength tests by hand dynamometers. Incidence of overall (n= 4008), ischemic (n= 3031), and hemorrhagic (n=1073) stroke was adjudicated during 11.5-year follow-up. RESULTS: Compared with the bottom muscle strength tertile, hazard ratios (95% CI) of stroke were 0.81 (0.75 to 0.87) and 0.76 (0.71 to 0.82) for the middle and top muscle strength tertiles, respectively, after adjustment for confounders and genetic risk; higher genetic risk was independently associated with higher stroke incidence. Stroke hazards for the top muscle strength tertile were consistently lower across genetic risk strata, with no evidence of interaction. Compared with individuals with high muscle strength and low genetic risk, stroke hazards were higher for individuals who had medium or high genetic risk combined with low or medium muscle strength but not for those who had medium genetic risk but high muscle strength. Associations were similar for ischemic and hemorrhagic stroke (although CIs were inconclusive for some of the associations). CONCLUSION: Higher muscle strength was associated with lower stroke incidence in all individuals, including those with high genetic susceptibility. The increased genetic risk of overall and ischemic stroke was partly attenuated through increased muscle strength