Working With Incremental Spatial Data During Parallel (GPU) Computation

Central to many complex systems, spatial actors require an awareness of their local environment to enable behaviours such as communication and navigation. Complex system simulations represent this behaviour with Fixed Radius Near Neighbours (FRNN) search. This algorithm allows actors to store data at spatial locations and then query the data structure to find all data stored within a fixed radius of the search origin. The work within this thesis answers the question: What techniques can be used for improving the performance of FRNN searches during complex system simulations on Graphics Processing Units (GPUs)? It is generally agreed that Uniform Spatial Partitioning (USP) is the most suitable data structure for providing FRNN search on GPUs. However, due to the architectural complexities of GPUs, the performance is constrained such that FRNN search remains one of the most expensive common stages between complex systems models. Existing innovations to USP highlight a need to take advantage of recent GPU advances, reducing the levels of divergence and limiting redundant memory accesses as viable routes to improve the performance of FRNN search. This thesis addresses these with three separate optimisations that can be used simultaneously. Experiments have assessed the impact of optimisations to the general case of FRNN search found within complex system simulations and demonstrated their impact in practice when applied to full complex system models. Results presented show the performance of the construction and query stages of FRNN search can be improved by over 2x and 1.3x respectively. These improvements allow complex system simulations to be executed faster, enabling increases in scale and model complexity

Mechanisms and outcome of severe mitral regulation after inoue balloon valvuloplasty

AbstractObjectives. The purpose of this study was to assess the incidence, mechanism and outcome of severe mitral regurgitation after treatment of mitral stenosis with percutaneous mitral valvuloplasty using the Inoue balloon.Background. Severe mitral regurgitation occurs in up to 15% of percutaneous balloon valvuloplasty procedures for acquired mitral stenosis. The incidence and mechanism of production of mitral regurgitation with the recently introduced single-ballon lnone technique have not been characterized.Methods. We examined the incidence, mechanism, predictors and outcome of severe mitral regurgitation after Inoue balloon valvuloplasty in 280 patients in the North American multicenter registry. Twenty-one patients who developed either clinically significant or angiographically severe regurgitation were identified, and their echocardiograms were reviewed to determine the mechanism of regurgitation. These patients were then compared with the remaining patients without severe regurgitation to identify predictors of this outcome.Results. The incidence of severe regurgitation in this study was 7.5%, and the mean grade of angiographic regurgitation in these patients increased from 0.9 ± 1.0 to 2.8 ± 0.7 (p < 0.05). The most common cause of regurgitation (43%) was rupture of clhordae tendineae to the anterior or posterior mitral leaflet. Tearing of a leaflet (usually the posterior one) occurred in 30% of patients; and no recognizable structural abnormality, with wide splitting of the commissures and a central regurgitant jet, was present in five patients (26%). All patients with definite posterior leaflet tears had heavily calcified leaflet. Patients who developed severe regurgitation had fewer balloon inflations and a higher grade of preexisting mitral regurgitation but were otherwish similar to the remaining patients without severe regurgitation. During 6-month follow-up, 71% of the patients with severe regurgitation were treated surgically; the grade of regurgitation decreased in four patients (19%), and five (24%) not required mitral valve replacement during 18 ± 5 month of follow-up.Conclusions. Severe mitral regurgitation is a relatively infrequent complication of Inoue balloon valvutoplasty and results from disruption of the valve integrity, chordal rapture and leaflet tearing. Careful balloon positioning may help avoid chordal rapture, and heavily calcified posterior lesflets may be at greater risk of tearing. Most patients who develop severe regurgitation will require nonemergency mitral valve replacement

Global Gene Expression of Prochlorococcus ecotypes in Response to Changes in Nitrogen Availability

Nitrogen (N) often limits biological productivity in the oceanic gyres where Prochlorococcus is the most abundant photosynthetic organism. The Prochlorococcus community is composed of strains, such as MED4 and MIT9313, that have different N utilization capabilities and that belong to ecotypes with different depth distributions. An interstrain comparison of how Prochlorococcus responds to changes in ambient nitrogen is thus central to understanding its ecology. We quantified changes in MED4 and MIT9313 global mRNA expression, chlorophyll fluorescence, and photosystem II photochemical efficiency (Fv/Fm) along a time series of increasing N starvation. In addition, the global expression of both strains growing in ammonium-replete medium was compared to expression during growth on alternative N sources. There were interstrain similarities in N regulation such as the activation of a putative NtcA regulon during N stress. There were also important differences between the strains such as in the expression patterns of carbon metabolism genes, suggesting that the two strains integrate N and C metabolism in fundamentally different ways

Nitrogen cost minimization is promoted by structural changes in the transcriptome of N-deprived Prochlorococcus cells

Prochlorococcus is a globally abundant marine cyanobacterium with many adaptations that reduce cellular nutrient requirements, facilitating growth in its nutrient-poor environment. One such genomic adaptation is the preferential utilization of amino acids containing fewer N-atoms, which minimizes cellular nitrogen requirements. We predicted that transcriptional regulation might further reduce cellular N budgets during transient N limitation. To explore this, we compared transcription start sites (TSSs) in Prochlorococcus MED4 under N-deprived and N-replete conditions. Of 64 genes with primary and internal TSSs in both conditions, N-deprived cells initiated transcription downstream of primary TSSs more frequently than N-replete cells. Additionally, 117 genes with only an internal TSS demonstrated increased internal transcription under N-deprivation. These shortened transcripts encode predicted proteins with an average of 21% less N content compared to full-length transcripts. We hypothesized that low translation rates, which afford greater control over protein abundances, would be beneficial to relatively slow-growing organisms like Prochlorococcus. Consistent with this idea, we found that Prochlorococcus exhibits greater usage of glycine-glycine motifs, which causes translational pausing, when compared to faster growing microbes. Our findings indicate that structural changes occur within the Prochlorococcus MED4 transcriptome during N-deprivation, potentially altering the size and structure of proteins expressed under nutrient limitation.Gordon and Betty Moore Foundation (Grant GBMF495)Simons Foundation (Award 329108)National Science Foundation (U.S.) (Grant DBI-0424599

Analysis of lesion localisation at colonoscopy: outcomes from a multi-centre U.K. study

Background: Colonoscopy is currently the gold standard for detection of colorectal lesions, but may be limited in anatomically localising lesions. This audit aimed to determine the accuracy of colonoscopy lesion localisation, any subsequent changes in surgical management and any potentially influencing factors. Methods: Patients undergoing colonoscopy prior to elective curative surgery for colorectal lesion/s were included from 8 registered U.K. sites (2012–2014). Three sets of data were recorded: patient factors (age, sex, BMI, screener vs. symptomatic, previous abdominal surgery); colonoscopy factors (caecal intubation, scope guide used, colonoscopist accreditation) and imaging modality. Lesion localisation was standardised with intra-operative location taken as the gold standard. Changes to surgical management were recorded. Results: 364 cases were included; majority of lesions were colonic, solitary, malignant and in symptomatic referrals. 82% patients had their lesion/s correctly located at colonoscopy. Pre-operative CT visualised lesion/s in only 73% of cases with a reduction in screening patients (64 vs. 77%; p = 0.008). 5.2% incorrectly located cases at colonoscopy underwent altered surgical management, including conversion to open. Univariate analysis found colonoscopy accreditation, scope guide use, incomplete colonoscopy and previous abdominal surgery significantly influenced lesion localisation. On multi-variate analysis, caecal intubation and scope guide use remained significant (HR 0.35, 0.20–0.60 95% CI and 0.47; 0.25–0.88, respectively). Conclusion: Lesion localisation at colonoscopy is incorrect in 18% of cases leading to potentially significant surgical management alterations. As part of accreditation, colonoscopists need lesion localisation training and awareness of when inaccuracies can occur

Insecticide Residues in Certain Texas Soils.

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Narrative exposure therapy for survivors of human trafficking: feasibility randomised controlled trial

Background Human trafficking is a grave human rights violation and a major public health concern. Survivors present with high rates of mental health problems including post-traumatic stress disorder (PTSD). Studies of effective treatments for PTSD in survivors of human trafficking are lacking. Narrative exposure therapy (NET) is an effective PTSD treatment for multiple, prolonged and complex trauma, but its efficacy has not been rigorously tested in survivors of human trafficking. Aims To test the feasibility and acceptability of a randomised controlled trial (RCT) offering NET as a treatment for PTSD in trafficking survivors with a history of multiple traumatic events, as well as providing preliminary evidence regarding its efficacy (trial registration: ISRCTN95136302). Method A single-blind RCT compared NET with a wait-list control in survivors of trafficking with PTSD (n = 25). In the NET arm of the study, participants attended a mean of 17 sessions. Results NET was well tolerated by participants. There were significant reductions in PTSD, depression and anxiety symptoms post-treatment in the NET group but no significant change in the wait-list group. Conclusions The results indicate that NET is a promising and acceptable treatment for trafficking survivors. Psychological therapy in an RCT design can be safely delivered to this vulnerable group, although modifications are required to ensure their holistic needs are properly addressed

Narrative exposure therapy for survivors of human trafficking: feasibility randomised controlled trial

BACKGROUND: Human trafficking is a grave human rights violation and a major public health concern. Survivors present with high rates of mental health problems including post-traumatic stress disorder (PTSD). Studies of effective treatments for PTSD in survivors of human trafficking are lacking. Narrative exposure therapy (NET) is an effective PTSD treatment for multiple, prolonged and complex trauma, but its efficacy has not been rigorously tested in survivors of human trafficking. AIMS: To test the feasibility and acceptability of a randomised controlled trial (RCT) offering NET as a treatment for PTSD in trafficking survivors with a history of multiple traumatic events, as well as providing preliminary evidence regarding its efficacy (trial registration: ISRCTN95136302). METHOD: A single-blind RCT compared NET with a wait-list control in survivors of trafficking with PTSD (n = 25). In the NET arm of the study, participants attended a mean of 17 sessions. RESULTS: NET was well tolerated by participants. There were significant reductions in PTSD, depression and anxiety symptoms post-treatment in the NET group but no significant change in the wait-list group. CONCLUSIONS: The results indicate that NET is a promising and acceptable treatment for trafficking survivors. Psychological therapy in an RCT design can be safely delivered to this vulnerable group, although modifications are required to ensure their holistic needs are properly addressed