Parallel Program Archetypes

A parallel program archetype is an abstraction that captures the common features of a class of problems with similar computational structure and combines them with a parallelization strategy to produce a pattern of dataflow and communication. Such abstractions are useful in application development, both as a conceptual framework and as a basis for tools and techniques. This paper describes an approach to parallel application development based on archetypes and presents two example archetypes with applications

Space Efficient Breadth-First and Level Traversals of Consistent Global States of Parallel Programs

Enumerating consistent global states of a computation is a fundamental problem in parallel computing with applications to debug- ging, testing and runtime verification of parallel programs. Breadth-first search (BFS) enumeration is especially useful for these applications as it finds an erroneous consistent global state with the least number of events possible. The total number of executed events in a global state is called its rank. BFS also allows enumeration of all global states of a given rank or within a range of ranks. If a computation on n processes has m events per process on average, then the traditional BFS (Cooper-Marzullo and its variants) requires $\mathcal{O}(\frac{m^{n-1}}{n})$ space in the worst case, whereas ou r algorithm performs the BFS requires $\mathcal{O}(m^2n^2)$ space. Thus, we reduce the space complexity for BFS enumeration of consistent global states exponentially. and give the first polynomial space algorithm for this task. In our experimental evaluation of seven benchmarks, traditional BFS fails in many cases by exhausting the 2 GB heap space allowed to the JVM. In contrast, our implementation uses less than 60 MB memory and is also faster in many cases

Integrating Task and Data Parallelism with the Collective Communication Archetype

A parallel program archetype aids in the development of reliable, efficient parallel applications with common computation/communication structures by providing stepwise refinement methods and code libraries specific to the structure. The methods and libraries help in transforming a sequential program into a parallel program via a sequence of refinement steps that help maintain correctness while refining the program to obtain the appropriate level of granularity for a target machine. The specific archetype discussed here deals with the integration of task and data parallelism by using collective (or group) communication. This archetype has been used to develop several applications

Molecular remission with arsenic trioxide in patients with newly diagnosed acute promyelocytic leukemia

Thirty six APML patients achieving hematological remission with As2O3 were serially monitored using RT-PCR. Though only 5.5% achieved molecular remission at induction remission, 94.5% became negative during consolidation. At 20 months follow-up, 85% remain in remission but longer follow up studies are needed to monitor late relapses

Fludarabine and cyclophosphamide based reduced intensity conditioning (RIC) regimens reduce rejection and improve outcome in Indian patients undergoing allogeneic stem cell transplantation for severe aplastic anemia

Thirty-five patients (25 men and 10 women) with a median age of 20 years with severe aplastic anaemia (SAA) underwent HLA identical stem cell transplantation (HSCT) using a combination of fludarabine and cyclophosphamideanti-thymocyte globulin between 2004 and 2006. Cyclosporine and mini methotrexate were used as GVHD prophylaxis. Graft source included peripheral blood stem cells (28) or G-CSF stimulated bone marrow (7). Two patients expired <7 days post-HSCT while 32 (91.5%) patients engrafted with a median neutrophil and platelet engraftment time of 12 days each. Three patients (8.5%) developed veno-occlusive disease while acute GVHD occurred in 29% of evaluable patients, with chronic GVHD in 32%. At a mean follow-up of 22 months, 29 (82.8%) are alive and well. When compared with 26 patients previously transplanted using Cy200/antilymphocyte globulin, there was faster neutrophil engraftment (12 vs 16 days; P=0.002) with significantly lower rejection rates (2.9 vs 30.7%; P=0.003) and a superior event-free (82.8 vs 38.4%; P=0.001) and overall survival (82.8 vs 46.1%; P=0.005). A combination of fludarabine with cyclophosphamideanti-thymocyte globulin reduces rejection and improves overall and event-free survival in Indian patients undergoing HSCT for severe aplastic anaemia

Malaria hotspot areas in a highland Kenya site are consistent in epidemic and non-epidemic years and are associated with ecological factors

BACKGROUND: Malaria epidemics in highland areas of East Africa have caused considerable morbidity and mortality in the past two decades. Knowledge of "hotspot" areas of high malaria incidence would allow for focused preventive interventions in resource-poor areas, particularly if the hotspot areas can be discerned during non-epidemic periods and predicted by ecological factors. METHODS: To address this issue, spatial distribution of malaria incidence and the relationship of ecological factors to malaria incidence were assessed in the highland area of Kipsamoite, Kenya, from 2001–2004. RESULTS: Clustering of disease in a single geographic "hotspot" area occurred in epidemic and non-epidemic years, with a 2.6 to 3.2-fold increased risk of malaria inside the hotspot, as compared to outside the area (P < 0.001, all 4 years). Altitude and proximity to the forest were independently associated with increased malaria risk in all years, including epidemic and non-epidemic years. CONCLUSION: In this highland area, areas of high malaria risk are consistent in epidemic and non-epidemic years and are associated with specific ecological risk factors. Ongoing interventions in areas of ecological risk factors could be a cost-effective method of significantly reducing malaria incidence and blunting or preventing epidemics, even in the absence of malaria early warning systems. Further studies should be conducted to see if these findings hold true in varied highland settings

Prevalence of Asymptomatic SARS-CoV-2 Infection in Children and Adults in Marion County, Indiana

Background and Objectives: Two community studies outside the US showed asymptomatic infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in adults, but not in children <10 years of age. In this study, we assessed the prevalence of asymptomatic SARS-CoV-2 infection in children and adults in Marion County, Indiana. Methods: Individuals living in Marion County with no symptoms of coronavirus 2019 disease (COVID-19) within seven days of enrollment were eligible for this cross-sectional household study. Study kits were delivered to the participant’s residence for self-swabbing, picked up by the study team, and tested by polymerase chain reaction (PCR) for SAR-CoV-2 infection. Results: Five hundred eleven nasal swabs were collected from 119 children and 392 adults ≥18 years of age. One participant (seven years of age) tested positive, for an overall study prevalence of 0.2% (95% CI 0, 0.6%). The participant had no known contact with a person with SARS-CoV-2 infection, and five family members tested negative for infection. The child and family members all tested negative for infection 10 and 20 days after the first test, and none developed symptoms of COVID-19 for 20 days after testing. Conclusions: Asymptomatic SARS-CoV-2 infection can occur in children <10 years with no known COVID-19 exposure. Large cohort studies should be conducted to determine prevalence of asymptomatic infection and risk of transmission from asymptomatic infection in children and adults over time

Malaria with neurological involvement in Ugandan children: effect on cognitive ability, academic achievement and behaviour

<p>Abstract</p> <p>Background</p> <p>Malaria is a leading cause of ill health and neuro-disability in children in sub-Saharan Africa. Impaired cognition is a common outcome of malaria with neurological involvement. There is also a possibility that academic achievement may be affected by malaria with neurological involvement given the association between cognitive ability and academic achievement. This study investigated the effect of malaria with neurological involvement on cognitive ability, behaviour and academic achievement.</p> <p>Methods</p> <p>This prospective case-control study was carried out in Kampala City, Uganda between February 2008 and October 2010. Sixty-two children with a history of malaria with neurological involvement were followed up and given assessments for cognitive ability (working memory, reasoning, learning, visual spatial skills and attention), behaviour (internalizing and externalizing problems) and academic achievement (arithmetic, spelling and reading) three months after the illness. Sixty-one community controls recruited from the homes or neighbouring families of the cases were also given the same assessments. Tests scores of the two groups were compared using analysis of covariance with age, sex, level of education, nutritional status and quality of the home environment as covariates. This study was approved by the relevant ethical bodies and informed consent sought from the caregivers.</p> <p>Results</p> <p>Children in the malaria group had more behavioural problems than the community controls for internalizing problems (estimated mean difference = -3.71, 95% confidence interval (CI), = -6.34 to -1.08, p = 0.007). There was marginal evidence of lower attention scores (0.40, CI = -0.05 to 0.86, p = 0.09). However, excluding one child from the analyses who was unable to perform the tests affected the attention scores to borderline significance (0.32, CI, = 0.01 to 0.62, p = 0.05). No significant differences were observed in other cognitive abilities or in academic achievement scores.</p> <p>Conclusion</p> <p>Malaria with neurological involvement affects behaviour, with a minimal effect on attention but no detectable effect on academic achievement at three months post discharge. This study provides evidence that development of cognitive deficits after malaria with neurological involvement could be gradual with less effect observed in the short term compared to the long term.</p

Evaluation of uroprotective efficacy of amifostine against cyclophosphamide induced hemorrhagic cystitis

The role of amifostine in the prevention of cyclophosphamide-induced hemorrhagic cystitis (HC) was evaluated in the rat model. Urinary bladders from control rats that received no drugs (group I) were compared with those from rats receiving cyclophosphamide alone at a dose of 150 mg/kg (group II), and two other groups receiving amifostine at 100 mg/kg (group III) and 200 mg/kg (group IV), 15 min prior to cyclophosphamide. Bladders were assessed macroscopically and histologically at 24 h and after 7 days. All the animals that received cyclophosphamide alone developed severe HC. On the basis of the scores of macroscopic and histologic changes, animals that received amifostine showed excellent uroprotection. Only 2/6 rats in group III and 1/6 rats in group IV developed mild HC at 24 h. None of the rats in either of these groups showed any evidence of HC at 7 days. It is concluded that amifostine protects the urothelium against cyclophosphamide-induced HC