A First Step Towards Automatically Building Network Representations

To fully harness Grids, users or middlewares must have some knowledge on the topology of the platform interconnection network. As such knowledge is usually not available, one must uses tools which automatically build a topological network model through some measurements. In this article, we define a methodology to assess the quality of these network model building tools, and we apply this methodology to representatives of the main classes of model builders and to two new algorithms. We show that none of the main existing techniques build models that enable to accurately predict the running time of simple application kernels for actual platforms. However some of the new algorithms we propose give excellent results in a wide range of situations

Identifying Logical Homogeneous Clusters for Efficient Wide-area Communications

Recently, many works focus on the implementation of collective communication operations adapted to wide area computational systems, like computational Grids or global-computing. Due to the inherently heterogeneity of such environments, most works separate "clusters" in different hierarchy levels. to better model the communication. However, in our opinion, such works do not give enough attention to the delimitation of such clusters, as they normally use the locality or the IP subnet from the machines to delimit a cluster without verifying the "homogeneity" of such clusters. In this paper, we describe a strategy to gather network information from different local-area networks and to construct "logical homogeneous clusters", better suited to the performance modelling.Comment: http://www.springerlink.com/index/TTJJL61R1EXDLCM

Design Issues for Qualitative Modelling of Biological Cells with Petri Nets

Abstract. Petri nets are a widely used formalism to qualitatively model concurrent systems such as a biological cell. We present techniques for modelling biological processes as Petri nets for further analyses and insilico experiments. Instead of extending the formalism with,,colours ” or rates, as is most often done, we focus on preserving the simplicity of the formalism and developing an execution semantics which resembles biology – we apply a principle of maximal parallelism and introduce the novel concept of bounded execution with overshooting. A number of modelling solutions are demonstrated using the example of the wellstudied C. elegans vulval development process. To date our model is still under development, but first results, based on Monte Carlo simulations, are promising.

An intervention to optimise the delivery of integrated tuberculosis and HIV services at primary care clinics: Results of the MERGE cluster randomised trial

Kielmann, Karina - ORCID 0000-0001-5519-1658 https://orcid.org/0000-0001-5519-1658Objectives: To evaluate the effect of an intervention to optimize TB/HIV integration on patient outcomes.Methods: Cluster randomised control trial at 18 primary care clinics in South Africa. The intervention was placement of a nurse (TB/HIV integration officer) to facilitate provision of integrated TB/HIV services, and a lay health worker (TB screening officer) to facilitate TB screening for 24 months. Primary outcomes were i) incidence of hospitalisation/death among individuals newly diagnosed with HIV, ii) incidence of hospitalisation/ death among individuals newly diagnosed with TB and iii) proportion of HIV-positive individuals newly diagnosed with TB who were retained in HIV care 12 months after enrolment.Results: Of 3328 individuals enrolled, 3024 were in the HIV cohort, 731 in TB cohort and 427 in TB-HIV cohort. For the HIV cohort, the hospitalisation/death rate was 12.5 per 100 person-years (py) (182/1459py) in the intervention arm vs. 10.4/100py (147/1408 py) in the control arms respectively (Relative Risk (RR) 1.17 [95% CI 0.92–1.49]).For the TB cohort, hospitalisation/ death rate was 17.1/100 py (67/ 392py) vs. 11.1 /100py (32/ 289py) in intervention and control arms respectively (RR 1.37 [95% CI 0.78–2.43]). For the TB-HIV cohort, retention in care at 12 months was 63.0% (213/338) and 55.9% (143/256) in intervention and control arms (RR 1.11 [95% 0.89–1.38]).Conclusions: The intervention as implemented failed to improve patient outcomes beyond levels at control clinics. Effective strategies are needed to achieve better TB/HIV service integration and improve TB and HIV outcomes in primary care clinics.Trial registration: South African Register of Clinical Trials (registration number DOH-27-1011-3846).This study was supported by the President's Emergency Plan for AIDS Relief (PEPFAR) through the Centers for Disease Control and Prevention (CDC) under the terms of [Cooperative agreement 5U2GPS000811]. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of CDC.https://doi.org/10.1016/j.cct.2018.07.01372pubpu

Prevalence of Mycobacterium tuberculosis in sputum and reported symptoms among clinic attendees compared to a community survey in rural South Africa

BACKGROUND: Tuberculosis (TB) case finding efforts typically target symptomatic people attending health facilities. We compared the prevalence of Mycobacterium tuberculosis (Mtb) sputum culture-positivity among adult clinic attendees in rural South Africa with a concurrent, community-based estimate from the surrounding demographic surveillance area (DSA). METHODS: Clinic: Randomly-selected adults (≥18 years) attending two primary healthcare clinics were interviewed and requested to give sputum for mycobacterial culture. HIV and antiretroviral therapy (ART) status were based on self-report and record review. Community: All adult (≥15 years) DSA residents were invited to a mobile clinic for health screening, including serological HIV testing; those with ≥1 TB symptom (cough, weight loss, night sweats, fever) or abnormal chest radiograph were asked for sputum. RESULTS: Clinic: 2,055 patients were enrolled (76.9% female, median age 36 years); 1,479 (72.0%) were classified HIV-positive (98.9% on ART) and 131 (6.4%) reported ≥1 TB symptom. Of 20/2,055 (1.0% [95% CI 0.6-1.5]) with Mtb culture-positive sputum, 14 (70%) reported no symptoms. Community: 10,320 residents were enrolled (68.3% female, median age 38 years); 3,105 (30.3%) tested HIV-positive (87.4% on ART) and 1,091 (10.6%) reported ≥1 TB symptom. Of 58/10,320 (0.6% [95% CI 0.4-0.7]) with Mtb culture-positive sputum, 45 (77.6%) reported no symptoms.In both surveys, sputum culture positivity was associated with male sex and reporting >1 TB symptom. CONCLUSIONS: In both clinic and community settings, most participants with Mtb culture-positive sputum were asymptomatic. TB screening based only on symptoms will miss many people with active disease in both settings

Assessing Contention Effects on MPI_Alltoall Communications

12 pagesInternational audienceOne of the most important collective communication patterns used in scientific applications is the complete exchange, also called All-to-All. Although efficient algorithms have been studied for specific networks, general solutions like those available in well-known MPI distributions (e.g. the MPI_Alltoall operation) are strongly influenced by the congestion of network resources. In this paper we present an integrated approach to model the performance of the All-to-All collective operation, which consists in identifying a contention signature that characterizes a given network environment, using it to augment a contention-free communication model. This approach, assessed by experimental results, allows an accurate prediction of the performance of the All-to-All operation over different network architectures with a small overhead

Mind the gap between policy imperatives and service provision: a qualitative study of the process of respiratory service development in England and Wales

The research was funded by the National Institute for Health Research Service Delivery and Organisation Programme. SDO/99/2005.Background: Healthcare systems globally are reconfiguring to address the needs of people with long-term conditions such as respiratory disease. Primary Care Organisations (PCOs) in England and Wales are charged with the task of developing cost-effective patient-centred local models of care. We aimed to investigate how PCOs in England and Wales are reconfiguring their workforce to develop respiratory services, and the background factors influencing service redesign. Methods: Semi-structured qualitative telephone interviews with the person(s) responsible for driving respiratory service reconfiguration in a purposive sample of 30 PCOs. Interviews were recorded, transcribed, coded and thematically analysed. Results: We interviewed representatives of 30 PCOs with diverse demographic profiles planning a range of models of care. Although the primary driver was consistently identified as the need to respond to a central policy to shift the delivery of care for people with long-term conditions into the community whilst achieving financial balance, the design and implementation of services were subject to a broad range of local, and at times serendipitous, influences. The focus was almost exclusively on the complex needs of patients at the top of the long-term conditions (LTC) pyramid, with the aim of reducing admissions. Whilst some PCOs seemed able to develop innovative care despite uncertainty and financial restrictions, most highlighted many barriers to progress, describing initiatives suddenly shelved for lack of money, progress impeded by reluctant clinicians, plans thwarted by conflicting policies and a PCO workforce demoralised by job insecurity. Conclusion: For many of our interviewees there was a large gap between central policy rhetoric driving workforce change, and the practical reality of implementing change within PCOs when faced with the challenges of limited resources, diverse professional attitudes and an uncertain organisational context. Research should concentrate on understanding these complex dynamics in order to inform the policymakers, commissioners, health service managers and professionals.Publisher PDFPeer reviewe

What 'outliers' tell us about missed opportunities for tuberculosis control: a cross-sectional study of patients in Mumbai, India

BACKGROUND: India's Revised National Tuberculosis Control Programme (RNTCP) is deemed highly successful in terms of detection and cure rates. However, some patients experience delays in accessing diagnosis and treatment. Patients falling between the 96th and 100th percentiles for these access indicators are often ignored as atypical 'outliers' when assessing programme performance. They may, however, provide clues to understanding why some patients never reach the programme. This paper examines the underlying vulnerabilities of patients with extreme values for delays in accessing the RNTCP in Mumbai city, India. METHODS: We conducted a cross-sectional study with 266 new sputum positive patients registered with the RNTCP in Mumbai. Patients were classified as 'outliers' if patient, provider and system delays were beyond the 95th percentile for the respective variable. Case profiles of 'outliers' for patient, provider and system delays were examined and compared with the rest of the sample to identify key factors responsible for delays. RESULTS: Forty-two patients were 'outliers' on one or more of the delay variables. All 'outliers' had a significantly lower per capita income than the remaining sample. The lack of economic resources was compounded by social, structural and environmental vulnerabilities. Longer patient delays were related to patients' perception of symptoms as non-serious. Provider delays were incurred as a result of private providers' failure to respond to tuberculosis in a timely manner. Diagnostic and treatment delays were minimal, however, analysis of the 'outliers' revealed the importance of social support in enabling access to the programme. CONCLUSION: A proxy for those who fail to reach the programme, these case profiles highlight unique vulnerabilities that need innovative approaches by the RNTCP. The focus on 'outliers' provides a less resource- and time-intensive alternative to community-based studies for understanding the barriers to reaching public health programmes