A hybrid MPI-OpenMP scheme for scalable parallel pseudospectral computations for fluid turbulence

A hybrid scheme that utilizes MPI for distributed memory parallelism and OpenMP for shared memory parallelism is presented. The work is motivated by the desire to achieve exceptionally high Reynolds numbers in pseudospectral computations of fluid turbulence on emerging petascale, high core-count, massively parallel processing systems. The hybrid implementation derives from and augments a well-tested scalable MPI-parallelized pseudospectral code. The hybrid paradigm leads to a new picture for the domain decomposition of the pseudospectral grids, which is helpful in understanding, among other things, the 3D transpose of the global data that is necessary for the parallel fast Fourier transforms that are the central component of the numerical discretizations. Details of the hybrid implementation are provided, and performance tests illustrate the utility of the method. It is shown that the hybrid scheme achieves near ideal scalability up to ~20000 compute cores with a maximum mean efficiency of 83%. Data are presented that demonstrate how to choose the optimal number of MPI processes and OpenMP threads in order to optimize code performance on two different platforms.Comment: Submitted to Parallel Computin

Prevalence of respiratory pathogens in nasal swabs from horses with acute respiratory disease in Belgium

Contagious respiratory infections are an important cause of respiratory disease in horses, resulting in impaired pulmonary function, poor performance and sometimes severe illness. Although bacterial infections are often suspected to be involved, viruses are frequently overlooked and are an underestimated cause of respiratory disease outbreaks in horses. In this study, nasal swabs of 103 horses with acute symptoms of respiratory disease were analyzed for the presence of 13 different respiratory pathogens. Gamma herpesviruses were the most commonly detected, with 60% of the samples being positive, followed by streptococcus equi subsp. zooepidemicus infection (30%). Rhinovirus B, streptococcus equi subsp. equi, adenovirus 1 and EHV-4 were more rarely detected. Further research is necessary to correctly interpret the importance of gamma herpesviruses in horses, for example by screening a healthy control population. National surveillance of respiratory viruses in horses by PCR analysis on nasal swabs might be a useful, early warning system for viral epidemics

Theoretical study of a cold atom beam splitter

A theoretical model is presented for the study of the dynamics of a cold atomic cloud falling in the gravity field in the presence of two crossing dipole guides. The cloud is split between the two branches of this laser guide, and we compare experimental measurements of the splitting efficiency with semiclassical simulations. We then explore the possibilities of optimization of this beam splitter. Our numerical study also gives access to detailed information, such as the atom temperature after the splitting

Description and Predictive Factors of individual outcomes in a refugee camp based mental health intervention (Beirut, Lebanon)

There is little evidence on the effectiveness of services for the care of people with mental disorders among refugee populations. Médecins sans Frontières (MSF) has established a mental health centre in a mixed urban-refugee population in Beirut to respond to the significant burden of mental health problems. Patients received comprehensive care through a multidisciplinary team. A cohort of people with common and severe mental disorders has been analysed between December 2008 and June 2011 to evaluate individual outcomes of treatment in terms of functionality

Boost-HiC: computational enhancement of long-range contacts in chromosomal contact maps

International audienceGenome-wide chromosomal contact maps are widely used to uncover the 3D organisation of genomes. They rely on the collection of millions of contacting pairs of genomic loci. Contact frequencies at short range are usually well measured in experiments, while there is a lot of missing information about long-range contacts. We propose to use the sparse information contained in raw contact maps to determine high-confidence contact frequency between all pairs of loci. Our algorithmic procedure, Boost-HiC, enables the detection of Hi-C patterns such as chromosomal compartments at a resolution that would be otherwise only attainable by sequencing a hundred times deeper the experimental Hi-C library

Clinico-radiological criteria versus GeneXpert for diagnosis of pediatric tuberculosis

Background: Diagnosing tuberculosis in children remains a challenge especially in low-income countries. The aim of this study was to assess the performance of the scoring system combined to chest x-ray images compared to GeneXpert for diagnosis of pediatric tuberculosis.Methods: A retrospective diagnostic accuracy study was carried out on hospitalized children aged 0 to 14 years old, tuberculosis suspect in the pediatric department of the Tsaralalana mother child university hospital center from August 2018 to June 2020.Results: Fifty-one medical files were retained. The mean age was 4±2 years old with a sex ratio of 1.55. The reason for consultation was dominated by respiratory signs (56.9%). The GeneXpert was positive in 58.9% of cases. The chest X-ray images were pathological in all cases, dominated by images of condensation or infiltration (72.5%). WHO score was positive (≥7) in 72.5% of cases. The clinico-radiological criteria had a sensitivity of 13.3-63.3%, a specificity of 61.9-95.2%, positive predictive values of 1.5-6.9% and negative predictive values of 98.8-99.3%.Conclusion: Clinico-radiological criteria could be useful in individual diagnosis of pediatric tuberculosis

Psychosocial experience of mothers of children with sickle cell disease in Antananarivo and Toamasina, Madagascar

Background: Sickle cell disease in children can disrupt life of their mothers who are at the forefront of care. The objectives of this study were to describe the psychosocial experience of these mothers, to identify factors associated to maternal anxiety and depressive disorders.Methods: A cross-sectional study was conducted from December 2017 to February 2018 with mothers of children with sickle cell disease under the age of 15 in Antananarivo and Toamasina. The abbreviated Beck and Hamilton scales were used to assess respectively depression and anxiety.Results: Of 134 mothers surveyed, 61.2% had depression and 35.8% had anxiety. Depression significantly affected mothers with more than one child with sickle cell disease (aOR=4.31, CI- 1.12-16.58) and mothers of children hospitalized at least three times per year for vaso-occlusive crisis (aOR=13.55, CI- 1.56-117.5). Anxiety was associated with blood transfusion more than three times (aOR=9.06, CI- 2.05-40.00). Pity (74.6%) and fear of death (55.2%) were the main feelings reported. Negative occupational repercussions were reported by 48.5% of mothers, marital conflict by 15.6%, financial difficulties by 43.3%.Conclusions: A global approach focused on the child and his family would be optimal for success in the management of pediatric sickle cell disease