Optimized Schwarz Waveform Relaxation for Advection Reaction Diffusion Equations in Two Dimensions

Optimized Schwarz Waveform Relaxation methods have been developed over the last decade for the parallel solution of evolution problems. They are based on a decomposition in space and an iteration, where only subproblems in space-time need to be solved. Each subproblem can be simulated using an adapted numerical method, for example with local time stepping, or one can even use a different model in different subdomains, which makes these methods very suitable also from a modeling point of view. For rapid convergence however, it is important to use effective transmission conditions between the space-time subdomains, and for best performance, these transmission conditions need to take the physics of the underlying evolution problem into account. The optimization of these transmission conditions leads to a mathematically hard best approximation problem of homographic type. We study in this paper in detail this problem for the case of linear advection reaction diffusion equations in two spatial dimensions. We prove comprehensively best approximation results for transmission conditions of Robin and Ventcel type. We give for each case closed form asymptotic values for the parameters, which guarantee asymptotically best performance of the iterative methods. We finally show extensive numerical experiments, and we measure performance corresponding to our analysisComment: 42 page

Comparative Evaluation of Three Automated Systems for DNA Extraction in Conjunction with Three Commercially Available Real-Time PCR Assays for Quantitation of Plasma Cytomegalovirus DNAemia in Allogeneic Stem Cell Transplant Recipients▿

Limited data are available on the performance of different automated extraction platforms and commercially available quantitative real-time PCR (QRT-PCR) methods for the quantitation of cytomegalovirus (CMV) DNA in plasma. We compared the performance characteristics of the Abbott mSample preparation system DNA kit on the m24 SP instrument (Abbott), the High Pure viral nucleic acid kit on the COBAS AmpliPrep system (Roche), and the EZ1 Virus 2.0 kit on the BioRobot EZ1 extraction platform (Qiagen) coupled with the Abbott CMV PCR kit, the LightCycler CMV Quant kit (Roche), and the Q-CMV complete kit (Nanogen), for both plasma specimens from allogeneic stem cell transplant (Allo-SCT) recipients (n = 42) and the OptiQuant CMV DNA panel (AcroMetrix). The EZ1 system displayed the highest extraction efficiency over a wide range of CMV plasma DNA loads, followed by the m24 and the AmpliPrep methods. The Nanogen PCR assay yielded higher mean CMV plasma DNA values than the Abbott and the Roche PCR assays, regardless of the platform used for DNA extraction. Overall, the effects of the extraction method and the QRT-PCR used on CMV plasma DNA load measurements were less pronounced for specimens with high CMV DNA content (>10,000 copies/ml). The performance characteristics of the extraction methods and QRT-PCR assays evaluated herein for clinical samples were extensible at cell-based standards from AcroMetrix. In conclusion, different automated systems are not equally efficient for CMV DNA extraction from plasma specimens, and the plasma CMV DNA loads measured by commercially available QRT-PCRs can differ significantly. The above findings should be taken into consideration for the establishment of cutoff values for the initiation or cessation of preemptive antiviral therapies and for the interpretation of data from clinical studies in the Allo-SCT setting

Study and interest of cellular load in respiratory samples for the optimization of molecular virological diagnosis in clinical practice

BACKGROUND: Respiratory viral diagnosis of upper respiratory tract infections has largely developed through multiplex molecular techniques. Although the sensitivity of different types of upper respiratory tract samples seems to be correlated to the number of sampled cells, this link remains largely unexplored. METHODS: Our study included 800 upper respiratory tract specimens of which 400 negative and 400 positive for viral detection in multiplex PCR. All samples were selected and matched for age in these 2 groups. For the positive group, samples were selected for the detected viral species. RESULTS: Among the factors influencing the cellularity were the type of sample (p < 0.0001); patient age (p < 0.001); viral positive or negative nature of the sample (p = 0.002); and, for the positive samples, the number of viral targets detected (0.004 < p < 0.049) and viral species. CONCLUSION: The cellular load of upper respiratory samples is multifactorial and occurs for many in the sensitivity of molecular detection. However it was not possible to determine a minimum cellularity threshold allowing molecular viral detection. The differences according to the type of virus remain to be studied on a larger scale

Développement et caractérisation de récepteurs d'anions et applications thérapeutiques dans les canalopathies

Les canalopathies représentent une famille de pathologies d'origines génétiques diverses touchant de nombreux organes. Il s'agit principalement de maladies d'origines génétiques dont les traitements sont uniquement symptomatiques. Pouvant toucher, le système nerveux, le système musculaire, le système respiratoire ou encore le système endocrinien, ces pathologies présentent des expressions phénotypiques variées rendant leur diagnostic complexe et pouvant entrainer des retards de prise en charge. De nombreuses approches thérapeutiques ont pu être développées pour subvenir au besoin des patients touchés par ces troubles, cependant de nombreux projets de recherches sont en cours pour mieux comprendre et traiter ces maladies. Nous nous proposons donc dans un premier temps de passer en revue les canalopathies, ainsi que leurs thérapeutiques actuelles et futures. Parmi les nombreuses approches développées, celle du remplacement des canaux ioniques par de petites molécules pouvant assurer la fonction des protéines mutées est prometteuse. Cette stratégie thérapeutique présente des avantages importants mais également un certain nombre de défis à surmonter pour permettre le développement de thérapeutiques innovantes et sûres pour les patients. Il s'agit de l'approche que nous avons pu développer. Dans ce travail, nous présenterons également les travaux expérimentaux nous ayant permis de réaliser la synthèse de composés capable de piéger les anions et de démontrer les mécanismes de complexation des ions à ceux-ci