Automated SNP genotype clustering algorithm to improve data completeness in high-throughput SNP genotyping datasets from custom arrays

High-throughput SNP genotyping platforms use automated genotype calling algorithms to assign genotypes. While these algorithms work efficiently for individual platforms, they are not compatible with other platforms, and have individual biases that result in missed genotype calls. Here we present data on the use of a second complementary SNP genotype clustering algorithm. The algorithm was originally designed for individual fluorescent SNP genotyping assays, and has been optimized to permit the clustering of large datasets generated from custom-designed Affymetrix SNP panels. In an analysis of data from a 3K array genotyped on 1,560 samples, the additional analysis increased the overall number of genotypes by over 45,000, significantly improving the completeness of the experimental data. This analysis suggests that the use of multiple genotype calling algorithms may be advisable in high-throughput SNP genotyping experiments. The software is written in Perl and is available from the corresponding author

Micro-Nano : des comportements différents, des procédés à adapter

6 pagesL'arrivée de nanomatériaux parmi les différents matériaux utilisés en pyrotechnie pose de nombreux problèmes de mise en œuvre. En effet, leurs propriétés texturales particulières ne permettent pas de les utiliser comme des matériaux classiques. Il est impératif d'adapter les procédés de mise en œuvre habituels. Pour obtenir l'adéquation de ces nouveaux matériaux et de nos procédés, des études spécifiques du comportement des nanomatériaux au cours des procédés de mise en œuvre par coulée ont été réalisés. L'observation des écarts de comportement des nanomatériaux par rapport aux "micro-matériaux" pour une même nature chimique et des conditions identiques de mise en œuvre permet d'établir des lois de comportement spécifiques, fonction de la taille des particules manipulées. Les mentalités, comme les procédés, doivent évoluer et prendre en compte l'élévation de surface spécifique qu'offre le passage à l'échelle nanométrique. Ainsi un chargement moindre en nanomatériaux ne sera pas forcement synonyme de lacunes sur les caractéristiques du produit fini (propriétés mécaniques ou pyrotechniques). Deux questions peuvent alors se poser : faut-il adapter les formulations aux procédés, en prenant en compte les caractéristiques des matières premières ou bien adapter des procédés devant supporter des taux de chargement élevés en nanomatériaux ? Le manque de connaissance et le recul sur le comportement des nanomatériaux sont un frein à leur intégration dans des composés pyrotechniques mais les propriétés exhibées laissent présagées d'un grand intérêt en vue de l'optimisation des propriétés des composés fabriqués

Acquired hemophilia as first manifestation of breast carcinoma in a man under long-term spironolactone therapy

A 69-year-old man under long-term spironolactone therapy (16 years) was hospitalized with spontaneous hematoma on the trunk and extremities. Coagulation studies disclosed an acquired hemophilia that was successfully treated with human factor VIII for a few days and immunosuppressive agents for several months. Physical examination revealed bilateral gynecomastia and an upper left quadrant breast nodule. Complete staging was unremarkable. Complete left mastectomy was performed. Histopathology showed invasive ductal carcinoma, expressing positivity for estrogen and progesterone receptors. The acquired hemophilia was considered to be a paraneoplasic syndrome. The question of a linkage between long-term spironolactone therapy and breast carcinoma is discusse

Intravenous ibandronate in men with osteoporosis: An open pilot study over 2 years

In the treatment of osteoporosis, the tolerance of oral bisphosphonates is often low. The high potency of ibandronate allows iv bolus injections that can be repeated every 2 to 3 months. However, the best dose and time interval of the treatment with iv ibandronate is still debated. Efficacy of 2-mg ibandronate injected every 3 months was tested in men with osteoporosis over 2 yr, in a prospective, open study. Fourteen men with primary osteoporosis, mean age 57±12 yr (range: 40-73), received 2-mg ibandronate iv every 3 months over 2 yr. All got 1 g/day calcium and 880 UI/day vitamin D for 2 yr. Bone mineral density (BMD) increased after 2 yr by 6.7±1.5% (mean change±SEM) at lumbar spine (p<0.001), by 3.2±08% at trochanter (p<0.001) and by 1.4±1.1% at femoral neck (ns). Serum ß-crosslaps and osteocalcin decreased significantly by 30-45 and 30%, respectively, during the 2 yr of treatment. Serum calcium increased from the lower to the middle tertile of the normal range during the 2 yr of the study. The observed decrease of bone remodelling and the increase of BMD are of the same magnitude as those described with oral bisphosphonates. The increase of plasma calcium confirms the positive effect of the supplementation with calcium and vitamin D. These results suggest that 3 months are a good interval between two doses of iv ibandronate, when 2 mg are give

What was your fracture risk evaluated by FRAX® the day before your osteoporotic fracture?

Osteoporotic fracture (OF) is one of the major causes of morbidity and mortality in industrialized countries. Switzerland is among the countries with the greatest risk. Our aim was (1) to calculate the FRAX® in a selected Swiss population the day before the occurrence of an OF and (2) to compare the results with the proposed Swiss FRAX® thresholds. The Swiss Association Against Osteoporosis proposed guidelines for the treatment of osteoporosis based on age-dependent thresholds. To identify a population at a very high risk of osteoporotic fracture, we included all consecutive patients in the active OF pathway cohort from the Lausanne University Hospital, Switzerland. FRAX® was calculated with the available data the day before the actual OF. People with a FRAX® body mass index (BMI) or a FRAX® (bone mineral density) BMD lower than the Swiss thresholds were not considered at high risk. Two-hundred thirty-seven patients were included with a mean age of 77.2years, and 80% were female. Major types of fracture included hip (58%) and proximal humerus (25%) fractures. Mean FRAX® BMI values were 28.0, 10.0, 13.0, 26.0, and 37.0% for age groups 50-59, 60-69, 70-79, and 80-89years old, respectively. Fifty percent of the population was not considered at high risk by the FRAX® BMI. FRAX® BMD was available for 95 patients, and 45% had a T score < −2.5 standard deviation. Only 30% of patients with a normal or osteopenic BMD were classified at high risk by FRAX® BMD. The current proposed Swiss thresholds were not able to classify at high risk in 50 to 70% of the studied population the day before a major O

“Inflammaging” and bone in the OsteoLaus cohort

In this large population-based cohort, we did not find a relation between the coined concept of “inflammaging” (hs-CRP, IL-6, IL-1β and TNF-α within the normal range) and bone parameters, measured in terms of prevalent and incident fractures, bone mass density and trabecular bone score

Comparative Effects of University of Wisconsin and Euro-Collins Solutions on Pulmonary Mitochondrial Function after Ischemia and Reperfusion

peer reviewedBACKGROUND: The aim of this study was to compare the effects of Euro-Collins and University of Wisconsin solutions on pulmonary mitochondrial function after cold ischemia and subsequent warm reperfusion. METHODS: Seventeen pigs underwent lung harvesting after classical lung flush with either University of Wisconsin or Euro-Collins solutions. The mitochondria were isolated from fresh swine lungs, from swine lungs subjected to 24 hr of cold ischemia, and from swine lungs subjected to 24 hr of ischemia followed by 30 min of subsequent ex vivo reperfusion at 37 degrees C with Krebs-Henseleit buffer solution and air ventilation. Mitochondrial oxidative phosphorylation parameters were determined in isolated mitochondria by in vitro measurement of oxygen consumption rates. During reperfusion, the lung function was assessed by the pulmonary aerodynamic parameters and the pulmonary vascular resistance. RESULTS: Relative to controls, mitochondria submitted to cold ischemia showed an alteration in the oxidoreductase activities of the respiratory chain. However, the yield of oxidative phosphorylation was conserved. After reperfusion, pulmonary mitochondria underwent a significant worsening in the oxidoreductase activities of the respiratory chain, and a decrease in the respiratory control and the efficiency of oxidative phosphorylation. Meanwhile, the reperfused lungs showed evidence of early dysfunction, assessed by the aerodynamic parameters and pulmonary vascular resistance. In this model, there was no advantage of University of Wisconsin solution over Euro-Collins solution. CONCLUSIONS: The mild mitochondrial alterations after cold ischemia were not sufficient to explain the limited tolerance of lung to ischemia. After reperfusion, the mitochondrial damage was more severe and could be involved in the posttransplant lung dysfunction

InAs quantum wires on InP substrate for VCSEL applications

International audienceQuantum dash based vertical cavity surface emitting lasers (VCSEL) on InP substrate are presented. Single and close stacking layers were successfully grown with molecular beam epitaxy. Optimized quantum dash layers exhibit a strong polarized 1.55 µm photoluminescence along the [1-10] crystallographic axis. Continuous wave laser emission is demonstrated at room temperature for the first time on a quantum dash VCSEL structure on InP susbtrate. The quantum dash VCSEL laser polarization appears stable on the whole sample and with excitation, no switching is observed. Its polarization is mainly oriented along [1-10], an extinction coefficient of 30 dB is measured. Those preliminary results demonstrate the interests of quantum dashes in the realization of controlled and stable polarization VCSEL device