A device for studying elementary plasticity fluctuations in granular media

In this manuscript, we describe a scientific device specifically designed for the study of the plasticity fluctuations preceding the fracture of granular media. Biaxial tests on model granular media are performed using a commercial uniaxial loading system. Strain field fluctuations are measured using a method based on the interference of coherent light scattered by the sample. We show that such a device enables discrete plasticity events to be unambiguously evidenced. Moreover, those discrete plasticity fluctuations depend only on the imposed strain, and not on the strain rate

Gestion de l’enherbement et biodiversité fonctionnelle contre pucerons en maraîchage biologique sous abris (Projet Ecophyto Placohb)

Pour la gestion des pucerons en maraîchage biologique sous abris, la mise en place de bandes fleuries dans les serres a pour objectif d’attirer leurs ennemis naturels le plus tôt possible. Par ailleurs, la gestion de l’enherbement sur les bords intérieurs des serres est parfois problématique, même avec la mise en place de paillages plastiques en bordure. Afin de concilier ces 2 objectifs, gestion des pucerons et maîtrise de l’enherbement au pied des bâches à l’intérieur des abris, le GRAB a mis en place en 2019 une étude destinée à rechercher les espèces vivaces les plus adaptées. Des espèces comme la centaurée, la marguerite, l’achillée, le lotier semblent pouvoir à la fois contrôler efficacement les plantes adventices et attirer un grand nombre d’auxiliaires

Mechanical characterization of the thoracic ascending aortae

International audienceIn this study the digital image correlation technique is used for characterizing the mechanical and fracture properties of aneurysmal tissues. The tissues which have been taken from the thoracic ascending aorta of diseased patients are tested in a bulge inflation test. The approach is original in the sense that it gives access to the local stress fields in the tissue and to local analysis of fracture. Applications to the dynamic behavior and fracture of vascular tissues are envisaged

Low-Wavelengths SOI CMOS Photosensors for Biomedical Applications

INTRODUCTION : Biological agents may be characterized (in terms of quantity (or concentration), purity, nature) using optical ways like spectrometry, fluorometry and real-time PCR for example. Most of these techniques are based on absorbance or fluorescence. Indeed, many biological molecules can absorb the light when excited at wavelengths close to blue and ultraviolet (UV). For example, DNA, RNA and proteins feature an absorption peak in the deep UV, more precisely around 260 and 280 nm (Karczemska & Sokolowska, 2001). This work is widely focused on those wavelengths. A biological sample concentration measurement method can be based on UV light absorbance or transmittance, as already known and realized with high-cost and large-size biomedical apparatus. But, often, the difficulties come from the limitation for measuring very small concentrations (close to a few ng/µL or lower) since the measurement of such small light intensity variations at those low wavelengths requires a precise light source, and very efficient photodetectors. Reducing the dimensions of such a characterization system further requires a small light source, a miniaturized photosensor and a processing system with high precision to reduce the measurement variations. Some light-emitting diodes (LED) performing at those UV wavelengths have recently appeared and may be used to implement the light source. Concerning the optical sensor, while accurate but high-cost photosensors in technologies such as AlGaN and SiC provide high sensitivities in UV low wavelengths thanks to their semiconductor bandgap (Yotter & Wilson, 2003), the silicon-on-insulator (SOI) layers absorb the photons in that specific range thanks to an appropriate thickness of the silicon. Adding excellent performances of low power consumption, good temperature behavior and high speed (Flandre et al., 1999; 2001), the SOI technology allows the designers for integrating a specific signal processing integrated CMOS circuit to transform the photocurrent into a digital signal for example. This opens the possibility to build a low-cost, complete and portable microsystem, including the light source, the photodetector and a recipient for the sample to characterize […

Unambiguous Detection of Multiple TP53 Gene Mutations in AAN-Associated Urothelial Cancer in Belgium Using Laser Capture Microdissection

In the Balkan and Taiwan, the relationship between exposure to aristolochic acid and risk of urothelial neoplasms was inferred from the A>T genetic hallmark in TP53 gene from malignant cells. This study aimed to characterize the TP53 mutational spectrum in urothelial cancers consecutive to Aristolochic Acid Nephropathy in Belgium. Serial frozen tumor sections from female patients (n = 5) exposed to aristolochic acid during weight-loss regimen were alternatively used either for p53 immunostaining or laser microdissection. Tissue areas with at least 60% p53-positive nuclei were selected for microdissecting sections according to p53-positive matching areas. All areas appeared to be carcinoma in situ. After DNA extraction, mutations in the TP53 hot spot region (exons 5-8) were identified using nested-PCR and sequencing. False-negative controls consisted in microdissecting fresh-frozen tumor tissues both from a patient with a Li-Fraumeni syndrome who carried a p53 constitutional mutation, and from KRas mutated adenocarcinomas. To rule out false-positive results potentially generated by microdissection and nested-PCR, a phenacetin-associated urothelial carcinoma and normal fresh ureteral tissues (n = 4) were processed with high laser power. No unexpected results being identified, molecular analysis was pursued on malignant tissues, showing at least one mutation in all (six different mutations in two) patients, with 13/16 exonic (nonsense, 2; missense, 11) and 3/16 intronic (one splice site) mutations. They were distributed as transitions (n = 7) or transversions (n = 9), with an equal prevalence of A>T and G>T (3/16 each). While current results are in line with A>T prevalence previously reported in Balkan and Taiwan studies, they also demonstrate that multiple mutations in the TP53 hot spot region and a high frequency of G>T transversion appear as a complementary signature reflecting the toxicity of a cumulative dose of aristolochic acid ingested over a short period of time

Impact of the spotted microarray preprocessing method on fold-change compression and variance stability

<p>Abstract</p> <p>Background</p> <p>The standard approach for preprocessing spotted microarray data is to subtract the local background intensity from the spot foreground intensity, to perform a log2 transformation and to normalize the data with a global median or a lowess normalization. Although well motivated, standard approaches for background correction and for transformation have been widely criticized because they produce high variance at low intensities. Whereas various alternatives to the standard background correction methods and to log2 transformation were proposed, impacts of both successive preprocessing steps were not compared in an objective way.</p> <p>Results</p> <p>In this study, we assessed the impact of eight preprocessing methods combining four background correction methods and two transformations (the log2 and the glog), by using data from the MAQC study. The current results indicate that most preprocessing methods produce fold-change compression at low intensities. Fold-change compression was minimized using the Standard and the Edwards background correction methods coupled with a log2 transformation. The drawback of both methods is a high variance at low intensities which consequently produced poor estimations of the p-values. On the other hand, effective stabilization of the variance as well as better estimations of the p-values were observed after the glog transformation.</p> <p>Conclusion</p> <p>As both fold-change magnitudes and p-values are important in the context of microarray class comparison studies, we therefore recommend to combine the Edwards correction with a hybrid transformation method that uses the log2 transformation to estimate fold-change magnitudes and the glog transformation to estimate p-values.</p

Regression applied to protein binding site prediction and comparison with classification

<p>Abstract</p> <p>Background</p> <p>The structural genomics centers provide hundreds of protein structures of unknown function. Therefore, developing methods enabling the determination of a protein function automatically is imperative. The determination of a protein function can be achieved by studying the network of its physical interactions. In this context, identifying a potential binding site between proteins is of primary interest. In the literature, methods for predicting a potential binding site location generally are based on classification tools. The aim of this paper is to show that regression tools are more efficient than classification tools for patches based binding site predictors. For this purpose, we developed a patches based binding site localization method usable with either regression or classification tools.</p> <p>Results</p> <p>We compared predictive performances of regression tools with performances of machine learning classifiers. Using leave-one-out cross-validation, we showed that regression tools provide better predictions than classification ones. Among regression tools, Multilayer Perceptron ranked highest in the quality of predictions. We compared also the predictive performance of our patches based method using Multilayer Perceptron with the performance of three other methods usable through a web server. Our method performed similarly to the other methods.</p> <p>Conclusion</p> <p>Regression is more efficient than classification when applied to our binding site localization method. When it is possible, using regression instead of classification for other existing binding site predictors will probably improve results. Furthermore, the method presented in this work is flexible because the size of the predicted binding site is adjustable. This adaptability is useful when either false positive or negative rates have to be limited.</p

Bone marrow graft versus peripheral blood graft in haploidentical hematopoietic stem cells transplantation: a retrospective analysis in1344 patients of SFGM-TC registry.

peer reviewedThe use of peripheral blood (PB) or bone marrow (BM) stem cells graft in haploidentical hematopoietic stem cell transplantation with post-transplant cyclophosphamide (PTCy) for graft-versus-host disease (GVHD) prophylaxis remains controversial. Moreover, the value of adding anti-thymoglobulin (ATG) to PTCy is unknown. A total of 1344 adult patients received an unmanipulated haploidentical transplant at 37 centers from 2012 to 2019 for hematologic malignancy. We compared the outcomes of patients according to the type of graft, using a propensity score analysis. In total population, grade II-IV and III-IV acute GVHD (aGVHD) were lower with BM than with PB. Grade III-IV aGVHD was lower with BM than with PB + ATG. All outcomes were similar in PB and PB + ATG groups. Then, in total population, adding ATG does not benefit the procedure. In acute leukemia, myelodysplastic syndrome and myeloproliferative syndrome (AL-MDS-MPS) subgroup receiving non-myeloablative conditioning, risk of relapse was twice greater with BM than with PB (51 vs. 22%, respectively). Conversely, risk of aGVHD was greater with PB (38% for aGVHD II-IV; 16% for aGVHD III-IV) than with BM (28% for aGVHD II-IV; 8% for aGVHD III-IV). In this subgroup with intensified conditioning regimen, risk of relapse became similar with PB and BM but risk of aGVHD III-IV remained higher with PB than with BM graft (HR = 2.0; range [1.17-3.43], p = 0.012)