Increasing the Number of Thyroid Lesions Classes in Microarray Analysis Improves the Relevance of Diagnostic Markers

BackgroundGenetic markers for thyroid cancers identified by microarray analysis have offered limited predictive accuracy so far because of the few classes of thyroid lesions usually taken into account. To improve diagnostic relevance, we have simultaneously analyzed microarray data from six public datasets covering a total of 347 thyroid tissue samples representing 12 histological classes of follicular lesions and normal thyroid tissue. Our own dataset, containing about half the thyroid tissue samples, included all categories of thyroid lesions. Methodology/Principal Findings Classifier predictions were strongly affected by similarities between classes and by the number of classes in the training sets. In each dataset, sample prediction was improved by separating the samples into three groups according to class similarities. The cross-validation of differential genes revealed four clusters with functional enrichments. The analysis of six of these genes (APOD, APOE, CLGN, CRABP1, SDHA and TIMP1) in 49 new samples showed consistent gene and protein profiles with the class similarities observed. Focusing on four subclasses of follicular tumor, we explored the diagnostic potential of 12 selected markers (CASP10, CDH16, CLGN, CRABP1, HMGB2, ALPL2, ADAMTS2, CABIN1, ALDH1A3, USP13, NR2F2, KRTHB5) by real-time quantitative RT-PCR on 32 other new samples. The gene expression profiles of follicular tumors were examined with reference to the mutational status of the Pax8-PPARγ, TSHR, GNAS and NRAS genes. Conclusion/Significance We show that diagnostic tools defined on the basis of microarray data are more relevant when a large number of samples and tissue classes are used. Taking into account the relationships between the thyroid tumor pathologies, together with the main biological functions and pathways involved, improved the diagnostic accuracy of the samples. Our approach was particularly relevant for the classification of microfollicular adenomas

Generation of thermal scattering laws with the CINEL code

The thermal scattering laws (TSL) take into account the crystalline structure and atomic motions of isotopes bound in materials. This paper presents the CINEL code, which was developed to generate temperature-dependent TSL for solid, liquid and free gas materials of interest for nuclear reactors. CINEL is able to calculate TSL from the phonon density of states (PDOS) of materials under the Gaussian-Incoherent approximations. The PDOS can be obtained by using theoretical approaches (e.g., ab initio density functional theory and molecular dynamics) or experimental results. In this work, the PDOS presented in the ENDF/BVIII.0 and NJOY-NCrystal libraries were used for numerical validation purposes. The CINEL results are in good agreement with those reported in these databases, even in the specific cases of TSL with the newly mixed elastic format. The coding flexibility offered by Python using the JupyterLab interface allowed to investigate limits of physical models reported in the literature, such as a four-site model for UO2, anharmonic behaviors of oxygen atoms bound in a Fm3m structure, texture in Zry4 samples and jump corrections in a roto-translational diffusion model for liquid water. The use of graphic processing units (GPU) is a necessity to perform calculations in a few minutes. The performances of the CINEL code is illustrated with the results obtained on actinide oxides having a Fm3m structure (UO2, ThO2, NpO2 and PuO2), low enriched fuel (UMo), cladding (Zry4) and moderators (H2O with a specific emphasis on ice)

Evidence of the presence of opticlike collective modes in a liquid from neutron scattering experiments

Inelastic neutron scattering data from liquid DF close to the melting point show, in addition to spectra comprising quasielastic and heavily damped acoustic motions, an intense, nondispersive band centered at about 27 meV along with a broader higher energy feature. Observation of the former band provides the first direct verification of the existence within the liquid state of collective opticlike excitations as predicted by molecular dynamics simulations. The latter corresponds to mainly reorientational motions assigned from mode eigenvector analysis carried out by computer simulations

Why is Asari (=Manila) clam Ruditapes philippinarum fitness poor in Arcachon Bay: A meta-analysis to answer?

© 2015 Elsevier Ltd Asari (=Manila) clam, Ruditapes philippinarum, is the second bivalve mollusc in terms of production in the world and, in many coastal areas, can beget important socio-economic issues. In Europe, this species was introduced after 1973. In Arcachon Bay, after a decade of aquaculture attempt, Asari clam rapidly constituted neo-naturalized population which is now fished. However, recent studies emphasized the decline of population and individual performances. In the framework of a national project (REPAMEP), some elements of fitness, stressors and responses in Arcachon Bay were measured and compared to international data (41 publications, 9 countries). The condition index (CI = flesh weight/shell weight) was the lowest among all compared sites. Variation in average Chla concentration explained 30% of variation of CI among different areas. Among potential diseases, perkinsosis was particularly prevalent in Arcachon Bay, with high abundance, and Asari clams underwent Brown Muscle Disease, a pathology strictly restricted to this lagoon. Overall element contamination was relatively low, although arsenic, cobalt, nickel and chromium displayed higher values than in other ecosystems where Asari clam is exploited. Finally, total hemocyte count (THC) of Asari clam in Arcachon Bay, related to the immune system activity, exhibited values that were also under what is generally observed elsewhere. In conclusion, this study, with all reserves due to heterogeneity of available data, suggest that the particularly low fitness of Asari clam in Arcachon Bay is due to poor trophic condition, high prevalence and intensity of a disease (perkinsosis), moderate inorganic contamination, and poor efficiency of the immune system