Search results for "mining"

RNA-Seq Atlas—a reference database for gene expression profiling in normal tissue by next-generation sequencing

2012

Abstract Motivation: Next-generation sequencing technology enables an entirely new perspective for clinical research and will speed up personalized medicine. In contrast to microarray-based approaches, RNA-Seq analysis provides a much more comprehensive and unbiased view of gene expression. Although the perspective is clear and the long-term success of this new technology obvious, bioinformatics resources making these data easily available especially to the biomedical research community are still evolving. Results: We have generated RNA-Seq Atlas, a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression pr…

Outlier detection with automatic modelling: TRAMO/SEATS versus X-12-ARIMA

2012

Efficient change point detection in genomic sequences of continuous measurements

2010

Abstract Motivation: Knowing the exact locations of multiple change points in genomic sequences serves several biological needs, for instance when data represent aCGH profiles and it is of interest to identify possibly damaged genes involved in cancer and other diseases. Only a few of the currently available methods deal explicitly with estimation of the number and location of change points, and moreover these methods may be somewhat vulnerable to deviations of model assumptions usually employed. Results: We present a computationally efficient method to obtain estimates of the number and location of the change points. The method is based on a simple transformation of data and it provides re…

Systematic handling of missing data in complex study designs : experiences from the Health 2000 and 2011 Surveys

2016

We present a systematic approach to the practical and comprehensive handling of missing data motivated by our experiences of analyzing longitudinal survey data. We consider the Health 2000 and 2011 Surveys (BRIF8901) where increased non-response and non-participation from 2000 to 2011 was a major issue. The model assumptions involved in the complex sampling design, repeated measurements design, non-participation mechanisms and associations are presented graphically using methodology previously defined as a causal model with design, i.e. a functional causal model extended with the study design. This tool forces the statistician to make the study design and the missing-data mechanism explicit…

A semiparametric approach to estimate reference curves for biophysical properties of the skin

2006

Reference curves which take one covariable into account such as the age, are often required in medicine, but simple systematic and efficient statistical methods for constructing them are lacking. Classical methods are based on parametric fitting (polynomial curves). In this chapter, we describe a new methodology for the estimation of reference curves for data sets, based on nonparametric estimation of conditional quantiles. The derived method should be applicable to all clinical or more generally biological variables that are measured on a continuous quantitative scale. To avoid the curse of dimensionality when the covariate is multidimensional, a new semiparametric approach is proposed. Th…

Electrochemical and DFT studies of the oxidative decomposition of the trihydride complexes Cp*M(dppe)H3 (M = Mo, W) in acetonitrile

2006

International audience; A detailed electrochemical study of the oxidative decomposition of the trihydride complexes Cp*M(dppe)H3 (M = Mo, W) in acetonitrile is presented. For the Mo complex, the decomposition occurs by four different pathways involving classical and non-classical tautomers, whereas only the classical form is accessible for the W derivative. Each of the decomposition pathways has been quantitatively assessed by analyses of the linear sweep voltammograms. In addition to the previously established (B. Pleune, D. Morales, R. Meunier-Prest, P. Richard, E. Collange, J. C. Fettinger and R. Poli, J. Am. Chem. Soc., 1999, 121, 2209–2225) deprotonation, disproportionation, and H2 red…

A theoretical study of carbon-carbon bond formation by a Michael-type addition.

2012

A theoretical study of the Michael-type addition of 1,3-dicarbonyl compounds to α,β-unsaturated carbonyl compounds has been performed in the gas phase by means of the AM1 semiempirical method and by density functional theory (DFT) calculations within the B3LYP and M06-2X hybrid functionals. A molecular model has been selected to mimic the role of a base, which is traditionally used as a catalyst in Michael reactions, an acetate moiety to modulate its basicity, and point charges to imitate the stabilization of the negative charge developed in the substrate during the reaction when taking place in enzymatic environments. Results of the study of six different reactions obtained at the three di…

Evaluating the microscopic effect of brushing stone tools as a cleaning procedure

2020

Cleaning stone tool surfaces is a common procedure in lithic studies. The first step widely applied at any archeological site (and/or at field laboratories) is the gross removal of sediment from the surfaces of artifacts. Lithic surface alterations due to mechanical action applied in wet or dry cleaning regimes have never been examined at a microscopic scale. This could have important implications in traceology, as any modern surface modifications inflicted on archeological artifacts might compromise their functional interpretations. The current trend toward quantification of use-wear traces makes the testing even more important, as even slight, apparently invisible surface alterations migh…

Soil REE patterns as tracers of the emplacement of metal-rich anthropogenic materials. A case study in Moa (Cuba)

2019

Purpose: Are rare earth element (REE) patterns employable as tracers in human interventions of bulk soil disturbances, when high concentrations of metals are involved in the in situ soil disturbance? In terms of bulk soil disturbance, it is difficult to distinguish between bulk soil disturbances and emplacement of new earthen material. Chemical fingerprinting, in particular REE plus yttrium, is applied across many fields, but predominantlyin tracking the sources of potential environmental contaminants. Materials and methods: The REE normalised patterns (HNO 3 :HF:HCl 3:1:1 digestion, ICP-MS) of two Calcaric Cambisols were compared with those of a Geric Ferralsol (Novic, Technic) originated …

Are Neural Networks Imitations of Mind?

2015

Artificial neural networks are often understood as a good way to imitate mind through the web structure of neurons in brain, but the very high complexity of human brain prevents to consider neural networks as good models for human mind;anyway neural networks are good devices for computation in parallel. The difference between feed-forward and feedback neural networks is introduced; the Hopfield network and the multi-layers Perceptron are discussed. In a very weak isomorphism (not similitude) between brain and neural networks, an artificial form of short term memory and of acknowledgement, in Elman neural networks, is proposed.