Preprocessing Procedures (preprocessing + procedure)

Distribution by Scientific Domains


Selected Abstracts


Finding starting points for Markov chain Monte Carlo analysis of genetic data from large and complex pedigrees

GENETIC EPIDEMIOLOGY, Issue 1 2003
Yuqun Luo
Abstract Genetic data from founder populations are advantageous for studies of complex traits that are often plagued by the problem of genetic heterogeneity. However, the desire to analyze large and complex pedigrees that often arise from such populations, coupled with the need to handle many linked and highly polymorphic loci simultaneously, poses challenges to current standard approaches. A viable alternative to solving such problems is via Markov chain Monte Carlo (MCMC) procedures, where a Markov chain, defined on the state space of a latent variable (e.g., genotypic configuration or inheritance vector), is constructed. However, finding starting points for the Markov chains is a difficult problem when the pedigree is not single-locus peelable; methods proposed in the literature have not yielded completely satisfactory solutions. We propose a generalization of the heated Gibbs sampler with relaxed penetrances (HGRP) of Lin et al., ([1993] IMA J. Math. Appl. Med. Biol. 10:1,17) to search for starting points. HGRP guarantees that a starting point will be found if there is no error in the data, but the chain usually needs to be run for a long time if the pedigree is extremely large and complex. By introducing a forcing step, the current algorithm substantially reduces the state space, and hence effectively speeds up the process of finding a starting point. Our algorithm also has a built-in preprocessing procedure for Mendelian error detection. The algorithm has been applied to both simulated and real data on two large and complex Hutterite pedigrees under many settings, and good results are obtained. The algorithm has been implemented in a user-friendly package called START. Genet Epidemiol 25:14,24, 2003. © 2003 Wiley-Liss, Inc. [source]


Preprocessing Steiner problems from VLSI layout

NETWORKS: AN INTERNATIONAL JOURNAL, Issue 1 2002
Eduardo Uchoa
Abstract VLSI layout applications yield instances of the Steiner tree problem over grid graphs with holes, which are considered hard to be solved by current methods. In particular, preprocessing techniques developed for Steiner problems over general graphs are not likely to reduce, significantly, such VLSI instances. We propose a new preprocessing procedure, extending earlier ideas from the literature and improving their application, so as to make them effective for VLSI problems. We report significant reductions within reasonable computational times, obtained with the application of this procedure to 116 instances of the SteinLib. These reductions allowed a branch and cut to solve 28 of 32 open instances of the SteinLib, some with more than 10,000 vertices and 20,000 edges. © 2002 Wiley Periodicals, Inc. [source]


Source-based morphometry: The use of independent component analysis to identify gray matter differences with application to schizophrenia

HUMAN BRAIN MAPPING, Issue 3 2009
Lai Xu
Abstract We present a multivariate alternative to the voxel-based morphometry (VBM) approach called source-based morphometry (SBM), to study gray matter differences between patients and healthy controls. The SBM approach begins with the same preprocessing procedures as VBM. Next, independent component analysis is used to identify naturally grouping, maximally independent sources. Finally, statistical analyses are used to determine the significant sources and their relationship to other variables. The identified "source networks," groups of spatially distinct regions with common covariation among subjects, provide information about localization of gray matter changes and their variation among individuals. In this study, we first compared VBM and SBM via a simulation and then applied both methods to real data obtained from 120 chronic schizophrenia patients and 120 healthy controls. SBM identified five gray matter sources as significantly associated with schizophrenia. These included sources in the bilateral temporal lobes, thalamus, basal ganglia, parietal lobe, and frontotemporal regions. None of these showed an effect of sex. Two sources in the bilateral temporal and parietal lobes showed age-related reductions. The most significant source of schizophrenia-related gray matter changes identified by SBM occurred in the bilateral temporal lobe, while the most significant change found by VBM occurred in the thalamus. The SBM approach found changes not identified by VBM in basal ganglia, parietal, and occipital lobe. These findings show that SBM is a multivariate alternative to VBM, with wide applicability to studying changes in brain structure. Hum Brain Mapp, 2009. © 2008 Wiley-Liss, Inc. [source]


Time-Domain and Morphological Analysis of the P-Wave.

PACING AND CLINICAL ELECTROPHYSIOLOGY, Issue 7 2008
Part I: Technical Aspects for Automatic Quantification of P-Wave Features
Introduction: Time-domain and morphological analysis of P-wave from surface electrocardiogram has been extensively used to identify patients prone to atrial arrhythmias, especially atrial fibrillation (AF). However, since no standard procedure exists for P-wave preprocessing, standardization of cut-off values for P-wave duration and morphological features is difficult. This study is a methodological investigation of P-wave preprocessing procedures for automatic time-domain and morphological analysis. Methods: We compared, on simulated and real data, the P-wave template obtained applying three alignment algorithms with that obtained without alignment, in terms of template error, shift error, P-wave duration, and morphological parameters. We also proposed automatic algorithms for estimation of P-wave duration. Results: We found that alignment is necessary for a reliable extraction of P-wave template by the averaging procedure, in order to perform time-domain and morphological analysis. On simulated and real data, the error on P-wave duration can be as high as 30 ms on a template obtained without alignment; if alignment procedure is performed, the error on P-wave duration is negligible. Analogously, morphological features are correctly estimated only on a P-wave template obtained with P-waves alignment. We also found that the proposed algorithm for the automatic estimation of the P-wave duration gave reliable results. [source]


Assessment of embryonic growth in chicken eggs by means of visible transmission spectroscopy

BIOTECHNOLOGY PROGRESS, Issue 2 2010
Bart J. Kemps
Abstract During this work, it was investigated whether spectral measurements can be used to monitor embryonic growth. An experiment was conducted in which both the transmission spectra and embryonic weight were determined on 240 eggs (Cobb, 37 weeks) between Day 5 and Day 10 of incubation. The spectral data were linked to embryonic weight by means of a partial least squares analysis. Different preprocessing procedures were compared during this work, that is, smoothing, multiplicative scatter correction (MSC), and first- and second-order derivative. Compared to the remainder of the preprocessing procedures, MSC leads to a considerable improvement of the prediction capability of the embryonic weight. The ratio of performance to deviation obtained for the MSC spectra equaled 4.5 indicating that a very accurate prediction of embryonic weight is feasible based on the VIS/NIR transmission measurements. Important regions for the prediction are situated around 685,740 nm. It is suggested that the spectral changes in these spectral regions result from the displacement of carotenoids from the yolk into the blood circuitry. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010 [source]