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941.
942.
PurposeAn investigation was carried out into the effect of three image registration techniques on the diagnostic image quality of contrast-enhanced magnetic resonance angiography (CE-MRA) images.MethodsWhole-body CE-MRA data from the lower legs of 27 patients recruited onto a study of asymptomatic atherosclerosis were processed using three deformable image registration algorithms. The resultant diagnostic image quality was evaluated qualitatively in a clinical evaluation by four expert observers, and quantitatively by measuring contrast-to-noise ratios and volumes of blood vessels, and assessing the techniques' ability to correct for varying degrees of motion.ResultsThe first registration algorithm (‘AIR’) introduced significant stenosis-mimicking artefacts into the blood vessels' appearance, observed both qualitatively (clinical evaluation) and quantitatively (vessel volume measurements). The two other algorithms (‘Slicer’ and ‘SEMI’), based on the normalised mutual information (NMI) concept and designed specifically to deal with variations in signal intensity as found in contrast-enhanced image data, did not suffer from this serious issue but were rather found to significantly improve the diagnostic image quality both qualitatively and quantitatively, and demonstrated a significantly improved ability to deal with the common problem of patient motion.ConclusionsThis work highlights both the significant benefits to be gained through the use of suitable registration algorithms and the deleterious effects of an inappropriate choice of algorithm for contrast-enhanced MRI data. The maximum benefit was found in the lower legs, where the small arterial vessel diameters and propensity for leg movement during image acquisitions posed considerable problems in making accurate diagnoses from the un-registered images. 相似文献
943.
Estimates of the fixation index, FST, have been used as measures of population differentiation for many decades. However, there have been persistent voices in the literature suggesting that these statistics do not measure true differentiation. In particular, the statistics Nei's GST and Wier and Cockerham's θ have been criticized for being ‘constrained’ to not equal one in some situations that seem to represent maximal differentiation. Here, we address the issue of how to evaluate exactly how much information a particular statistic contains about the process of differentiation. This criterion can be used to counter most concerns about the performance of GST (and related statistics), while also being reconciled with the insights of those who have proposed alternative measures of differentiation. In particular, the likelihood‐based framework that we put forward can justify the use of GST as an effective measure of differentiation, but also shows that in some situations GST is insufficient on its own and needs supplementing by another measure such as Jost's D or Hedrick's G′ST. This approach will become increasingly important in the future, as greater emphasis is placed on analysing large data sets. 相似文献
944.
945.
Y. Da P.M. VanRaden M. Ron J.E. Beever A. A. Paszek J. Song 《Animal biotechnology》2013,24(1-2):25-35
Abstract Large scale gene mapping efforts in domestic animals have generated and mapped a large number of genetic markers that are useful for mapping quantitative trait and disease loci and for DNA diagnostic purposes such as parentage testing. Marker polymorphism is an important criterion for selecting genetic markers in planning experiment for mapping quantitative trait loci or for DNA diagnostic purposes. Current formulations of marker polymorphism measures are functions of marker allele frequencies. In this study, two measures of marker polymorphism that are available from gene mapping studies and do not require allele frequencies were proposed and analyzed: the observed polymorphic information content (PIC) and the observed family information content (FIC). The observed FIC was more stable than the observed PIC because the observed FIC is unaffected by the variation in the frequency of heterozygous parents. However, both FIC and PIC are dependent on the gene mapping design. The effective number of alleles is recommended as a tool to standardize marker polymorphism measures so that polymorphism of different markers can be compared on an qual basis, and to obtain a new polymorphism measure (such an exclusion probability) from an existing measure (such as FIC). The usage of the effective number of alleles to standardize FIC, PIC and exclusion probabilities is illustrated using genetic markers in a published linkage map. 相似文献
946.
947.
The two‐component system (TCS) is a signal transduction system that involves a histidine kinase (HK) and a response regulator (RR). Although up to hundreds of TCSs may operate in parallel in a bacterial cell, the high‐fidelity of a TCS signaling is well maintained, minimizing irrelevant crosstalk between TCSs. When a HK gene and a RR gene in a given TCS system exist in neighboring positions, it is almost certain that their protein products (i.e., HK and RR) are interacting partners. However, large bacterial genomes often have multiple HK genes and/or cognate RR genes that are not neighboring positions. In many partially assembled genomes, some HK genes and RR genes belong to different contigs. In these cases, it is not clear which HK(s) and RR(s) interact. By combining information‐theoretic and graph‐theoretic approaches, we developed a computational method identifying co‐evolving residue pairs between HKs and cognate RRs and predicting the interacting HK:RR pairs for each TCS. In addition, we built a TCSppWWW webserver ( http://compath.org/platcom/tcs ) that takes query sequences of pairing candidates and predicts their HK:RR pairing using precomputed models. The current release of TCSppWWW provides predictors for 48 TCSs using over 20,000 protein sequences from about 900 bacterial genomes. Three different types of predictors using Random Forest, RBF Network, and Naïve Bayes are provided. Once a set of HK and RR candidate sequences are submitted, TCSppWWW aligns query sequences to the precomputed multiple sequence alignment of HK:RR pairs, extracts co‐evolving column positions, then returns prediction results with prediction margin and additional information. Proteins 2011. © 2010 Wiley‐Liss, Inc. 相似文献
948.
949.
It is well established that different sites within a protein evolve at different rates according to their role within the protein; identification of these correlated mutations can aid in tasks such as ab initio protein structure, structure function analysis or sequence alignment. Mutual Information is a standard measure for coevolution between two sites but its application is limited by signal to noise ratio. In this work we report a preliminary study to investigate whether larger sequence sets could circumvent this problem by calculating mutual information arrays for two sets of drug naïve sequences from the HIV gp120 protein for the B and C subtypes. Our results suggest that while the larger sequences sets can improve the signal to noise ratio, the gain is offset by the high mutation rate of the HIV virus which makes it more difficult to achieve consistent alignments. Nevertheless, we were able to predict a number of coevolving sites that were supported by previous experimental studies as well as a region close to the C terminal of the protein that was highly variable in the C subtype but highly conserved in the B subtype. 相似文献
950.
Urdy S 《Biological reviews of the Cambridge Philosophical Society》2012,87(4):786-803
In the 1950s, embryology was conceptualized as four relatively independent problems: cell differentiation, growth, pattern formation and morphogenesis. The mechanisms underlying the first three traditionally have been viewed as being chemical in nature, whereas those underlying morphogenesis have usually been discussed in terms of mechanics. Often, morphogenesis and its mechanical processes have been regarded as subordinate to chemical ones. However, a growing body of evidence indicates that the biomechanics of cells and tissues affect in striking ways those phenomena often thought of as mainly under the control of cell-cell signalling. This accumulation of data has led to a revival of the mechano-transduction concept in particular, and of complexity in general, causing us now to consider whether we should retain the traditional conceptualization of development. The researchers' semantic preferences for the terms 'patterning', 'pattern formation' or 'morphogenesis' can be used to describe three main 'schools of thought' which emerged in the late 1970s. In the 'molecular school', the term patterning is deeply tied to the positional information concept. In the 'chemical school', the term 'pattern formation' regularly implies reaction-diffusion models. In the 'mechanical school', the term 'morphogenesis' is more frequently used in relation to mechanical instabilities. Major differences among these three schools pertain to the concept of self-organization, and models can be classified as morphostatic or morphodynamic. Various examples illustrate the distorted picture that arises from the distinction among differentiation, growth, pattern formation and morphogenesis, based on the idea that the underlying mechanisms are respectively chemical or mechanical. Emerging quantitative approaches integrate the concepts and methods of complex sciences and emphasize the interplay between hierarchical levels of organization via mechano-chemical interactions. They draw upon recent improvements in mathematical and numerical morphogenetic models and upon considerable progress in collecting new quantitative data. This review highlights a variety of such models, which exhibit important advances, such as hybrid, stochastic and multiscale simulations. 相似文献