Multiple distributions for biased random test patterns

An efficient method has been presented to compute multiple distributions for random patterns, which can be applied successively. Using multiple distributions, all combinational circuits can be made random-testable, and complete fault coverage is provided by a few thousands of random patterns. The differently weighted random test sets can be applied to scan path circuits using an external chip, combining the advantages of a low cost test and of high fault coverage. Several facts about testing by random patterns have been proven. It has been shown that the number of random patterns required for a certain fault coverage can be computed without regarding the pseudorandom property and with the independence assumption for fault detection

Gene duplicability of core genes is highly consistent across all angiosperms

Gene duplication is an important mechanism for adding to genomic novelty. Hence, which genes undergo duplication and are preserved following duplication is an important question. It has been observed that gene duplicability, or the ability of genes to be retained following duplication, is a nonrandom process, with certain genes being more amenable to survive duplication events than others. Primarily, gene essentiality and the type of duplication (small-scale versus large-scale) have been shown in different species to influence the (long-term) survival of novel genes. However, an overarching view of "gene duplicability" is lacking, mainly due to the fact that previous studies usually focused on individual species and did not account for the influence of genomic context and the time of duplication. Here, we present a large-scale study in which we investigated duplicate retention for 9178 gene families shared between 37 flowering plant species, referred to as angiosperm core gene families. For most gene families, we observe a strikingly consistent pattern of gene duplicability across species, with gene families being either primarily single-copy or multicopy in all species. An intermediate class contains gene families that are often retained in duplicate for periods extending to tens of millions of years after whole-genome duplication, but ultimately appear to be largely restored to singleton status, suggesting that these genes may be dosage balance sensitive. The distinction between single-copy and multicopy gene families is reflected in their functional annotation, with single-copy genes being mainly involved in the maintenance of genome stability and organelle function and multicopy genes in signaling, transport, and metabolism. The intermediate class was overrepresented in regulatory genes, further suggesting that these represent putative dosage-balance-sensitive genes

Probability and Statistics for Particle Physicists

Lectures presented at the 1st CERN Asia-Europe-Pacific School of High-Energy Physics, Fukuoka, Japan, 14-27 October 2012. A pedagogical selection of topics in probability and statistics is presented. Choice and emphasis are driven by the author's personal experience, predominantly in the context of physics analyses using experimental data from high-energy physics detectors.Comment: Updated version of lectures given at the First Asia-Europe-Pacific School of High-Energy Physics, Fukuoka, Japan, 14-27 October 2012. Published as a CERN Yellow Report (CERN-2014-001) and KEK report (KEK-Proceedings-2013-8), K. Kawagoe and M. Mulders (eds.), 2014, p. 219. Total 28 pages, 36 figure

Coordinated functional divergence of genes after genome duplication in Arabidopsis thaliana

Gene and genome duplications have been rampant during the evolution of flowering plants. Unlike small-scale gene duplications, whole-genome duplications (WGDs) copy entire pathways or networks, and as such create the unique situation in which such duplicated pathways or networks could evolve novel functionality through the coordinated sub-or neofunctionalization of its constituent genes. Here, we describe a remarkable case of coordinated gene expression divergence following WGDs in Arabidopsis thaliana. We identified a set of 92 homoeologous gene pairs that all show a similar pattern of tissue-specific gene expression divergence following WGD, with one homoeolog showing predominant expression in aerial tissues and the other homoeolog showing biased expression in tip-growth tissues. We provide evidence that this pattern of gene expression divergence seems to involve genes with a role in cell polarity and that likely function in the maintenance of cell wall integrity. Following WGD, many of these duplicated genes evolved separate functions through subfunctionalization in growth/development and stress response. Uncoupling these processes through genome duplications likely provided important adaptations with respect to growth and morphogenesis and defense against biotic and abiotic stress

A new approach to measure reduction intensity on cores and tools on cobbles: the Volumetric Reconstruction Method

Knowing to what extent lithic cores have been reduced through knapping is an important step toward understanding the technological variability of lithic assemblages and disentangling the formation processes of archaeological assemblages. In addition, it is a good complement to more developed studies of reduction intensity in retouched tools, and can provide information on raw material management or site occupation dynamics. This paper presents a new methodology for estimating the intensity of reduction in cores and tools on cobbles, the Volumetric Reconstruction Method (VRM). This method is based on a correction of the dimensions (length, width, and thickness) of each core from an assemblage. The mean values of thickness and platform thickness of the assemblage’s flakes are used as corrections for the cores’ original dimensions, after its diacritic analysis. Then, based on these new dimensions, the volume or mass of the original blank are reconstructed using the ellipsoid volume formula. The accuracy of this method was experimentally tested, reproducing a variety of possible archaeological scenarios. The experimental results demonstrate a high inferential potential of the VRM, both in estimating the original volume or mass of the original blanks, and in inferring the individual percentage of reduction for each core. The results of random resampling demonstrate the applicability of VRM to non size-biased archaeological contexts.Introduction Methods - The Volumetric Reconstruction Method - Experimental design - Statistical procedures - Resamples Results - Geometric formulas - Reduction strategy and size - Resampling (randomly biased record) - Resampling (size bias) - Measuring the effect of number of generations Discussion and conclusion

Inferring the Distribution of Selective Effects from a Time Inhomogeneous Model

We have developed a Poisson random field model for estimating the distribution of selective effects of newly arisen nonsynonymous mutations that could be observed as polymorphism or divergence in samples of two related species under the assumption that the two species populations are not at mutation-selection-drift equilibrium. The model is applied to 91Drosophila genes by comparing levels of polymorphism in an African population of D. melanogaster with divergence to a reference strain of D. simulans. Based on the difference of gene expression level between testes and ovaries, the 91 genes were classified as 33 male-biased, 28 female-biased, and 30 sex-unbiased genes. Under a Bayesian framework, Markov chain Monte Carlo simulations are implemented to the model in which the distribution of selective effects is assumed to be Gaussian with a mean that may differ from one gene to the other to sample key parameters. Based on our estimates, the majority of newly-arisen nonsynonymous mutations that could contribute to polymorphism or divergence in Drosophila species are mildly deleterious with a mean scaled selection coefficient of -2.81, while almost 86% of the fixed differences between species are driven by positive selection. There are only 16.6% of the nonsynonymous mutations observed in sex-unbiased genes that are under positive selection in comparison to 30% of male-biased and 46% of female-biased genes that are beneficial. We also estimated that D. melanogaster and D. simulans may have diverged 1.72 million years ago

Storage of Natural Language Sentences in a Hopfield Network

This paper look at how the Hopfield neural network can be used to store and recall patterns constructed from natural language sentences. As a pattern recognition and storage tool, the Hopfield neural network has received much attention. This attention however has been mainly in the field of statistical physics due to the model's simple abstraction of spin glass systems. A discussion is made of the differences, shown as bias and correlation, between natural language sentence patterns and the randomly generated ones used in previous experiments. Results are given for numerical simulations which show the auto-associative competence of the network when trained with natural language patterns.Comment: latex, 10 pages with 2 tex figures and a .bib file, uses nemlap.sty, to appear in Proceedings of NeMLaP-