Morphological variation of Arabic queries

Although it has been shown that in test collection based studies, stemming improves retrieval effectiveness in an information retrieval system, morphological variations of queries searching on the same topic are less well understood. This work examines the broad morphological variation that searchers of an Arabic retrieval system put into their queries. In this study, 15 native Arabic speakers were asked to generate queries, morphological variants of query words were collated across users. Queries composed of either the commonest or rarest variants of each word were submitted to a retrieval system and the effectiveness of the searches was measured. It was found that queries composed of the more popular morphological variants were more likely to retrieve relevant documents that those composed of less popular

Large scale analysis of protein stability in OMIM disease related human protein variants

Modern genomic techniques allow to associate several Mendelian human diseases to single residue variations in different proteins. Molecular mechanisms explaining the relationship among genotype and phenotype are still under debate. Change of protein stability upon variation appears to assume a particular relevance in annotating whether a single residue substitution can or cannot be associated to a given disease. Thermodynamic properties of human proteins and of their disease related variants are lacking. In the present work, we take advantage of the available three dimensional structure of human proteins for predicting the role of disease related variations on the perturbation of protein stability

Evaluation of autosomal dominant retinal dystrophy genes in an unaffected cohort suggests rare or private missense variants may often be benign.

BackgroundMany genes have been reported as harboring autosomal dominant mutations causing retinal dystrophy. As newly available gene panel sequencing and whole exome sequencing will open these genes up to greater scrutiny, we assess the rate of rare coding variation in these genes among unaffected individuals to provide context for variants that will be discovered when clinical subjects are sequenced.MethodsPublicly available data from the Exome Variant Project were analyzed, focusing on 36 genes known to harbor mutations causing autosomal dominant macular dystrophy.ResultsRates of rare (minor allele frequency ≤0.1%) and private missense variants within autosomal dominant retinal dystrophy genes were found to occur at a high frequency in unaffected individuals, while nonsense variants were not.ConclusionsWe conclude that rare missense variations in most of these genes identified in individuals with retinal dystrophy cannot be confidently classified as disease-causing in the absence of additional information such as linkage or functional validation

A unified framework for Schelling's model of segregation

Schelling's model of segregation is one of the first and most influential models in the field of social simulation. There are many variations of the model which have been proposed and simulated over the last forty years, though the present state of the literature on the subject is somewhat fragmented and lacking comprehensive analytical treatments. In this article a unified mathematical framework for Schelling's model and its many variants is developed. This methodology is useful in two regards: firstly, it provides a tool with which to understand the differences observed between models; secondly, phenomena which appear in several model variations may be understood in more depth through analytic studies of simpler versions.Comment: 21 pages, 3 figure

Behavioural Genetics in Criminal Cases: Past, Present and Future

Researchers studying human behavioral genetics have made significant scientific progress in enhancing our understanding of the relative contributions of genetics and the environment in observed variations in human behavior. Quickly outpacing the advances in the science are its applications in the criminal justice system. Already, human behavioral genetics research has been introduced in the U.S. criminal justice system, and its use will only become more prevalent. This essay discusses the recent historical use of behavioral genetics in criminal cases, recent advances in two gene variants of particular interest in the criminal law, MAOA and SLC6A4, the recent expert testimony on behalf of criminal defendants with respect to these two gene variants, and the future direction of behavioral genetics evidence in criminal cases

Artificial table testing dynamically adaptive systems

Dynamically Adaptive Systems (DAS) are systems that modify their behavior and structure in response to changes in their surrounding environment. Critical mission systems increasingly incorporate adaptation and response to the environment; examples include disaster relief and space exploration systems. These systems can be decomposed in two parts: the adaptation policy that specifies how the system must react according to the environmental changes and the set of possible variants to reconfigure the system. A major challenge for testing these systems is the combinatorial explosions of variants and envi-ronment conditions to which the system must react. In this paper we focus on testing the adaption policy and propose a strategy for the selection of envi-ronmental variations that can reveal faults in the policy. Artificial Shaking Table Testing (ASTT) is a strategy inspired by shaking table testing (STT), a technique widely used in civil engineering to evaluate building's structural re-sistance to seismic events. ASTT makes use of artificial earthquakes that simu-late violent changes in the environmental conditions and stresses the system adaptation capability. We model the generation of artificial earthquakes as a search problem in which the goal is to optimize different types of envi-ronmental variations

Characterization of Coding Synonymous and Non-Synonymous Variants in ADAMTS13 Using Ex Vivo and In Silico Approaches

Synonymous variations, which are defined as codon substitutions that do not change the encoded amino acid, were previously thought to have no effect on the properties of the synthesized protein(s). However, mounting evidence shows that these “silent” variations can have a significant impact on protein expression and function and should no longer be considered “silent”. Here, the effects of six synonymous and six non-synonymous variations, previously found in the gene of ADAMTS13, the von Willebrand Factor (VWF) cleaving hemostatic protease, have been investigated using a variety of approaches. The ADAMTS13 mRNA and protein expression levels, as well as the conformation and activity of the variants have been compared to that of wild-type ADAMTS13. Interestingly, not only the non-synonymous variants but also the synonymous variants have been found to change the protein expression levels, conformation and function. Bioinformatic analysis of ADAMTS13 mRNA structure, amino acid conservation and codon usage allowed us to establish correlations between mRNA stability, RSCU, and intracellular protein expression. This study demonstrates that variants and more specifically, synonymous variants can have a substantial and definite effect on ADAMTS13 function and that bioinformatic analysis may allow development of predictive tools to identify variants that will have significant effects on the encoded protein