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Citas árabes en caracteres hebreos en el Pugio Fidei del dominico Ramón Martí: entre la autenticidad y la autoridad
Szpiech, Ryan
Al-Qantara : Revista de Estudios Arabes , 2011,
Abstract: This article presents and discusses the Arabic citations of Qur ān and adī , written in Hebrew characters and translated into Latin, that are found in the Puggio Fidei (Dagger of Faith) of the Dominican polemicist Raymond Martini (d. after 1284). The citations are of great interest because they constitute the only example of Arabic-language citations in his work and offer us information about his sources and about the direct connection between his use of original languages and the rhetorical strategy of his polemical work. En este artículo se presentan y analizan las citas árabes del Qur ān y el adī escritas en caracteres hebreos y traducidas al latín, que se hallan en el Pugio Fidei (Pu al de la fe) del polemista dominico Ramón Martí (m. después de 1284). éstas son de gran interés, pues constituyen el único ejemplo de citas en lengua árabe en su obra y nos proporcionan, además, información sobre las fuentes de Martí y sobre la conexión directa entre el uso de lenguas originales y la estrategia retórica de su obra polémica.
Selscan: an efficient multi-threaded program to perform EHH-based scans for positive selection
Zachary A Szpiech,Ryan D Hernandez
Quantitative Biology , 2014, DOI: 10.1093/molbev/msu211
Abstract: Haplotype-based scans to detect natural selection are useful to identify recent or ongoing positive selection in genomes. As both real and simulated genomic datasets grow larger, spanning thousands of samples and millions of markers, there is a need for a fast and efficient implementation of these scans for general use. Here we present selscan, an efficient multi-threaded application that implements Extended Haplotype Homozygosity (EHH), Integrated Haplotype Score (iHS), and Cross-population Extended Haplotype Homozygosity (XPEHH). selscan accepts phased genotypes in multiple formats, including TPED, and performs extremely well on both simulated and real data and over an order of magnitude faster than existing available implementations. It calculates iHS on chromosome 22 (22,147 loci) across 204 CEU haplotypes in 353s on one thread (33s on 16 threads) and calculates XPEHH for the same data relative to 210 YRI haplotypes in 578s on one thread (52s on 16 threads). Source code and binaries (Windows, OSX and Linux) are available at https://github.com/szpiech/selscan .
Comparing Evolutionary Rates Using An Exact Test for 2x2 Tables with Continuous Cell Entries
A. Morgan Thompson,M. Cyrus Maher,Lawrence H. Uricchio,Zachary A. Szpiech,Ryan D. Hernandez
Quantitative Biology , 2014,
Abstract: Assessing the statistical significance of an observed 2x2 contingency table can easily be accomplished using Fisher's exact test (FET). However, if the cell entries are continuous or represent values inferred from a continuous parametric model, then FET cannot be applied. Such tables arise frequently in areas of biostatistical research including population genetics and evolutionary genomics, where cell entries are estimated by computational methods and result in cell entries drawn from the non-negative real line R+. Simply rounding cell entries to conform to the assumptions of FET is an ill-suited approach that we show creates problems related to both type-I and type-II errors. Pearson's chi^2 test for independence, while technically applicable, is not often effective for these tables, as the test has several limiting assumptions that make application of this method inadvisable in many common instances (particularly with small cell entries). Here we develop a novel method for tables with continuous entries, which we term continuous Fisher's Exact Test (cFET). Through simulations, we show that cFET has a close-to-uniform distribution of p-values under the null hypothesis of independence, and more power when applied to tables where the null hypothesis is false (compared to FET applied to rounded cell entries). We apply cFET to an example from comparative genomics to confirm an overall increased evolutionary rate among primates compared to rodents, and identify several genes that show particularly elevated evolutionary rates in primates. Some of these genes exhibit signatures of continued positive selection along the human lineage since our divergence with chimpanzee 5-7 million years ago, as well as ongoing selection in modern humans.
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