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81.
Gustavo?Camps-VallsEmail author Alistair?M?Chalk Antonio?J?Serrano-López José?D?Martín-Guerrero Erik?LL?Sonnhammer 《BMC bioinformatics》2004,5(1):135
Background
This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules including 68 features each, inducing a problem well-suited to SVMs. The task of feature selection is crucial given the presence of noisy or redundant features, and the well-known problem of the curse of dimensionality. We propose a two-stage strategy to develop an optimal model: (1) feature selection using correlation analysis, mutual information, and SVM-based recursive feature elimination (SVM-RFE), and (2) AO prediction using standard and profiled SVM formulations. A profiled SVM gives different weights to different parts of the training data to focus the training on the most important regions. 相似文献82.
LOVE DALÉN EVA FUGLEI PÁLL HERSTEINSSON CHRISTIAN M. O. KAPEL JAMES D. ROTH GUSTAF SAMELIUS MAGNUS TANNERFELDT ANDERS ANGERBJÖRN 《Biological journal of the Linnean Society. Linnean Society of London》2005,84(1):79-89
The circumpolar arctic fox Alopex lagopus thrives in cold climates and has a high migration rate involving long-distance movements. Thus, it differs from many temperate taxa that were subjected to cyclical restriction in glacial refugia during the Ice Ages. We investigated population history and genetic structure through mitochondrial control region variation in 191 arctic foxes from throughout the arctic. Several haplotypes had a Holarctic distribution and no phylogeographical structure was found. Furthermore, there was no difference in haplotype diversity between populations inhabiting previously glaciated and unglaciated regions. This suggests current gene flow among the studied populations, with the exception of those in Iceland, which is surrounded by year-round open water. Arctic foxes have often been separated into two ecotypes: 'lemming' and 'coastal'. An analysis of molecular variance suggested particularly high gene flow among populations of the 'lemming' ecotype. This could be explained by their higher migration rate and reduced fitness in migrants between ecotypes. A mismatch analysis indicated a sudden expansion in population size around 118 000 BP, which coincides with the last interglacial. We propose that glacial cycles affected the arctic fox in a way opposite to their effect on temperate species, with interglacials leading to short-term isolation in northern refugia. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 79–89. 相似文献
83.
Frédéric D Chevalier Claudia LL Valentim Philip T LoVerde Timothy JC Anderson 《BMC genomics》2014,15(1)
Background
Identification of parasite genes that underlie traits such as drug resistance and host specificity is challenging using classical linkage mapping approaches. Extreme QTL (X-QTL) methods, originally developed by rodent malaria and yeast researchers, promise to increase the power and simplify logistics of linkage mapping in experimental crosses of schistosomes (or other helminth parasites), because many 1000s of progeny can be analysed, phenotyping is not required, and progeny pools rather than individuals are genotyped. We explored the utility of this method for mapping a drug resistance gene in the human parasitic fluke Schistosoma mansoni.Results
We staged a genetic cross between oxamniquine sensitive and resistant parasites, then between two F1 progeny, to generate multiple F2 progeny. One group of F2s infecting hamsters was treated with oxamniquine, while a second group was left untreated. We used exome capture to reduce the size of the genome (from 363 Mb to 15 Mb) and exomes from pooled F2 progeny (treated males, untreated males, treated females, untreated females) and the two parent parasites were sequenced to high read depth (mean = 95-366×) and allele frequencies at 14,489 variants compared. We observed dramatic enrichment of alleles from the resistant parent in a small region of chromosome 6 in drug-treated male and female pools (combined analysis: = 11.07, p = 8.74 × 10-29). This region contains Smp_089320 a gene encoding a sulfotransferase recently implicated in oxamniquine resistance using classical linkage mapping methods.Conclusions
These results (a) demonstrate the utility of exome capture for generating reduced representation libraries in Schistosoma mansoni, and (b) provide proof-of-principle that X-QTL methods can be successfully applied to an important human helminth. The combination of these methods will simplify linkage analysis of biomedically or biologically important traits in this parasite.Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-617) contains supplementary material, which is available to authorized users. 相似文献84.
Rhodri J. LL. Williams David Robertson A. J. S. Davies 《The Histochemical journal》1989,21(5):271-278
Summary The purpose of this study was to determine whether the plant lectin,Dolichos biflorus agglutinin (DBA), can be used to recognize capillary endothelial cells and their processes during angiogenesis. By means of a peroxidase conjugate of DBA, blood vessels were visualized in whole mounts and ultrathin sections of mouse omentum. A part of this mesentery normally comprises an avascular membrane that is approximately 30 µm in thickness. Changes in the vascular plexus bordering this membrane were induced by intraperitoneal injection of irradiated Landschutz cells. Vascular endothelial cells were precisely and intensely stained, and vasculogenic processes were reliably distinguished from those of other cells. This technique permitted observation of the structure and distribution of capillary sprouts, and their relationship to each other and to pre-existing blood vessels. It was discovered that filiform projections extend from sprout apices. These projections may fuse allowing adjacent sprouts to form a new capillary loop. 相似文献
85.
86.
The Pecten, considered from an Environmental Point of View. 总被引:1,自引:0,他引:1
87.
89.
In 1950, Raphael Patai published his research on Venta Prieta, a Mexican town in which some residents lived as Jews despite having little knowledge of Judaism. Like other visitors, Patai was perplexed. Why did they wish to live as Jews? While Patai never answered this question to his satisfaction, he believed the answer would be found by developing a psychological profile of the residents, an approach in keeping with culture and personality theorists of the day. The present article provides a different solution. Drawing on additional sources, and short visits, we argue that Venta Prieta was not only a stop on the Jewish tourist circuit by 1950 but also developed out of a unique exchange. While U.S. Jews, as evangelical Protestants before them, provided a model for upwardly mobile Mexicans, Venta Prieta enabled middle-class tourists to experience Judaism in a pastoral setting and to "repair the world" (tikkun). [Keywords: Judaism, tourism, dialogical anthropology, social change, social mobility] 相似文献
90.
LAURIE A. HALL PER J. PALSBØLL STEVEN R. BEISSINGER JAMES T. HARVEY MARTINE BÉRUBÉ MARTIN G. RAPHAEL S. KIM NELSON RICHARD T. GOLIGHTLY LAURA MCFARLANE‐TRANQUILLA SCOTT H. NEWMAN M. ZACHARIAH PEERY 《Molecular ecology》2009,18(24):5074-5085
Genetic assignment methods provide an appealing approach for characterizing dispersal patterns on ecological time scales, but require sufficient genetic differentiation to accurately identify migrants and a large enough sample size of migrants to, for example, compare dispersal between sexes or age classes. We demonstrate that assignment methods can be rigorously used to characterize dispersal patterns in a marbled murrelet (Brachyramphus marmoratus) population from central California that numbers approximately 600 individuals and is only moderately differentiated (FST~ 0.03) from larger populations to the north. We used coalescent simulations to select a significance level that resulted in a low and approximately equal expected number of type I and II errors and then used this significance level to identify a population of origin for 589 individuals genotyped at 13 microsatellite loci. The proportion of migrants in central California was greatest during winter when 83% of individuals were classified as migrants compared to lower proportions during the breeding (6%) and post‐breeding (8%) seasons. Dispersal was also biased toward young and female individuals, as is typical in birds. Migrants were rarely members of parent‐offspring pairs, suggesting that they contributed few young to the central California population. A greater number of migrants than expected under equilibrium conditions, a lack of individuals with mixed ancestry, and a small number of potential source populations (two), likely allowed us to use assignment methods to rigorously characterize dispersal patterns for a population that was larger and less differentiated than typically thought required for the identification of migrants. 相似文献