Search results for "Likelihood Function"
showing 10 items of 114 documents
Molecular basis of adaptive convergence in experimental populations of RNA viruses
2002
Abstract Characterizing the molecular basis of adaptation is one of the most important goals in modern evolutionary genetics. Here, we report a full-genome sequence analysis of 21 independent populations of vesicular stomatitis ribovirus evolved on the same cell type but under different demographic regimes. Each demographic regime differed in the effective viral population size. Evolutionary convergences are widespread both at synonymous and nonsynonymous replacements as well as in an intergenic region. We also found evidence for epistasis among sites of the same and different loci. We explain convergences as the consequence of four factors: (1) environmental homogeneity that supposes an id…
Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates.
2014
Legionella pneumophila is a strictly environmental pathogen and the etiological agent of legionellosis. It is known that non-vertical processes have a major role in the short-term evolution of pathogens, but little is known about the relevance of these and other processes in environmental bacteria. We report the whole-genome sequencing of 69 L. pneumophila strains linked to recurrent outbreaks in a single location (Alcoy, Spain) over 11 years. We found some examples where the genome sequences of isolates of the same sequence type and outbreak did not cluster together and were more closely related to sequences from different outbreaks. Our analyses identify 16 recombination events responsibl…
Deep metazoan phylogeny: When different genes tell different stories
2013
11 páginas, 4 figuras, 1 tabla.
Evidence of Recombination in Intrapatient Populations of Hepatitis C Virus.
2008
Hepatitis C virus (HCV) is a major cause of liver disease worldwide and a potential cause of substantial morbidity and mortality in the future. HCV is characterized by a high level of genetic heterogeneity. Although homologous recombination has been demonstrated in many members of the family Flaviviridae, to which HCV belongs, there are only a few studies reporting recombination on natural populations of HCV, suggesting that these events are rare in vivo. Furthermore, these few studies have focused on recombination between different HCV genotypes/subtypes but there are no reports on the extent of intra-genotype or intra-subtype recombination between viral strains infecting the same patient.…
Population genetic analysis of bi-allelic structural variants from low-coverage sequence data with an expectation-maximization algorithm
2014
Background Population genetics and association studies usually rely on a set of known variable sites that are then genotyped in subsequent samples, because it is easier to genotype than to discover the variation. This is also true for structural variation detected from sequence data. However, the genotypes at known variable sites can only be inferred with uncertainty from low coverage data. Thus, statistical approaches that infer genotype likelihoods, test hypotheses, and estimate population parameters without requiring accurate genotypes are becoming popular. Unfortunately, the current implementations of these methods are intended to analyse only single nucleotide and short indel variation…
Dental services utilization between 1977 and 1995 by Finnish adolescents of different socioeconomic levels.
1998
Equal distribution of health care services has long been a major goal of health policy in the Nordic countries. According to these guidelines, every child is expected to have an examination and treatment at least every second year. The aim of this study was to analyze the trends and, in particular, the socioeconomic differences in dental visits between 1977 and 1995. The data were collected as part of a nationwide research program, the Adolescent Health and Lifestyle Survey, which began in 1977. Every second year a self-administered questionnaire was mailed to a representative sample of 14-, 16- and 18-year-old Finns. The sample sizes in the surveys varied from 2422 to 9556, making a total …
Influence of immigration and other factors on caries in 12- and 15-yr-old children.
2007
In recent years the Valencia region has undergone mass immigration, mainly of people from eastern Europe, North Africa, and Latin America. The objective of this study was to assess the effect of immigration on caries prevalence and experience in 12- and 15-yr-old children in the Valencia region, and to relate this to other socio-economic and oral hygiene-related variables. The data were obtained from the epidemiological study of oral health carried out in the Valencia Region in 2004. The study group comprised 478, 12-yr-old children and 401, 15-yr-old children. Immigration status, age, toothbrushing frequency, and intake of cariogenic foods between meals showed significant association in a …
Nonparametric clustering of seismic events
2006
In this paper we propose a clustering technique, based on the maximization of the likelihood function defined from the generalization of a model for seismic activity (ETAS model, (Ogata (1988))), iteratively changing the partitioning of the events. In this context it is useful to apply models requiring the distinction between independent events (i.e. the background seismicity) and strongly correlated ones. This technique develops nonparametric estimation methods of the point process intensity function. To evaluate the goodness of fit of the model, from which the clustering method is implemented, residuals process analysis is used.
Mutations in KIAA0586 Cause Lethal Ciliopathies Ranging from a Hydrolethalus Phenotype to Short-Rib Polydactyly Syndrome
2015
KIAA0586, the human ortholog of chicken TALPID3, is a centrosomal protein that is essential for primary ciliogenesis. Its disruption in animal models causes defects attributed to abnormal hedgehog signaling; these defects include polydactyly and abnormal dorsoventral patterning of the neural tube. Here, we report homozygous mutations of KIAA0586 in four families affected by lethal ciliopathies ranging from a hydrolethalus phenotype to short-rib polydactyly. We show defective ciliogenesis, as well as abnormal response to SHH-signaling activation in cells derived from affected individuals, consistent with a role of KIAA0586 in primary cilia biogenesis. Whereas centriolar maturation seemed una…
Hessian PDF reweighting meets the Bayesian methods
2014
We discuss the Hessian PDF reweighting - a technique intended to estimate the effects that new measurements have on a set of PDFs. The method stems straightforwardly from considering new data in a usual $\chi^2$-fit and it naturally incorporates also non-zero values for the tolerance, $\Delta\chi^2>1$. In comparison to the contemporary Bayesian reweighting techniques, there is no need to generate large ensembles of PDF Monte-Carlo replicas, and the observables need to be evaluated only with the central and the error sets of the original PDFs. In spite of the apparently rather different methodologies, we find that the Hessian and the Bayesian techniques are actually equivalent if the $\Delta…