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## Proposta de sistema colaborativo cognitivo de baixo custo para análise e predição de sinais DTV; Proposal of a low cost collaborative cognitive system for analysis and prediction of DTV signals

Fonte: Biblioteca Digital da Unicamp
Publicador: Biblioteca Digital da Unicamp

Tipo: Tese de Doutorado
Formato: application/pdf

Publicado em 31/03/2015
PT

Relevância na Pesquisa

46.04%

#Redes de sensores#Televisão digital#Audiências de televisão#Espectro de frequência#Monitoramento#Computação em nuvem#Comunicações digitais#Sensor network#Digital television#TV audiences#Frequency spectrum

Esse trabalho inicialmente faz uma análise da evolução dos sistemas de comunicações digitais, enfatizando a evolução dos sistemas DTV (Digital TV) e explora através de aplicações, os conceitos de IoT (Internet of Things), computação em nuvem, mineração de dados, big data e rádios cognitivos, propondo o uso de redes de sensores e banco de dados para uma diversidade de aplicações relacionadas ao uso do espectro de frequências, entre elas: o sensoriamento do espectro, a medição da qualidade de sinais ao longo do tempo, a estatística de audiência e a detecção dos modelos de propagação mais adequados para cada região. Na proposta, a medição de qualidade dos sinais de radiodifusão é realizada por sensores em campo e a interface gráfica é realizada através de Web Map Services, possibilitando a filtragem das informações por tipo de medida, área e período de interesse. Distribui-se o processamento de dados entre servidores e máquinas locais para o melhor desempenho das aplicações. Para o sensoriamento, aplica-se o conceito de IoT ao se propor a conversão de receptores comerciais convencionais como Set-Top-Boxes e smartphones em sensores de qualidade de sinais, considera-se esse método como uma solução viável para a composição de redes com centenas a milhares de sensores. Os sensores ao ganharem a capacidade de varrer o espectro de frequências de forma automática...

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## The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations.

Fonte: PubMed
Publicador: PubMed

Tipo: Artigo de Revista Científica

Publicado em /01/2004
EN

Relevância na Pesquisa

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We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum...

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## The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele

Fonte: PubMed
Publicador: PubMed

Tipo: Artigo de Revista Científica

EN

Relevância na Pesquisa

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The sample frequency spectrum of a segregating site is the probability distribution of a sample of alleles from a genetic locus, conditional on observing the sample to be polymorphic. This distribution is widely used in population genetic inferences, including statistical tests of neutrality in which a skew in the observed frequency spectrum across independent sites is taken as a signature of departure from neutral evolution. Theoretical aspects of the frequency spectrum have been well studied and several interesting results are available, but they are usually under the assumption that a site has undergone at most one mutation event in the history of the sample. Here, we extend previous theoretical results by allowing for at most two mutation events per site, under a general finite alleles model in which the mutation rate is independent of current allelic state but the transition matrix is otherwise completely arbitrary. Our results apply to both nested and nonnested mutations. Only the former has been addressed previously, whereas here we show it is the latter that is more likely to be observed except for very small sample sizes. Further, for any mutation transition matrix, we obtain the joint sample frequency spectrum of the two mutant alleles at a triallelic site...

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## The Number of Alleles at a Microsatellite Defines the Allele Frequency Spectrum and Facilitates Fast Accurate Estimation of θ

Fonte: Oxford University Press
Publicador: Oxford University Press

Tipo: Artigo de Revista Científica

EN

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Theoretical work focused on microsatellite variation has produced a number of important
results, including the expected distribution of repeat sizes and the expected squared
difference in repeat size between two randomly selected samples. However, closed-form
expressions for the sampling distribution and frequency spectrum of microsatellite
variation have not been identified. Here, we use coalescent simulations of the stepwise
mutation model to develop gamma and exponential approximations of the microsatellite
allele frequency spectrum, a distribution central to the description of microsatellite
variation across the genome. For both approximations, the parameter of biological
relevance is the number of alleles at a locus, which we express as a function of
θ, the population-scaled mutation rate, based on simulated data.
Discovered relationships between θ, the number of alleles, and the
frequency spectrum support the development of three new estimators of microsatellite
θ. The three estimators exhibit roughly similar mean squared
errors (MSEs) and all are biased. However, across a broad range of sample sizes and
θ values, the MSEs of these estimators are frequently lower than
all other estimators tested. The new estimators are also reasonably robust to mutation
that includes step sizes greater than one. Finally...

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## The Yule Approximation for the Site Frequency Spectrum after a Selective Sweep

Fonte: Public Library of Science
Publicador: Public Library of Science

Tipo: Artigo de Revista Científica

Publicado em 10/12/2013
EN

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In the area of evolutionary theory, a key question is which portions of the genome of a species are targets of natural selection. Genetic hitchhiking is a theoretical concept that has helped to identify various such targets in natural populations. In the presence of recombination, a severe reduction in sequence diversity is expected around a strongly beneficial allele. The site frequency spectrum is an important tool in genome scans for selection and is composed of the numbers , where is the number of single nucleotide polymorphisms (SNPs) present in from individuals. Previous work has shown that both the number of low- and high-frequency variants are elevated relative to neutral evolution when a strongly beneficial allele fixes. Here, we follow a recent investigation of genetic hitchhiking using a marked Yule process to obtain an analytical prediction of the site frequency spectrum in a panmictic population at the time of fixation of a highly beneficial mutation. We combine standard results from the neutral case with the effects of a selective sweep. As simulations show, the resulting formula produces predictions that are more accurate than previous approaches for the whole frequency spectrum. In particular, the formula correctly predicts the elevation of low- and high-frequency variants and is significantly more accurate than previously derived formulas for intermediate frequency variants.

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## General Triallelic Frequency Spectrum Under Demographic Models with Variable Population Size

Fonte: Genetics Society of America
Publicador: Genetics Society of America

Tipo: Artigo de Revista Científica

EN

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It is becoming routine to obtain data sets on DNA sequence variation across several thousands of chromosomes, providing unprecedented opportunity to infer the underlying biological and demographic forces. Such data make it vital to study summary statistics that offer enough compression to be tractable, while preserving a great deal of information. One well-studied summary is the site frequency spectrum—the empirical distribution, across segregating sites, of the sample frequency of the derived allele. However, most previous theoretical work has assumed that each site has experienced at most one mutation event in its genealogical history, which becomes less tenable for very large sample sizes. In this work we obtain, in closed form, the predicted frequency spectrum of a site that has experienced at most two mutation events, under very general assumptions about the distribution of branch lengths in the underlying coalescent tree. Among other applications, we obtain the frequency spectrum of a triallelic site in a model of historically varying population size. We demonstrate the utility of our formulas in two settings: First, we show that triallelic sites are more sensitive to the parameters of a population that has experienced historical growth...

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## Recurrent bottlenecks in the malaria life cycle obscure signals of positive selection

Fonte: Cambridge University Press (CUP)
Publicador: Cambridge University Press (CUP)

Tipo: Artigo de Revista Científica

EN_US

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Detecting signals of selection in the genome of malaria parasites is a key to identify targets for drug and vaccine
development. Malaria parasites have a unique life cycle alternating between vector and host organism with a population
bottleneck at each transition. These recurrent bottlenecks could influence the patterns of genetic diversity and the power of
existing population genetic tools to identify sites under positive selection. We therefore simulated the site-frequency
spectrum of a beneficial mutant allele through time under the malaria life cycle. We investigated the power of current
population genetic methods to detect positive selection based on the site-frequency spectrum as well as temporal changes in
allele frequency. We found that a within-host selective advantage is difficult to detect using these methods. Although a
between-host transmission advantage could be detected, the power is decreased when compared with the classical Wright–
Fisher (WF) population model. Using an adjusted null site-frequency spectrum that takes the malaria life cycle into
account, the power of tests based on the site-frequency spectrum to detect positive selection is greatly improved. Our study
demonstrates the importance of considering the life cycle in genetic analysis...

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## Neurofeedbacktherapie bei Kindern mit einer Aufmerksamkeitsdefizit-Hyperaktivitäts-Störung: Zusammenhänge zwischen den langsamen kortikalen Potenzialen und dem EEG-Frequenzspektrum; Neurofeedback therapy for Children with Attention Deficit Hyperactivity Disorder: Relationship between Slow Cortical Potentials and EEG Frequency Spectrum

Fonte: Universidade de Tubinga
Publicador: Universidade de Tubinga

Tipo: Dissertação

DE_DE

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#Aufmerksamkeits-Defizit-Syndrom , Elektroencephalogramm , Langsames Hirnpotenzial , Theta-Aktivität , Biofeedback-Therapie#610#ADHS , Neurofeedback , Langsame Potenziale , Theta/Beta-Feedback , Frequenzspektrum , EEG#ADHD , Neurofeedback , Slow Cortical Potentials , Theta/beta feedback , Frequency Spectrum , EEG

Diese Arbeit ist Teil einer Studie, in der zwei verschiedene Neurofeedbacktherapien untersucht wurden. Die Stichprobe bestand aus 36 Kindern im Alter von 8 bis 13 Jahren mit ADHS oder ADS nach den DSM-IV-Kriterien, die randomisiert und parallelisiert den zwei Therapiegruppen zugeteilt wurden. Der einen Gruppe wurden ihre langsamen Potenziale zurückgemeldet (LP-Kinder), der anderen Gruppe ihre Theta- und Beta-Aktivität in Form des Theta/Beta-Quotienten (QT-Kinder). In beiden Gruppen erfolgte das Feedback akustisch und optisch. Das Therapieprogramm bestand aus insgesamt 35 Sitzungen mit je 4 Durchgängen, wobei in jedem Durchgang 38 bis 40 Aufgaben dargeboten wurden. Eine Aufgabe war es den zurückgemeldeten EEG-Parameter gegenüber der Baseline zu verkleinern (Aktivierungsaufgabe), die andere diesen zu vergrößern (Deaktivierungsaufgabe).
In dieser Arbeit wurde überprüft, ob das Feedback des einen EEG-Parameters zu Veränderungen des anderen EEG-Parameters führte, bzw. ob mit Veränderungen des einen EEG-Parameters Veränderungen des anderen EEG-Parameters einhergingen. Um diese Frage zu beantworten, wurden die Sitzungen 21 bis 30 auf Veränderungen im jeweils nicht zurückgemeldeten EEG-Parameter untersucht.
Hierbei wurden nur bei der Untergruppe von LP-Kindern...

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## Multitaper Methods for Time-Frequency Spectrum Estimation and Unaliasing of Harmonic Frequencies

Fonte: Quens University
Publicador: Quens University

Tipo: Tese de Doutorado
Formato: 1515276 bytes; application/pdf

EN; EN

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This thesis is concerned with various aspects of stationary and nonstationary time series analysis. In the nonstationary case, we study estimation of the Wold-Cram'er evolutionary spectrum, which is a time-dependent analogue of the spectrum of a stationary process. Existing estimators of the Wold-Cram'er evolutionary spectrum suffer from several problems, including bias in boundary regions of the time-frequency plane, poor frequency resolution, and an inability to handle the presence of purely harmonic frequencies. We propose techniques to handle all three of these problems.
We propose a new estimator of the Wold-Cram'er evolutionary spectrum
(the BCMTFSE) which mitigates the first problem. Our estimator is based on an extrapolation of the Wold-Cram'er evolutionary spectrum in time, using an estimate of its time derivative. We apply our estimator to a set of simulated nonstationary processes with known Wold-Cram'er evolutionary spectra to demonstrate its performance.
We also propose an estimator of the Wold-Cram'er evolutionary spectrum,
valid for uniformly modulated processes (UMPs). This estimator mitigates the second problem, by exploiting the structure of UMPs to improve the frequency resolution of the BCMTFSE. We apply this estimator to a simulated UMP with known Wold-Cram'er evolutionary spectrum.
To deal with the third problem...

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## The Hitchhiking Effect on the Site Frequency Spectrum of DNA Polymorphisms

Fonte: PubMed
Publicador: PubMed

Tipo: Artigo de Revista Científica

Publicado em /06/1995
EN

Relevância na Pesquisa

46.02%

The level of DNA sequence variation is reduced in regions of the Drosophila melanogaster genome where the rate of crossing over per physical distance is also reduced. This observation has been interpreted as support for the simple model of genetic hitchhiking, in which directional selection on rare variants, e.g., newly arising advantageous mutants, sweeps linked neutral alleles to fixation, thus eliminating polymorphisms near the selected site. However, the frequency spectra of segregating sites of several loci from some populations exhibiting reduced levels of nucleotide diversity and reduced numbers of segregating sites did not appear different from what would be expected under a neutral equilibrium model. Specifically, a skew toward an excess of rare sites was not observed in these samples, as measured by Tajima's D. Because this skew was predicted by a simple hitchhiking model, yet it had never been expressed quantitatively and compared directly to DNA polymorphism data, this paper investigates the hitchhiking effect on the site frequency spectrum, as measured by Tajima's D and several other statistics, using a computer simulation model based on the coalescent process and recurrent hitchhiking events. The results presented here demonstrate that under the simple hitchhiking model (1) the expected value of Tajima's D is large and negative (indicating a skew toward rare variants)...

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## Floristic, frequency, and vegetation life-form spectra of a cerrado site

Fonte: Instituto Internacional de Ecologia
Publicador: Instituto Internacional de Ecologia

Tipo: Artigo de Revista Científica
Formato: text/html

Publicado em 01/05/2004
EN

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We used Raunkiaer's system to classify in life-forms the vascular plants present in 12 random 25 m² quadrats of a cerrado site. The study area is covered by cerrado sensu stricto and is located in the Valério fragment, at about 22º13'S and 47º51'W, 760 m above sea level, in the Itirapina Ecological and Experimental Station, São Paulo State, southeastern Brazil. The floristic spectrum considers the life-form of each species, while in the frequency spectrum, each species is weighted by its frequency. The vegetation spectrum does not consider the species at all, but only the individuals in each life-form class. In the floristic spectrum, the most represented life-forms were the phanerophytes and the hemicryptophytes, as in other cerrado sites. This spectrum differed significantly from Raunkiaer's normal spectrum, mainly due to under-representation of therophytes and over-representation of phanerophytes. The floristic and frequency spectra were similar, but both differed from the vegetation spectrum. We recommend the floristic spectrum when working at larger scales and a description of the phytoclimate is wanted. The vegetation spectrum is preferable when working at smaller scales and wanting a quantitative description of the physiognomy. The frequency spectrum is not recommended at all.

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## The form of the asymptotic depth-limited wind-wave frequency spectrum

Fonte: American Geophysical Union
Publicador: American Geophysical Union

Tipo: Artigo de Revista Científica

Relevância na Pesquisa

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#Keywords: Bathymetry#Oceanography#Spectrum analysis#Velocity measurement#Wind#spectral analysis#water depth#wind velocity#wind wave

This paper presents a comprehensive set of field experiments investigating the form of the asymptotic, depth-limited wind wave frequency spectrum. Such a spectrum represents the upper limit to growth from active wind forcing in finite depth conditions. Th

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## Properties of neutrality tests based on allele frequency spectrum

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 05/11/2010

Relevância na Pesquisa

46%

#Quantitative Biology - Quantitative Methods#Quantitative Biology - Populations and Evolution#Statistics - Applications

One of the main necessities for population geneticists is the availability of
statistical tools that enable to accept or reject the neutral Wright-Fisher
model with high power. A number of statistical tests have been developed to
detect specific deviations from the null frequency spectrum in different
directions (i.e., Tajima's D, Fu and Li's F and D test, Fay and Wu's H).
Recently, a general framework was proposed to generate all neutrality tests
that are linear functions of the frequency spectrum. In this framework, a
family of optimal tests was developed to have almost maximum power against a
specific alternative evolutionary scenario. Following these developments, in
this paper we provide a thorough discussion of linear and nonlinear neutrality
tests. First, we present the general framework for linear tests and emphasize
the importance of the property of scalability with the sample size (that is,
the results of the tests should not depend on the sample size), which, if
missing, can guide to errors in data interpretation. The motivation and
structure of linear optimal tests are discussed. In a further generalization,
we develop a general framework for nonlinear neutrality tests and we derive
nonlinear optimal tests for polynomials of any degree in the frequency
spectrum.; Comment: 42 pages...

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## Modifications to the Cosmic 21-cm Background Frequency Spectrum by Scattering via electrons in Galaxy Clusters

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Relevância na Pesquisa

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The cosmic 21-cm background frequency spectrum related to the spin-flip
transition of neutral Hydrogen present during and before the era of
reionization is rich in features associated with physical processes that govern
transitions between the two spin states. The intervening electrons in
foreground galaxy clusters inversely Compton scatter the 21-cm background
spectrum and modify it just as the cosmic microwave background (CMB) spectrum
is modified by inverse-Compton scattering. Towards typical galaxy clusters at
low redshifts, the resulting modification is a few tenths milli-Kelvin
correction to the few tens milli-Kelvin temperature of 21-cm signal relative to
that of the cosmic microwave background black body spectrum. The modifications
are mostly associated with sharp changes in the cosmic 21-cm background
spectrum such as due to the onset of a Lyman-$\alpha$ radiation field or
heating of neutral gas. Though low frequency radio interferometers that are now
planned for 21-cm anisotropy measurements are insensitive to the mean 21-cm
spectrum, differential observations of galaxy clusters with these
interferometers can be utilized to indirectly establish global features in the
21-cm frequency spectrum. We discuss the feasibility to detect the spectrum
modified by clusters and find that for upcoming interferometers...

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## Compressive Wideband Spectrum Sensing for Fixed Frequency Spectrum Allocation

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 11/05/2010

Relevância na Pesquisa

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Too high sampling rate is the bottleneck to wideband spectrum sensing for
cognitive radio (CR). As the survey shows that the sensed signal has a sparse
representation in frequency domain in the mass, compressed sensing (CS) can be
used to transfer the sampling burden to the digital signal processor. An analog
to information converter (AIC) can randomly sample the received signal with
sub-Nyquist rate to obtained the random measurements. Considering that the
static frequency spectrum allocation of primary radios means the bounds between
different primary radios is known in advance, here we incorporate information
of the spectrum boundaries between different primary user as a priori
information to obtain a mixed l2/l1 norm denoising operator (MNDO). In the
MNDO, the estimated power spectrum density (PSD) vector is divided into block
sections with bounds corresponding different allocated primary radios.
Different from previous standard l1-norm constraint on the whole PSD vector, a
sum of the l2 norm of each section of the PSD vector is minimized to encourage
the local grouping distribution while the sparse distribution in mass, while a
relaxed constraint is used to improve the denoising performance. Simulation
demonstrates that the proposed method outperforms standard sparse spectrum
estimation in accuracy...

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## General triallelic frequency spectrum under demographic models with variable population size

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Relevância na Pesquisa

46.02%

It is becoming routine to obtain datasets on DNA sequence variation across
several thousands of chromosomes, providing unprecedented opportunity to infer
the underlying biological and demographic forces. Such data make it vital to
study summary statistics which offer enough compression to be tractable, while
preserving a great deal of information. One well-studied summary is the site
frequency spectrum---the empirical distribution, across segregating sites, of
the sample frequency of the derived allele. However, most previous theoretical
work has assumed that each site has experienced at most one mutation event in
its genealogical history, which becomes less tenable for very large sample
sizes. In this work we obtain, in closed-form, the predicted frequency spectrum
of a site that has experienced at most two mutation events, under very general
assumptions about the distribution of branch lengths in the underlying
coalescent tree. Among other applications, we obtain the frequency spectrum of
a triallelic site in a model of historically varying population size. We
demonstrate the utility of our formulas in two settings: First, we show that
triallelic sites are more sensitive to the parameters of a population that has
experienced historical growth...

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## The site frequency spectrum of dispensable genes

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 09/07/2014

Relevância na Pesquisa

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#Quantitative Biology - Populations and Evolution#Mathematics - Probability#92D20, 92D15, 60J25 (Primary) 60J70, 60C05 (Secondary)

The differences between DNA-sequences within a population are the basis to
infer the ancestral relationship of the individuals. Within the classical
infinitely many sites model, it is possible to estimate the mutation rate based
on the site frequency spectrum, which is comprised by the numbers
$C_1,...,C_{n-1}$, where n is the sample size and $C_s$ is the number of site
mutations (Single Nucleotide Polymorphisms, SNPs) which are seen in $s$
genomes. Classical results can be used to compare the observed site frequency
spectrum with its neutral expectation, $E[C_s]= \theta_2/s$, where $\theta_2$
is the scaled site mutation rate. In this paper, we will relax the assumption
of the infinitely many sites model that all individuals only carry homologous
genetic material. Especially, it is today well-known that bacterial genomes
have the ability to gain and lose genes, such that every single genome is a
mosaic of genes, and genes are present and absent in a random fashion, giving
rise to the dispensable genome. While this presence and absence has been
modeled under neutral evolution within the infinitely many genes model in
previous papers, we link presence and absence of genes with the numbers of site
mutations seen within each gene. In this work we derive a formula for the
expectation of the joint gene and site frequency spectrum...

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## Non-equilibrium theory of the allele frequency spectrum

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Relevância na Pesquisa

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A forward diffusion equation describing the evolution of the allele frequency
spectrum is presented. The influx of mutations is accounted for by imposing a
suitable boundary condition. For a Wright-Fisher diffusion with or without
selection and varying population size, the boundary condition is $\lim_{x
\downarrow 0} x f(x,t)=\theta \rho(t)$, where $f(\cdot,t)$ is the frequency
spectrum of derived alleles at independent loci at time $t$ and $\rho(t)$ is
the relative population size at time $t$. When population size and selection
intensity are independent of time, the forward equation is equivalent to the
backwards diffusion usually used to derive the frequency spectrum, but the
forward equation allows computation of the time dependence of the spectrum both
before an equilibrium is attained and when population size and selection
intensity vary with time. From the diffusion equation, we derive a set of
ordinary differential equations for the moments of $f(\cdot,t)$ and express the
expected spectrum of a finite sample in terms of those moments. We illustrate
the use of the forward equation by considering neutral and selected alleles in
a highly simplified model of human history. For example, we show that
approximately 30% of the expected heterozygosity of neutral loci is
attributable to mutations that arose since the onset of population growth in
roughly the last $150...

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## The frequency spectrum of periodically modulated sinusoidal oscillation

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 22/06/2009

Relevância na Pesquisa

46.04%

The mathematical model of periodically amplitude and phase modulated
sinusoidal oscillation is studied, and its Fourier spectrum is given
analytically. The Fourier spectrum of the model explains the main features of
the frequency spectrum of RR Lyrae stars showing light curve modulation called
the Blazhko effect: among others the appearance of multiplets, the rapid
decrease of their amplitudes in increasing orders, the asymmetry of the
amplitudes of the side frequency pairs, and the possibility of the occurrence
of frequency doublets instead of triplets in the spectrum. The good agreement
of the results of this mathematical model with observational facts favours
those physical models of the Blazhko effect which explain the phenomenon as a
modulation of the oscillation with the modulation frequency, f_m.; Comment: 13 pages, 3 figures, accepted for publication in CoAst

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## Decomposing the site frequency spectrum: the impact of tree topology on neutrality tests

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 22/10/2015

Relevância na Pesquisa

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We investigate the dependence of the site frequency spectrum (SFS) on the
topological structure of coalescent trees. We show that basic population
genetic statistics - for instance estimators of theta or neutrality tests such
as Tajima's D - can be decomposed into components of waiting times between
coalescent events and of tree topology. Our results clarify the relative impact
of the two components on these statistics. We provide a rigorous interpretation
of positive or negative values of neutrality tests in terms of the underlying
tree shape. In particular, we show that values of Tajima's D and Fay and Wu's H
depend in a direct way on a measure of tree balance which is mostly determined
by the root balance of the tree. We also compute the maximum and minimum values
for neutrality tests as a function of sample size.
Focusing on the standard coalescent model of neutral evolution, we discuss
how waiting times between coalescent events are related to derived allele
frequencies and thereby to the frequency spectrum. Finally, we show how tree
balance affects the frequency spectrum. In particular, we derive the complete
SFS conditioned on the root imbalance. We show that the conditional spectrum is
peaked at frequencies corresponding to the root imbalance and strongly biased
towards rare alleles.; Comment: 31 pages...

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