165 research outputs found
A unifying framework for seed sensitivity and its application to subset seeds
We propose a general approach to compute the seed sensitivity, that can be
applied to different definitions of seeds. It treats separately three
components of the seed sensitivity problem -- a set of target alignments, an
associated probability distribution, and a seed model -- that are specified by
distinct finite automata. The approach is then applied to a new concept of
subset seeds for which we propose an efficient automaton construction.
Experimental results confirm that sensitive subset seeds can be efficiently
designed using our approach, and can then be used in similarity search
producing better results than ordinary spaced seeds
Diffusion quantum Monte Carlo study of three-dimensional Wigner crystals
We report diffusion quantum Monte Carlo calculations of three-dimensional
Wigner crystals in the density range r_s=100-150. We have tested different
types of orbital for use in the approximate wave functions but none improve
upon the simple Gaussian form. The Gaussian exponents are optimized by directly
minimizing the diffusion quantum Monte Carlo energy. We have carefully
investigated and sought to minimize the potential biases in our Monte Carlo
results. We conclude that the uniform electron gas undergoes a transition from
a ferromagnetic fluid to a body-centered-cubic Wigner crystal at r_s=106+/-1.
The diffusion quantum Monte Carlo results are compared with those from
Hartree-Fock and Hartree theory in order to understand the role played by
exchange and correlation in Wigner crystals. We also study "floating" Wigner
crystals and give results for their pair-correlation functions
Limited Lifespan of Fragile Regions in Mammalian Evolution
An important question in genome evolution is whether there exist fragile
regions (rearrangement hotspots) where chromosomal rearrangements are happening
over and over again. Although nearly all recent studies supported the existence
of fragile regions in mammalian genomes, the most comprehensive phylogenomic
study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some
doubts about their existence. We demonstrate that fragile regions are subject
to a "birth and death" process, implying that fragility has limited
evolutionary lifespan. This finding implies that fragile regions migrate to
different locations in different mammals, explaining why there exist only a few
chromosomal breakpoints shared between different lineages. The birth and death
of fragile regions phenomenon reinforces the hypothesis that rearrangements are
promoted by matching segmental duplications and suggests putative locations of
the currently active fragile regions in the human genome
Cosmological parameters from SDSS and WMAP
We measure cosmological parameters using the three-dimensional power spectrum
P(k) from over 200,000 galaxies in the Sloan Digital Sky Survey (SDSS) in
combination with WMAP and other data. Our results are consistent with a
``vanilla'' flat adiabatic Lambda-CDM model without tilt (n=1), running tilt,
tensor modes or massive neutrinos. Adding SDSS information more than halves the
WMAP-only error bars on some parameters, tightening 1 sigma constraints on the
Hubble parameter from h~0.74+0.18-0.07 to h~0.70+0.04-0.03, on the matter
density from Omega_m~0.25+/-0.10 to Omega_m~0.30+/-0.04 (1 sigma) and on
neutrino masses from <11 eV to <0.6 eV (95%). SDSS helps even more when
dropping prior assumptions about curvature, neutrinos, tensor modes and the
equation of state. Our results are in substantial agreement with the joint
analysis of WMAP and the 2dF Galaxy Redshift Survey, which is an impressive
consistency check with independent redshift survey data and analysis
techniques. In this paper, we place particular emphasis on clarifying the
physical origin of the constraints, i.e., what we do and do not know when using
different data sets and prior assumptions. For instance, dropping the
assumption that space is perfectly flat, the WMAP-only constraint on the
measured age of the Universe tightens from t0~16.3+2.3-1.8 Gyr to
t0~14.1+1.0-0.9 Gyr by adding SDSS and SN Ia data. Including tensors, running
tilt, neutrino mass and equation of state in the list of free parameters, many
constraints are still quite weak, but future cosmological measurements from
SDSS and other sources should allow these to be substantially tightened.Comment: Minor revisions to match accepted PRD version. SDSS data and ppt
figures available at http://www.hep.upenn.edu/~max/sdsspars.htm
Temporal dynamics of the shrub and herbaceous layer of an area of moist grassland in Alto Paraíso de Goiás, Brazil
Este trabalho avaliou a dinâmica estrutural e fl orística de uma comunidade de espécies herbáceo-arbustivas
de uma área de campo limpo úmido em Alto Paraíso de Goiás, o primeiro inventário realizado em 2000 (T0) e o
segundo em 2007 (T1). A diversidade de Shannon entre os períodos foi comparada pelo teste-t de Hutcheson e a
similaridade fl orística, pelo índice de similaridade de Chao-Sørensen. As relações fl orísticas e a cobertura, entre os
períodos e as linhas, foram avaliadas por meio de análises de correspondência retifi cada (DCA). Foram amostradas
98 espécies, 88 no T0 e 67 no T1, sendo 31 exclusivas do T0 e 10 do T1. A diversidade fl orística na comunidade
foi elevada nos dois períodos, porém diferente entre esses (t = 7,12; p < 0,001), devido a variação no número e
cobertura das espécies. A similaridade entre os dois inventários foi alta (Chao-Sørensen ± IC = 0,841 ± 0,074). A
ordenação por DCA indicou relações entre a composição fl orística e a cobertura com o gradiente de umidade e
de matéria orgânica no solo identifi cados em T0. Houve modifi cações nas linhas em zonas sazonais, as quais se
tornaram mais semelhantes às linhas constantemente saturadas por água. Em um intervalo de sete anos o campo
limpo úmido apresentou mudanças na composição fl orística e, principalmente na estrutura devido o aumento da
cobertura de espécies perenes, cespitosas e entouceiradas, que foram favorecidas pela maior umidade no solo em
resposta à elevação da pluviosidade da região. __________________________________________________________________________________________ ABSTRACTTh is study evaluated the fl oristic and structural dynamics of a community of herbaceous-shrub species
in an area of moist grassland in Alto Paraíso de Goiás. Th e fi rst inventory was undertaken in 2000 (T0) and the
second in 2007 (T1). Shannon’s diversity between the periods was compared by Hutchesons´s t-test, and the
fl oristic similarity by the Chao-Sørensen similarity index. Floristic composition and cover, between periods and
lines, were evaluated by detrended correspondence analysis (DCA). We sampled 98 species, 88 at T0 and 67 at T1;
31 were unique to T0 and 10 to T1. Floristic diversity in the community was high in both periods, but diff erent
between them (t = 7.12, p <0.001), due to variation in species number and coverage. Similarity between the two
surveys was high (Chao-Sørensen CI = ± 0.841 ± 0.074). Th e DCA ordination indicated relationships between the
fl oristic composition and cover with a gradient of moisture and organic matter in the soil identifi ed in T0. Th ere
were changes in the lines in the seasonal zones, which became more similar in those constantly saturated with
water. During an interval of seven years the moist grassland showed changes in fl oristic composition and mainly
in structure due to increased cover of the clumped tussock perennial species, which were favored by higher soil
moisture due to high rainfall in the region
Astrometric Calibration and Performance of the Dark Energy Spectroscopic Instrument Focal Plane
The Dark Energy Spectroscopic Instrument (DESI), consisting of 5020 robotic
fiber positioners and associated systems on the Mayall telescope at Kitt Peak,
Arizona, is carrying out a survey to measure the spectra of 40 million galaxies
and quasars and produce the largest 3D map of the universe to date. The primary
science goal is to use baryon acoustic oscillations to measure the expansion
history of the universe and the time evolution of dark energy. A key function
of the online control system is to position each fiber on a particular target
in the focal plane with an accuracy of 11m rms 2-D. This paper describes
the set of software programs used to perform this function along with the
methods used to validate their performance.Comment: 27 pages, 16 figures submitted to A
Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function
Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of l
Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel
A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved
- …