On Counting the Number of Consistent Genotype Assignments for Pedigrees

Consistency checking of genotype information in pedigrees plays an important role in genetic analysis and for complex pedigrees the computational complexity is critical. We present here a detailed complexity analysis for the problem of counting the number of complete consistent genotype assignments. Our main result is a polynomial time algorithm for counting the number of complete consistent assignments for non-looping pedigrees. We further classify pedigrees according to a number of natural parameters like the number of generations, the number of children per individual and the cardinality of the set of alleles. We show that even if we assume all these parameters as bounded by reasonably small constants, the counting problem becomes computationally hard (#P-complete) for looping pedigrees. The border line for counting problems computable in polynomial time (i.e. belonging to the class FP) and #P-hard problems is completed by showing that even for general pedigrees with unlimited number of generations and alleles but with at most one child per individual and for pedigrees with at most two generations and two children per individual the counting problem is in FP

Exact solution of the Hu-Paz-Zhang master equation

The Hu-Paz-Zhang equation is a master equation for an oscillator coupled to a linear passive bath. It is exact within the assumption that the oscillator and bath are initially uncoupled . Here an exact general solution is obtained in the form of an expression for the Wigner function at time t in terms of the initial Wigner function. The result is applied to the motion of a Gaussian wave packet and to that of a pair of such wave packets. A serious divergence arising from the assumption of an initially uncoupled state is found to be due to the zero-point oscillations of the bath and not removed in a cutoff model. As a consequence, worthwhile results for the equation can only be obtained in the high temperature limit, where zero-point oscillations are neglected. In that limit closed form expressions for wave packet spreading and attenuation of coherence are obtained. These results agree within a numerical factor with those appearing in the literature, which apply for the case of a particle at zero temperature that is suddenly coupled to a bath at high temperature. On the other hand very different results are obtained for the physically consistent case in which the initial particle temperature is arranged to coincide with that of the bath

Shell-model calculations of neutrino scattering from 12C

Neutrino reaction cross-sections, $(\nu_\mu,\mu^-)$, $(\nu_e,e^-)$, $\mu$-capture and photoabsorption rates on $^{12}$C are computed within a large-basis shell-model framework, which included excitations up to $4\hbar\omega$. When ground-state correlations are included with an open $p$-shell the predictions of the calculations are in reasonable agreement with most of the experimental results for these reactions. Woods-Saxon radial wave functions are used, with their asymptotic forms matched to the experimental separation energies for bound states, and matched to a binding energy of 0.01 MeV for unbound states. For comparison purposes, some results are given for harmonic oscillator radial functions. Closest agreement between theory and experiment is achieved with unrestricted shell-model configurations and Woods-Saxon radial functions. We obtain for the neutrino-absorption inclusive cross sections: $\bar{\sigma} = 13.8 \times 10^{-40}$ cm$^2$ for the $(\nu_{\mu},\mu^{-})$ decay-in-flight flux in agreement with the LSND datum of $(12.4 \pm 1.8) \times 10^{-40}$ cm$^2$; and $\bar{\sigma} = 12.5 \times 10^{-42}$ cm$^2$ for the $(\nu_{e},e^{-})$ decay-at-rest flux, less than the experimental result of $(14.4 \pm 1.2) \times 10^{-42}$ cm$^2$.Comment: 19 pages. ReVTeX. No figure

Comportamento à flexão de vigas eco-eficientes de ultra elevada durabilidade

Atualmente, o ecossistema mundial tem vindo a ser confrontado com problemas de grande importância, a elevada poluição do meio ambiente e a limitação dos recursos energéticos. Estes problemas têm contribuído para que a sustentabilidade da construção seja uma prioridade cada vez maior no presente e no futuro. A manutenção e a reabilitação do património construído surge como uma das medidas mais eficazes para prevenir ou reduzir o consumo de energia no setor da construção. No caso da construção nova, a tendência é para verificar-se um aumento da utilização de elementos estruturais pré-fabricados com partes betonadas em obra, obtendose uma maior rapidez de execução associada a um maior controlo de qualidade. O betão de ultra elevada durabilidade, reforçado com fibras metálicas, é considerado um material inovador desenvolvido nas últimas décadas, apresentando um conjunto de caraterísticas especiais, como a durabilidade, a facilidade de aplicação, as elevadas resistências mecânicas, tornando-o num produto particularmente atraente para a reabilitação e reforço de estruturas de betão. No entanto, este betão não deve ser produzido em grandes quantidades devido ao elevado consumo de cimento e adições, resultando em elevados custos económicos e ambientais. Considerando estas desvantagens é proposto que o betão de ultra elevada durabilidade seja usado apenas na camada de recobrimento, formando-se assim uma superskin que protege o elemento estrutural dos ambientes mais agressivos, isto é, aumenta a durabilidade das estruturas de betão sem que, no entanto, seja criado um impacte ambiental muito significativo (a quantidade de CO2 libertada para a atmosfera é menor devido ao menor consumo de cimento e adições). A presente dissertação pretende explorar o conceito de superskin do ponto de vista do comportamento estrutural, nomeadamente, estudar o comportamento de vigas sujeitas a esforços de flexão, compostas por uma camada exterior de betão de ultra elevada durabilidade, associado a um núcleo com betão eco-eficiente, com baixa dosagem de cimento, de modo a obter uma solução mais durável e ao mesmo tempo, ecologicamente mais eficiente. Foram realizadas oito vigas com diferentes taxas de armadura: quatro vigas produzidas apenas com betão com baixa dosagem de cimento (usadas como vigas de referência) e quatro vigas produzidas com um betão de ultra elevada durabilidade na camada de recobrimento e com um betão com baixa dosagem de cimento no núcleo. As diferentes taxas de armadura longitudinal permitem avaliar a influência da superskin em vigas com roturas dúcteis e frágeis. Com base nos dados recolhidos durante os ensaios experimentais estudou-se: (i) relação cargadeslocamento; (ii) os valores teóricos e experimentais do momento resistente; (iii) a evolução da curvatura nas secções críticas; (iv) a evolução da rigidez à flexão com a carga aplicada; (v) a ductilidade; e (vi) a fendilhação e o tipo de rotura. Da análise de resultados foi possível verificar que o recobrimento em betão de ultra elevada durabilidade é uma solução com aspetos muito positivos, nomeadamente, aumenta a resistência à flexão das vigas

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

Effects of coastal urbanization on salt-marsh faunal assemblages in the northern Gulf of Mexico

Author Posting. © American Fisheries Society, 2014. This article is posted here by permission of American Fisheries Society for personal use, not for redistribution. The definitive version was published in Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 6 (2014): 89-107, doi:10.1080/19425120.2014.893467.Coastal landscapes in the northern Gulf of Mexico, specifically the Mississippi coast, have undergone rapid urbanization that may impact the suitability of salt-marsh ecosystems for maintaining and regulating estuarine faunal communities. We used a landscape ecology approach to quantify the composition and configuration of salt-marsh habitats and developed surfaces at multiple spatial scales surrounding three small, first-order salt-marsh tidal creeks arrayed along a gradient of urbanization in two river-dominated estuaries. From May 3 to June 4, 2010, nekton and macroinfauna were collected weekly at all six sites. Due to the greater abundance of grass shrimp Palaemonetes spp., brown shrimp Farfantepenaeus aztecus, blue crab Callinectes sapidus, Gulf Menhaden Brevoortia patronus, and Spot Leiostomus xanthurus, tidal creeks in intact natural (IN) salt-marsh landscapes supported a nekton assemblage that was significantly different from those in partially urbanized (PU) or completely urbanized (CU) salt-marsh landscapes. However, PU landscapes still supported an abundant nekton assemblage. In addition, the results illustrated a linkage between life history traits and landscape characteristics. Resident and transient nekton species that have specific habitat requirements are more likely to be impacted in urbanized landscapes than more mobile species that are able to exploit multiple habitats. Patterns were less clear for macroinfaunal assemblages, although they were comparatively less abundant in CU salt-marsh landscapes than in either IN or PU landscapes. The low abundance or absence of several macroinfaunal taxa in CU landscapes may be viewed as an additional indicator of poor habitat quality for nekton. The observed patterns also suggested that benthic sediments in the CU salt-marsh landscapes were altered in comparison with IN or PU landscapes. The amount of developed shoreline and various metrics related to salt marsh fragmentation were important drivers of observed patterns in nekton and macroinfaunal assemblages

Horizontal Branch Stars: The Interplay between Observations and Theory, and Insights into the Formation of the Galaxy

We review HB stars in a broad astrophysical context, including both variable and non-variable stars. A reassessment of the Oosterhoff dichotomy is presented, which provides unprecedented detail regarding its origin and systematics. We show that the Oosterhoff dichotomy and the distribution of globular clusters (GCs) in the HB morphology-metallicity plane both exclude, with high statistical significance, the possibility that the Galactic halo may have formed from the accretion of dwarf galaxies resembling present-day Milky Way satellites such as Fornax, Sagittarius, and the LMC. A rediscussion of the second-parameter problem is presented. A technique is proposed to estimate the HB types of extragalactic GCs on the basis of integrated far-UV photometry. The relationship between the absolute V magnitude of the HB at the RR Lyrae level and metallicity, as obtained on the basis of trigonometric parallax measurements for the star RR Lyrae, is also revisited, giving a distance modulus to the LMC of (m-M)_0 = 18.44+/-0.11. RR Lyrae period change rates are studied. Finally, the conductive opacities used in evolutionary calculations of low-mass stars are investigated. [ABRIDGED]Comment: 56 pages, 22 figures. Invited review, to appear in Astrophysics and Space Scienc

Variação sazonal na riqueza e na abundância de pequenos mamíferos, na estrutura da floresta e na disponibilidade de artrópodes em fragmentos florestais no Mato Grosso, Brasil

We captured small mammals in eight forest fragments (43 a 1.411 ha.) during the dry and wet seasons, in southwest Mato Grosso, Brazil, and investigated the variation in small mammal richness and abundance, as well as in forest structure variables (litter volume and canopy openness) and arthropod availability, between the two seasons. Sampling was carried out during the wet season between 2002 and 2003 and in the dry season of 2003. In each fragment, we used Sherman, Tomahawk, snap, and pitfall traps during 10 consecutive days per season, totaling 17,600 trap x nights. In total, we obtained 379 captures of 20 species, seven of marsupials and 13 of rodents. Overall capture success was 2.2% (1.6% during the wet season and 2.7% during the dry season). Total richness, richness of rodents, richness of marsupials, total abundance and abundance of rodents did not varied significantly between seasons. However, marsupial abundance was significantly lower in the dry season, when rainfall is high. Litter volume was significantly higher during the dry season, while arthropod availability was significantly higher during the wet season. Therefore, higher food availability during the wet season may have made trap baits less attractive. In general, the observed variations between dry and wet seasons are in accordance with patterns described in other studies

Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program

The genetic determinants of fasting glucose (FG) and fasting insulin (FI) have been studied mostly through genome arrays, resulting in over 100 associated variants. We extended this work with high-coverage whole genome sequencing analyses from fifteen cohorts in NHLBI’s Trans-Omics for Precision Medicine (TOPMed) program. Over 23,000 non-diabetic individuals from five race-ethnicities/populations (African, Asian, European, Hispanic and Samoan) were included. Eight variants were significantly associated with FG or FI across previously identified regions MTNR1B, G6PC2, GCK, GCKR and FOXA2. We additionally characterize suggestive associations with FG or FI near previously identified SLC30A8, TCF7L2, and ADCY5 regions as well as APOB, PTPRT, and ROBO1. Functional annotation resources including the Diabetes Epigenome Atlas were compiled for each signal (chromatin states, annotation principal components, and others) to elucidate variant-to-function hypotheses. We provide a catalog of nucleotide-resolution genomic variation spanning intergenic and intronic regions creating a foundation for future sequencing-based investigations of glycemic traits