Mixture models of nucleotide sequence evolution that account for heterogeneity in the substitution process across sites and across lineages

Molecular phylogenetic studies of homologous sequences of nucleotides often assume that the underlying evolutionary process was globally stationary, reversible, and homogeneous (SRH), and that a model of evolution with one or more site-specific and time-reversible rate matrices (e.g., the GTR rate matrix) is enough to accurately model the evolution of data over the whole tree. However, an increasing body of data suggests that evolution under these conditions is an exception, rather than the norm. To address this issue, several non-SRH models of molecular evolution have been proposed, but they either ignore heterogeneity in the substitution process across sites (HAS) or assume it can be modeled accurately using the distribution. As an alternative to these models of evolution, we introduce a family of mixture models that approximate HAS without the assumption of an underlying predefined statistical distribution. This family of mixture models is combined with non-SRH models of evolution that account for heterogeneity in the substitution process across lineages (HAL). We also present two algorithms for searching model space and identifying an optimal model of evolution that is less likely to over- or underparameterize the data. The performance of the two new algorithms was evaluated using alignments of nucleotides with 10 000 sites simulated under complex non-SRH conditions on a 25-tipped tree. The algorithms were found to be very successful, identifying the correct HAL model with a 75% success rate (the average success rate for assigning rate matrices to the tree's 48 edges was 99.25%) and, for the correct HAL model, identifying the correct HAS model with a 98% success rate. Finally, parameter estimates obtained under the correct HAL-HAS model were found to be accurate and precise. The merits of our new algorithms were illustrated with an analysis of 42 337 second codon sites extracted from a concatenation of 106 alignments of orthologous genes encoded by the nuclear genomes of Saccharomyces cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, S. castellii, S. kluyveri, S. bayanus, and Candida albicans. Our results show that second codon sites in the ancestral genome of these species contained 49.1% invariable sites, 39.6% variable sites belonging to one rate category (V1), and 11.3% variable sites belonging to a second rate category (V2). The ancestral nucleotide content was found to differ markedly across these three sets of sites, and the evolutionary processes operating at the variable sites were found to be non-SRH and best modeled by a combination of eight edge-specific rate matrices (four for V1 and four for V2). The number of substitutions per site at the variable sites also differed markedly, with sites belonging to V1 evolving slower than those belonging to V2 along the lineages separating the seven species of Saccharomyces. Finally, sites belonging to V1 appeared to have ceased evolving along the lineages separating S. cerevisiae, S. paradoxus, S. mikatae, S. kudriavzevii, and S. bayanus, implying that they might have become so selectively constrained that they could be considered invariable sites in these species.

Living arrangements and health

In line with major demographic changes in other Northern European and North American countries and Australia, being nonmarried is becoming increasingly common in Finland, and the proportion of cohabiters and of persons living alone has grown in recent decades. Official marital status no longer reflects an individual s living arrangement, as single, divorced and widowed persons may live alone, with a partner, with children, with parents, with siblings, or with unrelated persons. Thus, more than official marital status, living arrangements may be a stronger discriminator of one s social bonds and health. The general purpose of this study was to deepen our current understanding of the magnitude, trends, and determinants of ill health by living arrangements in the Finnish working-age population. Distinct measures of different dimensions of poor health, as well as an array of associated factors, provided a comprehensive picture of health differences by living arrangements and helped to assess the role of other factors in the interpretation of these differences . Mortality analyses were based on Finnish census records at the end of 1995 linked with cause-of-death registers for 1996 2000. The data included all persons aged 30 and over. Morbidity analyses were based on two comparable cross-sectional studies conducted twenty years apart (the Mini-Finland Survey in 1978 80 and the Health 2000 Survey in 2000 01). Both surveys were based on nationally representative samples of Finns aged 30 and over, and benefited from high participation rates. With the exception of mortality analyses, this study focused on health differences among the working-age population (mortality in age groups 30-64 and 65 and over, self-rated health and mental health in the age group 30-64, and unhealthy alcohol use in the age group 30-54). Compared with all nonmarried groups, married men and women exhibited the best health in terms of mortality, self-rated health, mental health and unhealthy alcohol use. Cohabiters did not differ from married persons in terms of self-rated health or mental health, but did exhibit excess unhealthy alcohol use and high mortality, particularly from alcohol-related causes. Compared with the married, persons living alone or with someone other than a partner exhibited elevated mortality as well as excess poor mental health and unhealthy alcohol use. By all measures of health, men and women living alone tended to be in the worst position. Over the past twenty years, SRH had improved least among single men and women and widowed women, and most among cohabiting women. The association between living arrangements and health has many possible explanations. The health-related selection theory suggests that healthy people are more likely to enter and maintain a marriage or a consensual union than those who are unhealthy (direct selection) or that a variety of health-damaging behavioural and social factors increase the likelihood of ill health and the probability of remaining without a partner or becoming separated from one s partner (indirect selection). According to the social causation theory, marriage or cohabitation has a health-promoting effect, whereas living alone or with others than a partner has a detrimental effect on health. In this study, the role of other factors that are mainly assumed to reflect selection, appeared to be rather modest. Social support, which reflects social causation, contributed only modestly to differences in unhealthy alcohol use by living arrangements, but had a larger effect on differences in poor mental health. Socioeconomic factors and health-related behaviour, which reflect both selection and causation, appeared to play a more important role in the excess poor health of cohabiters and of persons living alone or with someone other than a partner, than of married persons. Living arrangements were strongly connected to various dimensions of ill health. In particular, alcohol consumption appeared to be of great importance in the association between living arrangements and health. To the extent that the proportion of nonmarried persons continues to grow and their health does not improve at the same rate as that of married persons, the challenges that currently nonmarried persons pose to public health will likely increase.

Exploring novel methods to achieve sensitivity limits for high operating temperature infrared detectors

A review of high operating temperature (HOT) infrared (IR) photon detector technology vis-a-vis material requirements, device design and state of the art achieved is presented in this article. The HOT photon detector concept offers the promise of operation at temperatures above 120 K to near room temperature. Advantages are reduction in system size, weight, cost and increase in system reliability. A theoretical study of the thermal generation-recombination (g-r) processes such as Auger and defect related Shockley Read Hall (SRH) recombination responsible for increasing dark current in HgCdTe detectors is presented. Results of theoretical analysis are used to evaluate performance of long wavelength (LW) and mid wavelength (MW) IR detectors at high operating temperatures. (C) 2013 Elsevier B.V. All rights reserved.

Heteroepitaxy of Group IV and Group III-V semiconductor alloys for photovoltaic applications

Photovoltaic energy conversion represents a economically viable technology for realizing collection of the largest energy resource known to the Earth -- the sun. Energy conversion efficiency is the most leveraging factor in the price of energy derived from this process. This thesis focuses on two routes for high efficiency, low cost devices: first, to use Group IV semiconductor alloy wire array bottom cells and epitaxially grown Group III-V compound semiconductor alloy top cells in a tandem configuration, and second, GaP growth on planar Si for heterojunction and tandem cell applications.

Metal catalyzed vapor-liquid-solid grown microwire arrays are an intriguing alternative for wafer-free Si and SiGe materials which can be removed as flexible membranes. Selected area Cu-catalyzed vapor-liquid solid growth of SiGe microwires is achieved using chlorosilane and chlorogermane precursors. The composition can be tuned up to 12% Ge with a simultaneous decrease in the growth rate from 7 to 1 μm/min^-1. Significant changes to the morphology were observed, including tapering and faceting on the sidewalls and along the lengths of the wires. Characterization of axial and radial cross sections with transmission electron microscopy revealed no evidence of defects at facet corners and edges, and the tapering is shown to be due to in-situ removal of catalyst material during growth. X-ray diffraction and transmission electron microscopy reveal a Ge-rich crystal at the tip of the wires, strongly suggesting that the Ge incorporation is limited by the crystallization rate.

Tandem Ga_1-xIn_xP/Si microwire array solar cells are a route towards a high efficiency, low cost, flexible, wafer-free solar technology. Realizing tandem Group III-V compound semiconductor/Si wire array devices requires optimization of materials growth and device performance. GaP and Ga_1-xIn_xP layers were grown heteroepitaxially with metalorganic chemical vapor deposition on Si microwire array substrates. The layer morphology and crystalline quality have been studied with scanning electron microscopy and transmission electron microscopy, and they provide a baseline for the growth and characterization of a full device stack. Ultimately, the complexity of the substrates and the prevalence of defects resulted in material without detectable photoluminescence, unsuitable for optoelectronic applications.

Coupled full-field optical and device physics simulations of a Ga_0.51In_0.49P/Si wire array tandem are used to predict device performance. A 500 nm thick, highly doped "buffer" layer between the bottom cell and tunnel junction is assumed to harbor a high density of lattice mismatch and heteroepitaxial defects. Under simulated AM1.5G illumination, the device structure explored in this work has a simulated efficiency of 23.84% with realistic top cell SRH lifetimes and surface recombination velocities. The relative insensitivity to surface recombination is likely due to optical generation further away from the free surfaces and interfaces of the device structure.

Finally, GaP has been grown free of antiphase domains on Si (112) oriented substrates using metalorganic chemical vapor deposition. Low temperature pulsed nucleation is followed by high temperature continuous growth, yielding smooth, specular thin films. Atomic force microscopy topography mapping showed very smooth surfaces (4-6 Å RMS roughness) with small depressions in the surface. Thin films (~ 50 nm) were pseudomorphic, as confirmed by high resolution x-ray diffraction reciprocal space mapping, and 200 nm thick films showed full relaxation. Transmission electron microscopy showed no evidence of antiphase domain formation, but there is a population of microtwin and stacking fault defects.

Autoavaliação do estado de saúde: associação com fatores sociodemográficos, hábitos de vida, morbidade e experiência de discriminação racial em inquérito populacional no Brasil

A autoavaliação do estado de saúde (AAS) é um indicador de saúde amplamente utilizado e influenciado por uma grande variedade de fatores. Em particular, existem evidências crescentes de que a discriminação racial é um importante fator de risco para eventos mórbidos em saúde e seu impacto na saúde da população brasileira ainda é pouco explorado. No primeiro artigo, o objetivo principal é investigar a associação entre AAS e fatores sociodemográficos, comportamentais e de morbidade. No segundo artigo, o objetivo é estimar a associação entre discriminação racial e diferentes desfechos em saúde, a saber, AAS, morbidade física e depressão ajustando por variáveis sociodemográficas, comportamentos relacionados à saúde e Índice de Massa Corporal, na população de pretos e pardos. O presente estudo possui delineamento seccional, baseado nos dados do inquérito de abrangência nacional Pesquisa Dimensão Social das Desigualdades. Os entrevistados responderam a questionários estruturados e suas medidas antropométricas foram aferidas. No primeiro artigo, foram avaliados 12.324 indivíduos, entre chefes de família e cônjuges, com idade maior ou igual a 20 anos. No segundo artigo, foram avaliados 3.863 chefes de família que responderam a pergunta sobre discriminação racial e que se classificaram como pretos e pardos. AAS foi avaliada por meio de pergunta obtida do instrumento de qualidade de vida SF-36 e, para o primeiro artigo, foi analisada de forma dicotômica em AAS boa (categorias de resposta excelente, muito boa e boa) e AAS ruim (categorias de resposta razoável e ruim). No segundo artigo, esse desfecho foi analisado utilizando-se as 5 categorias de resposta. As análises foram realizadas utilizando-se modelos de regressão logística uni e multivariados, para dados binários (artigo 1) ou ordinais (artigo 2). Os resultados foram apresentados na forma de Odds Ratios com os respectivos intervalos de 95% de confiança. Maior faixa etária, analfabetismo, tabagismo, obesidade e doenças crônicas estiveram associados a maior chance de AAS ruim. Para cada incremento na faixa de renda, observou-se uma redução de 20% na chance de relatar AAS ruim. Atividade física esteve associada a menor chance de AAS ruim. No segundo artigo, exposição à discriminação racial esteve associada com aumento na chance de relato de pior AAS, de morbidade física e de depressão. O presente estudo identificou a influência de diversos fatores sociais, demográficos, comportamentos relacionados à saúde e morbidade física na AAS. O estudo demonstrou ainda que a discriminação racial está associada negativamente aos três desfechos em saúde avaliados (AAS, morbidade física e depressão). Esses resultados podem traçar um perfil de subgrupos populacionais mais vulneráveis, ou seja, com maior risco de contrair doenças ou de procurar o serviço de saúde por uma doença já existente, auxiliando na definição de populações-alvo para o adequado planejamento de políticas e de programas de promoção de saúde.

Air quality and public health impacts of UK airports. Part I: Emissions

The potential adverse human health and climate impacts of emissions from UK airports have become a significant political issue, yet the emissions, air quality impacts and health impacts attributable to UK airports remain largely unstudied. We produce an inventory of UK airport emissions - including aircraft landing and takeoff (LTO) operations and airside support equipment - with uncertainties quantified. The airports studied account for more than 95% of UK air passengers in 2005. We estimate that in 2005, UK airports emitted 10.2 Gg [-23 to +29%] of NOx, 0.73 Gg [-29 to +32%] of SO2, 11.7 Gg [-42 to +77%] of CO, 1.8 Gg [-59 to +155%] of HC, 2.4 Tg [-13 to +12%] of CO2, and 0.31 Gg [-36 to +45%] of PM2.5. This translates to 2.5 Tg [-12 to +12%] CO2-eq using Global Warming Potentials for a 100-year time horizon. Uncertainty estimates were based on analysis of data from aircraft emissions measurement campaigns and analyses of aircraft operations.The First-Order Approximation (FOA3) - currently the standard approach used to estimate particulate matter emissions from aircraft - is compared to measurements and it is shown that there are discrepancies greater than an order of magnitude for 40% of cases for both organic carbon and black carbon emissions indices. Modified methods to approximate organic carbon emissions, arising from incomplete combustion and lubrication oil, and black carbon are proposed. These alterations lead to factor 8 and a 44% increase in the annual emissions estimates of black and organic carbon particulate matter, respectively, leading to a factor 3.4 increase in total PM2.5 emissions compared to the current FOA3 methodology. Our estimates of emissions are used in Part II to quantify the air quality and health impacts of UK airports, to assess mitigation options, and to estimate the impacts of a potential London airport expansion. © 2011 Elsevier Ltd.

Updated correlation between aircraft smoke number and black carbon concentration

Aircraft emissions of black carbon (BC) contribute to anthropogenic climate forcing and degrade air quality. The smoke number (SN) is the current regulatory measure of aircraft particulate matter emissions and quantifies exhaust plume visibility. Several correlations between SN and the exhaust mass concentration of BC (CBC) have been developed, based on measurements relevant to older aircraft engines. These form the basis of the current standard method used to estimate aircraft BC emissions (First Order Approximation version 3 [FOA3]) for the purposes of environmental impact analyses. In this study, BC with a geometric mean diameter (GMD) of 20, 30, and 60 nm and filter diameters of 19 and 35 mm are used to investigate the effect of particle size and sampling variability on SN measurements. For BC with 20 and 30 nm GMD, corresponding to BC emitted by modern aircraft engines, a smaller SN results from a given CBC than is the case for BC with 60 nm GMD, which is more typical of older engines. An updated correlation between CBC and SNthat accounts for typical size of BC emitted by modern aircraft is proposed. An uncertainty of ±25% accounts for variation in GMD in the range 20-30 nm and for the range of filter diameters. The SN-CBC correlation currently used in FOA3 underestimates by a factor of 2.5-3 for SN <15, implying that current estimates of aircraft BC emissions derived from SN are underestimated by the same factor. Copyright © American Association for Aerosol Research.

The effect of multiple chronic conditions on self-rated health, disability and quality of life among the older populations of Northern Ireland and the Republic of Ireland: a comparison of two nationally representative cross-sectional surveys

Objectives: Multimorbidity is common in the older population, but the impact of combinations of chronic conditions on disability and quality of life (QoL) is not well known. This analysis explores the effect of specific combinations of chronic diseases on disability, QoL and self-rated health (SRH).

Design: We used data from two population representative cross-sectional studies, the Northern Ireland Health and Social Wellbeing Survey (NIHSWS) 2005 and the Survey of Lifestyle, Attitudes and Nutrition (SLAN) 2007 (conducted in the Republic of Ireland).

Setting: Randomly selected community-living participants were interviewed at home.

Participants: A total of 6159 participants aged 50 years and older were included in the analysis.

Outcome measures: Chronic conditions were classified as cardiovascular disease, chronic pain,diabetes or respiratory disease. Interaction terms estimated by logistic regression were used to examine the effects of multiple chronic conditions on disability, SRH and QoL.

Results: Each chronic condition group was correlated with each of the others after adjusting for sociodemographic factors. Those from Northern Ireland were more likely to report a limitation in daily activities (45%) compared to those from the Republic of Ireland (21%). Each condition had an independent effect on disability, SRH and QoL, and those with multiple chronic conditions reported the worst outcomes. However, there were no statistically significant positive interactions between chronic condition groups with respect to any outcome.

Conclusions: Chronic conditions affect individuals largely independent of each other with respect to their effect on disability, SRH and QoL. However, a significant proportion of the population aged 50 years and over across the island of Ireland lives with multimorbidity,and this group is at the highest risk of disability, poor SRH and poor QoL.

Les relations entre les compétences des professionnels en ressources humaines, les caractéristiques des clients et leur satisfaction par l’approche des constituantes multiples

Cette étude empirique que nous avons appliquée à l’ingénierie-conseil, vise principalement deux objectifs ; (1) la validation des relations entre certaines caractéristiques des clients des services de ressources humaines et leur niveau de satisfaction face à ces services et (2) l’étude des relations entre les compétences des professionnels RH et le niveau de satisfaction des clients. Nous avons retenu un cadre théorique qui est constitué principalement de l’approche des constituantes multiples. Notre modèle d’analyse suppose que la satisfaction des groupes-clients d’un SRH est influencée par onze facteurs. De ces facteurs, cinq reflètent les caractéristiques des clients ; 1-l’engagement, 2-le sexe, 3-l’âge, 4-l’ancienneté et 5-la fréquence des contacts. Les six autres facteurs représentent les compétences des professionnels en ressources humaines ; 1-expert en ressources humaines, 2-allié de l’organisation, 3-gestion de la culture et du changement, 4-architecte stratégique, 5-gestion de talent et 6-activiste crédible. Pour les fins de notre recherche, nous retenons une approche quantitative et qualitative. Les résultats des analyses bivariées ne confirment pas nos hypothèses. Par contre, l’ancienneté et l’âge des clients semblent avoir une relation négative avec la satisfaction des clients. Quant à l’analyse de contenu des entrevues effectuées auprès des professionnels ressources humaines d’une organisation, elle permet de faire ressortir les liens entre la satisfaction et cinq compétences. Celles-ci sont l’expert en ressources humaines, l’allié de l’organisation, la gestion de la culture et du changement, la gestion du talent et l’activiste crédible. Ainsi, cinq propositions sont supportées.