Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Machine Vision Enhanced Post-Earthquake Inspection and Rapid Loss Estimation

Manual inspection is required to determine the condition of damaged buildings after an earthquake. The lack of available inspectors, when combined with the large volume of inspection work, makes such inspection subjective and time-consuming. Completing the required inspection takes weeks to complete, which has adverse economic and societal impacts on the affected population. This paper proposes an automated framework for rapid post-earthquake building evaluation. Under the framework, the visible damage (cracks and buckling) inflicted on concrete columns is first detected. The damage properties are then measured in relation to the column's dimensions and orientation, so that the column's load bearing capacity can be approximated as a damage index. The column damage index supplemented with other building information (e.g. structural type and columns arrangement) is then used to query fragility curves of similar buildings, constructed from the analyses of existing and on-going experimental data. The query estimates the probability of the building being in different damage states. The framework is expected to automate the collection of building damage data, to provide a quantitative assessment of the building damage state, and to estimate the vulnerability of the building to collapse in the event of an aftershock. Videos and manual assessments of structures after the 2009 earthquake in Haiti are used to test the parts of the framework.

Single event molecular signalling for estimation and control

Cell biology is characterised by low molecule numbers and coupled stochastic chemical reactions with intrinsic noise permeating and dominating the interactions between molecules. Recent work [9] has shown that in such environments there are hard limits on the accuracy with which molecular populations can be controlled and estimated. These limits are predicated on a continuous diffusion approximation of the target molecule (although the remainder of the system is non-linear and discrete). The principal result of [9] assumes that the birth rate of the signalling species is linearly dependent on the target molecule population size. In this paper, we investigate the situation when the entire system is kept discrete, and arbitrary non-linear coupling is allowed between the target molecule and downstream signalling molecules. In this case it is possible, by relying solely on the event triggered nature of control and signalling reactions, to define non-linear reaction rate modulation schemes that achieve improved performance in certain parameter regimes. These schemes would not appear to be biologically relevant, raising the question of what are an appropriate set of assumptions for obtaining biologically meaningful results. © 2013 EUCA.

Estimation of the detection probability for Yangtze finless porpoises (Neophocaena phocaenoides asiaeorientalis) with a passive acoustic method

Yangtze finless porpoises were surveyed by using simultaneous visual and acoustical methods from 6 November to 13 December 2006. Two research vessels towed stereo acoustic data loggers, which were used to store the intensity and sound source direction of the high frequency sonar signals produced by finless porpoises at detection ranges up to 300 m on each side of the vessel. Simple stereo beam forming allowed the separation of distinct biosonar sound source, which enabled us to count the number of vocalizing porpoises. Acoustically, 204 porpoises were detected from one vessel and 199 from the other vessel in the same section of the Yangtze River. Visually, 163 and 162 porpoises were detected from two vessels within 300 m of the vessel track. The calculated detection probability using acoustic method was approximately twice that for visual detection for each vessel. The difference in detection probabilities between the two methods was caused by the large number of single individuals that were missed by visual observers. However, the sizes of large groups were underestimated by using the acoustic methods. Acoustic and visual observations complemented each other in the accurate detection of porpoises. The use of simple, relatively inexpensive acoustic monitoring systems should enhance population surveys of free-ranging, echolocating odontocetes. (C) 2008 Acoustical Society of America.

Estimation of wind erosion rates by using Cs-137 tracing technique: A case study in Tariat-Xilin Gol transect, Mongolian Plateau

Wind erosion is one of the major environmental problems in semi-arid and arid regions. Here we established the Tariat-Xilin Gol transect from northwest to southeast across the Mongolian Plateau, and selected seven sampling sites along the transect. We then estimated the soil wind erosion rates by using the Cs-137 tracing technique and examined their spatial dynamics. Our results showed that the Cs-137 inventories of sampling sites ranged from 265.63 +/- 44.91 to 1279.54 +/- 166.53 Bq.m(-2), and the wind erosion rates varied from 64.58 to 419.63 t.km(-2).a(-1) accordingly. In the Mongolia section of the transect (from Tariat to Sainshand), the wind erosion rate increased gradually with vegetation type and climatic regimes; the wind erosion process was controlled by physical factors such as annual precipitation and vegetation coverage, etc., and the impact of human activities was negligible. While in the China section of the transect (Inner Mongolia), the wind erosion rates of Xilin Hot and Zhengxiangbai Banner were thrice as much as those of Bayannur of Mongolia, although these three sites were all dominated by typical steppe. Besides the physical factors, higher population density and livestock carrying level should be responsible for the higher wind erosion rates in these two regions of Inner Mongolia.

Working at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae).

New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeographical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylogenetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar's Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. While the phylogeny cannot determine whether Africa or Madagascar was the centre of origin for the species investigated, it serves as the essential backbone for the application of coalescent and population genetic methods. From the application of these methods, we conclude that a hypothesis of two independent but unidirectional dispersal events from Africa to Madagascar is best supported by the data.

Estimation of survival rate and extinction probability for stage-structured populations with overlapping life stages

The development of methods providing reliable estimates of demographic parameters (e. g., survival rates, fecundity) for wild populations is essential to better understand the ecology and conservation requirements of individual species. A number of methods exist for estimating the demographics of stage-structured populations, but inherent mathematical complexity often limits their uptake by conservation practitioners. Estimating survival rates for pond-breeding amphibians is further complicated by their complex migratory and reproductive behaviours, often resulting in nonobservable states and successive cohorts of eggs and tadpoles. Here we used comprehensive data on 11 distinct breeding toad populations (Bufo calamita) to clarify and assess the suitability of a relatively simple method [the Kiritani-Nakasuji-Manly (KNM) method] to estimate the survival rates of stage-structured populations with overlapping life stages. The study shows that the KNM method is robust and provides realistic estimates of amphibian egg and larval survival rates for species in which breeding can occur as a single pulse or over a period of several weeks. The study also provides estimates of fecundity for seven distinct toad populations and indicates that it is essential to use reliable estimates of fecundity to limit the risk of under- or overestimating the survival rates when using the KNM method. Survival and fecundity rates for B. calamita populations were then used to define population matrices and make a limited exploration of their growth and viability. The findings of the study recently led to the implementation of practical conservation measures at the sites where populations were most vulnerable to extinction. © 2010 The Society of Population Ecology and Springer.

Estimation of contribution of changes in classic risk factors to trends in coronary-event rates across the WHO MONICA Project populations

Background. From the mid-1980s to mid-1990s, the WHO MONICA Project monitored coronary events and classic risk factors for coronary heart disease (CHD) in 38 populations from 21 countries. We assessed the extent to which changes in these risk factors explain the variation in the trends in coronary-event rates, across the populations. Methods. In men and women aged 35-64 years, non-fatal myocardial infarction and coronary deaths were registered continuously to assess trends in rates of coronary events. We carried out population surveys to estimate trends in risk factors. Trends in event rates were regressed on trends in risk score and in individual risk factors. Findings. Smoking rates decreased in most male populations but trends were mixed in women; mean blood pressures and cholesterol concentrations decreased, body-mass index increased, and overall risk scores and coronary-event rates decreased. The model of trends in 10-year coronary-event rates against risk scores and single risk factors showed a poor fit, but this was improved with a 4-year time lag for coronary events. The explanatory power of the analyses was limited by imprecision of the estimates and homogeneity of trends in the study populations. Interpretation. Changes in the classic risk factors seem to partly explain the variation in population trends in CHD. Residual variance is attributable to difficulties in measurement and analysis, including time lag, and to factors that were not included, such as medical interventions. The results support prevention policies based on the classic risk factors but suggest potential for prevention beyond these.

ESTIMATION OF PURITY FOR A QUANTUM HARMONIC OSCILLATOR INITIALLY PREPARED IN A DISPLACED THERMAL STATE

We address the estimation of purity for a quantum oscillator initially prepared in a displaced thermal state and probed by a suitably prepared qubit interacting with the oscillator via Jaynes-Cummings Hamiltonian without the rotating-wave approximation. We evaluate the quantum Fisher information (QFI) and show that optimal estimation of purity can be achieved by measuring the population of the qubit after a properly chosen interaction time. We also address the estimation of purity at fixed total energy and show that the corresponding precision is independent of the presence of a coherent amplitude.

Arsenic Speciation in Food and Estimation of the Dietary Intake of Inorganic Arsenic in a Rural Village of West Bengal, India

Arsenic (As) species were quantified by HPLC-HG-AFS in water and vegetables from a rural area of West Bengal (India). Inorganic species predominated in vegetables (including rice) and drinking water; in fact, inorganic arsenic (i-As) represented more than 80% of the total arsenic (t-As) content. To evaluate i-As intake in an arsenic affected rural village, a food survey was carried out on 129 people (69 men and 60 women). The data from the survey showed that the basic diet, of this rural population, was mainly rice and vegetables, representing more than 50% of their total daily food intake. During the periods when nonvegetarian foods (fish and meat) were scarce, the importance of rice increased, and rice alone represented more than 70% of the total daily food intake. The food analysis and the food questionnaires administrated led us to establish a daily intake of i-As of about 170 mu g i-As day(-1), which was above the tolerable daily intake of 150 mu g i-As day(-1), generally admitted. Our results clearly demonstrated that food is a very important source of i-As and that this source should never be forgotten in populations depending heavily on vegetables (mainly rice) for their diet.

Contribution of water and cooked rice to an estimation of the dietary intake of inorganic arsenic in a rural village of West Bengal, India

Arsenic contamination of rice plants by arsenic-polluted irrigation groundwater could result in high arsenic concentrations in cooked rice. The main objective of the study was to estimate the total and inorganic arsenic intakes in a rural population of West Bengal, India, through both drinking water and cooked rice. Simulated cooking of rice with different levels of arsenic species in the cooking water was carried out. The presence of arsenic in the cooking water was provided by four arsenic species (arsenite, arsenate, methylarsonate or dimethylarsinate) and at three total arsenic concentrations (50, 250 or 500 mu g l(-1)). The results show that the arsenic concentration in cooked rice is always higher than that in raw rice and range from 227 to 1642 mu g kg(-1). The cooking process did not change the arsenic speciation in rice. Cooked rice contributed a mean of 41% to the daily intake of inorganic arsenic. The daily inorganic arsenic intakes for water plus rice were 229, 1024 and 2000 mu g day(-1) for initial arsenic concentrations in the cooking water of 50, 250 and 500 g arsenic l(-1), respectively, compared with the tolerable daily intake which is 150 mu g day(-1).

Anthropometric within-country Inequality and the Estimation of Skill Premia with Anthropometric Indicators

Recently, a method to measure inequality has been proposed that is based on an- thropometric indicators. Baten (1999, 2000) argued that the coefficient of variation of human stature (henceforth ‘CV’) is correlated with overall inequality in a society, and that it can be used as indicator, especially where income inequality measures are lack- ing. This correlation has been confirmed in further analyses, for example by Pradhan et al. (2003), Moradi and Baten (2005), Sunder (2003), Guntupalli and Baten (2006), Blum (2010a), van Zanden et al. (2010), see also Figure 1 and Table 1. The idea is that average height reflects nutritional conditions during early childhood and youth. Since wealthier people have better access to food, shelter and medical resources, they tend to be taller than the poorer part of the population. Hence, the variation of height of a cer- tain cohort may be indicative of income distribution during the decade of their birth. The aim of this study is firstly to provide an overview of different forms of within- country height inequality. Previous studies on the aspects of height inequality are re- viewed. Inequalities between ethnic groups, gender, inhabitants of different regions and income groups are discussed. In the two final sections, we compare height CVs of anthropological inequality with another indicator of inequality, namely skill premia. We also present estimates of skill premia for a set of countries and decades for which “height CVs”, as they will be called in the following, are available.

Cavity-aided quantum parameter estimation in a bosonic double-well Josephson junction

We describe an apparatus designed to make non-demolition measurements on a Bose-Einstein condensate (BEC) trapped in a double-well optical cavity. This apparatus contains, as well as the bosonic gas and the trap, an optical cavity. We show how the interaction between the light and the atoms, under appropriate conditions, can allow for a weakly disturbing yet highly precise measurement of the population imbalance between the two wells and its variance. We show that the setting is well suited for the implementation of quantum-limited estimation strategies for the inference of the key parameters defining the evolution of the atomic system and based on measurements performed on the cavity field. This would enable {\it de facto} Hamiltonian diagnosis via a highly controllable quantum probe.

Molecular pedigree reconstruction and estimation of evolutionary parameters in a wild Atlantic salmon river system with incomplete sampling: a power analysis

Background: Pedigree reconstruction using genetic analysis provides a useful means to estimate fundamental population biology parameters relating to population demography, trait heritability and individual fitness when combined with other sources of data. However, there remain limitations to pedigree reconstruction in wild populations, particularly in systems where parent-offspring relationships cannot be directly observed, there is incomplete sampling of individuals, or molecular parentage inference relies on low quality DNA from archived material. While much can still be inferred from incomplete or sparse pedigrees, it is crucial to evaluate the quality and power of available genetic information a priori to testing specific biological hypotheses. Here, we used microsatellite markers to reconstruct a multi-generation pedigree of wild Atlantic salmon (Salmo salar L.) using archived scale samples collected with a total trapping system within a river over a 10 year period. Using a simulation-based approach, we determined the optimal microsatellite marker number for accurate parentage assignment, and evaluated the power of the resulting partial pedigree to investigate important evolutionary and quantitative genetic characteristics of salmon in the system.

Results: We show that at least 20 microsatellites (ave. 12 alleles/locus) are required to maximise parentage assignment and to improve the power to estimate reproductive success and heritability in this study system. We also show that 1.5 fold differences can be detected between groups simulated to have differing reproductive success, and that it is possible to detect moderate heritability values for continuous traits (h(2) similar to 0.40) with more than 80% power when using 28 moderately to highly polymorphic markers.

Conclusion: The methodologies and work flow described provide a robust approach for evaluating archived samples for pedigree-based research, even where only a proportion of the total population is sampled. The results demonstrate the feasibility of pedigree-based studies to address challenging ecological and evolutionary questions in free-living populations, where genealogies can be traced only using molecular tools, and that significant increases in pedigree assignment power can be achieved by using higher numbers of markers.

Overweight and obesity on the island of Ireland: an estimation of costs

Objectives The increasing prevalence of overweight and obesity worldwide continues to compromise population health and creates a wider societal cost in terms of productivity loss and premature mortality. Despite extensive international literature on the cost of overweight and obesity, findings are inconsistent between Europe and the USA, and particularly within Europe. Studies vary on issues of focus, specific costs and methods. This study aims to estimate the healthcare and productivity costs of overweight and obesity for the island of Ireland in 2009, using both top-down and bottom-up approaches.

Methods Costs were estimated across four categories: healthcare utilisation, drug costs, work absenteeism and premature mortality. Healthcare costs were estimated using Population Attributable Fractions (PAFs). PAFs were applied to national cost data for hospital care and drug prescribing. PAFs were also applied to social welfare and national mortality data to estimate productivity costs due to absenteeism and premature mortality.

Results The healthcare costs of overweight and obesity in 2009 were estimated at €437 million for the Republic of Ireland (ROI) and €127.41 million for NI. Productivity loss due to overweight and obesity was up to €865 million for ROI and €362 million for NI. The main drivers of healthcare costs are cardiovascular disease, type II diabetes, colon cancer, stroke and gallbladder disease. In terms of absenteeism, low back pain is the main driver in both jurisdictions, and for productivity loss due to premature mortality the primary driver of cost is coronary heart disease.

Conclusions The costs are substantial, and urgent public health action is required in Ireland to address the problem of increasing prevalence of overweight and obesity, which if left unchecked will lead to unsustainable cost escalation within the health service and unacceptable societal costs.