Bayesian Inference in Exponential and Pareto populations in the presence of Outliers

This thesis Entitled Bayesian inference in Exponential and pareto populations in the presence of outliers. The main theme of the present thesis is focussed on various estimation problems using the Bayesian appraoch, falling under the general category of accommodation procedures for analysing Pareto data containing outlier. In Chapter II. the problem of estimation of parameters in the classical Pareto distribution specified by the density function. In Chapter IV. we discuss the estimation of (1.19) when the sample contain a known number of outliers under three different data generating mechanisms, viz. the exchangeable model. Chapter V the prediction of a future observation based on a random sample that contains one contaminant. Chapter VI is devoted to the study of estimation problems concerning the exponential parameters under a k-outlier model.

Enlarging a training set for genomic selction by imputation of un-genotyped animals in populations of varying genetic architecture

Background: The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. ----- Methods: Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. ----- Results: Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. ----- Conclusions: Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.

Heat stress response for physiological traits in dairy and dual purpose cattle populations on phenotypic and genetic scales

The main objective of this thesis was to determine the potential impact of heat stress (HS) on physiological traits of lactating cows and semen quality of bulls kept in a temperate climate. The thesis is comprised of three studies. An innovative statistical modeling aspect common to all three studies was the application of random regression methodology (RRM) to study the phenotypic and genetic trajectory of traits in dependency of a continuous temperature humidity index (THI). In the first study, semen quality and quantity traits of 562 Holstein sires kept on an AI station in northwestern Germany were analyzed in the course of THI calculated from data obtained from the nearest weather station. Heat stress was identified based on a decline in semen quality and quantity parameters. The identified general HS threshold (THI = 60) and the thermoneutal zone (THI in the range from 50 to 60) for semen production were lower than detected in studies conducted in tropical and subtropical climates. Even though adult bulls were characterized by higher semen productivity compared to younger bulls, they responded with a stronger semen production loss during harsh environments. Heritabilities (low to moderate range) and additive genetic variances of semen characteristics varied with different levels of THI. Also, based on genetic correlations genotype, by environment interactions were detected. Taken together, these findings suggest the application of specific selection strategies for specific climate conditions. In the second study, the effect of the continuous environmental descriptor THI as measured inside the barns on rectal temperatures (RT), skin temperatures (ST), vaginal temperatures (VT), respiration rates (RR), and pulse rate (PR) of lactating Holstein Friesian (HF) and dual-purpose German black pied cattle (DSN) was analyzed. Increasing HS from THI 65 (threshold) to THI 86 (maximal THI) resulted in an increase of RT by 0.6 °C (DSN) and 1 °C (HF), ST by 3.5 °C (HF) and 8 °C (DSN), VT by 0.3 °C (DSN), and RR by 47 breaths / minute (DSN), and decreased PR by 7 beats / minute (DSN). The undesired effects of rising THI on physiological traits were most pronounced for cows with high levels of milk yield and milk constituents, cows in early days in milk and later parities, and during summer seasons in the year 2014. In the third study of this dissertation, the genetic components of the cow’s physiological responses to HS were investigated. Heat stress was deduced from indoor THI measurements, and physiological traits were recorded on native DSN cows and their genetically upgraded crosses with Holstein Friesian sires in two experimental herds from pasture-based production systems reflecting a harsh environment of the northern part of Germany. Although heritabilities were in a low range (from 0.018 to 0.072), alterations of heritabilities, repeatabilities, and genetic components in the course of THI justify the implementation of genetic evaluations including heat stress components. However, low repeatabilities indicate the necessity of using repeated records for measuring physiological traits in German cattle. Moderate EBV correlations between different trait combinations indicate the potential of selection for one trait to simultaneously improve the other physiological attributes. In conclusion, bulls of AI centers and lactating cows suffer from HS during more extreme weather conditions also in the temperate climate of Northern Germany. Monitoring physiological traits during warm and humid conditions could provide precious information for detection of appropriate times for implementation of cooling systems and changes in feeding and management strategies. Subsequently, the inclusion of these physiological traits with THI specific breeding values into overall breeding goals could contribute to improving cattle adaptability by selecting the optimal animal for extreme hot and humid conditions. Furthermore, the recording of meteorological data in close distance to the cow and visualizing the surface body temperature by infrared thermography techniques might be helpful for recognizing heat tolerance and adaptability in cattle.

Análisis del Proyecto Mesoaméricano y su incidencia en la integración de la Región Centroaméricana y Colombia : Período de Estudio 2001-2007

El Proyecto Mesoamericano es un proyecto de integración entre los países de Mesoamerica; es decir, que es una integración entre los nueves Estados del Sureste de México (Campeche, Chiapas, Guerrero, Oaxaca, Puebla, Quintana Roo, Tabasco, Veracruz y Yucatán)y los territorios de Guatemala, El Salvador, Belice, Honduras, Nicaragua, Costa Rica y Panamá. Aunque a partir del 2006 Colombia ingresó con todos los derechos de participación. El proyecto busca principalmente aumentar la calidad de vida de los habitantes potencializando el desarrollo económico, reduciendo la pobreza, aumentando el capital humano y natural de la región, dentro de un contexto de respeto a la diversidad cultural, étnica e inclusión social. Para esto el Proyecto Mesoamericano se ha dividido en 9 Iniciativas las cuales a cada país le corresponde desarrollar cada una. Es por esto que a México le correspondió desarrollar la Iniciativa de Desarrollo Humano; a Belice la iniciativa de Turismo; a Guatemala la Iniciativa Energética; a El Salvador, Telecomunicaciones; a Costa Rica, Transporte; a Honduras Facilitación Comercial y Competitividad; a Nicaragua, Desarrollo Sostenible; a Panamá, Prevención y Mitigación de Desastres Naturales y finalmente a Colombia le correspondió desarrollar el tema de los biocombustibles. estas Iniciativas todas tienen la misma importancia pero a diferencia de las otras; la Iniciativa Energética es la más desarrollada y ejecutada hasta el momento por ser la más grande; entre sus proyectos están: El Sistema de Interconexión Eléctrica SIEPAC, la Interconexión Eléctrica entre México y Guatemala, la Interconexión Eléctrica entre Panamá y Colombia, el Proyecto de Biocombustibles y las Energías Renovables. Esta Iniciativa ha hecho que la integración entre los países de la región se afiance mucho más. Aunque todavía existe mucho rechazo por parte de la población campesina e indígena por el temor a perder sus recursos naturales y que estos sean privatizados. De igual forma Colombia es muy importante para el proyecto puesto que Colombia geoestratégicamente es el puente entre Centroamérica y Suramérica y es un factor clave para el Proyecto Mesoamericano.

Lupus nephritis in colombians: Contrasts and comparisons with other populations

Lupus nephritis (LN) is one of the most serious complications of systemic lupus erythematosus (SLE) since it is the major predictor of poor prognosis. The purpose of this study was to examine the clinical and immunological characteristics associated with LN development during the course of SLE in Colombians. Therefore, patients with SLE followed at five different referral centers in Medellin, Bogota, and Cali were included in this cross-sectional and multicenter study. Factors influencing LN were assessed by conditional logistic regression analysis, adjusting by gender, age at onset, duration of disease, and city of origin. The entire sample population included 467 patients, of whom 51% presented with LN. The presence of anti-dsDNA antibodies (adjusted odds ratio (AOR), 2.06; 95% confidence interval (CI), 1.16–3.65), pleuritis (AOR, 3.82; 95% CI, 1.38–10.54), and hypertension (AOR, 2.63; 95% CI, 1.23–5.62) were positively associated with LN, whereas the presence of anti-La antibodies was a protective factor against LN development (AOR, 0.4; 95% CI, 0.19–0.85). A review of literature on LN in different populations is made. The identified clinical- and laboratory-associated factors would assist earlier diagnosis and guide decisions on therapeutic interventions on this critical and frequent complication of SLE.

Interpretation, emotional reactions and daily life implications of hallucination-like experiences in clinical and nonclinical populations

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Some biological data on cetaceans populations present in the western coasts of Ireland

Ireland’s waters constitute one of the richest habitats for cetaceans in Europe. Marine mammals, particularly cetaceans, are known to be definitive hosts of digestive parasites from the Fm.Anisakidae. The main aim of this study is to collect and compile all the information available out there regarding parasites of the Fm. Anisakidae and their definitive hosts. Secondary objectives are to relate the presence of cetacean species with the presence of parasites of the Fm. Anisakidae and to determine whether this greater number of cetaceans relates to a greater level of parasitism. Prevalence and burdens of anisakids in definitive hosts vary widely with host species, geographic location, and season. Results from several post-mortem exams are given. However, they cannot be compared due to differences in collecting techniques. Anisakis simplex is the most commonly and widespread parasite found in the majority of the samples and in a major number of hosts, which include harbour porpoise, short-beaked common dolphin and bottlenose dolphin. Studies on harbour porpoise obtained prevalences of Anisakis spp. of 46% (n=26) and of 100% (n= 12). Another study in common dolphin reported a prevalence of 68% (n=25). Several reasons could influence the variations in the presence of Anisakis. Studies on commercially exploited fish have reported prevalences of Anisakis simplex ranging from 65-100% in wild Atlantic salmon and from 42-53.4% in Atlantic cod

The comparison of vestibular functions in hearing and hearing impaired populations

This study investigates possible vestibular dysfunctions in the deaf using a typical clinical assessment battery and discerns whether there is a trend between these disorders in meningitic children as compared to children with unknown origins of deafness.

The relationship between popular culture awareness and socialization in the deaf/hard of hearing and hearing populations

A sample of deaf/hard of hearing students and hearing students ages 11-14 were surveyed to examine social perceptions about intellect and popularity related to popular culture knowledge. Participants also provided descriptive responses to their popular culture favorites.

Promoting the health of marginalized populations in Ecuador through international collaboration and educational innovations

This paper examines two innovative educational initiatives for the Ecuadorian public health workforce: a Canadian-funded Masters programme in ecosystem approaches to health that focuses on building capacity to manage environmental health risks sustainably; and the training of Ecuadorians at the Latin American School of Medicine in Cuba (known as Escuela Latinoamericana de Medicina in Spanish). We apply a typology for analysing how training programmes address the needs of marginalized populations and build capacity for addressing health determinants. We highlight some ways we can learn from such training programmes with particular regard to lessons, barriers and opportunities for their sustainability at the local, national and international levels and for pursuing similar initiatives in other countries and contexts. We conclude that educational efforts focused on the challenges of marginalization and the determinants of health require explicit attention not only to the knowledge, attitudes and skills of graduates but also on effectively engaging the health settings and systems that will reinforce the establishment and retention of capacity in low- and middle-income settings where this is most needed.

Changes in heron and egret populations on the Laurentian Great Lakes and connecting channels, 1977-2009

Canadian and U.S. federal wildlife agencies completed four decadal surveys, spanning the years 1977 to 2009, to census colonial waterbirds breeding on the Great Lakes and adjoining bodies of water. In this paper, we reports abundance, distribution, and general population trends of three species: Black-crowned Night-Heron (Nycticorax nycticorax), Great Egret (Ardea alba), and Great Blue Heron (Ardea herodias). Estimates of nest numbers ranged from approximately 4000-6100 for the Black-crowned Night-Heron, 250-1900 for the Great Egret, and 3800-6400 for the Great Blue Heron. Average annual rates of change in nest numbers between the first (1977) and fourth (2008) census were −1% for the Black-crowned Night-Heron, +23% for the Great Egret, and −0.27% for the Great Blue Heron. Across the 30-year census, Black-crowned Night-Heron estimates decreased in U.S. (−57%) but increased (+18%) in Canadian waters, Great Egret nests increased 1381% in Canadian waters with a smaller, but still substantial increase in the number of nests at U.S. colonies (+613%), and Great Blue Heron numbers increased 148% in Canadian waters and 713% in U.S. waters. Although a single factor cannot be clearly linked to changes observed in each species’ distribution, hydrological variation, habitat succession, nest competition with Double-crested Cormorants (Phalacrocorax auritus), and land use changes likely all contributed. Management activities should support both breeding and foraging conditions including restoration of early successional habitats and anticipate continued northward expansions in the distributions of these waterbirds.

Accumulated metal speciation in earthworm populations with multi-generational exposure to metalliferous soils: cell fractionation and high energy synchrotron analyses

Predicting metal bioaccumulation and toxicity in soil organisms is complicated by site-specific biotic and abiotic parameters. In this study we exploited tissue fractionation and digestion techniques, combined with X-ray absorption spectroscopy (XAS), to investigate the whole-body and subcellular distributions, ligand affinities, and coordination chemistry of accumulated Pb and Zn in field populations of the epigeic earthworm Lumbricus rubellus inhabiting three contrasting metalliferous and two unpolluted soils. Our main findings were (i) earthworms were resident in soils with concentrations of Pb and Zn ranging from 1200 to 27 000 mg kg(-1) and 200 to 34 000 mg kg(-1), respectively; (ii) Pb and Zn primarily accumulated in the posterior alimentary canal in nonsoluble subcellular fractions of earthworms; (iii) site-specific differences in the tissue and subcellular partitioning profiles of populations were observed, with earthworms from a calcareous site partitioning proportionally more Pb to their anterior body segments and Zn to the chloragosome-rich subcellular fraction than their acidic-soil inhabiting counterparts; (iv) XAS indicated that the interpopulation differences in metal partitioning between organs were not accompanied by qualitative differences in ligand-binding speciation, because crystalline phosphate-containing pyromorphite was a predominant chemical species in the whole-worm tissues of all mine soil residents. Differences in metal (Pb, Zn) partitioning at both organ and cellular levels displayed by field populations with protracted histories of metal exposures may reflect their innate ecophysiological responses to essential edaphic variables, such as Ca2+ status. These observations are highly significant in the challenging exercise of interpreting holistic biomarker data delivered by "omic" technologies.

Comparison of subcellular partitioning, distribution, and internal speciation of Cu between Cu-tolerant and naive populations of Dendrodrilus rubidus Savigny

When considering contaminated site ecology and ecological risk assessment a key question is whether organisms that appear unaffected by accumulation of contaminants are tolerant or resistant to those contaminants. A population of Dendrodrilus rubidus Savigny earthworms from the Coniston Copper Mines, an area of former Cu mining, exhibit increased tolerance and accumulation of Cu relative to a nearby non-Cu exposed population. Distribution of total Cu between different body parts (posterior, anterior, body wall) of the two populations was determined after a 14 day exposure to 250 mg Cu kg(-1) in Cu-amended soil. Cu concentrations were greater in Coniston earthworms but relative proportions of Cu in different body parts were the same between populations. Cu speciation was determined using extended X-ray absorption fine structure spectroscopy (EXAFS). Cu was coordinated to 0 atoms in the exposure soil but to S atoms in the earthworms. There was no difference in this speciation between the different earthworm populations. In another experiment earthworms were exposed to a range of Cu concentrations (200-700 mg Cu kg(-1)). Subcellular partitioning of accumulated Cu was determined. Coniston earthworms accumulated more Cu but relative proportions of Cu in the different fractions (cytosol > granular > tissue fragments, cell membranes, and intact cells) were the same between populations. Results suggest that Coniston D. rubidus are able to survive in the Cu-rich Coniston Copper Mines soil through enlargement of the same Cu storage reservoirs that exist in a nearby non-Cu exposed population.