Includes bibliographical references / Many large, sparsely distributed raptors are threatened by a host of anthropogenic factors, while a minority may actually benefit from some aspects of development and environmental change. Clarity on the size and trajectory of such populations is essential for effective conservation management, but can be difficult to achieve. One solution is to use multivariate habitat association models to derive critical estimates of distribution and abundance. The South African population of Martial Eagle Polemaetus bellicosus is currently estimated at < 800 adult birds , with the bulk of the known population believed to be residing in the larger protected areas. However, Martial Eagles also build nests on pylons that support high voltage transmission lines running through the largely treeless, semiarid landscapes of the Karoo. The main aim of this study was to develop a better understanding of the environmental factors that influence Martial Eagle territory densities and locations along South African transmission lines, and thereby estimate the size of this population and its relative importance to the national conservation status of this globally threatened species. I used habitat association models to d escribe Martial Eagle territory density in relation to eight environmental covariates. Models were first fitted to eagle territory data for the central Karoo regions, collected and pooled over the period 2002 - 2006, and then applied to predict the number of pairs present on each of three adjacent sections of unsurveyed line (northern, southern and eastern lines) . Once these model predictions were verified by a series of aerial and ground surveys, I fitted the models to all the known Martial Eagle territory records for the transmission network and extrapolated from these back to the rest of the network using the fitted relationships. Ultimately, the models predicted 52 additional Martial Eagle territories on the remaining transmission network with a confidence interval ranging from 38 to 67 (based on models that explained up to 39 % of the total variance in terms of only two explanatory terms – rainfall and the proportion of cultivated land). I then examined the role of territoriality and social structure in the eagle population in determining the location and dispersion of pylon nests. To do this I used the location of active nests from the original central Karoo data and a similar number of randomly selected points. I then asked whether I could predict the nest locations from each of the eight environmental covariates and distance to its nearest conspecific active nest or its nearest nest of any other large eagle species. Using a logistic generalised linear model with regression splines for distance to nearest other nest, I found that Martial Eagles strongly avoid proximity to conspecific nests (mean distance to conspecific nest = 28.2 km, range 2.5 - 167.1 km, n = 306). This result shows that minimum spacing should be considered in predicting the distribution of eagles on unsurveyed transmission lines. Lastly, I further investigated the geographical extent of pylon nesting in South African Martial Eagles, with particular focus on variation in the frequency of this behaviour in relation to biome - scale variation in the availability of trees as natural nest sites. To do this, I related Martial Eagle reporting rates generated by citizen - science bird atlas data to the density of transmission lines and biome types across South Africa. While these analyses yielded some suggestive results, such as significant positive and negative relationships between reporting rates and line density in the Desert (P = 0.02) versus the Savanna (P < 0.001) biomes respectively, data sparseness in arid areas and a generally low detection probability limited the conclusiveness of these results. The refined habitat association models developed in this study predict that the South African transmission grid supports 130 - 159 breeding pairs of Martial Eagle. This figure has never been estimated or calculated before, and suggests that 36 % of the national breeding population could reside largely in the commercial ranchland and nest on man - made structures. This result, which is at odds with the generally held belief that the Martial Eagle is increasingly confined to large protected areas, has significant implications for the thinking around the conservation management of this globally threatened species.

In Sweden, reporting is voluntary for most common felled game, and the number of voluntary reports can vary between hunting teams, HMP, and counties. In 2020, an improved harvest estimation model was developed, which reduced the sensitivity to low reporting. However, there were still some limits to the model, where large, credible intervals were estimated. Therefore, additional variables were considered as the model does not take into account landcover among HMPs, [2] the impact of climate, [4] wildlife accidents, and [4] geographical distribution, creating the covariate model. This study aimed to compare the new model with the covariate model to see if covariates would reduce the large, credible intervals. Two hypothesis tests were performed: evaluation of predictive performance using leave one out cross-validation and evaluation of the 95 % credible interval. Evaluation of predictive performance was performed by examining the difference in expected log-pointwise predictive density (ELPD) and standard error (SE) for each species and model. The results show that the covariates model ranked highest for all ten species, and out of the ten species, six had an (ELPD) difference of two to four, which implies that there is support that the covariate model will be a better predictor for other datasets than this one. At least one covariate had an apparent effect on harvest estimates for nine out of ten species. Finally, the covariate model reduced the large uncertainties, which was an improvement of the null model, indicating that harvest estimates can be improved by taking covariates into account.

No description available.

The goal of genetic-based cancer research is often to identify which genes behave differently in cancerous and healthy tissue. This difference in behavior, referred to as differential expression, may lead researchers to more targeted preventative care and treatment. One way to measure the expression of genes is though a process called RNA-Seq, that takes physical tissue samples and maps gene products and fragments in the sample back to the gene that created it, resulting in a large read-count matrix with genes in the rows and a column for each sample. The read-counts for tumor and normal samples are then compared in a process called differential expression analysis. However, normalization of these read-counts is a necessary pre-processing step, in order to account for differences in the read-count values due to non-expression related variables. It is common in recent RNA-Seq normalization methods to also account for gene-level covariates, namely gene length in base pairs and GC-content, the proportion of bases in the gene that are Guanine and Cytosine. Here a colorectal cancer RNA-Seq read-count data set comprised of 30,220 genes and 378 samples is examined. Two of the normalization methods that account for gene length and GC-content, CQN and EDASeq, are extended to account for protein coding status as a third gene-level covariate. The binary nature of protein coding status results in unique computation issues. The results of using the normalized read counts from CQN, EDASeq, and four new normalization methods are used for differential expression analysis via the nonparametric Wilcoxon Rank-Sum Test as well as the lme4 pipeline that produces per-gene models based on a negative binomial distribution. The resulting differential expression results are compared for two genes of interest in colorectal cancer, APC and CTNNB1, both of the WNT signaling pathway.

No description available.

No description available.

<p>In diagnostic accuracy studies, sensitivity and specificity are the most common measures to assess the performance of diagnostic or screening tests. The estimation of these measures can be done using empirical or model-based methods. The primary objective of this thesis is to use both the empirical and the model-based (logistic regression) approach to assess the effects of covariates on the performance of the visual inspection with acetic acid (VIA) and lugol iodine (VILI) tests using the data from women screened for cervical cancer in Kinshasa, the Democratic Republic of Congo. The secondary objectives are: first, to adjust for the false negative and false positive error rates by the two tests through latent class models (LCM), and second, to evaluate the effects of covariates on the agreement between the measurements of the two tests taken by nurse and physician through Kappa statistic.</p> <p>No particular pattern could be observed in the trend of empirically estimated sensitivity and specificity of the VIA and VILI tests measured by the nurse and by the physician across age and parity categories. From the logistic regression models, both age, parity, and their respective quadratic terms have significant effects on the probability of VIA and VILI tests to detect cervical cancer. However, there is no significant effect of marital status, smoking, and hybrid capture2 (HPV DNA) on the probability of VIA and VILI tests measured by nurse to detect cervical cancer while HPV DNA does in the probability of VIA and VILI tests measured by physician to detect cervical cancer. The trend of the estimated sensitivity of VIA and VILI tests measured by the nurse is not different across age groups but the specificity does vary. The trend of both the sensitivity and specificity of VIA and VILI tests are significantly different across parity groups. The reverse is the case for the sensitivity and specificity of VIA and VILI tests measured by physician across age and parity groups. The false negative and false positive error rates in the sensitivity and specificity of VIA and VILI tests measured by nurse are higher compared to that of physician. With Kappa statistic results, there is almost perfect agreement between the ratings by the nurse and physician for the dichotomized VIA and VILI test outcomes.</p> <p>In conclusion, there is a significant effects of age, parity and the quadratic term of age on the performance of VIA and VILI tests outcomes measured by nurse. On the VIA and VILI test outcomes measured by physician, age, parity, HPV DNA and quadratic term of age have shown significant effects on the performance of VIA and VILI tests outcomes measured by physician alone.</p> / Master of Science (MSc)

This study examined longitudinal changes in coping and defense mechanisms in an age- and gender-stratified sample of 392 European-American adults. Nonlinear age-related changes were found for the coping mechanisms of sublimation and suppression and the defense mechanisms of intellectualization, doubt, displacement, and regression. The change trajectories for sublimation and suppression showed that their use increased from adolescence to late middle age and early old age, and remained mostly stable into late old age. The change trajectory for intellectualization showed that the use of this defense mechanism increased from adolescence to middle age, remained stable until late midlife, and started to decline thereafter. The defense mechanisms of doubt, displacement, and regression showed decreases from adolescence until early old age, with increases occurring again after the age of 65. Linear age-related decreases were found for the coping mechanism of ego regression and the defense mechanisms of isolation and rationalization. Gender and socioeconomic status were associated with the mean levels of several coping and defense mechanisms, but did not moderate age-related changes. Increases in ego level were associated with increased use of the defense mechanism intellectualization and decreased use of the defense mechanisms of doubt and displacement. Overall, these findings in a European-American sample suggest that most individuals showed development in the direction of more adaptive and less maladaptive coping and defense strategies from adolescence until late middle age or early old age. However, in late old age this development was reversed, presenting potential challenges to the adaptive capacity of older adults.

In public health, biomedical, epidemiological, and other applications, data collected are often measured with error. When mismeasured data is used in a regression analysis, not accounting for the measurement error can lead to incorrect inference about the relationships between the covariates and the response. We investigate measurement error in the covariates of two types of regression models.  For each we propose a fully Bayesian approach that treats the variable measured with error as a latent variable to be integrated over, and a semi-Bayesian approach which uses a first order Laplace approximation to marginalize the variable measured with error out of the likelihood. The first model is the matched case-control study for analyzing clustered binary outcomes. We develop low-rank thin plate splines for the case where a variable measured with error has an unknown, nonlinear relationship with the response. In addition to the semi- and fully Bayesian approaches, we propose another using expectation-maximization to detect both parametric and nonparametric relationships between the covariates and the binary outcome. We assess the performance of each method via simulation terms of mean squared error and mean bias. We illustrate each method on a perturbed example of 1--4 matched case-control study. The second regression model is the generalized linear model (GLM) with unknown link function. Usually, the link function is chosen by the user based on the distribution of the response variable, often to be the canonical link. However, when covariates are measured with error, incorrect inference as a result of the error can be compounded by incorrect choice of link function. We assess performance via simulation of the semi- and fully Bayesian methods in terms of mean squared error. We illustrate each method on the Framingham Heart Study dataset. The simulation results for both regression models support that the fully Bayesian approach is at least as good as the semi-Bayesian approach for adjusting for measurement error, particularly when the distribution of the variable of measure with error and the distribution of the measurement error are misspecified. / Ph. D.

La variabilité des concentrations plasmatiques mesurées lors d’une anesthésie générale avec le propofol est directement reliée à une variabilité inter-animale, sa pharmacocinétique. L’objectif de cette étude est de caractériser la pharmacocinétique du propofol et de rechercher les effets des caractéristiques démographiques sur la variation des paramètres pharmacocinétiques. Les chiens (n=44) ayant participé à cette étude ont été anesthésiés au propofol à 6 mois (n=29), 12 (n=21) mois et/ou 24 mois (n=35). L’anesthésie a été induite avec du propofol (en moyenne 5 mg) et maintenue avec une perfusion (débit initial de 360 mg/kg/h). Des ajustements de perfusion ainsi que des bolus supplémentaires seront administrés si le comportement de l’animal l’exige. Une randomisation stratifiée des sexes aux deux groupes de prémédication, le premier recevant de l’acépropmazine (0,05 mg/kg en I.M.) et le deuxième une association d’acépromazine (0.05 mg/kg IM) et de butorphanol (0.1mg/kg IM). Des échantillons sanguins ont été prélevés de t=0 jusqu'à t=300 minutes ou plus. Au total 1339 prélèvements ont été analysés. Un modèle mamillaire à 3 compartiments décrit de manière adéquate nos données. Les valeurs moyennes de CLt V1, CL2, V2, CL3 and V3 sont respectivement égales à 0.65 L/min (SD=0.24), 2.6 L (SD=2.04), 2.24 L/min (1.43), 9.6 L (SD=7.49), 0.42 L/min (SD=0.199), 46.4 L (SD=40.6). Les paramètres pharmacocinétiques obtenus ont révélé une grande variabilité interindividuelle, en particulier CL2, V1, V2 et V3 .Le poids est une co-variable significative pour CLt et V2. L’âge est une co-variable significative pour CL3 et V3. L’ajout de la parenté pour V2 et V3 au modèle a amélioré la qualité de l’ajustement du modèle. Les paramètres V1 et CL2 sont indépendants des facteurs physiologiques étudiés. / The variability of plasma concentrations measured during general anesthesia with propofol is directly related to inter-animal variability of its pharmacokinetics. The objective of this study was to characterize the pharmacokinetics of propofol and to investigate the effects of demographic variables on the pharmacokinetic parameters. Dogs (n = 44) that participated in this study were anesthetized with propofol at 6 months (n = 29), 12 (n = 21) and/or 24 months (n = 35). Anesthesia was induced with propofol (average dose of 5 mg) and maintained with an infusion (initial rate of 360 mg/kg/h). Infusion adjustment and bolus doses were performed if required by the behavior of the animal . A stratified randomization of both sexes on two premedications groups [acepropmazine (0.05 mg /kg I.M) or Acepropmazine (0.05 mg /kg I.M) and butorphanol (0.1 mg /kg IM)]. Blood samples were collected from t = 0 to t = 300 minutes or more. A total of 1339 samples were analyzed. A 3-compartment mamillary model showed good predictive performances. The average values of CLt V1, CL2, V2, CL3 and V3 were 0.65 L/min (SD=0.24), 2.6 L (SD=2.04), 2.24 L/min (1.43), 9.6 L (SD=7.49), 0.42 L/min (SD=0.199), 46.4 L (SD=40.6) respectively. The pharmacokinetic parameters obtained showed a large inter-individual variability, in particular CL2, V1, V2 and V3. Adding to the model the covariates weight to CLt and V2, age to CL3 and V3, and kinship to V2 and V3 to the model to improved the performance and the quality of adjustment. Therefore, V1 and CL2 are constant parameters in this population.