Use of posterior predictive assessments to evaluate model fit in multilevel logistic regression

Assessing the fit of a model is an important final step in any statistical analysis, but this is not straightforward when complex discrete response models are used. Cross validation and posterior predictions have been suggested as methods to aid model criticism. In this paper a comparison is made between four methods of model predictive assessment in the context of a three level logistic regression model for clinical mastitis in dairy cattle; cross validation, a prediction using the full posterior predictive distribution and two “mixed” predictive methods that incorporate higher level random effects simulated from the underlying model distribution. Cross validation is considered a gold standard method but is computationally intensive and thus a comparison is made between posterior predictive assessments and cross validation. The analyses revealed that mixed prediction methods produced results close to cross validation whilst the full posterior predictive assessment gave predictions that were over-optimistic (closer to the observed disease rates) compared with cross validation. A mixed prediction method that simulated random effects from both higher levels was best at identifying the outlying level two (farm-year) units of interest. It is concluded that this mixed prediction method, simulating random effects from both higher levels, is straightforward and may be of value in model criticism of multilevel logistic regression, a technique commonly used for animal health data with a hierarchical structure.

Anopheles darlingi polytene chromosomes: revised maps including newly described inversions and evidence for population structure in Manaus

Salivary gland polytene chromosomes of 4th instar Anopheles darlingi Root were examined from multiple locations in the Brazilian Amazon. Minor modifications were made to existing polytene photomaps. These included changes to the breakpoint positions of several previously described paracentric inversions and descriptions of four new paracentric inversions, two on the right arm of chromosome 3 and two on the left arm of chromosome 3 that were found in multiple locations. A total of 18 inversions on the X (n = 1) chromosome, chromosome 2 (n = 7) and 3 (n = 11) were scored for 83 individuals from Manaus, Macapá and Porto Velho municipalities. The frequency of 2Ra inversion karyotypes in Manaus shows significant deficiency of heterozygotes (p < 0.0009). No significant linkage disequilibrium was found between inversions on chromosome 2 and 3. We hypothesize that at least two sympatric subpopulations exist within the An. darlingi population at Manaus based on inversion frequencies.

Design of bicycling suitability maps for hilly cities

Post-print version. Pictures and tables separated from main text and presented at the end.

Studies of MHC class I antigen presentation & the origins of the immunopeptidome

La présentation d'antigène par les molécules d'histocompatibilité majeure de classe I (CMHI) permet au système immunitaire adaptatif de détecter et éliminer les agents pathogènes intracellulaires et des cellules anormales. La surveillance immunitaire est effectuée par les lymphocytes T CD8 qui interagissent avec le répertoire de peptides associés au CMHI présentés à la surface de toutes cellules nucléées. Les principaux gènes humains de CMHI, HLA-A et HLA-B, sont très polymorphes et par conséquent montrent des différences dans la présentation des antigènes. Nous avons étudié les différences qualitatives et quantitatives dans l'expression et la liaison peptidique de plusieurs allotypes HLA. Utilisant la technique de cytométrie de flux quantitative nous avons établi une hiérarchie d'expression pour les quatre HLA-A, B allotypes enquête. Nos résultats sont compatibles avec une corrélation inverse entre l'expression allotypique et la diversité des peptides bien que d'autres études soient nécessaires pour consolider cette hypothèse. Les origines mondiales du répertoire de peptides associés au CMHI restent une question centrale à la fois fondamentalement et dans la recherche de cibles immunothérapeutiques. Utilisant des techniques protéogénomiques, nous avons identifié et analysé 25,172 peptides CMHI isolées à partir des lymphocytes B de 18 personnes qui exprime collectivement 27 allotypes HLA-A,B. Alors que 58% des gènes ont été la source de 1-64 peptides CMHI par gène, 42% des gènes ne sont pas représentés dans l'immunopeptidome. Dans l'ensemble, l’immunopeptidome présenté par 27 allotypes HLA-A,B ne couvrent que 17% des séquences exomiques exprimées dans les cellules des sujets. Nous avons identifié plusieurs caractéristiques des transcrits et des protéines qui améliorent la production des peptides CMHI. Avec ces données, nous avons construit un modèle de régression logistique qui prédit avec une grande précision si un gène de notre ensemble de données ou à partir d'ensembles de données indépendants génèrerait des peptides CMHI. Nos résultats montrent la sélection préférentielle des peptides CMHI à partir d'un répertoire limité de produits de gènes avec des caractéristiques distinctes. L'idée que le système immunitaire peut surveiller des peptides CMHI couvrant seulement une fraction du génome codant des protéines a des implications profondes dans l'auto-immunité et l'immunologie du cancer.

AN ASSESSMENT OF FLOW REGIME MAPS AND A NUMERICAL HEAT TRANSFER CORRELATION FOR THE STRATIFIED/ANNULAR REGIME OF SHEAR-DRIVEN INTERNAL CONDENSING FLOWS

Several modern-day cooling applications require the incorporation of mini/micro-channel shear-driven flow condensers. There are several design challenges that need to be overcome in order to meet those requirements. The difficulty in developing effective design tools for shear-driven flow condensers is exacerbated due to the lack of a bridge between the physics-based modelling of condensing flows and the current, popular approach based on semi-empirical heat transfer correlations. One of the primary contributors of this disconnect is a lack of understanding caused by the fact that typical heat transfer correlations eliminate the dependence of the heat transfer coefficient on the method of cooling employed on the condenser surface when it may very well not be the case. This is in direct contrast to direct physics-based modeling approaches where the thermal boundary conditions have a direct and huge impact on the heat transfer coefficient values. Typical heat transfer correlations instead introduce vapor quality as one of the variables on which the value of the heat transfer coefficient depends. This study shows how, under certain conditions, a heat transfer correlation from direct physics-based modeling can be equivalent to typical engineering heat transfer correlations without making the same apriori assumptions. Another huge factor that raises doubts on the validity of the heat-transfer correlations is the opacity associated with the application of flow regime maps for internal condensing flows. It is well known that flow regimes influence heat transfer rates strongly. However, several heat transfer correlations ignore flow regimes entirely and present a single heat transfer correlation for all flow regimes. This is believed to be inaccurate since one would expect significant differences in the heat transfer correlations for different flow regimes. Several other studies present a heat transfer correlation for a particular flow regime - however, they ignore the method by which extents of the flow regime is established. This thesis provides a definitive answer (in the context of stratified/annular flows) to: (i) whether a heat transfer correlation can always be independent of the thermal boundary condition and represented as a function of vapor quality, and (ii) whether a heat transfer correlation can be independently obtained for a flow regime without knowing the flow regime boundary (even if the flow regime boundary is represented through a separate and independent correlation). To obtain the results required to arrive at an answer to these questions, this study uses two numerical simulation tools - the approximate but highly efficient Quasi-1D simulation tool and the exact but more expensive 2D Steady Simulation tool. Using these tools and the approximate values of flow regime transitions, a deeper understanding of the current state of knowledge in flow regime maps and heat transfer correlations in shear-driven internal condensing flows is obtained. The ideas presented here can be extended for other flow regimes of shear-driven flows as well. Analogous correlations can also be obtained for internal condensers in the gravity-driven and mixed-driven configuration.