Social meets molecular: Combining phylogenetic and latent class analyses to understand HIV-1 transmission in Switzerland.

Switzerland has a complex human immunodeficiency virus (HIV) epidemic involving several populations. We examined transmission of HIV type 1 (HIV-1) in a national cohort study. Latent class analysis was used to identify socioeconomic and behavioral groups among 6,027 patients enrolled in the Swiss HIV Cohort Study between 2000 and 2011. Phylogenetic analysis of sequence data, available for 4,013 patients, was used to identify transmission clusters. Concordance between sociobehavioral groups and transmission clusters was assessed in correlation and multiple correspondence analyses. A total of 2,696 patients were infected with subtype B, 203 with subtype C, 196 with subtype A, and 733 with recombinant subtypes (mainly CRF02_AG and CRF01_AE). Latent class analysis identified 8 patient groups. Most transmission clusters of subtype B were shared between groups of gay men (groups 1-3) or between the heterosexual groups "heterosexual people of lower socioeconomic position" (group 4) and "injection drug users" (group 8). Clusters linking homosexual and heterosexual groups were associated with "older heterosexual and gay people on welfare" (group 5). "Migrant women in heterosexual partnerships" (group 6) and "heterosexual migrants on welfare" (group 7) shared non-B clusters with groups 4 and 5. Combining approaches from social and molecular epidemiology can provide insights into HIV-1 transmission and inform the design of prevention strategies.

Measures of fit in multiple correspondence analysis of crisp and fuzzy coded data

When continuous data are coded to categorical variables, two types of coding are possible: crisp coding in the form of indicator, or dummy, variables with values either 0 or 1; or fuzzy coding where each observation is transformed to a set of "degrees of membership" between 0 and 1, using co-called membership functions. It is well known that the correspondence analysis of crisp coded data, namely multiple correspondence analysis, yields principal inertias (eigenvalues) that considerably underestimate the quality of the solution in a low-dimensional space. Since the crisp data only code the categories to which each individual case belongs, an alternative measure of fit is simply to count how well these categories are predicted by the solution. Another approach is to consider multiple correspondence analysis equivalently as the analysis of the Burt matrix (i.e., the matrix of all two-way cross-tabulations of the categorical variables), and then perform a joint correspondence analysis to fit just the off-diagonal tables of the Burt matrix - the measure of fit is then computed as the quality of explaining these tables only. The correspondence analysis of fuzzy coded data, called "fuzzy multiple correspondence analysis", suffers from the same problem, albeit attenuated. Again, one can count how many correct predictions are made of the categories which have highest degree of membership. But here one can also defuzzify the results of the analysis to obtain estimated values of the original data, and then calculate a measure of fit in the familiar percentage form, thanks to the resultant orthogonal decomposition of variance. Furthermore, if one thinks of fuzzy multiple correspondence analysis as explaining the two-way associations between variables, a fuzzy Burt matrix can be computed and the same strategy as in the crisp case can be applied to analyse the off-diagonal part of this matrix. In this paper these alternative measures of fit are defined and applied to a data set of continuous meteorological variables, which are coded crisply and fuzzily into three categories. Measuring the fit is further discussed when the data set consists of a mixture of discrete and continuous variables.

Computation of multiple correspondence analysis, with code in R

The generalization of simple correspondence analysis, for two categorical variables, to multiple correspondence analysis where they may be three or more variables, is not straighforward, both from a mathematical and computational point of view. In this paper we detail the exact computational steps involved in performing a multiple correspondence analysis, including the special aspects of adjusting the principal inertias to correct the percentages of inertia, supplementary points and subset analysis. Furthermore, we give the algorithm for joint correspondence analysis where the cross-tabulations of all unique pairs of variables are analysed jointly. The code in the R language for every step of the computations is given, as well as the results of each computation.

Multiple correspondence analysis of a subset of response categories

In the analysis of multivariate categorical data, typically the analysis of questionnaire data, it is often advantageous, for substantive and technical reasons, to analyse a subset of response categories. In multiple correspondence analysis, where each category is coded as a column of an indicator matrix or row and column of Burt matrix, it is not correct to simply analyse the corresponding submatrix of data, since the whole geometric structure is different for the submatrix . A simple modification of the correspondence analysis algorithm allows the overall geometric structure of the complete data set to be retained while calculating the solution for the selected subset of points. This strategy is useful for analysing patterns of response amongst any subset of categories and relating these patterns to demographic factors, especially for studying patterns of particular responses such as missing and neutral responses. The methodology is illustrated using data from the International Social Survey Program on Family and Changing Gender Roles in 1994.

Perceptual mapping of practical ethics along the value chain: A multiple correspondence analysis with industry and cultural indices as supplementary variables

This paper presents findings from a study investigating a firm s ethical practices along the value chain. In so doing we attempt to better understand potential relationships between a firm s ethical stance with its customers and those of its suppliers within a supply chain and identify particular sectoral and cultural influences that might impinge on this. Drawing upon a database comprising of 667 industrial firms from 27 different countries, we found that ethical practices begin with the firm s relationship with its customers, the characteristics of which then influence the ethical stance with the firm s suppliers within the supply chain. Importantly, market structure along with some key cultural characteristics were also found to exert significant influence on the implementation of ethical policies in these firms.

A method for multiple sequential analyses of macrophage functions using a small single cell sample

Microbial pathogens such as bacillus Calmette-Guérin (BCG) induce the activation of macrophages. Activated macrophages can be characterized by the increased production of reactive oxygen and nitrogen metabolites, generated via NADPH oxidase and inducible nitric oxide synthase, respectively, and by the increased expression of major histocompatibility complex class II molecules (MHC II). Multiple microassays have been developed to measure these parameters. Usually each assay requires 2-5 x 10(5) cells per well. In some experimental conditions the number of cells is the limiting factor for the phenotypic characterization of macrophages. Here we describe a method whereby this limitation can be circumvented. Using a single 96-well microassay and a very small number of peritoneal cells obtained from C3H/HePas mice, containing as little as <=2 x 10(5) macrophages per well, we determined sequentially the oxidative burst (H2O2), nitric oxide production and MHC II (IAk) expression of BCG-activated macrophages. More specifically, with 100 µl of cell suspension it was possible to quantify H2O2 release and nitric oxide production after 1 and 48 h, respectively, and IAk expression after 48 h of cell culture. In addition, this microassay is easy to perform, highly reproducible and more economical.

Gene by environment QTL mapping through multiple trait analyses in blood pressure salt-sensitivity: identification of a novel QTL in rat chromosome 5

Background The genetic mechanisms underlying interindividual blood pressure variation reflect the complex interplay of both genetic and environmental variables. The current standard statistical methods for detecting genes involved in the regulation mechanisms of complex traits are based on univariate analysis. Few studies have focused on the search for and understanding of quantitative trait loci responsible for gene × environmental interactions or multiple trait analysis. Composite interval mapping has been extended to multiple traits and may be an interesting approach to such a problem. Methods We used multiple-trait analysis for quantitative trait locus mapping of loci having different effects on systolic blood pressure with NaCl exposure. Animals studied were 188 rats, the progenies of an F2 rat intercross between the hypertensive and normotensive strain, genotyped in 179 polymorphic markers across the rat genome. To accommodate the correlational structure from measurements taken in the same animals, we applied univariate and multivariate strategies for analyzing the data. Results We detected a new quantitative train locus on a region close to marker R589 in chromosome 5 of the rat genome, not previously identified through serial analysis of individual traits. In addition, we were able to justify analytically the parametric restrictions in terms of regression coefficients responsible for the gain in precision with the adopted analytical approach. Conclusion Future work should focus on fine mapping and the identification of the causative variant responsible for this quantitative trait locus signal. The multivariable strategy might be valuable in the study of genetic determinants of interindividual variation of antihypertensive drug effectiveness.

Social Meets Molecular: Combining Phylogenetic and Latent Class Analyses to Understand HIV-1 Transmission in Switzerland

Switzerland has a complex human immunodeficiency virus (HIV) epidemic involving several populations. We examined transmission of HIV type 1 (HIV-1) in a national cohort study. Latent class analysis was used to identify socioeconomic and behavioral groups among 6,027 patients enrolled in the Swiss HIV Cohort Study between 2000 and 2011. Phylogenetic analysis of sequence data, available for 4,013 patients, was used to identify transmission clusters. Concordance between sociobehavioral groups and transmission clusters was assessed in correlation and multiple correspondence analyses. A total of 2,696 patients were infected with subtype B, 203 with subtype C, 196 with subtype A, and 733 with recombinant subtypes (mainly CRF02_AG and CRF01_AE). Latent class analysis identified 8 patient groups. Most transmission clusters of subtype B were shared between groups of gay men (groups 1-3) or between the heterosexual groups "heterosexual people of lower socioeconomic position" (group 4) and "injection drug users" (group 8). Clusters linking homosexual and heterosexual groups were associated with "older heterosexual and gay people on welfare" (group 5). "Migrant women in heterosexual partnerships" (group 6) and "heterosexual migrants on welfare" (group 7) shared non-B clusters with groups 4 and 5. Combining approaches from social and molecular epidemiology can provide insights into HIV-1 transmission and inform the design of prevention strategies.

A aprendizagem de conceitos estatísticos numa amostra de alunos do ensino secundário - análise univariada e multivariada

Trabalho de projecto apresentado como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Physiotherapy practice in the private sector: organizational characteristics and models.

BACKGROUND: Even if a large proportion of physiotherapists work in the private sector worldwide, very little is known of the organizations within which they practice. Such knowledge is important to help understand contexts of practice and how they influence the quality of services and patient outcomes. The purpose of this study was to: 1) describe characteristics of organizations where physiotherapists practice in the private sector, and 2) explore the existence of a taxonomy of organizational models. METHODS: This was a cross-sectional quantitative survey of 236 randomly-selected physiotherapists. Participants completed a purpose-designed questionnaire online or by telephone, covering organizational vision, resources, structures and practices. Organizational characteristics were analyzed descriptively, while organizational models were identified by multiple correspondence analyses. RESULTS: Most organizations were for-profit (93.2%), located in urban areas (91.5%), and within buildings containing multiple businesses/organizations (76.7%). The majority included multiple providers (89.8%) from diverse professions, mainly physiotherapy assistants (68.7%), massage therapists (67.3%) and osteopaths (50.2%). Four organizational models were identified: 1) solo practice, 2) middle-scale multiprovider, 3) large-scale multiprovider and 4) mixed. CONCLUSIONS: The results of this study provide a detailed description of the organizations where physiotherapists practice, and highlight the importance of human resources in differentiating organizational models. Further research examining the influences of these organizational characteristics and models on outcomes such as physiotherapists' professional practices and patient outcomes are needed.

Dynamic patterns of flow in the workplace: characterizing within-individual variability using a complexity science approach

As a result of the growing interest in studying employee well-being as a complex process that portrays high levels of within-individual variability and evolves over time, this present study considers the experience of flow in the workplace from a nonlinear dynamical systems approach. Our goal is to offer new ways to move the study of employee well-being beyond linear approaches. With nonlinear dynamical systems theory as the backdrop, we conducted a longitudinal study using the experience sampling method and qualitative semi-structured interviews for data collection; 6981 registers of data were collected from a sample of 60 employees. The obtained time series were analyzed using various techniques derived from the nonlinear dynamical systems theory (i.e., recurrence analysis and surrogate data) and multiple correspondence analyses. The results revealed the following: 1) flow in the workplace presents a high degree of within-individual variability; this variability is characterized as chaotic for most of the cases (75%); 2) high levels of flow are associated with chaos; and 3) different dimensions of the flow experience (e.g., merging of action and awareness) as well as individual (e.g., age) and job characteristics (e.g., job tenure) are associated with the emergence of different dynamic patterns (chaotic, linear and random).

La pratique médicale des omnipraticiens : influence des contextes organisationnel et géographique

L’utilisation des services de santé est au centre de l’organisation des soins. La compréhension des processus qui déterminent cette utilisation est essentielle pour agir sur le système de santé et faire en sorte qu’il réponde mieux aux besoins de la population. L’objectif de cette thèse est de comprendre le phénomène complexe qu’est l’utilisation des services de santé en s’intéressant à la pratique des médecins omnipraticiens. En nous appuyant sur le cadre théorique de Donabedian, nous décomposons les déterminants de l’utilisation des services de santé en trois niveaux : le niveau individuel, le niveau organisationnel, et le niveau environnemental. Pour tenir compte de la complexité des phénomènes de cette étude nous proposons de nous appuyer sur l’approche configurationnelle. Notre question de recherche est la suivante : dans quelle mesure le mode d’exercice des omnipraticiens influence-t-il la prestation des services et comment l’environnement géographique et la patientèle modulent-ils cette relation ? Nous avons utilisé des bases de données jumelées du Collège des médecins du Québec, de la Régie d’assurance maladie du Québec et de la banque de données iCLSC. Notre échantillon est constitué des médecins omnipraticiens de l’année 2002, ayant satisfait aux critères d’inclusion, ce qui représente près de 70% de la population totale. Des analyses de correspondances multiples et des classifications ascendantes hiérarchiques ont été utilisées pour réaliser la taxonomie des modes d’exercice et des contextes géographiques. Nous avons construit des indicateurs d’utilisation des services de santé pour apprécier la continuité, la globalité, l’accessibilité et la productivité. Ces indicateurs ont été validés en les comparant à ceux d’une enquête populationnelle. Nous présentons tout d’abord les modes d’exercice des médecins qui sont au nombre de sept. Deux modes d’exercice à lieu unique ont émergé : le mode d’exercice en cabinet privé d'une part, caractérisé par des niveaux de continuité et productivité élevés, le mode d’exercice en CLSC d'autre part présentant un niveau de productivité faible et des niveaux de globalité et d'accessibilité légèrement au-dessus de la moyenne. Dans les cinq autres modes d’exercice, les médecins exercent leur pratique dans une configuration de lieux. Deux modes d’exercice multi-institutionnel réunissent des médecins qui partagent leur temps entre les urgences, les centres hospitaliers et le cabinet privé ou le CLSC. Les médecins de ces deux groupes présentent des niveaux d’accessibilité et de productivité très élevés. Le mode d’exercice le moins actif réunit des médecins travaillant en cabinet privé et en CHLSD. Leur niveau d’activité est inférieur à la moyenne. Ils sont caractérisés par un niveau de continuité très élevé. Le mode d’exercice ambulatoire regroupe des médecins qui partagent leur pratique entre le CLSC, le cabinet privé et le CHLSD. Ces médecins présentent des résultats faibles sur tous les indicateurs. Finalement le mode d’exercice hospitaliste réunit des médecins dont la majorité de la pratique s’exerce en milieu hospitalier avec une petite composante en cabinet privé. Dans ce mode d’exercice tous les indicateurs sont faibles. Les analyses ont mis en évidence quatre groupes de territoires de CSSS : les ruraux, les semi-urbains, les urbains et les métropolitains. La prévalence des modes d’exercice varie selon les contextes. En milieu rural, le multi-institutionnel attire près d’un tiers des médecins. En milieu semi-urbain, les médecins se retrouvent de façon plus prédominante dans les modes d’exercice ayant une composante CLSC. En milieu urbain, les modes d’exercice ayant une composante cabinet privé attirent plus de médecins. En milieu métropolitain, les modes d’exercice moins actif et hospitaliste attirent près de 40% des médecins. Les omnipraticiens se répartissent presque également dans les autres modes d’exercice. Les niveaux des indicateurs varient en fonction de l’environnement géographique. Ainsi l’accessibilité augmente avec le niveau de ruralité. De façon inverse, la productivité augmente avec le niveau d’urbanité. La continuité des soins est plus élevée en régions métropolitaines et rurales. La globalité varie peu d’un contexte à l’autre. Pour pallier à la carence de l’analyse partielle de l’organisation de la pratique des médecins dans la littérature, nous avons créé le concept de mode d’exercice comme la configuration de lieux professionnels de pratique propre à chaque médecin. A notre connaissance, il n’existe pas dans la littérature, d’étude qui ait analysé simultanément quatre indicateurs de l’utilisation des services pour évaluer la prestation des services médicaux, comme nous l’avons fait. Les résultats de nos analyses montrent qu’il existe une différence dans la prestation des services selon le mode d’exercice. Certains des résultats trouvés sont documentés dans la littérature et plus particulièrement quand il s’agit de mode d’exercice à lieu unique. La continuité et la globalité des soins semblent évoluer dans le même sens. De même, la productivité et l’accessibilité sont corrélées positivement. Cependant il existe une tension, entre les premiers indicateurs et les seconds. Seuls les modes d’exercice à lieu unique déjouent l’arbitrage entre les indicateurs, énoncé dans l’état des connaissances. Aucun mode d’exercice ne présente de niveaux élevés pour les quatre indicateurs. Il est donc nécessaire de travailler sur des combinaisons de modes d’exercice, sur des territoires, afin d’offrir à la population les services nécessaires pour l’atteinte concomitante des quatre objectifs de prestation des services. Les modes d’exercice émergents (qui attirent les jeunes médecins) et les modes d’exercice en voie de disparition (où la prévalence des médecins les plus âgés est la plus grande) sont préoccupants. A noter que les modes d’exercice amenés à disparaître répondent mieux aux besoins de santé de la population que les modes d’exercice émergents, au regard de tous nos indicateurs. En conclusion, cette thèse présente trois contributions théoriques et trois contributions méthodologiques. Les implications pour les recherches futures et la décision indiquent que, si aucune mesure n’est mise en place pour renverser la tendance, le Québec risque de vivre des pénuries dans la prestation des services en termes de continuité, globalité et accessibilité.

Factores asociados a mortalidad en pacientes colombianos con enfermedades autoinmunes en la unidad de cuidado intensivo, de un hospital de tercer nivel en Bogotá Colombia

Antecedentes: El interés en las enfermedades autoinmunes (EA) y su desenlace en la unidad de cuidado intensivo (UCI) han incrementado debido al reto clínico que suponen para el diagnóstico y manejo, debido a que la mortalidad en UCI fluctúa entre el 17 – 55 %. El siguiente trabajo representa la experiencia de un año de nuestro grupo en un hospital de tercer nivel. Objetivo: Identificar factores asociados a mortalidad particulares de los pacientes con enfermedades autoinmunes que ingresan a una UCI, de un hospital de tercer nivel en Bogotá, Colombia. Métodos: El uso de análisis de componentes principales basado en el método descriptivo multivariado y análisis de múltiple correspondencia fue realizado para agrupar varias variables relacionadas con asociación significativa y contexto clínico común. Resultados: Cincuenta pacientes adultos con EA con una edad promedio de 46,7 ± 17,55 años fueron evaluados. Los dos diagnósticos más comunes fueron lupus eritematoso sistémico y esclerosis sistémica, con una frecuencia de 45% y 20% de los pacientes respectivamente. La principal causa de admisión en la UCI fue la infección seguido de actividad aguda de la EA, 36% y 24% respectivamente. La mortalidad durante la estancia en UCI fue del 24%. El tiempo de hospitalización antes de la admisión a la UCI, el choque, soporte vasopresor, ventilación mecánica, sepsis abdominal, Glasgow bajo y plasmaféresis fueron factores asociados con mortalidad. Dos fenotipos de variables fueron definidos relacionadas con tiempo en la UCI y medidas de soporte en UCI, las cuales fueron asociadas supervivencia y mortalidad. Conclusiones: La identificación de factores individuales y grupos de factores por medio del análisis de componentes principales permitirá la implementación de medidas terapéutica de manera temprana y agresiva en pacientes con EA en la UCI para evitar desenlaces fatales.