Genetic determinants of clinical heterogeneity in sickle cell disease

L’anémie falciforme est une maladie monogénique causée par une mutation dans le locus de la β-globine. Malgré le fait que l’anémie falciforme soit une maladie monogénique, cette maladie présente une grande hétérogénéité clinique. On présume que des facteurs environnementaux et génétiques contribuent à cette hétérogénéité. Il a été observé qu’un haut taux d’hémoglobine fœtale (HbF) diminuait la sévérité et la mortalité des patients atteints de l’anémie falciforme. Le but de mon projet était d’identifier des variations génétiques modifiant la sévérité clinique de l’anémie falciforme. Dans un premier temps, nous avons effectué la cartographie-fine de trois régions précédemment associées avec le taux d’hémoglobine fœtale. Nous avons ensuite effectué des études d’association pan-génomiques avec deux complications cliniques de l’anémie falciforme ainsi qu’avec le taux d’hémoglobine fœtale. Hormis les régions déjà identifiées comme étant associées au taux d’hémoglobine fœtale, aucun locus n’a atteint le niveau significatif de la puce de génotypage. Pour identifier des groupes de gènes modérément associés au taux d’hémoglobine fœtale qui seraient impliqués dans de mêmes voies biologiques, nous avons effectué une étude des processus biologiques. Finalement, nous avons effectué l’analyse de 19 exomes de patients Jamaïcains ayant des complications cliniques mineures de l’anémie falciforme. Compte tenu de la taille des cohortes de réplication disponibles, nous n’avons pas les moyens de valider statistiquement les variations identifiées par notre étude. Cependant, nos résultats fournissent de bons gènes candidats pour des études fonctionnelles et pour les réplications futures. Nos résultats suggèrent aussi que le β-hydroxybutyrate en concentration endogène pourraient influencer le taux d’hémoglobine fœtale. De plus, nous montrons que la cartographie-fine des régions associées par des études pan-génomiques peut identifier des signaux d’association additionnels et augmenter la variation héritable expliquée par cette région.

Éducation alimentaire, nutritionnelle et sensorielle combinée au jardinage chez les jeunes : rôle des animateurs non professionnels de la nutrition

Les programmes éducatifs de jardinage alimentaire avec les jeunes offrent l’opportunité d’agir sur leurs connaissances nutritionnelles, préférences pour des légumes, sentiment d'efficacité personnelle à consommer des fruits et légumes, envie d'y goûter et leur consommation. Dans ces activités, certains obstacles peuvent freiner l'éducation alimentaire et nutritionnelle faite par des animateurs qui ne sont pas professionnels de la nutrition ou de la santé. Le présent projet consistait à développer un volet alimentaire et nutritionnel éducatif pour les "Jardins-jeunes" (JJ), un camp d'été en jardinage du Jardin botanique de Montréal, à offrir une courte formation en nutrition à ses animatrices, puis à évaluer leurs niveaux d'intérêt et de confiance personnelle à intégrer ce volet à l'édition 2013. Les méthodes d'évaluation auprès des animatrices comprenaient des entrevues de groupe, des questionnaires et une observation-terrain. La taille d'échantillon permettait uniquement une analyse qualitative des résultats. La formation semble avoir maintenu ou élevé les niveaux de confiance et de connaissances des animatrices sur plusieurs sujets alimentaires et nutritionnels. Les animatrices évoquent que les trois activités de trente minutes en alimentation et nutrition, intégrées aux JJ 2013, auraient favorisé l'éducation nutritionnelle, qui par ailleurs, fut limitée par manque de temps. Elles rapportent avoir perçu des effets positifs du programme sur les connaissances, attitudes et comportements alimentaires des jeunes. Nos résultats suggèrent qu'un volet d’éducation alimentaire et nutritionnelle peut être intégré à un programme de jardinage par des animateurs non spécialisés dans ces domaines, outillés et encadrés pour se sentir motivés et confiants dans leur rôle.

Attachement, tempérament et déclaration de l’enfant victime d’agression sexuelle durant l’audition

Cette thèse a pour objectif principal d’explorer les contributions de l’attachement et du tempérament sur la quantité d’informations dévoilées par les enfants victimes d’agression sexuelle. Les auditions de 25 enfants âgés de trois à sept ans ont été codifiées sur le plan du type de questions et du nombre de détails. Le tempérament de l’enfant a été évalué par un questionnaire rempli par le parent. Les représentations d’attachement et les habiletés verbales ont été évaluées par l’entremise de tâches auprès de sous-échantillons d’enfants. Pour répondre à la question de recherche principale, le questionnaire de tempérament TABC-r a d’abord été traduit en français puis validé auprès de 231 parents issus de la population générale, ce qui a constitué un objectif secondaire de la thèse. Les résultats indiquent que le TABC-r version canadienne-française présente des propriétés psychométriques adéquates et similaires à la version originale. La structure factorielle, la cohérence interne, la fidélité inter-juge, la stabilité temporelle et la validité divergente sont très satisfaisantes. La validité convergente est soutenue par des relations attendues avec les problèmes de comportements et les relations familiales, mis à part des liens non retrouvés avec les habiletés cognitives. Ces résultats, les limites de l’étude et les pistes de recherche futures sont discutés. Les résultats obtenus concernant l’audition indiquent que les enfants victimes d’agression sexuelle présentant un attachement plus sécurisé et moins évitant rapportent davantage de détails en moyenne aux questions proposant un choix. Les associations modérées, quoique non significatives, entre le manque de persistance à la tâche et la quantité moyenne de détails aux questions proposant un choix, et entre l’attachement sécurisé et évitant et la quantité moyenne d’informations rapportées globalement sont décrites compte tenu de la petite taille de l’échantillon. Lorsqu’ils sont considérés simultanément, la sécurité d’attachement et le manque de persistance à la tâche contribuent potentiellement de façon complémentaire à expliquer une part de variance du nombre moyen de détails aux questions de reconnaissance lorsque l’âge est contrôlé, mais seul l’apport de la sécurité d’attachement est significatif. Ces résultats, les limites de l’étude, les pistes de recherches futures et les implications pour la conduite d’auditions sont discutés.

fNIRS-EEG study of focal interictal epileptiform discharges

Functional near-infrared spectroscopy (fNIRS) acquired with electroencephalography (EEG) is a relatively new non-invasive neuroimaging technique with potential for long term monitoring of the epileptic brain. Simultaneous EEG-fNIRS recording allows the spatio-temporal reconstruction of the hemodynamic response in terms of the concentration changes in oxy-hemoglobin (HbO) and deoxy-hemoglobin (HbR) associated with recorded epileptic events such as interictal epileptic discharges (IEDs) or seizures. While most previous studies investigating fNIRS in epilepsy had limitations due to restricted spatial coverage and small sample sizes, this work includes a sufficiently large number of channels to provide an extensive bilateral coverage of the surface of the brain for a sample size of 40 patients with focal epilepsies. Topographic maps of significant activations due to each IED type were generated in four different views (dorsal, frontal, left and right) and were compared with the epileptic focus previously identified by an epileptologist. After excluding 5 patients due to the absence of IEDs and 6 more with mesial temporal foci too deep for fNIRS, we report that significant HbR (respectively HbO) concentration changes corresponding to IEDs were observed in 62% (resp. 38%) of patients with neocortical epilepsies. This HbR/HbO response was most significant in the epileptic focus region among all the activations in 28%/21% of patients.

Whither RDS? An investigation of respondent driven sampling as a method of recruiting mainstream marijuana users.

Background: An important challenge in conducting social research of specific relevance to harm reduction programs is locating hidden populations of consumers of substances like cannabis who typically report few adverse or unwanted consequences of their use. Much of the deviant, pathologized perception of drug users is historically derived from, and empirically supported, by a research emphasis on gaining ready access to users in drug treatment or in prison populations with higher incidence of problems of dependence and misuse. Because they are less visible, responsible recreational users of illicit drugs have been more difficult to study. Methods: This article investigates Respondent Driven Sampling (RDS) as a method of recruiting experienced marijuana users representative of users in the general population. Based on sampling conducted in a multi-city study (Halifax, Montreal, Toronto, and Vancouver), and compared to samples gathered using other research methods, we assess the strengths and weaknesses of RDS recruitment as a means of gaining access to illicit substance users who experience few harmful consequences of their use. Demographic characteristics of the sample in Toronto are compared with those of users in a recent household survey and a pilot study of Toronto where the latter utilized nonrandom self-selection of respondents. Results: A modified approach to RDS was necessary to attain the target sample size in all four cities (i.e., 40 'users' from each site). The final sample in Toronto was largely similar, however, to marijuana users in a random household survey that was carried out in the same city. Whereas well-educated, married, whites and females in the survey were all somewhat overrepresented, the two samples, overall, were more alike than different with respect to economic status and employment. Furthermore, comparison with a self-selected sample suggests that (even modified) RDS recruitment is a cost-effective way of gathering respondents who are more representative of users in the general population than nonrandom methods of recruitment ordinarily produce. Conclusions: Research on marijuana use, and other forms of drug use hidden in the general population of adults, is important for informing and extending harm reduction beyond its current emphasis on 'at-risk' populations. Expanding harm reduction in a normalizing context, through innovative research on users often overlooked, further challenges assumptions about reducing harm through prohibition of drug use and urges consideration of alternative policies such as decriminalization and legal regulation.

La bioéthique et les conflits armés : la réflexion éthique des médecins militaires

Le but de la recherche est d’étudier les tensions éthiques que peuvent vivre les médecins militaires, qui doivent agir à la fois comme soignants, militaires (même s’ils sont non combattants) et parfois comme acteurs humanitaires. Parmi la littérature sur l’éthique de la médecine militaire, les dilemmes la concernant sont souvent présentés comme le fruit de pressions réelles ou perçues provenant de l’institution militaire, des règles, codes, lois ou de politiques, ceci afin de détourner le médecin de son but premier, soit l’intérêt du patient. Pour mieux comprendre les défis éthiques auxquels sont confrontés les médecins militaires canadiens et comment ceux-ci les traitent, la recherche utilise une approche de bioéthique empirique. À partir d’une analyse de la littérature, nous examinons les dilemmes éthiques des médecins militaires, le concept de profession, ainsi que les codes d’éthique (médicaux et militaires) canadiens. L’expérience éthique est ensuite explorée à partir d’entrevues semi-directives effectuées auprès de quatorze médecins militaires ayant participé à des missions opérationnelles, notamment à Kandahar en Afghanistan, entre 2006 et 2010. Les résultats, tant conceptuels qu’empiriques, nous indiquent que plusieurs nuances s’imposent. Tout d’abord, les médecins militaires canadiens ne vivent pas les dilemmes tels qu’ils sont présentés dans la littérature, ni en nombre ni en fréquence. Ils sont conscients qu’ils doivent à la fois tenir compte de l’intérêt du patient et du bien commun, mais n’en ressentent pas pour autant un sentiment de double loyauté professionnelle. De plus, ils ont l’impression de partager l’objectif de la mission qui est de maintenir la force de combat. Des distinctions s’imposent aussi entre les médecins eux-mêmes, dans la conception qu’ils se font de leur profession, ainsi que dans les contextes (opération ou garnison), selon le type de travail qu’ils exercent (généraliste ou spécialiste). Les principaux défis éthiques rapportés portent sur les inégalités de soins entre les soldats de la coalition et les victimes locales (soldats et civils), ainsi que sur le manque de ressources, engendrant des décisions cliniques éprouvantes. Un résultat étonnant des entrevues est la présence de deux groupes distincts au plan de l’identification professionnelle. Huit médecins militaires se considèrent avant tout comme médecin, alors que les six autres ne sont pas arrivés à accorder une priorité à l’une ou l’autre des professions. Ces deux groupes se différencient également sur d’autres plans, comme le nombre et le type de défis éthiques identifiés, ainsi que les mécanismes de résolution des dilemmes utilisés. Malgré les formations éthiques offertes par l’institution, des lacunes subsistent dans la capacité d’identification des expériences éthiques et des valeurs impliquées, de même que des mécanismes de résolution utilisés. Compte tenu du faible échantillonnage, ces résultats sont difficilement généralisables. Néanmoins, ils peuvent nous inspirer au niveau théorique en faisant ressortir le caractère multidimensionnel de la médecine militaire, ainsi qu’au niveau pratique en nous permettant de suggérer des éléments de formation facilitant la réflexion éthique des médecins militaires.

Capital expenditure decision in private and public sector entreprises in India A comparative evaluation

This study is focussed on public and private sector The study is confined to industrial Public companies in the states of Kerala and Orissa along with companies in India. undertakings only. sector and private sector private sector companies in other states were studied. Even though the original plan of 190 companies as the sample size could not be accomplished, as the responses were very poor, but data could be collected frmn 6 public and 5 private sector companies in Kerala, 8 public and 8 private sector companies in Orissa along with 27 private sector companies in other states totalling to 54 companies. The number of years of data collected varies from 2 years to 6 years. Factors which are affecting capital expenditures and hence leading to the performance of private sector compared to public sector companies are studied. After the study and analysis, comparisons are made between public sector and private sector, and suitable recomendations are made so that public sector industries can also perform equally well as the private sector industries in India.

A new fast stream cipher: MAJE4

A new fast stream cipher, MAJE4 is designed and developed with a variable key size of 128-bit or 256-bit. The randomness property of the stream cipher is analysed by using the statistical tests. The performance evaluation of the stream cipher is done in comparison with another fast stream cipher called JEROBOAM. The focus is to generate a long unpredictable key stream with better performance, which can be used for cryptographic applications.

Message Integrity in the World Wide Web: Use of Nested Hash Function and a Fast Stream Cipher

The focus of this work is to provide authentication and confidentiality of messages in a swift and cost effective manner to suit the fast growing Internet applications. A nested hash function with lower computational and storage demands is designed with a view to providing authentication as also to encrypt the message as well as the hash code using a fast stream cipher MAJE4 with a variable key size of 128-bit or 256-bit for achieving confidentiality. Both nested Hash function and MAJE4 stream cipher algorithm use primitive computational operators commonly found in microprocessors; this makes the method simple and fast to implement both in hardware and software. Since the memory requirement is less, it can be used for handheld devices for security purposes.

Evaluation Of A Novel Method Of Real Time Computer Assisted Spine Surgery

In this paper the effectiveness of a novel method of computer assisted pedicle screw insertion was studied using testing of hypothesis procedure with a sample size of 48. Pattern recognition based on geometric features of markers on the drill has been performed on real time optical video obtained from orthogonally placed CCD cameras. The study reveals the exactness of the calculated position of the drill using navigation based on CT image of the vertebra and real time optical video of the drill. The significance value is 0.424 at 95% confidence level which indicates good precision with a standard mean error of only 0.00724. The virtual vision method is less hazardous to both patient and the surgeon

Socio-Economic Aspects of Sustainable Ecotourism Development: The Case of Kerala

The paper is an attempt to shed light on the socio-economic aspects of the local communities on the development of ecotourism in Kerala. Most of the local communities in the ecotourism destinations are tribes who have been excluded from the mainstream society and are not a part of Kerala’s overall development setting. The paper also tries to situate the community perception on the sustainable livelihood of ecotourism sites of Kerala. Data for the study is obtained from a primary survey by dividing the ecotourism destinations in Kerala into three zones, 230 from south zone, 220 from central zone and 200 from north zone with a total sample size of 650 based on the notion of community based ecotourism initiatives of the state. The result of the study confirms that ecotourism has helped to enhance the livelihood of the marginalized community. With well-knit policies it is possible to tag ecotourism of Kerala as an important tourism destination in the global tourism map

Digital image analysis as a tool to estimate legume contributions in legume-grass swards

Summary: Productivity and forage quality of legume-grass swards are important factors for successful arable farming in both organic and conventional farming systems. For these objectives the botanical composition of the swards is of particular importance, especially, the content of legumes due to their ability to fix airborne nitrogen. As it can vary considerably within a field, a non-destructive detection method while doing other tasks would facilitate a more targeted sward management and could predict the nitrogen supply of the soil for the subsequent crop. This study was undertaken to explore the potential of digital image analysis (DIA) for a non destructive prediction of legume dry matter (DM) contribution of legume-grass mixtures. For this purpose an experiment was conducted in a greenhouse, comprising a sample size of 64 experimental swards such as pure swards of red clover (Trifolium pratense L.), white clover (Trifolium repens L.) and lucerne (Medicago sativa L.) as well as binary mixtures of each legume with perennial ryegrass (Lolium perenne L.). Growth stages ranged from tillering to heading and the proportion of legumes from 0 to 80 %. Based on digital sward images three steps were considered in order to estimate the legume contribution (% of DM): i) The development of a digital image analysis (DIA) procedure in order to estimate legume coverage (% of area). ii) The description of the relationship between legume coverage (% area) and legume contribution (% of DM) derived from digital analysis of legume coverage related to the green area in a digital image. iii) The estimation of the legume DM contribution with the findings of i) and ii). i) In order to evaluate the most suitable approach for the estimation of legume coverage by means of DIA different tools were tested. Morphological operators such as erode and dilate support the differentiation of objects of different shape by shrinking and dilating objects (Soille, 1999). When applied to digital images of legume-grass mixtures thin grass leaves were removed whereas rounder clover leaves were left. After this process legume leaves were identified by threshold segmentation. The segmentation of greyscale images turned out to be not applicable since the segmentation between legumes and bare soil failed. The advanced procedure comprising morphological operators and HSL colour information could determine bare soil areas in young and open swards very accurately. Also legume specific HSL thresholds allowed for precise estimations of legume coverage across a wide range from 11.8 - 72.4 %. Based on this legume specific DIA procedure estimated legume coverage showed good correlations with the measured values across the whole range of sward ages (R2 0.96, SE 4.7 %). A wide range of form parameters (i.e. size, breadth, rectangularity, and circularity of areas) was tested across all sward types, but none did improve prediction accuracy of legume coverage significantly. ii) Using measured reference data of legume coverage and contribution, in a first approach a common relationship based on all three legumes and sward ages of 35, 49 and 63 days was found with R2 0.90. This relationship was improved by a legume-specific approach of only 49- and 63-d old swards (R2 0.94, 0.96 and 0.97 for red clover, white clover, and lucerne, respectively) since differing structural attributes of the legume species influence the relationship between these two parameters. In a second approach biomass was included in the model in order to allow for different structures of swards of different ages. Hence, a model was developed, providing a close look on the relationship between legume coverage in binary legume-ryegrass communities and the legume contribution: At the same level of legume coverage, legume contribution decreased with increased total biomass. This phenomenon may be caused by more non-leguminous biomass covered by legume leaves at high levels of total biomass. Additionally, values of legume contribution and coverage were transformed to the logit-scale in order to avoid problems with heteroscedasticity and negative predictions. The resulting relationships between the measured legume contribution and the calculated legume contribution indicated a high model accuracy for all legume species (R2 0.93, 0.97, 0.98 with SE 4.81, 3.22, 3.07 % of DM for red clover, white clover, and lucerne swards, respectively). The validation of the model by using digital images collected over field grown swards with biomass ranges considering the scope of the model shows, that the model is able to predict legume contribution for most common legume-grass swards (Frame, 1992; Ledgard and Steele, 1992; Loges, 1998). iii) An advanced procedure for the determination of legume DM contribution by DIA is suggested, which comprises the inclusion of morphological operators and HSL colour information in the analysis of images and which applies an advanced function to predict legume DM contribution from legume coverage by considering total sward biomass. Low residuals between measured and calculated values of legume dry matter contribution were found for the separate legume species (R2 0.90, 0.94, 0.93 with SE 5.89, 4.31, 5.52 % of DM for red clover, white clover, and lucerne swards, respectively). The introduced DIA procedure provides a rapid and precise estimation of legume DM contribution for different legume species across a wide range of sward ages. Further research is needed in order to adapt the procedure to field scale, dealing with differing light effects and potentially higher swards. The integration of total biomass into the model for determining legume contribution does not necessarily reduce its applicability in practice as a combined estimation of total biomass and legume coverage by field spectroscopy (Biewer et al. 2009) and DIA, respectively, may allow for an accurate prediction of the legume contribution in legume-grass mixtures.

Improving food and nutritional security of small and marginal coconut growers through diversification of crops and enterprises

This paper presents the impact of integrating interventions like nutrition gardening, livestock rearing, product diversification and allied income generation activities in small and marginal coconut homesteads along with nutrition education in improving the food and nutritional security as well as the income of the family members. The activities were carried out through registered Community Based Organizations (CBOs) in three locations in Kerala, India during 2005-2008. Data was collected before and after the project periods through interviews using a pre-tested questionnaire containing statements indicating the adequacy, quality and diversity of food materials. Fifty respondents each were randomly selected from the three communities, thereby resulting in a total sample size of 150. The data was analysed using SPSS by adopting statistical tools like frequency, average, percentage analysis, t – test and regression. Participatory planning and implementation of diverse interventions notably intercropping and off-farm activities along with nutrition education brought out significant improvements in the food and nutritional security, in terms of frequency and quantity of consumption as well as diet diversity. At the end of the project, 96%of the members became completely food secure and 72% nutritionally secure. The overall consumption of fruits, vegetables and milk by both children and adults and egg by children recorded increase over the project period. Consumption of fish was more than the Recommended Dietary Intake (RDI) level during pre and post project periods. Project interventions like nutrition gardening could bring in surplus consumption of vegetables (35%) and fruits (10%) than RDI. In spite of the increased consumption of green leafy vegetables and milk and milk products over the project period, the levels of consumption were still below the RDI levels. CBO-wise analysis of the consumption patterns revealed the need for location-specific interventions matching to the needs and preferences of the communities.

Selecting Relevant Genes with a Spectral Approach

Array technologies have made it possible to record simultaneously the expression pattern of thousands of genes. A fundamental problem in the analysis of gene expression data is the identification of highly relevant genes that either discriminate between phenotypic labels or are important with respect to the cellular process studied in the experiment: for example cell cycle or heat shock in yeast experiments, chemical or genetic perturbations of mammalian cell lines, and genes involved in class discovery for human tumors. In this paper we focus on the task of unsupervised gene selection. The problem of selecting a small subset of genes is particularly challenging as the datasets involved are typically characterized by a very small sample size ?? the order of few tens of tissue samples ??d by a very large feature space as the number of genes tend to be in the high thousands. We propose a model independent approach which scores candidate gene selections using spectral properties of the candidate affinity matrix. The algorithm is very straightforward to implement yet contains a number of remarkable properties which guarantee consistent sparse selections. To illustrate the value of our approach we applied our algorithm on five different datasets. The first consists of time course data from four well studied Hematopoietic cell lines (HL-60, Jurkat, NB4, and U937). The other four datasets include three well studied treatment outcomes (large cell lymphoma, childhood medulloblastomas, breast tumors) and one unpublished dataset (lymph status). We compared our approach both with other unsupervised methods (SOM,PCA,GS) and with supervised methods (SNR,RMB,RFE). The results clearly show that our approach considerably outperforms all the other unsupervised approaches in our study, is competitive with supervised methods and in some case even outperforms supervised approaches.

Intrinsic test of independence in contingency tables

A condition needed for testing nested hypotheses from a Bayesian viewpoint is that the prior for the alternative model concentrates mass around the small, or null, model. For testing independence in contingency tables, the intrinsic priors satisfy this requirement. Further, the degree of concentration of the priors is controlled by a discrete parameter m, the training sample size, which plays an important role in the resulting answer regardless of the sample size. In this paper we study robustness of the tests of independence in contingency tables with respect to the intrinsic priors with different degree of concentration around the null, and compare with other “robust” results by Good and Crook. Consistency of the intrinsic Bayesian tests is established. We also discuss conditioning issues and sampling schemes, and argue that conditioning should be on either one margin or the table total, but not on both margins. Examples using real are simulated data are given