Validation of Coded Aperture Coherent Scatter Spectral Imaging for Differentiation of Normal and Neoplastic Breast Tissues via Surgical Pathology

This study intends to validate the sensitivity and specificity of coded aperture coherent scatter spectral imaging (CACSSI) by comparison to clinical histological preparation and pathologic analysis methods currently used for the differentiation of normal and neoplastic breast tissues. A composite overlay of the CACSSI rendered image and pathologist interpreted, stained sections validate the ability of coherent scatter imaging to differentiate cancerous tissues from normal, healthy breast structures ex-vivo. Via comparison to the pathologist annotated slides, the CACSSI system may be further optimized to maximized sensitivity and specificity for differentiation of breast carcinomas.

Global and local perceptual style, field-independence, and central coherence: an attempt at concept validation

Historically, the concepts of field-independence, closure flexibility, and weak central coherence have been used to denote a locally, rather globally, dominated perceptual style. To date, there has been little attempt to clarify the relationship between these constructs, or to examine the convergent validity of the various tasks purported to measure them. To address this, we administered 14 tasks that have been used to study visual perceptual styles to a group of 90 neuro-typical adults. The data were subjected to exploratory factor analysis. We found evidence for the existence of a narrowly defined weak central coherence (field-independence) factor that received loadings from only a few of the tasks used to operationalise this concept. This factor can most aptly be described as representing the ability to dis-embed a simple stimulus from a more complex array. The results suggest that future studies of perceptual styles should include tasks whose theoretical validity is empirically verified, as such validity cannot be established merely on the basis of a priori task analysis. Moreover, the use of multiple indices is required to capture the latent dimensions of perceptual styles reliably.

The relationship between adipokines and the onset of type 2 diabetes in middle-aged men: The PRIME study

Aims: Epidemiological evidence suggests that adipokines may be associated with the onset of type 2 diabetes, but the evidence to date is limited and inconclusive. This study examined the association between adiponectin and leptin and the subsequent diagnosis of type 2 diabetes in a UK population based cohort of non-diabetic middle-aged men.
Methods: Baseline serum levels of leptin and adiponectin were measured in 1839 nondiabetic men aged 50–60 years who were participating in the prospective populationbased PRIME study. Over a mean follow-up of 14.7 years, new cases of type 2 diabetes were determined from self-reported clinical information with subsequent validation by general practitioners.
Results: 151 Participants developed type 2 diabetes during follow-up. In Cox regression models adjusted for age, men in the top third of the leptin distribution were at increased risk (hazard ratio (HR) 4.27, 95% CI 2.67–6.83) and men in the top third of the adiponectin
distribution at reduced risk (HR 0.24, 95% CI 0.14–0.42) relative to men in the bottom third. However, significance was lost for leptin after additional adjustment for BMI, waist to hip ratio, lifestyle factors and biological risk factors, including C-reactive protein (CRP). Further adjustment for HOMA-IR also resulted in loss of significance for adiponectin.
Conclusions: This study provides evidence that adipokines are associated with men’s future type 2 diabetes risk but not independently of other risk factors.

Studies on Bio-Geochemistry, Bio-Optical Properties and Satellite Validation of Coastal Waters of South Eastern Arabian Sea

In situ methods used for water quality assessment have both physical and time constraints. Just a limited number of sampling points can be performed due to this, making it difficult to capture the range and variability of coastal processes and constituents. In addition, the mixing between fresh and oceanic water creates complex physical, chemical and biological environment that are difficult to understand, causing the existing measurement methodologies to have significant logistical, technical, and economic challenges and constraints. Remote sensing of ocean colour makes it possible to acquire information on the distribution of chlorophyll and other constituents over large areas of the oceans in short periods. There are many potential applications of ocean colour data. Satellite-derived products are a key data source to study the distribution pattern of organisms and nutrients (Guillaud et al. 2008) and fishery research (Pillai and Nair 2010; Solanki et al. 2001. Also, the study of spatial and temporal variability of phytoplankton blooms, red tide identification or harmful algal blooms monitoring (Sarangi et al. 2001; Sarangi et al. 2004; Sarangi et al. 2005; Bhagirathan et al., 2014), river plume or upwelling assessments (Doxaran et al. 2002; Sravanthi et al. 2013), global productivity analyses (Platt et al. 1988; Sathyendranath et al. 1995; IOCCG2006) and oil spill detection (Maianti et al. 2014). For remote sensing to be accurate in the complex coastal waters, it has to be validated with the in situ measured values. In this thesis an attempt to study, measure and validate the complex waters with the help of satellite data has been done. Monitoring of coastal ecosystem health of Arabian Sea in a synoptic way requires an intense, extensive and continuous monitoring of the water quality indicators. Phytoplankton determined from chl-a concentration, is considered as an indicator of the state of the coastal ecosystems. Currently, satellite sensors provide the most effective means for frequent, synoptic, water-quality observations over large areas and represent a potential tool to effectively assess chl-a concentration over coastal and oceanic waters; however, algorithms designed to estimate chl-a at global scales have been shown to be less accurate in Case 2 waters, due to the presence of water constituents other than phytoplankton which do not co-vary with the phytoplankton. The constituents of Arabian Sea coastal waters are region-specific because of the inherent variability of these optically-active substances affected by factors such as riverine input (e.g. suspended matter type and grain size, CDOM) and phytoplankton composition associated with seasonal changes.

Validation of stress indicators for the assessment of animal welfare and prediction of pork meat quality variation at commercial level

Les procédures appliquées avant l’abattage des animaux influencent directement la qualité de la viande en modulant l’état physiologique des porcs; ainsi, l’augmentation de la température corporelle, les taux élevés de lactate sanguin et l’épuisement des réserves de glycogène entre autres, occasionnent la majorité des baisses de qualité. L’objectif de cette thèse était de valider des outils indicateurs de stress porcin pour les fermes et les abattoirs. Ceux-ci seraient appliqués à la surveillance du bien-être animal et à la prédiction de variation de qualité de la viande porcine au niveau commercial. Premierement, les résultats de la thèse ont permis de conclure qu’un des outils développés (analyseur portatif de lactate) mesure la variation du niveau de lactate sanguin associé à l’état physiologique des porcs dans la phase péri-mortem et aide à expliquer la variation de la qualité de la viande chez le porc à l’abattoir, en particulier dans les muscles du jambon. Deuxièmement, les résultats des audits du bien-être animal appliqués de la ferme à l’abattoir ont démontré que la qualité du système d’élevage à la ferme d’origine et les compétences du chauffeur de camion sont d’importants critères affectant la réponse comportementale des porcs à la manipulation avant l’abattage. Ces résultats ont également démontré que les conditions de logement à la ferme (la faible densité et l’enrichissement dans les enclos), le comportement des porcs en période pré-abattage (glissade), ainsi que les interventions du manipulateur (utilisation du bâton électrique) dans la zone d’étourdissement de l’abattoir affectent négativement la variation de la qualité de la viande. L’application des protocoles d’audits dans la filière porcine a également démontré que le respect des critères de bien-être animal fixés par un outil de vérification est primordiale et permet de contrôler les conditions de bien-être des porcs à chaque étape de la période pré-abattage, de produire une viande de qualité supérieure et de réduire les pertes. Les audits de bien-être animal sont donc un outil qui apporte des resultats très pertinents pour aider a éviter les variations de la qualité de la viande chez le porc. Troisièmement, la thermographie infrarouge s’est avéré être une technique prometteuse permettant d’évaluer la variation de température corporelle de l’animal pendant et après un stress physique, en particulier lorsque cette mesure est prise derrière les oreilles. En conclusion, les outils validés à travers cette thèse représentent des méthodologies non invasives et potentiellement complémentaires à d’autres approches d’évaluation de l’état physiologique et du bien-être animal par rapport au stress, permettant de réduire les pertes de qualité de viande (par exemple en utilisation conjointe avec le niveau de lactate sanguin et les indicateurs de stress comportemental, entre autres).

Multicentric Genome-Wide Association Study for Primary Spontaneous Pneumothorax

Despite elevated incidence and recurrence rates for Primary Spontaneous Pneumothorax (PSP), little is known about its etiology, and the genetics of idiopathic PSP remains unexplored. To identify genetic variants contributing to sporadic PSP risk, we conducted the first PSP genome-wide association study. Two replicate pools of 92 Portuguese PSP cases and of 129 age- and sex-matched controls were allelotyped in triplicate on the Affymetrix Human SNP Array 6.0 arrays. Markers passing quality control were ranked by relative allele score difference between cases and controls (|RASdiff|), by a novel cluster method and by a combined Z-test. 101 single nucleotide polymorphisms (SNPs) were selected using these three approaches for technical validation by individual genotyping in the discovery dataset. 87 out of 94 successfully tested SNPs were nominally associated in the discovery dataset. Replication of the 87 technically validated SNPs was then carried out in an independent replication dataset of 100 Portuguese cases and 425 controls. The intergenic rs4733649 SNP in chromosome 8 (between LINC00824 and LINC00977) was associated with PSP in the discovery (P = 4.07E-03, ORC[95% CI] = 1.88[1.22-2.89]), replication (P = 1.50E-02, ORC[95% CI] = 1.50[1.08-2.09]) and combined datasets (P = 8.61E-05, ORC[95% CI] = 1.65[1.29-2.13]). This study identified for the first time one genetic risk factor for sporadic PSP, but future studies are warranted to further confirm this finding in other populations and uncover its functional role in PSP pathogenesis.

Conception, développement et validation expérimentale d’une boussole haptique

Ce mémoire présente la conception, le contrôle et la validation expérimentale d’une boussole haptique servant à diriger les utilisateurs aux prises avec une déficience visuelle, et ce, dans tous les environnements. La revue de littérature décrit le besoin pour un guidage haptique et permet de mettre en perspective cette technologie dans le marché actuel. La boussole proposée utilise le principe de couples asymétriques. Son design est basé sur une architecture de moteur à entraînement direct et un contrôle en boucle ouverte étalonné au préalable. Cette conception permet d’atteindre une vaste plage de fréquences pour la rétroaction haptique. Les propriétés mécaniques de l’assemblage sont évaluées. Puis, l’étalonnage des couples permet d’assurer que le contrôle en boucle ouverte produit des couples avec une précision suffisante. Un premier test avec des utilisateurs a permis d’identifier que les paramètres de fréquence entre 5 et 15 Hz combinés avec des couples au-delà de 40 mNm permettent d’atteindre une efficacité intéressante pour la tâche. L’expérience suivante démontre qu’utiliser une rétroaction haptique proportionnelle à l’erreur d’orientation améliore significativement les performances. Le concept est ensuite éprouvé avec dix-neuf sujets qui doivent se diriger sur un parcours avec l’aide seule de cette boussole haptique. Les résultats montrent que tous les sujets ont réussi à rencontrer tous les objectifs de la route, tout en maintenant des déviations latérales relativement faibles (0:39 m en moyenne). Les performances obtenues et les impressions des utilisateurs sont prometteuses et plaident en faveur de ce dispositif. Pour terminer, un modèle simplifié du comportement d’un individu pour la tâche d’orientation est développé et démontre l’importance de la personnalisation de l’appareil. Ce modèle est ensuite utilisé pour mettre en valeur la stratégie d’horizon défilant pour le placement de la cible intermédiaire actuelle dans un parcours sur une longue distance.

miRNAs as therapeutic agents in neurodegeneration, a pilot study

L’échec des différents essais cliniques souligne la nécessité de développer des nouvelles thérapies pour la maladie d’Alzheimer (MA), la cause la plus commune de démence. Les microARNs (miARNs) sont les ARNs non-codants les plus étudiés et ils jouent un rôle important dans la modulation de l’expression des gènes et de multiples voies de signalisation. Des études antérieures, dont celles de mon laboratoire d’accueil, ont permis de développer l’hypothèse que certains membres de la famille miR-15/107 (c.-à-d. miR-15ab, miR-16, miR-195, miR-424, and miR-497) pourraient être utilisés comme agents thérapeutiques dans MA. En effet, cette famille avait le potentiel de réguler de multiples gènes associés à MA, tels que la protéine précurseur de l’amyloïde (APP), la β-secrétase (BACE1), et la protéine Tau. Tel que démontré dans ce projet de thèse, j’ai choisi miR-16 comme cible thérapeutique potentielle pour MA parmi tous les membres de la famille. L’essai luciférase dans ce projet confirme que miR-16 peut réguler simultanément APP et BACE1, directement par une interaction avec la région non-codante en 3’ de l’ARNm). Notamment, nous observons aussi une réduction de la production des peptides amyloïdes et de la phosphorylation de Tau après une augmentation de miR-16 en cellule. J’ai ensuite validé mes résultats in vivo dans la souris en utilisant une méthode de livraison de miR-16 via une pompe osmotique implanté dans le cerveau. Dans ce cas, l’expression des protéines d’intérêts (APP, BACE1, Tau) a été mesurée par immunobuvardage et PCR à temps réel. Après validation, ces résultats ont été complémentés par une étude protéomique (iTRAQ) du tronc cérébral et de l’hippocampe, deux régions associées à la maladie. Ces données m’ont permis d’identifier d’autres protéines régulées par miR-16 in vivo, incluant α-Synucléine, Transferrine receptor1, et SRm300. Une autre observation intéressante : les voies régulées par miR-16 in vivo sont directement en lien avec le stress oxydatif et la neurodégénération. En résumé, ce travail démontre l’efficacité et la faisabilité d’utiliser un miARN comme outil thérapeutique pour la maladie d’Alzheimer. Ces résultats rentrent dans un cadre plus vaste de découvrir de nouvelles cibles pour MA, et en particulier la forme sporadique de la maladie qui représente plus de 95% de tous les cas. Évidemment, la découverte d’une molécule pouvant cibler simultanément les deux pathologies de la maladie (plaques amyloïdes et hyper phosphorylation de tau) est nouvelle et intéressante, et ce domaine de recherche ouvre la porte aux autres petits ARNs non-codants dans MA et les maladies neurodégénératives connexes.

Validation Française de l’Échelle de la Personnalité Temporelle (French Validation of the Time Personality Indicator)

RÉSUMÉ Certains auteurs ont développé un intérêt pour la compréhension des aptitudes associées à la gestion du temps. Ainsi, plusieurs définitions théoriques ont été proposées afin de mieux cerner ce concept et une multitude de questionnaires a été développée afin de le mesurer. La présente étude visait à valider la traduction française d’un de ces outils, soit le Time Personality Indicator (TPI). Des analyses exploratoires et confirmatoires ont été effectuées sur l’ensemble des données recueillies auprès de 1 267 étudiants et employés de l’Université Laval ayant complété la version française du TPI ainsi que d’autres mesures de la personnalité. Les résultats ont révélé qu’une solution à huit facteurs permet de mieux décrire les données de l’échantillon. La discussion présente les raisons pour lesquelles la version française du TPI est valide, identifie certaines limites de la présente étude et souligne l’utilité de cet outil pour la recherche sur la gestion du temps. (ABSTRACT: Numerous authors have developed an interest towards the understanding of the abilities related to time management. As a consequence, multiple theoretical definitions have been proposed to explain time management. Likewise, several questionnaires have been developed in order to measure this concept. The aim of this study was to validate a French version of one of these tools, namely the Time Personality Indicator (TPI). The French version of the TPI and other personality questionnaires were completed by 1267 students and employees of Université Laval. The statistical approach used included exploratory and confirmatory analyses. Results revealed that an eight factor model provided a better adjustment to the data. The discussion provides arguments supporting the validity of the French version of the TPI and underlines the importance of such a tool for the research on time management)

Validation of the self-regulated online learning questionnaire

Abstract The number of students engaged in Massive Open Online Courses (MOOCs) is increasing rapidly. Due to the autonomy of students in this type of education, students in MOOCs are required to regulate their learning to a greater extent than students in traditional, face-to-face education. However, there is no questionnaire available suited for this online context that measures all aspects of self-regulated learning (SRL). In this study, such a questionnaire is developed based on existing SRL questionnaires. This is the self-regulated online learning ques- tionnaire. Exploratory factor analysis (EFA) on the first dataset led to a set of scales differing from those theoretically defined beforehand. Confirmatory factor analysis (CFA) was conducted on a second dataset to compare the fit of the theoretical model and the exploratively obtained model. The exploratively obtained model provided much better fit to the data than the theoretical model. All models under investigation provided better fit when excluding the task strategies scale and when merging the scales measuring metacognitive activities. From the results of the EFA and the CFA it can be concluded that further development of the questionnaire is necessary.

Experimental study of forces and energies during shearing of steel sheet with angled tools

Shearing is a fast and inexpensive method to cut sheet metal that has been used since the beginning of the industrialism. Consequently, published experimental studies of shearing can be found from over a century back in time. Recent studies, however, are due to the availability of low cost digital computation power, mostly based on finite element simulations that guarantees quick results. Still, for validation of models and simulations, accurate experimental data is a requisite. When applicable, 2D models are in general desirable over 3D models because of advantages like low computation time and easy model formulation. Shearing of sheet metal with parallel tools is successfully modelled in 2D with a plane strain approximation, but with angled tools the approximation is less obvious. Therefore, plane strain approximations for shearing with angled tools were evaluated by shear experiments of high accuracy. Tool angle, tool clearance, and clamping of the sheet were varied in the experiments. The results showed that the measured forces in shearing with angled tools can be approximately calculated using force measurements from shearing with parallel tools. Shearing energy was introduced as a quantifiable measure of suitable tool clearance range. The effects of the shearing parameters on forces were in agreement with previous studies. Based on the agreement between calculations and experiments, analysis based on a plane strain assumption is considered applicable for angled tools with a small (up to 2 degrees) rake angle.

A qualitative study of the emotional coping and support needs of children living with a parent with a brain injury

Primary objective: To examine emotional coping and support needs in children of persons with acquired brain injury, with a view to understanding what interventions would be helpful for these children. Design: The study was qualitative, using a thematic analysis approach. Methods and procedure: Six children between 9 and 18 years of age, six parents (three with ABI), and three support workers were interviewed either at home or at a support centre, using a semi-structured interview guide. Results: Children reported using a variety of adaptive and maladaptive emotional coping strategies, but were consistent in expressing a need for credible validation, i.e. sharing experiences with peers. The results are presented under four overarching themes: difficulties faced; emotions experienced; coping strategies; and reported support needs. Conclusions: The results reveal an interaction between the child’s experiences of complex loss that is difficult to acknowledge, emotional distancing between parent and child, and the children’s need for credible validation. All children expressed a desire for talking to peers in a similar situation to themselves, but had not had this opportunity. Interventions should set up such peer interaction to create credible validation for the specific distress suffered by this population.

Validation of Electronic Health Record Phenotyping of Bipolar Disorder Cases and Controls

Objective: The study was designed to validate use of elec-tronic health records (EHRs) for diagnosing bipolar disorder and classifying control subjects. Method: EHR data were obtained from a health care system of more than 4.6 million patients spanning more than 20 years. Experienced clinicians reviewed charts to identify text features and coded data consistent or inconsistent with a diagnosis of bipolar disorder. Natural language processing was used to train a diagnostic algorithm with 95% specificity for classifying bipolar disorder. Filtered coded data were used to derive three additional classification rules for case subjects and one for control subjects. The positive predictive value (PPV) of EHR-based bipolar disorder and subphenotype di- agnoses was calculated against diagnoses from direct semi- structured interviews of 190 patients by trained clinicians blind to EHR diagnosis. Results: The PPV of bipolar disorder defined by natural language processing was 0.85. Coded classification based on strict filtering achieved a value of 0.79, but classifications based on less stringent criteria performed less well. No EHR- classified control subject received a diagnosis of bipolar dis- order on the basis of direct interview (PPV=1.0). For most subphenotypes, values exceeded 0.80. The EHR-based clas- sifications were used to accrue 4,500 bipolar disorder cases and 5,000 controls for genetic analyses. Conclusions: Semiautomated mining of EHRs can be used to ascertain bipolar disorder patients and control subjects with high specificity and predictive value compared with diagnostic interviews. EHRs provide a powerful resource for high-throughput phenotyping for genetic and clinical research.

Critère de validation croisée pour le choix des modèles des petits domaines au niveau des unités

Ce mémoire s’intéresse à l’étude du critère de validation croisée pour le choix des modèles relatifs aux petits domaines. L’étude est limitée aux modèles de petits domaines au niveau des unités. Le modèle de base des petits domaines est introduit par Battese, Harter et Fuller en 1988. C’est un modèle de régression linéaire mixte avec une ordonnée à l’origine aléatoire. Il se compose d’un certain nombre de paramètres : le paramètre β de la partie fixe, la composante aléatoire et les variances relatives à l’erreur résiduelle. Le modèle de Battese et al. est utilisé pour prédire, lors d’une enquête, la moyenne d’une variable d’intérêt y dans chaque petit domaine en utilisant une variable auxiliaire administrative x connue sur toute la population. La méthode d’estimation consiste à utiliser une distribution normale, pour modéliser la composante résiduelle du modèle. La considération d’une dépendance résiduelle générale, c’est-à-dire autre que la loi normale donne une méthodologie plus flexible. Cette généralisation conduit à une nouvelle classe de modèles échangeables. En effet, la généralisation se situe au niveau de la modélisation de la dépendance résiduelle qui peut être soit normale (c’est le cas du modèle de Battese et al.) ou non-normale. L’objectif est de déterminer les paramètres propres aux petits domaines avec le plus de précision possible. Cet enjeu est lié au choix de la bonne dépendance résiduelle à utiliser dans le modèle. Le critère de validation croisée sera étudié à cet effet.

New tools for cognitive and motor rehabilitation: development and clinical validation

Nervous system disorders are associated with cognitive and motor deficits, and are responsible for the highest disability rates and global burden of disease. Their recovery paths are vulnerable and dependent on the effective combination of plastic brain tissue properties, with complex, lengthy and expensive neurorehabilitation programs. This work explores two lines of research, envisioning sustainable solutions to improve treatment of cognitive and motor deficits. Both projects were developed in parallel and shared a new sensible approach, where low-cost technologies were integrated with common clinical operative procedures. The aim was to achieve more intensive treatments under specialized monitoring, improve clinical decision-making and increase access to healthcare. The first project (articles I – III) concerned the development and evaluation of a web-based cognitive training platform (COGWEB), suitable for intensive use, either at home or at institutions, and across a wide spectrum of ages and diseases that impair cognitive functioning. It was tested for usability in a memory clinic setting and implemented in a collaborative network, comprising 41 centers and 60 professionals. An adherence and intensity study revealed a compliance of 82.8% at six months and an average of six hours/week of continued online cognitive training activities. The second project (articles IV – VI) was designed to create and validate an intelligent rehabilitation device to administer proprioceptive stimuli on the hemiparetic side of stroke patients while performing ambulatory movement characterization (SWORD). Targeted vibratory stimulation was found to be well tolerated and an automatic motor characterization system retrieved results comparable to the first items of the Wolf Motor Function Test. The global system was tested in a randomized placebo controlled trial to assess its impact on a common motor rehabilitation task in a relevant clinical environment (early post-stroke). The number of correct movements on a hand-to-mouth task was increased by an average of 7.2/minute while the probability to perform an error decreased from 1:3 to 1:9. Neurorehabilitation and neuroplasticity are shifting to more neuroscience driven approaches. Simultaneously, their final utility for patients and society is largely dependent on the development of more effective technologies that facilitate the dissemination of knowledge produced during the process. The results attained through this work represent a step forward in that direction. Their impact on the quality of rehabilitation services and public health is discussed according to clinical, technological and organizational perspectives. Such a process of thinking and oriented speculation has led to the debate of subsequent hypotheses, already being explored in novel research paths.