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Correlated mutation analysis is an effective approach for predicting functional and structural residue interactions from protein multiple sequence alignments. A prediction pipeline over the Pfam database was developed to predict residue contacts within protein domains. Cross- reference with the PDB showed these contacts are spatially close. Furthermore, we found our predictions to be biochemically reasonable and correspond closely with known contact matrices. This large-scale search for coevolving regions within protein domains revealed that if two sites in an alignment covary, then neighboring sites in the alignment would also typically covary, resulting in clusters of covarying residues. The program PatchD was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibited strong covariation identified multiple residues that were generally nearby in the protein structures, suggesting that the detection of covarying patches can be used in addition to traditional CMA approaches to reveal functional interaction partners.

Correlated mutation analysis is an effective approach for predicting functional and structural residue interactions from protein multiple sequence alignments. A prediction pipeline over the Pfam database was developed to predict residue contacts within protein domains. Cross- reference with the PDB showed these contacts are spatially close. Furthermore, we found our predictions to be biochemically reasonable and correspond closely with known contact matrices. This large-scale search for coevolving regions within protein domains revealed that if two sites in an alignment covary, then neighboring sites in the alignment would also typically covary, resulting in clusters of covarying residues. The program PatchD was developed to measure the covariation between disconnected sequence clusters to reveal patch covariation. Patches that exhibited strong covariation identified multiple residues that were generally nearby in the protein structures, suggesting that the detection of covarying patches can be used in addition to traditional CMA approaches to reveal functional interaction partners.

De nombreuses recherches ont mis en évidence les difficultés rencontrées par les élèves relativement au concept de fonction. Néanmoins, peu de chercheurs se sont penchés sur les sources possibles de ces difficultés qui sont liées au développement, chez les élèves du premier cycle du secondaire, du concept de covariation entre deux grandeurs, ni sur les moyens envisageables pour remédier à ces difficultés. C’est donc ce que nous faisons dans cette recherche. Évidemment, la problématique est très vaste et les angles pour l’aborder aussi. Nous avons donc choisi de nous concentrer sur les transferts entre modes de représentation, particulièrement le transfert de la situation au graphique. Ce choix est dû, entre autres, au fait que ce transfert en est un de ceux qui pose le plus de difficultés aux élèves alors qu’on le retrouve très tôt dans les objectifs des programmes de formation de l’école secondaire (MEQ, 1994 et MELS, 2003). Nos hypothèses sur la source de ces difficultés sont l’incompréhension du concept de covariation entre deux grandeurs par les élèves et le manque de prise en considération de la complexité des transferts entre modes de représentation dans l’enseignement. Afin d’approfondir cette deuxième hypothèse, nous nous sommes intéressé aux travaux de Duval (1988, 1993) en ce qui concerne les registres de représentation sémiotiques, ce qui nous a permis d’analyser précisément en quoi consiste le transfert de la situation au graphique. Nous avons alors élaboré sur la conversion d’une situation présentée à l’aide de deux registres, « verbal » et « figural », au registre « graphique », ce qui nous a permis par la suite d’analyser les résultats de l’expérimentation. Nous avons en effet conçu une séquence d’enseignement permettant de développer le concept de covariation et d’introduire le graphique comme étant la représentation visuelle de cette covariation chez des élèves de secondaire 2, puis nous l’avons expérimentée auprès de trois groupes d’élèves de niveaux académiques différents (faible, régulier et fort). Cette séquence d’enseignement repose principalement sur une perspective constructiviste de l’enseignement et de l’apprentissage, ainsi que sur la considération des représentations spontanées des élèves. Elle propose donc une situation-problème menant les élèves à la construction de la représentation graphique à partir de leurs représentations spontanées. Notre analyse des résultats met principalement en évidence les caractéristiques des représentations spontanées des élèves, ainsi que leur évolution tout au long de l’expérimentation. Elle nous permet donc de tirer plusieurs conclusions relativement au développement du concept de covariation et à l’introduction de la représentation graphique chez les élèves du premier cycle du secondaire.

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Ce travail de thèse porte sur l'intégration des structures craniofaciales au sein de la famille des hominidés. Au cours de l'évolution, une réduction du prognathisme et une diminution de la longueur de la face sont observées chez les taxons appartenant au rameau humaine. Cette réduction des structures faciales est associée à une base du crâne plus fléchie et à une mandibule plus gracile. L'objectif de ce travail est de définir le rôle joué par les changements basicrâniens et mandibulaires dans la mise en place de la face courte et droite des humains modernes. Dans ce contexte, les schémas d'intégration liant la face et les autres structures crâniennes (basicrâne et mandibule) ont été décrits et quantifiés dans ce mémoire. Ce travail a été effectué sur la base d'un échantillon de crânes incluant l'ensemble des genres d'hominidés actuels : les humains modernes, les chimpanzés, les gorilles et les orangs-outans. Les crânes ont été préalablement numérisés à l'aide d'un scanner médical. Les schémas d'intégration craniofaciaux ont alors été étudiés à l'aide d'outils statistiques et de méthodes d'analyses en morphométrie géométrique. Ce travail a permis de mettre en avant plusieurs mécanismes d'intégration craniofaciale, propres aux humains modernes. Ces schémas d'intégration spécifiques permettent d'expliquer en grande partie la mise en place de la face réduite des humains modernes. Ces résultats permettent donc d'éclairer les mécanismes d'évolution et de mise en place des structures faciales chez les hominidés et dans le rameau humain. / This thesis dissertation is dedicated to the study of craniofacial structures within the hominid family. Throughout evolution, a reduction of facial prognathism and a diminution of the facial length are observed in the taxa which belong to the human lineage. This reduction of facial structures is associated to a more flexed cranial base and to a shorter mandible. The aim of this work is to define the role played by the basicranial and mandibular changes in the set up of the short and straight face of modern humans. In this context, the patterns of integration linking the face and the other cranial structures (basicranium and mandible) are decrypted and quantified in this thesis dissertation. This work has been done with a sample including all the extant hominid genera: modern humans, chimpanzees, gorillas, orang-utans. The skulls were first scanned using a medical scanner. Patterns of craniofacial integration were then studied using statistical tools and geometric morphometric analysis methods. This work underlined several mechanisms of craniofacial integration, unique to modern humans. These specific patterns of integration can explain an important part of the set up of modern humans reduced face. Thus, these results enlighten the evolution mechanisms and the set up of facial structures in hominids and in the human lineage.

My goal was to examine potential moderators that affect emotional coordination between romantic partners. I conducted three separate empirical studies that are conceptually related. I used data collected in conjunction with Dr. Emily Butler (all 3 papers), and Dr. Shanmukh Kamble of Karnatak University, India (paper 3). Using models of two forms of emotional coordination in partners - emotion transmission and synchrony - I examined the moderating effects of attachment, cooperation and marriage type on emotional coordination between partners. The purpose of first paper was to examine the role that individual factors, specifically differences in attachment avoidance and anxiety, have on the transmission of emotions between partners. Interestingly, results were counter to hypotheses based on attachment differences in emotion regulation, which suggests the limitations of taking an individual perspective within dyadic contexts. The second paper examined how cooperation impacts emotional coordination between partners. I found that cooperation produces different emotional coordination patterns for men and women. Specifically, when both partners were at high levels of cooperation, men showed an in-phase emotional coordination pattern (changes in unison), whereas women showed an anti-phase emotional coordination (changes in opposite directions). Therefore, while both partners were engaging in similar behaviors their emotional experience was different. In the third paper, I moved to a more global analysis of factors that moderate emotional synchrony between partners. Specifically, I examined how different marriage-types in American and Indian cultures (love versus arranged marriages) impact emotional synchrony between partners. I expected that Indian-love marriages would show similar synchronization patterns to American marriages, and that both would show more synchrony in comparison with Indian-arranged marriages. Unexpectedly, Indian-love and Indian-arranged marriages were similar and both displayed lower synchrony than American couples. These findings suggest that emotional experience between partners may be influenced by the boarder culture, irrespective of marriage type. Taken together, these papers provide evidence for when emotional coordination between couples can have beneficial or detrimental effects on the relationship, depending on individual, dyadic and cultural factors.

Uncertainty represents a robust threat that can amplify aversive experiences and exaggerate negative expectations about uncertain future outcomes. Mindfulness – an open and receptive attention to present moment experiences -- has been shown to facilitate adaptive regulation when faced with a variety of distinct emotional threats. Reduced experiential avoidance and equanimity in the face of unpleasant emotional experiences have been theorized as central to these emotional regulatory benefits. The present study explored whether dispositional mindfulness would promote adaptive responses to uncertainty during the anticipation of, and after exposure to emotional stimuli, as indicated by self-reports and neural (event-related potential) markers of anticipation and appraisal. Participants were exposed to stimulus cues that informed them about the valence of a subsequent emotional picture as neutral, aversive, or uncertain. Consistent with past research, uncertainty during the anticipation of an emotional stimulus amplified unpleasant stimulus appraisals, and participants demonstrated biased expectations to associate uncertainty with aversiveness. Dispositional mindfulness was associated with lower expectations for unpleasant stimuli, and was found to amplify the effect of uncertainty on a cortical marker of stimulus appraisal called the late positive potential (LPP). Traits that contrasted with mindfulness predicted opposite patterns of association with these measures. However, these findings were directly the opposite of findings from past research. A theoretically defensible explanation is discussed for these findings and suggestions were made for future research on the role of mindfulness on ERP variability. The results from the present study contribute to a growing body of evidence that suggests that uncertainty during the anticipation of potentially negative future outcomes can exert a potent downstream influence on emotional anticipation and appraisal processes. Further research is needed to clarify the role of dispositional mindfulness during emotional stimulus anticipation and appraisal following uncertainty.

Graphing is a fundamental topic in algebra that is notoriously difficult for students. Much of the past research has focused on conceptions and misconceptions. This study extends past research by looking at the mathematical practices of a practitioner, specifically one instructor of a function-based covariation-focused algebra class in the linear functions unit. Considering practices in addition to conception adds dramatically to our understanding of mathematical activity because it leads to explicit descriptions of normative purposes that are connected to particular situations or problems and also specifies how tools and symbols are coordinated to achieve these purposes. The results of this study are three levels of empirically proven practices associated with the conception of one advanced level of covariational reasoning, chunky continuous covariation. This study not only describes how practices may be described at different levels of complexity, but also demonstrates how smaller practices may be combined to form larger, more complex practices. These practices can be used to guide instruction of those who want to participate in and become practitioners in the community of teachers of function-based covariation-focused algebra curricula.