The study aimed at giving a thick description of African families' experiences, views, cultural beliefs and interpretations of traumatic brain injury (TBI), and making recommendations for rehabilitation. It was conducted from the qualitative research paradigm, adopting a phenomenological research method. Twenty-two pairs of participants (patients and their caregivers )were interviewed about their perception of TBI. The semi-structured interviews were conducted at the participants' homes in Sesotho, and where necessary in their home languages. The consequences of TBI were found to follow universal trends (Oddy, 1984). However, participants' perceptions, as shaped by their experiences, views and cultural beliefs, were found to be unique. On analysing the gathered data, using inductive data analysis, it was found that African families' interpretations of TBI were based on beliefs about witchcraft, thwasa, Satanism, ancestral anger and God's wish. Based on these findings, rehabilitation services in the form of education, advocacy, networking and family therapy are recommended. / Psychology / M.A.(Clinical Psychology)

There is currently a large increase in the speed of production of DNA sequence data as next generation sequencing technologies become more widespread. As such there is a need for rapid computational techniques to functionally annotate data as it is generated. One computational method for the functional annotation of protein-coding genes is via detection of interaction partners. If the putative partner has a functional annotation then this annotation can be extended to the initial protein via the established principle of “guilt by association”. This work presents a method for rapid detection of functional interaction partners for proteins through the use of the comparative method. Functional links are sought between proteins through analysis of their patterns of presence and absence amongst a set of 54 eukaryotic organisms. These links can be either direct or indirect protein interactions. These patterns are analysed in the context of a phylogenetic tree. The method used is a heuristic combination of an established accurate methodology involving comparison of models of evolution the parameters of which are estimated using maximum likelihood, with a novel technique involving the reconstruction of ancestral states using Dollo parsimony and analysis of these reconstructions through the use of logistic regression. The methodology achieves comparable specificity to the use of gene coexpression as a means to predict functional linkage between proteins. The application of this method permitted a genome-wide analysis of the human genome, which would have otherwise demanded a potentially prohibitive amount of computational resource. Proteins within the human genome were clustered into orthologous groups. 10 of these proteins, which were ubiquitous across all 54 eukaryotes, were used to reconstruct a phylogeny. An application of the heuristic predicted a set of functional protein interactions in human cells. 1,142 functional interactions were predicted. Of these predictions 1,131 were not present in current protein-protein interaction databases.

L’inférence de génomes ancestraux est une étape essentielle pour l’étude de l’évolution des génomes. Connaissant les génomes d’espèces éteintes, on peut proposer des mécanismes biologiques expliquant les divergences entre les génomes des espèces modernes. Diverses méthodes visant à résoudre ce problème existent, se classant parmis deux grandes catégories : les méthodes de distance et les méthodes de synténie. L’état de l’art des distances génomiques ne permettant qu’un certain répertoire de réarrangements pour le moment, les méthodes de synténie sont donc plus appropriées en pratique. Nous proposons une méthode de synténie pour la reconstruction de génomes ancestraux basée sur une définition relaxée d’adjacences de gènes, permettant un contenu en gène inégal dans les génomes modernes causé par des pertes de gènes de même que des duplications de génomes entiers (DGE). Des simulations sont effectuées, démontrant une capacité de former une solution assemblée en un nombre réduit de régions ancestrales contigües par rapport à d’autres méthodes tout en gardant une bonne fiabilité. Des applications sur des données de levures et de plantes céréalières montrent des résultats en accord avec d’autres publications, notamment la présence de fusion imbriquée de chromosomes pendant l’évolution des céréales. / Ancestral genome inference is a decisive step for studying genome evolution. Knowing genomes from extinct species, one can propose biological mecanisms explaining divergences between extant species genomes. Various methods classified in two categories have been developped : distance based methods and synteny based methods. The state of the art of distance based methods only permit a certain repertoire of genomic rearrangements, thus synteny based methods are more appropriate in practice for the time being. We propose a synteny method for ancestral genome reconstruction based on a relaxed defenition of gene adjacencies, permitting unequal gene content in extant genomes caused by gene losses and whole genome duplications (WGD). Simulations results demonstrate our method’s ability to form a more assembled solution rather than a collection of contiguous ancestral regions (CAR) with respect to other methods, while maintaining a good reliability. Applications on data sets from yeasts and cereal species show results agreeing with other publications, notably the existence of nested chromosome fusion during the evolution of cereals.

The archaeofaunal remains left by the Ancestral Puebloan people of Goodman Point Unit provides a valuable, yet underutilized resource into pit structure function. This thesis explores temporal changes in pit structure use and evaluates if a final feast occurred during a kiva decommissioning. The results from zooarchaeological analyses of a pithouse and two great kivas suggest that changes in pit structures at Goodman Point mimic the regional trend toward specialization until late Pueblo III. Cross-cultural studies on feasts, southwest ethnographies and previous zooarchaeological work established methods for identifying a feast. The analysis of differences in faunal remains from a great kiva and multiple room block middens imply that the remains in the kiva were from a final feast prior to a decommissioning ceremony and were not fill. Spatially and temporally the great kiva appears to be a unique, specialized structure in the cultural development of the Goodman Point community.

This study focuses on the burial practices in the Bronze Age Xiaohe-Gumugou cemeteries, north-west China, in order to understand how people constructed their social identities and delivered the social cognitions through generations. The Xiaohe-Gumugou cemeteries, as the main sites of the Xiaohe cultural horizon, have central roles for the understanding of the formation of the Bronze Age cultural groups and the cultural interactions between the west and the east in the Tarim Basin. However, current research is lacking in-depth examinations of the material culture of the cemeteries, and the contexts of the surrounding archaeological cultures in a timespan from Bronze Age to Iron Age. Through detailed comparisons of the construction of coffins and monuments, the dress of the dead, and the burial goods assemblages, this study provides an overview of the social structural development, from the Gumugou group’s heterogenous condition to the Xiaohe group’s homogeneous and mature state. Also, through relating to the results of biological and osteological analyses, and applying geographical analyses to the material, this study suggests that the early settlers in the Tarim Basin, the Xiaohe-Gumugou people have created their own social identities. Although the Xiaohe-Gumugou people might have migrated from southern Siberia or Central Asia, the archaeological material shows indications of their own typical features. When newcomers joined the society, the local burial customs were accepted and applied in a new cultural setting. / Denna studie fokuserar på gravskick på gravfälten Xiaohe och Gumugou i nordvästra Kina, för att förstå hur människor konstruerade social identitet och överförde kulturella föreställningar mellan generationer. Xiaohe-Gumugou-gravfälten, som de viktigaste platserna i Xiaohe-kulturhorisonten, är centrala för förståelsen av bildandet av bronsålderns kulturgrupper och de kulturella växelverkningarna mellan väst och öst i Tarimbäckenet. Tidigare forskning saknar fördjupade undersökningar av gravfältens materiella kultur samt den historiska kontexten med de omgivande arkeologiska kulturerna under tidsperioden från bronsålder till järnålder. Genom detaljerade jämförelser av konstruktionen av kistor och monument samt de dödas klädsel och gravgåvor, ger denna studie en översikt över utvecklingen av sociala strukturer, från Gumugou-gruppens heterogena situation till Xiaohe-gruppens homogena och mogna tillstånd. Genom att relatera till resultaten från biologiska och osteologiska analyser och tillämpa geografiska analyser på materialet, tyder den här studien på att de tidiga bosättarna i Tarimbäckenet, Xiaohe-Gumugou-folket, har utvecklat egna sociala identiteter. Trots att Xiaohe-Gumugou-folket kan ha migrerat från södra Sibirien eller Centralasien visar det arkeologiska materialet indikationer på egna typiska egenskaper. När nykomlingar anslöt till samhället accepterades de lokala begravningssederna och tillämpades i ett nytt kulturellt sammanhang.

O objetivo desta dissertação é verificar como se deu o registro da história de uma prática ancestral como a capoeira que, a despeito de ter-se originado nas senzalas no período colonial, ainda não teve o devido reconhecimento social. Dadas as lacunas desse registro, foram entrevistados alguns mestres de capoeira com extensa experiência na transmissão dessa cultura com o objetivo de reconstruir, por meio de suas narrativas de vida, as contribuições dessa prática ancestral para a formação de gerações de jovens afrodescendentes. Embora as Leis Federais 10.639/03 e 11.645/08 reconheçam sua importância histórica, cultural e política e a considere fundamental para a formação das novas gerações, prevendo, além disso, sua introdução nas escolas, sua prática ainda encontra obstáculos nesse âmbito. Daí serem propostas, como parte da pesquisa, experiências de docência compartilhada de capoeira na Escola de Aplicação FEUSP, visando contribuir para a formação de professores para o ensino da história e cultura afro-brasileira e africana. O conceito de reconhecimento nos planos subjetivo, jurídico e cultural defendido por Axel Honneth, bem como a reconstrução da história da capoeira nos estados de São Paulo, Rio de Janeiro e Bahia, como parte das lutas de resistência dos escravizados no Brasil, foram essenciais para interpretar o conteúdo crítico das letras das músicas e o significado simbólico do jogo da capoeira e de seus rituais, além de contribuir para o reconhecimento de uma cultura afro-brasileira amplamente difundida em praticamente todos os continentes. / The objective of this project was to research on how the history of an ancient practice, such as capoeira, was registered. In spite of having originated at the slave quarters in the colonial period, the capoeira has not yet seen its social recognition. . Due to the gaps within such registration, we have interviewed some capoeira masters with extensive experience in the transmission of its culture aiming at rebuilding, the capoeira contributions to the upbringing of generations of African descendant youngsters. Although the Federal Laws 10.639/03 and 11.645/08 which recognizes the historical, cultural and political importance of capoeira, and considers it crucial for the formation of new generations, foreseeing its implementation in schools, its practice still faces obstacles in this scope. Therefore, we propose as part of the research, experiences of shared teaching of capoeira at FEUSP\'S Application School, seeking to contribute to the teachers\' formation for the teaching of history and Afro-Brazilian and African culture. The concept of recognition - in the subjective, legal and cultural perspectives, defended by Axel Honneth, as well as the reconstruction of the history of capoeira in the states of São Paulo, Rio de Janeiro and Bahia. It as part of the enslaved resistance in Brazil, were essential to interpret the critical content of the lyrics and the symbolic meaning of the game of capoeira and its rituals. They also contributed to the recognition of a widespread Afro-Brazilian culture on practically all the continents.

Auf der Basis von Fossilien wird angenommen, dass die ersten Säugetiere nachtaktiv waren. Diese Arbeit untersucht diese Hypothese mit bioinformatischen und molekularbiologischen Techniken. Der Fokus liegt auf dem Rhodopsin, ein Sehpigment im Wirbeltierauge, das für Sehen unter schlechten Lichtverhältnissen verantwortlich ist. Zunächst wurde das Rhodopsin der monotrematen Echidna, einem basalen Säugetier, sequenziert und mit zwei Mutanten mit Mutationen an Positionen 158 und 169 in vitro exprimiert. Die biochemische und funktionelle Charakterisierung ergab, dass das Echidna-Rhodopsin farbpigment-typische Charakteristika aufweist, was auf eine Expression auch in Zapfen hindeutet. Dies ist die erste Charakterisierung eines Rhodopsins eines nachtaktiven Tieres. Dann wurden anzestrale Rhodopsinsequenzen für die Knotenpunkte Amniota, Mammalia und Theria mithilfe der Maximum-Likelihood-Methode berechnet. Die in vitro Expression und biochemische und funktionelle Charakterisierung zeigt funktionale und rhodopsin-typische Sehpigmente. Das Mammalia- und Theria-Rhodopsin zeigen eine hohe Meta II Halbwertszeit. Dieses Ergebnis wird als eventuelle Anpassung an Sehen unter schlechten Lichtverhältnissen interpretiert, wobei, aufgrund von Unstimmigkeiten in der Literatur, Schlussfolgerungen auf ökologisch-bedingte Anpassungen basierend auf einzelnen Funktionstests problematisch sind, da die visuelle Signalkaskade ein sehr komplexes und durch viele Proteine vernetztes System darstellt. Zuletzt zeigen Selektionsanalysen, dass das Rhodopsin entlang der Theria-Linie positive Selektion auf nicht-synonyme Substitutionen erfahren hat, was zu Anpassungen in einem Protein führt. Der Fossilbericht belegt entlang dieser Linie mehrere Einnischungsevents in neue Lebensräume. Entlang der Mammalia-Linie wurde positive Selektion auf synonyme Substitutionen gemessen, was zu einer Zunahme an Rhodopsin-Molekülen führt und damit eine Anpassung an Sehen unter schlechten Lichtverhältnissen darstellt. / Based on information from the fossil record, the first mammals are thought to have been nocturnal. This thesis investigates this popular hypothesis using bioinformatic and molecular techniques, focusing on the rhodopsin, a visual pigment in the vertebrate eye that is responsible for vision at low-light levels. First, the rhodopsin gene of the monotreme echidna, a basal mammal, was sequenced and successfully expressed in vitro, together with two mutants with substitutions at sites 158 and 169. Biochemical and functional analyses revealed that the echidna rhodopsin displays cone-like characteristics, likely due to being also expressed in cones. With the echidna being nocturnal, this thesis comprises the first characterisation of a rhodopsin of a nocturnal animal. Second, ancestral rhodopsin sequences for the tetrapod nodes Amniota, Mammalia, and Theria were inferred using Maximum likelihood estimates. All expressed pigments were successfully expressed in vitro, functional and rod-like. Mammalia and Theria rhodopsins display a high meta II half life time, a pattern that is usually interpreted to facilitate better vision at low-light levels. However, due to inconsistency in the available data, the result also suggests that, with the visual signaling cascade being a complex and interconnected system, erecting ecological interpretations based on single biochemical and functional reactions is problematic. Third, selective constraint analyses performed on a set of tetrapod rhodopsin sequences indicate that positive selection on non-synonymous sites, was acting along the branch leading to Theria. This result reflects the rapid diversification into modern ecological habitats during the Triassic and Jurassic, as indicated by the fossil record. In addition, positive selection on synonymous sites, leading to an increase of rhodopsin molecules, was found along the branch leading to Mammalia and suggests adaptations to vision at low-light levels.

La théorie de l’évolution repose sur la biologie moderne. Toutes les nouvelles espèces émergent d’une espèce existante. Il en résulte que différentes espèces partagent une ascendance commune, telle que représentée dans la classification phylogénétique. L’ascendance commune peut expliquer les similitudes entre tous les organismes vivants, tels que la chimie générale, la structure cellulaire, l’ADN comme matériau génétique et le code génétique. Les individus d’une espèce partagent les mêmes gènes mais (d’ordinaire) différentes séquences d’allèles de ces gènes. Un individu hérite des allèles de leur ascendance ou de leurs parents. Le but des études phylogénétiques est d’analyser les changements qui se produisent dans différents organismes pendant l’évolution en identifiant les relations entre les séquences génomiques et en déterminant les séquences ancestrales et leurs descendants. Une étude de phylogénie peut également estimer le temps de divergence entre les groupes d’organismes qui partagent un ancêtre commun. Les arbres phylogénétiques sont utiles dans les domaines de la biologie, comme la bio informatique, pour une phylogénétique systématique et comparative. L’arbre évolutif ou l’arbre phylogénétique est une exposition ramifiée les relations évolutives entre divers organismes biologiques ou autre existence en fonction des différences et des similitudes dans leurs caractéristiques génétiques. Les arbres phylogénétiques sont construits à partir de données moléculaires comme les séquences d’ADN et les séquences de protéines. Dans un arbre phylogénétique, les nœuds représentent des séquences génomiques et s’appellent des unités taxonomiques. Chaque branche relie deux nœuds adjacents. Chaque séquence similaire sera un voisin sur les branches extérieures, et une branche interne commune les reliera à un ancêtre commun. Les branches internes sont appelées unités taxonomiques hypothétiques. Ainsi, les unités taxonomiques réunies dans l’arbre impliquent d’être descendues d’un ancêtre commun. Notre recherche réalisée dans cette dissertation met l’accent sur l’amélioration des prototypes évolutifs appropriés et des algorithmes robustes pour résoudre les problèmes d’inférence phylogénétiques et ancestrales sur l’ordre des gènes et les données ADN dans l’évolution du génome complet, ainsi que leurs applications.[...] / The theory of evolution is based on modern biology. All new species emerge of an existing species. As a result, different species share common ancestry,as represented in the phylogenetic classification. Common ancestry may explainthe similarities between all living organisms, such as general chemistry, cell structure,DNA as genetic material and genetic code. Individuals of one species share the same genes but (usually) different allele sequences of these genes. An individual inheritsalleles of their ancestry or their parents. The goal of phylogenetic studies is to analyzethe changes that occur in different organisms during evolution by identifying therelationships between genomic sequences and determining the ancestral sequences and theirdescendants. A phylogeny study can also estimate the time of divergence betweengroups of organisms that share a common ancestor. Phylogenetic trees are usefulin the fields of biology, such as bioinformatics, for systematic phylogeneticsand comparative. The evolutionary tree or the phylogenetic tree is a branched exposure the relationsevolutionary between various biological organisms or other existence depending on the differences andsimilarities in their genetic characteristics. Phylogenetic trees are built infrom molecular data such as DNA sequences and protein sequences. Ina phylogenetic tree, the nodes represent genomic sequences and are calledtaxonomic units. Each branch connects two adjacent nodes. Each similar sequencewill be a neighbor on the outer branches, and a common internal branch will link them to acommon ancestor. Internal branches are called hypothetical taxonomic units. Thus,Taxonomic units gathered in the tree involve being descended from a common ancestor. Ourresearch conducted in this dissertation focuses on improving evolutionary prototypesappropriate and robust algorithms to solve phylogenetic inference problems andancestral information about the order of genes and DNA data in the evolution of the complete genome, as well astheir applications.

La puissance de la biopile enzymatique à glucose/oxygène est limitée par sa partiecathodique. Afin de contourner cette limitation, nous avons étudié les enzymescathodiques : les Bilirubine oxydases (BODs). Dans le but de mieux appréhender ces BODs, lemécanisme réactionnel, la nature de l’étape limitante et l’effet des sels ont alors été étudiés.Deux mécanismes différents sont retrouvés en fonction du mode de transfert des protons etdes électrons (4 fois 1H+/1e- ou 2 fois 2H+/2e-). De plus, nous avons démontré que l’étapelimitante est l’oxydation du substrat pour les trois substrats testés et que les sels agissent auniveau du cuivre T1. Les principales limitations des BODs sont leur stabilité à 37 °C ainsi queleur inhibition par le NaCl. Deux techniques ont alors été utilisées pour identifier des BODsplus résistantes. La première méthode est l’extraction de nouvelles enzymes à partird’organismes extremophiles. Elle a permis d’isoler la BOD d’Anaerophaga thermohalophilaqui possède une bonne résistance au NaCl mais une densité de courant faible. Dans unsecond temps, afin de reconstruire des séquences ancestrales, la phylogénie de la familledes Bacillus Bacterium a été effectuée. Cette technique a permis l’identification de troisBODs possédant des caractéristiques très intéressantes : la BOD de Bacillus nakamurai etdeux BODs ancestrales (Noeud 10 et Noeud 13). Par exemple, après une heure à 37°C et 140mM de NaCl, le Noeud 10 possède une meilleure densité de courant que la BOD de Bacilluspumilus, qui est l’enzyme utilisée comme base de la phylogénie. La seconde technique estdonc une méthode de choix permettant la découverte de nouvelles enzymes à la fois plusstables et plus résistantes que les enzymes actuelles. Elle ouvre de grandes perspectivespour l’utilisation des BODs comme enzymes cathodiques ou pour d’autres applicationsbiotechnologiques. Enfin, nous avons montré que l’immobilisation de la BOD de B. pumilusdans le matériau Si-(HIPE) permet la décoloration cyclique de colorants chimiques surplusieurs mois. / Power of glucose/oxygen enzymatic biofuel cell is limited by the cathodic part. In order to prevent this limitation, we studied cathodic enzymes: Bilirubin oxidases (BODs). For this purpose, the kinetic mechanism, rate-limiting step and salts effect were determined. Two different mechanisms are observed depending on the electron/proton transfer (4 times1H+/1e- or 2 times 2H+/2e-). We also demonstrated that the rate-limiting step is the substrate oxidation for the three substrates tested and salts act around the T1 copper. Main BODs limitations are their stability at 37°C and their inhibition by NaCl. Two methods were used toidentify the most resistant BODs. The first one was the identification of new enzymes from extremophile organisms. It allows to isolate BOD from Anaerophaga thermohalophila whichhas good NaCl resistance but low current density. In addition, in order to reconstructancestral sequences, phylogeny of Bacillus Bacterium family was performed. This methodidentified three BODs with interesting features: BOD from Bacillus nakamurai and twoancestral BODs (Noeud 10 and Noeud 13). For example, after one hour at 37°C and 140 mMNaCl, Noeud 10 has a better current density than the BOD from Bacillus pumilus, which is theenzyme used as basis for the phylogeny. This second method allowed the discovery of newenzymes that were both more stable and more resistant than actual enzymes. Thistechnique opens up valuable prospects for the use of BODs as cathodic enzymes or for otherbiotechnological applications. In the end, we demonstrated that BOD from B. pumilusimmobilization in Si-(HIPE) materials allows cyclic discoloration of chemical dyes duringseveral months.

This paper is a summary of the methods and key results of my analysis of 7,997 sherds from 14 sites in Beef Basin, Utah. I discuss physical attributes of the collection, the results of mean ceramic dating, the results of neutron activation analysis, and the results of refiring a sample of nips in an oxidizing atmosphere. I briefly summarize the architecture at each site , as well as possible Fremont cultural material found in and near Beef Basin. I conclude that Beef Basin was likely occupied in the early Pueblo III period and that the occupation was sudden and brief. I determined that paste color can be used as a general indicator of clay procurement locale north of the Abajo Mountains, just as it is in the Comb Ridge vicinity (Glowacki et al. 2015), that there was ceramic production in Beef Basin using local materials, and that the people of Beef Basin had similar connections as, or connections with the east of the Comb Ridge area, as evinced by similar sources for light-paste ceramics found in both areas.