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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
101

Exploring Different Experience Modalities of Tennis Electronic Line Calling : Key elements of the interaction between players and the system / Utforska olika upplever av Tennis vid assisterat domslut : Avgörande faktor i samspelet mellan spelare och systemet

Rignanese, Leonardo January 2022 (has links)
New technologies have made sports more entertaining, safe, and fair in recent years. This study focuses on electronic line calling, a technology that is revolutionizing tennis. A set of sensors and complex algorithms enable umpires and players to determine with a certain degree of precision whether the ball has bounced inside or outside the court. Numerous technological solutions have been developed in this ambit, but little research has been conducted on the interaction between players and the system during a match. The research follows the Research trough Design approach and the Double-Diamond design process. I collaborated with the company PlayReplay AB, that has developed an electronic judging system. At first, I used research methods such as interviews with experts to understand the user needs and narrow down the problem. Secondly, I explored different modalities and iterated on several user interfaces to generate a final design proposal for PlayReplay's system. The findings demonstrate that the player experience with an electronic line call system depends on various elements. First, the system must adhere to certain requirements like discretion, punctuality, and reliability, otherwise will feel unreliable or disturbing. Second, the interaction modalities should comply with some specifics: the output should be easily identifiable but not obtrusive, and the input must be easy to use but also well incorporated into the game. / Ny teknik har gjort sport mer underhållande, säkrare och mer rättvis de senaste åren. Denna studie fokuserar på elektroniskt linjeanrop (ELC), en teknik som revolutionerar tennis. Sensorer och komplexa algoritmer gör det möjligt för domare och spelare att med en viss precision avgöra om bollen har studsat innanför eller utanför planen. Många tekniska lösningar har utvecklats inom detta område, men lite forskning har gjorts på interaktionen mellan spelare och systemet under en match. Jag samarbetade med företaget PlayReplay AB som har utvecklat ett elektroniskt bedömningssystem. Min forskning följer ”Research trough Design”-metoden och designprocessen ”Double Diamond”. Till en början använde jag forskningsmetoder som intervjuer med experter för att förstå användarnas behov och begränsa problemet. För det andra utforskade jag olika modaliteter och itererade på flera användargränssnitt för att generera ett slutgiltigt designförslag för PlayReplays ELC-system. Resultaten visar att spelarens erfarenhet av ett elektroniskt linjesamtalssystem beror på olika faktorer. För det första måste systemet följa vissa krav som diskretion, punktlighet och tillförlitlighet, annars kommer det att kännas opålitligt eller störande. För det andra bör interaktionen mellan användaren och systemet överensstämma med följande principer: Resultatet ska vara lätt identifierbart men inte påträngande, och interaktionen måste vara lättanvänd men också väl integrerad i spelet. / Uudet teknologiat ovat tehneet urheilusta viihdyttävämpää, turvallisempaa ja oikeudenmukaisempaa viime vuosina. Tämä tutkimus keskittyy Electronic line calling -teknologiaan (ELC), joka parhaillaan mullistaa tennistä. Nopeat anturit ja monimutkaiset algoritmit antavat tuomareille ja pelaajille mahdollisuuden määrittää tietyllä tarkkuudella, onko pallo pomppinut kentän sisällä vai ulkopuolella. Alalla on kehitetty lukuisia teknisiä ratkaisuja, mutta pelaajien ja järjestelmien välistä vuorovaikutusta ottelun aikana on tutkittu vähän. Tein yhteistyötä PlayReplay AB:n kanssa, joka on kehittänyt sähköisen tuomarointijärjestelmän. Tutkimus noudattaa Research trough Design -lähestymistapaa ja Double diamond -suunnitteluprosessia. Ensin käytin tutkimusmenetelmiä, kuten asiantuntijoiden haastatteluja käyttäjien tarpeiden ymmärtämiseksi ja ongelman rajaamiseksi. Toiseksi tutkin erilaisia modaliteetteja ja iteroin useammalla käyttöliittymällä luodakseni lopullisen suunnitteluehdotuksen PlayReplayn ELC-järjestelmästä. Löydökset osoittavat, että pelaajan kokemus sähköisestä linjapuhelujärjestelmästä koostuu useista osista. Ensinnäkin järjestelmän on täytettävä tietyt vaatimukset, kuten harkintakyky, täsmällisyys ja luotettavuus. Sitten vuorovaikutusmenetelmien tulee noudattaa joitain erityispiirteitä: tulosteen tulee olla helposti tunnistettavissa, mutta ei häiritsevä, ja syötteen on oltava helppokäyttöinen, mutta se on myös sisällytettävä kunnolla peliin. / Negli ultimi anni, l'avvento di nuove tecnologie ha reso gli sport più divertenti, sicuri e corretti. Questa ricerca si concentra sui sistemi di chiamata di linea automatizzati (ELC), una tecnologia che sta rivoluzionando il tennis. Sensori ad alta precisione e algoritmi complessi consentono agli arbitri e ai giocatori di determinare, con un certo grado di precisione, se la palla è rimbalzata all'interno o all'esterno del campo. In questo ambito sono state sviluppate numerose soluzioni tecnologiche, ma poche sono state le ricerche condotte sull'interazione tra i giocatori e il sistema durante una partita. Ho collaborato con l'azienda PlayReplay AB, che ha sviluppato un sistema di arbitraggio elettronico. Questa tesi segue l'approccio della ricerca attraverso il design (Research through Design) e il processo di progettazione a doppio diamante (Double Diamond). Inizialmente, si è fatto uso di metodi di ricerca, come interviste ad esperti, per comprendere le esigenze degli utenti e restringere il problema; in secondo luogo, si sono esplorate differenti modalità di interazione attraverso l'iterazione con diverse interfacce utente. Il fine è stato quello di generare una interfaccia utente da utilizzare nel sistema ELC di PlayReplay. I risultati dimostrano che l'esperienza del giocatore è composta da varie componenti. Innanzitutto, il sistema deve rispettare determinati requisiti come discrezione, puntualità e affidabilità. Inoltre, le modalità di interazione con il sistema devono rispettare alcune specifiche: l'output dovrebbe essere facilmente identificabile ma allo stesso tempo non invadente e l'input deve essere semplice da utilizzare e ben integrato nel gioco.
102

The phenomenon of Xenophobia as experienced by immigrant learners in inner city schools of Johannesburg

Osman, Razia 11 1900 (has links)
There has been a significant increase in immigrant learners in South African schools. This research study captures the experiences of immigrant learners in selected inner city schools of Johannesburg. The May 2008 xenophobic violence prompted the researcher to investigate the extent of xenophobia. A survey of immigrant learners, South African learners and educators was conducted by means of interviews that allowed the research participants to express their feelings and experiences regarding the phenomenon of xenophobia. The result of the study revealed that immigrant learners do experience xenophobia in various forms by South African learners and, in some cases, educators as well. Immigrant learners were predominantly exposed to prejudice and xenophobic comments. They perceived South Africa as positive, giving them hope and opportunities. This research provided a baseline for more extensive research into this phenomenon. / Thesis (M. Ed. (Guidance and Counselling)
103

Berufung zur Ehelosigkeit : eine seelsorgerliche Hilfe für Singles? / The call to celibacy : a pastoral aid for singles?

Fuisting, Dirk 08 1900 (has links)
German text / Singles sind Menschen mit speziellen Problemen und Bedürfnissen – insbesondere, wenn sie unfreiwillig Single sind und lieber in einer Partnerschaft leben wollen. Viele Singles leiden unter ihrem Dasein als Single, ihre Probleme können vielfältig sein: Einsamkeit, unbefriedigte sexuelle Wünsche, mangelndes Selbstwertgefühl, fehlende Elternschaft, Leere und Antriebslosigkeit. Diese Probleme stellen die Seelsorge vor eine wichtige Aufgabe: Wie kann man diesen leidenden Singles helfend begegnen? Mein poimenischer Ansatz besteht darin, die Frage nach der Berufung zur Ehelosigkeit zu stellen(1 Korinther 7,17). Wenn Singles ihr Dasein nicht mehr als gescheiterte Existenz betrachten, sondern als Stand, zu dem sie von Gott berufen worden sind, hilft das vielleicht, eine positivere Lebenseinstellung zu bekommen und ein zufriedeneres Leben zu führen. / Singles are people with special problems and needs – particularly when they are involuntary singles and would prefer to live in a partner relationship. Many singles suffer with their condition as a single, and their problems can be manifold: loneliness, unsatisfied sexual desires, feelings of low self-worth, missing parenthood, emptiness and listlessness. These problems present the pastoral carer with an important task: How can these suffering singles be helped? My poimenics orientated approach is to raise the question regarding the call to singleness (1 Corinthians 7:17). When singles no longer consider their life as a failed existence, but rather as a state to which they have been called by God, perhaps that would help them have a more positive attitude to life, and to lead a satisfying life. / Practical Theology / M. Th. (Practical Theology)
104

The phenomenon of Xenophobia as experienced by immigrant learners in inner city schools of Johannesburg

Osman, Razia 11 1900 (has links)
There has been a significant increase in immigrant learners in South African schools. This research study captures the experiences of immigrant learners in selected inner city schools of Johannesburg. The May 2008 xenophobic violence prompted the researcher to investigate the extent of xenophobia. A survey of immigrant learners, South African learners and educators was conducted by means of interviews that allowed the research participants to express their feelings and experiences regarding the phenomenon of xenophobia. The result of the study revealed that immigrant learners do experience xenophobia in various forms by South African learners and, in some cases, educators as well. Immigrant learners were predominantly exposed to prejudice and xenophobic comments. They perceived South Africa as positive, giving them hope and opportunities. This research provided a baseline for more extensive research into this phenomenon. / Thesis (M. Ed. (Guidance and Counselling)
105

“Dando las gracias a mis papás”: A discursive analysis of perceptions of policy and callings across generations of Latinx immigrants

Virginia Sanchez (6951713) 15 August 2019 (has links)
<p>U.S. rhetoric that embraces immigration is juxtaposed with the lived experiences of Latinx immigrants, the country’s largest immigrant group. Intergenerational research shows how immigrants’ social mobility depends on socioeconomic and environmental factors, impacting occupational attainment. Immigration policies portray immigrants negatively—contrasting deserving/good with undeserving/bad. This study uses d/Discourse (i.e., everyday talk/societal understandings) to investigate how immigrants from different generations make sense of policy, immigrant portrayals, and their lives through the lens of “calling.” Here, calling is used to understand differences across generations, rather than positioned as an individual pull toward an occupation. Specifically, this study answered three questions: (1) What occupational and intergenerational d/Discourses are perceived by immigrants?; (2) Whose interests are served by these d/Discourses and who is marginalized?; (3) How do immigrants experience “callings” across generations? Semi-structured interviews were conducted with different generations of immigrants (N=36). Generational and intergenerational sensemaking themes are identified using d/Discourse, while critical discourse analysis is used to explain inequalities and in whose interests d/Discourses are created. The main theoretical contribution of this study suggests that callings can be enacted and fulfilled intergenerationally. Within immigrant families, first-generation immigrants often hold visions of who their children (second-generation immigrants) will become. This vision often includes high educational attainment, a prestigious occupation, and documentation in the United States. Second-generation immigrants felt a pressure to perform well in school and validate the sacrifices made by their parents. They recognized that the visions for their future constructed by their first-generation parents were riddled with tensions. The occupational decisions of the second-generation immigrants often tried to find a middle ground between fulfilling their parents’ vision but also practicing in occupations that they were personally interested in. Several barriers made the path to fulfilling intergenerational callings more difficult. Second-generation immigrants recognized the privileges they held that their parents did not, including language barriers and acceptance into the country tied to documentation and acceptance based on racial models in the United States. While first-generation immigrants accepted these challenges as part of their intergenerational calling, the second-generation struggled to do the same. Finally, in fulfilling intergenerational callings many immigrants unintentionally reproduced deservingness narratives. In short, this study contributes theoretically and practically by challenging immigrant portrayals and viewing callings as intergenerational but filled with internal and external challenges.</p>
106

Mating behavior as non-invasive biomarker in Xenopus laevis for the assessment of endocrine disrupting compounds

Hoffmann, Frauke 23 May 2012 (has links)
Hormonell wirksame Chemikalien, wie Pflanzenschutzmittel oder Pharmaka gelangen durch Abwässer in die Umwelt und akkumulieren vor allem in Oberflächengewässern. Ein erhöhtes Augenmerk liegt auf Substanzen, die durch (anti)androgene und (anti)östrogene Wirkungsweise die Reproduktion von Tieren und Menschen beeinträchtigen. Bei den bisherigen Nachweismethoden für diese Stoffe handelt es sich um invasive Methoden, die das Töten der Tiere beinhalten. Diesen Methoden mangelt es jedoch an der nötigen Sensitivität, um umweltrelevante Konzentrationen der endokrinen Disruptoren (EDs) nach Kurzzeitexposition nachweisen zu können, sowie am Vermögen, alle vier Wirkmechanismen (androgen, antiandrogen, östrogen und antiöstrogen) mit einer einzelnen Testmethode feststellen und unterscheiden zu können. In dieser Studie wurde deshalb mit Hilfe männlicher Afrikanischer Krallenfrösche (Xenopus laevis) eine Testmethode entwickelt, bei der die Frösche verschiedenen (anti)androgenen und (anti)östrogenen EDs ausgesetzt wurden und ihr Rufverhalten untersucht wurde. Diese nicht-invasive Methode erwies sich als schnell und höchst sensitiv. Zudem war es erstmals möglich, die vier verschiedenen Wirkmechanismen allein anhand veränderter Ruftypen und Rufparameter zu bestimmen und zu unterscheiden. Darüber hinaus konnte gezeigt werden, dass bei Anwendung dieser Methode die Möglichkeit besteht, die Versuchstiere in weiteren Tests wiederzuverwenden, da die Rufparameter nach einer expositionsfreien Zeit von sechs Wochen wieder Kontrollwerte erreichten. Zusammengefasst kann die hier vorgestellte verhaltensphysiologische und damit nicht-invasive Methode als Biomarker für den Nachweis von (anti)androgenen und (anti)östrogenen EDs verwendet werden. Ferner zeigt die hohe Sensitivität des Tests, sowie die Möglichkeit der vollautomatischen Analyse enormer Datenmengen, dass dieser schnelle Verhaltenstest ein großes Potential hat, ein sensitiver, standardisierter und nicht-invasiver Biomarker zu werden. / Endocrine disrupting compounds (EDCs), such as herbicides, pesticides or pharmaceuticals enter the environment via sewage effluents and especially accumulate in surface waters. Research efforts so far mainly focused on EDCs with (anti)androgenic and (anti)estrogenic modes of action (MOAs), which can interfere with reproductive biology of vertebrates. To date, biomarkers for the assessment of such compounds are invasive techniques, which are not sensitive enough to detect EDCs after short-term exposures and which cannot distinguish between the four MOAs. Hence, in this study a non-invasive method for the assessment of EDCs was developed using male African clawed frogs (Xenopus laevis) as model species. Frogs were exposed to individual (anti)androgenic and (anti)estrogenic EDCs in the surrounding water and their calling behavior was analyzed. This non-invasive method turned out to be a fast and highly sensitive biomarker for the detection of (anti)androgenic and (anti)estrogenic EDCs. Moreover, this method was able to differentiate between the four different MOAs solely by determining affected parameters of the calling behavior. It was also shown that by using this method, it might be possible to reuse already tested experimental animals, because the measured affected parameters were reversed after a period of six weeks under control conditions. Taken together the here established non-invasive behavioral method can be used as biomarker for the detection of (anti)androgenic and (anti)estrogenic EDCs. Furthermore, the high sensitivity of this testing method, as well as the possibility of analyzing vast datasets rapidly in a completely automated fashion indicate the huge potential for this rapid behavior test to become a sensitive, standardized, non-invasive biomarker.
107

Using new tools to study the neural mechanisms of sensation : auditory processing in locusts and translational motion vision in flies

Isaacson, Matthew David January 2019 (has links)
This thesis describes work from both the University of Cambridge in the lab of Berthold Hedwig and from the HHMI Janelia Research Campus in the lab of Michael Reiser. At the University of Cambridge, my work involved the development and demonstration of a method for electrophoretically delivering dyes and tracers for anatomical and functional imaging into animals that are not amenable to genetic labelling techniques. Using this method in locusts and crickets - model systems of particular interest for their acoustic communication - I successfully delivered polar fluorescent dyes and tracers through the sheath covering the auditory nerve, simultaneously staining both the peripheral sensory structures and the central axonal projections without destroying the nerve's function. I could label neurons which extend far from the tracer delivery site on the nerve as well as local neuron populations through the brain's surface. I used the same method to deliver calcium indicators into central neuropils for in vivo optical imaging of sound-evoked activity, as well as calling song-evoked activity in the brain. The work completed at the Janelia Research Campus began with the development of a modern version of a modular LED display and virtual reality control system to enable research on the visual control of complex behaviors in head-fixed animals. The primary advantages of our newly developed LED-based display over other display technologies are its high-speed operation, brightness uniformity and control, precise synchronization with analog inputs and outputs, and its ability to be configured into a variety of display geometries. Utilizing the system's fast display refresh rates, I conducted the first accurate characterization of the upper limits of the speed sensitivity of Drosophila for apparent motion during flight. I also developed a flexible approach to presenting optic flow scenes for functional imaging of motion-sensitive neurons. Finally, through the on-line analysis of behavioral measures, image rendering, and display streaming with low latency to multi-color (UV/Green) LED panels, I demonstrated the ability to create more naturalistic stimuli and interactive virtual visual landscapes. Lastly, I used this new visual display system to explore a newly discovered cell-type that had been implicated in higher-order motion processing from a large genetic screen of visually-guided behavior deficits. Using genetic silencing and activation methods, and by designing stimuli that modeled the optic flow encountered during different types of self-motion, colleagues in the Reiser lab and I showed that this cell-type - named Lobula Plate Columnar 1 (LPC1) - is required for the stopping behavior of walking flies caused by back-to-front translation motion but is not involved in the rotational optomotor response. Using calcium imaging, I found that LPC1 was selectively excited by back-to-front motion on the eye ipsilateral to the neuron population and inhibited by front-to-back motion on the contralateral eye, demonstrating a simple mechanism for its selectivity to translation over rotation. I also examined an anatomically similar cell type - named Lobula-Lobula Plate Columnar type 1 (LLPC1) - and found that its selectivity results from a similar but opposite calculation for the detection of front-to-back translational motion. The detection of back-to-front motion had previously been hypothesized to be useful for collision avoidance, and this work provides a neural mechanism for how this detection could be accomplished, as well as providing a platform from which to explore the larger network for translation optic flow.
108

Seguimento de Jesus na cristologia de Jon Sobrino

Bombonatto, Ivanise 29 October 2012 (has links)
Made available in DSpace on 2016-04-29T14:27:22Z (GMT). No. of bitstreams: 1 Ivanise Bombonatto.pdf: 1269045 bytes, checksum: 914fc8b8d8494a096ce4d0f81596b6f2 (MD5) Previous issue date: 2012-10-29 / The aim of this research is to answer the following question: what is the meaning, the relevance and the reaching of knowing Jesus and its implications for the Christian existence, in the actual context, determined by deep and quick changes in all fields of knowledge and human activity. The answer to this question is given having as support the theologian Jon Sobrino s Christology. His Christological reflection arises from an engaged life with victims cry, it s at life s service, completely linked to the historical reality and it is developed in the perspective of knowing Jesus. The aim was to identify the original and renewed feelings in relation to knowing Jesus and the aspects directly related with this theme. Knowing Jesus is the fundamental idea of Jon Sobrino s Christology, not as historical, spiritual or moral basis, but, as Christological category, epistemological place, hermeneutical principle, totalizing reality, structuring of Christian life. Knowing Jesus is to reproduce the fundamental structure of your life: incarnation, mission, cross and resurrection; it is to be and to live as Jesus. Knowing Jesus is the only way to establish a correct relationship with Christ and to answer to the light of the spirit to the question: And you who say who I am? (Mc 8,29) / Esta pesquisa busca responder à seguinte questão: qual o significado, a relevância e a abrangência do seguimento de Jesus e suas implicações para a existência cristã, no contexto atual, marcado por profundas e rápidas transformações em todos os campos do saber e da atividade humana. A resposta a esta questão é dada tendo por base a cristologia do teólogo Jon Sobrino. Sua reflexão cristológica brota de uma vida comprometida com o clamor das vítimas, está a serviço da vida, profundamente vinculada à realidade histórica e se desenvolve na perspectiva do seguimento de Jesus. O objetivo foi identificar as intuições originais e inovadoras em relação ao seguimento de Jesus e os aspectos diretamente relacionados com este tema. O seguimento de Jesus é o eixo fundamental da cristologia de Jon Sobrino, não como dado histórico, espiritual ou moral, mas como categoria cristológica, lugar epistemológico, princípio hermenêutico, realidade totalizante, estruturadora da vida cristã. Seguir Jesus é reproduzir a estrutura fundamental de sua vida: encarnação, missão, cruz e ressurreição; é ser e viver como Jesus. O seguimento é o único caminho que leva a estabelecer uma correta relação com Cristo e a responder à luz do Espírito à pergunta: E vos quem dizeis que eu sou? (Mc 8,29)
109

Statistical Methods to Combine SPN and CNV Information in Genome-Wide Association Studies : An Application to Bladder Cancer / Utilisation conjointe de l'information apportée par les différents polymorphismes, SNPs et CNVs, dans les études d'association pangénomique : application au cancer de la vessie

Marenne, Gaëlle 28 September 2012 (has links)
Les variations en nombre de copies (CNV) sont des gains ou pertes d’une séquence d’ADN et peuvent avoir un rôle dans la susceptibilité à certaines maladies. Les CNVs peuvent être détectés par les puces de SNPs de haute résolution en analysant les intensités des allèles avec des algorithmes de détection des CNVs tels que CNV partition, PennCNV et QuantiSNP. Dans cette thèse, nous avons évalué les performances de ces outils pour la détection des CNVs au niveau pangénomique et pour les tests d'association. Nous avons également étudié des stratégies d'association combinant les informations de l'allèle et du nombre de copies pour des SNP situés dans des CNV. Nous avons appliqué ces outils pour mener une étude d’association pan-génomique avec les CNV en utilisant les données de l'étude espagnole du cancer de lavessie (SBC)/EPICURO générées par la puce Illumina 1M.Nos résultats montrent une faible fiabilité et une faible sensibilité des algorithmes de détection des CNV. Dans la région du gène GSTM1 où un CNV très fréquent existe qui est associé au risque de cancer de la vessie, nous avons constaté que les algorithmes de détection des CNV ont de faibles performances. Néanmoins, l’utilisation de la mesure d'intensité des allèles dans les tests d'association peut alors être une alternative intéressante car cela nous a permis de détecter cette association connue. Pour les SNPs situés dans des CNVs, nous avons étudié plusieurs stratégies de tests d'association et nous avons montré que la plus puissante était d’utiliser un modèle avec deux termes correspondant respectivement à la somme et à la différence du nombre de copies des deux allèles. Finalement, en appliquant ces stratégies à l'étude (SBC)/EPICURO, nous avons identifié des CNVs potentiellement associés au risque de cancer de la vessie, ainsi que des SNP dont l'allèle et le nombre de copies pourraient être impliqués dans le risque de cancer de la vessie. / Copy number variations (CNVs) are losses or gains of DNA sequences that may play a role in specific disease susceptibility. CNVs can be detected by high-resolution SNP-arrays through the analysis of allele intensities with CNV calling algorithms such as CNVpartition, PennCNV and QuantiSNP. In this thesis, we identified and assessed the performances of available tools for CNV calling and for association testing, at the genome-wide level. We also investigatedassociation strategies that combine information on both the allele and the number of copies for SNPs located in CNV regions. We applied these tools to conduct a genome-wide association study with CNV using data from the Spanish Bladder Cancer (SBC)/EPICURO Study generated by the Illumina 1M SNP-array. Our results showed a low reliability and a low sensitivity of the investigated CNV calling algorithms applied to SNP-array data. The GSTM1 locus shows a very frequent CNV that is associated with bladder cancer (BC) risk. We reported that the calling algorithms performed very poorly in identifying this CNV. We proposed using allele intensity measures (LRR) as a screening step to assess association as it allowed the detection of the GSTM1 CNV association with BC. To combine the allele and the number of copies for SNPs located in CNV regions, we investigated several strategies of association testing and we showed that the more powerfulone used a two-term model with the sum and the difference of the number of copies of both alleles. Finally, by applying these strategies to the (SBC)/EPICURO Study, we identified CNV regions potentially associated with BC risk, as well as SNPs for which both the allele and the number of copies could be involved in BC risk.
110

Interrogation of Nucleic Acids by Parallel Threading

Pettersson, Erik January 2007 (has links)
Advancements in the field of biotechnology are expanding the scientific horizon and a promising era is envisioned with personalized medicine for improved health. The amount of genetic data is growing at an ever-escalating pace due to the availability of novel technologies that allow massively parallel sequencing and whole-genome genotyping, that are supported by the advancements in computer science and information technologies. As the amount of information stored in databases throughout the world is growing and our knowledge deepens, genetic signatures with significant importance are discovered. The surface of such a set in the data mining process may include causative- or marker single nucleotide polymorphisms (SNPs), revealing predisposition to disease, or gene expression signatures, profiling a pathological state. When targeting a reduced set of signatures in a large number of samples for diagnostic- or fine-mapping purposes, efficient interrogation and scoring require appropriate preparations. These needs are met by miniaturized and parallelized platforms that allow a low sample and template consumption. This doctoral thesis describes an attempt to tackle some of these challenges by the design and implementation of a novel assay denoted Trinucleotide Threading (TnT). The method permits multiplex amplification of a medium size set of specific loci and was adapted to genotyping, gene expression profiling and digital allelotyping. Utilizing a reduced number of nucleotides permits specific amplification of targeted loci while preventing the generation of spurious amplification products. This method was applied to genotype 96 individuals for 75 SNPs. In addition, the accuracy of genotyping from minute amounts of genomic DNA was confirmed. This procedure was performed using a robotic workstation running custom-made scripts and a software tool was implemented to facilitate the assay design. Furthermore, a statistical model was derived from the molecular principles of the genotyping assay and an Expectation-Maximization algorithm was chosen to automatically call the generated genotypes. The TnT approach was also adapted to profiling signature gene sets for the Swedish Human Protein Atlas Program. Here 18 protein epitope signature tags (PrESTs) were targeted in eight different cell lines employed in the program and the results demonstrated high concordance rates with real-time PCR approaches. Finally, an assay for digital estimation of allele frequencies in large cohorts was set up by combining the TnT approach with a second-generation sequencing system. Allelotyping was performed by targeting 147 polymorphic loci in a genomic pool of 462 individuals. Subsequent interrogation was carried out on a state-of-the-art massively parallelized Pyrosequencing instrument. The experiment generated more than 200,000 reads and with bioinformatic support, clonally amplified fragments and the corresponding sequence reads were converted to a precise set of allele frequencies. / QC 20100813

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