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1
Iodice, Domenico. "Construction and characterization of probiotic Lactobacillus rhamnosus GG deletion mutant for extracellular polysaccharide (EPS) biosynthesis regulator." Doctoral thesis, Università di Siena, 2018. http://hdl.handle.net/11365/1037713.
Full textAbstract:
Lactobacillus rhamnosus GG ATCC 53103 (LGG) is a probiotic microorganism
producing a galactose-rich exopolysaccharide (EPS) surrounding the cell wall
involved in adhesion and biofilm formation. The EPS gene cluster is composed
by 16 genes associated to EPS biosynthesis. The wzb gene is an ortholog of the
Streptococcus pneumoniae cpsB, encoding a protein phosphatase involved in
the regulation of capsule production. In order to study the role of wzb gene in
EPS biosynthesis, a L. rhamnosus GG wzb deletion mutant was constructed.
Deletion of wzb produced a 12 minutes reduction of duplication time during
growth. Deletion mutant strain produced smaller colonies than wild-type strain.
Alcian Blue and India Ink staining denoted a strong reduction of the halo
surrounding cells likely associated to EPS in Δwzb strain. Zeta potential analysis
showed 2 bacterial populations in the Δwzb strain, while a single population was
present in wild type indicating different Zeta potential values and consequently
different electrokinetic properties of bacterial surfaces in the isogenic strains.
Flow cytometry and dot blot analyses were used to assess the binding of Wheat
Germ Agglutinin (WGA) and Chum Salmon Lectin 3 (CSL-3) lectins to the Nacetylglucosamine
and rhamnose residues of EPS. In presence of WGA, 2
bacterial populations were observed in Δwzb strain, while a single population in
wild type strain. In Δwzb strain a strong reduction of CSL-3 binding was
observed. Furthermore, deletion of wzb is responsible of a significant reduction in
biofilm production as estimated by crystal violet coloration. A general reduction of
gene expression level of the EPS gene cluster was observed in Δwzb strain from
the mid exponential to the early stationary growth phases. The present data
reported the first inactivation of wzb gene in L. rhamnosus and the functional
characterization of the Δwzb strain confirmed a role of Wzb phosphatase in EPS
production.
2
Neveu, Françoise. "Des gens et des lettres, et www?" Paris 7, 1997. http://www.theses.fr/1997PA070102.
Full textAbstract:
La problématique de départ était, au travers d'une démarche ethnométhodologique, d'aller a la rencontre de professionnels de la lettre. Qui sont ces "gens" qui tournent autour de la "lettre", la dessinent, l'écrivent, la composent, la regardent, la mettent en regard de l'image, la mettent en recherche ? Sous la figure emblématique du "WWW", quels sont leurs rapports avec les objets lettre et livre, avec la macroculture environnante ? La méthodologie pour en rendre compte n'est pas du tout extérieure au champ de l'étude : elle est au contraire au cœur de la recherche. Utiliser les arguments (au sens mathématique du terme) fondamentaux des savoir-faire pour donner a voir les gens qui les utilisent. Les termes de "balisage", "navigation", "niveaux de lecture", "connotation" (sens second), sont des termes de métier. S'appuyer sur les concepts d'ethnométhodologie (notion de membre, réflexivité, indexicalitée, distance) dans une représentation qui ne soit pas simplement métaphorique : le voyage de Marco Polo, mais un parcours selon les procédures et modalités même des réseaux multimédia. La thèse est de contribuer par la pratique a une réflexion sur l'ébauche de la réalisation d'un "objet" : la cartographie d'un service web, qui pose les trois paradigmes, "gens", "lettres", "WWW" et les traverse en un syntagme qui ne soit pas linéaire mais en maillage, en réseau. Cette optique "d'objet" n'est ni en rupture (objet séparé), ni totalisante (objet auto-suffisant), mais en ouverture, en prolongements, ou les changements d'angle, la navigation, offrent la possibilité de dimensions multiples. L'objet, dont l'architecture rejoint la structure de la recherche, est mis en mouvement par une transversalité la moins linéaire possible, par le choix d'un acte d'écrire, the act of writing, et de "l'oralité". Son décryptage révèle des mots-clés dans les paradigmes, qui indiquent la possibilité d'autres parcours et l'ouverture a une complémentarité (jointe ou disjointe) en devenirThe starting point for this thesis was te use an ethnomethodological approach to look at professionals in the print trade. Who are these "people" who spend their time with "letters", drawing them, writing them, composing them, looking at them, making them into images and sending them in research ? Looking at them from the angle of the emblematic "WWW", what relation do they have with objects letter and book, and with the surrounding culture as a whole ? The methodology applied actually lies at the heart of the research field itself. It involves using the fundamental arguments (in the mathematical sense) of a set of skills to render the people who use these skills sisible. The terms "marking up", "navigation", "levels of reading", "connotation" (associated meaning) are trade terms. The ethnomethodological concepts of member, reflexivity, indexicality and distance are used to produce a representation that is not purely metaphorical - Marco Polo's travels but also a journey using the very same principle as multimedia networks. This thesis is an attempt to think practically about how "objects" are created - the cartography of a web service, based on thre paradigms of "people", "letters", "WWW", using a network-looped rather than a linear syntagmatics. This approach to "objects" neither breaks them up into separate objects nor elevated them into total self-sufficient wholes ; it broadens and extends the perspective, so that the change of angles, the process of navigation opens up a broad range of dimensions. The architecture of the objects resembles the structure of the search. It is set in motion by a cross- functionality which is maximally non-linear, trough the act of writing and "orality". Deciphering this cross-functionality reveals key-words in the paradigms, and by choosing one, one can set off on other navigation, offering an emerging form of complementarity (joint or disjoint)
3
Santini, Marina. "Automatic identification of genre in Web pages." Thesis, University of Brighton, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439208.
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4
DEETER, ANTHONY E. Deeter. "A Web-Based Software System Utilizing Consensus Networks to Infer Gene Interactions." University of Akron / OhioLINK, 2018. http://rave.ohiolink.edu/etdc/view?acc_num=akron152302071289795.
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Bara, Olivier. "Le théâtre de l'opéra-comique entre 1822 et 1827 la difficile recherche d'un genre moyen /." Lille : A.N.R.T, Université de Lille III, 1998. http://bibpurl.oclc.org/web/24931.
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France, Jacques. "Theadelpheia in de Romeinse Periode : Een bijdrage op basis van onuitgegeven papyri in de universiteitsbibliotheek te Gent /." Online version, 1994. http://bibpurl.oclc.org/web/21981.
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Ullestad, Ove. "La légende des sept dormants les gens de la caverne (Ahl al-Kahf): exégèses islamiques d'une légende hagiographique /." Online version, 1993. http://bibpurl.oclc.org/web/25559.
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8
Kennedy, Alistair. "Automatic genre classification of home pages on the web /." Halifax, N.S. : Dalhousie University, 2004. http://torch.cs.dal.ca/%7Ekennedy/genre%5Fthesis.pdf.
Full textAbstract:
Thesis (B.C.S.)--Dalhousie University, Halifax."Submitted in partial fulfillment of the requirements for the degree of bachelor of computer science with honours at Dalhousie University, Halifax, Nova Scotia, April 2004." Includes bibliographical references (p. 33-35). Also available in PDF via the World Wide Web.
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Santa-Maria, Luis. "Visual genre conventions and user performance on the web." Thesis, University of Reading, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515751.
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L'Étoile, Jeannine de. "Amorce de caractérisation textuelle du genre site Web informatif." Mémoire, Université de Sherbrooke, 2003. http://savoirs.usherbrooke.ca/handle/11143/2400.
Full textAbstract:
La présente recherche se penche sur l'étude du cyberdocument dont la visée est d'informer. Elle se propose de reconnaître et de recenser différents mécanismes--langagiers et visuels--propres au site Web informatif afin de caractériser un modèle émergent du genre. Réalisée à partir d'un corpus de dix sites tant des secteurs public que parapublic ou privé, l'exploration s'est faite au regard de deux principaux niveaux structurels du texte, à savoir la microstructure et la superstructure. Ainsi, dans un premier temps, l'application de deux formules qui rendent compte d'approches différentes de la lisibilité (test évaluant l'indice de brouillard, de Gunning, et formule simplifiée de Flesch) a permis une évaluation nuancée de cette variable retenue au niveau microstructurel. Nous appuyant ensuite sur divers principes du modèle de l'Architecture textuelle, développé par Jacques Virbel (1985) et Elsa Pascual (1991), nous nous sommes attardés, dans un deuxième temps, à des mécanismes qui concernent la superstructure: marqueurs d'appartenance, organisateurs énumératifs, spatiaux et temporels ainsi que procédés de segmentation. Il est ressorti de l'analyse un certain défaut de lisibilité, conséquent de phrases et de mots longs. L'observation a aussi mis en lumière la forte segmentation des contenus, et ce, tant au plan local que global du cybertexte. Enfin, il apparaît que la mise en forme matérielle, tout en participant à la structuration et à la hiérarchisation des composantes textuelles, signe également l'appartenance des parties au tout qui les englobe. Sans être exhaustive, la présente recherche brosse toutefois un portrait assez précis des pratiques mises en oeuvre dans les sites du corpus par rapport aux variables observées. Sans conteste, elle ouvre la voie à la réflexion critique d'autres chercheurs du domaine.
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L'Étoile, Jeannine de. "Amorce de caractérisation textuelle du genre Site Web Informatif." Sherbrooke : Université de Sherbrooke, 2003.
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12
Chetry, Roshan. "Web genre classification using feature selection and semi-supervised learning." Kansas State University, 2011. http://hdl.handle.net/2097/8855.
Full textAbstract:
Master of ScienceDepartment of Computing and Information Sciences
Doina Caragea
As the web pages continuously change and their number grows exponentially, the need for genre classification of web pages also increases. One simple reason for this is given by the need to group web pages into various genre categories in order to reduce the complexities of various web tasks (e.g., search). Experts unanimously agree on the huge potential of genre classification of web pages. However, while everybody agrees that genre classification of web pages is necessary, researchers face problems in finding enough labeled data to perform supervised classification of web pages into various genres. The high cost of skilled manual labor, rapid changing nature of web and never ending growth of web pages are the main reasons for the limited amount of labeled data. On the contrary unlabeled data can be acquired relatively inexpensively in comparison to labeled data. This suggests the use of semi-supervised learning approaches for genre classification, instead of using supervised approaches. Semi-supervised learning makes use of both labeled and unlabeled data for training - typically a small amount of labeled data and a large amount of unlabeled data. Semi-supervised learning have been extensively used in text classification problems. Given the link structure of the web, for web-page classification one can use link features in addition to the content features that are used for general text classification. Hence, the feature set corresponding to web-pages can be easily divided into two views, namely content and link based feature views. Intuitively, the two feature views are conditionally independent given the genre category and have the ability to predict the class on their own. The scarcity of labeled data, availability of large amounts of unlabeled data, richer set of features as compared to the conventional text classification tasks (specifically complementary and sufficient views of features) have encouraged us to use co-training as a tool to perform semi-supervised learning. During co-training labeled examples represented using the two views are used to learn distinct classifiers, which keep improving at each iteration by sharing the most confident predictions on the unlabeled data. In this work, we classify web-pages of .eu domain consisting of 1232 labeled host and 20000 unlabeled hosts (provided by the European Archive Foundation [Benczur et al., 2010]) into six different genres, using co-training. We compare our results with the results produced by standard supervised methods. We find that co-training can be an effective and cheap alternative to costly supervised learning. This is mainly due to the two independent and complementary feature sets of web: content based features and link based features.
13
Asonov, Dmitri. "Querying databases privately : a new approach to private information retrieval /." Berlin : Springer, 2004. http://springerlink.metapress.com/openurl.asp?genre=issue&issn=0302-9743&volume=3128.
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Hoddinott, Simon Matthew. "Web mining for translators: automatic construction of comparable, genre-driven corpora." Bachelor's thesis, Alma Mater Studiorum - Università di Bologna, 2016. http://amslaurea.unibo.it/10775/.
Full textAbstract:
The aim of this paper is to evaluate the efficacy of the application WebBootCaT to create specialised corpora automatically, investigating the translation of articles of association from Italian into English. The first section reflects on the relevant literature and proposes the utility of corpora for translators. The second section discusses the methodology employed, and the third section analyses the results obtained and comments on how language professionals could possibly exploit the application to its full. The fourth section provides a few concrete usage examples of the thus built corpora, to then conclude that WebBootCaT is a genuinely powerful tool that could be implemented by professional translators in order to save time and improve their translations in the long term.
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May, Patrick, Jan-Ole Christian, Stefan Kempa, and Dirk Walther. "ChlamyCyc : an integrative systems biology database and web-portal for Chlamydomonas reinhardtii." Universität Potsdam, 2009. http://opus.kobv.de/ubp/volltexte/2010/4494/.
Full textAbstract:
Background:
The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic
model organism for the study of photosynthesis and plant growth. In the era of modern highthroughput technologies there is an imperative need to integrate large-scale data sets from highthroughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism.
Results:
In the framework of the German Systems Biology initiative GoFORSYS, a pathway
database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.
Conclusion:
ChlamyCyc provides a curated and integrated systems biology repository that will
enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.
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Cheng, Beethoven. "Development of genre and function types for web page classification and rating." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/42804.
Full textAbstract:
Thesis (S.B. and M.Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1996.Includes bibliographical references (leaves 58-59).
by Beethoven Cheng.
S.B.and M.Eng.
17
Dillon, Andrew, and Barbara Grushowski. "Genres and the Web - is the home page the first digital genre?" Wiley, 2000. http://hdl.handle.net/10150/105166.
Full textAbstract:
Genre conventions emerge across discourse communities over time to support the communication of ideas and information in socially and cognitively compatible forms. Digital genres frequently borrow heavily from the paper world even though the media are very different. This research sought to identify the existence and form of a truly digital genre. Preliminary results from a survey of user perceptions of the form and content of web home pages reveal a significant correlation between commonly found elements on such home pages and user preferences and expectations of type. Results suggest that the personal home page has rapidly evolved into a recognizable form with stable, user-preferred elements and thus can be considered the first truly digital genre.
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AraÃjo, JÃlio CÃsar Rosa de. "Chat na web: um estudo de gÃnero hipertextual." Universidade Federal do CearÃ, 2003. http://www.teses.ufc.br/tde_busca/arquivo.php?codArquivo=3476.
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CoordenaÃÃo de AperfeiÃoamento de Pessoal de NÃvel SuperiorEsta pesquisa investiga as hipÃteses de que o chat à um gÃnero do discurso formado pela transmutaÃÃo do diÃlogo cotidiano para a Web e de que um grupo especÃfico de internautas, que se autodenomina Tananans, constitui-se em uma comunidade discursiva. As bases teÃricas utilizadas para a verificaÃÃo dessas hipÃteses foram a teoria enunciativa de Bakhtin (1981; 1997) e a noÃÃo de comunidade discursiva de Swales (1990; 1992). O corpus à resultado de uma pesquisa de cunho etnogrÃfico, realizada em uma sala especÃfica de chat. Focalizou-se, primeiramente, a superposiÃÃo de elementos semiÃticos, que confere ao chat marcas da esfera na qual o evento se insere, para, posteriormente, realizar a aplicaÃÃo dos critÃrios de comunidade discursiva de Swales ao grupo Tananans. O estudo mostra que o chat à o principal gÃnero que dà suporte verbal à comunicaÃÃo entre os internautas estudados. Tal gÃnero à marcado por um jogo intenso de semioses que simulam gestos, sons e expressÃes prÃprias da interaÃÃo oral, permitindo a conclusÃo de que a intersemiose som-imagem-escrita, por suprir as lacunas paralingÃÃsticas, mostra-se como marca da transposiÃÃo do diÃlogo cotidiano para a Web. Verificou-se, ainda, que embora a prÃtica comunicativa dos Tananans tenha iniciado das interaÃÃes via chat, esta se expande para outros mecanismos e gÃneros apropriados pelo grupo, permitindo a validaÃÃo da hipÃtese de que este grupo à uma comunidade discursiva no sentido que lhe dà Swales.
This research investigates the hypotheses that the chat is a class of the discourse formed by the transformation of the daily dialogue for the Web and that an specific group of internauts is a discoursing community. The theoretical bases used for checking these hypotheses are the enunciative theory of Bakhtin (1981; 1997) and the concept of discoursing community of Swales (1990; 1992). The corpus is the result of a research of ethnographic character, conducted in a specific chat room. Firstly, we focussed on the application of the criteria of Swalesâ discoursing community to the Tananans group. This is a group of virtual friends who interact with each other by chatting. Next, we observed the overlap of semiotical elements, which gives to the chat characteristics of the domain in which the event occurs, namely the Web. The analysis shows that, although the communicative practice of the Tananans has begun from the interactions through chatting, this practice expands towards other mechanisms and classes developed by the group, allowing the validation of the hypothesis that this group is a discoursing community in the sense attributed by Swales. Furthermore, we verified that chat is the main class which gives verbal support to the communication among the internauts. Such a class is characterized by an intense game of semioses that simulate gestures, sounds and expressions which are proper to the oral interaction. The analysis makes us conclude that the intersemiosis sound-image- writing reveals itself as a feature of the transformation of the daily dialogue for the Web, since it stops the paralinguistical gaps.
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Araújo, Júlio César Rosa de. "Chat na web: um estudo de gênero hipertextual." www.teses.ufc.br, 2003. http://www.repositorio.ufc.br/handle/riufc/8753.
Full textAbstract:
ARAÚJO, Júlio César Rosa de. Chat na web: um estudo de gênero hipertextual. 2003. 179f. – Dissertação (Mestrado) – Universidade Federal do Ceará, Departamento de Letras Vernáculas, Programa de Pós-graduação em Linguística, Fortaleza (CE), 2003.Submitted by Márcia Araújo (marcia_m_bezerra@yahoo.com.br) on 2014-08-19T13:22:12Z No. of bitstreams: 1 2003_dis_jcraraujo.pdf: 1446843 bytes, checksum: 1bd8310fb83f0c53246a7d5deadeaadc (MD5)
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This research investigates the hypotheses that the chat is a class of the discourse formed by the transformation of the daily dialogue for the Web and that an specific group of internauts is a discoursing community. The theoretical bases used for checking these hypotheses are the enunciative theory of Bakhtin (1981; 1997) and the concept of discoursing community of Swales (1990; 1992). The corpus is the result of a research of ethnographic character, conducted in a specific chat room. Firstly, we focussed on the application of the criteria of Swales’ discoursing community to the Tananans group. This is a group of virtual friends who interact with each other by chatting. Next, we observed the overlap of semiotical elements, which gives to the chat characteristics of the domain in which the event occurs, namely the Web. The analysis shows that, although the communicative practice of the Tananans has begun from the interactions through chatting, this practice expands towards other mechanisms and classes developed by the group, allowing the validation of the hypothesis that this group is a discoursing community in the sense attributed by Swales. Furthermore, we verified that chat is the main class which gives verbal support to the communication among the internauts. Such a class is characterized by an intense game of semioses that simulate gestures, sounds and expressions which are proper to the oral interaction. The analysis makes us conclude that the intersemiosis sound-image- writing reveals itself as a feature of the transformation of the daily dialogue for the Web, since it stops the paralinguistical gaps.
Esta pesquisa investiga as hipóteses de que o chat é um gênero do discurso formado pela transmutação do diálogo cotidiano para a Web e de que um grupo específico de internautas, que se autodenomina Tananans, constitui-se em uma comunidade discursiva. As bases teóricas utilizadas para a verificação dessas hipóteses foram a teoria enunciativa de Bakhtin (1981; 1997) e a noção de comunidade discursiva de Swales (1990; 1992). O corpus é resultado de uma pesquisa de cunho etnográfico, realizada em uma sala específica de chat. Focalizou-se, primeiramente, a superposição de elementos semióticos, que confere ao chat marcas da esfera na qual o evento se insere, para, posteriormente, realizar a aplicação dos critérios de comunidade discursiva de Swales ao grupo Tananans. O estudo mostra que o chat é o principal gênero que dá suporte verbal à comunicação entre os internautas estudados. Tal gênero é marcado por um jogo intenso de semioses que simulam gestos, sons e expressões próprias da interação oral, permitindo a conclusão de que a intersemiose som-imagem-escrita, por suprir as lacunas paralingüísticas, mostra-se como marca da transposição do diálogo cotidiano para a Web. Verificou-se, ainda, que embora a prática comunicativa dos Tananans tenha iniciado das interações via chat, esta se expande para outros mecanismos e gêneros apropriados pelo grupo, permitindo a validação da hipótese de que este grupo é uma comunidade discursiva no sentido que lhe dá Swales.
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Yang, Yanming. "Design, construction and implementation of a Web-based database system for tumor suppressor genes." [Gainesville, Fla.] : University of Florida, 2003. http://purl.fcla.edu/fcla/etd/UFE0000827.
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FRANCAVILLA, MARCELLA. "Geni modificatori della Beta talassemia e sviluppo di un algoritmo per la predizione della severità clinica." Doctoral thesis, Università degli Studi di Cagliari, 2015. http://hdl.handle.net/11584/266611.
Full textAbstract:
Introduction
Many genetic factors influence Beta Thalassemia severity, recessive autosomal disorder with a
highly variable phenotype, beyond mutations in the causative Beta-globin gene (chr 11).
These factors are Alpha-globin genes defects and Fetal Hemoglobin modulators (HBG2:g.-
158C>T polymorphism, HBS1L-MYB intergenic region and the BCL11A gene).
Metods
In this work we studied an International cohort of 890 Beta Thalassemic patients to build a
predictive severity model of the pathology.
In order to achieve this goal we characterized 54 genetic variants at these loci robustly
associated with the amelioration of Beta Thalassemia phenotype. Subsequently we assessed,
using Cox proportional hazard analysis on a training set, the effect of these loci on the age at
which patients start regular transfusions. Finally we built a Thalassemia Severity Score and
validated it on a testing set.
Results
Discriminatory power of the model was high (C-index=0.705; R2=0.343) and the validation
conducted on the testing set confirmed its predictive accuracy with transfusion free
survival probability (p<0.001) and with transfusion dependency status (Area Under the
Receiver Operating Characteristic Curve=0.774, <0.001). Finally, an automatized online
calculation of the score was made available at http://tss.unica.it. Besides the accurate
assessment of genetic predictors effect, the presented results could be helpful in the
management of patients, both as a predictive score for screening and a standardized
scale of severity to overcome the major-intermedia dichotomy and suport clinical decisions
22
Xin, Jing. "The Chinese Approach To Web Journalism: A Comparative Analysis." Thesis, University of Canterbury. Social and Political Sciences, 2010. http://hdl.handle.net/10092/5117.
Full textAbstract:
This thesis explores the distinctive forms of journalism that have emerged in mainstream news websites in mainland China. Two case studies, the 2008 Beijing Olympic Games and the H1N1 influenza pandemic in 2009, are employed to identify features in Chinese and Western news online. Specifically, a comparison is made between the in-depth news sections of popular mainstream news websites in China and those in the United States, the United Kingdom, and New Zealand. The study finds that the Chinese version of mainstream web news genre differs significantly from the Western version. This thesis argues that journalists’ practice is strongly context dependent. Distinctive economic, organizational, social and cultural factors contribute to shaping Chinese web journalism in a way that contradicts the notion of a homogeneous worldwide journalism or of a single set of norms for journalism. The study challenges the dominance of the political explanatory framework that considers political factors as the most important approach to study Chinese web-based media. In the face of a sparse literature and sporadic studies concerning the development of the internet as a novel platform in China for news production and transmission, this thesis aims to bring more academic interest to an overlooked research area and to contribute to a broader understanding of the actual diversity of global communication research.
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Dodda, Srinivasa Rao. "Improvements and extensions of a web-tool for finding candidate genes associated with rheumatoid arthritis." Thesis, University of Skövde, School of Humanities and Informatics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:his:diva-26.
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QuantitativeTraitLocus (QTL) is a statistical method used to restrict genomic regions contributing to specific phenotypes. To further localize genes in such regions a web tool called “Candidate Gene Capture” (CGC) was developed by Andersson et al. (2005). The CGC tool was based on the textual description of genes defined in the human phenotype database OMIM. Even though the CGC tool works well, the tool was limited by a number of inconsistencies in the underlying database structure, static web pages and some gene descriptions without properly defined function in the OMIM database. Hence, in this work the CGC tool was improved by redesigning its database structure, adding dynamic web pages and improving the prediction of unknown gene function by using exon analysis. The changes in database structure diminished the number of tables considerably, eliminated redundancies and made data retrieval more efficient. A new method for prediction of gene function was proposed, based on the assumption that similarity between exon sequences is associated with biochemical function. Using Blast with 20380 exon protein sequences and a threshold E-value of 0.01, 639 exon groups were obtained with an average of 11 exons per group. When estimating the functional similarity, it was found that on the average 72% of the exons in a group had at least one Gene Ontology (GO) term in common.
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Ayuso, Anna Maria E. "Automation of Drosophila gene expression pattern image annotation : development of web-based image annotation tool and application of machine learning methods." Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/66403.
Full textAbstract:
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2011.Cataloged from PDF version of thesis.
Includes bibliographical references (p. 91-92).
Large-scale in situ hybridization screens are providing an abundance of spatio-temporal patterns of gene expression data that is valuable for understanding the mechanisms of gene regulation. Drosophila gene expression pattern images have been generated by the Berkeley Drosophila Genome Project (BDGP) for over 7,000 genes in over 90,000 digital images. These images are currently hand curated by field experts with developmental and anatomical terms based on the stained regions. These annotations enable the integration of spatial expression patterns with other genomic data sets that link regulators with their downstream targets. However, the manual curation has become a bottleneck in the process of analyzing the rapidly generated data therefore it is necessary to explore computational methods for the curation of gene expression pattern images. This thesis addresses improving the manual annotation process with a web-based image annotation tool and also enabling automation of the process using machine learning methods. First, a tool called LabelLife was developed to provide a systematic and flexible way of annotating images, groups of images, and shapes within images using terms from a controlled vocabulary. Second, machine learning methods for automatically predicting vocabulary terms for a given image based on image feature data were explored and implemented. The results of the applied machine learning methods are promising in terms of predictive ability, which has the potential to simplify and expedite the curation process hence increasing the rate that biologically significant data can be evaluated and new insights can be gained.
by Anna Maria E. Ayuso.
M.Eng.
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Cadenas, Sevilla Beatriz. "Refining and improving a next-generation sequencing gene panel for clinical diagnosis of hereditary hematologic diseases and development of bioinformatic tools for biomedical analysis." Doctoral thesis, Universitat de Vic - Universitat Central de Catalunya, 2019. http://hdl.handle.net/10803/668181.
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En este doctorado industrial, el objetivo era cumplir los objetivos innovadores de Whole Genix, que incluyen: dominar los protocolos de secuenciación masiva de próxima generación (en inglés next-generation sequencing, NGS), cubrid un espectro más amplio de enfermedades, desarrollar nuevas herramientas bioinformáticas y de telemedicina para el análisis de diferentes datos ómicos; y consecuentemente, progresar hacia la medicina personalizada. Se han llevado a cabo cuatro proyectos para cubrir estos objetivos.
1. Refinar y mejorar un panel de genes NGS para el diagnóstico clínico de enfermedades hematológicas hereditarias e investigación sobre enfermedades con alteraciones de la ferritina.
2. CODYSAN: una herramienta web para el diagnóstico de anemia diseritropoyética congénita
3. BEA (BioMark Expression Analysis): una herramienta web para realizar análisis de expresión relativa de datos provenientes del sistema BioMark-Fluidigm.
4. Pipeline para la construcción de firmas de expresión génica para predicción y pronóstico utilizando datos de pacientes con cáncer de vejiga músculo-invasivo.In this industrial doctorate, the aim was to fulfill the Whole Genix innovative objectives, including: master Next Generation Sequencing (NGS) protocols; cover a bigger spectrum of diseases; develop new bioinformatic and telemedicine tools for analysis of different omics data; and consequently, progress towards personalized medicine. Four independent projects have been carried out to cover these objectives. 1. Refining and improving an NGS gene panel for clinical diagnosis of hereditary hematologic diseases and focus on diseases with ferritin alterations. 2. CODYSAN: a web tool for the diagnosis of Congenital Dyserythropoietic Anemia 3. BEA (BioMark Expression Analysis): a web tool to perform relative expression analysis from Fluidigm – BioMark data. 4. Pipeline to construction of gene expression signatures for prediction and prognosis using data from patients with muscle-invasive bladder cancer.
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Guardia, Gabriela Der Agopian. "Suporte ao desenvolvimento e à composição de serviços web semânticos para a análise de expressão gênica." Universidade de São Paulo, 2016. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-28102016-101702/.
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Estudos de expressão gênica geralmente envolvem a realização de processos de análise integrados para a obtenção de respostas biológicas de interesse. A realização destes processos frequentemente requer o uso combinado de uma série de ferramentas de software. No entanto, o processo de integração manual de ferramentas pode ser demorado e propenso a erros devido ao crescente número de ferramentas e formatos de dados disponíveis no domínio. De modo a automatizar o processo de integração, algumas abordagens têm sido propostas tanto para a adaptação das ferramentas de análise existentes como serviços web semânticos, quanto para o desenvolvimento de ambientes de suporte à integração (composição) de serviços web semânticos. Embora estas abordagens representem avanços, nenhuma solução adequada para o desenvolvimento e composição de serviços foi especificamente definida para o domínio de genômica funcional. Neste contexto, o principal objetivo deste projeto foi investigar uma solução completa para o desenvolvimento e composição de serviços web semânticos para a análise de expressão gênica. Como parte da solução proposta, definimos uma metodologia integrada para a implementação de serviços web semânticos criados a partir de ferramentas de software existentes e para a anotação semântica destes serviços. Nossa metodologia fornece diretrizes concretas para o desenvolvimento sistemático de serviços, considerando também os principais aspectos técnicos associados ao processo de desenvolvimento. Esta metodologia foi aplicada a um conjunto representativo de serviços que fornecem suporte às principais atividades de análise realizadas em diferentes tipos de dados de expressão gênica. De forma complementar, definimos uma solução completa para a composição semântica de serviços no domínio de análise de expressão gênica. A solução proposta foi implementada em uma plataforma de suporte semi-automático à composição de serviços web semânticos, chamada SemanticSCo. Esta plataforma fornece suporte flexível a todas as atividades envolvidas no processo de composição de serviços, incluindo a criação, publicação, requisição, descoberta, seleção, composição e execução de serviços. Além disto, a plataforma SemanticSCo foi projetada para prover suporte adequado a diferentes tipos de usuários, incluindo biologistas e bioinformatas. Neste sentido, a plataforma fornece aos usuários um alto nível de abstração para a definição de seus processos de análise, permitindo que os mesmos se concentrem mais nas questões de pesquisa biológicas do que nos aspectos subjacentes do processo de composição. Adicionalmente, a plataforma SemanticSCo suporta a definição e incorporação não apenas de serviços simples, definidos em termos de uma única operação, mas também de serviços complexos, definidos em termos de um conjunto de condições que restringem a ordem de invocação de suas operações. Finalmente, de modo a avaliar a plataforma de suporte desenvolvida, definimos diferentes cenários de composição para a análise (integrada) de dados de expressão gênica. O uso da plataforma SemanticSCo facilitou a definição destes cenários, permitindo assim a reprodução dos resultados obtidos a partir de diferentes estudos de expressão gênica previamente documentados na literaturaGene expression studies usually involve the creation of integrated analysis processes for obtaining responses for a biological question. The creation of such processes often require the combined use of a number of software tools. However, the manual integration of tools can be cumbersome and error prone due to the increasing number of tools and data formats available in the domain. In order to automate the integration process, some approaches have been proposed for the adaptation of existing analysis tools as semantic web services as well as for the development of software environments to support the integration (composition) of semantic web services. Although these approaches present advances, to the best of our knowledge, no suitable solution has been proposed for the development and composition of web services in the functional genomics domain. In this context, this project aimed at investigating a complete solution for the development and composition of semantic web services to support gene expression analysis. As part of the proposed solution, we have defined an integrated methodology for the implementation of semantic web services created from existing software tools and the semantic annotation of such services. Our methodology provides concrete guidelines for the systematic development of services, also taking into account the main technical aspects associated with the development process. This methodology has been applied in the development of a representative set of services that support the main analysis activities performed on different types of gene expression data. Complementary to our methodology, we have defined a complete solution for the semantic composition of web services in the gene expression analysis domain. The proposed solution has been implemented in a software platform to support the semi-automatic composition of semantic web services, named SemanticSCo. This platform provides flexible support to all activities involved in the service composition process including service creation, publication, request, discovery, selection, composition and execution. Additionally, the SemanticSCo platform has been designed to support different types of users, including biologists and bioinformaticians. In this sense, the platform provides users with a high level of abstraction in the definition of their analysis processes, thus allowing them to focus more on biological research issues rather than on underlying details of the composition process. In addition, the SemanticSCo platform supports not only the definition and incorporation of (simple) services defined in terms of a single operation, but also (complex) services defined in terms of a set of conditions that constrain the order in which service operations should be invoked. Finally, in order to evaluate the developed support platform, we have defined a number of composition scenarios for the (integrated) analysis of gene expression data. The use of the SemanticSCo platform has facilitated the definition of these scenarios, thus allowing the reproduction of the results obtained from different gene expression studies previously documented in the literature.
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Brock, Erin Lynn. "Please Type Here: Digital Petitions and the Intersections of the Web and Democracy." Miami University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=miami1408023321.
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Vaughan, Misha, and Andrew Dillon. "Why structure and genre matter to users of digital information: a longitudinal study with readers of a web-based newspaper." Elsevier, 2006. http://hdl.handle.net/10150/105924.
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In an effort to understand the impact of designing for digital genres on usersâ mental representations of structure, a two-phase study was conducted. In phase 1, six expert news readers and a panel of HCI experts were solicited for input regarding genre-conforming and
genre-violating web news page design, navigation, and story categorization. In phase 2, a longitudinal experiment with a group of 25 novice web news readers who were exposed to one of the two designs over 5 sessions is reported. During these sessions a variety of user data were captured, including: comprehension (recall, recognition), usability (time on task, accuracy, user satisfaction), and navigation
(path length, category node hits).
The between-group difference of web site design was signiï¬ cant for comprehension, usability, and navigation with the users of the
genre-conforming design demonstrating better performance. The within-group difference of time was signiï¬ cant across these three
measures as well, with performance improving over time. No interaction effect was found between web site design and time on
comprehension or usability. However, a surprising interaction effect was found on navigation; speciï¬ cally the breadth of navigation (i.e.
the number of nodes visited for two classes of tasks) increased over time more dramatically for the genre-violating group than for the
genre-conforming group. By examining the changes in these data over time and between the two designs, evidence for the development of
usersâ mental representations of structure was captured.
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Silva, Wilson Daniel da. "Suporte à acessibilidade, reprodutibilidade e transparência em uma plataforma integrada de análise de dados de expressão gênica." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/59/59143/tde-08122018-112207/.
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Modernas tecnicas de biologia molecular sao utilizadas para quantificar os niveis de expressao genica de amostras celulares, frequentemente submetidas a diferentes condicoes experimentais. A genomica funcional e a area da bioinformatica responsavel pela caracterizacao do papel funcional dos genes e processos biologicos associados. A analise de expressao genica requer o uso (integrado) de diversas ferramentas de analise para a obtencao de respostas as questoes biologicas de interesse. Uma plataforma de analise pode ser utilizada para facilitar a integracao sintatica e semantica destas ferramentas. Tal plataforma deve oferecer acessibilidade, reprodutibilidade e transparencia, de modo a promover a colaboracao e a disseminacao da pesquisa cientifica. A plataforma SemanticSCo foi concebida para prover suporte a composicao semantica de servicos de analise de expressao genica. Contudo, esta plataforma, em sua versao standalone, apresenta baixa acessibilidade, alem de nao prover suporte para a reproducao e o compartilhamento dos workflows desenvolvidos por seus usuarios. O principal objetivo deste projeto foi ampliar a acessibilidade da plataforma SemanticSCo, bem como introduzir suporte para a reproducao e compartilhamento de workflows. Como resultado principal, desenvolvemos uma nova versao da plataforma SemanticSCo, chamada SemanticSCo Web. A plataforma SemanticSCo Web possui uma interface simples e amigavel, contribuindo para o desenvolvimento colaborativo de pesquisa cientifica reproduzivel no dominio da genomica funcional. Adicionalmente, desenvolvemos uma API chamada SIBRI para permitir a execucao automatica, via framework Activiti, de servicos RESTful modelados como processos BPMN. O uso desta API facilita a integracao de aplicacoes desenvolvidas na linguagem Java e que fazem uso de servicos RESTful, dado que esta API prove suporte a interacao com o usuario em um ambiente web para que o mesmo possa prover valores de parametros que serao utilizados na execucao de um dado servico. Desta forma, a API SIBRI simplifica a incorporacao de novos servicos na plataforma SemanticSCo Web.Modern molecular biology techniques are used to quantify the levels of gene expression of cellular samples, often submitted to different experimental conditions. Functional genomics is the area of bioinformatics responsible for the characterization of the functional role of genes and associated biological processes. The analysis of gene expression requires the (integrated) use of several analysis tools to obtain answers to a given biological question. An analysis platform can be used to facilitate the syntactic and semantic integration of these tools. Such platform should offer accessibility, reproducibility and transparency in order to promote collaboration and dissemination of scientific research. The SemanticSCo platform was designed to provide support for the semantic composition of gene expression analysis services. However, this platform, in its standalone version, presents low accessibility, and does not provide support for the reproduction and sharing of developed workflows. The main objective of this project was to increase the accessibility of the SemanticSCo platform, as well as to introduce support for the reproduction and sharing of workflows (transparency). As a main result, we have developed a new version of the SemanticSCo platform, called SemanticSCo Web. The SemanticSCo Web platform has a simple and user-friendly interface, contributing to the collaborative development of reproducible scientific research in the functional genomics domain. Additionally, we have developed an API called SIBRI to allow the automatic execution, via Activity framework, of RESTful services modeled as BPMN processes. The use of this API facilitates the integration of applications developed in Java that uses RESTful services, since this API provides support for the interaction with the end user in a web environment so s/he can provide parameters to be used in the execution of a given service. In this way, the API SIBRI simplifies the incorporation of new services in the SemanticSCo Web platform.
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Nunes, Rosangela Brandão. "Território de gente e de música: Jovens no Centro cultural Cartola e o cotidiano de uma experiência." Universidade do Estado do Rio de Janeiro, 2015. http://www.bdtd.uerj.br/tde_busca/arquivo.php?codArquivo=8748.
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Conselho Nacional de Desenvolvimento Científico e TecnológicoEste trabalho busca compor um quadro das práticas cotidianas de jovens frequentadores das oficinas de jazz oferecidas pelo Centro Cultural Cartola (CCC). Contextualizado dentro de um universo tradicionalmente conhecido por sua origem no samba, esse território de arte e de expressão através do corpo e da música contempla outros movimentos musicais, principalmente o jazz e o moderno, possibilitando um conjunto de múltiplos sentidos e ressignificações na vida destes participantes. Como fundamentação epistemológica, foi utilizada a Teoria Ator-Rede (TAR), concebida como forma de abordar a fabricação dos fatos, ao abranger, simetricamente, natureza e sociedade, humano e não humano. Foram igualmente consideradas as possíveis configurações de interação e sociabilidade que envolvem território, sujeito e demais atores da rede, os quais conseguem reconhecer-se diante do outro, do diferente, e construírem um projeto individual e coletivo frente à sociedade multicultural em que estão inseridos. Para isso, foram realizadas entrevistas que, por sua vez, são complementos à descrição interpretativa registrada no diário de campo, permitindo a dimensão de improviso, de manejo das situações e de envolvimento nas incessantes redefinições processuais. O campo explorado foi, estritamente, o de jovens adolescentes, num recorte etário de 14 a 21 anos. Todos deveriam estar matriculados na escola ensino fundamental e médio e residir em comunidade, não sendo necessariamente a Mangueira. As abordagens contemplaram também as incontáveis participações do professor da oficina de jazz. Durante o processo, emanou-se a existência de um apaixonamento e de uma apropriação por parte de todos os envolvidos com a oficina: parte administrativa, pedagógica e docente, garantindo autonomia e diferencial no universo social do grupo, cujas escolhas legitimam o quanto o investimento na cultura produz artistas conscientes da beleza inerente à própria arte e aos afetamentos daí advindos. Interessante ressaltar que o samba funciona como marca histórica e temporal do CCC, mas a principal motivação ali percebida estava no encontro mediado pela dança, junção corpo/música, presente na vida dos participantes desde a infância, além do prazer de pertencerem a um grupo afim, movido por histórias semelhantes. Junto a isso, o professor exercia o papel de liderança velada, a mediar as relações e a produzir efeitos de coesão grupal, com suas ideias e incentivo à expressão pela dança, de modo a dar lugar a novas descobertas e ressignificação
This paper aims to compose a picture of the young peoples daily practices who attend the jazz workshops offered by Centro Cultural Cartola (CCC) - Top Hat Cultural Centre. Within the context of a universe traditionally known for its origins in the samba, this territory of art and expression through body and music that includes other musical movements, mainly jazz and modern, allowing a set of multiple meanings and new meanings in the lives of these attendees. On an epistemological foundation, we used the Actor-Network Theory (ART), designed to address the manufacturing of facts, when it covers symmetrically, nature and society, human and nonhuman. We also considered the possible configurations of interaction and sociability involving the territory, subject and other actors in the network, which can recognize each other to the other, to the different, and build an individual and collective project before the multicultural society where they are inserted. For this, interviews were conducted that, in turn, are added to the "interpretative" description recorded in the diary of field, allowing the dimension of improvisation, management of situations and engaging in endless procedural resets. The explored field was, strictly, the young adolescents, in an age cut from 14 to 21. They all should be enrolled in school - primary and secondary education - and live in a community, not necessarily the Mangueira community. The approaches also regarded the countless contributions of the jazz workshop teacher. Along the process, there was the falling in love and an appropriation of all the ones involved in the workshop: the administrative, pedagogical and teaching members, ensuring autonomy and differential in the social universe of the group, whose choices legitimize how the investment in culture can produce artists aware of texisting art beauty and its coming results. It is interesting to make evidente that the samba works as a temporal milestone for CCC, but the main motivation that was noticed there, was the in meeting mediated by dance, junction body/music, present in the lives of the attendees since their childhood, beyond the pleasure of belonging to a group , influenced by similar stories. Along with that, the teacher held the role of a veiled leadership, to mediate the relationships and to produce effects of group cohesion, with his ideas and incentive for the dance expression, in order to make way for new discoveries and reframing
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Jean, Daniel. "La scène utopique : le théâtre des poètes modernistes W.B. Yeats, T.S. Eliot et W.H. Auden." Paris 4, 2006. http://www.theses.fr/2006PA040075.
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Les trois poètes majeurs de l’ère moderne en Angleterre, W. B. Yeats, T. S Eliot et W. H. Auden, au delà de leur identité poétique propre ont en commun d’avoir consacré une partie significative de leur carrière au théâtre. Leurs contributions à l’art dramatique ont fait l’objet de nombreuses études au moment de leur gloire, mais caractérisées par l’inscription de leur parcours dans le genre contestable de théâtre en vers (« verse drama »). Une telle approche nie la spécificité moderniste de leur réflexion et de leur pratique du théâtre, en particulier en négligeant l’importance des problématiques européennes d’un théâtre utopique, que l’on trouve à la fois chez Wagner et Mallarmé. L’objet de cette thèse est d’intégrer la dimension utopique à une relecture des œuvres de ces poètes, qu’elles soient explicitement destinées à la scène, ou qu‘elles contiennent une théâtralité latente, avec comme horizon une redéfinition de leur place dans l’histoire du théâtre britanniqueThe three major English-speaking poets of the modern age, W. B. Yeats, T. S. Eliot and W. H. Auden have all devoted a significant part of their careers to the theatre. There were many studies of their contributions to drama at the time of their success, but the concept of “verse drama”, which was coined to characterize them, has proved of doubtful value. It denies the specifically modernist nature of their reflection and a approach to the theatre, particularly by underestimating the importance of the European theories of drama as utopia, such as Wagner’s and Mallarmé’s. The aim of the present thesis is to offer a new reading of the dramatic works of these poets, whether they were explicitly intended for the stage or they are implicitly dramatic in form and content, taking into account their utopian dimension and attempting to redefine their place in the history of British drama
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Boldrini, Ester. "EMOTIBLOG: a model to learn subjetive information detection in the new textual genres of the web 2.0 -a multilingual and multi-genre approach." Doctoral thesis, Universidad de Alicante, 2012. http://hdl.handle.net/10045/24316.
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Castello, Edna. "Le Net participatif, levier d’acquisition des littératies traditionnelle et numérique : étude sur deux terrains, en FLE et auprès d'un public migrant faiblement scolarisé." Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAL007/document.
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Cette recherche vise à comprendre de quelle manière l’exploitation des sites du Net participatif et de leur dimension sociale peut favoriser les apprentissages en classe de langue. Notre recherche s’appuie sur deux expériences de terrain réalisées auprès de deux publics différents, un public en FLE en 2012 et en 2013, à l’Alliance française Paris Île-de-France, et un public faiblement ou non scolarisé, en 2014, aux Cours Municipaux pour Adultes de la Ville de Paris, en post-alphabétisation. Dans une approche sociocritique, nous avons analysé des dispositifs pédagogiques dans lesquels les apprenants ont posté des messages sur des forums de discussion, des avis et des commentaires sur différents sites dont TripAdvisor, YouTube, Doctissimo, Le Parisien. Essentiellement qualitative, notre analyse a tout particulièrement interrogé la prise en compte de la dimension interactionnelle et sociale du Net participatif qui est sa caractéristique et son avantage principal. L’expérience en FLE nous a permis, en adoptant une approche émique, de repérer un certain nombre de conditions, favorables et défavorables, à l’intégration du Net participatif en classe de langue, de montrer le rôle déterminant de la culture d’usage dans l’appropriation de l’outil par les apprenants et de mettre en avant les notions de besoin et d’utilité de la tâche. À partir de ces conclusions, nous montrons qu’en post-alphabétisation les sites du Net participatif utilisés semblent avoir répondu aux besoins des apprenants faiblement ou non scolarisés. Grâce à la socialisation des écrits qu’il permet, et à l’engouement certain qu’il suscite chez ce public, le Web participatif, crée un effet d’entraînement dans les tâches de lecture-écriture. Nous émettons l’hypothèse que l’hybridité entre oral et écrit et entre langage et action des messages de forums de discussion et des sections commentaires lève certaines inhibitions généralement constatées chez ce public et facilite le processus d’écriture. Ainsi, nous avons repéré sur ce deuxième terrain le potentiel du Net participatif en tant que levier d’acquisition de la littératie traditionnelle et numérique chez un public en insécurité scripturale, et examiné les liens synergiques qui peuvent se créer entre ces deux littératies. Nous dégageons l’intérêt heuristique que présente le Net participatif dans les tâches de lecture-écriture, quel que soit le public, et nous montrons les avantages d’une démarche centrée sur l’apprenantThe aim of this research was to understand and evaluate the use of some sites of the participative web, viewed in their social dimension, to meet the learning needs of learners in language courses. Our study was based on two field experiments conducted on two different types of audiences, one in 2012 and 2013 with French as a Foreign Language (FFL) students at the Alliance française Paris Île-de-France, and another in 2014 with learners with low levels of education at the Cours Municipaux d’Adultes de la Ville de Paris (adult training provider of the City of Paris) in a post–literacy programme. Following a sociocritical approach, we worked on case-based scenarios in which learners were asked to post messages on discussion forums and in the comments section of online magazines on websites such as TripAdvisor, YouTube, Doctissimo and Le Parisien. In a qualitative analysis, we took into account the interactional and social dimensions of the Web 2.0 which are its distinctive features and main advantages. In FFL our experiment enabled us, through an emic approach, to pinpoint some conditions necessary for the effective use of the participative web in language courses, to show the decisive role of culture of use in tool appropriation and to underline the two notions of need and purpose. Our first results led us to show in a second experiment that in post-literacy programmes, the participative websites seemed to answer the needs of learners with low levels of education. Socialization of writing skills and the keen interest these tools arouse in this type of audience were the main factors of improved achievements. The fact that the participative web seemed to improve the performance of reading and writing tasks leads us to formulate the hypothesis that the hybridization of written and oral languages and of language and action found in discussion forum messages and comments section frees this second type of learners from some of the anxieties generally observed at a low education level and helps the writing process. We suggest from our findings that the participative web is a potential lever for the acquisition of traditional and digital literacies in learners with writing skill insecurities, and examine the synergies that could be created in the acquisition of these two literacies. We look into the heuristic value of the participative web in writing-reading skills, regardless of the learner's level of education, and we discuss the benefits of a learner-centered approach
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Silva, Lucas Felipe da. "Integração de dados e desenvolvimento de métricas escalável para análise de fatores de transcrição." PROGRAMA DE PÓS-GRADUAÇÃO EM BIOINFORMÁTICA, 2018. https://repositorio.ufrn.br/jspui/handle/123456789/25393.
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Atualmente há diversas ferramentas propostas para análise de Fatores de Transcrição (TF), tais como TFCheckpoint, JASPAR, SSTAR, GTRD, Enrichr. No entanto, nenhuma dessas ferramentas oferece uma experiência completa, em que se possa avaliar a confiabilidade do TF, ou seja, se de fato uma proteína analisada é um TF e a sua associação com o gene alvo. Ao longo do tempo, foram construídas inúmeras bases de dados, todas elas com riquíssimas informações, porém a complexidade intrínseca do dado, o volume de informações, problemas de nomenclatura dos genes e diversos outros fatores fizeram com que tais ferramentas não oferecessem um espectro completo da análise. Por outro lado, para se trabalhar com um grande volume de dados, se requer conhecimentos avançados de computação. Entretanto, o grande público interessado em analisar esses dados são os profissionais procedentes das áreas biológicas, configurando-se como uma barreira, uma vez que a formação acadêmica desta área não oferece em seus componentes curriculares disciplinas de programação. Diante desta situação, este trabalho tem como objetivo criar uma ferramenta web destinada exclusivamente para análise dos TFs. Desse modo, foi idealizado e desenvolvido o Transcription Factor Analysis Tools (TFAT), contendo a integração de diferentes bases de dados e um conjunto de scripts para manipular estas informações, juntamente com os parâmetros cruciais definidos pelo usuário em sua análise. O cerne desta ferramenta é a análise para identificar os TFs chaves na modularização da transcrição gênica, ou seja, o enriquecimento dos TFs reguladores de uma lista de genes submetida pelo usuário, que através dos componentes da ferramenta, consulta sua base de dados, identificam os TFs que estão associados aos genes da lista e calcula o p-valor de enriquecimento. Além disso, a ferramenta verifica a confiabilidade do TF, disponibiliza as predições realizadas e converte os itens de uma lista para o GeneID ou Symbol do Entrez Gene. Outro recurso presente neste trabalho é a utilização da confiabilidade do TF aplicado em toda a ferramenta. Esse grau de confiabilidade leva em consideração evidências de diferentes bases de dados, experimentos, predições e outras características dos TFs. Este recurso de confiabilidade possui um modo padrão e um modo com parâmetros definidos pelo próprio usuário, que permite toda uma personalização por meio de filtros nas consultas e controle de análise para o usuário final.
Currently there are several tools proposed for analysis of Transcription Factors (TF), such as TFCheckpoint, JASPAR, SSTAR, GTRD, Enrichr. However, none of these tools offer a complete experience in assessing the reliability of TF, checking if an analyzed protein is a TF and its association with the target gene. Over time, numerous databases were built, all of them with rich information, but the intrinsic complexity of the data, the volume of information, problems of nomenclature of the genes and several other factors led these tools to do not offer a complete spectrum of analyses. On the other hand, working with a large volume of data requires advanced computer skills. However, the general public interested in analyzing these data are professionals from the biological areas, forming a barrier since the academic formation of this area does not offer in its curricular components programming disciplines. From this situation, this work aims to create a web tool exclusively for the analysis of TFs. In this way, the Transcription Factor Analysis Tools (TFAT) was conceived and developed, containing the integration of different databases and a set of scripts to manipulate this information, along with the crucial parameters defined by the user in the analysis. The core of this tool is the analysis to identify the key TFs in the modulation of gene transcription, namely the enrichment of the regulatory TFs of a user-submitted gene list, which through the components of the tool, consults its database, identifies the TFs that are associated with those genes and computes the p-value of enrichment. In addition, the tool verifies TF reliability, makes available predictions, and converts items from a list to the Entrez Gene's GeneID or Symbol. Another feature of this work is the use of TF reliability applied throughout the tool. This degree of reliability takes into account evidences from different databases, experiments, predictions and other characteristics of TFs. This reliability feature has a standard mode and a userdefined parameter mode, which allows full customization through filters in the queries and analysis control for the end user.
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Kumar, Vivek. "Computational Prediction of Protein-Protein Interactions on the Proteomic Scale Using Bayesian Ensemble of Multiple Feature Databases." University of Akron / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=akron1322489637.
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Stigliani, Arnaud. "Modélisation de la liaison à l'ADN et des mécanismes d'action de facteurs de transcription floraux Building Transcription Factor Binding Site Models to Understand Gene Regulation in Plants JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework." Thesis, Université Grenoble Alpes (ComUE), 2019. https://thares.univ-grenoble-alpes.fr/2019GREAV032.pdf.
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Chez les angiospermes, la floraison est un processus qui prend part en plusieurs étapes. Le méristème caulinaire, un réservoir de cellule souche d’où émergent la totalité des organes aériens de la plante, va d’abord se différencier en méristème d’inflorescence. Des méristèmes floraux vont alors émerger des flancs du méristème d’inflorescence pour donner naissance aux différents organes qui composent la fleur : les pétales, les sépales, les étamines et le carpelle. Chacune de ces phases est régulée avec finesse par des facteurs de transcription, une famille de protéines se liant à l’ADN pour induire l’activation ou la répression des gènes. Si cette thèse nous a permis de contribuer à la mise à jour de JASPAR, une base de données qui recense des profils liaison de facteurs de transcription, elle a avant tout pour but d’apporter un regard nouveau sur la compréhension des phénomènes qui contrôlent le développement des fleurs à travers l’étude d’une poignée de facteurs de transcription clé dans ce processus. Nous essayerons au mieux d’expliquer les paramètres qui influent sur la liaison de ces facteurs de transcription en utilisant des modèles bioinformatiques associés à des expériences de génomique.Nous nous pencherons d’abord sur les facteurs de réponse à l’auxine à travers l’étude de deux représentants de cette famille de 23 protéines : ARF2 et ARF5. Si les facteurs de transcription de cette famille sont connus pour se lier en dimères, nous avons montré que ARF2 et ARF5 préféraient des espacements différents entre les sites de liaison monomériques sur l’ADN. Nous avons également montré que certaines configurations semblent favoriser l’activation des gènes liés.Ensuite, nous avons étudié LFY, un facteur de transcription maître du développement floral. Nous avons amélioré un modèle de liaison existant et nous avons pu voir que l’intégration de données génomiques de natures diverse permettait de mieux comprendre la liaison du facteur de transcription in vivo.Enfin, nous avons analysé les préférences des facteurs de transcription à boîte MADS, connus pour lier les mêmes séquences d’ADN et dont le rôle est de déterminer l’identité des organes floraux. À travers l’étude du complexe SEP3/AG, qui contrôle la formation du carpelle, nous avons montré que le domaine de tétramérisation de ces facteurs confère une spécificité de liaison expliquant potentiellement que des groupes de facteurs de transcription à boîte MADS régulent la formation d’organes floraux différents en activant des gènes distinctsIn angiosperms, the development of flowers takes place in several stages. The meristem, a stem cell reservoir from which all the plant’s aerial organs emerge, first differentiate into an inflorescence meristem. Floral meristems then emerge from the flanks of the inflorescence meristem to give birth to the different organs that compose the flower : the petals, sepals, stamens and carpel. Each of these phases is finely regulated by transcription factors, a family of proteins that bind to DNA to induce gene activation or repression. If this thesis allowed us to contribute to the JASPAR database, which gather transcription factor binding profiles, its main goal is to provide a new perspective on the understanding of the phenomena that control flower development through the study of a handful of key transcription factors in the regulation of floral development. We have tried to explain the parameters that influence the binding of these transcription factors using bioinformatics models associated with genomics experiments.We have analysed the auxin response factors (ARF) through the study of two representatives of this family of 23 proteins : ARF2 and ARF5. The transcription factors of this family are known to bind in dimers and we have shown that ARF2 and ARF5 prefer different spacings between monomeric binding sites on DNA. We have also shown that some configurations seem to favour the activation of bound genes.Then, we have studied LFY, a master transcription factor of floral development. We have improved an existing binding model and have seen that the integration of genomic data of various kinds provides a better understanding of the binding of the transcription factor in vivo.Finally, we have analyzed the preferences of MADS box transcription factors, known to bind the same DNA sequences and whose role is to determine the identity of floral organs. Through the study of the SEP3/AG complex, which controls the formation of the carpel, we have found that the tetramerization domain of these factors confers binding specificity, potentially explaining that groups of MADS box transcription factors regulate the formation of different floral organs by activating distinct genes
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Bergström, Marie. "Au bonheur des rencontres : sexualité, classe et rapports de genre dans la production et l’usage des sites de rencontres en France." Thesis, Paris, Institut d'études politiques, 2014. http://www.theses.fr/2014IEPP0032.
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La fréquentation des sites de rencontres est désormais une pratique répandue en France et un objet de débat important. À partir d’une recherche empirique originale qui croise des enquêtes qualitatives et quantitatives, cette thèse propose une sociologie de ces services de rencontres sur Internet. Se plaçant d’abord du côté de la production des sites, elle montre la constitution d’un nouveau marché économique – celui de la rencontre – dont elle dissèque les différentes logiques. Elle explique en particulier la forte standardisation des plateformes, et la diffusion plus récente de sites spécialisés, comme autant de dynamiques propres à un marché en développement. Étudiant les usages au sein de la population hétérosexuelle, elle interroge ensuite les modes d’appropriation – sociaux et sexués – des sites et l’organisation des relations qui en découlent. Ce faisant, l’enquête révèle que, si les sites promeuvent les rencontres amoureuses, ils contribuent en réalité peu à la formation des couples, favorisant davantage une hétérosexualité non conjugale. La discrétion des rencontres en ligne, qui se déroulent en dehors et à l’insu des cercles de sociabilité, contribue à ce fait. Alors que les pratiques numériques sont habituellement associées à une publicisation croissante de la vie intime, les sites de rencontres participent donc d’un mouvement contraire de privatisation de la sociabilité sexuelle. Cette caractéristique des sites autorise une plus grande marge de manœuvre dans l’exercice de la sexualité, et ce en premier lieu pour les femmes, mais ne déroge pas pour autant au double standard de sexe qui structure les relations hétérosexuelles, sur Internet comme ailleursOnline dating is a widespread phenomenon in France today as well as an important topic of debate. Based on original empirical research, interweaving qualitative and quantitative methods, this thesis offers a sociological understanding of these sites. By first examining the production of dating sites, the thesis shows how a new economic market has been established – the dating market – whose different logics are then analysed. In particular, the high degree of standardisation of these platforms, as well as the more recent spread of specialised sites, are seen as characteristics of a developing market. Dating site use within the heterosexual population is then examined through an analysis of the different modes of appropriation – social and sexual – of the sites, as well as the structure of resulting relations. In so doing, the investigation reveals that although these sites do foster romantic encounters, they seldom result in couple formation, favouring instead a non-conjugal heterosexuality. The privacy afforded by online dating, external and unbeknownst to one’s social circle, contributes to this. Whilst the use of information technologies is typically associated with increasing public exposure of intimate life, dating sites thus have the opposite effect of rendering sexual sociability more private. This characteristic of the sites allows for a larger degree of freedom in the expression of sexuality, particularly for women; however, it does not circumvent the sexual double standard that structures heterosexual relations, on the Internet as elsewhere
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Anjos, Joelma Sá Teles dos. "Práticas de linguagem em situação de trabalho - chat: um novo gênero digital." Pontifícia Universidade Católica de São Paulo, 2011. https://tede2.pucsp.br/handle/handle/13546.
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Previous issue date: 2011-11-21Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Some companies have been offering online chats named as Web Call Centers besides traditional Call Centers. This is a new tool for communication between companies and clients which aims for more productivity and commitment. Considering this new work activity and through qualitative methodology and epistemological interpretative orientation, this research examines online chat interactions to understand the characteristics of the discursive practices in this given context. This work has looked for answering two major questions: what are the characteristics of the situation of work of Web Call Center attendants?; and what is the discursive status of the online chat in this work situation? Theoretically, we have recurred to language studies that consider online chats as a genre, specifically Marchurschi s contibutions (2010). We have also recurred to language studies that consider online chats as a hypergenre like Dominique Maingueneau s work (2001) and, we have recurred to studies of work, specifically Ergology, which is considered an innovative theory to approach work activities (Schwartz, 1997, 2006). The corpus considered in the analysis consists of registers of online chats in customer service with interactions between insurance technicians as attendants and their clients who were insurance agents. By doing the analysis of these registers and by discussing them, we have come to the conclusion that in work situation the online chat goes under coercion that allows us to classify it as a genre. Some other aspects were revealed in the study as well, such as the normalization, done by the attendants, that points to the dialectics among the instituted pieces of knowledge, i. e., the rules that precede the activity, and the invested knowledge, the experience that comes with practice
Algumas empresas têm instituído, ao lado dos Call Center, intitulados atualmente de Web Call Center, o chat como uma nova modalidade de atendimento agente-cliente, visando, sobretudo, ao aumento da produtividade e engajamento com a nova tecnologia. Considerando essa nova atividade de trabalho, esta pesquisa, pautada em metodologia qualitativa, de base epistemológica interpretativista de observação, teve como objetivo investigar e analisar interações ocorridas em situação de atendimento ao cliente, via chat, para compreender as características das práticas discursivas nesse contexto. Nesse sentido, procurou responder a duas questões: Qual(is) a(s) característica(s) da situação de trabalho das atendentes do Web Call Center? Qual o estatuto discursivo do chat em situação de trabalho? Do ponto de vista teórico, recorreu aos estudos da linguagem - mais especificamente às contribuições de Marcuschi (2010), que considera o chat como gênero, e de Dominique Maingueneau (2001), que o vê como hipergênero - e aos estudos do trabalho, mais especificamente à Ergologia, entendida como um modelo teórico-metodológico inovador para abordar a atividade de trabalho (Schwartz, 1997, 2006). O corpus considerado para análise constituiu-se de registros de atendimento ao cliente por meio do chat, entre técnicos de seguros na função de agentes de atendimento de uma Seguradora Nacional e, seus clientes - corretores de seguros. Por meio da análise e discussão desses registros, concluiu-se que o chat em situação de trabalho sofre várias coerções que permitem caracterizá-lo como gênero. Ficaram claras também as várias renormalizações feitas pelas atendentes, as quais indicam a dialética entre os saberes instituídos, isto é, as normas que antecedem a atividade, e os saberes investidos, a experiência advinda da prática
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Peña, Salas Juan Pablo. "Clickbait como recurso que altera los criterios de jerarquización en el periodismo digital informativo. Caso: COVID-19 en el Perú (6 al 15 de marzo del 2020), en la web del Diario La República, RPP Noticias y América Noticias." Bachelor's thesis, Universidad Peruana de Ciencias Aplicadas (UPC), 2020. http://hdl.handle.net/10757/655066.
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El tema de la presente tesis es la influencia de las nuevas tecnologías en la evolución del periodismo digital informativo y cómo su uso ha alterado sus criterios de jerarquización tradicionales (en forma de pirámide invertida, en donde lo principal iba al inicio y el resto de la nota era su desarrollo o descripción). En este caso, la investigación se basará en cómo emplean el clickbait los medios de comunicación peruanos para el desarrollo de sus notas informativas y cómo este uso ha cambiado la estructura de la noticia. Se revisaron las plataformas en línea de tres medios: el Diario La República como prensa escrita, Radio RPP como prensa radial, y América Noticias como prensa televisiva; escogidos al haber sido pioneros en sus rubros en la transición al mundo digital y además por el alto nivel de lectoría y audiencia. Para el logro del objetivo planteado, se realizó un análisis de contenido con un periodo de tiempo delimitado por la aparición del paciente cero de COVID-19 en el Perú (6 de marzo), que fue el momento en que el público peruano tomó conciencia de que la enfermedad había llegado a nuestro país; hasta que se decretó el inicio de la cuarentena (15 de marzo), fecha en el que el Estado reaccionó y tomó medidas para combatir y/o prevenir la expansión del virus. El hallazgo más importante en los tres medios es que sí existe una variación en la estructura de las notas informativas que contienen un clickbait, utilizando una jerarquización principalmente romboide (estructura de redacción donde la información principal o la respuesta al titular de la nota está al medio y no al inicio).The subject of this thesis is the influence of new technologies in the evolution of digital journalism and how its use has altered its traditional hierarchical criteria (in the form of an inverted pyramid, where the main thing was at the beginning and the rest of the note is its development or description). In this case, the research will be based on how the Peruvian media use clickbait for the development of their informative notes and how this use has changed the structure of the news. The online platforms of three media were reviewed: Diario La República as the written press, Radio RPP as the radio press, and América Noticias as the television press; chosen for having been pioneers in their fields in the transition to the digital world and also for the high level of readership and audience. To achieve the proposed objective, a content analysis was carried out with a period of time delimited by the appearance of the zero COVID-19 patient in Peru (March 6), which was the moment when the Peruvian public became aware of that the disease had reached our country; until the beginning of the quarantine was decreed (March 15), the date on which the State reacted and took measures to combat and / or prevent the spread of the virus. The most important finding in the three media is that there is a variation in the structure of the informative notes that contain a clickbait, using a mainly rhomboid hierarchization (writing structure where the main information or the response to the note holder is in the middle and not at the beginning).
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Ruiz, Ugo. "Le blog d'écrivain : la littérature à l'épreuve d'Internet." Thesis, Paris 4, 2015. http://www.theses.fr/2015PA040025.
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Ce travail se propose d’étudier les effets d’Internet sur la littérature : le web se prête-t-il à l’activité littéraire ou représente-t-il pour elle au contraire une limite, voire une menace pour son avenir ? Nous menons notre interrogation à partir de l’analyse de trois blogs d’écrivain dont les auteurs publient aussi des romans dans des maisons d’édition reconnues : François Bon, Éric Chevillard et Chloé Delaume. À l’aide d’outils empruntés au domaine de l’analyse du discours, nous abordons des problèmes théoriques relatifs aux effets du support numérique sur la perception des genres et sur la notion d’auteur. Tout d’abord, nous montrons que le web ne permet pas l’émergence d’œuvres littéraires, puisque ce processus repose sur le circuit éditorial et la hiérarchie imposée par les catégories textuelles. La toile compromet également le statut d’auteur au sens fort du terme, dans la mesure où les écrivains sont amenés à établir un contact direct avec leurs lecteurs. Nous mettons en évidence que cet exercice d’écriture est ainsi soumis à une double contrainte : la notoriété de leurs blogs se fait au détriment d’une pratique littéraire gratifiante à laquelle les écrivains ne veulent pourtant pas renoncer. Cette situation ressort dans la manière dont les écrivains introduisent leur projet littéraire sur Internet : Bon veut mettre l’œuvre sur la toile, Chevillard se pose en défenseur de la « bonne » littérature et Delaume crée son salon littéraireThis study focuses on three blogs kept by writers who have published novels in renowned publishing houses: François Bon, Éric Chevillard and Chloé Delaume. This new writing practice raises the question of whether literature can be transferred to the Internet: does this medium admit literary activity or, on the contrary, does it represent a limit or even a threat to the future of literature? By using theoretical tools from the field of discourse analysis, the study discusses theoretical problems related to the impact of digital media on the perception of genres and on the notion of authorship. First, the study shows that the web does not allow the emergence of literary works, because this process is based on the editorial circuit and the hierarchy between textual categories. The existence of authors in the strongest meaning of the term is also compromised by the web, since the writers establish direct contact with their readers. The writer blog thus implies a dilemma: its success is necessarily to the detriment of a rewarding literary practice that the writer does not want to give up. This double bind is apparent in the way the writers use their blog: Bon wishes to open the literary field to the Internet, Chevillard is defending ”good” literature and Delaume intends to make her blog a performance
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Harlig, Alexandra M. "Social Texts, Social Audiences, Social Worlds: The Circulation of Popular Dance on YouTube." The Ohio State University, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=osu1557161706452516.
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Le, Caroff Coralie. "Les usages sociopolitiques de l'actualité en ligne. S'informer, partager et commenter sur Facebook." Thesis, Paris 2, 2015. http://www.theses.fr/2015PA020080/document.
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La thèse porte sur les usages sociopolitiques de l’actualité en ligne par les profanes sur Facebook. Initialement conçu pour l’échange privé, ce réseau social est également devenu un espace pour s’informer, partager et commenter les nouvelles. Ces pratiques sont analysées à partir de trois entrées : les spécificités du dispositif technique, le rapport au politique des participants et, enfin, le rôle du genre dans les prises de parole sur Facebook. Ce travail se fonde sur l’analyse comparée de la participation sur une sélection de pages Facebook de médias et de profils personnels sur ce réseau. La méthodologie repose sur une observation ethnographique en ligne et sur une enquête qualitative par entretiens.Les principaux résultats démontrent que les actualités politiques débouchent sur des réactions davantage fondées sur l’émotion que sur la rationalité et sur des affrontements de camps d’opinion. Ces débats se déroulent essentiellement sur les pages publiques des médias alors que les Timelines sont plutôt des espaces de diffusion et de partage d’actualités. Les femmes manifestent autant que les hommes un intérêt pour les questions publiques et Facebook est un espace commun d’indignation. En dépit d’opinions affirmées, les modes d’interaction des participantes sont plutôt modérés à l’inverse de ceux des hommes, plus investis dans des confrontations. Si Facebook contribue, en un sens, à un élargissement de l’espace public, la participation étudiée demeure limitée et ne s’apparente pas à des débats susceptibles de revivifier la démocratieThe thesis focuses on the socio-political uses of online news for laymen, specifically on Facebook. Originally designed for the private exchange, this social network has also become a place to access, share and comment the news. These practices are analysed through three inputs: the specifics of the technical device, the relation to politics by participants, and, finally, the role of gender in speaking out on Facebook.This work is based on a comparative analysis of participation around political events on selected Facebook media pages and on personal profiles of the social network. The methodology is based on an online ethnographic observation and on qualitative interviews.The main results show that political events lead to reactions based more on emotion than on rationality and on opinion camps clashes. These debates mainly take place on the media public pages while the timelines are rather dissemination areas, by sharing news. Women manifest as much as men their interest for public issues and Facebook is a common area to express indignation. Despite asserted opinions, women get involved in more moderate forms of interaction unlike men who are more invested in conflictual exchanges. In a sense, if Facebook contributes to an extension of the public space, participation remains limited and does not akin to discussions that are likely to revive democracy
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Fuller, Roger Jason. "Threads in a Tapestry: An Ethnographic Evaluation of Milken Community High School’s Tiferet Fellowship Program." Antioch University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=antioch1285863435.
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Lee, Sungeun. "Virus-host interactions across a soil pH gradient at the community and individual scale." Thesis, Lyon, 2020. http://www.theses.fr/2020LYSEC020.
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Les virus du sol sont capables d'influencer la structure de la communauté microbienne et le fonctionnement de l'écosystème en affectant l'abondance des cellules hôtes par lyse et par leurs caractéristiques à transférer des gènes entre les hôtes. Bien que notre compréhension sur la diversité et la fonction virales s’améliore, la connaissance des interactions hôte-virus dans le sol reste limitée. Pour mieux comprendre les interactions hôte-virus, un gradient du sol à long terme manipulé par le pH dans lequel la communauté microbienne change à travers, a été étudié. Les principaux objectifs de cette thèse ont consisté à (1) déterminer l'influence de la structure de la communauté microbienne et du pH du soil sur les virus par séquençage d’ADN haut-débit (Chapitre II), (2) déterminer l’infectivité des populations virales à partir de niches de sol co-localisées et non co-localisées avec son hôte grâce à une approche de l’essai de plaque combinée à un séquençage hybride (Chapitre III), (3) identifier les populations virales infectant des groupes fonctionnels microbiens spécifiques du sol, en particulier les méthanotrophes (Chapitre IV) et les nitrifiants (Chapitre V ), à l’aide d’une sonde isotopique stable à l'ADN. Nos premiers résultats ont montré que la structure de la communauté virale change selon le pH du sol, ce qui souligne que la communauté virale est étroitement liée aux populations hôtes. L’analyse de CRISPR systèmes a révélé des interactions virus-hôte dynamiques, avec le nombre et la taille des CRISPR systèmes distincts selon le soil à pH contrasté. L’analyse taxonomique de cette CRISPR systèmes suggère que les virus jouent un rôle essentiel dans la composition et de la fonction de la communauté procaryote du sol. Les processus co-évolutionnaires entre l'hôte (le système de restriction-modification et le CRISPR-Cas système) et les populations virales co-localisées (la mutation d’une séquence espaceur « spacer » et la méthyltransférase codée par le virus) fournissent des preuves de l'adaptation locale et que les interactions virus-hôte jouent un rôle important dans la susceptibilité d'un hôte à l'infection et par conséquent la régulation des populations bactériennes du sol. L'ADN-SIP-métagénomique ciblant des groupes fonctionnels microbiens spécifiques a permis l’analyse des populations hôte-virus individuelles. Le suivi du flux de carbone à travers les populations procaryotes et virales a révélé des interactions actives entre les virus et les hôtes méthanotrophes et nitrifiants, et les préférences de niches de pH du sol. Notre étude a montré une preuve de transfert horizontal de gènes et des gènes métaboliques auxiliaires codés par le virus, indiquant que les virus contribuent de manière significative aux cycles biogéochimiques dans le sol, tels que le carbone (les gènes qui codent pour les familles GH, peptidases et la sous-unité C de méthane monooxygénase particulaire), et l'azote (les gènes qui codent pour la nitrogénase et le cytochrome cd1-nitrite réductase). Dans l’ensemble, ces résultats ont montré que les virus du sol sont des régulateurs importants des communautés microbiennes par la lyse spécifique de l’hôte et des interactions dynamiques virus-hôteSoil viruses have potential to influence microbial community structure and subsequent ecosystem functioning by directly affecting the abundance of host cells by lysis and through their ability to transfer genes between hosts. Although our understanding of soil viral diversity and functioning has increased, the role of viruses and their interactions with prokaryotes in soil is limited. To gain a better understanding of virus-host interactions in soil, a long-term pH-manipulated soil gradient, which microbial community structure changes across, was investigated. The main objectives of this thesis were to 1) determine the influence of microbial community structure and soil pH on viruses using metagenomics and viromics (Chapter II), 2) determine the infectivity of soil viral populations from co-localized and foreign pH soil niches using a plaque assay approach combined with hybrid metagenomics sequencing (Chapter III) and 3) identify virus populations infecting specific soil microbial functional groups, specifically methanotrophs (Chapter IV) and nitrifiers (Chapter V), using DNA stable isotope probing combined with metagenomic deep sequencing. Viral community structure was found to change with soil pH, demonstrating that viral communities are tightly linked to host populations, but also may have narrow host ranges. Analysis of clustered regularly interspaced short palindromic repeats (CRISPR) arrays revealed dynamic virus-host interactions, with the number and size of CRISPR arrays distinct across contrasting pH soil. Profiling of the host-virus linkages between soil pH, suggests that viruses play a critical role in shaping the composition and function of the soil prokaryotic community. Surprisingly, greater infectivity of a host bacterium by virus populations was found when viruses and host bacterium were not co-localized in the same pH soil. Coevolutionary processes between the host and virus populations, such as restriction modification/virus-encoded methyltransferase and CRISPR-Cas system/spacer mutation, provide evidence for local adaptation, and that virus-bacterial host interactions play an integral part in the susceptibility of a host to infection and consequently in the regulation of soil bacterial populations. Targeting specific microbial functional groups via stable isotope probing allowed analysis of individual host-virus populations. Tracking carbon flow through prokaryotic and viral populations revealed active interactions between viruses and methanotroph and nitrifier hosts, and soil pH niche preferences. Evidence of horizontal gene transfer and virus-encoded auxiliary metabolic genes, such as glycoside hydrolase families, peptidases, particulate methane monooxygenase subunit C (pmoC), nitrogenase (nifH) and cytochrome cd1-nitrite reductase, supports that viruses are significant contributors to host functioning and carbon and nitrogen cycling in soil. Overall, this work demonstrated that soil viruses are important regulators of microbial communities through specific host lysis and dynamic virus-host interactions
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Denecker, Thomas. "Bioinformatique et analyse de données multiomiques : principes et applications chez les levures pathogènes Candida glabrata et Candida albicans Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata Efficient, quick and easy-to-use DNA replication timing analysis with START-R suite FAIR_Bioinfo: a turnkey training course and protocol for reproducible computational biology Label-free quantitative proteomics in Candida yeast species: technical and biological replicates to assess data reproducibility Rendre ses projets R plus accessibles grâce à Shiny Pixel: a content management platform for quantitative omics data Empowering the detection of ChIP-seq "basic peaks" (bPeaks) in small eukaryotic genomes with a web user-interactive interface A hypothesis-driven approach identifies CDK4 and CDK6 inhibitors as candidate drugs for treatments of adrenocortical carcinomas Characterization of the replication timing program of 6 human model cell lines." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL010.
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Plusieurs évolutions sont constatées dans la recherche en biologie. Tout d’abord, les études menées reposent souvent sur des approches expérimentales quantitatives. L’analyse et l’interprétation des résultats requièrent l’utilisation de l’informatique et des statistiques. Également, en complément des études centrées sur des objets biologiques isolés, les technologies expérimentales haut débit permettent l’étude des systèmes (caractérisation des composants du système ainsi que des interactions entre ces composants). De très grandes quantités de données sont disponibles dans les bases de données publiques, librement réutilisables pour de nouvelles problématiques. Enfin, les données utiles pour les recherches en biologie sont très hétérogènes (données numériques, de textes, images, séquences biologiques, etc.) et conservées sur des supports d’information également très hétérogènes (papiers ou numériques). Ainsi « l’analyse de données » s’est petit à petit imposée comme une problématique de recherche à part entière et en seulement une dizaine d’années, le domaine de la « Bioinformatique » s’est en conséquence totalement réinventé. Disposer d’une grande quantité de données pour répondre à un questionnement biologique n’est souvent pas le défi principal. La vraie difficulté est la capacité des chercheurs à convertir les données en information, puis en connaissance. Dans ce contexte, plusieurs problématiques de recherche en biologie ont été abordées lors de cette thèse. La première concerne l’étude de l’homéostasie du fer chez la levure pathogène Candida glabrata. La seconde concerne l’étude systématique des modifications post-traductionnelles des protéines chez la levure pathogène Candida albicans. Pour ces deux projets, des données « omiques » ont été exploitées : transcriptomiques et protéomiques. Des outils bioinformatiques et des outils d’analyses ont été implémentés en parallèle conduisant à l’émergence de nouvelles hypothèses de recherche en biologie. Une attention particulière et constante a aussi été portée sur les problématiques de reproductibilité et de partage des résultats avec la communauté scientifiqueBiological research is changing. First, studies are often based on quantitative experimental approaches. The analysis and the interpretation of the obtained results thus need computer science and statistics. Also, together with studies focused on isolated biological objects, high throughput experimental technologies allow to capture the functioning of biological systems (identification of components as well as the interactions between them). Very large amounts of data are also available in public databases, freely reusable to solve new open questions. Finally, the data in biological research are heterogeneous (digital data, texts, images, biological sequences, etc.) and stored on multiple supports (paper or digital). Thus, "data analysis" has gradually emerged as a key research issue, and in only ten years, the field of "Bioinformatics" has been significantly changed. Having a large amount of data to answer a biological question is often not the main challenge. The real challenge is the ability of researchers to convert the data into information and then into knowledge. In this context, several biological research projects were addressed in this thesis. The first concerns the study of iron homeostasis in the pathogenic yeast Candida glabrata. The second concerns the systematic investigation of post-translational modifications of proteins in the pathogenic yeast Candida albicans. In these two projects, omics data were used: transcriptomics and proteomics. Appropriate bioinformatics and analysis tools were developed, leading to the emergence of new research hypotheses. Particular and constant attention has also been paid to the question of data reproducibility and sharing of results with the scientific community
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Hung, Wei-Hsin, and 洪偉欣. "A Comprehensive Web Server for Human Gene Regulation." Thesis, 2012. http://ndltd.ncl.edu.tw/handle/61676662675720721531.
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碩士國立中興大學
基因體暨生物資訊學研究所
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Previously, we constructed a composite regulatory signature database (CRSD http://biochip.nchu.edu.tw/crsd1). In this work, based on our previous framework, we established CRSD release 2 (CRSD2, http://syslab.nchu.edu.tw/crsd2). The CRSD2 can predict target genes for microRNAs and transcription factors. Users can use CRSD2 in investigating complex regulatory behaviors involving the microRNA regulatory signatures and TF regulatory signatures. We integrated six large-scale databases to construct two core genome-wide databases. The former are those for microRNAs, promoters, transcription factors, pathways and gene functions, while the latter are microRNA regulatory signatures and transcription factor signatures. In addition, CRSD2 also provides information for single nucleotide polymorphisms.
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Vellguth, Martin. "OrfMapper : a web-based application for querying and visualizing gene metadata /." 2007. http://digitool.hbz-nrw.de:1801/webclient/DeliveryManager?pid=2147615&custom_att_2=simple_viewer.
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Cheng, Po-Ying, and 鄭博營. "Web-based visualization system for individual gene variants and their associated diseases." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/p762w9.
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碩士國立陽明大學
生物醫學資訊研究所
106
Precision medicine is an emerging approach for disease treatment and prevention that takes into account individual variability in genes, environment, and lifestyle for each person. The development of precision medicine relies on the improvement of high-throughput techniques and the astonishingly rapid accumulation of genomic data derived from large-scale research projects for investigation of the association between diseases and genes. Here, we have developed a disease risk assessment system based on personal genetic variation data to help better diagnosis and earlier intervention. We collected the NHGRI-EBI Catalog of published genome-wide association studies and the human gene variation and genotype data from 1000 Genome Project as references, and applied a polygenic risk score to predict the risks of an individual suffering from known diseases. Then we used the normal tissue of cancer patients in The Cancer Genome Atlas to evaluate the predictive power of our system. Our developed system provides a good performance for risk estimation and a user-friendly query and visualization interface for users to assess and browse the potential diseases associated with individual gene variants.
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CHEN, YEN-CHEN, and 陳彥臣. "Establishment of a web-based system for gene identifier navigation among databases and Microarray platform annotation：DIPLEX (Database Interrogation Platform for Gene Expression)." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/43715086964667220774.
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碩士臺北醫學大學
醫學資訊研究所
93
Microarray and other gene expression technologies often result in hundreds and thousands of gene raw data; thus, correct and comprehensive gene annotations certainly will help the biomedical researchers interpret more complex work beyond gene lists. Since each gene has embedded valuable information among separate databases where the researchers often find difficult to access and not to mention to obtain the data in a convenient way. The big challenge for this project is the process to put together various identifiers from all databases and further to define the corresponding relationship between each identifier in order to produce correct annotations. As a result, we have developed a service tool DIPLEX (Database Interrogation Platform for Gene Expression) that offers the automatic annotation, the basic gene expression levels in normal tissues and carcinomas using public accessible microarray data, and the relevant biochemical pathways, in an aim to help the biomedical experts to make sense of each gene and the relationships among a gene list obtained from their research. The MatchMiner developed by NCI is one of the similar researches, and we use the most update data and different algorithm from MatchMiner, with NCBI Entrez GeneID as the main identifier to set up its relationship with all other databases. Gene identifier submitted by user will first be transferred into Entrez GeneID and all kinds of gene-related information can then be retrieved according to the user’s need simply by clicking the functional keys. Likewise, user can also review the valuable gene expression level data in microarrays and allocate the position of each gene played in the pathways from KEGG and Biocarta. DIPLEX is located at http://bio.tmu.edu.tw/diplex/ .
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Murray, Gerald Laurence. "The role of wzz genes in Salmonella typhimurium virulence." 2005. http://hdl.handle.net/2440/58482.
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Title page, abstract and table of contents only. The complete thesis in print form is available from the University of Adelaide Library.Salmonella is a genus of Gram-negative bacteria responsible for food-borne enteritis and systemic fever. Salmonellosis continues to be a serious health burden worldwide. Lipopolysaccharide (LPS) is the dominant lipid component of the outer membrane of Salmonella. LPS is composed of lipid A, an oligosaccharide core, and a polymer of O units known as O antigen. Wzz proteins control the length of O antigen by an unknown mechanism. While O antigen is essential for S. typhimurium virulence, the significance of length regulation by Wzz is not known. This study investigates the pathogenic relevance of the wzz genes in S. typhimurium. In addition to the previously recognised wzz gene (WZZ[subscript]ST), a second gene with this function (WZZ[subscript]fepE) was identified in the S. typhimurium genome. Whereas WZZ[subscript]ST specifies the production of long LPS chains with a modal length of 16-35 O antigen repeat units, WZZ[subscript]fepE conferred very long chains containing> 100 O antigen repeat units. Strains carrying mutations in one or both wzz genes were constructed to investigate the role of wzz genes in virulence. It was found that wzz-controlled regulation of O antigen length was essential for resistance to the bactericidal activity of serum complement, while studies in the mouse model of infection found that wzz genes are essential for full virulence. The wzz double mutant was complemented with heterologous wzz genes from a variety of bacterial sources. Despite variable sequence similarity of the encoded Wzz proteins each was functional in the S. typhimurium host, generating a panel of isogenic O antigen length variants. This panel of variants was used to define a minimum length requirement for complement resistance and identified relationships between O antigen length and complement consumption. Finally, the regulation of O antigen chain length was investigated. It was found that growth either in iron limiting conditions or in serum caused an increased production of LPS with very long O antigen chains (conferred by WZZ[subscript]fepE), resulting in increased complement resistance. The constitutive activation mutation of the phoPQ regulator (Phop) results in an altered O antigen distribution phenotype consistent with down-regulation of wzz genes. However PhoPQ had no effect on production of Wzz[subscript]sT as determined by immunoblotting with an antiWZZ[subscript]ST antiserum.
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Thesis (Ph.D.) -- University of Adelaide, School of Molecular and Biomedical Science, 2005