Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Exploring the use of prediction and summarization to increase students' listening and reading comprehension /

This study examined the effect of expHcitly instructing students to use a repertoire of reading comprehension strategies. Specifically, this study examined whether providing students with a "predictive story-frame" which combined the use of prediction and summarization strategies improved their reading comprehension relative to providing students with generic instruction on prediction and summarization. Results were examined in terms of instructional condition and reading ability. Students from 2 grade 4 classes participated in this study. The reading component of the Canadian Achievement Tests, Second Edition (CAT/2) was used to identify students as either "average or above average" or "below average" readers. Students received either strategic predication and summarization instruction (story-frame) or generic prediction and summarization instruction (notepad). Students were provided with new but comparable stories for each session. For both groups, the researcher modelled the strategic tools and provided guided practice, independent practice, and independent reading sessions. Comprehension was measured with an immediate and 1-week delayed comprehension test for each of the 4 stories, hi addition, students participated in a 1- week delayed interview, where they were asked to retell the story and to answer questions about the central elements (character, setting, problem, solution, beginning, middle, and ending events) of each story. There were significant differences, with medium to large effect sizes, in comprehension and recall scores as a fimction of both instructional condition and reading ability. Students in the story-frame condition outperformed students in the notepad condition, and average to above average readers performed better than below average readers. Students in the story-frame condition outperformed students in the notepad condition on the comprehension tests and on the oral retellings when teacher modelling and guidance were present. In the cued recall sessions, students in the story-frame instructional condition recalled more correct information and generated fewer errors than students in the notepad condition. Average to above average readers performed better than below average readers across comprehension and retelling measures. The majority of students in both instructional conditions reported that they would use their strategic tool again.

String figures : a study of Cat`s-Cradle in many lands

UANL

Évaluation objective de la douleur chronique secondaire à l’arthrose chez le chat

La prévalence de l’arthrose féline augmente fortement avec l’âge atteignant plus de 80% des chats de plus de 11 ans. L'arthrose induit une douleur chronique s’exprimant par des changements de comportements et une diminution de la mobilité. Il n'existe aucun outil validé pour évaluer la douleur chronique associée à l’arthrose chez le chat. Conséquemment, aucun traitement ciblant cette douleur n’a pu être validé. Notre hypothèse de recherche est que la douleur arthrosique chez le chat induit des handicaps fonctionnels, des changements neurophysiologiques et un état d'hypersensibilité qu'il faut évaluer pour quantifier de manière fiable cette douleur et ses répercussions sur la qualité de vie de l'animal. Nos objectifs étaient 1) de développer des outils adaptés aux chats mesurant les handicaps fonctionnels grâce à des outils cinématiques, cinétiques et de suivi de l'activité motrice ; 2) de caractériser les changements fonctionnels et neurophysiologiques secondaires à la douleur arthrosique et de tester avec ces outils un traitement analgésique à base d'anti-inflammatoire non stéroïdien ; 3) de développer une technique adaptée aux chats pouvant caractériser la présence du phénomène de sensibilisation centrale à l'aide d'une évaluation de la sommation temporelle mécanique ; 4) de tester la possibilité de mesurer le métabolisme glucidique cérébral par tomographie d’émission par positrons comme marqueur des changements supraspinaux secondaires à la chronicisation de la douleur. Grâce au développement d’outils de mesure de douleur chronique objectifs, sensibles et répétables nous avons caractérisé la douleur chez les chats arthrosiques. Ils présentent des signes de boiterie quantifiée par une diminution de l’amplitude de l’articulation ou par une diminution de la force verticale d’appui au sol et une diminution de l’activité motrice quotidienne. Ces deux derniers outils ont permis de démontrer qu’un anti-inflammatoire non stéroïdien (le méloxicam) administré pendant quatre semaines réduit la douleur arthrosique. De plus, grâce au développement de tests sensoriels quantitatifs et à l'utilisation d'imagerie cérébrale fonctionnelle, nous avons démontré pour la première fois que la douleur arthrosique conduisait à des modifications du système nerveux central chez le chat. Particulièrement, les chats arthrosiques développent le phénomène de sensibilisation centrale mis en évidence par un seuil de retrait aux filament de von Frey diminué (mesure réflexe) mais aussi par une facilitation de la sommation temporelle mécanique (mesure tenant compte de la composante cognitive et émotionnelle de la douleur). L'augmentation du métabolisme cérébral dans le cortex somatosensoriel secondaire, le thalamus et la substance grise périaqueducale, souligne aussi l'importance des changements liés à la chronicisation de la douleur. Un traitement analgésique adapté à l’arthrose permettra d’améliorer la qualité de vie des chats atteints, offrira une option thérapeutique valide aux praticiens vétérinaires, et profitera aux propriétaires qui retrouveront un chat actif et sociable. La découverte de l'implication du phénomène de sensibilisation central combiné à l'investigation des changements cérébraux secondaires à la douleur chronique associée à l'arthrose par imagerie fonctionnelle ouvre de nouvelles avenues de recherche chez le chat (développement et/ou validation de traitements adaptés à l'état d'hypersensibilité) et les humains (potentiel modèle naturel de douleur chronique associée à l'arthrose).

Human Rights as tools for political progress

La pratique des droits de l'homme est souvent décrite comme une entreprise qui vise à établir des standards minimaux pour guider l'action des États et des individus. Dans cet article, je tente de remettre en question la position minimaliste défendue par deux auteurs, James Nickel et James Griffin, en défendant une thèse selon laquelle la philosophie et la morale ne devraient pas être limitées par la pratique et les circonstances du monde. Sans apporter une réponse précise à la question de la faisabilité des droits de l'homme tels qu'on les connaît, je soutiens que le minimalisme défendu par Griffin et Nickel n'est pas nécessaire, ni souhaitable, dans la lutte pour la défense des droits de l'homme, lutte dans laquelle la philosophie a un rôle de premier ordre à jouer.

Physiology of the blood of cat fishes

The vast areas of derelict swamps covered by macrophyton and swarmed by insects scattered in different parts of India are at present either under total negligence or utilized as waste disposal dumps. Eventhough Indian subcontinent is ranked among the first ten fish producing countries in the world, the fish production is not at par with the increasing need of protein in the average Indian diet. So the water areas which become unusable for conventional human activities like the swamps could be used for fish culture which would increase the availability of protein in the form of fish flesh, thus providing new opportunities to the fishermen. But the conversion of swamps for fish culture would entail considerable expenditure. Hence the significance of a group of fresh water fishes which have made their favourable abode the muddy swamps of tropics depending partly on accessory _respiration to survive in the inimical environment. The homeostasis achieved in such a hostile, hypoxic medium make them excellent choices for culture in the derelict freshwater bodies of India. These air breathing fishes form an economically important group which are highly esteemed as food fishes in many parts of South Asia and Africa. Though their natural habitat seems to be the marshes, they have also conquered other freshwater bodies like ponds, tanks, rivers and flooded paddy fields. They can also tolerate slightly brackish waters. They are known for their nutritive, invigorating and therapeutic qualities and are recommended by physicians as diet during convalescence (Jhingran, 1982)

ICT Tools for Teaching & Learning

Page 1. ICT Tools for Teaching & Learning G Santhosh Kumar Cochin University Page 2. Agenda • What is ICT? • Why integrate ICT in Education? • What are the Challenges? • What are the good resources? Page 3. Questions # “Despite the increasing use of ICT, the need for teachers is as great as ever” # “Placing ICT in schools will automatically improve the quality of education that children receive” #”The Internet is unsafe for children to use because there is so much dangerous material available on it” Page 4. What is ICT? • ICT is short for ..

Exploration tools in formal concept analysis

The development of conceptual knowledge systems specifically requests knowledge acquisition tools within the framework of formal concept analysis. In this paper, the existing tools are presented, and furhter developments are discussed.

Cat??logo ayudas t??cnicas

Cat??logo que recoge las ayudas t??cnicas que facilita la Consejer??a de Educaci??n, ciencia e Investigaci??n de la Regi??n de Murcia, destinadas a los alumnos con necesidades educativas especiales. Se especifican las caracter??sticas t??cnicas, medidas, destinatarios y objetivos de uso de las mismas. El objetivo del presente Cat??logo es que todos los profesionales que trabajan con alumnos con necesidades educativas especiales (acnees) conozcan la existencia de estas ayudas t??cnicas y el tipo de alumno a quien van dirigidas, con el fin de que una vez detectada la necesidad puedan solicitarlas f??cilmente. As?? mismo se especifican las caracter??sticas t??cnicas y medidas de cada ayuda, estableciendo un sistema de c??digos seg??n medidas y accesorios, con el fin de poder concretar al m??ximo el tipo de material necesario y agilizar el procedimiento de dotaci??n. Se recogen en anexos el procedimiento de solicitud y los formularios

The Architect's Collaborator: Toward Intelligent Tools for Conceptual Design

In early stages of architectural design, as in other design domains, the language used is often very abstract. In architectural design, for example, architects and their clients use experiential terms such as "private" or "open" to describe spaces. If we are to build programs that can help designers during this early-stage design, we must give those programs the capability to deal with concepts on the level of such abstractions. The work reported in this thesis sought to do that, focusing on two key questions: How are abstract terms such as "private" and "open" translated into physical form? How might one build a tool to assist designers with this process? The Architect's Collaborator (TAC) was built to explore these issues. It is a design assistant that supports iterative design refinement, and that represents and reasons about how experiential qualities are manifested in physical form. Given a starting design and a set of design goals, TAC explores the space of possible designs in search of solutions that satisfy the goals. It employs a strategy we've called dependency-directed redesign: it evaluates a design with respect to a set of goals, then uses an explanation of the evaluation to guide proposal and refinement of repair suggestions; it then carries out the repair suggestions to create new designs. A series of experiments was run to study TAC's behavior. Issues of control structure, goal set size, goal order, and modification operator capabilities were explored. In addition, TAC's use as a design assistant was studied in an experiment using a house in the process of being redesigned. TAC's use as an analysis tool was studied in an experiment using Frank Lloyd Wright's Prairie houses.

Interactions between grain size and composition of sediments: two examples

Two contrasting case studies of sediment and detrital mineral composition are investigated in order to outline interactions between chemical composition and grain size. Modern glacial sediments exhibit a strong dependence of the two parameters due to the preferential enrichment of mafic minerals, especially biotite, in the fine-grained fractions. On the other hand, the composition of detrital heavy minerals (here: rutile) appears to be not systematically related to grain-size, but is strongly controlled by location, i.e. the petrology of the source rocks of detrital grains. This supports the use of rutile as a well-suited tracer mineral for provenance studies. The results further suggest that (i) interpretations derived from whole-rock sediment geochemistry should be flanked by grain-size observations, and (ii) a more sound statistical evaluation of these interactions require the development of new tailor-made statistical tools to deal with such so-called two-way compositions

Bayesian tools for zero counts in compositional data

The log-ratio methodology makes available powerful tools for analyzing compositional data. Nevertheless, the use of this methodology is only possible for those data sets without null values. Consequently, in those data sets where the zeros are present, a previous treatment becomes necessary. Last advances in the treatment of compositional zeros have been centered especially in the zeros of structural nature and in the rounded zeros. These tools do not contemplate the particular case of count compositional data sets with null values. In this work we deal with \count zeros" and we introduce a treatment based on a mixed Bayesian-multiplicative estimation. We use the Dirichlet probability distribution as a prior and we estimate the posterior probabilities. Then we apply a multiplicative modi¯cation for the non-zero values. We present a case study where this new methodology is applied. Key words: count data, multiplicative replacement, composition, log-ratio analysis

Cat??logo de ??rboles y arbustos

Los profesores del Departamento de Biolog??a y Geolog??a de este IES elaboraron esta gu??a como ayuda a aquellos que se acercan por primera vez al conocimiento de los ??rboles y arbustos de su entorno m??s cercano, aquel que se circunscribe a los jardines del Instituto y al ??rea recreativa pr??xima, ambos situados en Vegadeo (Asturias). La mayor parte de las especies descritas son plantas cultivadas procedentes de jardines y viveros cuya utilizaci??n ornamental se encuentra muy extendida por lo que a pesar no formar parte de la flora aut??ctona de Asturias su presencia en calles y parques urbanos es tan com??n que no resultan extra??as al observador. Este material forma parte de un programa del Departamento, en el que adem??s de visitas, salidas, estudios fuera del recinto y tareas de mantenimiento del jard??n del IES se editaron varios trabajos relacionados con el mismo. En ??l se encuentran una introducci??n explicativa a la gu??a; el cat??logo de ??rboles y arbustos (nombre popular, nombre cient??fico, clasificaci??n, descripci??n, h??bitat, origen y distribuci??n, usos, ilustraciones); un glosario, un ??ndice de especies, clave dicot??mica para principiantes y un plano del ??rea catalogado con la ubicaci??n de cada especie.

Enhancing learning beyond the classroom: blogging and other social networking tools

Blogging has become one of the key ingredients of the so-called socials networks. This phenomenon has indeed invaded the world of education. Connections between people, comments on each other posts, and assessment of innovation are usually interesting characteristics of blogs related to students and scholars. Blogs have become a kind of new form of authority, bringing about (divergent) discussions which lead to creation of knowledge. The use of blogs as an innovative, educational tool is not at all new. However, their use in universities is not very widespread yet. Blogging for personal affairs is rather commonplace, but blogging for professional affairs – teaching, research and service, is scarce, despite the availability of ready-to-use, free tools. Unfortunately, Information Society has not reached yet enough some universities: not only are (student) blogs scarcely used as an educational tool, but it is quite rare to find a blog written by University professors. The Institute of Computational Chemistry of the University of Girona and the Department of Chemistry of the Universitat Autònoma de Barcelona has joined forces to create “InnoCiència”, a new Group on Digital Science Communitation. This group, formed by ca. ten researchers, has promoted the use of blogs, twitters. wikis and other tools of Web 2.0 in activities in Catalonia concerning the dissemination of Science, like Science Week, Open Day or Researchers’ Night. Likewise, its members promote use of social networking tools in chemistry- and communication-related courses. This communication explains the outcome of social-network experiences with teaching undergraduate students and organizing research communication events. We provide live, hands-on examples and interactive ground to show how blogs and twitters can be used to enhance the yield of teaching and research. Impact of blogging and other social networking tools on the outcome of the learning process is very depending on the target audience and the environmental conditions. A few examples are provided and some proposals to use these techniques efficiently to help students are hinted