京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第17927号 / 情博第509号 / 新制||情||90(附属図書館) / 30747 / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 吉川 正俊, 教授 石田 亨, 教授 田中 克己 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DGAM

No description available.

Home automation systems is something that has risen in popularity over the last decade. More and more real estate is equipped with various IoT systems in order to keep effective- ness and efficiency on a high level. With these systems comes highly advanced technical systems connected to various devices that report data collected from their environments. The data that is collected is then reformatted into tag lists in the software with a very specific name that follows a certain naming convention. The problem is that there is no transparency amongst companies when it comes to the standards they follow when it comes to naming their tags. This is investigated in this thesis by conducting a literature review and creating a design to interpret existing tag lists to make it easier to understand the structure. The thesis is made with the intent of answering the question to what the current state of research when it comes to standardization in tag lists. It is also exploring what a potential effective design for translating tags into a manageable format would look like. At the time of making this thesis there were not very extensive research when it comes to standards and naming convention in IoT tag lists, therefore a lot of the compiled research in this thesis refers to related ways of structuring names in other topics. The design was developed with the help of an scale-up company called Sensative that works with IoT tags on a daily basis. The end result of the design is a translation service that is able to sugges- tion relatable tags to translate when a user is manually renaming tags that are imported into the service. The design is built with the potential to later add artificial intelligence to suggest related tags for translation.

Festakt zum Tag der Deutschen Einheit im Plenarsaal des Sächsischen Landtages

Master of Science / Department of Computing and Information Sciences / Doina Caragea / The vast amount of data present on the internet calls for ways to label and organize this data according to specific categories, in order to facilitate search and browsing activities. This can be easily accomplished by making use of folksonomies and user provided tags. However, it can be difficult for users to provide meaningful tags. Tag recommendation systems can guide the users towards informative tags for online resources such as websites, pictures, etc. The aim of this thesis is to build a system for recommending tags to URLs available through a bookmark sharing service, called BibSonomy. We assume that the URLs for which we recommend tags do not have any prior tags assigned to them. Two approaches are proposed to address the tagging problem, both of them based on Latent Dirichlet Allocation (LDA) Blei et al. [2003]. LDA is a generative and probabilistic topic model which aims to infer the hidden topical structure in a collection of documents. According to LDA, documents can be seen as mixtures of topics, while topics can be seen as mixtures of words (in our case, tags). The first approach that we propose, called topic words based approach, recommends the top words in the top topics representing a resource as tags for that particular resource. The second approach, called topic distance based approach, uses the tags of the most similar training resources (identified using the KL-divergence Kullback and Liebler [1951]) to recommend tags for a test untagged resource. The dataset used in this work was made available through the ECML/PKDD Discovery Challenge 2009. We construct the documents that are provided as input to LDA in two ways, thus producing two different datasets. In the first dataset, we use only the description and the tags (when available) corresponding to a URL. In the second dataset, we crawl the URL content and use it to construct the document. Experimental results show that the LDA approach is not very effective at recommending tags for new untagged resources. However, using the resource content gives better results than using the description only. Furthermore, the topic distance based approach is better than the topic words based approach, when only the descriptions are used to construct documents, while the topic words based approach works better when the contents are used to construct documents.

Doctor of Philosophy / Department of Entomology / Larry L. Buschman / Kun Yan Zhu / Genomic information for lepidopteran insects, particularly agricultural pest species, is very limited but urgently needed due to their economic importance and biodiversity. The huge economic losses ($ 1-2 billons / year) caused by the European corn borer (Ostrinia nubilalis, Hübner, ECB) makes this insect species one of the major pests of corn in the United States and western world. Management of ECB by conventional methods is limited but has had a great success by transgenic Bt (Bacillus thuringiensis) corn, which targets insect gut. However, the widespread use of Bt corn may lead to the development of Bt resistance in ECB. Knowledge of genes expressed in the insect gut is considered crucial for understanding basic physiology of food digestion, their interactions with Bt toxins and pathogens, and for discovering new targets for pest management. A large database of 15,000 expressed sequence tags (ESTs) was established from the ECB larval gut. To our knowledge, this database represents the largest gut-specific EST database from a lepidopteran pest. Analysis of 10 aminopeptidase-like genes between Cry1Ab–resistant and –susceptible ECB larvae revealed that aminopeptidase P-like (OnAPP) gene is a strong candidate for its role in Bt toxicity and resistance. The RNA interference mediated reduction in the transcript level of OnAPP gene in ECB larvae resulted in their reduced susceptibily to Cry1Ab. Analysis of the chitinase-like gene (OnCht) revealed its essential role in regulating chitin content of peritrophic membrane (PM). Our results suggest that OnCht may influence food digestion, nutrient absorption or movement of digestive enzymes through the PM and can be an important target for insect management. We also identified and characterized six genes involved in the innate immune defense response in ECB and showed that the expression of these genes were induced when challenged with bacteria. In addition to these results, this research generated significant genomic information for the development of microarray from the larval gut of ECB. The establishment of the feeding-based RNA interference technique could potentially help in delivering dsRNA orally to ECB for high throughput screening of effective genes to be targeted for insect pest management.

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.

La première partie de la thèse traite de la recherche de biomarqueurs du cancer. Lors de la transcription, il apparaît que certains nucléotides peuvent être remplacés par un autre nucléotide. On s'intéresse alors à la comparaison des probabilités de survenue de ces infidélités de transcription dans des ARNm cancéreux et dans des ARNm sains. Pour cela, une procédure de tests multiples menée sur les positions des séquences de référence de 17 gènes est réalisée via les EST (Expressed Sequence Tag). On constate alors que ces erreurs de transcription sont majoritairement plus fréquentes dans les tissus cancéreux que dans les tissus sains. Ce phénomène conduirait ainsi à la production de protéines dites aberrantes, dont la mesure permettrait par la suite de détecter les patients atteints de formes précoces de cancer. La deuxième partie de la thèse s'attache à l'étude de l'allergie à l'arachide. Afin de diagnostiquer l'allergie à l'arachide et de mesurer la sévérité des symptômes, un TPO (Test de Provocation Orale) est réalisé en clinique. Le protocole consiste à faire ingérer des doses croissantes d'arachide au patient jusqu'à l'apparition de symptômes objectifs. Le TPO pouvant se révéler dangereux pour le patient, des analyses discriminantes de l'allergie à l'arachide, du score du TPO, du score du premier accident et de la dose réactogène sont menées à partir d'un échantillon de 243 patients, recrutés dans deux centres différents, et sur lesquels sont mesurés 6 dosages immunologiques et 30 tests cutanés. Les facteurs issus d'une Analyse Factorielle Multiple sont également utilisés comme prédicteurs. De plus, un algorithme regroupant simultanément en classes des intervalles comprenant les doses réactogènes et sélectionnant des variables explicatives est proposé, afin de mettre ensuite en compétition des règles de classement. La principale conclusion de cette étude est que les mesures de certains anticorps peuvent apporter de l'information sur l'allergie à l'arachide et sa sévérité, en particulier ceux dirigés contre rAra-h1, rAra-h2 et rAra-h3. / The first part of this doctoral dissertation deals with the research of cancer biomarkers. During transcription it was observed that some nucleotides are replaced mistakenly by others. We sought to compare the probabilities of these transcription infidelities in mRNA originating from normal and cancerous tissues. To do this, a multiple testing procedure was performed on the positions of 17 genes by considering their ESTs (Expressed Sequence Tag). The conclusion was reached that the proportions of these transcription errors are mainly increased in cancer tissues as compared to normal ones. This phenomenon would lead to the translation of aberrant proteins, whose detection could help in identifying patients with cancer. The main goals of the second part are the diagnosis of peanut allergy and the prediction of its severity. Diagnosing peanut allergy and evaluating the intensity of the symptoms are currently accomplished with a double blind placebo controlled food challenge (DBPCFC). Patients are given increasing peanut doses until the first clinical reaction appears. Since DBPCFC can result in life-threatening responses, we propose an alternate procedure with the long term goal of replacing invasive allergy tests. Discriminant analyses of peanut allergy, DBPCFC score, the eliciting dose and the first accidental exposure score were performed in 243 allergic patients using 6 immunoassays and 30 skin prick tests. A Multiple Factorial Analysis was performed to use new factors as predictors. We also developed an algorithm for simultaneously clustering eliciting dose values and selecting discriminant variables. Our main conclusion is that antibody measurements provide information on the allergy and its severity, especially those directed against the peanut allergens rAra-h1, rAra-h2 and rAra-h3.

Mes travaux de thèse concernent la fabrication de micro et de nanostructures en silicium dans le but de développer des surfaces non-mouillantes et d’outils analytiques pour des applications en biochimie et en microfluidique. Pour ce faire, nous avons utilisé d’une part la gravure chimique humide qu’est la « metal-assisted electroless etching » (approche descendante) et d’autre part la croissance de nanofils par « Chemical Vapor Deposition » via le mécanisme « Vapor-Liquid-Solid » (approche ascendante). Des surfaces structurées possédant des morphologies différentes ont été obtenues. Grâce à ces méthodes de fabrication nous avons préparé des structurations simple et double, à savoir des structurations nanométriques et micrométriques et des doubles structurations micro-nanométriques. Dans une première partie, les surfaces structurées ont permis de développer des surfaces superomniphobes, capables de repousser des liquides présentant des tensions de surface très variables. Les surfaces présentant une double structuration donnant les meilleures propriétés non-mouillantes. Dans une deuxième partie, ces surfaces nanostructurées ont été utilisées comme matrices inorganiques pour la désorption/ionisation assistée par laser permettant l’analyse en spectrométrie de masse de petites molécules sans l’utilisation de matrice organique. Nous avons étudié l’influence de la morphologie, du type de dopage et de la terminaison chimique sur l’analyse en spectrométrie de masse d’un mélange de peptide standard. Finalement, nous avons réalisé l’enrichissement d’un peptide et son analyse en spectrométrie de masse à partir d’un mélange donné, grâce à l’introduction d’un ligand spécifique. / This work concerns the fabrication of micro/nanostructured silicon substrates and their application as non-wetting surfaces, and analytical tools for biomolecules’ analysis and in microfluidic devices. Two different techniques were investigated for the formation of nanostructured silicon substrates: chemical wet etching via metal-assisted electroless etching (Top-down approach) and nanowire growth by « Chemical Vapor Deposition » via Vapor-Liquid-Solid mechanism (Bottom-up approach). Different structured surface morphologies were then obtained. These were either simple structured such as: Micro or Nanoscale, or double structured such as: Micro-Nano or Nano-Nanoscale. The first part of the thesis deals with the preparation of superominiphobic surfaces capable of repelling almost any liquid. The surfaces consisting of double structured substrates gave the best non-wetting properties. Secondly, nanostructured silicon substrates were used as inorganic matrices for the detection of small molecules without using an organic matrix in laser desorption/ionization mass spectrometry. Herein, we investigated the influence of surface morphology, doping type and chemical termination on mass spectrometry analysis of a standard peptide mixture. Finally, functionalized silicon nanowires surfaces with a specific ligand were used to perform peptide enrichment and its subsequent analysis by mass spectrometry from a mixture solution.

Visualizing proteins in living cells without perturbing biological function remains a key challenge in chemical biology. A chemical approach to this problem is the synthesis of small molecule fluorophores that react specifically with a protein of interest (POI). We have developed a site-specific labelling method based on a Fluorogenic Addition Reaction (FlARe). The FlARe probe’s fluorescence is quenched until it undergoes thiol addition with a small, genetically encoded dicysteine peptide tag fused to the POI. Recent blue coumarin probes were shown to be highly selective for target proteins over other cellular thiols; however, fluorogens that can label in the red and green channels of the fluorescence microscope are more desirable for cellular imaging, as red light is lower in energy and therefore less photo-toxic. In the work presented herein, we use DFT calculations to guide the design of red-shifted, PeT-quenched BODIPY based dimaleimide fluorogens. Driven by the preliminary results of a FlARe probe (YC29) that emitted in the red channel, we attempted to prepare the hit compound through a new synthetic approach to further evaluate kinetics and in cellulo labelling. Given the time available, this compound was unable to be synthesized through an SNAr or Pd-catalyzed approach. Alternatives probes lacking the red-shifting substituent were synthesized and evaluated in vitro and in cellulo. The fluorescent enhancement and reaction kinetics of these probes were evaluated in detail, in order to determine the suitability of their application to cellular labelling. A green-BODIPY fluorogen was synthesized that exhibits suitable kinetics for labelling and a dramatic fluorescent enhancement of ~800-fold upon tagging. This probe was successfully applied to the specific, fluorescent labelling of a nuclear histone protein in cellulo.