A coccidiose aviária é uma doença entérica causada por protozoários parasitas do gênero Eimeria. Visando uma maior compreensão dos mecanismos moleculares envolvidos na regulação do ciclo de vida dos parasitas, foram geradas 15.000 seqüências expressas (ORESTES) para cada uma das três espécies mais importantes: E. tenella, E. maxima e E. acervulina. O presente trabalho consistiu no desenvolvimento de componentes de anotação automática de seqüências para o sistema EGene, plataforma previamente desenvolvida pelo nosso grupo (Durham et al. Bioinformatics 21: 2812-2813, 2005) para a construção de processamentos encadeados (pipelines). Estes componentes foram utilizados para a construção de pipelines de anotação automática de seqüências-consenso obtidas a partir da montagem dos ORESTES de Eimeria spp. A anotação consistiu na identificação dos genes e atribuição da função dos respectivos produtos protéicos, baseando-se em um conjunto de evidências. As seqüências também foram classificadas e quantificadas utilizando-se um vocabulário controlado de termos de ontologia gênica (GO). / Avian coccidiosis is an enteric disease caused by protozoan parasites of the genus Eimeria. Aiming at obtaining a better understanding of the molecular mechanisms that regulate the life cycle of the parasites, our group generated 15,000 expressed sequences (ORESTES) for each one of the three most important species: E. tenella, E. maxima and E. acervulina. In the present work, we report the development of a set of components for the automated sequence annotation through EGene, a platform for pipeline construction previously described by our group (Durham et al. Bioinformatics 21: 2812-2813, 2005). These components were used to construct pipelines for the automated annotation of assembled sequences of ORESTES of Eimeria spp. The annotation process consisted in the identification of genes and the corresponding protein function based on a set of evidences. The sequences were also mapped and quantified using a controlled vocabulary of gene ontology (GO) terms.

Made available in DSpace on 2014-12-17T14:55:45Z (GMT). No. of bitstreams: 1 AugustoCPSM_DISSERT.pdf: 2233012 bytes, checksum: 89758cdc093b113084eb987f29899b36 (MD5) Previous issue date: 2010-12-21 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / In recent years, the radio frequency identification technology (RFID) has gained great interest both industrial communities as scientific communities. Its ability to locate and monitor objects, animals and persons with active or passive tags allows easy development, with good cost-benefice and still presents undeniable benefits in applications ranging from logistics to healthcare, robotics, security, among others. Within this aspect what else comes excelling are RFID tags and the antennas used in RFID readers. Most tags have antennas omnidirectional and are usually manufactured as dipoles modified printed. The primary purpose of a project of antenna for tag is to achieve the required input impedance to perform a good marriage impedance with the load impedance of the chip. Already the objective principal in project of antennas for readers is to achieve reduced sizes and structures with good data transmission capacity. This work brings the numerical characterization of antennas for RFID applications, being these divided into tags RFID and antennas for RFID readers. Three tags RFID and two antennas for RFID readers, found in literature, are analyzed. The analysis of these structures is made using the Method of Waves - WCIP. Initial results found in the literature are compared with those obtained through simulations in WCIP with objective to show that the Method of Waves is able to analyze such structures. To illustrate the results obtained in simulations is presented the behavior of electric and magnetic fields. It also performed a literature review on the characteristics and principles of RFID technology. Suggestions for continuity to this work are presented / Nos ?ltimos anos, a tecnologia de Identifica??o por Radiofrequ?ncia (RFID) tem ganhado grande interesse tanto de comunidades industriais como de comunidades cient?ficas. A sua capacidade de localizar e monitorar objetos, animais e pessoas com etiquetas passivas ou ativas permite o desenvolvimento f?cil, com uma boa rela??o custo-benef?cio e ainda apresenta ineg?veis benef?cios em aplica??es que variam de log?stica a cuidados de sa?de, rob?tica, seguran?a, entre outras. Dentro desse aspecto o que mais vem se destacando s?o as etiquetas RFID e as antenas usadas em leitores RFID. A maioria das etiquetas possui antenas omnidirecionais e normalmente s?o fabricadas como dipolos modificados impressos. O objetivo principal de um projeto de antena para etiqueta ? conseguir a imped?ncia de entrada necess?ria para realizar um bom casamento de imped?ncia com a imped?ncia de carga do chip. J? o objetivo principal no projeto de antenas para leitores ? conseguir estruturas de tamanhos reduzidos e com boa capacidade de transmiss?o de dados. Este trabalho traz a caracteriza??o num?rica de antenas para aplica??es RFID, sendo estas divididas em etiquetas RFID e antenas para leitores. S?o analisadas tr?s etiquetas RFID e duas antenas para leitores RFID encontradas na literatura. A an?lise dessas estruturas ? feita utilizando o M?todo das Ondas - WCIP. S?o comparados os resultados iniciais encontrados na literatura com os obtidos atrav?s de simula??es no WCIP com o objetivo de mostrar que o M?todo das Ondas ? capaz de analisar tais estruturas. Para ilustrar os resultados obtidos nas simula??es, ? apresentado o comportamento dos campos el?trico e magn?tico. ? realizada tamb?m uma revis?o bibliogr?fica a respeito das caracter?sticas e princ?pios da Tecnologia RFID. S?o apresentadas, ainda, sugest?es de continuidade para este trabalho

This study analyses the translation of pragmatic markers from English into Swedish. The source text that was translated and used as a basis for the study is an article called “Black Books”, which was published in the British music magazine Prog in January 2013. The study is limited to question tags, general extenders and single-word pragmatic markers. It aims to investigate how these types of pragmatic markers can be translated in a dynamic and natural way, as well as how a careful analysis can facilitate the search for appropriate translation equivalents. Previous research and theories were used to determine the functions of the pragmatic markers in the source text, and the translation choices made on the basis of these findings were supported by corpus searches in the English-Swedish Parallel Corpus and Korp. The study revealed that because of the different ways in which pragmatic functions are expressed in English and Swedish, almost none of the pragmatic markers in the source text could be translated directly into Swedish. Formally equivalent solutions such as tja as a translation of well were generally considered too unnatural. While the study is too small to provide any general guidelines, it shows how a careful analysis may help the translator find more dynamically equivalent and natural solutions in the form of, for instance, other Swedish pragmatic markers, modal particles, adverbs and conjunctions.

This project focuses on the use of sponge genetic transcripts in the form of expressed sequence tags (ESTs) readily available in Genbank to search for novel genes using bioinformatics analysis tools. Marine sponge species are known to house a diversity of marine microbes and are known as the ‘living fossils’ of the animal kingdom because of the large number of ancient genes they house. Genomic mining can be a useful tool in discovering these orthologous genes. This study utilized the techniques of genomic mining of 11 previously described sponge species transcripts. The results of this study provide a better understanding of the genomic structure of the organisms studied by creating a more detailed genetic map and examining a specific environmental snapshot of the genes in each sponge. Novel methods for dissecting beneficial information from large scale data sets available in genomic libraries utilizing bioinformatics search tool MGRAST were examined. The results of this study indicate that sponges house numerous genes that are likely to be evolutionary predecessors of genes in higher eukaryotes. Support was also given to the notion that microbial communities play a role in metabolic pathways of sponges.

In response to the drastic decline of the European eel (Anguilla anguilla (L.)) fisheries have been reduced and elvers are stocked in areas where natural abundances are low. Are these measures adequate? To answer different aspects of this question, we have analysed more than a century of eel tagging, using both traditional and more novel capture – recapture analyses. Based on these long-term data, we have evaluated the impact of the Swedish eel coastal fisheries using Survival analysis. Our analysis indicates that the fishing mortality just prior the 2009 fishing restrictions were in the order of 10%. More recent tagging programs have focused on issues related to the fate of stocked fish. If and how they migrate out of the Baltic Sea and further on towards the Atlantic Ocean. Both earlier and our new studies reveal that all eels recaptured on the Swedish East Coast, no matter of their origin, migrate at a reasonable speed and direction towards the outlets of the Baltic Sea. Even though it is sometimes difficult to determine their origin, our analyses indicate that stocked fish were scarce among the recaptures. In an experiment on the Swedish West Coast, we knew the individuals’ origin (stocked or wild) and they had similar migration patterns. In contrast, silver eel in Lake Mälaren – assumed to have been stocked as elvers or bootlace eels – seemed to have difficulties in finding the outlets. Instead they overwintered and lost weight. However, weight losses are also significant among non-stocked individuals in the Baltic Sea, both if they overwinter and if they appear to be on their way out from the area. It remains an open question whether eels from the Baltic region in general, and whether the overwintered fish in particular, manage to reach the spawning area in the Atlantic Ocean. Based on current knowledge, I advocate invoking the precautionary approach and to concentrate Swedish eel stockings to the West Coast and allow the young fish to spread out on their own. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.</p><p> </p>

A produção de aves no Brasil vem crescendo na ordem de 10% a cada ano, o que se explica pela atualização constante da tecnologia do setor (http://www.abef.com.br). Sendo a carne de frango a fonte de proteína animal mais barata e acessível ao consumidor, há necessidade de se produzir cada vez mais animais com maior acúmulo de massa muscular. Para isso, o entendimento dos mecanismos celulares e moleculares envolvidos na formação da musculatura esquelética é de extrema relevância. Os fatores miogênicos, genes responsáveis pela determinação e diferenciação de células musculares, foram clonados e progressos significativos foram desenvolvidos quanto ao controle da expressão dos mesmos. A utilização da técnica de seqüenciamento de DNA possibilita a identificação e caracterização de novos genes envolvidos na complexa rede de fatores que regulam a formação da musculatura esquelética em aves. Neste estudo, foram construídas duas bibliotecas de cDNA (fase embrionária e pós-eclosão) de músculo peitoral de uma linhagem de corte (TT) e uma biblioteca da fase embrionária de uma linhagem de postura (CC). A análise das seqüências EST (Expressed Sequence Tags) foi utilizada para identificar possíveis novos genes envolvidos no processo de formação da musculatura esquelética. As seqüências EST identificadas possibilitaram a construção de um banco com 6247 ESTs da musculatura peitoral das linhagens de corte e postura nas duas fases de desenvolvimento. Com o intuito de estabelecer uma relação entre o perfil de expressão dos fatores miogênicos: MyoD, MRF4 e miogenina; e dos genes Pax-3 e miostatina e a formação e maturação das fibras musculares, foi utilizada a técnica de PCR em tempo real. Em geral, a expressão dos fatores miogênicos foi maior na linhagem de corte em relação à de postura nas idades estudadas. Este estudo deverá contribuir para as áreas celular e molecular de desenvolvimento, além de fornecer recursos úteis aos programas de melhoramento genético de aves que visam obter animais com maior acúmulo de massa muscular. / Brazilian’s chicken production is increasing annually around 10%, which can be explained by the current technology applied to this sector (http://www.abef.com.br). Being chicken’s meat the cheapest animal protein source for consumers, there is a need to produce even more animals with increased muscular mass. For this purpose, understanding the molecular and cellular mechanisms involved with the skeletal muscle development is of great relevance. The myogenic factors, genes responsible for the determination and differentiation of muscle cells, were cloned and significant progress was made on the control of their expression. The use of DNA sequencing technique allows the identification and characterization of new genes involved in the complex chain of factors signalling systems that regulates the expression of avian skeletal muscles. In this study, two cDNA libraries (embryonic and post-hatching phases) were constructed from the breast muscle of a chicken broiler line (TT) and one library, from the embryonic phase, from a chicken layer line (CC). The EST (Expressed Sequencing Tags) analysis was used to identify probable new genes involved in the skeletal muscle development. The identified ESTs were used to generate a database containing 6247 breast muscle ESTs from two chicken lines in two development phases. Real time PCR was employed with the aim of establishing a relationship among the expression profile of myogenic factors (MyoD, MFR4, and myogenin), Pax-3 and myostatin genes with the formation and maturation of muscle fibers. In general, the expression of myogenic factors was greater in the broiler than in the layer chicken line in the phases under study. These results should contribute to other cellular and molecular development studies besides providing useful resources for chicken breeding programs whose objective is the deposition of skeletal muscle mass.

Organic phosphorescence at room temperature is a strongly growing field of research. Together with fluorescence, it describes the radiative transitions of organic molecules after excitation with light of appropriate wavelength. While fluorescence is a process on the nanosecond timescale, organic phosphorescence is known to show afterglow emission in the lifetime range of microseconds to seconds. These long timescales result from quantum-mechanical restrictions in the transition processes underlying the phosphorescence. Namely, the involved electrons of the molecule have to undergo a spin flip, which is forbidden in zeroth-order approximation due to the necessity of conservation of angular momentum. In consequence, this emission feature of organic materials in general is obstructed at ambient temperature by dominating nonradiative deactivation channels. However, by careful design of the system, efficient phosphorescence at room temperature can be realized. In recent years, the number of publications introducing new organic phosphorescent emitters has continuously increased. However, to that date, the high quantity of described materials is not matched by an adequate amount of proposed applications. In fact, most publications present the synthesis of the substances as well as the morphology of the system, but only briefly address possible subsequent developing steps. In this thesis, as a first step, recent developments in that area are compiled to a broad overview, which includes proposed applications like sensing and optical data storage. Beyond that, a newly detected photophysical effect is introduced and evaluated, which enables the reversible activation of phosphorescence in a thin and transparent film. Since for many emitter materials the presence of adjacent molecular oxygen leads to a complete vanishing of phosphorescence, this emission can locally be tuned by manipulating the respective oxygen concentration. It is shown that a very elegant, non-contact way of achieving that is by using light of different wavelengths only. In detail, radiation in the near UV or blue regime can induce a chemical reaction of the oxygen and its environment, leading to an oxygen depletion at the illuminated regions. By covering the system with suitable barrier layers, no fresh oxygen can refill the system and phosphorescence becomes visible at the respective areas. By that, any luminescent image can be programmed into the transparent layers and be read out on demand. In addition, subsequent illumination with infrared radiation leads to a rise of the overall temperature, which consequently increases the permeability of the oxygen barrier. Therefore, the system is refilled with molecular oxygen and the pattern is erased. In a next step, new images can be written into the device. When not read out by illumination with appropriate light, the system is completely transparent and does not reveal the programmed information. That enables the fabrication of programmable luminescent tags, which allow multiple cycles of writing, reading and erasing, and thus may be used for temporary labeling in logistics or for invisible document security. Prototypes of the mentioned applications are manufactured and tested in this work, revealing the feasibility of their realization. The overall procedure as well as the device structure are part of patent applications. As a further part of the thesis, the characterization of multiple organic emitters and additives reveals that the effect of switchable phosphorescence is not limited to a particular material combination, but is rather a very general behavior. In consequence, device features like emission color, pattern contrast, or wavelength sensitivity are successfully optimized using suitable available organic systems. In order to facilitate a targeted development of new phosphorescent emitters in the future, the decisive demands on the materials to enable programmable tags are defined. Conclusively, more application pathways are depicted, of which one already successfully gained funding by the Federal Ministry of Education and Research of Germany. In this follow-up study, the suitability of the discovered results on sensing of UV radiation will be examined. With two more submitted proposals building up on the presented developments, the results of this thesis open up a broad range of further work both from the scientific and the engineering point of view.:1. Introduction 2. Theory 3. Methods 4. Basic Principles of Programmable Luminescent Tags (PLTs) 5. Characterization of Guest Materials 6. Optimization via Diversification: PLTs with Various Material Systems 7. Conclusions and Outlook / Organische Phosphoreszenz bei Raumtemperatur ist ein aktuell stark wachsendes Forschungsgebiet. Gemeinsam mit der Fluoreszenz beschreibt sie strahlende Übergänge von organischen Molekülen nach der Anregung mit Licht passender Wellenlänge. Während Fluoreszenz ein Prozess auf einer Zeitskala von Nanosekunden ist, zeigt organische Phosphoreszenz typischerweise ein längeres Nachleuchten im Bereich von Mikrosekunden bis Sekunden. Dieses resultiert daraus, dass die Übergangsprozesse, die zur Phosphoreszenz führen, quantenmechanisch nicht erlaubt sind. Die beteiligten Elektronen müssen sich einem Spin-Flip unterziehen, welcher in nullter Näherung aufgrund der Drehimpulserhaltung verboten ist. Infolgedessen wird die Phosphoreszenz organischer Materialien bei Umgebungstemperatur üblicherweise durch dominierende nichtstrahlende Relaxationswege unterdrückt. Durch gezielte Materialentwicklung lässt sich dennoch effiziente Phosphoreszenz realisieren. In den letzten Jahren ist die Zahl der Publikationen, in denen neue organische phosphoreszierende Emitter vorgestellt wurden, kontinuierlich gestiegen. Dieser hohen Auswahl an Materialien steht aktuell jedoch keine ausreichende Anzahl von Vorschlägen potentieller Anwendungen gegenüber. Tatsächlich stellen die meisten Publikationen die Synthese der Substanzen und die Morphologie des Systems vor, gehen aber nur kurz auf mögliche weitere Entwicklungsschritte ein. In dieser Arbeit werden nun zunächst die jüngsten Entwicklungen auf diesem Gebiet zu einem breiten Überblick zusammengestellt, der auch einige der vorgeschlagenen Anwendungen wie Sensorik und optische Datenspeicherung umfasst. Darüber hinaus wird ein neu entdeckter photophysikalischer Effekt vorgestellt und bewertet, der die reversible Aktivierung von Phosphoreszenz in einem dünnen und transparenten Film ermöglicht. Da bei vielen organischen Emittermaterialien die Nähe zu molekularem Sauerstoff zu einem vollständigen Verschwinden der Phosphoreszenz führt, kann diese Emission lokal durch Veränderung der Sauerstoffkonzentration beeinflusst werden. Eine sehr elegante, berührungslose Methode hierfür ist die zielgerichtete Bestrahlung mit Licht verschiedener Wellenlängen. So kann Strahlung im nahen UV- oder im blauen Bereich eine chemische Reaktion des Sauerstoffs mit seiner Umgebung auslösen, die zu einer Abnahme der Sauerstoffmenge in den beleuchteten Bereichen führt. Durch eine zusätzlich aufgebrachte Barriereschicht kann kein frischer Sauerstoff in das System nachströmen, weshalb an den entsprechenden beleuchteten Stellen nach ausreichender Bestrahlung Phosphoreszenz sichtbar wird. Dadurch kann ein beliebiges lumineszentes Muster in die transparenten Schichten einprogrammiert und bei Bedarf ausgelesen werden. Durch die Beleuchtung mit Infrarotstrahlung hingegen wird die Temperatur und damit auch die Durchlässigkeit der Sauerstoffbarriere erhöht. So wird das System mit molekularem Sauerstoff wieder aufgefüllt und die Phosphoreszenz verschwindet. Daraufhin können erneut Bilder in die Folie geschrieben werden. Wenn nicht durch Bestrahlung mit entsprechendem Licht ausgelesen, ist das System völlig transparent und lässt das eingeschriebene Muster nicht erkennen. Dies ermöglicht die Herstellung von programmierbaren lumineszenten Etiketten, die mehrere Schreib-, Lese- und Löschzyklen ermöglichen und somit zur temporären Beschriftung in der Logistik oder zur unsichtbaren Dokumentensicherung eingesetzt werden können. Die Machbarkeit der genannten Anwendungen wird in der Arbeit durch die Herstellung funktionierender Prototypen aufgezeigt. Sowohl das Gesamtverfahren von Aktivierung und Deaktivierung als auch der Aufbau des Systems sind Teil von Patentanmeldungen. Die im Rahmen dieser Arbeit erfolgte Charakterisierung weiterer organischer Emitter und Additive zeigt, dass der Effekt der schaltbaren Phosphoreszenz nicht auf eine bestimmte Materialkombination beschränkt ist, sondern ein sehr allgemeingültiges Verhalten darstellt. Deshalb werden Eigenschaften der Materialsysteme wie die Emissionsfarbe, der Kontrast der Muster oder die Empfindlichkeit gegenüber verschiedenen Lichtwellenlängen mit geeigneten Kombinationen optimiert. Um in Zukunft eine gezielte Entwicklung von organischen phosphoreszierenden Emittern zu ermöglichen, werden die entscheidenden Anforderungen an die Materialien bezüglich ihres Einsatzes in programmierbaren Etiketten dargestellt. Abschließend werden potentielle weitere Entwicklungsrichtungen hin zu weiteren Anwendungen beschrieben, von denen eine bereits Gegenstand von erfolgreich eingeworbener Förderung durch das Bundesministerium für Bildung und Forschung ist. In dieser Folgestudie wird die Eignung der gefundenen Ergebnisse zur Messung von UV-Strahlung untersucht. Mit zwei weiteren eingereichten Anträgen, die auf den vorgestellten Entwicklungen aufbauen, eröffnen die Ergebnisse dieser Arbeit sowohl aus wissenschaftlicher als auch aus technischer Sicht ein breites Spektrum weiterer Forschungsarbeiten.:1. Introduction 2. Theory 3. Methods 4. Basic Principles of Programmable Luminescent Tags (PLTs) 5. Characterization of Guest Materials 6. Optimization via Diversification: PLTs with Various Material Systems 7. Conclusions and Outlook

This paper is dealing with the detection clothes characteristics in the picture, for the use of person identification. These characteristics are described and categorized. It also deals with the design of the database structure, which works with masks and categories of characteristics for their processing. This work uses haar cascades to detect face and to determine the position of clothing for the purpose of color detection

This thesis focuses on the possibility of using current methods in the field of computer vision to re-identify graffiti tags. The work examines the possibility of using convolutional neural networks to re-identify graffiti tags, which are the most common type of graffiti. The work experimented with various models of convolutional neural networks, the most suitable of which was MobileNet using the triplet loss function, which managed to achieve a mAP of 36.02%.

This research investigated the connection between the Medicare star rating system and E-tags on emergency preparedness of nursing homes for disasters in Hampton Roads, Virginia. Emergency preparedness in nursing homes has been a topic of growing interest within the past decade. Hampton Roads, Virginia, has a history of natural disasters including hurricanes and flooding, which necessitates a proper and efficient emergency preparedness plan in nursing home facilities. The primary purpose of this research was to review the secondary Centers for Medicare and Medicaid Services (CMS) data regarding the star rating system and E-tag surveys of each of the 37 nursing facilities that were not connected to a hospital or part of a continuing care retirement community to find a correlation, if any, between emergency preparedness and CMS star rating. The theoretical foundation for the research was the diffusions of innovation theory, which addresses innovation that is communicated between members of a team or social group, inclusive of gaining knowledge of an innovation, persuading others to move toward that innovation, team decision making on the innovation, and implementation/confirmation of that innovation. The statistical analysis provided inconclusive answers to research questions. The potential social change from this study is it may inform nursing home administrators of the 4 most frequent E-tag deficiencies found in this research; and their nonlinear relationship to total bed count and variables such as individual Medicare star rating categories so that administrators can apply this new knowledge to their field in general and their facility in particular; to achieve better overall disaster preparedness coordination.