O presente trabalho foi organizado em cinco capítulos. No primeiro é apresentada uma breve revisão da bibliografia relacionada ao DNA barcode, apontando as aplicações e os limites desse marcador. Os resultados obtidos são apresentados nos três capítulos subsequentes. O segundo capítulo teve como objetivo avaliar o potencial do método de DNA barcoding na distinção de 783 amostras de 228 espécies diferentes de aves neotropicais de 16 ordens baseado na diferença dos valores de divergências intra- e interespecíficas. O DNA barcode permitiu a diagnose da maioria das espécies tanto utilizando os valores de distância quanto os agrupamentos nas árvores de Neighbor-joining (NJ), mostrando ser um marcador muito útil na identificação rápida de aves neotropicais. Além disso, verificamos que ele gera informações que podem ser relevantes a estudos biogeográficos. Foram identificadas espécies proximamente relacionadas que não puderam ser identificadas seguindo essa metodologia, todas pertencentes aos psitaciformes. Assim, o objetivo do capítulo seguinte foi investigar se há caracteres diagnósticos no coxI de pares de espécies irmãs de psitacídeos neotropicais (gêneros Amazona, Ara, Aratinga, Brotogeris e Graydidascalus) e de grupos que não puderam ser identificados nas análises anteriores devido a baixas distâncias interespecíficas ou por não formarem clados reciprocamente monofiléticos nas árvores de NJ (espécies dos gêneros Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura e Rhynchopsitta). As espécies irmãs apresentaram de quatro a 39 sítios diagnósticos puros e as espécies proximamente relacionadas apresentaram de um a 11 sítios diagnósticos. Apenas as espécies Rhynchopsitta pachyrhyncha e R. terrisi e as espécies Amazona aestiva e A. ochrochephala, não apresentaram caracteres diagnósticos exclusivos e, portanto não puderam ser identificadas. Os resultados mostraram que é possível identificar grande parte das espécies proximamente relacionadas desse grupo de aves utilizando caracteres diagnósticos do DNA barcode. O penúltimo capítulo teve como objetivo identificar espécies de embriões de aves apreendidos do tráfico internacional de animais, utilizando o DNA barcode. Das 58 amostras totais, 93% foram identificadas, sendo três amostras de Ara ararauna, duas de Triclaria malachitacea e 49 de Alipiopsitta xanthops. As quatro amostras restantes (7%) foram identificadas como Amazona aestiva e/ou Amazona ochrochephala. Essas espécies formam um complexo já descrito em alguns trabalhos de filogenia molecular, o que inviabiliza qualquer sistema de identificação de espécies ao nível molecular. O DNA barcoding parece ser eficaz na correta identificação de espécies de aves e é especialmente útil em casos nos quais dados morfológicos não são acessíveis, como o presente exemplo. Por fim são descritas as principais conclusões de cada capítulo. / The present study was organized in five chapters. The first one is a brief review of the literature on DNA barcode, pointing out its applications and limits. The results are presented in the three subsequent chapters. The second chapter aimed to evaluate the potential of the DNA barcoding method in the distinction of 783 samples of 228 different Neotropical birds species from 16 orders, based on the difference of values of intra- and interspecific distances. DNA barcode was able to diagnose most of the species using distance values and Neighbor-joining (NJ) trees. Thus, it is a useful tool for rapid identification of Neotropical birds and it can provide information that may be relevant to biogeography studies. Some closely related species, all psitaciformes, could not be identified. Thus, the following chapter attempted to identify diagnostic characters in the DNA barcode sequences of sister species pairs of Neotropical parrots (genera Amazona, Ara, Aratinga, Brotogeris and Graydidascalus) and groups of species that could not be identified due to low interspecific distances or lack of monophyly in NJ trees (species of the genera Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura, Rhynchopsitta). The pairs of sister species had four to 39 pure diagnostic sites and closely related species had one to 11 diagnostic sites. Only the pair of species Rhynchopsitta pachyrhyncha and R. terrisi, and Amazona aestiva and A. ochrochephala did not have exclusive characters and therefore could not be identified with this method. The results showed that it is possible to identify the majority of the closely related species of this avian group using DNA barcode characters. The next chapter intended to identify the species of bird embryos apprehended from the illegal animal trade using DNA barcodes. From the total of 58 samples, 93% were identified as: three Ara ararauna, two Triclaria malachitacea and 49 Alipiopsitta xanthops. The four remaining samples (7%) were identified as Amazona aestiva and/or A. ochrochephala. These species form a complex that was already suggested in previous molecular phylogeny studies. Thus, it seems to be impossible to distinguish them based on molecular markers. DNA barcoding seems to be efficient in the identification of species of birds and is especially useful in cases where morphological data is not accessible, as the present example. Finally the main conclusions are described in the last chapter.

O presente trabalho foi organizado em cinco capítulos. No primeiro é apresentada uma breve revisão da bibliografia relacionada ao DNA barcode, apontando as aplicações e os limites desse marcador. Os resultados obtidos são apresentados nos três capítulos subsequentes. O segundo capítulo teve como objetivo avaliar o potencial do método de DNA barcoding na distinção de 783 amostras de 228 espécies diferentes de aves neotropicais de 16 ordens baseado na diferença dos valores de divergências intra- e interespecíficas. O DNA barcode permitiu a diagnose da maioria das espécies tanto utilizando os valores de distância quanto os agrupamentos nas árvores de Neighbor-joining (NJ), mostrando ser um marcador muito útil na identificação rápida de aves neotropicais. Além disso, verificamos que ele gera informações que podem ser relevantes a estudos biogeográficos. Foram identificadas espécies proximamente relacionadas que não puderam ser identificadas seguindo essa metodologia, todas pertencentes aos psitaciformes. Assim, o objetivo do capítulo seguinte foi investigar se há caracteres diagnósticos no coxI de pares de espécies irmãs de psitacídeos neotropicais (gêneros Amazona, Ara, Aratinga, Brotogeris e Graydidascalus) e de grupos que não puderam ser identificados nas análises anteriores devido a baixas distâncias interespecíficas ou por não formarem clados reciprocamente monofiléticos nas árvores de NJ (espécies dos gêneros Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura e Rhynchopsitta). As espécies irmãs apresentaram de quatro a 39 sítios diagnósticos puros e as espécies proximamente relacionadas apresentaram de um a 11 sítios diagnósticos. Apenas as espécies Rhynchopsitta pachyrhyncha e R. terrisi e as espécies Amazona aestiva e A. ochrochephala, não apresentaram caracteres diagnósticos exclusivos e, portanto não puderam ser identificadas. Os resultados mostraram que é possível identificar grande parte das espécies proximamente relacionadas desse grupo de aves utilizando caracteres diagnósticos do DNA barcode. O penúltimo capítulo teve como objetivo identificar espécies de embriões de aves apreendidos do tráfico internacional de animais, utilizando o DNA barcode. Das 58 amostras totais, 93% foram identificadas, sendo três amostras de Ara ararauna, duas de Triclaria malachitacea e 49 de Alipiopsitta xanthops. As quatro amostras restantes (7%) foram identificadas como Amazona aestiva e/ou Amazona ochrochephala. Essas espécies formam um complexo já descrito em alguns trabalhos de filogenia molecular, o que inviabiliza qualquer sistema de identificação de espécies ao nível molecular. O DNA barcoding parece ser eficaz na correta identificação de espécies de aves e é especialmente útil em casos nos quais dados morfológicos não são acessíveis, como o presente exemplo. Por fim são descritas as principais conclusões de cada capítulo. / The present study was organized in five chapters. The first one is a brief review of the literature on DNA barcode, pointing out its applications and limits. The results are presented in the three subsequent chapters. The second chapter aimed to evaluate the potential of the DNA barcoding method in the distinction of 783 samples of 228 different Neotropical birds species from 16 orders, based on the difference of values of intra- and interspecific distances. DNA barcode was able to diagnose most of the species using distance values and Neighbor-joining (NJ) trees. Thus, it is a useful tool for rapid identification of Neotropical birds and it can provide information that may be relevant to biogeography studies. Some closely related species, all psitaciformes, could not be identified. Thus, the following chapter attempted to identify diagnostic characters in the DNA barcode sequences of sister species pairs of Neotropical parrots (genera Amazona, Ara, Aratinga, Brotogeris and Graydidascalus) and groups of species that could not be identified due to low interspecific distances or lack of monophyly in NJ trees (species of the genera Amazona, Aratinga, Myiopsitta, Pionites, Pyrrhura, Rhynchopsitta). The pairs of sister species had four to 39 pure diagnostic sites and closely related species had one to 11 diagnostic sites. Only the pair of species Rhynchopsitta pachyrhyncha and R. terrisi, and Amazona aestiva and A. ochrochephala did not have exclusive characters and therefore could not be identified with this method. The results showed that it is possible to identify the majority of the closely related species of this avian group using DNA barcode characters. The next chapter intended to identify the species of bird embryos apprehended from the illegal animal trade using DNA barcodes. From the total of 58 samples, 93% were identified as: three Ara ararauna, two Triclaria malachitacea and 49 Alipiopsitta xanthops. The four remaining samples (7%) were identified as Amazona aestiva and/or A. ochrochephala. These species form a complex that was already suggested in previous molecular phylogeny studies. Thus, it seems to be impossible to distinguish them based on molecular markers. DNA barcoding seems to be efficient in the identification of species of birds and is especially useful in cases where morphological data is not accessible, as the present example. Finally the main conclusions are described in the last chapter.

In this thesis we apply the idea of a barcode from persistent homology to four hierarchical clustering methods: single, average, complete, and Ward's linkage. Desirable theoretical properties of dendrograms, the standard tool to visualize the output of hierarchical clustering methods, were described by Carlsson. We define analogous properties for hierarchical clustering quasi-barcodes and prove that average and complete quasi-barcodes possess a property that dendrograms do not. We discuss how to decide where to "cut" the output of hierarchical clustering quasi-barcodes based on the distance between the heights at which clusters merge. We find the best possible matching for calculating the Wasserstein distance between quasi-barcodes built from the same number of data points all born at time 0. We also prove that single, average, and complete quasi-barcodes are stable in the sense that small perturbations in distances between points produce small changes in quasi-barcodes. In order to test the efficiency of quasi-barcodes and the cut-off criteria, we generate datasets of points arranged in blobs or concentric circles and look whether the combination of the quasi-barcode with the cut-off criteria successfully finds the right amount of clusters in the dataset and whether it places points in the correct clusters. Finally, we apply these tools to datasets from New York University and Peking University of typically developed controls and attention hyperactivity deficit disorder subjects between the ages of 7 and 18.

¡@¡@The main objectives of this study is to: (1) understand the recruitment pattern and mechanisms of fish larvae in the kenting waters, such as seasonal variation, distance from shoreline, depth, and diurnal migration of the assemblages of larvae fish. The correlation of the tempo-spatial variations of larval fish communities with temperature, salinity, and chlorophyll were also investigated; (2) to apply DNA barcode technique to identify fish larvae to lower taxonomic categories so as to reveal the temporal or spatial variation of the community structure of fish larvae that was unclear if the identification could only up to higher level. Additionally, DNA barcoding can help us to compile the diagnostic keys for larval fish species identifications. ¡@¡@For fish larval communities studies, fish larvae were collected from four seasons and two different depths during 2001-2002, and every two hours in a day during 10-11 April 2004 by the standard ORI net in Kenting. 527 specimens belonging to 86 taxa and 51 families of fish larvae were collected during 2001-2002. Randomization tests show significant differences between fish larval abundance vs. depths, and the number of families vs. seasons. Canonical correspondence analysis (CCA) shows that temperature and salinity were the main environmental factors, and chlorophyll was the second. 158 specimens belonging to 44 taxa and 34 families of fish larvae were collected during 24 hour survey. The abundance and diversity of fish larvae increase after sunset, and reach to their climax in the midnight. ¡@¡@For COI species identification, 1,505 of the post-flexion stage fish larvae specimens belong to 44 taxa and 34 families were collected by the four-time surveys of light trap in Kenting coral reef area during 2005-2007. Fifteen types of damaselfish larvae and five types of butterflyfish larvae were identified based on their morphological characters. The COI were used to identify the morphological types of damselfishes and butterflyfishes to species level. Fifteen morphological types of damselfishes (Pomacentridae) can be identified to 11 species and three genera. Five morphological types of butterflyfishes (Chaetodontidae) can be assigned to four species and one genus. After COI identification to the lower taxonomic levels, the ordination analysis can clearly reveal the seasonal variation. The result shows that applying DNA barcode technique to identify fish larvae to lower taxonomic categories indeed can reveal temporal or spatial variation of the community structure of fish larvae.

Recent improvements in sequencing technologies have caused various interesting problems to arouse. Having millions of read sequences as the final product of sequencing genome at a lower cost compared to micro array era, has encouraged scientists to enhance previous methods in various areas of bioinformatics. Genotyping and generating genetic maps to study inherited genotypes in order to analyze specific traits in a population is one of the fields of bioinformatics that involves generating different genetic markers and identify polymorphisms in different individuals of a population. Presence/absence markers are the main focus of this thesis. This is one type of Restriction site Associate DNA (RAD) markers which is present in some samples and absent in others and is the sign of variation in the cut site of a restriction enzyme. However, the counts of markers in an experiment are highly correlated and calling true absence and presence is not a straightforward task which means any marker with zero count is not necessarily absent in the sample under study. This is also the case for non-zero count markers which are not necessarily present. A good model that can fit the data is able to make true calls. We propose two different contexts for designing such models as a solution to this problem and investigate their performance. On the other hand, utilizing features of next generation sequencing technology in an even more efficient way, requires the ability to multiplex high number of samples in a single experiment run. In that case, appropriate barcoding, that is robust to various sources of noise in the machine, becomes paramount. Designing such barcodes in an efficient way is a challenging task which is addressed in detail as another problem of this thesis. We make two contributions. One, we propose an algorithm for barcoding multiplexed RADSeq samples. Two, we propose an algorithm for the statistical selection of presence/absence markers on the basis of RADSeq data on two related individuals. Operating characteristics of our methods are explored using both simulated and real data.

This work deals with localization and decoding of the linear barcode EAN-13 in the image. It describes types and qualities of barcodes and pose posibble accesses into the localization and decoding. The practical part concerns with the concept and implementation of the algorithm having regard to effectiveness for processing in real time. The localization is established on finding similar features of the barcode among the read rows of the image and decoding is made by finding of the supreme conformity towards referential code figures.

Darbo esmė giliau pažvelgti į brūkšninių kodų rūšis, panaudojimo galimybes ir išsiaiškinti jų privalumus bei trūkumus. Darbo tikslas išnagrinėti QR brūkšninio kodo sandarą, kiekvienos sudedamos dalies svarbą ir savybes. Taip pat sukurti programinę įrangą QR kodo lokalizavimui vaize ir palyginti su praktikoje naudojamais produktais. / This paper investigates different barcodes, use cases, advantages and disadvantages. Aim of this paper is to analyse stucture and characteristics of QR code, develop software to locate QR code in picture, compare results with other software.

Automation in warehouses has been improved in a very certain manner, combining sensors for perception of the environment and mapping of the warehouse. The most common characteristic, which makes the products and the pallet rack cells discriminative, are the barcodes placed on them. This means that the warehouse management system should successfully perceive all the necessary information of the detected barcodes, which also includes their position in the warehouse and build a barcode map of the environment. For this process a barcode reader is needed, with extended capabilities such as estimation of the 3-dimensional coordinates of the barcodes. The main idea of this research was the development of a system to be used in future work, placed on the roof of a forklift, which will be able to detect the barcodes and localize itself using an existing map of the warehouse and update new information in this map. However, the purpose of this project was the investigation of a suitable system for barcode mapping. The main challenge of this project was the development of a barcode reader, which fulfills all the referred capabilities and the comparison with a commercial reader in order to evaluate the performance of the system. In this project a barcode reader was developed using software libraries and a camera for industrial use. The performance of the system was compared with a commercial barcode reader. Moreover, an algorithm was implemented, for estimation of the position of each detected barcode, with reference to the position of the camera's lens.  According to the results of all the investigations the performance of the developed system was quiet satisfying and promising. The comparison of the two systems proved that the commercial barcode reader had a better performance than the implemented system. However, it lacked the ability to provide the required information for mapping also the flexibility for integration with other systems. Overall, the developed system proved to be suitable for integration with a warehouse management system for barcode mapping of the environment.

Submitted by Inácio de Oliveira Lima Neto (inacio.neto@inpa.gov.br) on 2018-10-01T14:07:32Z No. of bitstreams: 2 eduardo_carlo_amat_garcia.pdf: 9255988 bytes, checksum: 1e3954df1b9d7f68db70c2e0e00098d0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-10-01T14:07:32Z (GMT). No. of bitstreams: 2 eduardo_carlo_amat_garcia.pdf: 9255988 bytes, checksum: 1e3954df1b9d7f68db70c2e0e00098d0 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-12-15 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The blow fly fauna of Northwest South America was studied based in three main approaches: 1. Local diversity of assemblages; 2. geographical distribution of their species; and 3. efficacy of short DNA sequences (Mini barcode) to identify their species. In order to study the patterns of species richness, abundance and dominance of local assemblages, three scenarios were chosen: the Amazonian interfluvial region; an altitudinal gradient in the Andean belt and the Páramo ecosystem. By the other hand, the geographical information of 13.474 specimens belonging to 28 species, deposited in eleven entomological collection of Brazil, Colombia, Ecuador and Venezuela was retrieved. Based on this data, it was possible to make a preliminary regionalization into six natural divisions: Amazon, Andes, Caribbean, Orinoquia, Pacific and Tepuyan region. It was also possible to identify preliminary patterns of geographical distribution and classify the blow fly species according to the biographic origin as follow: Tropical (25 spp); Temperate (4 spp) and Introduced (4spp). According to the altitudinal distribution, 17 species come from lowlands; 27 of montane and 8 of high elevations. Finally according to the level of synanthropy: 14 species were asynanthropic; 13 hemisynanthropic and 14 eusynanthropic. We recovered short mitochondrial DNA sequences (Mini barcodes of 317bp) from 143 specimens of thirty Neotropical species. This molecular marker allow the species identification of Calliphora, Chrysomya, Cochliomyia, Compsomyiops, Sarconesia, and Hemilucilia. However, it was not suitable for the correct identification of Lucilia species. In addition, we recovered genetic information from old preserved specimens deposited in museums for up to 57 year. The global diversity patterns together with the local assemblages assessed demostrated that the existence of an altitudinal gradient affects the composition of the blow fly fauna in the region. Being the most diverse assemblages, those located at intermediate elevations and the less diverse the perennial páramo ecosystem. The noticeable sensibility of blow flies to anthropized environments, the relative low number of species and their ubiquity, together with their relatively stable taxonomy, makes this group of flies as an ideal indicator of the level of human influence in environments of Northwest South America. / Estudou-se a fauna de Calliphoridae (Diptera) na região noroeste da América do Sul, abordando três aspectos principais: 1. Diversidade local das assembleias; 2. Distribuição geográfica das espécies; e 3. Uso de sequências de DNA na identificação genética das espécies. Para estudar os padrões de diversidade local e avaliar os padrões de riqueza, abundância e dominância foram escolhidos três cenários: o interflúvio amazônico, o gradiente altitudinal nos Andes Colombianos e o ecossistema de Páramo andino. Além disso, foi compilada a informação geográfica de 13.474 espécimes de 28 espécies, depositados em onze coleções entomológicas localizadas no Brasil, Colômbia, Equador e Venezuela. Com base nessa informação foi possível dividir a área de estudo em seis regiões naturais: Amazônia, Andes, Caribe, Orinoquia, Pacífica e Tepuiana. Também foi possível identificar padrões preliminares de distribuição espacial e classificar a fauna de califorídeos segundo a origem biogeográfica: espécies tropicais (25 spp.) temperadas (4 spp.) e introduzidas (4 spp.); segundo a distribuição altitudinal: espécies de terras baixas (17 spp.), espécies de montanha (27 spp.) e espécies de altas elevações (8 spp.) e segundo o grau de sinantropia em espécies assinantrópicas (14 spp.), hemissiantrópicas (13 spp.) e sinantrópicas (14 spp.). Finalmente, foram fornecidas as sequências curtas de DNA mitocondrial com 317 pares de bases (mini-barcode) para trinta espécies, possibilitando a identificação molecular das de Calliphora, Chrysomya, Cochliomyia, Compsomyiops, Sarconesia e Hemilucilia. Contudo, o marcador escolhido não foi adequado para identificar as espécies de Lucilia. Além disso, foram recuperadas as sequências genéticas de exemplares antigos depositados em coleções por até 57 anos. Os padrões de diversidade global e os encontrados em cada assembleia avaliada demostraram que a existência de um gradiente altitudinal afeta a composição da fauna de Califorídeos. Foi demostrado que as elevações intermediarias andinas são as mais ricas em espécies e que os Paramos andinos são pobres em califorídeos. A evidente sensibilidade dos Calliphoridae aos ambientes antropogênicos, seu número baixo de espécies e sua taxonomia relativamente estável faz deste um grupo ideal para utilização como indicador de ambientes antropisádos na região norte da América do Sul.

A fiber optic system for measuring magnetic heading and pitch of one or more compass heads in a towed acoustic array has been developed as a cooperative effort between engineers at Fiber Dynamics, Inc., and faculty and graduate students at Texas A&M. An unconventional photolithographic process for producing a bar-code pattern on a curved (spherical) surface was successfully implemented. First, an absorption process for applying a thin layer of photoresist uniformly to the gold-coated surface of a glass sphere was perfected. Then, a system for defining the patterns in the metal was assembled. A LabView computer program controlled the system as required to define the bar code pattern in the metal. High-quality bar code patterns were produced on floating spheres by this method. The data acquisition/signal processing system digitized and processed the raw data returning from the compass heads, and computed magnetic heading and pitch from the data. Processing of the signal from a single compass head required readout of a 7-bit binary code giving coarse heading, using timing information to obtain fine heading, and measuring the apparent width of an analog bar to determine pitch. When monitoring multiple compass heads distributed along the fiber, a time-division demultiplexing technique was used for separating the data from the individual compass heads. For testing the system, the cylindrical sensor head was mounted on a machinist's table for rotating it through 360?? in the horizontal plane to vary the heading, and through ??10?? about a horizontal axis to vary pitch. Measured resolutions of the system were 0.044?? for heading, and 0.85?? for pitch.