High-throughput sequencing technologies are improving in quality, capacity, and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag, index, or barcode that is attached to the sequencing or amplification primer and hence accompanies every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence. Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and codes based on the Levenshtein distance. Levenshtein-based codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this thesis we demonstrate the decreased error correction capability of Levenshtein-based codes in a DNA context and suggest an adaptation of Levenshtein-based codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaptation, we take any DNA context into account and impose more strict rules for the selection of barcode sets. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. We present an adaptation of Levenshtein-based codes to DNA contexts capable of guaranteed correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of correcting on average more random mutations than traditional Levenshtein-based or Hamming codes. As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance. However, not every platform is susceptible to a large number of both indel and substitution errors. The Illumina “Sequencing by Synthesis” platform shows a very large number of substitution errors as well as a very specific shift of the read that results in inserted and deleted bases at the 5’-end and the 3’-end (which we call phaseshifts). We argue in this scenario that the application of Sequence-Levenshtein-based codes is not efficient because it aims for a category of errors that barely occurs on this platform, which reduces the code size needlessly. As a solution, we propose the “Phaseshift distance” that exclusively supports the correction of substitutions and phaseshifts. Additionally, we enable the correction of arbitrary combinations of substitution and phaseshift errors. Thus, we address the lopsided number of substitutions compared to phaseshifts on the Illumina platform. To compare codes based on the Phaseshift distance to Hamming Codes as well as codes based on the Sequence-Levenshtein distance, we simulated an experimental scenario based on the error pattern we identified on the Illumina platform. Furthermore, we generated a large number of different sets of DNA barcodes using the Phaseshift distance and compared codes of different lengths and error correction capabilities. We found that codes based on the Phaseshift distance can correct a number of errors comparable to codes based on the Sequence-Levenshtein distance while offering the number of DNA barcodes comparable to Hamming codes. Thus, codes based on the Phaseshift distance show a higher efficiency in the targeted scenario. In some cases (e.g., with PacBio SMRT in Continuous Long Read mode), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives. For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements.

High-throughput sequencing technologies are improving in quality, capacity, and costs, providing versatile applications in DNA and RNA research. For small genomes or fraction of larger genomes, DNA samples can be mixed and loaded together on the same sequencing track. This so-called multiplexing approach relies on a specific DNA tag, index, or barcode that is attached to the sequencing or amplification primer and hence accompanies every read. After sequencing, each sample read is identified on the basis of the respective barcode sequence. Alterations of DNA barcodes during synthesis, primer ligation, DNA amplification, or sequencing may lead to incorrect sample identification unless the error is revealed and corrected. This can be accomplished by implementing error correcting algorithms and codes. This barcoding strategy increases the total number of correctly identified samples, thus improving overall sequencing efficiency. Two popular sets of error-correcting codes are Hamming codes and codes based on the Levenshtein distance. Levenshtein-based codes operate only on words of known length. Since a DNA sequence with an embedded barcode is essentially one continuous long word, application of the classical Levenshtein algorithm is problematic. In this thesis we demonstrate the decreased error correction capability of Levenshtein-based codes in a DNA context and suggest an adaptation of Levenshtein-based codes that is proven of efficiently correcting nucleotide errors in DNA sequences. In our adaptation, we take any DNA context into account and impose more strict rules for the selection of barcode sets. In simulations we show the superior error correction capability of the new method compared to traditional Levenshtein and Hamming based codes in the presence of multiple errors. We present an adaptation of Levenshtein-based codes to DNA contexts capable of guaranteed correction of a pre-defined number of insertion, deletion, and substitution mutations. Our improved method is additionally capable of correcting on average more random mutations than traditional Levenshtein-based or Hamming codes. As part of this work we prepared software for the flexible generation of DNA codes based on our new approach. To adapt codes to specific experimental conditions, the user can customize sequence filtering, the number of correctable mutations and barcode length for highest performance. However, not every platform is susceptible to a large number of both indel and substitution errors. The Illumina “Sequencing by Synthesis” platform shows a very large number of substitution errors as well as a very specific shift of the read that results in inserted and deleted bases at the 5’-end and the 3’-end (which we call phaseshifts). We argue in this scenario that the application of Sequence-Levenshtein-based codes is not efficient because it aims for a category of errors that barely occurs on this platform, which reduces the code size needlessly. As a solution, we propose the “Phaseshift distance” that exclusively supports the correction of substitutions and phaseshifts. Additionally, we enable the correction of arbitrary combinations of substitution and phaseshift errors. Thus, we address the lopsided number of substitutions compared to phaseshifts on the Illumina platform. To compare codes based on the Phaseshift distance to Hamming Codes as well as codes based on the Sequence-Levenshtein distance, we simulated an experimental scenario based on the error pattern we identified on the Illumina platform. Furthermore, we generated a large number of different sets of DNA barcodes using the Phaseshift distance and compared codes of different lengths and error correction capabilities. We found that codes based on the Phaseshift distance can correct a number of errors comparable to codes based on the Sequence-Levenshtein distance while offering the number of DNA barcodes comparable to Hamming codes. Thus, codes based on the Phaseshift distance show a higher efficiency in the targeted scenario. In some cases (e.g., with PacBio SMRT in Continuous Long Read mode), the position of the barcode and DNA context is not well defined. Many reads start inside the genomic insert so that adjacent primers might be missed. The matter is further complicated by coincidental similarities between barcode sequences and reference DNA. Therefore, a robust strategy is required in order to detect barcoded reads and avoid a large number of false positives or negatives. For mass inference problems such as this one, false discovery rate (FDR) methods are powerful and balanced solutions. Since existing FDR methods cannot be applied to this particular problem, we present an adapted FDR method that is suitable for the detection of barcoded reads as well as suggest possible improvements.

Det här examensarbetet genomfördes på Silvent ABs huvudkontor i Borås. Syftet med arbetet var att se på vilka sätt företaget kunde förbättra sin saldokvalitet. Vikten av att lagersaldot är korrekt blir viktigare för varje år. Flera begrepp såsom Lean, prognostisering, beställningspunkter och lagerpåfyllning är alla baserade på att lagersaldot är korrekt. För att undersöka orsakerna till varför felaktigt lagersaldo uppstod gjordes intervjuer med personal som är centrala för att uppnå ett korrekt lagersaldo. Utöver intervjuerna observerades flödet för den avgränsade produktgruppen. Eftersom det finns flera faktorer som påverkar lagersaldot undersöker analysen flera metoder som är möjliga att använda sig av för att uppnå ett säkrare lagersaldo.De tre viktigaste slutsatserna som undersökningen kom fram till är följande: Rutiner för mätning och dokumentation.Dokumentering av mätningar är viktigt för att använda som underlag för att synliggöra problemområden och motiv för eventuella förbättringar. Därför är det inte bara viktigt att införa tydliga rutiner för hur mätningar ska utföras och utan även hur dokumentationen av dessa mätningar ska ske så att man i efterhand kan spåra och jämföra med tidigare mätningar. RFIDMed implementationen av någon form av digital uppmärkning och ett automatiserat identifieringssystem finns stor potential för att förbättra saldokvaliteten. Bevis för att RFID skulle kunna förbättra saldokvaliteten med ungefär 26 % finns i en tidigare studie, gjord av Hardgrave et. al. 2015. Företaget rekommenderas därför att undersöka om det finns möjligheter för implementation av detta. KanbanEtt lätt sätt att hantera artiklar som är svåra eller kostnadskrävande att föra ett lagersaldo över är tvåbingesystem där påfyllning av lagret sker på ett mer visuellt sätt. Att inte föra ett lagersaldo över artiklarna gör det dock svårt att redovisa siffror på hur mycket av artiklarna som faktiskt lagerhålls ifall någon efterfrågar efter det. / This bachelor thesis took place at Silvent AB’s headquarters in Borås. The purpose of this inquiry was to identify in which ways the company could improve their stock-on-hand accuracy. The importance of having a correct inventory balance is growing for every year that passes. Concepts like Lean, forecasting, re-ordering point, and stock replenishment are all based on having a correct stock balance. In order to investigate the reasons for an incorrect inventory balance, interviews were conducted with staff that is central to achieving a correct stock balance. In addition to the interviews, the flow of the demarcated product group was observed. Since there are several factors that affect inventory balance, the analysis explores several methods that are possible to use to achieve a more secure inventory balance.The three main conclusions of the inquiry are as follows: Procedures for measurment and documentation.Documentation of measurements is important as a basis to visualize problem areas and motives for possible improvements. Therefore, it is not only important to introduce clear procedures for how measurements are to be performed but also how the documentation of these measurements should be done, making it possible to backtrack and compare with previous measurements. RFIDWith the implementation of some form of digital markup and an automated identification system, there is great potential for improving the quality of the stock balance. Evidence that RFID could reduce the inaccuracy of inventory balance by about 26% is found in a previous study by Hardgrave et. al. 2015. The company is therefore recommended to investigate if there are possibilities for implementing this. KanbanAn easy way to handle items that are difficult or costly to keep an inventory balance is a two-bin system where replenishment of the stock is done in a more visual way. However, by not keeping a proper record of stock balance of the articles makes it difficult to report figures on how many items that is available if it is required.

De par leurs propriétés d’autorenouvellement et de multipotentialité, les cellules souches hématopoïétiques (CSH) présentent un intérêt médical majeur et sont au cœur de nombreuses thérapies génique et cellulaire. Cependant, leur utilisation en clinique est encore limitée par leur rareté, leur hétérogénéité fonctionnelle, et leur perte durant l’étape de manipulation in vitro qui précède la transplantation.Dans ce contexte, nous avons mis au point une stratégie de marquage cellulaire par des codes-barres moléculaires afin d’évaluer simultanément et quantitativement les capacités de repopulation des CSH in vivo. Cette stratégie nous a permis de cribler 1200 composés chimiques afin d’identifier des molécules capables (1) d’améliorer l’efficacité de transduction des CSH par un vecteur lentiviral, (2) de maintenir voire d’expandre, lors de l’étape de culture in vitro, les CSH capables de repopulation à long terme. Plusieurs molécules candidates sont en cours de validation.Par ailleurs, grâce au marquage par des codes-barres, nous avons révélé l’hétérogénéité des CSH en comparant leur capacité d’autorenouvellement, la taille de la descendance qu’elles génèrent et leur capacité de différenciation. Notre technique nous a permis non seulement de confirmer l’existence de CSH biaisées vers le lignage myéloïde ou vers le lignage lymphoïde, mais aussi de quantifier leur fréquence.L’application de cette stratégie à un autre système cellulaire nous a permis d’étudier l’influence de facteurs environnementaux et génétiques sur la croissance cellulaire de populations exprimant différentiellement l’-synucléine, une protéine impliquée dans la maladie de Parkinson et certains cancers. / Considerable hope is placed on the use of hematopoietic stem cells (HSC) in engineered gene- and cell- based therapy protocols. Their clinical utilization is, however to some extent, limited by their scarce representation, their heterogeneity and their loss during the ex vivo manipulation procedure. Within this context, we developed a barcode tagging strategy to simultaneously evaluate in vivo the repopulating capacity of HSC cultured in vitro. Barcode deconvolution demonstrated that our strategy constitute a powerful tool for tracking HSC quantitatively even using several dozens of different conditions. Using this strategy, we screened 1200 chemical compounds in order to identify molecules acting (1) on HSC transduction efficiency using a lentiviral vector, (2) on maintenance or even amplification during the in vitro culture step of long-term repopulating HSC. Several candidate molecules are currently under validation. In addition, using this barcoding strategy, we reveal heterogeneous behaviour of HSC examining their proliferation capacity, self-renewal ability and their differentiation lineage option. Our technique allowed us not only to confirm the occurrence of myeloid- and lymphoid-biased HSC, but also to quantify their frequency.We apply this strategy to another cell system to address the effect of different genetic and environmental factors on proliferation of cells expressing -synuclein, a protein involved in Parkinson disease and some cancers.

Made available in DSpace on 2016-12-12T17:38:31Z (GMT). No. of bitstreams: 1 Marlon Alcantara.pdf: 7618831 bytes, checksum: 4f3eda2c23fb87ff3373687e72470feb (MD5) Previous issue date: 2012-05-28 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Barcodes, already common in commercial environments and supermarkets, are applied in various situations as a way to record and acquire data automatically and quickly, using electronic devices. Barcodes do not incorporate features that allow identification of their position and orientation during the reading process, these resources are essential in everal areas, such as Augmented Reality (AR) and Mobile Robotics (MR). This paper shows a survey of applications in AR and MR and it was observed that several technologies are used for data logging and acquisition of position and orientation, at the same time or not, such as sensors, cameras and maps. Therefore, we developed a barcode with capacity to acquire position and orientation in a three-dimensional space. The development of barcode enriched, called QRPO, was reached through the calculation of the Direct Linear Transformation on a standard two-dimensional barcode, like QR Code with square shape, which allowed the extraction of translation, rotation and scale parameters using the capture device as reference, in this case, a low-cost webcam. With this, we developed QRPO versions to be applied both in Augmented Reality (using no edge) and in Mobile Robotics (using an edge): for the first, we made programs and tests which validated the robustness and efficiency calculating the position and orientation, and correctness of reading data, for the second, we created a solution to the problem of exploring an unknown environment, called mouse-cheese problem, from its conception to the definition of the movement control strategy, passing through deployment and testing. This application demonstrated that it is possible, with a single camera, to conduct a mobile robot acquiring position, orientation and data efficiently and avoiding the use of additional sensors, only using the QRPO. Thus, the result of this work, the QRPO, represents a new enriched barcode with the capacity of data representation and acquisition of position and orientation with wide applicability. / Os códigos de barras, já comuns em ambientes comerciais e supermercados, são aplicados em diversas situações como meio de registrar e adquirir, automática e rapidamente, dados por meio de leitura por dispositivos eletrônicos. Os códigos de barras não incorporam recursos que permitam a identificação de sua posição e orientação nos momentos de leitura, recursos estes essenciais em diversas áreas, como a Realidade Aumentada (RA) e Robótica Móvel (RM). Este trabalho fez um levantamento das aplicações em RA e RM e constatou-se que diversas tecnologias são utilizadas para registro de dados e aquisição de posição e orientação, às vezes juntas e às vezes isolada, tais como sensores, câmeras e mapas. Por isto, foi desenvolvido um código de barras com capacidade de aquisição de posição e orientação no espaço tridimensional. A elaboração do código de barras enriquecido, denominado QRPO, foi alcançada por meio do cálculo da Transformada Linear Direta sobre um código de barra bidimensional padronizado, do tipo QR Code e com forma quadrada, o que permitiu a extração dos parâmetros de translação, rotação e escala com referência ao dispositivo de captura, no caso uma webcam de baixo custo. Com isto, foram desenvolvidas versões do QRPO para serem aplicadas tanto para Realidade Aumentada (sem uso de uma borda) quanto para Robótica Móvel (com o uso da borda): para a primeira, foram feitos programas e testes que validaram a robustez e eficiência no cálculo da posição e orientação e a corretude na leitura de dados; para a segunda, foi elaborada uma solução para o problema de exploração de um ambiente desconhecido, denominado problema do rato-queijo , desde a sua concepção até a definição da estratégia de controle de movimentação, passando pela implantação e testes. Esta aplicação demonstrou que é possível com uma única câmera, conduzir um robô móvel adquirindo posição, orientação e dados de forma eficiente e dispensando o uso de sensores adicionais, apenas com o uso do QRPO. Assim, o resultado deste trabalho, o QRPO, representa um novo código de barras enriquecido com a capacidade de representação de dados e aquisição de posição e orientação e com ampla aplicabilidade.

Actuellement, l’asthme est la 1ère maladie professionnelle respiratoire. L’utilisation de produits de nettoyage et de désinfection est un facteur de risque émergent de l’asthme lié au travail, surtout dans le secteur de la santé. Cependant, les produits spécifiques en cause dans l’asthme restent à identifier. L’évaluation de l’exposition professionnelle aux produits de nettoyage et de désinfection est difficile dans les études épidémiologiques. De plus, le biais du travailleur sain (HWE) est important à considérer dans les études épidémiologiques sur l’asthme lié au travail.L’objectif de la thèse comportait deux aspects : 1) un aspect méthodologique visant à améliorer l’évaluation des expositions professionnelles aux produits de nettoyage et de désinfection en développant des méthodes novatrices ; 2) un aspect étiologique visant à estimer le rôle des expositions professionnelles dans le contrôle de l’asthme en prenant en compte un potentiel HWE.Tout d’abord, des matrices emplois-expositions (MEE) et emplois-tâches¬-expositions (METE) ont été développées via les données de femmes non-asthmatiques tirées au sort dans une cohorte prospective d’infirmières américaine (NHSII : Nurse’s Health Study II). Puis, une méthode d’évaluation des expositions professionnelles aux produits de nettoyage et de désinfection utilisant une application smartphone scannant les codes-barres de produits et une base de données (BDD) a été développée. L’étude du rôle des expositions professionnelles aux produits de nettoyage et de désinfection dans le contrôle de l’asthme a été réalisée dans l’étude Épidémiologique des facteurs Génétiques et Environnementaux de l'Asthme disposant de données longitudinales détaillées sur l’histoire professionnelle et les phénotypes d’asthme. Afin de prendre en compte un potentiel HWE, un modèle marginal structural (MMS) a été appliqué.Une hétérogénéité de l’estimation des expositions par les MEE et METE était observée dans la plupart des métiers infirmiers, sauf pour les infirmières exerçant aux urgences et dans l’administration/la formation. Nous avons montré que la METE était plus adaptée que la MEE pour estimer les expositions, en particulier pour les métiers infirmiers ayant des tâches hétérogènes. Via l’application, 126 produits ont été recueillis auprès de 14 personnels hospitaliers de l’étude pilote, et des informations sur les composés étaient disponibles pour tous les produits via la BDD associée. Cette étude a montré que ce nouvel outil était simple à mettre en place, facile et rapide à utiliser pour les participants, et permettait d’évaluer de façon précise les expositions aux différentes substances. Ces résultats confirment la faisabilité et l’intérêt de cette méthode et suggèrent son déploiement dans les études épidémiologiques. Dans la partie étiologique, nous avons observé la présence d’un HWE dans notre échantillon d’étude. Malgré la prise en compte de ce HWE en utilisant un MMS, les résultats des associations ne permettaient pas de conclure sur le rôle des expositions professionnelles dans le contrôle de l’asthme. / Currently, asthma is the first occupational respiratory disease. The use of disinfectants and cleaning products has been identified as an emerging risk factor for work-related asthma, especially in the healthcare industry. However, identifying the specific products at risk for asthma remains challenging, partly because assessment of occupational exposure to disinfectants/cleaning products is difficult in epidemiological studies and needs improvement. Moreover, taking into account possible healthy worker effect (HWE) is essential in work-related asthma study.The aims of the thesis were to improve the methods for assessment of occupational exposure to disinfectants/cleaning products by developing new methods; and to study the association between occupational exposure to disinfectants/cleaning products and asthma control taking into account a possible HWE.First, job-exposure (JEM) and job-task-exposure matrices (JTEM) have been created using data from a random sample of women without asthma from a large prospective cohort of US nurses (NHSII: Nurse’s Health Study II). Second a new assessment method using a smartphone application with a barcode scanner and a database was designed to evaluate occupational exposure to disinfectants and cleaning products. The study of the association between occupational exposure to disinfectants and cleaning products and asthma control has used data from the French Epidemiological study on the genetics and environment of asthma. Longitudinal data were available on occupational history and asthma phenotypes. To control for a possible HWE, a marginal structural model (MSM) was used.For the first part, JEM and JTEM exposure estimates were heterogeneous in most nursing jobs, except in emergency room and education/administration. The JTEM may provide more accurate estimates than the JEM, especially for nursing jobs with heterogeneous tasks. Through the smartphone application, 126 products were registered for 14 hospital workers of the pilot study. Information on components was available for all products in the database. The method developed is feasible and applicable to larger epidemiological studies. In the etiological part, a HWE was observed in the study sample. Even after controlling for a HWE, results did not allow concluding on the association between occupational exposures and control of asthma.

This thesis describes barcodes which are used in postal services. Specifically, it is concerned with Intelligent Mail Barcode, the GS1-128 code, the C128 code of Ceska posta (Czech Postal Services) and the QR code. The thesis attempts to analyze methods of encoding information into barcodes and error detection algorithms used for error correction during the decoding processes. Most importantly, there is described Reed-Solomon error correction in the QR code. There are presented and evaluated different methods of code detecting which are suggested by authors of various academic articles. The thesis also describes the method of creating test sets of images and proposed appearances of the scanning scene. Additionally, there are described algorithms for detection and decoding barcodes GS1-128, C128 and IMB in the image which was created during the work on this thesis. Finally, there is the evaluation of the percentage success of algorithms.

The door manufacturing industry still heavily relies on manual technology for its production and quality assurance systems, which poses certain challenges. However, in recent years, the industry has witnessed a growing demand for personalized products, leading to a need for more adaptable production methods and shorter product life cycles. Unfortunately, this reliance on manual technologies has resulted in increased errors and inaccuracies. Moreover, manual technology requires significant time and effort investment, which reduces production efficiency and product quality. To address these issues, the purpose of this thesis is to address the issue of inefficiency at a door manufacturing company by examining its existing production systems and quality assurance system. The thesis aims to provide recommendations for improvement by exploring the integration of automated tracing and tracking technology. Furthermore, it would result in recommendations for feasible methods that may be used in Swedish production systems, as well as further study fields.