The two techniques aqueoustwo-phase partitioning and expanded bed adsorption that bothare suitable for primary protein recovery were studied. Most ofthe work was focused on partition in aqueous two-phase systemsand in particular on the possibility to effect the partitionbehaviour by fusion of short peptide tags or protein domains tothe target protein. The partitioning of fusionproteins between different variants of the domain tag Z and thenaturally occurring protein DNA Klenow polymerase were studiedin Breox/Reppal aqueous two-phase systems. Most studies wereperformed with cell homogenate. The Breox/Reppal system was infocus because if the fusion protein can be partitioned to theBreox-rich top phase the next step can be a thermoseparatingaqueous two-phase system. When the Breox phase is heated to50°C it switches from a one-phase system to a two-phasesystem resulting in an almost pure water rich top phase andhighly concentrated Breox-rich bottom phase. The Breox can thenbe reused and the protein recovered from the water phase. TheZ-domain was genetically modified in different ways to Zbasic1, Zacid2and Ztrp12and fused to the Klenow protein to try toenhance partitioning to the Breox-rich phase. From theexperiments it was not possible to observe any effects on thepartition behaviour irrespectively of tested properties of thedomain tag. Despite the absence of domain tag effects highK-values, i.e. partition to the Breox-rich top phase, wereobserved in the Breox/Reppal system. However, the proteinK-values seemed to be rather sensitive to the cell homogenateload and showed a tendency to decrease with increased cellhomogenate load. Also increased phosphate concentration reducedthe K-values. The partitioning of cell debris also seemed todependent on the cell homogenate load. At higher homogenateload (&lt;=20g DW/L) clear Breox-rich top phases were observedwith the cell debris collected in Reppal-rich bottomphases. Two different tetrapeptides,AlaTrpTrpPro and AlaIleIlePro were inserted near the C-terminusof the protein ZZT0. The Trp-rich peptide unit stronglyincreased both the partitioning of ZZT0 into the poly(ethyleneglycol) (PEG)-rich phase in a PEG/potassium phosphate aqueoustwo-phase system and its retention on PEG and propylhydrophobic interaction chromatographic columns with potassiumphosphate as eluent in isocratic systems. Both the partitioningand the retention increased with increasing number of Trp-richpeptide units inserted into ZZT0. Insertion of Ile-richtetrapeptide units affected the partitioning and retention to amuch lesser extent. Partition and modelling data also indicateda folding of inserted Trp and Ile tetrapeptide units, probablyto minimise their water contact. It was also investigated howto predict the partitioning of proteins in isoelectricPEG/phosphate aqueous two-phase systems. The capture ofß-galactosidase fromE. colicell homogentate (50g DW/L) by metal chelatexpanded bed adsorption was studied. These experiments showedthat capture, with a certain degree of selectivity, andclarification of ß-galactosidase could be achieved from acell homogenate. However, a rather low recovery of about 35 %was obtained at a capacity of 0.25mg/mL of gel. Thus, severalparameters remain to be optimised like the load buffercomposition and the cell homogenate load. <b>Keywords:</b>E. coli, aqueous two-phase systems, fusion proteins,hydrophobic interaction chromatography, expanded bedadsorption, ß-galactosidase, Klenow polymerase, Z-domain,peptide tags / NR 20140805

Plick is an online platform with the intention of being a marketplace where users may buy and sell second-hand fashion. The platform caters to younger users, and as such borrows many ideas from well-known social network platforms - such as putting more focus on user profiles and expression, rather than just the products themselves. One of these ideas is to allow users free reign over tagging their items, rather than having them select from some constrained, pre-approved, group of categories, styles, sizes - et cetera. A problem of letting users tag products however they see fit is that a subset of users will inevitably try to 'game' the system by knowingly tagging their products using incorrect labels - resulting in inaccurate search results for many of these incorrect tags.The aim of this project is to firstly develop a pre-processing algorithm to normalize the user generated tagging data - to handle situations such as a tag having multiple different (albeit possibly all correct) spellings, capitalizations, typos, languages etc. The processed data will then be used to develop two different approaches to solve the problem of incorrect tagging. The first approach involves using the normalized data to create a graph representation of the tags and their relations to each other. Each node in the graph will represent an individual tag, and each edge between nodes will explain how closely related those two tags are. An algorithm will then be developed to, utilizing the tag relation graph, describe the relatedness of an arbitrary group of tags. The algorithm should also be able to identify any tags that are outliers among the group. The second approach entails the development of a gaussian naive bayes classifier, with the goal of identifying whether an article is anomalistic or not - given the group of tags it's been assigned.

Microalgae hold much promise as a feedstock in liquid biofuel production. Lipid content of microalgae cells range from 30-80% dry weight of biomass. It is projected that microalgae can produce between 1,000-6,500 gallons/acre/year of oil. Currently, production of industrial algae operates in open raceway ponds that use minimal capital and energy inputs to culture algae. Raceway ponds can also be used to grow microalgae from municipal waste streams. Although high biomass productivity can be achieved in these systems, there remains a large production gap between large volumes of biomass cultivation and high lipid content from microalgae cells. Low lipid content has been ameliorated through laboratory manipulations of nitrogen availability and light intensity. This two-part project measured microalgae lipid levels in open raceway ponds located at the San Luis Obispo Water Reclamation Facility (SLO WRF) grown in primary clarifier effluent and then performed nitrogen depletion and light-shift methods on cultures to increase triglyceride (TAG) content. The raceway ponds reached maximum biomass productivity of 24 g/m2-day, but with minimal TAG reserves. Optimization of both biomass productivity and TAG content can be achieved in April and September with 13 g/m2-day productivity and 13% TAG content. Investigation of increased TAG production responses were performed on wastewater microalgae (predominately Scenedesmus sp.) through N-depletion and three light treatments: light-shift on day 3 (before N-depletion), light-shift on day 5 (near N-depletion), and a double-illumination treatment. Highest levels of TAG content were observed in the double-illumination treatment and reached a maximum of 49% TAG in 9 days.

Sewer and oil pipeline spillage issues have become major causes of pollution in urban and rural areas usually caused by blockages in the water storage and drainage system, and oil spillage of underground oil pipelines. An effective way of avoiding this problem will be by deploying some mechanism to monitor these installations at each point in time and reporting unusual liquid activity to the relevant authorities for prompt action to avoid a flooding or spillage occurrence. This research work presents a low cost energy efficient liquid level monitoring technique using Radio Frequency Identification Technology. Passive UHF RFID tags have been designed, modelled and optimized. A simple rectangular tag, the P-shaped tag and S-shaped tag with UHF band frequency of operation (850-950 MHz) has been designed and modelled. Detailed parametric analysis of the rectangular tag is made and the optimised design results analysed and presented in HFSS and Matlab. The optimised rectangular tag designs are then deployed as level sensors in a gully pot. Identical tags were deployed to detect 4 distinct levels in alternate positions and a few inches in seperation distance within the gully pot height (Low, Mid, High and Ultra high). The radiation characteristic of tag sensors in deployment as modelled on HFSS is observed to show consistent performance with application requirements. An in-manhole chamber antenna for an underground communication system is analysed, designed, deployed and measured. The antenna covers dual-band impedance bandwidths (i.e. 824 to 960 MHz, and 1710 to 2170 MHz). The results show that the antenna prototype exhibits sufficient impedance bandwidth, suitable radiation characteristics, and adequate gains for the required underground wireless sensor applications. Finally, a Linearly Shifted Quadrifilar Helical Antenna (LSQHA) designed using Genetic Algorithm optimisation technique for adoption as an RFID reader antenna is proposed and investigated. The new antenna confirms coverage of the RFID bandwidth 860-960 MHz with acceptable power gain of 13.1 dBi. / Petroleum Technology Development Fund (PTDF) and National Space Research and Development Agency (NASRDA).

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.

Avec l'ouverture de la bande 57-66 GHz en Europe, de nouvelles technologies de communication sans fil à haut débit sont en cours de développement. De nombreux avantages liés à cette bande de fréquence ont notamment conduit à envisager la transposition du principe de l'identification par radiofréquence (RFID) en bande millimétrique : la MMID. Les réglementations internationales font notamment apparaître une bande passante commune de 5 GHz qui permettrait la mise en place de solutions universelles. De plus la sécurisation des communications point-à-point et la directivité des réseaux d'antennes offrent des perspectives intéressantes.Les travaux présentés dans cette thèse visent à contribuer au développement de la MMID. Ils soulignent les principaux verrous de cette technologie et présentent les différentes solutions proposées qui couvrent de multiples aspects : conception d'antennes et de réseaux d'antennes, conception de prototypes de tags MMID passifs, caractérisation et méthodologie de mesure dont la conception intégrale d'un banc de mesure en bande V, amélioration des performances des tags, et étude de fonctionnalités de capteur intégrées aux tags. Les différents prototypes de tags MMID fabriqués ont permis de réaliser des communications passives de type rétro-modulation jusqu'à 20 cm. De plus, des fonctions de capteur d'humidité et capteur de pression intégrées aux tags MMID ont été montrées expérimentalement. L'ensemble de ces résultats ouvre la voie à de nouvelles perspectives pour les domaines des télécommunications et des réseaux de capteurs en bande millimétrique. / With the opening of the 57-66 GHz band in Europe, new high data-rate wireless communication technologies are currently under development. Numerous advantages linked to the frequency band conducted to consider the transposition of the radiofrequency identificaion (RFID) principle to the millimeter frequency band: the MMID. The international regulations provide a common bandwidth of 5 GHz allowing universal solutions. Moreover, the communication security of point-to-point networks and the directivities of the antennas present interesting perspectives.The presented work in this thesis looks for contributing to the development of MMID. The work underlines the principal locks of this technology and it presents the different proposed solutions covering multiple aspects: conception of antennas and antennas arrays, conception of MMID tags prototypes, characterization and measurement methodology including the complete conception of a measurement bench in V-band, improvement of the tags performances and study of sensing functionalities integrated in the tags. Different prototypes of MMID tags are fabricated and passive communications based on the backscattering of the tags were demonstrated up to 20 cm. In addition, humidity and pressure sensing functionalities were proved by experimentations. The overall of these results pave the way for new perspectives for the wireless communication domain and sensors networks in the millimeter-wave band.

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.

The performance of commercial Radio Frequency Identification (RFID) tags is primarily limited by present techniques used for tag antenna design. Currently, industry techniques rely on identifying the RFID tag application (books, clothing, etc.) and then building antenna prototypes of different configurations in order to satisfy minimum read range requirements. However, these techniques inherently lack an electromagnetic basis and are unable to provide a low cost solution to the tag antenna design process. RFID tag performance characteristics (read-range, chip-antenna impedance matching, surrounding environment) can be very complex, and a thorough understanding of the RFID tag antenna design may be gained through an electromagnetic approach in order to reduce the tag antenna size and the overall cost of the RFID system. The research presented in this thesis addresses RFID tag antenna design process for passive RFID tags. With the growing number of applications (inventory, supply-chain, pharmaceuticals, etc), the proposed RFID antenna design process demonstrates procedures to design tag antennas for such applications. Electrical/geometrical properties of the antennas designed were investigated with the help of computer electromagnetic simulations in order to achieve optimal tag performance criteria such as read range, chip-impedance matching, antenna efficiency, etc. Experimental results were performed on the proposed antenna designs to compliment computer simulations and analytical modelling.

Considérées comme des moyens incontournables de participation à la société, les technologies de l’information et de la communication (TIC) constituent une piste de solution prometteuse pour l’enseignement et l’apprentissage auprès des élèves qui ont des incapacités intellectuelles. Toutefois, plusieurs auteurs dénoncent la faible utilisation des TIC en éducation de ces élèves. Pire encore, les recherches sur le sujet génèrent des résultats intéressants, mais d’une contribution limitée pour l’avancement des connaissances dans le domaine. Guidées par l’intuition et par un enthousiasme empirique évident, ces recherches s’appuient rarement sur des cadres de référence. Certes la documentation scientifique foisonne de champs de savoirs qui peuvent contribuer à ce domaine, mais ces contributions sont parcellaires et peu adaptées aux spécificités de ce dernier. L’intervention avec les TIC auprès des élèves qui ont des incapacités intellectuelles demeure donc un champ conceptuel mal défini qui n'est légitimé par aucun cadre de référence en particulier. Cette recherche doctorale se situe en phase de préconception d’un modèle de l’intervention avec les TIC auprès des élèves qui ont des incapacités intellectuelles. Elle vise à mettre en place des balises solides pouvant servir de cadre à l’élaboration d’un modèle de cette intervention. Dans cette phase de préconception, nous poursuivons deux objectifs, à savoir : 1) la mise au point d’un référentiel qui constitue un cadre intégrateur des connaissances existantes en la matière, qui servira avant tout à structurer et à organiser les informations disponibles à l’intérieur d’une synthèse validée par des experts et des intervenants oeuvrant auprès de ce type d’élèves et 2) l’élaboration d’un cahier des charges fonctionnel qui s’appuie sur le référentiel développé et qui précise les fonctions qu’un modèle idéal de l’intervention avec les TIC auprès des élèves qui ont des incapacités intellectuelles devrait remplir pour répondre pleinement aux besoins de ses différents utilisateurs. Ces balises (le référentiel et le cahier des charges fonctionnel) sont destinées, principalement, à des chercheurs, des concepteurs de technologies, des formateurs d’enseignants, etc. Les élèves, les enseignants et autres agents de l'éducation pourront en bénéficier indirectement à travers les applications dérivées de ces balises (programmes de formation, technologies, recherches, scénarios pédagogiques, etc.). / Regarded as essential means of participation in society, information and communication technologies (ICT) are a promising track for teaching and learning of students with intellectual disabilities. However, several authors denounce the low use of ICT in education of these students. Worse yet, research on the subject generate interesting results, but a limited support to contribute to the advancement of knowledge in the field. Guided by intuition and empirical enthusiasm, theses researches often rely on reference frames. While the literature abounds with fields of knowledge that can contribute to this area, these proposals are fragmented and poorly adapted to the specifics of the latter. The educational intervention with ICT with students with intellectual disabilities remains an ill-defined conceptual field that is not legitimized by any particular reference frame. This doctoral research precedes the conception of an educational intervention model using ICT with students who have intellectual disabilities. It aims to establish strong tags that can serve as a framework for developing this model. In this phase of preconception, we pursue two objectives: 1) developing a repository consisting in a framework for integrating existing knowledge on the subject that will serve primarily to structure and organize the information available within the a synthesis validated by experts and practitioners; 2) developing a tender specification of the functions that a perfect model of this intervention should meet to fully satisfy the needs of different users. These tags (the repository and the tender specification) are intended, mainly, to researchers, technology developers, teacher educator, etc. Students, teachers and other educational agents will benefit indirectly from these tags through their applications by the first users of (training programs, technologies, studies, lesson plans, etc.).

This study explores how the social tags are employed by users of LibraryThing, a popular web 2.0 social networking site for cataloging books, to describe works on Asian women in representing themes within the context of intersectionality. Background literature in the domain of subject description of works has focused on race and gender representation within traditional controlled vocabularies such as the Library of Congress Subject Headings (LCSH). This study explores themes related to intersectionality in order to analyze how users construct meaning in their social tags. The collection of works used to search for social tags came from the Association of College and Research Libraries’ list on East Asian, South and Southeast Asian, and Middle Eastern women. A pilot study was conducted comprising of a limited sample in each of the three domains, which helped generate a framework of analysis that was used in application for the larger sample of works on Asian women. The full study analyzed 1231 social tags collected from 122 works on Asian women. Findings from this study showed that users construct a variety of intersections relating to gender and ethnicity for works on Asian women. Overall findings from this showed that gender and gender-related constructs were the most common subject of tags employed for works on Asian women. Users more often referred to geography rather than ethnicity when describing the materials on Asian women. Interesting themes to emerge involved how gender and other constructs differed among the three domains. Tags describing the majority of East Asia, such as Chinese and Japanese were most common in the East Asian dataset. Countries not considered the “majority” in South and Southeast Asia were often used, such as Indonesia and the Philippines. Themes of sexuality and religion were much more prevalent in the Middle Eastern set of tags. Social tags act as a mechanism for social commentary. Researchers have access to a plethora of constructions available to them through these social tags; such abundance of information is a valuable resource to understanding how the general populace understands intersections and constructs identity.