Doctor of Philosophy / Department of Statistics / Suzanne Dubnicka / DNA barcodes are short strands of nucleotide bases taken from the cytochrome c oxidase subunit 1 (COI) of the mitochondrial DNA (mtDNA). A single barcode may have the form C C G G C A T A G T A G G C A C T G . . . and typically ranges in length from 255 to around 700 nucleotide bases. Unlike nuclear DNA (nDNA), mtDNA remains largely unchanged as it is passed from mother to offspring. It has been proposed that these barcodes may be used as a method of differentiating between biological species (Hebert, Ratnasingham, and deWaard 2003). While this proposal is sharply debated among some taxonomists (Will and Rubinoff 2004), it has gained momentum and attention from biologists. One issue at the heart of the controversy is the use of genetic distance measures as a tool for species differentiation. Current methods of species classification utilize these distance measures that are heavily dependent on both evolutionary model assumptions as well as a clearly defined "gap" between intra- and interspecies variation (Meyer and Paulay 2005). We point out the limitations of such distance measures and propose a character-based method of species classification which utilizes an application of Bayes' rule to overcome these deficiencies. The proposed method is shown to provide accurate species-level classification. The proposed methods also provide answers to important questions not addressable with current methods.

<p>Advances in sequencing technologies constantly improves the throughput andaccuracy of sequencing instruments. Together with this development comes newdemands and opportunities to fully take advantage of the massive amounts of dataproduced within a sequence run. One way of doing this is by analyzing a large set ofsamples in parallel by pooling them together prior to sequencing and associating thereads to the corresponding samples using DNA sequence tags. Amplicon sequencingis a common application for this technique, enabling ultra deep sequencing andidentification of rare allelic variants. However, a common problem for ampliconsequencing projects is formation of unspecific PCR products and primer dimersoccupying large portions of the data sets.</p><p>This thesis is based on two papers exploring these new kinds of possibilities andissues. In the first paper, a method for including thousands of samples in the samesequencing run without dramatically increasing the cost or sample handlingcomplexity is presented. The second paper presents how the amount of high qualitydata from an amplicon sequencing run can be maximized.</p><p>The findings from the first paper shows that a two-tagging system, where the first tagis introduced by PCR and the second tag is introduced by ligation, can be used foreffectively sequence a cohort of 3500 samples using the 454 GS FLX Titaniumchemistry. The tagging procedure allows for simple and easy scalable samplehandling during sequence library preparation. The first PCR introduced tags, that arepresent in both ends of the fragments, enables detection of chimeric formation andhence, avoiding false typing in the data set.</p><p>In the second paper, a FACS-machine is used to sort and enrich target DNA covered emPCR beads. This is facilitated by tagging quality beads using hybridization of afluorescently labeled target specific DNA probe prior to sorting. The system wasevaluated by sequencing two amplicon libraries, one FACS sorted and one standardenriched, on the 454 showing a three-fold increase of quality data obtained.</p> / QC20100907

Visually impaired (VI) individuals struggle with grocery shopping and have to rely on either friends, family or grocery store associates for shopping. ShopMobile 2 is a proof-of-concept system that allows VI shoppers to shop independently in a grocery store using only their smartphone. Unlike other assistive shopping systems that use dedicated hardware, this system is a software only solution that relies on fast computer vision algorithms. It consists of three modules - an eyes free barcode scanner, an optical character recognition (OCR) module, and a tele-assistance module. The eyes-free barcode scanner allows VI shoppers to locate and retrieve products by scanning barcodes on shelves and on products. The OCR module allows shoppers to read nutrition facts on products and the tele-assistance module allows them to obtain help from sighted individuals at remote locations. This dissertation discusses, provides implementations of, and presents laboratory and real-world experiments related to all three modules.

Title page, abstract and table of contents only. The complete thesis in print form is available from the University of Adelaide Library. / A combination of Radio Frequency Identification technology and ubiquitous computing are revolutionising the manner in which we look at simple objects. Radio Frequency Identification (RFID) allows RFID labeled objects to be identified at a distance without physical contact, and ubiquitous computing provides a virtually connected environment for the objects. RFID labels are frequently referred to as the next generation barcodes. RFID Systems provide increased productivity, efficiency, convenience and many advantages over bar codes for numerous applications, especially global supply chain management. RFID labeling has a number of advantages over conventional bar code systems. The optics based bar code systems could be rendered useless by common everyday environments containing dirt, dust, smoke, grease, condensation and by misorientation and misalignment. Furthermore bar codes are subject to fraudulent duplication and counterfeiting with minimal effort. However, there are limitations and constraints inherent to RFID technology: semiconductor thresholds, limits on transmitted power, costs, antenna and coupling inefficiencies. Thus it is important for RFID designers to understand these limitations and constraints in order to optimise system designs and overcome inefficiencies where possible. Therefore the work presented in this dissertation seeks to improve the performance of advanced RFID systems by overcoming a number of these limitations. Prior to a discussion of improving performance, the author's interpretation of a modem RFID system along its evolutionary path as a ubiquitous RFID network and its application to supply chain management is described. Performance improvements are achieved by: the development of electromagnetic theory for RFID system analysis and optimisation; design and development of interrogator antennas; analysis of electrically small and tiny antennas for RFID labels; and development and utilisation of a design methodology for creating high performance label antennas and antennas for tagging metallic objects. Implementations of RFID systems have raised concerns regarding information security and possible violations of end-user privacy. The most profound concerns are raised against low cost RFID technology because of its potential for mass scale deployment, its pervasive nature, and the resource limitations preventing the provision of strong cryptographic solutions. There is a growing need in the RFID community to discover and develop techniques and methods to overcome various hurdles posed by the above-mentioned concerns. Thus, the thesis also considers the vulnerabilities of low cost RFID systems and associated insecurities and privacy concerns resulting from the latter. Prior to addressing such concerns impeding the deployment of low cost RFID technology, a framework within which to provide security services is also detailed. It has become important to both defme and identity a framework based around low cost RFID systems since RFID has become a "catch all" phrase for various other forms of technology. Addressing security and privacy of low cost RFID systems requires novel thinking. The later parts of the thesis outline design considerations for security mechanisms and a number of practicable solutions for providing the features of: mutual authentication; confidentiality; message content security; product authentication; anonymity and untraceability, that are necessary for low cost RFID systems to overcome the weaknesses identified in this dissertation. Implementing these security mechanisms requires the generation of true random tag parameters and true random numbers. Achieving these objectives using a hardware based true random number generator is also described and analysed. A final part of the thesis focuses on active RFID labels and improving their performance. The primary concern with active labels is the life of the onboard battery. Turn-on circuits provide a method of turning "on" and "off" an active label remotely to conserve valuable battery power. Analysis, development and testing of a turn-on circuit concept, based on interrogator field sensing, have provided a means of remotely activating and deactivating active RFID labels and conserving battery power. The final chapter of this thesis provides a detailed analysis, based on coupling relations between electromechanical systems, for evaluating the feasibility of a theft detection sensor, based on a turn-on circuit for an active RFID label, for preventing the theft of high value items. While low cost RFID needs to overcome certain security and privacy related barriers, RFID technology does provide novel and valid approaches to such security related applications as product authentication, anti-counterfeiting and theft detection. It is believed that the contributions from this thesis will extend and elaborate on the existing knowledge base, paving the way forward to allow further significant deployment of advanced RFID techno logy. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1368084 / Thesis (Ph.D.) -- University of Adelaide, School of Electrical and Electronic Engineering, 2007

Visually impaired (VI) individuals struggle with grocery shopping and have to rely on either friends, family or grocery store associates for shopping. ShopMobile 2 is a proof-of-concept system that allows VI shoppers to shop independently in a grocery store using only their smartphone. Unlike other assistive shopping systems that use dedicated hardware, this system is a software only solution that relies on fast computer vision algorithms. It consists of three modules - an eyes free barcode scanner, an optical character recognition (OCR) module, and a tele-assistance module. The eyes-free barcode scanner allows VI shoppers to locate and retrieve products by scanning barcodes on shelves and on products. The OCR module allows shoppers to read nutrition facts on products and the tele-assistance module allows them to obtain help from sighted individuals at remote locations. This dissertation discusses, provides implementations of, and presents laboratory and real-world experiments related to all three modules.

Title page, abstract and table of contents only. The complete thesis in print form is available from the University of Adelaide Library. / A combination of Radio Frequency Identification technology and ubiquitous computing are revolutionising the manner in which we look at simple objects. Radio Frequency Identification (RFID) allows RFID labeled objects to be identified at a distance without physical contact, and ubiquitous computing provides a virtually connected environment for the objects. RFID labels are frequently referred to as the next generation barcodes. RFID Systems provide increased productivity, efficiency, convenience and many advantages over bar codes for numerous applications, especially global supply chain management. RFID labeling has a number of advantages over conventional bar code systems. The optics based bar code systems could be rendered useless by common everyday environments containing dirt, dust, smoke, grease, condensation and by misorientation and misalignment. Furthermore bar codes are subject to fraudulent duplication and counterfeiting with minimal effort. However, there are limitations and constraints inherent to RFID technology: semiconductor thresholds, limits on transmitted power, costs, antenna and coupling inefficiencies. Thus it is important for RFID designers to understand these limitations and constraints in order to optimise system designs and overcome inefficiencies where possible. Therefore the work presented in this dissertation seeks to improve the performance of advanced RFID systems by overcoming a number of these limitations. Prior to a discussion of improving performance, the author's interpretation of a modem RFID system along its evolutionary path as a ubiquitous RFID network and its application to supply chain management is described. Performance improvements are achieved by: the development of electromagnetic theory for RFID system analysis and optimisation; design and development of interrogator antennas; analysis of electrically small and tiny antennas for RFID labels; and development and utilisation of a design methodology for creating high performance label antennas and antennas for tagging metallic objects. Implementations of RFID systems have raised concerns regarding information security and possible violations of end-user privacy. The most profound concerns are raised against low cost RFID technology because of its potential for mass scale deployment, its pervasive nature, and the resource limitations preventing the provision of strong cryptographic solutions. There is a growing need in the RFID community to discover and develop techniques and methods to overcome various hurdles posed by the above-mentioned concerns. Thus, the thesis also considers the vulnerabilities of low cost RFID systems and associated insecurities and privacy concerns resulting from the latter. Prior to addressing such concerns impeding the deployment of low cost RFID technology, a framework within which to provide security services is also detailed. It has become important to both defme and identity a framework based around low cost RFID systems since RFID has become a "catch all" phrase for various other forms of technology. Addressing security and privacy of low cost RFID systems requires novel thinking. The later parts of the thesis outline design considerations for security mechanisms and a number of practicable solutions for providing the features of: mutual authentication; confidentiality; message content security; product authentication; anonymity and untraceability, that are necessary for low cost RFID systems to overcome the weaknesses identified in this dissertation. Implementing these security mechanisms requires the generation of true random tag parameters and true random numbers. Achieving these objectives using a hardware based true random number generator is also described and analysed. A final part of the thesis focuses on active RFID labels and improving their performance. The primary concern with active labels is the life of the onboard battery. Turn-on circuits provide a method of turning "on" and "off" an active label remotely to conserve valuable battery power. Analysis, development and testing of a turn-on circuit concept, based on interrogator field sensing, have provided a means of remotely activating and deactivating active RFID labels and conserving battery power. The final chapter of this thesis provides a detailed analysis, based on coupling relations between electromechanical systems, for evaluating the feasibility of a theft detection sensor, based on a turn-on circuit for an active RFID label, for preventing the theft of high value items. While low cost RFID needs to overcome certain security and privacy related barriers, RFID technology does provide novel and valid approaches to such security related applications as product authentication, anti-counterfeiting and theft detection. It is believed that the contributions from this thesis will extend and elaborate on the existing knowledge base, paving the way forward to allow further significant deployment of advanced RFID techno logy. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1368084 / Thesis (Ph.D.) -- University of Adelaide, School of Electrical and Electronic Engineering, 2007

Submitted by Marco Antonio de Freitas Contessoto (marco_contessoto@hotmail.com) on 2018-06-19T06:27:03Z No. of bitstreams: 1 Marcoeditado.pdf: 1251669 bytes, checksum: 5fe5c25a4002aeefa7831bd4137fb1f8 (MD5) / Approved for entry into archive by Elza Mitiko Sato null (elzasato@ibilce.unesp.br) on 2018-06-19T14:26:54Z (GMT) No. of bitstreams: 1 contessoto_maf_me_sjrp.pdf: 1242012 bytes, checksum: e5b5acc9695b0f3103a68a1f1f32edac (MD5) / Made available in DSpace on 2018-06-19T14:26:54Z (GMT). No. of bitstreams: 1 contessoto_maf_me_sjrp.pdf: 1242012 bytes, checksum: e5b5acc9695b0f3103a68a1f1f32edac (MD5) Previous issue date: 2018-03-09 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O objetivo dessa dissertação é apresentar parte do artigo [2] de Gunnar Carlsson, onde se discute a adaptação de métodos da teoria usual de homologia para problemas de reconhecimento topológico de padrões em conjuntos de dados. Esta adaptação conduz aos conceitos de homologia de persistência e de barcodes. Atualmente, várias aplicações são obtidas com o uso deste método. Apresentaremos alguns casos onde a homologia de persistência é usada, ilustrando diferentes modos em que podem ser aplicados. Descreveremos, também baseado no artigo de Carlsson, um novo método para estudar a persistência de características topológicas através de uma família de conjuntos de dados, chamado persistência zig-zag . Este método generaliza a teoria de homologia de persistência e chama atenção de situações que não são cobertas pela outra teoria. Além disso, são apresentadas algumas aplicações dessa ferramenta para a obtenção de informações de alguns conjuntos de dados / The main goal of this work is to present a part of the Gunnar Carlsson paper [2], where the adaptation of the theory of usual homology to topological pattern recognition problems in point cloud data sets is discussed. This adaptation leads to the concepts of persistence homology and barcodes. Several applications have been obtained using this method. We will present some cases where persistence homology is used, illustrating different ways in which the method can be applied. We will describe,alsobasedintheCarlsson’spaper,anewmethodtostudythepersistence oftopologicalfeaturesthroughpointclouddatasets,calledzig-zagpersistence. This method generalizes the homology persistent theory and we will pay attention to situations that are not covered by the other theory. In addition, some applications of this tool are presented to obtain information from some data sets. / 2016/25659-3

This diploma work analyzes the problem of logistic and invertory management with using barcode. This diploma work is based on cooperation with Identcode company. DataPro Solutions is customer of Identcode company. The task is project warehouse system based on portable computers Dolphin from Hanhedl. The output of this diploma is proposal of warehouse inventory system for customer - DataPro Solutions company.

Pooled cell strain libraries are a powerful tool allowing to investigate the influence of genetic modifications on phenotypes in high throughput single-cell assays. To link the genotype to phenotype in each cell of the library, unique 20 base pairs (bp) long barcodes are used to allow in situ genotyping after phenotyping via fluorescence microscopy. In previous studies, these barcode sequences were expressed from high copy number plasmids resulting in a high number of targets for detection via fluorescence in situ hybridization (FISH) and thus, a strong readout signal. However, constant selection pressure must be applied on the cells to maintain the foreign plasmid DNA which may influence the phenotype. Inserting unique barcodes on the chromosome ensures stability of the construct which is required for some genomic library applications. However, the low copy number of the barcode sequence often requires an additional step of DNA amplification for efficient detection. In this study, two methods for barcode amplification were investigated. First, amplification from the double stranded DNA upon binding of peptide nucleic acids and subsequent amplification via rolling circle amplification (AmPPR). Second, amplification from genomic DNA or cDNA via loop-mediated isothermal amplification (LAMP). Whereas the AmPPR approach remained unsuccessful, chromosomal barcode sequences were successfully amplified in situ via LAMP and subsequently detected using FISH. I show that LAMP can potentially be a quick, specific, and elegant amplification technique for in situ genotyping in microfluidic devices. However, nonspecific amplification and partly nonspecific readout signals when using LAMP remain a problem and need to be further investigated before implementing this method on pooled libraries.

Advances in sequencing technologies constantly improves the throughput andaccuracy of sequencing instruments. Together with this development comes newdemands and opportunities to fully take advantage of the massive amounts of dataproduced within a sequence run. One way of doing this is by analyzing a large set ofsamples in parallel by pooling them together prior to sequencing and associating thereads to the corresponding samples using DNA sequence tags. Amplicon sequencingis a common application for this technique, enabling ultra deep sequencing andidentification of rare allelic variants. However, a common problem for ampliconsequencing projects is formation of unspecific PCR products and primer dimersoccupying large portions of the data sets. This thesis is based on two papers exploring these new kinds of possibilities andissues. In the first paper, a method for including thousands of samples in the samesequencing run without dramatically increasing the cost or sample handlingcomplexity is presented. The second paper presents how the amount of high qualitydata from an amplicon sequencing run can be maximized. The findings from the first paper shows that a two-tagging system, where the first tagis introduced by PCR and the second tag is introduced by ligation, can be used foreffectively sequence a cohort of 3500 samples using the 454 GS FLX Titaniumchemistry. The tagging procedure allows for simple and easy scalable samplehandling during sequence library preparation. The first PCR introduced tags, that arepresent in both ends of the fragments, enables detection of chimeric formation andhence, avoiding false typing in the data set. In the second paper, a FACS-machine is used to sort and enrich target DNA covered emPCR beads. This is facilitated by tagging quality beads using hybridization of afluorescently labeled target specific DNA probe prior to sorting. The system wasevaluated by sequencing two amplicon libraries, one FACS sorted and one standardenriched, on the 454 showing a three-fold increase of quality data obtained. / QC20100907