<div>In the U.S., unitary residential air conditioners are rated using standard AHRI 210/240 that is inadequate to credit equipment with advanced controls and variable-speed components since the ratings are based on results of steady-state laboratory tests. Contrarily, a load-based testing and rating approach is presented in this work that can capture equipment performance with its integrated controls and thermostat responses that is more representative of the field. In this approach, representative building sensible and latent loads are emulated in a psychrometric test facility at different indoor and outdoor test conditions utilizing a virtual building model. The indoor test room conditions are continuously adjusted to emulate the dynamic response of the virtual building to the test equipment sensible and latent cooling rates and the equipment dynamic response is measured. Meanwhile, the inlet temperatures to the test equipment thermostat are independently controlled to track the same virtual building response using a thermostat environment emulator that encloses the test thermostat, that provides typical flow conditions and of which the design and control are presented in this work. Climate-specific cooling seasonal performance ratings can be determined by propagating load-based test results through a temperature-bin method to estimate a seasonal coefficient of performance (SCOP). In addition, a next-generation rating approach is developed that extends load-based testing for performance mapping, such that the SCOP can be obtained using building simulations that incorporate specific building types, climates and an equipment-specific performance map. </div><div> </div><div>In this work, the proposed approaches were implemented to test and rate a variable-speed residential heat pump operating in cooling mode. Trained with results from only 12 load-based test intervals carried out using the test equipment, a quasi-steady-state mapping model was able to map the equipment performance across almost the entire operating envelope within $\pm10\%$ errors and the $R^2$ values were very close to 1. Using the identified performance map, the next-generation SCOP was obtained based on an annual simulation deployed in EnergyPlus, where the map was coupled to a typical single-family building in Albuquerque,NM. Compared to the temperature-bin-based rating, this simulation-based rating is able to comprehensively and appropriately reflect equipment annual field performance associated with a specific building type and climate, as the rating is extended from automated laboratory load-based testing and performance mapping.</div>

The application of Y-chromosome analysis is expanding in fields such as forensic science and genealogy. By researching the potential polymorphisms this chromosome can present, we can further our ability to assess DNA profiles for these disciplines to avoid erroneous exclusions of paternal linkage, wrongful convictions based on forensic evidence, and other misinformed genetic conclusions. The conservation of Y-haplotypes during transmission occurs due to a relative lack of genetic recombination events in the inheritance of the Y-chromosome [1]. However, random mutation events can occur in a paternal line resulting in haplotype changes. These changes can include allele duplications and deletions that occur at the STR and SNP loci used in forensic DNA analysis. This can become important in cases of sexual assault where male-female mixture samples have low amounts of male DNA such that the male signal is not amplified in currently used STR multiplexes [7]. In this study, we analyzed a father and his eleven sons using two different methodologies for genetic analysis; next generation sequencing and capillary electrophoresis. The samples were obtained from the Coriell Institute for Medical Research located in Hamden, NJ, in the form of frozen DNA extracts isolated from a blood-sourced lymphocyte cell culture [22]. DNA from these samples was tested with the ForenSeqTM DNA Signature Prep Kit [14] (Verogen, San Diego, CA) primer set A and the YFilerTM Plus PCR Amplification Kit [24] (Thermo Fisher Scientific, Waltham, MA). Using these two platforms, three Y-STR loci were identified as discordant between the father and all of his eleven sons. In all three instances, the father possessed the same allele as the sons as well as one additional allele. At two of these loci (DYS449 and DYS635), the additional allele was one repeat (4bp) longer than that of the shared allele. At the other locus (DYS458), the additional allele was three repeats (12bp) longer than that of the shared allele. Following read count and peak height analysis, it was concluded that these double allele loci are not the product of stutter and are potentially the product of a non-inheritable mutation. With the knowledge that the DNA was extracted from a blood lymphocyte cell culture, it is believed that a somatic mutation may be present in the cell line. We are not able to determine whether the mutations exist in the blood of the father (true somatic mutations) or occurred as a result of the cell culture process. Throughout the study, details concerning the position of these loci on the Y-chromosome, the repeat motifs of the alleles, and the potential for duplication and/or stutter as the originating event are discussed in an effort to further understand this phenomenon. Potential locus duplications were compared to those reported on the National Institute of Standards and Technology STRBase [21] list of allele variations and also to information found in literature. The observed DYS635 locus had an allele designation of 21,22 which is reported on STRBase. The DYS449 and DYS458 loci showed potential allele-specific locus duplications that were not found on STRBase. The implications of potentially undocumented non-inheritable allele patterns in the Y-chromosome, such as this, are significant when considering comparisons between DNA obtained from germline cells (sperm) versus a known casework sample which is usually obtained from blood or saliva [7].

This work summarizes the results of a research inquiring into relatively rare neuroendocrine tumors - pheochromocytomas and paragangliomas (PHEO/PGL) These tumors may arise on a hereditary genetic predisposition basis. On that account we primarily focused on a genetic examination of patients with PHEO/PGL. Methods for diagnostics of changes in SDHD, SDHB and RET genes were implemented. The number of examined genes has been (and is still being) extended. Currently we are investigating these genes: ATRX, BRAF, CDH1, CDKN2A, CDKN2B, FGFR1, FH, FHIT, GNAS, HIF2A (EPAS1), H-RAS, IDH1, IDH2, KIF1Bß, KMT2D, K-RAS, MAML3, MAX, MDH2, MET, NF1, NGFR, N-RAS, PHD2/EGLN1, RET, SDHA, SDHAF2, SDHB, SDHC, SDHD, TERT, TMEM 127, TP53 and VHL, using next generation sequencing. The number of variations of the above mentioned genes is different (23%) in Czech patients with PHEO/PGL in comparison with some foreign studies (27%, 40%). This may be caused by geographical influences or selection of patients. PHEO/PGL occur mainly (75%) in a benign form. A malignant form may be indicated by the presence of chromaffin tissue in locations where these tumors do not usually occur - liver, lungs, bones. In our study we focused on characteristics indicating the malignancy, for example, the lower age of patients with the first manifestation...

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

During the last decade, the use of Next-Generation Sequencing(NGS) technologies has sky-rocketed. The vast amount of data produced by these platforms require processing and analysis. This is usually performed at locations remote from the sequencing facilities thereby introducing the need for data-transportation to the place of analysis. The use of internet transfer would greatly facilitate the process, however since NGS data is considered to be personal sensitive information the handling of the data is highly regulated by the General Data Protection Regulation(GDPR). During this project, a web-based application was developed for the privacy-protecting transfer of personal sensitive data, implementing an in-motion encryption scheme which ensures data integrity and authenticity. The application consists of three scripts: the HTML web page with JavaScript functionality, a PHP script responsible for connection establishment and integrity verification, and a Python script executing the majority of the server-side operations. The resulting application uses the symmetric encryption algorithm AES in GCM mode, using a key size of 128 bits and transfers 60 Kibibytes of the file at a time. The key is established by using the asymmetric RSA encryption scheme with a 4096 bit key pair. SHA-256 is used for verifying the integrity of the transferred files. The JavaScript encryption speed is 584 MB/s and the Python decryption speed 251 MB/s. While the focus of the project was to optimize the application for NGS data, it is not limited to this type of file and can transfer different formats, enabling the use in multiple different fields.

Hepatitis B Virus (HBV) is a DNA virus and belongs to the genus Orthohepadnavirus of the Hepadnaviridae family which represents one of two animal viruses with a DNA genome which replicates by reverse transcription of a viral RNA intermediate. Nucleotide variation led to further sub-classification into 8 genotypes (A to H). The reverse transcription step within its life cycle is prone to the introduction of errors and recombination when dually infected. This leads to a viral quasispecies which forms during the course of infection with many minor population variants; such variants can however only be detected by means of ultra-deep sequencing. A recent study in the Department of Medical Virology (UP) by Mayaphi et al. identified a number of the specimens that partitioned away from the typical subgenotype A1 clades with high bootstrap values and longer branch lengths. Thus, the main objective of the current study was to characterize the full genome of all variants for the outliers observed in the aforementioned study, inclusive of potential recombination, dual infection and minor populations. Twenty samples were selected from a previous cohort for purposes of the present study. The viral DNA was extracted and amplified by PCR according to the methods described by Günther et al. with modified primer sets. Nineteen of the samples were successfully amplified and 15 of these were sequenced. Specimens were sequenced by NGS on the Illumina MiSeq™ sequencer and sequence data used to reconstruct the viral quasispecies of each specimen. Further analyses of the reconstructed variants included molecular characterization as well as phylogenetic analysis and screening for recombination and drug resistance mutations. Full genome coverage was obtained for twelve of the fifteen samples and full genome variants reconstructed, generating nearly 40 full genomes. Phylogenetic analysis showed that the majority of the samples are of genotype A, more specifically of subgenotype A1, differing by less than 4% from known sequences. The phylogenetic analysis revealed a similar clade of outliers, where four samples clustered together with significant bootstrap support (75%) and a fifth sample partitioned separate from, yet close to, this clade, away from the typical African A1 clade. This clade was assigned to genogroup III. Three samples were of the Asian A1 clade (genogroup I) with remaining specimens grouping within genotype D and E. The variants showed low diversity within each specimen with some differing at but a few positions across the genome while even the most diverse quasispecies differed by less than a percentage (32 positions). Several unique and atypical positional variations were observed amongst study samples of which some were present in but one of the variants for that sample. Twenty-six lead to shared amino acid changes. Some observed changes, such as A1762T/G1764A and G1896A, could explain the serological patterns such as HBeAg negativity while others, such as C2002T, were previously implicated in disease progression and severity. Sample N199 presented a longer branch length and revealed short regions within the genome that display evidence of recombination between HBV/A1 and HBV/A2. The results illustrate the utility of NGS technology in characterizing viral variants. / Dissertation (MSc)--University of Pretoria, 2014. / lk2014 / Medical Virology / MSc / Unrestricted

High-throughput next-generation sequencing techniques have hugely decreased the cost and increased the speed of sequencing, resulting in an explosion of sequencing data. This motivates the development of high-efficiency sequence alignment algorithms. In this thesis, I present multiple bit-parallel and Single Instruction Multiple Data (SIMD) algorithms that greatly accelerate the processing of biological sequences. The first chapter describes the BitPAl bit-parallel algorithms for global alignment with general integer scoring, which assigns integer weights for match, mismatch, and insertion/deletion. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations. Bit-parallelism has previously been applied to other pattern matching problems, producing fast algorithms. In timed tests, we show that BitPAl runs 7 - 25 times faster than a standard iterative algorithm. The second part involves two approaches to alignment with substitution scoring, which assigns a potentially different substitution weight to every pair of alphabet characters, better representing the relative rates of different mutations. The first approach extends the existing BitPAl method. The second approach is a new SIMD algorithm that uses partial sums of adjacent score differences. I present a simple partial sum method as well as one that uses parallel scan for additional acceleration. Results demonstrate that these algorithms are significantly faster than existing SIMD dynamic programming algorithms. Finally, I describe two extensions to the partial sums algorithm. The first adds support for affine gap penalty scoring. Affine gap scoring represents the biological likelihood that it is more likely for gaps to be continuous than to be distributed throughout a region by introducing a gap opening penalty and a gap extension penalty. The second extension is an algorithm that uses the partial sums method to calculate the tandem alignment of a pattern against a text sequence using a single pattern copy. Next generation sequencing data provides a wealth of information to researchers. Extracting that information in a timely manner increases the utility and practicality of sequence analysis algorithms. This thesis presents a family of algorithms which provide alignment scores in less time than previous algorithms.

Aujourd’hui, le marché des services est devenu de plus en plus concurrentiel. Les exigences des clients pour des offres de service en adéquation avec leurs usages et leurs préférences conduisent les fournisseurs à proposer de nouveaux services qui répondent à ce nouveau besoin pour se démarquer des concurrents et attirer de nouveaux clients. Avec la convergence des réseaux et celle des services de nouvelle génération (NGN/NGS), de nouveaux services sont apparus. Les utilisateurs sont nomades et veulent utiliser leurs services de différentes manières n’importe où, n’importe quand et par n’importe quel type de terminal, et cela avec une continuité de service et une qualité de service de bout en bout. Ainsi, fournir des services personnalisés aux clients dans un environnement hétérogène et mobile devient un challenge pour les opérateurs et les fournisseurs de service pour améliorer le retour sur investissement (ROI) et le délai de mise sur le marché (TTM). Nos réflexions à propos de la fourniture des services personnalisés selon les besoins fonctionnels et non-fonctionnels (QoS) des usagers, nous ont conduits à identifier les besoins du nouveau contexte NGN/NGS défini par l’intersection de ces trois éléments «user-centric, mobilité et QoS». Comment piloter dynamiquement la QoS de bout en bout pour une session unique «user-centric»? Comment assurer le « service Delivery» dans un contexte de mobilité et d’ubiquité? Ces nouveaux besoins, nous ont motivé à proposer des solutions à travers trois contributions principales qui prennent en considération la vision utilisateur et opérateur. Notre première contribution porte sur le modèle organisationnel. Nous proposons une nouvelle organisation avec un maximum de flexibilité, d’adaptabilité et d’autogestion, qui permet de piloter la QoS à chaque niveau de l’architecture (équipement, réseau et service). Dans cette organisation nous avons défini des acteurs et le rôle que joue chacun d’eux par rapport à la prise de décision au cours de la session de l’utilisateur, et cela pour maintenir la QoS de bout en bout dans un environnement qui est totalement hétérogène et mobile.Notre deuxième contribution traite du composant de service autonomique. Avec la complexité de la personnalisation des services dans un contexte hétérogène et mobile et le besoin de satisfaire la QoS de bout en bout, les ressources services doivent être prises en compte au même titre que les ressources réseaux. Donc, un degré élevé d’autosuffisance, d’autogestion et d’automatisation est demandé dans la ressource service (composant de service) pour améliorer le service delivery. Pour cela, nous proposons un composant de service autonomique «ASC: Autonomic Service Component» basé sur un agent de QoS intégré qui s’autocontrôle et s’autogère pour adapter dynamiquement ses ressources en réponse à un changement de situations au cours de la session de l’utilisateur. Notre troisième proposition couvre le modèle protocolaire. La session de services personnalisés nécessite des interactions plus flexibles au niveau service pour avoir une session unique avec une continuité de service. Nous proposons un protocole de signalisation SIP+ qui permet la négociation de la QOS des services personnalisés dès la phase d’initialisation de la session et de la renégociation de la QoS pendant l’usage, pour maintenir le service avec la QoS requise à travers une session unique.De façon plus concrète, nous présentons nos expérimentations à travers un scenario et une plate-forme de démonstration qui nous permet de tester la faisabilité et la performance de nos contributions. Les apports et les perspectives de cette thèse sont consignés en conclusion. / Nowadays, the services market has become increasingly competitive. Customer requirements for service offerings in line with their uses and preferences led providers to offer new services to meet this new need and to stand out from competitors and attract new customers. With the success of the network and service convergence (NGN / NGS), new services have emerged. A mobile user desires to access his services anywhere, anytime and on any type of terminal.Thus, providing customized services to clients while ensuring the service continuity and the end-to-end quality of service in a heterogeneous and mobile environment became a challenge for mobile operators and service providers to improve the return on investment (ROI) and time-to-market (TTM). Our thinking about the provision of customized services according to the functional and non-functional (QoS) needs of the users has led us to identify the needs of the new context NGN / NGS defined by the intersection of these three elements "user-centric, mobility and QoS". How to dynamically control the end-to-end QoS for a single "user-centric" session? How to ensure the "Service Delivery" in the context of mobility and ubiquity? These new needs have led us to propose solutions through three main contributions that take into account the user and the operator vision. Our first contribution concerns the organizational model. We have proposed a new organization with a maximum of flexibility, adaptability and self-management which allows the control of the QoS at each level of the architecture (equipment, network and service). In this organization, we have defined actors and the role of each one in relation to the decision-making process during the user session in order to maintain the end-to-end QoS in an environment that is totally heterogeneous and mobile. Our second contribution addresses the autonomic service component. With the complexity of services personalization in a heterogeneous and mobile context and the need to satisfy the end to end QoS, services and network resources must be taken into account. Therefore, a high degree of self-sufficiency, self-management and automation is required in the resource service to improve the service delivery. We have therefore proposed an autonomic service component based on an integrated QoS-agent which is self-controlled and self-managed to dynamically adapt its resources in response to changing situations during the user’s session. Our third proposal covers the model protocol. The personalized services session requires more flexible interactions at the service level in order to obtain a single session with service continuity. We have proposed a signalling protocol SIP + that allows the negotiation of the QoS of personalized services at the session initialization phase and the renegotiation of the QoS during the utilization to maintain the service with the required QoS through a unique session. More concretely, we have presented our experiments through a scenario and demonstration platform that allows us to test the feasibility and the performance of our contributions. The contributions and perspectives of this thesis are stated in the conclusion.

De nos jours, l'avènement de la dérégulation et l'ouverture à la concurrence stimulent les fournisseurs de services à être de plus en plus compétitifs et à attirer de plus en plus d'abonnés afin de faire face aux fortes pressions du marché. Pour ce faire, les fournisseurs d'aujourd'hui favorisent une approche user-centric qui consiste à fournir le plus rapidement possible des services orientés utilisateurs. Cette approche user-centric gagne de plus en plus d'ampleur suite à l'émergence du contexte de nouvelle génération de réseaux et de services (NGN/NGS). Dans ce contexte où les convergences de réseaux et de services sont omniprésentes, l'utilisateur devient de plus en plus nomade et il réclame l'accès à n'importe quel service, n'importe où, n'importe quand et par n'importe quel moyen. Son but est de composer dynamiquement une session personnalisée de services, dans laquelle converge un ensemble de services multi-domaines (Telco, Web et IT). Ensuite, il désire maintenir la continuité de cette session de services tout au long de sa mobilité spatiale et temporelle. Dans le cadre de cette thèse, nous proposons une nouvelle architecture de services, dénommée NGN/NGS Middleware qui suit une approche horizontale distribuée évènementielle et orientée service, et qui s'appuie sur un nouveau modèle de services. De plus, nous proposons deux solutions de gestion de la continuité de services, basées sur des communautés virtuelles et sur un handover sémantique. Ces solutions tiennent compte des préférences de l'utilisateur ainsi que de son contexte ambiant. Enfin, nous pensons apporter une réponse au monde du cloud en intégrant nos solutions pour gérer les utilisateurs du cloud. / Nowadays, with the advent of deregulation, service providers aim to be more competitive and to attract more subscribers in order to cope with the high market pressure. For this purpose, today's providers support a user-centric approach that consists on quickly providing user oriented services. This user-centric approach becomes more and more significant with the emergence of the next generation networks and services (NGN/NGS) context. Within this context, where network convergence and service convergence are omnipresent, the end-user becomes more nomadic and claims the access to any service, anywhere, anytime and by any means. His goal is to dynamically compose a personalized service session while converging a set of multi-domain services (Telco, Web and IT). Then, he wants to maintain the continuity of this service session throughout his spatial and temporal mobility. Within the scope of this thesis, we propose a novel service architecture, namely the NGN/NGS Middleware, that adopts an horizontal distributed event-driven and service oriented approachn and that is based on a novel service model. In addition, we propose two solutions for service continuity management, that are based on virtual communities and on a semantic handover. These solutions take into consideration the user's preferences and ambiant context. At the end, we think we could answer some cloud computing challenges by integrating our solutions to manage cloud users.

The North American genus Speyeria is an especially challenging radiation of butterflies due to ongoing hybridization, incomplete lineage sorting, and similar morphological characters among species. Adaptive radiations often require considerable evidence in order to resolve the evolutionary relationships of closely related individuals. Previous studies of this genus have found paraphyly among species and have been unable to disentangle these taxa due to a lack of data and/or incomplete sampling of the genus. As a result, the interspecific relationships among Speyeria remain unresolved. In an attempt to achieve phylogenetic resolution of the genus, we conducted population genomic and phylogenomic analyses of all North American Speyeria species, as well as several subspecies, based on genome wide markers using the SbfI restriction enzyme and restriction site associated DNA sequencing (RADseq). Together, our analyses recovered 16 species within Speyeria, validating previous taxonomic work. However, consistent with recent molecular analyses, internal relationships have poor support. This lack of resolution indicates Speyeria represent an ongoing adaptive radiation, with incomplete lineage sorting, hybridization, and lack of postzygotic reproductive barriers, supporting this hypothesis.