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

Bakgrund Akutmottagningen är en central punkt i hälso- och sjukvården och där sker en ständig samverkan med andra vårdenheter så som ambulansen. Sjuksköterskor som arbetar inom akutsjukvården behöver kompetens som innefattar avancerade kliniska färdigheter, förmåga att skapa ett helhetsgrepp i en akut situation och medicinska kunskaper. Enligt tidigare studier framkommer anhörigas behov av information, kommunikation och bemötande inom akutsjukvården. Sjuksköterskan bör eftersträva ett partnerskap med övriga professioner samt patient och anhöriga inom akutsjukvården. Syfte Syftet med litteraturstudien är att beskriva sjuksköterskors upplevelser av när anhöriga är delaktiga i det akuta omhändertagandet prehospitalt och på akutmottagning. Metod Examensarbetet har genomförts som en strukturerad litteraturstudie med inslag av den metodologi som används vid systematiska översikter. I litteraturstudien har kvalitativa orginalstudier inkluderats Resultat Från analysen identifieras två tydliga huvudkategorier; sjuksköterskors positiva och negativa upplevelser av delaktiga anhöriga i det akuta omhändertagandet. Orealistiska förväntningar, kommunikationshinder, exkludering av anhöriga, tidskrävande, en potentiell ojämlik omvårdnad, informationsutbyte och tidssparande, integrerat partnerskap, närvaro av anhöriga skapar en bättre omvårdnad och det känslomässiga utbytet var underkategorier som identifierades. Sjuksköterskor såg det som positivt när anhöriga deltog och kunde förmedla information kring patienten, samtidigt fanns negativa upplevelser kring att anhöriga förmedlade irrelevant information. Slutsats Sjuksköterskors upplevelser av delaktiga anhöriga skiljer sig åt. Både fördelar och nackdelar med anhörigas närvaro beroende på hur den akuta situationen ser ut framkom. Upplevelserna är individuella och skulle kunna bero på olika personlighetstyper hos sjuksköterskor / Background The emergency department is a central point in the health care system and there is a constant collaboration with other units such as the ambulance. Nurses working in emergency care need skills that include advanced clinical skills, the ability to create a holistic approach to an emergency situation and medical knowledge. According to previous studies, relatives need for information, communication and treatment in emergency care emerge. The nurse should strive for a partnership with other professions as well as the patient and relatives in the emergency care. Aim The aim of the literature study is to describe nurses’ experiences of when relatives areinvolved in the acute care prehospitalt and in the emergency department.MethodThe degree project has been carried out as a structured literature study whit elements ofthe methodology used in systematic reviews. Qualitative original studies have beenincluded in the literature study.ResultsFrom the analysis two clear main categories were identified; nurses` positive and negativeexperiences of participating relatives in the emergency care.: Unrealistic expectations,communication barriers, exclusion of relatives, time consuming, a potentially unequalcare, information exchange and time saving, integrated partnership, presence of relatives creates better care and the exchange were subcategories that were identified. Nurses saw it as positive when relatives participated and were able to convey information about the patient, at the same time there were negative experience about relatives conveying irrelevant information. Conclusions Nurses´ experiences of participating relatives differ. Both advantages and disadvantages of the presence of relatives depending on what the emergency situation looks like emerged. The experiences are individual and could depend on different personality types of nurses.

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.

Bakgrund: Palliativ vård syftar till att förbättra livskvaliteten för patienter och närstående genom förebyggande och lindring av lidandet i ett tidigt skede vid livshotande sjukdomar. Patienter inom palliativ vård har ofta närstående omkring sig vilket är de närmaste personerna i patientens umgänge. Närstående har en viktig betydelse för patientens mående och välbefinnande och de har därav en viktig roll inom vården. Att vara närstående till en palliativ patient kan ha olika inverkan på närstående. Närstående blir ofta själva drabbade på något vis av att befinna sig i denna situation.  Syfte: Syftet var att beskriva närståendes upplevelser i samband med palliativ vård. Metod: En litteraturöversikt valdes som metod. Elva vetenskapliga originalartiklar inkluderades i resultatet, varav tio var av kvalitativ metod och en var mixad metod. Författarna använde sig av Fribergs (2017) tillvägagångssätt under analysförfarandet.  Resultat: Tre huvudteman med åtta underteman identifierades i resultatet; Sista tiden tillsammans med subtemana; Meningsskapande och kvalitetstid samt Närvaro vid dödstillfället. Det andra huvudtemat är Känslor i samband med palliativ vårdmed subtemana; Skuld och åsidosättning, Stöd i sorghanteringensamt Efter patientens bortgång. Det sista huvudtemat består av Mötet med vårdpersonal med subtemana; Delaktighet och bekräftelse, Oro och maktlöshet ochKommunikation och information. Diskussion: I metoddiskussionen behandlas författarnas samarbete och gjorda överväganden i arbetet tillsammans med arbetets styrkor och svagheter. Resultatdiskussionen tar upp stöd och sorg som kopplats till Erikssons caritativa teori. Resultatet diskuteras även mot bakgrunden samt ny forskning där författarna även tar upp kulturella och religiösa aspekter på palliativ vård. / Background: Palliative care aims to improve the patients and the next of kin’s quality of life, through prevention and relief of suffering at an early stage in life-threatening sickness. Patients in palliative care are often surrounded by next of kin’s, which are the closest persons in the patient’s relations. Next of kin have a great importance for the patient's mood and well-being, thus they have an important role in nursing. To be a next of kin to a patient in palliative care can impact the next of kin in different ways. The next of kin often becomes affected in some way by being in this situation.  Aim: The aim of this study was to describe next of kin’s experiences in conjunction with palliative care. Method: The chosen method for this essay was a literature review. Eleven scientific articles were included in the result of the essay, ten which was of qualitative method, and one of mixed method. The authors used Friberg’s (2017) approach during the analysis procedure. Results: Three main themes with eight subthemes were identified in the result; The last time together with the subthemes;Meaning and quality timeand Presence at the time of death. The second main theme is; Feelings in conjunction with palliative care with the subthemes; Guilt and putting aside own needs, Support in grief management and After the patient passed away. The final main theme consists of the Meeting with health professionalswith the subthemes; Participation and affirmation, Worry and powerless andCommunication and information. Discussion: The method discussion presents the authors work procedure and their considerations along with strengths and weaknesses of the essay. The results discussion procures support and guilt related to the caritative theory of Eriksson, as well as traditional and religious aspects of palliative care.

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 aim of this study is to report selected perceptions and attitudes of adolescents placed in the “attention home” at Hood River, Oregon, as an early aid towards improved understanding and treatment, and program assessment.

Bakgrund: Möten med anhöriga ingår i sjuksköterskans dagliga arbete inom slutenvården och plötslig död är något som kan inträffa på alla vårdavdelningar. Syfte: Syftet med litteraturöversikten var att sammanställa sjusköterskors upplevelser av att möta anhöriga till patienter som drabbats av plötslig död inom slutenvården. Metod: Litteraturöversikten genomfördes med kvalitativ ansats och baserades på 10 vetenskapliga studier. Databassökningar gjordes i CINAHL och PubMed. Resultat: Analysen av de utvalda studiernas resultat visade sjuksköterskors upplevda otrygghet i mötet med anhöriga som drabbats av plötslig förlust, svårigheter att hantera de egna känslorna relaterat till döden samt sjuksköterskornas upplevda betydelse av att etablera goda relationer med anhöriga för att kunna tillgodose deras omvårdnadsbehov. Konklusion: Det råder osäkerhet bland sjuksköterskor gällande möten och kommunikation med anjöriga till patienter som drabbats av plötslig död och många sjuksköterskor önskar mer stöd gällande den egna känslohanteringen i relation till mötet med dessa anhöriga. / Background: Encounters with the people having close relationships with patients occurs daily for nurses working in a hospital setting and sudden death is something that can arrive in any department of care. Aim: The aim of this litterature review was to assemble nurses´ experiences of caring for the suddenly bereaved. Method: The litterature review was conducted with a qualitative approach using Friberg´s method book (2017) and is based on 10 scientific studies collected from the two databases CINAHL and PubMed. Result: The analysis of the chosen studies showed how the nurses felt uncertain in the encounters with the suddenly bereaved, the struggle of dealing with their own emotions related to death and the nurses´ perceptions of the importance of establishing good relationships with the next of kin to be able to provide good care for them. Conclusion: There is a general feeling of uncertainty among nurses regarding the encounters with, and the communication with next of kin suffering from sudden loss. Many nurses need further emotional support regarding their own feelings in relation to the encounters with the suddensly bereaved next of kin.

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.

京都大学 / 0048 / 新制・課程博士 / 博士(理学) / 甲第18831号 / 理博第4089号 / 新制||理||1588(附属図書館) / 31782 / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 阿形 清和, 教授 緒方 博之, 教授 高田 彰二 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM