The genetic requirements for Influenza virus to infect and adapt to new species is largely unknown. To understand the evolutionary steps required by a virus to become virulent, a human virus (A/HK/1/68) (HK), avirulent in mice, was subjected to 20 and 21 serial lung-to-lung passages in mouse. Sequence analysis revealed the emergence of eleven mutations within the NS1 gene of the new virulent strains, many of which occurred in binding sites for transcriptional and translational cellular factors. In the present study we have rescued viruses containing each of the NS1 mouse adapted mutations onto A/PR/8/34 (PR8) backbone. We found 9 of 16 NS1 mutants were adaptive by inducing mortality, body weight loss in BALB/c mice and enhanced virus replication in MDCK cells with properties of host cell interferon transcription inhibition. Sequence comparisons with the highly pathogenic A/Hong Kong/156/1997 (H5N1) and the most severe pandemic A/Brevig Mission/1/1918 (H1N1) NS1 genes showed convergent evolution with some of the mouse adapted viruses for F103L plus M106I and V226I plus R227K mutations respectively. The F103L and M106I mutations in the HK NS1 gene were shown to be adaptive by assessment with respect to replication, early viral protein synthesis, interferon-β antagonism and tropism in the mouse lung. We extended the study and proved increased virulence associated with F103L+M106I mutations in their respective H5N1 NS1 gene on the PR8 and HK backbones, as well as the PR8 NS1 gene and the H9N2 (A/Ck/Bj/1/95) gene in the PR8 and A/WSN/33 backbones respectively. However the V226I and R227K mutations in their respective HK and 1918 NS1 genes slightly enhanced virulence and viral growth at later stages of infection. This study demonstrates that NS1 is a virulence factor; involved in multiple viral processes including interferon antagonism and viral protein synthesis. Furthermore, NS1 mutations acquired during mouse adaptation are proven to be adaptive in human, mouse and avian NS1 genes.

Purpose: This study asks whether active horizontal angular Vestibulo-Ocular Reflex (VOR) gain is capable of monocular adaptation after 4 hours of wearing 10 dioptres (D) of induced anisometropia in healthy human adults. Method: The participants (average age 28 years) wore a contact lenses/spectacles combination for 4 hours. The power of the spectacle was +5. 00D (magnified images 8. 65%) in front of the right eye and ?5. 00D (minified images 5. 48%) for the left eye, while the power of the contact lenses was equal to the subjects? habitual correction, summed with the opposite power of the spectacle lens. Eye and head position data was collected in complete darkness, in one-minute trials before adaptation and every 30 minutes for 2 hours after adaptation. Eye and head position data obtained using a video-based eye tracking system, was analyzed offline using Fast Fourier Transform in MATHCADTM 11. 1 software to calculate VOR gain. The VOR gain was compared between the right eyes and left eyes for the trials before and after adaptation. Results: In the first post-adaptation trial, a significant decrease in VOR gain (? 6%) occurred in the left eye in response to the miniaturizing lens. The right eye VOR gain did not show a significant change in the first post-adaptation trial (?2% decrease). During the remaining trials in the 2 hour follow-up time, both eyes showed a significant decrease compared to the baseline trial. This might indicate habituation of the VOR from repeated testing, or fatigue. Conclusion: There was monocular adaptation of VOR in response to the combined contact lenses/spectacles, but it was not complete and it was not as we expected. However, trying different amounts of anisometropia in one or two directions, a longer adaptation period (more than 4 hours) or monitoring the gain for more than 2 hours after adaptation with a longer separation between trials, might show different results.

This thesis discusses the challenges and opportunities facing the field of accessibility, particularly as computing becomes ubiquitous. It is argued that a new approach is needed that centres around adaptations (specific, atomic changes) to user interfaces and content in order to improve their accessibility for a wider range of people than targeted by present Assistive Technologies (ATs). Further, the approach must take into consideration the capabilities of people at the human level and facilitate collaboration, in planned and ad-hoc environments. There are two main areas of focus: (1) helping people experiencing minor-to-moderate, transient and potentially-overlapping impairments, as may be brought about by the ageing process and (2) supporting collaboration between people by reasoning about the consequences, from different users perspectives, of the adaptations they may require. A theoretical basis for describing these problems and a reasoning process for the semi-automatic application of adaptations is developed. Impairments caused by the environment in which a device is being used are considered. Adaptations are drawn from other research and industry artefacts. Mechanical testing is carried out on key areas of the reasoning process, demonstrating fitness for purpose. Several fundamental techniques to extend the reasoning process in order to take temporal factors (such as fluctuating user and device capabilities) into account are broadly described. These are proposed to be feasible, though inherently bring compromises (which are defined) in interaction stability and the needs of different actors (user, device, target level of accessibility). This technical work forms the basis of the contribution of one work-package of the Sustaining ICT use to promote autonomy (Sus-IT) project, under the New Dynamics of Ageing (NDA) programme of research in the UK. Test designs for larger-scale assessment of the system with real-world participants are given. The wider Sus-IT project provides social motivations and informed design decisions for this work and is carrying out longitudinal acceptance testing of the processes developed here.

The New World Junonia butterflies include well-studied model organisms yet their phylogeny remains unresolved by traditional cox1 DNA barcodes. Sixteen Junonia mitochondrial genomes were sequenced using next generation MiSeq technology. Junonia lemonias, an Old World species, has mitochondrial genome features typical of Ditrysian Lepidoptera, and synteny is maintained throughout Junonia. Analysis of Junonia mitogenomes produced a robust phylogeny that was used with biogeographic information to infer that Junonia crossed the Pacific Ocean to invade the New World on 3 separate occasions. Junonia vestina, a high elevation species from the Andes Mountains, shows high altitude adaptation in the mitochondrial protein coding loci atp6, atp8, cox1, cob, nad1, and nad2, with the strongest effects seen in cox1 and nad1. There is some overlap between these genes with human loci that have disease associations with the same amino acid positions which could help elucidate the function of high elevation mutations in J. vestina. / February 2016

Biologists have taken the concept of organism largely for granted. However, advances in the study of chimerism, symbiosis, bacterial-eukaryote associations, and microbial behavior have prompted a redefinition of organisms as biological entities exhibiting low conflict and high cooperation among their parts. This expanded view identifies organisms in evolutionary time. However, the ecological processes, mechanisms, and traits that drive the formation of organisms remain poorly understood. Recognizing that organismality can be context dependent, we advocate elucidating the ecological contexts under which entities do or do not act as organisms. Here we develop a "contextual organismality" framework and provide examples of entities, such as honey bee colonies, tumors, and bacterial swarms, that can act as organisms under specific life history, resource, or other ecological circumstances. We suggest that context dependence may be a stepping stone to the development of increased organismal unification, as the most integrated biological entities generally show little context dependence. Recognizing that organismality is contextual can identify common patterns and testable hypotheses across different entities. The contextual organismality framework can illuminate timeless as well as pressing issues in biology, including topics as disparate as cancer emergence, genomic conflict, evolution of symbiosis, and the role of the microbiota in impacting host phenotype.

Master of Science / Department of Computing and Information Sciences / Doina Caragea / Machine learning is the subfield of Artificial intelligence that gives computers the ability to learn without being explicitly programmed, as it was defined by Arthur Samuel - the American pioneer in the field of computer gaming and artificial intelligence who was born in Emporia, Kansas. Supervised Machine Learning is focused on building predictive models given labeled training data. Data may come from a variety of sources, for instance, social media networks. In our research, we use Twitter data, specifically, user-generated tweets about disasters such as floods, hurricanes, terrorist attacks, etc., to build classifiers that could help disaster management teams identify useful information. A supervised classifier trained on data (training data) from a particular domain (i.e. disaster) is expected to give accurate predictions on unseen data (testing data) from the same domain, assuming that the training and test data have similar characteristics. Labeled data is not easily available for a current target disaster. However, labeled data from a prior source disaster is presumably available, and can be used to learn a supervised classifier for the target disaster. Unfortunately, the source disaster data and the target disaster data may not share the same characteristics, and the classifier learned from the source may not perform well on the target. Domain adaptation techniques, which use unlabeled target data in addition to labeled source data, can be used to address this problem. We study single-source and multi-source domain adaptation techniques, using Nave Bayes classifier. Experimental results on Twitter datasets corresponding to six disasters show that domain adaptation techniques improve the overall performance as compared to basic supervised learning classifiers. Domain adaptation is crucial for many machine learning applications, as it enables the use of unlabeled data in domains where labeled data is not available.

No description available.

With increasing awareness of the potential impacts posed by climate change, many ports and their surrounding regions have undertaken adaptation planning and proactive actions so as to build a resilient and sustained business. However, most of them are still at the embryonic stage in understanding the problem and find it very challenging regarding adaptation planning and implementation. This thesis addresses the current issue in adaptation to climate change impacts at ports, regions and supply chains through quantitative and qualitative analyses. A global survey is designed to investigate port decision-makers’ perceptions and knowledge about climate change adaption. It explores the existing impacts posed by sea level rise (SLR), and high winds and storms, and demonstrates the potential impacts of adaptation measures. Analytical results suggest that, despite the forecast of more serious impacts posed by these climate change risks in the near future, port decision-makers still have strong doubts about the effectiveness of adaptation measures and planning. In-depth interviews in a case study on Port Metro Vancouver (Canada) are conducted to further investigate the barriers (especially institutional ones) that hinder the process of climate change adaptation, and thus calls attention for its regional efforts. Based on the literature review and analysis, this study argues that a paradigm shift in adaptation planning, notably from ‘go it alone’ to ‘collaborative’ approach involving all major port stakeholders, is urgently needed. The thesis also highlights the pivotal role of tailor-made adaptation methods in accordance with a specific climate change risk in the adaptation planning. Besides, two innovative, ‘paradigm shift’ recommendations are proposed to climate adaptation planning: (1) a method based on usage unit to allocate investment responsibility; and (2) the establishment of a neutral agency (e.g., a collaborative network) with the power to promote the adaptation process. In addition, a flexible combination of engagement in collaborative projects and individual efforts for ports is suggested so as to implement adaptation works. / October 2016

The purpose of this report was to investigate how municipals in the county of Västra Götaland work with climate adaptation of storm water management and to identify problems that occur in the work. As with the rest of the world, Sweden will be affected by expected climate changes and it is therefore important that Swedish municipalities work with climate adaptation and to help them make the work manageable. The method used was semi-structural qualitative interviews where 13 municipalities were interviewed in April 2016. The result of the interviews shows that there is an ambition to work with climate adaptation of storm water management but that there are different problems associated with the work that have made it difficult to start. 69% of the municipalities include climate adaptation to some extent when they work with master plans and 5 out of 8 municipalities are or will be including climate adaptation strategies in their storm water management document. A majority of the municipalities don’t prioritize climate adaptation and could be doing more to include climate adaptation in their work. The most common problems reported by the municipalities were too little resources/lack of finance, undecided responsibility and not clear enough laws regarding the subject.

Bakgrund: Cancer är ett hälsoproblem som är stort över hela världen och mer än var tredje person riskerar att bli drabbad under sin livstid. Varje år ökar antalet människor som drabbas av cancer, men även överlevnaden ökar. Syfte: Att beskriva hur vuxna personer med obotlig cancersjukdom hanterar sin livssituation med hjälp av coping strategier vid livets slutskede samt metodologiskt granska hur undersökningsgrupp och urvalsmetod är beskrivet i granskade artiklar. Metod: En litteraturstudie med deskriptiv design som baserades på 10 artiklar med både kvalitativ och kvantitativ ansats. Artiklarna hittades i databasen Pubmed. Huvudresultat: Familj, vänner och trosuppfattning var viktiga källor för att personer med obotlig cancer sjukdom skulle kunna hantera faktumet att livets slut var nära. Socialt stöd och religiös tro var nyckelkomponenterna för att personer som levde sin sista tid i livet skulle klara av att hantera sin livssituation, antingen genom att finna en mening i den pågående situationen eller genom stöd från sina nära och kära. Resultatet baserades på fyra kvantitativa artiklar och sex kvalitativa artiklar. I granskningen av de ingående artiklarnas datainsamlingsmetod framkom både urvalsmetod och undersökningsgrupp. I studierna förekommer semistrukturerade intervjuer, strukturerade intervjuer och enkäter. Slutsats: Coping strategier i form av socialt stöd och religiöst stöd var nyckelkomponenter för att personer med obotlig cancersjukdom skulle klara av att hantera sin sista tid i livet. Personerna såg olika på komponenterna, vilka coping strategier de använde och vilka som fungerade, men även vilket stöd som var av betydelse. De flesta personerna upplevde att stöd från familj och anhöriga var viktigt för att kunna hantera livets slutskede, men likaså stödet från en religiös bakgrund. / Background: Cancer is a major health problem worldwide and more than every third person has got the risk to get cancer during their lifetime. The number of people getting diagnosed with cancer is increasing, but the survival rate is increasing as well. Aim: To describe how adults with incurable cancer manage their lives with the help of coping strategies at the end of life as well as methodologically review how the selection of the study group and the selection method in the reviewed articles were described. Method: A literature study with a descriptive design based on ten articles with both qualitative and quantitative approach. The articles were found in the database PubMed. Findings: Family, friends and religious beliefs were important sources for people with terminally ill cancer to cope with the fact that life was about to come to an end. Social support and religious beliefs were the main important facts for the people who were facing end of life to be able to cope with their situation, either trying to find meaning in the current situation or through support from loved ones. The findings were based on four quantitave articles and six qualitative articles. The selection of the study group and the selection method in the reviewed articles were described in each article. The data collection methods that the included articles used were semistructed interwievs, unstructed interwievs and surveys. Conclusion: Coping strategies as in social support and religious support were the main facts for people to cope with end of life. People had different views on both of the facts, which coping strategies they used and which ones that worked, but also what kind of support that was more important. Most of the people felt that support from family and friends were important to have so that they could cope with the end of life, but religious support was just as much important.