The International market of crude oil and natural gas is well established and very competitive. Knowledge about costs is important in helping to understand the current position of producers within the industry. In the eyes of the producers, the lower the costs the more profitable they will become given the price of crude. This thesis focuses on an economic analysis of crude oil exploration in Saskatchewan and Alberta. In a competitive market, the producers require estimates of finding costs in both regions. The public policies that are designed to encourage crude exploration also rely heavily on reliable estimates of these costs. The results show that Saskatchewans per-unit finding cost is significantly lower than Albertas in spite of the geological differences between the two provinces. The finding costs are estimated by using a methodology (Uhler 1979) that has been widely accepted within economic literature of non-renewable resources. The results support the hypothesis that finding costs in both regions are increasing and the argument that these costs will converge in the long-run, except for the last six years of the analysis.

Background: There is an unacceptable delay in diagnosis of axial Spondyloarthritis (axSpA) especially in its early stages among patients with inflammatory bowel disease (IBD). Objective: to develop a sensible and reliable questionnaire to identify undetected axSpA among IBD patients. Methods: Candidate items for the questionnaire were selected on 3 domains (IBD, inflammatory back symptoms, and extra-axial features). Sensibility of the Toronto axSpA Questionnaire (TASQ) was assessed leading to drafting 18 items. Test-retest reliability study was conducted among 77 patients with established IBD and axSpA and kappa agreement coefficients were calculated for items. Results: The TASQ was developed using multiple steps of sensibility assessment resulting in 16 items. Kappa coefficients ranged from 0.81 to 1.00 for all items indicating almost perfect agreement. Conclusion: TASQ is a newly developed, sensible and reliable questionnaire that should facilitate identification and referral of IBD patients to rheumatologists and should avoid delay in diagnosis of axSpA.

Background: There is an unacceptable delay in diagnosis of axial Spondyloarthritis (axSpA) especially in its early stages among patients with inflammatory bowel disease (IBD). Objective: to develop a sensible and reliable questionnaire to identify undetected axSpA among IBD patients. Methods: Candidate items for the questionnaire were selected on 3 domains (IBD, inflammatory back symptoms, and extra-axial features). Sensibility of the Toronto axSpA Questionnaire (TASQ) was assessed leading to drafting 18 items. Test-retest reliability study was conducted among 77 patients with established IBD and axSpA and kappa agreement coefficients were calculated for items. Results: The TASQ was developed using multiple steps of sensibility assessment resulting in 16 items. Kappa coefficients ranged from 0.81 to 1.00 for all items indicating almost perfect agreement. Conclusion: TASQ is a newly developed, sensible and reliable questionnaire that should facilitate identification and referral of IBD patients to rheumatologists and should avoid delay in diagnosis of axSpA.

Consensus pattern problem (CPP) aims at finding conserved regions, or motifs, in unaligned sequences. This problem is NP-hard under various scoring schemes. To solve this problem for protein sequences more efficiently,a new scoring scheme and a randomized algorithm based on substitution matrix are proposed here. Any practical solutions to a bioinformatics problem must observe twoprinciples: (1) the problem that it solves accurately describes the real problem; in CPP, this requires the scoring scheme be able to distinguisha real motif from background; (2) it provides an efficient algorithmto solve the mathematical problem. A key question in protein motif-finding is how to determine the motif length. One problem in EM algorithms to solve CPP is how to find good startingpoints to reach the global optimum. These two questions were both well addressed under this scoring scheme,which made the randomized algorithm both fast and accurate in practice. A software, COPIA (COnsensus Pattern Identification and Analysis),has been developed implementing this algorithm. Experiments using sequences from the von Willebrand factor (vWF)familyshowed that it worked well on finding multiple motifs and repeats. COPIA's ability to find repeats makes it also useful in illustrating the internal structures of multidomain proteins. Comparative studies using several groups of protein sequences demonstrated that COPIA performed better than the commonly used motif-finding programs.

Consensus pattern problem (CPP) aims at finding conserved regions, or motifs, in unaligned sequences. This problem is NP-hard under various scoring schemes. To solve this problem for protein sequences more efficiently,a new scoring scheme and a randomized algorithm based on substitution matrix are proposed here. Any practical solutions to a bioinformatics problem must observe twoprinciples: (1) the problem that it solves accurately describes the real problem; in CPP, this requires the scoring scheme be able to distinguisha real motif from background; (2) it provides an efficient algorithmto solve the mathematical problem. A key question in protein motif-finding is how to determine the motif length. One problem in EM algorithms to solve CPP is how to find good startingpoints to reach the global optimum. These two questions were both well addressed under this scoring scheme,which made the randomized algorithm both fast and accurate in practice. A software, COPIA (COnsensus Pattern Identification and Analysis),has been developed implementing this algorithm. Experiments using sequences from the von Willebrand factor (vWF)familyshowed that it worked well on finding multiple motifs and repeats. COPIA's ability to find repeats makes it also useful in illustrating the internal structures of multidomain proteins. Comparative studies using several groups of protein sequences demonstrated that COPIA performed better than the commonly used motif-finding programs.

The International market of crude oil and natural gas is well established and very competitive. Knowledge about costs is important in helping to understand the current position of producers within the industry. In the eyes of the producers, the lower the costs the more profitable they will become given the price of crude. This thesis focuses on an economic analysis of crude oil exploration in Saskatchewan and Alberta. In a competitive market, the producers require estimates of finding costs in both regions. The public policies that are designed to encourage crude exploration also rely heavily on reliable estimates of these costs. The results show that Saskatchewans per-unit finding cost is significantly lower than Albertas in spite of the geological differences between the two provinces. The finding costs are estimated by using a methodology (Uhler 1979) that has been widely accepted within economic literature of non-renewable resources. The results support the hypothesis that finding costs in both regions are increasing and the argument that these costs will converge in the long-run, except for the last six years of the analysis.

Bakgrund: Palliativ vård syftar till att lindra symtom vid livshotande sjukdom och innefattar en helhetsvård av patienten och dess familj samt en tydlig vårdfilosofi. Då arbetet rymmer en hög komplexitet och sjuksköterskan utsätts för emotionell påfrestning i mötet med sorg och död kan motivationen att stanna kvar i yrket komma att ifrågasättas.Syfte: Syftet är att beskriva sjuksköterskors upplevelser och hantering av svårigheter inom palliativ vård. Metod: En litteraturöversikt med analys av tio vetenskapliga artiklar har gjorts. Utifrån detta har två teman, upplevelser av svårigheter vid vård i livets slutskede samt hantering av svårigheter vid vård i livets slutskede framträtt med tre respektive fyra åtföljande kategorier.Resultat: Svårigheter blev framträdande i möten med patientlidande, död och sorg samt i anslutning till gränssättande. Meningsskapande var ett starkt motiv i sjuksköterskors val att stanna inom yrket och hantera de svårigheter som uppstod. Ett stödjande team och tidigare erfarenheter underlättade i arbetet med döende människor där de ansåg emotionell balans vara viktig att finna.Diskussion: Svårigheter och dess hantering är beroende av varandra. Meningsskapande bildar ett sammanhang genom ökad förståelse för svårigheter och går att härleda till KASAM komponenten begriplighet. Resurser för att möjliggöra meningsskapande bidrog med hanterbarhet. Det finns anledning att betrakta modellen 6S som ett redskap för sjuksköterskor i hanteringen av svårigheter inom vård i livets slut, då säkerställandet av en god död för patienten även ökar möjligheten till sjuksköterskors tillfredställelse i arbetet. / Background: The aim of palliative care is to alleviate symptoms that occur with life-threatening disease and involves a holistic care of the patient and family and a clear philosophy of care. As the work holds a high complexity and the nurse is exposed to emotional strain in the meeting with bereavement and death, the motivation to stay in the profession can be compromised.Aim: The aim of this study is to describe nurse’s experiences and management of difficulties in palliative care. Method: A literature overview containing an analysis of ten scientific articles has been done. Out of this two head themes emerged, experiences of difficulties in end of life care and managing difficulties in end of life care. Three and four subcategories came out of the two head themes.Result: Difficulties were prominent in the meeting with patient suffering, death and bereavement and in accession to limit setting. Finding meaning where a strong motive to nurses choice to stay in the profession and managing difficulties that occurred. A supportive team and past experiences facilitated the work with dying people where finding an emotional balance were important.Discussion: Difficulties and its management is interdependent. Finding meaning create coherence through increased understanding towards difficulties and is possible to trace to the component comprehensibility in Sense Of Coherence (SOC). The resources to enable finding meaning contributed to manageability. There is reason to consider the model of 6S as a tool for nurses in the management of difficulties in end of life care, since ensuring of a good death increases the possibility of work satisfaction for the nurses.

This thesis presents novel methods for analysis of short viral sequences and identifying biologically significant regions based on their statistical properties. The first section of this thesis describes the ab initio method for identifying genes in viral genomes of varying type, shape and size. This method uses statistical models of the viral protein-coding and non-coding regions. We have created an interactive database summarizing the results of the application of this method to viral genomes currently available in GenBank. This database, called VIOLIN, provides an access to the genes identified for each viral genome, allows for further analysis of these gene sequences and the translated proteins, and displays graphically the distribution of protein-coding potential in a viral genome. The next two sections of this thesis describe individual projects for two specific viral genomes analyzed with the new method. The first project was devoted to the recently sequenced Herpes B virus from Rhesus macaque. This genome was initially thought to lack an ortholog of the gamma-34.5 gene encoding for a neurovirulence factor necessary for viability of the two close relatives, human herpes simplex viruses 1 and 2. The genome of Rhesus macaque Herpes B virus was annotated using the new gene finding procedure and an in-depth analysis was conducted to find a gamma-34.5 ortholog using a variety of tools for a similarity search. A profound similarity in codon usage between B virus and its host was also identified, despite the large difference in their GC contents (74% and 51%, respectively). The last thesis section describes the analysis of the Mouse Cytomegalovirus (MCMV) genome by the combination of methods such as sequence segmentation, gene finding and protein identification by mass spectrometry. The MCMV genome is a challenging subject for statistical sequence analysis due to the heterogeneity of its protein coding regions. Therefore the MCMV genome was segmented based on its nucleotide composition and then each segment was considered independently. A thorough analysis was conducted to identify previously unnoticed genes, incorrectly annotated genes and potential sequence errors causing frameshifts. All the findings were then corroborated by the mass spectrometry analysis.

Navigation of a group of autonomous agents that are needed to maintain a formation is a challenging task which has not been studied much in especially 3-D terrains. This thesis presents a novel approach to collision free path finding of multiple agents preserving a predefined formation in a 3-D terrain. The proposed method could be used in many areas like navigation of semi-automated forces (SAF) at unit level in military simulations and non player characters (NPC) in computer games. The proposed path finding algorithm first computes an optimal path from an initial point to a target point after analyzing the 3-D terrain data from which it constructs a weighted graph. Then, it employs a real-time path finding algorithm specifically designed to realize the navigation of the group from one way point to the successive one on the optimal path generated at the previous stage, preserving the formation and avoiding collision both. A software was developed to test the methods discussed here.

The aim of the current study was to test the effectiveness of the written disclosure paradigm on psychological health, cognitive processing, dispositional and social factors and to improve the paradigm on the basis of the underlying mechanisms responsible for its benefits. Participants consisting of 73 Middle East Technical University students were randomly assigned to one of three groups to write during 30-min sessions on 3 consecutive days: (1) Guided Disclosure Group (GDG) / (2) Standard Disclosure Group (SDG) / (3) Control Group (CG). GDG wrote about their most upsetting life events according to exposure, cognitive reappraisal, and benefit-finding instructions, respectively. SDG wrote about their deepest thoughts and feelings related to their most upsetting life events. CG described familiar environments without including any emotion or opinion. All participants completed measures of psychological health (i.e., general psychological distress symptoms), cognitive processing (i.e., intrusive thoughts, avoidance, and appraisal of the event), dispositional (i.e., trait anxiety, alexithymia, coping styles) and social factors (i.e., perceived social support, and severity of negative life events) prior to the first writing session, following the third writing session, and a 1-month follow-up. It was expected that GDG would report more improvements in outcome measures, relative to SDG. In turn, SDG was expected to display greater improvements, relative to CG. All groups reported similar improvements in psychological distress symptoms, cognitive processing and alexithymia. The findings were discussed in terms of relevant literature.