The similarities between psychosis and different mystical experiences are striking. Professor Jens-Ivar Nergård (1998, 2006) has pointed out similarities between the calling of the Sami shaman/nåjd and the state of psychosis and high-lights the reciprocal meanings andpurposes of these similarities in a Saami context where the calling and the called are regarded as meaningful for the community. By comparing what psychodynamic theorynames psychosis with the calling process of the nåjd the aim of this work is to investigatethe question of how the latter’s discourse finds individual and contextual purpose andmeaning in the psychological functions leading to the former. Since this comparison andinvestigation concerns two different ontologies and discourses, with their own conceptsand views on the psychological functions mentioned, it is done in a qualitative comparativemethod of discourse analysis.The psychodynamic discourse through the books of professor Johan Cullberg classifiespsychosis as a psychological regression to a more primitive psychological state in whichthe individual is caught in primary process thoughts; characterized by dilutions, hallucinations and magical thinking. The psychodynamic discourse sees no contextual, and verylittle individual, meaning or purpose with these functions. This theory is what I will compare to the material given by primarily Jens-Ivar Nergård from a Saami discourse.What I find in the discourse material is an ontology - simultaneously psychological, spiritual, practical and religious (hence the interest from the perspective of psychology of religion) – which differs from the ontology of the psychodynamic discourse in crucial ways.In the Saami discourse the individual experiencing what the theory would name hallucinations, dilutions or psychosis is never disconnected from his or her community and contextbut is instead seen as an important and strong bringer of insights and knowledge. This isconnected to the ontology mentioned above in which relating to - seeing, hearing and interacting with - non-human persons is viewed as a natural experience to understand andrelate to nature, the community, the past and present. The psychological functions in which these interactions take place are regarded as meaningful, significant and sacred.

This master's thesis deals with the creation of a tool for the extraction of methylation level from transposon sequences. Transposons are DNA elements with ability to move or copy themselves and their activity is regulated by DNA methylation. Sequence methylation information is stored in the bisulfite data and their processing is done with parts of two existing tools in a combination with implemented modules. Created tool takes into consideration unique challenges brought in the methylation calling process by transposable elements and it's functionality is presented on a set of experiments with simulated and real data.

Massive parallel sequencing (NGS) is useful in detecting and later classifying somatic driver mutations in cancer tumours. False-positive variants occur in the NGS workflow and they may be mistaken for low frequency somatic cancer mutations in a patient sample. This pushes the need for decreasing the noise rate in the NGS workflow since it may improve the detection of rare allele frequency variants, in particular cancer mutations. In this project, the aim was to reduce the level of false-positive variants in an NGS workflow. The scope was limited to looking at substitution errors and their neighbouring nucleotides. Alongside this, it was also a way to understand how different types of substitution errors are distributed in the data, if their frequencies are affected by neighbouring nucleotides and how data processing may affect these substitution rates. A bioinformatic pipeline was set up where a commercially available genomic DNA sample with known variants was subjected to different trimming and filtering settings. The goal was to reduce the substitution error rate as much as possible, without removing any true variants from the data. The optimised settings were trimming the sequencing reads with 5 bp from the tail and filtering sequencing reads that contained 5 or more substitutions. Three additional samples, whereof two were clinical and the third commercial, were tested with these settings. The results showed that in all samples, C:G>T:A substitutions were of a higher frequency compared to the rest of the substitution types. For all samples, A:T>C:G substitutions, where the neighbouring nucleotide was a C or a G on each side, had a higher frequency compared to A:T>C:G substitutions with other neighbouring nucleotides on both sides. Those substitution types were especially targeted by the trimming. For the two commercial samples, substitutions that resulted in the nucleotide combinations >XAA or >XTT were of a higher frequency compared to the same substitution types that did not result in those nucleotide combinations. Filtering reads with 5 or more substitutions particularly targeted these substitution types. Consequently, filtering had a greater effect on the commercial samples, compared to the clinical samples. Overall, trimming and filtering helped reduce transversions more than the transitions, increasing the transition/transversion ratio after processing the data. The results suggest that trimming and filtering can be a useful method to computationally reduce the transversion errors introduced in an NGS workflow, but transition errors to a lesser extent, in particular A:T>G:C transitions. To confirm these findings, more samples should be tested using this methodology. To better understand the effect of trimming and filtering on variant calling, the scope could in the future be expanded to also look at small insertions and deletions.

No description available.

As cars become more integrated into people’s lives, the design of in-car infotainment systems has become increasingly important. This thesis explores the user experience and Usability design principles of the calling functionality within the infotainment systems of five of the most common cars in Romania. The research examines the design principles that underpin these systems, using the European Statement of Principles on Human-Machine Interface (HMI) as a reference. The primary methodology involved two stages of surveys. The first survey gathered demographic information, car ownership details, and participants' experiences with their infotainment systems. This data was then used to identify the most common cars for the second survey, which further investigated user preferences for different infotainment interfaces. Analysis of the survey results reveals significant patterns in user preferences, with ease of use and convenience emerging as crucial factors in user satisfaction. The study highlights the importance of button placement, interface design, and layout in determining user experience. The most preferred interfaces were those which aligned with HMI principles, emphasizing simplicity, clarity of information, and ease of navigation. Despite certain limitations, such as the small sample size and potential for self-reporting bias, the research provides important insights into user preferences and the impact of design principles on user experience. The findings underscore the need for interface designs that are both user-friendly and align with established HMI guidelines. The implications of these findings extend to the broader fields of Human-Computer Interaction and Automotive User Interfaces, emphasizing the importance of user-centered design in enhancing user experience and satisfaction. Future research could expand upon these findings, exploring the impact of aesthetic design factors and the potential for personalized interface options.

Digital Selective Calling (DSC) is a vital maritime communications and safety system, enabling ships in distress to alert nearby vessels and coast guard stations of their emergency. While DSC is suitable for calling, its technical format is substandard from a cybersecurity perspective. Specifically, this work aims to demonstrate that Very High Frequency (VHF) DSC distress calls can be spoofed using Software Defined Radio (SDR). A VHF DSC distress call encoder and VHF DSC SDR signal constructor were developed. The forged distress call was transmitted using various techniques to two different DSC decoder programs, as well as to the maritime VHF transceiver ICOM IC-M510. It was shown that all of the targeted DSC decoders were susceptible to spoofing. This thesis concludes that VHF DSC distress calls can be spoofed using SDR, and infers that the DSC system as a whole has inherent security vulnerabilities that need to be addressed to assure the safety of future seafaring.

The development of high-throughput next-generation sequencing (NGS) techniques produces massive amount of data, allowing the identification of biomarkers in early disease diagnosis and driving the transformation of most disciplines in biology and medicine. A greater concentration is needed in developing novel, powerful, and efficient tools for NGS data analysis. This dissertation focuses on modeling ``omics'' data in various NGS applications with a primary goal of developing novel statistical methods to identify sequence variants, find transcription factor (TF) binding patterns, and decode the relationship between TF and gene expression levels. Accurate and reliable identification of sequence variants, including single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (INDELs), plays a fundamental role in NGS applications. Existing methods for calling these variants often make simplified assumption of positional independence and fail to leverage the dependence of genotypes at nearby loci induced by linkage disequilibrium. We propose vi-HMM, a hidden Markov model (HMM)-based method for calling SNPs and INDELs in mapped short read data. Simulation experiments show that, under various sequencing depths, vi-HMM outperforms existing methods in terms of sensitivity and F1 score. When applied to the human whole genome sequencing data, vi-HMM demonstrates higher accuracy in calling SNPs and INDELs. One important NGS application is chromatin immunoprecipitation followed by sequencing (ChIP-seq), which characterizes protein-DNA relations through genome-wide mapping of TF binding sites. Multiple TFs, binding to DNA sequences, often show complex binding patterns, which indicate how TFs with similar functionalities work together to regulate the expression of target genes. To help uncover the transcriptional regulation mechanism, we propose a novel nonparametric Bayesian method to detect the clustering pattern of multiple-TF bindings from ChIP-seq datasets. Simulation study demonstrates that our method performs best with regard to precision, recall, and F1 score, in comparison to traditional methods. We also apply the method on real data and observe several TF clusters that have been recognized previously in mouse embryonic stem cells. Recent advances in ChIP-seq and RNA sequencing (RNA-Seq) technologies provides more reliable and accurate characterization of TF binding sites and gene expression measurements, which serves as a basis to study the regulatory functions of TFs on gene expression. We propose a log Gaussian cox process with wavelet-based functional model to quantify the relationship between TF binding site locations and gene expression levels. Through the simulation study, we demonstrate that our method performs well, especially with large sample size and small variance. It also shows a remarkable ability to distinguish real local feature in the function estimates. / Doctor of Philosophy / The development of high-throughput next-generation sequencing (NGS) techniques produces massive amount of data and bring out innovations in biology and medicine. A greater concentration is needed in developing novel, powerful, and efficient tools for NGS data analysis. In this dissertation, we mainly focus on three problems closely related to NGS and its applications: (1) how to improve variant calling accuracy, (2) how to model transcription factor (TF) binding patterns, and (3) how to quantify of the contribution of TF binding on gene expression. We develop novel statistical methods to identify sequence variants, find TF binding patterns, and explore the relationship between TF binding and gene expressions. We expect our findings will be helpful in promoting a better understanding of disease causality and facilitating the design of personalized treatments.

<p dir="ltr">Pedicels are the slender stalks that attach the fruit to the plant. They play a crucial role in fruit development. The characteristics of the pedicel comprise complex traits that are controlled by multiple genes. To study whether genetic control of fruit mass was via control of pedicel characteristics, we used two unique hybrid apple populations: ‘20 Ounce’ x ‘Prairie Fire’ and ‘Edward VII’ x ‘Prairie Fire’. Both ‘20 Ounce’ and ‘Edward VII’ x ‘Prairie Fire’ produce large fruit over 200 g, whereas ‘Prairie Fire’ is a small-fruited crabapple with fruit size less than 2 g. These populations offer the potential to investigate how pedicel attributes relate to apple fruit size. Previous work established a correlation between pedicel characteristics and apple fruit mass. Specifically, pedicel length showed an inverse relationship, while pedicel diameter was directly related to fruit mass. Shorter and broader pedicels were expected to offer the least resistance to water and nutrient flows. We hypothesize that among the genes that control fruit mass, some govern pedicel length and diameter. Quantitative Trait Loci (QTLs) analysis (Linkage mapping) was performed, and 5 QTLs were associated with characteristics such as fruit mass, pedicel length and pedicel diameter with LOD scores of 4 and above. That being said, no common region was associated with both the fruit mass and pedicel characteristics. This does not support our hypothesis and suggests that different regions may be controlling all these traits. Knowledge of QTLs and subsequently genes that affect fruit mass and pedicel characteristics in apple have potential applications in apple breeding and fruit production. The identification and manipulation of these genes holds the promise of developing new apple cultivars with improved pedicel traits and ultimately fruit mass and enhanced fruit quality.</p>

This thesis contends that the pastoral role is significant to the effective functioning and well-being of the church. Therefore, the initial selection of a pastor is a vital component and contributes to those desirable outcomes. The question being considered within this thesis is: What are the factors within a church hiring process which may play a role in successful or unsuccessful pastoral ministry? As there are many variables even within this process, the scope of this thesis is limited to the identification and selection of pastoral leadership from the perspective of the pastoral participants. This perspective is drawn from one denominational association in Ontario —the Fellowship of Evangelical Baptists (FEB hereafter) within the Central region of Canada. In examining this question, an empirical, mixed-methodology is used. The triangulation of a literature review, surveys, personal interviews and a biblical, theological treatment allowed for the most comprehensive perspective and treatment of the research question (Leedy, 2010, p. 99). There is a significant amount of inductive reasoning included, based upon personal interactions within cultural contexts and experiences. This is due to the inadequacy or lack of current theories and available literature relative to the question being studied. This motivates me towards the inclusion of a grounded theory methodology as a component of this study (Leedy, 2010, p. 142). Hiring the right pastor is a challenge at the best of times. As the church struggles to respond to a rapidly changing and diverse culture it presents greater challenges. Rates of pastoral turnover are high and the general duration of pastoral ministry is low. This, in turn, impacts ministry effectiveness. This study of hiring practices and pastoral experiences begins to identify elements as to why some pastors are successful and others are not. It allows for the reflection and consideration of whether the church is, what I have termed, “Equipping the Called, or Calling the Equipped”. There is cause for hope, as there always is within God’s church. This thesis identifies concerns, as well as some positive practices and experiences that can be helpful to inform practice and potential change. As Osmer acknowledges, “observing good practice in other congregations is a powerful source of normative guidance” (Osmer, 2008, p. 152). / Practical Theology / M. Th. (Practical Theology)

This thesis contends that the pastoral role is significant to the effective functioning and well-being of the church. Therefore, the initial selection of a pastor is a vital component and contributes to those desirable outcomes. The question being considered within this thesis is: What are the factors within a church hiring process which may play a role in successful or unsuccessful pastoral ministry? As there are many variables even within this process, the scope of this thesis is limited to the identification and selection of pastoral leadership from the perspective of the pastoral participants. This perspective is drawn from one denominational association in Ontario —the Fellowship of Evangelical Baptists (FEB hereafter) within the Central region of Canada. In examining this question, an empirical, mixed-methodology is used. The triangulation of a literature review, surveys, personal interviews and a biblical, theological treatment allowed for the most comprehensive perspective and treatment of the research question (Leedy, 2010, p. 99). There is a significant amount of inductive reasoning included, based upon personal interactions within cultural contexts and experiences. This is due to the inadequacy or lack of current theories and available literature relative to the question being studied. This motivates me towards the inclusion of a grounded theory methodology as a component of this study (Leedy, 2010, p. 142). Hiring the right pastor is a challenge at the best of times. As the church struggles to respond to a rapidly changing and diverse culture it presents greater challenges. Rates of pastoral turnover are high and the general duration of pastoral ministry is low. This, in turn, impacts ministry effectiveness. This study of hiring practices and pastoral experiences begins to identify elements as to why some pastors are successful and others are not. It allows for the reflection and consideration of whether the church is, what I have termed, “Equipping the Called, or Calling the Equipped”. There is cause for hope, as there always is within God’s church. This thesis identifies concerns, as well as some positive practices and experiences that can be helpful to inform practice and potential change. As Osmer acknowledges, “observing good practice in other congregations is a powerful source of normative guidance” (Osmer, 2008, p. 152). / Philosophy, Practical and Systematic Theology / M. Th. (Practical Theology)