Novel Statistical Methods in Quantitative Genetics : Modeling Genetic Variance for Quantitative Trait Loci Mapping and Genomic Evaluation

This thesis develops and evaluates statistical methods for different types of genetic analyses, including quantitative trait loci (QTL) analysis, genome-wide association study (GWAS), and genomic evaluation. The main contribution of the thesis is to provide novel insights in modeling genetic variance, especially via random effects models. In variance component QTL analysis, a full likelihood model accounting for uncertainty in the identity-by-descent (IBD) matrix was developed. It was found to be able to correctly adjust the bias in genetic variance component estimation and gain power in QTL mapping in terms of precision.  Double hierarchical generalized linear models, and a non-iterative simplified version, were implemented and applied to fit data of an entire genome. These whole genome models were shown to have good performance in both QTL mapping and genomic prediction. A re-analysis of a publicly available GWAS data set identified significant loci in Arabidopsis that control phenotypic variance instead of mean, which validated the idea of variance-controlling genes.  The works in the thesis are accompanied by R packages available online, including a general statistical tool for fitting random effects models (hglm), an efficient generalized ridge regression for high-dimensional data (bigRR), a double-layer mixed model for genomic data analysis (iQTL), a stochastic IBD matrix calculator (MCIBD), a computational interface for QTL mapping (qtl.outbred), and a GWAS analysis tool for mapping variance-controlling loci (vGWAS).

Translating and testing the Alberta Context Tool for use among nurses in Swedish elder care

Background. There is emerging evidence that context is important for successful transfer of research knowledge into health care practice. The Alberta Context Tool (ACT) is a Canadian developed research-based instrument that assesses 10 modifiable concepts of organizational context considered important for health care professionals’ use of evidence. Swedish and Canadian health care have similarities in terms of organisational and professional aspects, suggesting that the ACT could be used for measuring context in Sweden. This paper reports on the translation of the ACT to Swedish and a testing of preliminary aspects of its validity, acceptability and reliability in Swedish elder care. Methods. The ACT was translated into Swedish and back-translated into English before being pilot tested in ten elder care facilities for response processes validity, acceptability and reliability (Cronbach’s alpha). Subsequently, further modification was performed. Results. In the pilot test, the nurses found the questions easy to respond to (52%) and relevant (65%), yet the questions’ clarity were mainly considered ‘neither clear nor unclear’ (52%). Missing data varied between 0 (0%) and 19 (12%) per item, the most common being 1 missing case per item (15 items). Internal consistency (Cronbach’s Alpha > .70) was reached for 5 out of 8 contextual concepts. Translation and back translation identified 21 linguistic- and semantic related issues and 3 context related deviations, resolved by developers and translators. Conclusion. Modifying an instrument is a detailed process, requiring time and consideration of the linguistic and semantic aspects of the instrument, and understanding of the context where the instrument was developed and where it is to be applied. A team, including the instrument’s developers, translators, and researchers is necessary to ensure a valid translation. This study suggests preliminary validity, reliability and acceptability evidence for the ACT when used with nurses in Swedish elder care.

PANA V : Evaluation of a Literacy Project

PANA V Evaluation of a Literacy ProjectSUMMARY AND CONCLUSIONSThis evaluation set out to explore the impact of the literacy work carried out through PANA V. It focussed on clarifying effects such as empowerment and poverty reduction in relation to the civil society. Two specific objectives were to evaluate the methodological approach and the didactic materials and to evaluate the sustainability of the project.Although the focus of the evaluation has been PANA V, the project has been evaluated in its context, as one in a series of five projects located in Rwanda ten years after the war and genocide. The conclusion will consider future plans in this field.The evaluator has striven to create a holistic picture of the effects of the project, although the given time for the evaluation was short. Only three weeks were spent in the field study and only ten days in the actual field. Although there were some organisational and logistic problems, as is common when carrying out a study like this in a poor country, many literacy sites were visited and quite many participators were interviewed. The overall impression from the study is overwhelmingly positive. So many people commit themselves in this task of teaching Rwandans reading, writing and numeracy. Despite harsh conditions learners strive to learn and group leaders devote themselves to the task. Many leaders on different levels try their very best to manage their difficult and demanding task. The main objective was to explore the impact of the project on poverty reduction, particularly on empowerment and strategies for everyday life. Women were to be regarded particularly. From the results it is clear that the project has a strong, positive impact both on poverty reduction and empowerment of marginalised groups. Among those who have benefited from the alphabetisation are mainly women. Unfortunately, when it comes to leaders in PANA, who may also be said to have benefited from the project, only a small minority is women. This is something that is recommended that it be reconsidered inside the organisation. As a majority of the targeted learners are women, and as the economic and social situation of women in Rwanda is generally weak, this is a question that I recommend the Pentesostal church and ADEPR to look particularly into. With many women being single breadwinners of their households, it is important that also women get access to positions that may bring benefits of different kind.It is also clear that the project has positive effects for the civil society. In the present situation in Rwanda, during the process of reconciliation and rapid progress, basic education for the poor majority is a democratic issue. In a country with a plethora of internet-cafés in the capital and a small minority that use cars and mobile-telephones to communicate nation-wide, it is of outmost importance that the majority acquires basic education, of which literacy is a central part. To strengthen the civil society in Rwanda literacy is important. One central issue is then that Rwanda develops toward becoming a country where literacy is used for the benefit of the citizens and it is a democratic issue that all citizens get an opportunity to participate. Crucial for this is that strong efforts are put into primary schools nation-wide. Literacy projects for adults, like PANA, may only complement these efforts, but they constitute important and necessary complements. Other relevant ways to promote literacy are campaigns in Radio and TV and through cultural events such as festivals, music and theatre. News papers, magazines and books are natural parts of such campaigns as well as adult education. As stated under the results not much can be said about the didactics in this evaluation. On the whole the methodology and the materials fill their function well and receive a high reputation. As people learn to read and write under very simple conditions, obviously the approach is appropriate. A few suggestions may be given from the study:•Focus groups leaders’ attention on clearness, that they show very clearly what is to be read. Good structuring is probably of great importance for many learners.•Make clear what is tested in the tests and consider the possibility to use a holistic test that would be more congruent with the methodology. The possibility to use only one grade, pass, would enable a more practical test, such as reading a short, relevant text, writing something relevant and solving practical mathematic problems. Avoid tests that demand school knowledge.•Avoid using methaphors such as “fight against illiteracy” and connections between illiteracy/literacy and darkness/light. It is not true that illiteracy causes bad things and that literacy only brings good. •Be prepared that it may be more difficult in the future to achieve the goals as it may be the case that the early learners where the ones who achieved easily. The goal of “literacy in six month” in PANA will probably hold only for some learners but also those who do not manage in six months need literacy skills.A third objective was to secure sustainability. As for sustainability of the project in itself, and of the literacy process, the main conclusion is that there is a good potential. The commitment and devotedness among many involved in PANA proves good. One weakness is individual leaders in ADEPR who do not see this as an important task for the Pentecostal church in Rwanda. Other weaknesses are the unwillingness to mention explicitly the wish, for example among group leaders, to get some kind of incentive and the fear of loosing believers by cooperation with other organisations. A higher degree of transparency in this issue would probably solve some irritations and tensions.As for the sustainability of the literacy skills much may be done to improve. The acquired skills seem to be comparably relevant. The level achieved, and the level tested, may be defined as basic literacy skills, consisting of basic reading, writing and numeracy skills. However, these skills are very restricted and there is a high risk that the skills will decline, which means that there is a high risk that people will forget how to read and write because of lack of exercising. From these conclusions a few suggestions for future development will be given.

Health system context and implementation of evidence-based practices-development and validation of the Context Assessment for Community Health (COACH) tool for low- and middle-income settings

Background: The gap between what is known and what is practiced results in health service users not benefitting from advances in healthcare, and in unnecessary costs. A supportive context is considered a key element for successful implementation of evidence-based practices (EBP). There were no tools available for the systematic mapping of aspects of organizational context influencing the implementation of EBPs in low- and middle-income countries (LMICs). Thus, this project aimed to develop and psychometrically validate a tool for this purpose. Methods: The development of the Context Assessment for Community Health (COACH) tool was premised on the context dimension in the Promoting Action on Research Implementation in Health Services framework, and is a derivative product of the Alberta Context Tool. Its development was undertaken in Bangladesh, Vietnam, Uganda, South Africa and Nicaragua in six phases: (1) defining dimensions and draft tool development, (2) content validity amongst in-country expert panels, (3) content validity amongst international experts, (4) response process validity, (5) translation and (6) evaluation of psychometric properties amongst 690 health workers in the five countries. Results: The tool was validated for use amongst physicians, nurse/midwives and community health workers. The six phases of development resulted in a good fit between the theoretical dimensions of the COACH tool and its psychometric properties. The tool has 49 items measuring eight aspects of context: Resources, Community engagement, Commitment to work, Informal payment, Leadership, Work culture, Monitoring services for action and Sources of knowledge. Conclusions: Aspects of organizational context that were identified as influencing the implementation of EBPs in high-income settings were also found to be relevant in LMICs. However, there were additional aspects of context of relevance in LMICs specifically Resources, Community engagement, Commitment to work and Informal payment. Use of the COACH tool will allow for systematic description of the local healthcare context prior implementing healthcare interventions to allow for tailoring implementation strategies or as part of the evaluation of implementing healthcare interventions and thus allow for deeper insights into the process of implementing EBPs in LMICs.

From a traditional academic library to a modern learning environment : Dalarna University Library - expectations and results

This report describes the ideas and vision behind Dalarna University's award-winning library in Falun. A description of the planning and construction processes and an evaluation of the final outcome are presented together with experiences and observations drawn from the project.