Construction of a global map of human gene expression : the process, tools and analysis

This thesis studies human gene expression space using high throughput gene expression data from DNA microarrays. In molecular biology, high throughput techniques allow numerical measurements of expression of tens of thousands of genes simultaneously. In a single study, this data is traditionally obtained from a limited number of sample types with a small number of replicates. For organism-wide analysis, this data has been largely unavailable and the global structure of human transcriptome has remained unknown. This thesis introduces a human transcriptome map of different biological entities and analysis of its general structure. The map is constructed from gene expression data from the two largest public microarray data repositories, GEO and ArrayExpress. The creation of this map contributed to the development of ArrayExpress by identifying and retrofitting the previously unusable and missing data and by improving the access to its data. It also contributed to creation of several new tools for microarray data manipulation and establishment of data exchange between GEO and ArrayExpress. The data integration for the global map required creation of a new large ontology of human cell types, disease states, organism parts and cell lines. The ontology was used in a new text mining and decision tree based method for automatic conversion of human readable free text microarray data annotations into categorised format. The data comparability and minimisation of the systematic measurement errors that are characteristic to each lab- oratory in this large cross-laboratories integrated dataset, was ensured by computation of a range of microarray data quality metrics and exclusion of incomparable data. The structure of a global map of human gene expression was then explored by principal component analysis and hierarchical clustering using heuristics and help from another purpose built sample ontology. A preface and motivation to the construction and analysis of a global map of human gene expression is given by analysis of two microarray datasets of human malignant melanoma. The analysis of these sets incorporate indirect comparison of statistical methods for finding differentially expressed genes and point to the need to study gene expression on a global level.

Suomen Taideyhdistyksestä Ateneumiin : Fredrik Cygnaeus, Carl Gustaf Estlander ja taidekokoelman roolit

From the Finnish Art Society to the Ateneum: Fredrik Cygnaeus, Carl Gustaf Estlander and the Roles of the Art Collection My dissertation deals with the Finnish Art Society and the development of its collection in the evolving field of the visual arts from the foundation of the society in 1846 to its exhibition in the Ateneum, a palace of art that was opened to the public in Helsinki in 1888. The main questions that it addresses are why and how the collection came into being, what its purpose was and what kind of future prospects were projected for it in the rapidly evolving field of the visual arts. I have examined the subject of my study from the perspectives of institutional history, the organisation of the field of art and the history of art collections. The prisms through which I have viewed the subject are the history of museums in Europe, the written history of art, the art association movement and the organisation of art education in relation to an ideology of enlightenment. Thus the activities of the Finnish Art Society are here mirrored for the first time in a wider context and the history of its collection located on the map of European collections. My research shows that the history of the collection of the Finnish Art Society initially depended on certain players in the visual arts and their particular leanings. The most important of these custodians were two long-serving chairmen of the society, Fredrik Cygnaeus (1807 1881) and Carl Gustaf Estlander (1834 1910). When the foundations for art activities had been laid through the establishment of the society, Cygnaeus and Estlander began to plan how the field of art might be moulded so as to improve the level of training for artists and to improve the quality of the collections and the opportunities for their display. Cygnaeus campaigned for the establishment of the Finnish Fine Arts Academy, while Estlander saw opportunities to combine the visual and applied arts. The findings of my research bring new information about the history of the collection of the Finnish Art Society, its profile, the professional abilities of those who were mainly responsible for developing it and the relationship between it and plans for reforming art education. The major findings are connected with the position of the collection in the field of art at different stages of its development. Despite the central monopoly of the Finnish Art Society in the field of art, the position of the collection was closely bound up with leading players in the field of art and their personal interests. This subservience also created an impediment to its full-blown enhancement and purposeful profiling, and it remained evident for a long time when the collection was seeking its own place in the Finnish art world.

Onnistuneen ikääntymisen ymmärrystä rakentamassa : Fysioterapeuttiopiskelijoiden oppiminen kestävää kehitystä edistävän kasvatuksen kehyksessä

The purpose of the present study was to investigate the possibilities and interconnec-tions that exist concerning the relationship between the University of Applied Sci-ences and the Learning by Developing action model (LbD), on the one hand, and education for sustainable development and high-quality learning as a part of profes-sional competence development on the other. The research and learning environment was the Coping at Home research project and its Caring TV project, which provided the context of the Physiotherapy for Elderly People professional study unit. The re-searcher was a teacher and an evaluator of her own students learning. The aims of the study were to monitor and evaluate learning at the individual and group level using tools of high-quality learning − improved concept maps − related to understanding the projects core concept of successful ageing. Conceptions were evaluated through aspects of sustainable development and a conceptual basis of physiotherapy. As edu-cational research this was a multi-method case study design experiment. The three research questions were as follows. 1. What kind of individual conceptions and conceptual structures do students build concerning the concept of successful ageing? How many and what kind of concepts and propositions do they have a) before the study unit, b) after the study unit, c) after the social-knowledge building? 2. What kind of social-knowledge building exists? a) What kind of social learn-ing process exists? b) What kind of socially created concepts, propositions and conceptual structures do the students possess after the project? c) What kind of meaning does the social-knowledge building have at an individual level? 3. How do physiotherapy competences develop according to the results of the first and second research questions? The subjects were 22 female, third-year Bachelor of Physiotherapy students in Laurea University of Applied Sciences in Finland. Individual learning was evaluated in 12 of the 22 students. The data was collected as a part of the learning exercises of the Physiotherapy for Elderly People study unit, with improved concept maps both at individual and group levels. The students were divided into two social-knowledge building groups: the first group had 15 members and second 7 members. Each group created a group-level concept map on the theme of successful ageing. These face-to-face interactions were recorded with CMapTools and videotaped. The data consists of both individually produced concept maps and group-produced concept maps of the two groups and the videotaped material of these processes. The data analysis was carried out at the intersection of various research traditions. Individually produced data was analysed based on content analysis. Group-produced data was analysed based on content analysis and dialogue analysis. The data was also analysed by simple statistical analysis. In the individually produced improved concept maps the students conceptions were comprehensive, and the first concept maps were found to have many concepts unrelated to each other. The conceptual structures were between spoke structures and chain structures. Only a few professional concepts were evident. In the second indi-vidual improved concept maps the conception was more professional than earlier, particulary from the functional point of view. The conceptual structures mostly re-sembled spoke structures. After the second individual concept mapping social map-ping interventions were made in the two groups. After this, multidisciplinary concrete links were established between all concepts in almost all individual concept maps, and the interconnectedness of the concepts in different subject areas was thus understood. The conceptual structures were mainly net structures. The concepts in these individual concept maps were also found to be more professional and concrete than in the previ-ous concept maps of these subjects. In addition, the wider context dependency of the concepts was recognized in many individual concept maps. This implies a conceptual framework for specialists. The social-knowledge building was similar to a social learning process. Both socio-cultural processes and cognitive processes were found to develop students conceptual awareness and the ability to engage in intentional learning. In the knowl-edge-building process two aspects were found: knowledge creation and pedagogical action. The discussion during the concept-mapping process was similar to a shared thinking process. In visualising the process with CMapTools, students easily comple-mented each others thoughts and words, as if mutually telepathic . Synthesizing, supporting, asking and answering, peer teaching and counselling, tutoring, evaluating and arguing took place, and students were very active, self-directed and creative. It took hundreds of conversations before a common understanding could be found. The use of concept mapping in particular was very effective. The concepts in these group-produced concept maps were found to be professional, and values of sustainable development were observed. The results show the importance of developing the contents and objectives of the European Qualification Framework as well as education for sustainable development, especially in terms of the need for knowledge creation, global responsibility and systemic, holistic and critical thinking in order to develop clinical practice. Keywords: education for sustainable development, learning, knowledge building, improved concept map, conceptual structure, competence, successful ageing

Routine Measurement of Health-Related Quality of Life in Assessing Cost-Effectiveness in Secondary Health Care

Aims: The aims of this study were 1) to identify and describe health economic studies that have used quality-adjusted life years (QALYs) based on actual measurements of patients' health-related quality of life (HRQoL); 2) to test the feasibility of routine collection of health-related quality of life (HRQoL) data as an indicator of effectiveness of secondary health care; and 3) to establish and compare the cost-utility of three large-volume surgical procedures in a real-world setting in the Helsinki University Central Hospital, a large referral hospital providing secondary and tertiary health-care services for a population of approximately 1.4 million. Patients and methods: So as to identify studies that have used QALYs as an outcome measure, a systematic search of the literature was performed using the Medline, Embase, CINAHL, SCI and Cochrane Library electronic databases. Initial screening of the identified articles involved two reviewers independently reading the abstracts; the full-text articles were also evaluated independently by two reviewers, with a third reviewer used in cases where the two reviewers could not agree a consensus on which articles should be included. The feasibility of routinely evaluating the cost-effectiveness of secondary health care was tested by setting up a system for collecting HRQoL data on approximately 4 900 patients' HRQoL before and after operative treatments performed in the hospital. The HRQoL data used as an indicator of treatment effectiveness was combined with diagnostic and financial indicators routinely collected in the hospital. To compare the cost-effectiveness of three surgical interventions, 712 patients admitted for routine operative treatment completed the 15D HRQoL questionnaire before and also 3-12 months after the operation. QALYs were calculated using the obtained utility data and expected remaining life years of the patients. Direct hospital costs were obtained from the clinical patient administration database of the hospital and a cost-utility analysis was performed from the perspective of the provider of secondary health care services. Main results: The systematic review (Study I) showed that although QALYs gained are considered an important measure of the effectiveness of health care, the number of studies in which QALYs are based on actual measurements of patients' HRQoL is still fairly limited. Of the reviewed full-text articles, only 70 reported QALYs based on actual before after measurements using a valid HRQoL instrument. Collection of simple cost-effectiveness data in secondary health care is feasible and could easily be expanded and performed on a routine basis (Study II). It allows meaningful comparisons between various treatments and provides a means for allocating limited health care resources. The cost per QALY gained was 2 770 for cervical operations and 1 740 for lumbar operations. In cases where surgery was delayed the cost per QALY was doubled (Study III). The cost per QALY ranges between subgroups in cataract surgery (Study IV). The cost per QALY gained was 5 130 for patients having both eyes operated on and 8 210 for patients with only one eye operated on during the 6-month follow-up. In patients whose first eye had been operated on previous to the study period, the mean HRQoL deteriorated after surgery, thus precluding the establishment of the cost per QALY. In arthroplasty patients (Study V) the mean cost per QALY gained in a one-year period was 6 710 for primary hip replacement, 52 270 for revision hip replacement, and 14 000 for primary knee replacement. Conclusions: Although the importance of cost-utility analyses has during recent years been stressed, there are only a limited number of studies in which the evaluation is based on patients own assessment of the treatment effectiveness. Most of the cost-effectiveness and cost-utility analyses are based on modeling that employs expert opinion regarding the outcome of treatment, not on patient-derived assessments. Routine collection of effectiveness information from patients entering treatment in secondary health care turned out to be easy enough and did not, for instance, require additional personnel on the wards in which the study was executed. The mean patient response rate was more than 70 %, suggesting that patients were happy to participate and appreciated the fact that the hospital showed an interest in their well-being even after the actual treatment episode had ended. Spinal surgery leads to a statistically significant and clinically important improvement in HRQoL. The cost per QALY gained was reasonable, at less than half of that observed for instance for hip replacement surgery. However, prolonged waiting for an operation approximately doubled the cost per QALY gained from the surgical intervention. The mean utility gain following routine cataract surgery in a real world setting was relatively small and confined mostly to patients who had had both eyes operated on. The cost of cataract surgery per QALY gained was higher than previously reported and was associated with considerable degree of uncertainty. Hip and knee replacement both improve HRQoL. The cost per QALY gained from knee replacement is two-fold compared to hip replacement. Cost-utility results from the three studied specialties showed that there is great variation in the cost-utility of surgical interventions performed in a real-world setting even when only common, widely accepted interventions are considered. However, the cost per QALY of all the studied interventions, except for revision hip arthroplasty, was well below 50 000, this figure being sometimes cited in the literature as a threshold level for the cost-effectiveness of an intervention. Based on the present study it may be concluded that routine evaluation of the cost-utility of secondary health care is feasible and produces information essential for a rational and balanced allocation of scarce health care resources.

Quality Assessment of a Forest Inventory Based on Airborne Laser Scanning

In this study, a quality assessment method based on sampling of primary laser inventory units (microsegments) was analysed. The accuracy of a laser inventory carried out in Kuhmo was analysed as a case study. Field sample plots were measured on the sampled microsegments in the Kuhmo inventory area. Two main questions were considered. Did the ALS based inventory meet the accuracy requirements set for the provider and how should a reliable, cost-efficient and independent quality assessment be undertaken. The agreement between control measurement and ALS based inventory was analysed in four ways: 1) The root mean squared errors (RMSEs) and bias were calculated. 2) Scatter plots with 95% confidence intervals were plotted and the placing of identity lines was checked. 3) Bland-Altman plots were drawn so that the mean difference of attributes between the control method and ALS-method was calculated and plotted against average value of attributes. 4) The tolerance limits were defined and combined with Bland-Altman plots. The RMSE values were compared to a reference study from which the accuracy requirements had been set to the service provider. The accuracy requirements in Kuhmo were achieved, however comparison of RMSE values proved to be difficult. Field control measurements are costly and time-consuming, but they are considered to be robust. However, control measurements might include errors, which are difficult to take into account. Using the Bland-Altman plots none of the compared methods are considered to be completely exact, so this offers a fair way to interpret results of assessment. The tolerance limits to be set on order combined with Bland-Altman plots were suggested to be taken in practise. In addition, bias should be calculated for total area. Some other approaches for quality control were briefly examined. No method was found to fulfil all the required demands of statistical reliability, cost-efficiency, time efficiency, simplicity and speed of implementation. Some benefits and shortcomings of the studied methods were discussed.

Selenium and its effects on growth, yield and tuber quality in potato

Selenium (Se) has been demonstrated to be an essential trace element for maintenance of animal and human health. Although it has not been confirmed to be an essential micronutrient in higher plants, there is increasing evidence that Se functions as an antioxidant in plants. Selenium has been shown to exert a beneficial effect on crop growth and promotes stress tolerance at low concentrations. However, the specific physiological mechanisms that underlie the positive effects of Se in plants have not been clearly elucidated. The aims of this study were to determine the Se concentration in potato (Solanum tuberosum L.) and the effects of Se on the accumulation of carbohydrates, growth and yield in potato plants. An additional aim was to study the impact of Se on the total glycoalkaloid concentration in immature potato tubers. The distribution of Se in different biochemical Se fractions and the effect of storage on the Se concentration were studied in Se-enriched tubers. Furthermore, the effect of Se on raw darkening and translocation of Se from seed tubers to the next tuber generation was investigated. Due to the established anti-ageing properties of Se, it was of interest to study if Se affects physiological age and growth vigour of seed tubers. The Se concentrations in the upper leaves, roots, stolons and tubers of potato increased with increasing Se supplementation. The highest Se concentration was reached in young upper leaves, roots and stolons, indicating that added selenate was efficiently utilized and taken up at an early stage. During the growing period the Se concentration declined in the aerial parts, roots and stolons of potato plants whereas an intensive accumulation took place in immature and mature tubers. Selenium increased carbohydrate accumulation in the young upper leaves and in stolons, roots and tubers at maturity. This could not be explained by increased production of photoassimilates as net photosynthesis did not differ among Se treatments. The Se treated plants produced higher tuber yields than control plants, and at the highest Se concentration (0.3 mg kg-1) lower numbers of larger tubers were harvested. Increased yield of Se treated plants suggested that Se may enhance the allocation of photoassimilates for tuber growth, acting as a strong sink for both Se and for carbohydrates. Similarly as for other plant species, the positive impact of Se on the yield of potato plants could be related to its antioxidative effect in delaying senescence. The highest Se supplementation (0.9 mg kg-1) slightly decreased the glycoalkaloid concentration of immature tubers. However, at this level the Se concentration in tubers was about 20 µg g-1 DW. A 100 g consumption of potato would provide about 500 mg of Se, which exceeds the upper safe intake level of 400 µg per day for human dietary. The low Se applications (0.0035 and 0.1 mg kg-1) diminished and retarded the degree of raw darkening in tubers stored for one and eight months, which can be attributed to the antioxidative properties of Se. The storage for 1 to 12 months did not affect the Se concentrations of tubers. In the Se enriched tubers Se was allocated to the organic Se fraction, indicating that it was incorporated into organic compounds in tubers. Elevated Se concentration in the next-generation tubers produced by the Se enriched seed tubers indicated that Se could be translocated from the seed tubers to the progeny. In the seed tubers stored for 8 months, at high levels, Se had some positive effects on the growth vigour of sprouts, but Se had no consistent effect on the growth vigour of seed tubers of optimal physiological age. These results indicate that Se is a beneficial trace element in potato plants that exerts a positive effect on yield formation and improves the processing and storage quality of table potato tubers. These positive effects of Se are, however, dependent on the Se concentration and the age of the potato plant and tuber.