Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

Stress testing practices in risk management - Empirical evidence from the Finnish banking and insurance sectors

The main purpose of this study was to analyze how stress tests are used in risk management in the Finnish banking and insurance sectors. In order to enhance understanding of the topic, stress testing was explored in the context of corporate governance and regulato-ry implications of Basel II and Solvency II on stress testing were examined. In addition, the effects of the global financial crisis on stress testing were mapped and the differences in stress testing practices between the banking and insurance sector were discussed. The research method was qualitative case study and it was conducted by interviewing risk managers from ten institutions and a representative from FIN-FSA. Findings pointed out that stress testing practices vary significantly between different institutions. Interesting observations were made in terms of stress testing practices in the banking and insurance sectors. The increasing importance and use of stress tests were recognized as a result of the financial crisis. Stress testing was even considered more like art than science given the amount of challenges it involves. In general, improvements in stress tests were suggested, with an emphasis on stress concentration between different types of risks.

Solution marketing characteristics and practices

The first objective of this master's thesis is to find out how the concepts solution and solution marketing are defined in the literature. In order to do so, solution marketing literature is reviewed widely. Another target is to identify the characteristics of solution marketing and to explain how solution marketing can be carried out. The final objective is to determine how well the described solution marketing practices are executed in the target company, and this will be studied with a survey. A solution can be described as a co-created and customized combination of products and services. Solution marketing aims at developing and anticipating customer's business needs and it involves close collaboration between customer and supplier. Solution marketing communication is targeted to a specific audience. It entails deep customer intimacy and is focused on understanding customer's business problem. Solution marketing also requires close collaboration between sales and marketing as well as customer focused mindset. Solution marketing can be executed by promoting thought leadership, presenting solution offering, creating close customer relationships and treating customers as individuals. Solution provider's whole organization must engage customer focus.

The relationship between a virtual leader’s communication practices and a virtual team’s performance

A lot of research has been carried out into virtual teams and virtual leadership, yet there is hardly any research available on the communication behaviour of virtual leaders within a real business context. This research assessed the communication practices of virtual leaders and analysed the relationship between these practices and the performance of virtual teams. The objective of this research was to examine the distinctions of virtual teams, to study the leader’s role in a virtual team and its performance, and to examine the leader’s communication practices within virtual teams. The research involves a case study in which interviews have been carried out within an international technology company headquartered in Finland. Qualitative research methods were applied in the research. Based on the results of the study it can be said that there is a strong relationship between a virtual leader’s communication practices and a virtual team member’s job satisfaction. Through their communication practices, activities and message contents, leaders can affect the job satisfaction of virtual team members. In virtual leadership the focus is not in virtual but in leadership. It does not matter if the context is virtual or face-to-face; similar communication practices are good in both cases. As the global economic crisis strongly affected the sales results of the between a leader’s communication practices and a virtual team’s objective performance cannot be made.

Eye Fundus Image Analysis for Automatic Detection of Diabetic Retinopathy

Diabetes is a rapidly increasing worldwide problem which is characterised by defective metabolism of glucose that causes long-term dysfunction and failure of various organs. The most common complication of diabetes is diabetic retinopathy (DR), which is one of the primary causes of blindness and visual impairment in adults. The rapid increase of diabetes pushes the limits of the current DR screening capabilities for which the digital imaging of the eye fundus (retinal imaging), and automatic or semi-automatic image analysis algorithms provide a potential solution. In this work, the use of colour in the detection of diabetic retinopathy is statistically studied using a supervised algorithm based on one-class classification and Gaussian mixture model estimation. The presented algorithm distinguishes a certain diabetic lesion type from all other possible objects in eye fundus images by only estimating the probability density function of that certain lesion type. For the training and ground truth estimation, the algorithm combines manual annotations of several experts for which the best practices were experimentally selected. By assessing the algorithm’s performance while conducting experiments with the colour space selection, both illuminance and colour correction, and background class information, the use of colour in the detection of diabetic retinopathy was quantitatively evaluated. Another contribution of this work is the benchmarking framework for eye fundus image analysis algorithms needed for the development of the automatic DR detection algorithms. The benchmarking framework provides guidelines on how to construct a benchmarking database that comprises true patient images, ground truth, and an evaluation protocol. The evaluation is based on the standard receiver operating characteristics analysis and it follows the medical practice in the decision making providing protocols for image- and pixel-based evaluations. During the work, two public medical image databases with ground truth were published: DIARETDB0 and DIARETDB1. The framework, DR databases and the final algorithm, are made public in the web to set the baseline results for automatic detection of diabetic retinopathy. Although deviating from the general context of the thesis, a simple and effective optic disc localisation method is presented. The optic disc localisation is discussed, since normal eye fundus structures are fundamental in the characterisation of DR.

Patient Seclusion and Restraint Practices in Psychiatric Hospitals - Towards Evidence Based Clinical Nursing

The overall goal of this study was to support evidence based clinical nursing regarding patient seclusion and restraint practices. This was done by ensuring professional competence through innovative learning methods. The data were collected in three phases between March 2007 and May 2009 on acute psychiatric wards. Firstly, psychiatric inpatients’ experiences and suggestions for seclusion and restraint practices were explored (n=30). Secondly, nursing and medical personnel’s perceptions of seclusion and restraint practices were explored (n=27). Thirdly, the impacts of a continuing vocational eLearning course on nurses’ professional competence was evaluated (n=158). Patients’ perspectives received insufficient attention during the seclusion and restraint process. Improvements and alternatives to seclusion and restraint as suggested by the patients focused on essential parts of clinical nursing, but were not extensively adopted. Also nursing and medical personnel thought that patients’ subjective perspective received little attention. Personnel proposed a number of alternatives to seclusion and restraint, and they expressed a need for education and support to adopt these in clinical nursing. Evaluation of impacts of eLearning course on nurses’ professional competence showed no statistical differences between an eLearning group and an education-as-usual group. This dissertation provides evidence based knowledge about the realization of seclusion and restraint practices and the impacts of eLearning course on nurses’ professional competence in psychiatric hospitals. In order to improve clinical nursing the patient perspective must be accentuated. To ensure personnel’s professional competence, there is a need for written clinical guidelines, education and support. Continuing vocational education should bring together written clinical guidelines, ethical and legal issues and the support for personnel. To achieve the ambitious goal of such integration, achievable and affordable educational programmes are required. This, in turn, yields a call for innovative learning methods.

Integrating environmental education in primary school education in Tanzania : teachers’ perceptions and teaching practices

The study focuses on primary school teachers’ perceptions of environmental education, its integration into primary school education and teachers’ teaching practices in Tanzania. The thesis is based on empirical research. The theoretical underpinnings of the study are based on Palmer’s (1998) model of environmental education. According to the model, meaningful environmental education should include education about, in or through and for the environment. The study is supported by national and international literature from research done on environmental education and education for sustainable development and policy statements. The study is qualitative in nature, adopting phenomenography and phenomenology as points of departure. The empirical data was collected from four primary schools in Morogoro region in Tanzania. The study sample consisted of 31 primary school teachers. Data was collected through interviews and lesson observations. According to the results of the study, primary school teachers expressed variations in their perceptions of environmental education and education for sustainable development. Most of the teachers focused on the aspect of knowledge acquisition. According to Tanzanian education and training policy, environmental education has to be integrated into all subjects. Although there is environmental education in the primary school curriculum, it is not integrated on an equal footing in all subjects. Some subjects like science, social studies and geography have more environmental content than other subjects. Teachers claim that the approach used to integrate environmental education into the school curriculum was not favoured because many claimed that what is to be taught as environmental education in the various subjects is not shown clearly. As a result, many teachers suggested that to ensure that it is taught properly it should be included in the curriculum as an independent subject or as specific topics. The study revealed that teachers’ teaching practices in integrating environmental education varied from one subject to another. Although most of the teachers said that they used participatory methods, lesson observations showed that they limited themselves to question and answer and group discussion. However, the teachers faced a number of barriers in the teaching of environmental education, some of which include lack of teaching and learning resources, time and large class size. The role of teachers in the implementation of environmental education in developing an environmentally literate citizenry is of great significance. The responsibility of the government in developing a curriculum with clear goals and content, developing teachers’ capacity in the teaching of environmental education and provision of teaching and learning materials needs to be taken seriously by the government in educational plans and programs.

Identifying first graders at risk of reading and writing difficulties : creating a group-based screening tool in kiswahili in Tanzania

Early identification of beginning readers at risk of developing reading and writing difficulties plays an important role in the prevention and provision of appropriate intervention. In Tanzania, as in other countries, there are children in schools who are at risk of developing reading and writing difficulties. Many of these children complete school without being identified and without proper and relevant support. The main language in Tanzania is Kiswahili, a transparent language. Contextually relevant, reliable and valid instruments of identification are needed in Tanzanian schools. This study aimed at the construction and validation of a group-based screening instrument in the Kiswahili language for identifying beginning readers at risk of reading and writing difficulties. In studying the function of the test there was special interest in analyzing the explanatory power of certain contextual factors related to the home and school. Halfway through grade one, 337 children from four purposively selected primary schools in Morogoro municipality were screened with a group test consisting of 7 subscales measuring phonological awareness, word and letter knowledge and spelling. A questionnaire about background factors and the home and school environments related to literacy was also used. The schools were chosen based on performance status (i.e. high, good, average and low performing schools) in order to include variation. For validation, 64 children were chosen from the original sample to take an individual test measuring nonsense word reading, word reading, actual text reading, one-minute reading and writing. School marks from grade one and a follow-up test half way through grade two were also used for validation. The correlations between the results from the group test and the three measures used for validation were very high (.83-.95). Content validity of the group test was established by using items drawn from authorized text books for reading in grade one. Construct validity was analyzed through item analysis and principal component analysis. The difficulty level of most items in both the group test and the follow-up test was good. The items also discriminated well. Principal component analysis revealed one powerful latent dimension (initial literacy factor), accounting for 93% of the variance. This implies that it could be possible to use any set of the subtests of the group test for screening and prediction. The K-Means cluster analysis revealed four clusters: at-risk children, strugglers, readers and good readers. The main concern in this study was with the groups of at-risk children (24%) and strugglers (22%), who need the most assistance. The predictive validity of the group test was analyzed by correlating the measures from the two school years and by cross tabulating grade one and grade two clusters. All the correlations were positive and very high, and 94% of the at-risk children in grade two were already identified in the group test in grade one. The explanatory power of some of the home and school factors was very strong. The number of books at home accounted for 38% of the variance in reading and writing ability measured by the group test. Parents´ reading ability and the support children received at home for schoolwork were also influential factors. Among the studied school factors school attendance had the strongest explanatory power, accounting for 21% of the variance in reading and writing ability. Having been in nursery school was also of importance. Based on the findings in the study a short version of the group test was created. It is suggested for use in the screening processes in grade one aiming at identifying children at risk of reading and writing difficulties in the Tanzanian context. Suggestions for further research as well as for actions for improving the literacy skills of Tanzanian children are presented.

High-Throughput Screening for Novel Prostate Cancer Drug Targets –Getting Personal

Prostate cancers form a heterogeneous group of diseases and there is a need for novel biomarkers, and for more efficient and targeted methods of treatment. In this thesis, the potential of microarray data, RNA interference (RNAi) and compound screens were utilized in order to identify novel biomarkers, drug targets and drugs for future personalized prostate cancer therapeutics. First, a bioinformatic mRNA expression analysis covering 9873 human tissue and cell samples, including 349 prostate cancer and 147 normal prostate samples, was used to distinguish in silico prevalidated putative prostate cancer biomarkers and drug targets. Second, RNAi based high-throughput (HT) functional profiling of 295 prostate and prostate cancer tissue specific genes was performed in cultured prostate cancer cells. Third, a HT compound screen approach using a library of 4910 drugs and drug-like molecules was exploited to identify potential drugs inhibiting prostate cancer cell growth. Nine candidate drug targets, with biomarker potential, and one cancer selective compound were validated in vitro and in vivo. In addition to androgen receptor (AR) signaling, endoplasmic reticulum (ER) function, arachidonic acid (AA) pathway, redox homeostasis and mitosis were identified as vital processes in prostate cancer cells. ERG oncogene positive cancer cells exhibited sensitivity to induction of oxidative and ER stress, whereas advanced and castrate-resistant prostate cancer (CRPC) could be potentially targeted through AR signaling and mitosis. In conclusion, this thesis illustrates the power of systems biological data analysis in the discovery of potential vulnerabilities present in prostate cancer cells, as well as novel options for personalized cancer management.

Making Sense of Shared Leadership. A case study of leadership processes and practices without formal leadership structure in the team context

Leadership is essential for the effectiveness of the teams and organizations they are part of. The challenges facing organizations today require an exhaustive review of the strategic role of leadership. In this context, it is necessary to explore new types of leadership capable of providing an effective response to new needs. The presentday situations, characterized by complexity and ambiguity, make it difficult for an external leader to perform all leadership functions successfully. Likewise, knowledge-based work requires providing professional groups with sufficient autonomy to perform leadership functions. This study focuses on shared leadership in the team context. Shared leadership is seen as an emergent team property resulting from the distribution of leadership influence across multiple team members. Shared leadership entails sharing power and influence broadly among the team members rather than centralizing it in the hands of a single individual who acts in the clear role of a leader. By identifying the team itself as a key source of influence, this study points to the relational nature of leadership as a social construct where leadership is seen as social process of relating processes that are co-constructed by several team members. Based on recent theoretical developments concerned with relational, practice-based and constructionist approaches to the study of leadership processes, this thesis proposes the study of leadership interactions, working processes and practices to focus on the construction of direction, alignment and commitment. During the research process, critical events, activities, working processes and practices of a case team have been examined and analyzed with the grounded theory –approach in the terms of shared leadership. There are a variety of components to this complex process and a multitude of factors that may influence the development of shared leadership. The study suggests that the development process of shared leadership is a common sense -making process and consists of four overlapping dimensions (individual, social, structural, and developmental) to work with as a team. For shared leadership to emerge, the members of the team must offer leadership services, and the team as a whole must be willing to rely on leadership by multiple team members. For these individual and collective behaviors to occur, the team members must believe that offering influence to and accepting it from fellow team members are welcome and constructive actions. Leadership emerges when people with differing world views use dialogue and collaborative learning to create spaces where a shared common purpose can be achieved while a diversity of perspectives is preserved and valued. This study also suggests that this process can be supported by different kinds of meaning-making and process tools. Leadership, then, does not reside in a person or in a role, but in the social system. The built framework integrates the different dimensions of shared leadership and describes their relationships. This way, the findings of this study can be seen as a contribution to the understanding of what constitutes essential aspects of shared leadership in the team context that can be of theoretical value in terms of advancing the adoption and development process of shared leadership. In the real world, teams and organizations can create conditions to foster and facilitate the process. We should encourage leaders and team members to approach leadership as a collective effort that the team can be prepared for, so that the response is rapid and efficient.

The Forms and Functions of Multilingual Practices in Early Modern School Drama from the King‟s School, Canterbury

Käsittelen tutkimuksessani monikielisyyden ilmenemistä Canterburyn katedraalikoulun oppilaiden 1600-luvun loppupuoliskolla esittämissä näytelmissä, jotka löytyvät käsikirjoituksesta Lit.Ms.E41 (Canterburyn katedraalin arkisto). Tämä käsikirjoitus sisältää puheita ja näytelmiä, joiden kielinä ovat englanti, latina ja vähemmissä määrin myös kreikka. Useissa näytelmissä esiintyy koodinvaihtoa näiden kielten välillä, ja tutkielmassani selvitän, millaisia syntaktisia ilmenemismuotoja ja pragmaattisia merkityksiä koodinvaihdolla on. Teoreettinen viitekehykseni on yhdistelmä filologista ja lingvististä lähestymistapaa. Olen sisällyttänyt tutkielmaani aiemman koodinvaihdon tutkimuksen lisäksi Brownin ja Levinsonin kohteliaisuusteorian, jonka avulla erityisesti puhujien välisiin sosiaalisiin suhteisiin liittyviä koodinvaihdon funktioita voidaan luokitella. Koska historiallinen koodinvaihto on tutkimusaiheena vielä melko tuore, käsittelen perusteellisesti erilaisia metodologisia ratkaisuja. Valitsemani metodi yhdistää perinteisen filologisen lähiluvun pragmaattiseen analyysiin, jonka kautta työssäni vaikuttavat muun muassa rationaalisuuden ja empatian käsitteet. Analyysini perusteella kävi ilmi, että erityisen yleinen koodinvaihdon funktio on mahdollistaa intertekstuaalisuus, jolla edelleen voidaan ilmaista esimerkiksi solidaarisuutta eli sosiaalista läheisyyttä tai loukata puhuteltavaa. Solidaarisuus oli myös ilman intertekstuaalisuutta yleinen koodinvaihdon funktio. Näiden lisäksi koodinvaihdon funktioita olivat muun muassa kasvoja uhkaavat teot, eufemismit, stilistiset efektit sekä diskurssin avustaminen. Syntaktisten ilmenemismuotojen osalta keskeisin havainto oli, että koodinvaihdon ja lainaamisen erottaminen ei ole tarpeellista tai edes kannattavaa kaikissa tilanteissa. Lisäksi voitiin todeta, että valittu metodi soveltui hyvin aineiston analysoimiseen, ja sitä tulisi soveltaa mahdollisuuksien mukaan laajempaan materiaaliin sekä muiden pragmaattisten ilmiöiden tutkimiseen.

A Case Study of Agile Software Engineering Methods and Practices in the MeeGo Harmattan Open Source and Product Context

The aim of this master’s thesis is to study how Agile method (Scrum) and open source software are utilized to produce software for a flagship product in a complex production environment. The empirical case and the used artefacts are taken from the Nokia MeeGo N9 product program, and from the related software program, called as the Harmattan. The single research case is analysed by using a qualitative method. The Grounded Theory principles are utilized, first, to find out all the related concepts from artefacts. Second, these concepts are analysed, and finally categorized to a core category and six supported categories. The result is formulated as the operation of software practices conceivable in circumstances, where the accountable software development teams and related context accepts a open source software nature as a part of business vision and the whole organization supports the Agile methods.

Indicent reporting in shipping. Experiences and best practices for the Baltic Sea

Incident and near miss reporting is one of the proactive tools of safety management. By analyzing incidents and near misses and by corrective actions, severe accidents can potentially be avoided. Near miss and incident reporting is widely used in many riskprone industries such as aviation or chemical industry. In shipping incident and near miss reporting is required by the mandatory safety management system International Safety Management Code (ISM Code). However, in several studies the conclusion has been that incidents are reported poorly in the shipping industry. The aim of this report is to highlight the best practices for incident reporting in shipping and to support the shipping industry in the better utilization of incident reporting information. The study consists of three parts: 1) voluntary, shared reporting systems in shipping (international experiences), 2) interview study at four shipping companies in Sweden and in Finland (best practices), 3) expert workshop on incident reporting (problems and solutions). Preconditions for a functional reporting system are an existing no blame culture, commitment of the top management, feedback, good communication, training and an easy-to-use system. Although preconditions are met, problems can still appear, for example due to psychological, interpersonal or nationality-related reasons. In order to keep the reporting system functioning, the shipping company must be committed to maintain and develop the system and to tackle the problems. The whole reporting process from compiling, handling and analyzing a report, creating corrective actions and implementing them has to be handled properly in order to gain benefits from the reporting system. In addition to avoiding accidents, the functional reporting system can also offer other benefits by increasing safety awareness, by improving the overall safety and working conditions onboard, by enhancing team work and communication onboard and between ships and the land-based organization of shipping companies. Voluntary shared reporting systems are supported in the shipping industry in principle, but their development in the Baltic Sea is still in its infancy and the potential benefits of sharing the reports have not been realized. On the basis of this study we recommend that a common reporting system be developed for the Baltic Sea area which all the ships operating in the area could use regardless of their flag. Such a wider system could prevent some of the problems related to the current national systems. There would be more incident cases available in the database and this would support anonymity and thus encourage shipping companies to report to a shared database more frequently. A shared reporting system would contribute to the sharing of experiences and to the wider use of incident information in the shipping industry.