Design of an Event Based Messaging System

B2B document handling is moving from paper to electronic networks and electronic domain very rapidly. Moving, handling and transforming large electronic business documents requires a lot from the systems handling them. This paper explores new technologies such as SOA, event-driven systems and ESB and a scalable, event-driven enterprise service bus is created to demonstrate these new approaches to message handling. As an end result, we have a small but fully functional messaging system with several different components. This is the first larger Java-project done in-house, so on the side we developed our own set of best practices of Java development, setting up configurations, tools, code repositories and class naming and much more.

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.

Optimization of wind blade design including its energetic characteristics

The goal of the Master’s thesis is to develop and to analyze the optimization method for finding a geometry shape of classical horizontal wind turbine blades based on set of criteria. The thesis develops a technique that allows the designer to determine the weight of such factors as power coefficient, sound pressure level and the cost function in the overall process of blade shape optimization. The optimization technique applies the Desirability function. It was never used before in that kind of technical problems, and in this sense it can claim to originality of research. To do the analysis and the optimization processes more convenient the software application was developed.

Simplified sample handing in mass spectrometry based protein research - focus on protein phosphorylation

The human genome comprises roughly 20 000 protein coding genes. Proteins are the building material for cells and tissues, and proteins are functional compounds having an important role in many cellular responses, such as cell signalling. In multicellular organisms such as humans, cells need to communicate with each other in order to maintain a normal function of the tissues within the body. This complex signalling between and within cells is transferred by proteins and their post-translational modifications, one of the most important being phosphorylation. The work presented here concerns the development and use of tools for phosphorylation analysis. Mass spectrometers have become essential tools to study proteins and proteomes. In mass spectrometry oriented proteomics, proteins can be identified and their post-translational modifications can be studied. In this Ph.D. thesis the objectives were to improve the robustness of sample handling methods prior to mass spectrometry analysis for peptides and their phosphorylation status. The focus was to develop strategies that enable acquisition of more MS measurements per sample, higher quality MS spectra and simplified and rapid enrichment procedures for phosphopeptides. Furthermore, an objective was to apply these methods to characterize phosphorylation sites of phosphopeptides. In these studies a new MALDI matrix was developed which allowed more homogenous, intense and durable signals to be acquired when compared to traditional CHCA matrix. This new matrix along with other matrices was subsequently used to develop a new method that combines multiple spectra from different matrises from identical peptides. With this approach it was possible to identify more phosphopeptides than with conventional LC/ESI-MS/MS methods, and to use 5 times less sample. Also, phosphopeptide affinity MALDI target was prepared to capture and immobilise phosphopeptides from a standard peptide mixture while maintaining their spatial orientation. In addition a new protocol utilizing commercially available conductive glass slides was developed that enabled fast and sensitive phosphopeptide purification. This protocol was applied to characterize the in vivo phosphorylation of a signalling protein, NFATc1. Evidence for 12 phosphorylation sites were found, and many of those were found in multiply phosphorylated peptides

IDEAS for Strategic Technology Management: Design of an electronically mediated scenario method

The age-old adage goes that nothing in this world lasts but change, and this generation has indeed seen changes that are unprecedented. Business managers do not have the luxury of going with the flow: they have to plan ahead, to think strategies that will meet the changing conditions, however stormy the weather seems to be. This demand raises the question of whether there is something a manager or planner can do to circumvent the eye of the storm in the future? Intuitively, one can either run on the risk of something happening without preparing, or one can try to prepare oneself. Preparing by planning for each eventuality and contingency would be impractical and prohibitively expensive, so one needs to develop foreknowledge, or foresight past the horizon of the present and the immediate future. The research mission in this study is to support strategic technology management by designing an effective and efficient scenario method to induce foresight to practicing managers. The design science framework guides this study in developing and evaluating the IDEAS method. The IDEAS method is an electronically mediated scenario method that is specifically designed to be an effective and accessible. The design is based on the state-of-the-art in scenario planning, and the product is a technology-based artifact to solve the foresight problem. This study demonstrates the utility, quality and efficacy of the artifact through a multi-method empirical evaluation study, first by experimental testing and secondly through two case studies. The construction of the artifact is rigorously documented as justification knowledge as well as the principles of form and function on the general level, and later through the description and evaluation of instantiations. This design contributes both to practice and foundation of the design. The IDEAS method contributes to the state-of-the-art in scenario planning by offering a light-weight and intuitive scenario method for resource constrained applications. Additionally, the study contributes to the foundations and methods of design by forging a clear design science framework which is followed rigorously. To summarize, the IDEAS method is offered for strategic technology management, with a confident belief that it will enable gaining foresight and aid the users to choose trajectories past the gales of creative destruction and off to a brighter future.

Cognitively Empowering Internet-Based Patient Education for Ambulatory Orthopaedic Surgery Patients

Tiedollista voimavaraistumista tukeva internet-perustainen ohjaus päiväkirurgisille ortopedisille potilaille Tutkimuksen tarkoituksena oli kehittää tiedollista voimavaraistumista tukeva Internetperustainen potilasohjausohjelma sekä arvioida sitä. Tutkimusprosessi jaettiin kahteen vaiheeseen. Ensimmäisessä vaiheessa luotiin sisältö tiedollista voimavaraistumista tukevalle Internet-perustaiselle ohjaukselle päiväkirurgisia ortopedisia potilaita varten. Toisessa vaiheessa arvioitiin Internet-perustaisen ohjauksen (koeryhmä) hyväksyttävyyttä käyttäjien arvioimana ja ohjauksen tuloksia sekä verrattiin Internet-perustaisen ohjauksen (koeryhmä) tuloksia tiedollisesti voimavaraistumista tukevan sairaanhoitajan välittämään ohjauksen (kontrolliryhmä) tuloksiin. Tutkimuksen tavoitteena oli luoda uusi potilasohjausmuoto joka tarjoaa yksilöllisen, osallistavan ja aikaan ja paikkaan sitomattoman ohjauksen päiväkirurgiseen ortopediseen leikkaukseen tulevalle potilaalle. Tutkimuksen ensimmäisessä vaiheessa käytettiin kuvailevaa ja vertailevaa tutkimusmenetelmää (ennen ja jälkeen testaus). Tutkimukseen osallistui 120 päiväkirurgista ortopedista potilasta joiden tiedon odotuksia ja heille välitettyä tietoa tarkasteltiin. Tutkimuksen ensimmäisen vaiheen tuloksien ja aikaisemman voimavaraistumista käsittävän tiedon perusteella luotiin sisältö tiedollista voimavaraistumista tukevalle Internet-perustaiselle ohjaukselle. Sisältö rakentui voimavaraistavan tiedon kuudesta eri osa-alueesta. Tutkimuksen toisessa vaiheessa käytettiin randomoitua kokeellista tutkimusasetelmaa. Päiväkirurgiseen ortopediseen leikkaukseen tulevat potilaat randomoitiin koeryhmään (n=72) Internetperustaiseen ohjaukseen ja kontrolliryhmään (n=75) sairaanhoitajan välittämään ohjaukseen. Aineisto kerättiin strukturoitujen mittareiden avulla ja tulokset analysoitiin tilastollisesti. Tutkimuksen tulokset osoittavat, että kehitettyä tiedollisesti voimavaraistumista tukevaa Internet-perustaista potilasohjausmenetelmää voidaan suositella käytettäväksi ortopedisten päiväkirurgisten potilaiden ohjauksessa ja potilailla on hyvät mahdollisuudet voimavaraistua tiedollisesti sen avulla. Monipuolista tietoa sisältävä Internet-perustainen ohjaus osoittautui käyttäjien näkökulmasta hyväksyttäväksi. Vaikka Internet ohjauksen hyväksyttävyys koettiin osittain heikommaksi kuin sairaanhoitajan välittämän ohjauksen, potilaat käyttivät nettisivustoa ongelmitta ja arvioivat sen helppokäyttöiseksi. Ohjausmuodolla ei ollut vaikutusta hoidosta aiheutuneisiin kustannuksiin. Sen sijaan kustannuksista organisaatiolle voitiin puolittaa sairaanhoitajan ohjaukseen käyttämä aika Internet-perustaisen ohjauksen avulla. Internet-perustaiseen ohjaukseen osallistuneiden potilaiden tiedon taso ja kokemus tiedon riittävyydestä lisääntyivät ohjauksen jälkeen enemmän kuin sairaanhoitajan välittämään potilasohjaukseen osallistuneiden potilaiden tiedot. Ohjausmuodolla ei ollut vaikutusta potilaiden kokemien tunteiden ja oireiden voimakkuuteen. Yhteenvetona voidaan todeta, että tiedollisesti voimavaraistava Internet-perustaista ohjausta voidaan suositella vaihtoehtoiseksi menetelmäksi sairaanhoitajan välittämälle ohjaukselle päiväkirurgiseen ortopediseen leikkaukseen tuleville potilaille.