Biomolecular screening for inhibitors of butyrylcholinesterase : identification and characterization using in vitro and in silico tools

Drug discovery is a continuous process where researchers are constantly trying to find new and better drugs for the treatment of various conditions. Alzheimer’s disease, a neurodegenerative disease mostly affecting the elderly, has a complex etiology with several possible drug targets. Some of these targets have been known for years while other new targets and theories have emerged more recently. Cholinesterase inhibitors are the major class of drugs currently used for the symptomatic treatment of Alzheimer’s disease. In the Alzheimer’s disease brain there is a deficit of acetylcholine and an impairment in signal transmission. Acetylcholinesterase has therefore been the main target as this is the main enzyme hydrolysing acetylcholine and ending neurotransmission. It is believed that by inhibiting acetylcholinesterase the cholinergic signalling can be enhanced and the cognitive symptoms that arise in Alzheimer’s disease can be improved. Butyrylcholinesterase, the second enzyme of the cholinesterase family, has more recently attracted interest among researchers. Its function is still not fully known, but it is believed to play a role in several diseases, one of them being Alzheimer’s disease. In this contribution the aim has primarily been to identify butyrylcholinesterase inhibitors to be used as drug molecules or molecular probes in the future. Both synthetic and natural compounds in diverse and targeted screening libraries have been used for this purpose. The active compounds have been further characterized regarding their potencies, cytotoxicity, and furthermore, in two of the publications, the inhibitors ability to also inhibit Aβ aggregation in an attempt to discover bifunctional compounds. Further, in silico methods were used to evaluate the binding position of the active compounds with the enzyme targets. Mostly to differentiate between the selectivity towards acetylcholinesterase and butyrylcholinesterase, but also to assess the structural features required for enzyme inhibition. We also evaluated the compounds, active and non-active, in chemical space using the web-based tool ChemGPS-NP to try and determine the relevant chemical space occupied by cholinesterase inhibitors. In this study, we have succeeded in finding potent butyrylcholinesterase inhibitors with a diverse set of structures, nine chemical classes in total. In addition, some of the compounds are bifunctional as they also inhibit Aβ aggregation. The data gathered from all publications regarding the chemical space occupied by butyrylcholinesterase inhibitors we believe will give an insight into the chemically active space occupied by this type of inhibitors and will hopefully facilitate future screening and result in an even deeper knowledge of butyrylcholinesterase inhibitors.

Business intelligence viewpoint on managerial decision-making : Ill-structured problems and decision support systems

Vaikka liiketoimintatiedon hallintaa sekä johdon päätöksentekoa on tutkittu laajasti, näiden kahden käsitteen yhteisvaikutuksesta on olemassa hyvin rajallinen määrä tutkimustietoa. Tulevaisuudessa aiheen tärkeys korostuu, sillä olemassa olevan datan määrä kasvaa jatkuvasti. Yritykset tarvitsevat jatkossa yhä enemmän kyvykkyyksiä sekä resursseja, jotta sekä strukturoitua että strukturoimatonta tietoa voidaan hyödyntää lähteestä riippumatta. Nykyiset Business Intelligence -ratkaisut mahdollistavat tehokkaan liiketoimintatiedon hallinnan osana johdon päätöksentekoa. Aiemman kirjallisuuden pohjalta, tutkimuksen empiirinen osuus tunnistaa liiketoimintatiedon hyödyntämiseen liittyviä tekijöitä, jotka joko tukevat tai rajoittavat johdon päätöksentekoprosessia. Tutkimuksen teoreettinen osuus johdattaa lukijan tutkimusaiheeseen kirjallisuuskatsauksen avulla. Keskeisimmät tutkimukseen liittyvät käsitteet, kuten Business Intelligence ja johdon päätöksenteko, esitetään relevantin kirjallisuuden avulla – tämän lisäksi myös dataan liittyvät käsitteet analysoidaan tarkasti. Tutkimuksen empiirinen osuus rakentuu tutkimusteorian pohjalta. Tutkimuksen empiirisessä osuudessa paneudutaan tutkimusteemoihin käytännön esimerkein: kolmen tapaustutkimuksen avulla tutkitaan sekä kuvataan toisistaan irrallisia tapauksia. Jokainen tapaus kuvataan sekä analysoidaan teoriaan perustuvien väitteiden avulla – nämä väitteet ovat perusedellytyksiä menestyksekkäälle liiketoimintatiedon hyödyntämiseen perustuvalle päätöksenteolle. Tapaustutkimusten avulla alkuperäistä tutkimusongelmaa voidaan analysoida tarkasti huomioiden jo olemassa oleva tutkimustieto. Analyysin tulosten avulla myös yksittäisiä rajoitteita sekä mahdollistavia tekijöitä voidaan analysoida. Tulokset osoittavat, että rajoitteilla on vahvasti negatiivinen vaikutus päätöksentekoprosessin onnistumiseen. Toisaalta yritysjohto on tietoinen liiketoimintatiedon hallintaan liittyvistä positiivisista seurauksista, vaikka kaikkia mahdollisuuksia ei olisikaan hyödynnetty. Tutkimuksen merkittävin tulos esittelee viitekehyksen, jonka puitteissa johdon päätöksentekoprosesseja voidaan arvioida sekä analysoida. Despite the fact that the literature on Business Intelligence and managerial decision-making is extensive, relatively little effort has been made to research the relationship between them. This particular field of study has become important since the amount of data in the world is growing every second. Companies require capabilities and resources in order to utilize structured data and unstructured data from internal and external data sources. However, the present Business Intelligence technologies enable managers to utilize data effectively in decision-making. Based on the prior literature, the empirical part of the thesis identifies the enablers and constraints in computer-aided managerial decision-making process. In this thesis, the theoretical part provides a preliminary understanding about the research area through a literature review. The key concepts such as Business Intelligence and managerial decision-making are explored by reviewing the relevant literature. Additionally, different data sources as well as data forms are analyzed in further detail. All key concepts are taken into account when the empirical part is carried out. The empirical part obtains an understanding of the real world situation when it comes to the themes that were covered in the theoretical part. Three selected case companies are analyzed through those statements, which are considered as critical prerequisites for successful computer-aided managerial decision-making. The case study analysis, which is a part of the empirical part, enables the researcher to examine the relationship between Business Intelligence and managerial decision-making. Based on the findings of the case study analysis, the researcher identifies the enablers and constraints through the case study interviews. The findings indicate that the constraints have a highly negative influence on the decision-making process. In addition, the managers are aware of the positive implications that Business Intelligence has for decision-making, but all possibilities are not yet utilized. As a main result of this study, a data-driven framework for managerial decision-making is introduced. This framework can be used when the managerial decision-making processes are evaluated and analyzed.

Before internationalisation : reflections of lateral rigidity on managerial decision making

The purpose of the study is to analyse lateral rigidity in the framework of pre-internationalisation to find out its reflections on managerial decision making. The interest of the study lies in the intersection of the meaningful but relatively stagnant concept of lateral rigidity, and the pre-internationalisation phase of companies that has received only a limited amount of research attention. The theoretical basis for the study is drawn from managerial decision making and internationalisation literatures. Firstly, the study aims to define the concept of lateral rigidity in order to secondly find out how it influences managers’ pre-internationalisation decision making. The study is theoretical in nature, and is based solely on literature examination. Concept analysis method is used to determine the attributes of lateral rigidity for the purpose of recognising the concept in the pre-internationalisation framework. The attributes that are found to comprise lateral rigidity are culture, know-how, uncertainty and attitude. Furthermore, these attributes are more specifically found to consist of environmental, personal and operational matters. Through the analysis of the pre-internationalisation literature it is discovered that all the attributes appear there, and present a variety of influences on pre-internationalisation decision making that can be characterised as being negative. The study finds that culture influences managers’ decision making via subjective reasoning and behaviour that stem from a domestic inclination, and via unfamiliarity with foreign markets. Against assumption, home cultural factors, e.g. values and customs, do not appear to have an influence. Know-how is found to influence decision making via managers’ previous experiences, subjective abiding perceptions, and the usage of previous operation patterns. Uncertainty, then again, influences managers’ risk perception, unfamiliarity avoidance, and the scope of potential international operations. Attitude is found to have a robust influence on managerial decision making via the usage of familiar processes and decision regimes, subjective preference of convention, and plausible results of operations. Ergo, the effects of lateral rigidity on managers show to represent an encumbrance in the pre-internationalisation phase; even though internationalisation would take place, the related decisions and actions are highly constrained. Especially the subjectivity of managers is seen to have a meaningful role in the decision making process.

Enabling Change in Universities: Enhancing Education for Sustainable Development with Tools for Quality Assurance

Enabling Change in Universities: Enhancing Education for Sustainable Development with Tools for Quality Assurance This thesis deals with enabling change in universities, more explicitly enhancing education for sustainable development with tools for quality assurance. Change management is a discipline within management that was developed in the 1980s because business changed from being predictable to unpredictable. The PEST mnemonic is a method to categorize factors enabling change; such as political, economic, socio-cultural and technological factors, which all affect higher education. A classification of a change, in either hard or soft, can help understanding the type of change that an organization is facing. Hard changes are more applied to problems that have clear objectives and indicators, with a known cause of the problem. Soft changes are applied to larger problems that affect the entire organization or beyond it. The basic definition for sustainable development is: the future generations should have similar opportunities as the previous. The UN has set as a global goal an integration of education for sustainable development (ESD) at all levels of education during 2005- 2014. The goal is set also in universities, the graduates of which are future leaders for all labor markets. The objective for ESD in higher education is that graduates obtain the competence to take economic, social and environmental costs and benefits into account when making decisions. Knowledge outcomes should aim for systematic and holistic thinking, which requires cross disciplinary education. So far, the development of ESD has not achieved its goals. The UN has identified a need for more transdisclipnary research in ESD. A joint global requirement for universities is quality assurance, the aim of which is to secure and improve teaching and learning. Quality, environmental and integrated management systems are used by some universities for filling the quality assurance requirements. The goal of this thesis is to open up new ways for enhancing ESD in universities, beyond the forerunners; by exploring how management systems could be used as tools for promoting ESD. The thesis is based on five studies. In the first study, I focus on if and how tools for quality assurance could be benefitted for promoting ESD. It is written from a new perspective, the memetic, for reaching a diversity of faculty. A meme is an idea that diffuses from brain to brain. It can be applied for cultural evolution. It is a theory that is based on the evolutionary theory by Darwin, applied for social sciences. In the second Paper, I present the results from the development of the pilot process model for enhancing ESD with management systems. The development of the model is based on a study that includes earlier studies, a survey in academia and an analysis of the practice in 11 universities in the Nordic countries. In the third study, I explore if the change depends on national culture or if it is global. It is a comparative study on both policy and implementation level, between the Nordic countries and China. The fourth study is a single case study based on change management. In this study, I identify what to consider in order to enable the change: enhancing ESD with tools for quality assurance in universities. In the fifth Paper, I present the results of the process model for enhancing ESD with management systems. The model was compared with identified drivers and barriers for enhancing ESD and for implementing management systems. Finally, the process model was piloted and applied for identifying sustainability aspects in curricula. Action research was chosen as methodology because there are not already implemented approaches using quality management for promoting ESD, why the only way to study this is to make it happen. Another reason for choosing action research is since it is essential to involve students and faculty for enhancing ESD. Action based research consists of the following phases: a) diagnosing, b) planning action, c) taking action and d) evaluating action. This research was made possible by a project called Education for Sustainable Development in Academia in the Nordic countries, ESDAN, in which activities were divided into these four phases. Each phase ended with an open seminar, where the results of the study were presented. The objective for the research project was to develop a process for including knowledge in sustainable development in curricula, which could be used in the quality assurance work. Eleven universities from the Nordic countries cooperated in the project. The aim was, by applying the process, to identify and publish examples of relevant sustainability aspects in different degree programs in universities in the Nordic countries. The project was partly financed by the Nordic Council of Ministers and partly by the participating pilot universities. Based on the results of my studies, I consider that quality, environmental and integrated management systems can be used for promoting ESD in universities. Relevant sustainability aspects have been identified in different fields of studies by applying the final process model. The final process model was compared with drivers and barriers for enhancing ESD and for implementing management systems in universities and with succeeding with management systems in industry. It corresponds with these, meaning that drivers are taken into account and barriers tackled. Both ESD and management systems in universities could be considered successful memes, which can reflect an effective way of communication among individuals. I have identified that management systems could be used as tools for hard changes and to support the soft change of enhancing ESD in universities with management system. Based on the change management study I have summarized recommendations on what to consider in order to enable the studied change. The main practical implications of the results are that the process model could be applied for assessment, benchmarking and communication of ESD, connected to quality assurance, when applied. This is possible because the information can be assembled in one picture, which facilitates comparison. The memetic approach can be applied for structuring. It is viable to make comparative studies between cultures, for getting insight in special characteristics of the own culture. Action based research is suitable for involving faculty. Change management can be applied for planning a change, which both enhancing ESD and developing management systems are identified to be.

Matrix Mind : on managerial reframing in multidimensional problem solving

Det är inte ovanligt att man i organisationer ställs inför problem som inte kan hanteras inom befintlig organisationsstruktur. Skälen kan vara att frågorna har många – ibland konflikterande – dimensioner och perspektiv som samtidigt måste beaktas. I den här avhandlingen studeras vilka tankemönster och föreställningar som fanns när grupper av chefer försökte lösa komplexa problem, som inte hade en naturlig organisatorisk hemvist och hur de omsatte dessa tankemönster i handling. Vad kännetecknade det ledarskap som utövades under problemlösningsprocessen? Avhandlingens empiri hämtas från ledarutvecklingsprogram i två internationellt verksamma företag i Sverige, och omfattar 14 verkliga affärsproblem i dessa företag och den process varigenom de löstes. De 14 seminarierna utgör exempel på hur mångdimensionella frågeställningar framgångsrikt hanteras utanför den befintliga organisationsstrukturen. Studien ger, genom att adressera frågor kring tankesätt och ledningsprocesser, en djupare förståelse för förutsättningarna för detta, och lyfter särskilt fram betydelsen av ett ledarskap som inbegriper begreppen intervention, förmåga och omtolkning. Som ett samlat begrepp introduceras bilden att utöva ledarskapet utifrån ett matrix mind. Att påverka strukturer (i vid mening) och därigenom de förmågor som utvecklas, är del i detta ledarskap. Det sker genom interventioner (ingrepp som påverkar relationer i t ex en grupp) och baserades i den aktuella empirin på uppfattningar om värdet av problematisering, erfarenhetsutbyte och av ett språk, som både beskriver och anger inriktning för aktiviteter. Interventioner i strukturer (och till dem knutna processer) beskriver dock bara delvis detta ledarskap. Att leda med ett matrix mind innefattar också ett nyfiket och kreativt förhållningssätt, och att utifrån detta leda omtolkning av problem. I empirin finns flera exempel på detta. Avhandlingen avser att ge ett bidrag inom såväl organisations- som ledarskapsteori.

Phytosociological surveys: tools for weed science?

In simple terms, a phytosociological survey is a group of ecological evaluation methods whose aim is to provide a comprehensive overview of both the composition and distribution of plant species in a given plant community. To understand the applicability of phytosociological surveys for weed science, as well as their validity, their ecological basis should be understood and the most suitable ones need to be chosen, because cultivated fields present a relatively distinct group of selecting factors when compared to natural plant communities. For weed science, the following sequence of steps is proposed as the most suitable: (1) overall infestation; (2) phytosociological tables/graphs; (3) intra-characterization by diversity; (4) inter-characterization and grouping by cluster analysis. A summary of methods is established in order to assist Weed Science researchers through their steps into the realm of phytosociology.

Project Management Tools in Agile Embedded Systems Development

Agile methods have become increasingly popular in the field of software engineering. While agile methods are now generally considered applicable to software projects of many different kinds, they have not been widely adopted in embedded systems development. This is partly due to the natural constraints that are present in embedded systems development (e.g. hardware–software interdependencies) that challenge the utilization of agile values, principles and practices. The research in agile embedded systems development has been very limited, and this thesis tackles an even less researched theme related to it: the suitability of different project management tools in agile embedded systems development. The thesis covers the basic aspects of many different agile tool types from physical tools, such as task boards and cards, to web-based agile tools that offer all-round solutions for application lifecycle management. In addition to these two extremities, there is also a wide range of lighter agile tools that focus on the core agile practices, such as backlog management. Also other non-agile tools, such as bug trackers, can be used to support agile development, for instance, with plug-ins. To investigate the special tool requirements in agile embedded development, the author observed tool related issues and solutions in a case study involving three different companies operating in the field of embedded systems development. All three companies had a distinct situation in the beginning of the case and thus the tool solutions varied from a backlog spreadsheet built from scratch to plug-in development for an already existing agile software tool. Detailed reports are presented of all three tool cases. Based on the knowledge gathered from agile tools and the case study experiences, it is concluded that there are tool related issues in the pilot phase, such as backlog management and user motivation. These can be overcome in various ways epending on the type of a team in question. Finally, five principles are formed to give guidelines for tool selection and usage in agile embedded systems development.

Digital Preservation Tools, Practices, and Policies in Islandora

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Geo-enabling repositories - techniques, tools, and challenges

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Development of remote monitoring process tools for biomass fired bubbling fluidized bed boilers

Remote monitoring of a power boiler allows the supplying company to make sure that equipment is used as supposed to and gives a good chance for process optimization. This improves co-operation between the supplier and the customer and creates an aura of trust that helps securing future contracts. Remote monitoring is already in use with recovery boilers but the goal is to expand especially to biomass-fired BFB-boilers. To make remote monitoring possible, data has to be measured reliably on site and the link between the power plant and supplying company’s server has to work reliably. Data can be gathered either with the supplier’s sensors or with measurements originally installed in the power plant if the plant in question is not originally built by the supplying company. Main goal in remote monitoring is process optimization and avoiding unnecessary accidents. This can be achieved for instance by following the efficiency curves and fouling in different parts of the process and comparing them to past values. The final amount of calculations depends on the amount of data gathered. Sudden changes in efficiency or fouling require further notice and in such a case it’s important that dialogue toward the power plant in question also works.

Macroalgae across environmental gradients : tools for managing rocky coastal areas of the northern Baltic Sea

Macroalgae are the main primary producers of the temperate rocky shores providing a three-dimensional habitat, food and nursery grounds for many other species. During the past decades, the state of the coastal waters has deteriorated due to increasing human pressures, resulting in dramatic changes in coastal ecosystems, including macroalgal communities. To reverse the deterioration of the European seas, the EU has adopted the Water Framework Directive (WFD) and the Marine Strategy Framework Directive (MSFD), aiming at improved status of the coastal waters and the marine environment. Further, the Habitats Directive (HD) calls for the protection of important habitats and species (many of which are marine) and the Maritime Spatial Planning Directive for sustainability in the use of resources and human activities at sea and by the coasts. To efficiently protect important marine habitats and communities, we need knowledge on their spatial distribution. Ecological knowledge is also needed to assess the status of the marine areas by involving biological indicators, as required by the WFD and the MSFD; knowledge on how biota changes with human-induced pressures is essential, but to reliably assess change, we need also to know how biotic communities vary over natural environmental gradients. This is especially important in sea areas such as the Baltic Sea, where the natural environmental gradients create substantial differences in biota between areas. In this thesis, I studied the variation occurring in macroalgal communities across the environmental gradients of the northern Baltic Sea, including eutrophication induced changes. The aim was to produce knowledge to support the reliable use of macroalgae as indicators of ecological status of the marine areas and to test practical metrics that could potentially be used in status assessments. Further, the aim was to develop a methodology for mapping the HD Annex I habitat reefs, using the best available data on geology and bathymetry. The results showed that the large-scale variation in the macroalgal community composition of the northern Baltic Sea is largely driven by salinity and exposure. Exposure is important also on smaller spatial scales, affecting species occurrence, community structure and depth penetration of algae. Consequently, the natural variability complicates the use of macroalgae as indicators of human-induced changes. Of the studied indicators, the number of perennial algal species, the perennial cover, the fraction of annual algae, and the lower limit of occurrence of red and brown perennial algae showed potential as usable indicators of ecological status. However, the cumulated cover of algae, commonly used as an indicator in the fully marine environments, showed low responses to eutrophication in the area. Although the mere occurrence of perennial algae did not show clear indicator potential, a distinct discrepancy in the occurrence of bladderwrack, Fucus vesiculosus, was found between two areas with differing eutrophication history, the Bothnian Sea and the Archipelago Sea. The absence of Fucus from many potential sites in the outer Archipelago Sea is likely due to its inability to recover from its disappearance from the area 30-40 years ago, highlighting the importance of past events in macroalgal occurrence. The methodology presented for mapping the potential distribution and the ecological value of reefs showed, that relatively high accuracy in mapping can be achieved by combining existing available data, and the maps produced serve as valuable background information for more detailed surveys. Taken together, the results of the theses contribute significantly to the knowledge on macroalgal communities of the northern Baltic Sea that can be directly applied in various management contexts.

Cardiac Troponin Specific Autoantibodies: Analytical Tools for Exploring Their Impact on Cardiac Troponin I Testing

Cardiac troponin (cTn) I and T are the recommended biomarkers for the diagnosis and risk stratification of patients with suspected acute coronary syndrome (ACS), a major cause of cardiovascular death and disability worldwide. It has recently been demonstrated that cTn-specific autoantibodies (cTnAAb) can negatively interfere with cTnI detection by immunoassays to the extent that cTnAAb-positive patients may be falsely designated as cTnI-negative. The aim of this thesis was to develop and optimize immunoassays for the detection of both cTnI and cTnAAb, which would eventually enable exploring the clinical impact of these autoantibodies on cTnI testing and subsequent patient management. The extent of cTnAAb interference in different cTnI assay configurations and the molecular characteristics of cTnAAbs were investigated in publications I and II, respectively. The findings showed that cTnI midfragment targeting immunoassays used predominantly in clinical practice are affected by cTnAAb interference which can be circumvented by using a novel 3+1-type assay design with three capture antibodies against the N-terminus, midfragment and C-terminus and one tracer antibody against the C-terminus. The use of this assay configuration was further supported by the epitope specificity study, which showed that although the midfragment is most commonly targeted by cTnAAbs, the interference basically encompasses the whole molecule, and there may be remarkable individual variation at the affected sites. In publications III and IV, all the data obtained in previous studies were utilized to develop an improved version of an existing cTnAAb assay and a sensitive cTnI assay free of this specific analytical interference. The results of the thesis showed that approximately one in 10 patients with suspected ACS have detectable amounts of cTnAAbs in their circulation and that cTnAAbs can inhibit cTnI determination when targeted against the binding sites of assay antibodies used in its immunological detection. In the light of these observations, the risk of clinical misclassification caused by the presence of cTnAAbs remains a valid and reasonable concern. Because the titers, affinities and epitope specificities of cTnAAbs and the concentration of endogenous cTnI determine the final effect of circulating cTnAAbs, appropriately sized studies on their clinical significance are warranted. The new cTnI and cTnAAb assays could serve as analytical tools for establishing the impact of cTnAAbs on cTnI testing and also for unraveling the etiology of cTn-related autoimmune responses.