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.

Effect of forest-based biofuels production on carbon footprint, Case: Integrated LWC paper mill

International energy and climate strategies also set Finland’s commitments to increasing the use of renewable energy sources and reducing greenhouse gas emissions. The target can be achieved by, for example, increasing the use of energy wood. Finland’s forest biomass potential is significant compared with current use. Increased use will change forest management and wood harvesting methods however. The thesis examined the potential for integrated pulp and paper mills to increase bioenergy production. The effects of two bioenergy production technologies on the carbon footprint of an integrated LWC mill were studied at mill level and from the cradle-to-customer approach. The LignoBoost process and FT diesel production were chosen as bioenergy cases. The data for the LignoBoost process were obtained from Metso and for the FT diesel process from Neste Oil. The rest of the information is based on the literature and databases of the KCL-ECO life-cycle computer program and Ecoinvent. In both case studies, the carbon footprint was reduced. From the results, it can be concluded that it is possible to achieve a fossil-fuel-free pulp mill with the LignoBoost process. By using steam from the FT diesel process, the amount of auxiliary fuel can be reduced considerably and the bark boiler can be replaced. With a choice of auxiliary fuels for use in heat production in the paper mill and the production methods for purchased electricity, it is possible to affect the carbon footprints even more in both cases.

Design and Analysis of Forward Error Control Coding and Signaling for Guaranteeing QoS in Wireless Broadcast Systems

Broadcasting systems are networks where the transmission is received by several terminals. Generally broadcast receivers are passive devices in the network, meaning that they do not interact with the transmitter. Providing a certain Quality of Service (QoS) for the receivers in heterogeneous reception environment with no feedback is not an easy task. Forward error control coding can be used for protection against transmission errors to enhance the QoS for broadcast services. For good performance in terrestrial wireless networks, diversity should be utilized. The diversity is utilized by application of interleaving together with the forward error correction codes. In this dissertation the design and analysis of forward error control and control signalling for providing QoS in wireless broadcasting systems are studied. Control signaling is used in broadcasting networks to give the receiver necessary information on how to connect to the network itself and how to receive the services that are being transmitted. Usually control signalling is considered to be transmitted through a dedicated path in the systems. Therefore, the relationship of the signaling and service data paths should be considered early in the design phase. Modeling and simulations are used in the case studies of this dissertation to study this relationship. This dissertation begins with a survey on the broadcasting environment and mechanisms for providing QoS therein. Then case studies present analysis and design of such mechanisms in real systems. The mechanisms for providing QoS considering signaling and service data paths and their relationship at the DVB-H link layer are analyzed as the first case study. In particular the performance of different service data decoding mechanisms and optimal signaling transmission parameter selection are presented. The second case study investigates the design of signaling and service data paths for the more modern DVB-T2 physical layer. Furthermore, by comparing the performances of the signaling and service data paths by simulations, configuration guidelines for the DVB-T2 physical layer signaling are given. The presented guidelines can prove useful when configuring DVB-T2 transmission networks. Finally, recommendations for the design of data and signalling paths are given based on findings from the case studies. The requirements for the signaling design should be derived from the requirements for the main services. Generally, these requirements for signaling should be more demanding as the signaling is the enabler for service reception.

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.

Integrating eco-innovation principles into regional strategy and policy: case of Päijät-Häme region, Finland

This study focuses on the integration of eco-innovation principles into strategy and policy at the regional level. The importance of regions as a level for integrating eco-innovative programs and activities served as the point of interest for this study. Eco-innovative activities and technologies are seen as means to meet sustainable development objective of improving regions’ quality of life. This study is conducted to get an in-depth understanding and learning about eco-innovation at regional level, and to know the basic concepts that are important in integrating eco-innovation principles into regional policy. Other specific objectives of this study are to know how eco-innovation are developed and practiced in the regions of the EU, and to analyze the main characteristic features of an eco-innovation model that is specifically developed at Päijät-Häme Region in Finland. Paijät-Häme Region is noted for its successful eco-innovation strategies and programs, hence, taken as casework in this study. Both primary (interviews) and secondary data (publicly available documents) are utilized in this study. The study shows that eco-innovation plays an important role in regional strategy as reviewed based on the experience of other regions in the EU. This is because of its localized nature which makes it easier to facilitate in a regional setting. Since regional authorities and policy-makers are normally focused on solving its localized environmental problems, eco-innovation principles can easily be integrated into regional strategy. The case study highlights Päijät-Häme Region’s eco-innovation strategies and projects which are characterized by strong connection of knowledge-producing institutions. Policy instruments supporting eco-innovation (e.g. environmental technologies) are very much focused on clean technologies, hence, justifying the formation of cleantech clusters and business parks in Päijät-Häme Region. A newly conceptualized SAMPO model of eco-innovation has been developed in Päijät-Häme Region to better capture the region’s characteristics and to eventually replace the current model employed by the Päijät-Häme Regional Authority. The SAMPO model is still under construction, however, review of its principles points to some of its three important spearheads – practice-based innovation, design (eco-design) and clean technology or environmental technology (environment).

Economic optimization method to design telescope irrigation of multiples outlets

In this study is presented an economic optimization method to design telescope irrigation laterals (multidiameter) with regular spaced outlets. The proposed analytical hydraulic solution was validated by means of a pipeline composed of three different diameters. The minimum acquisition cost of the telescope pipeline was determined by an ideal arrangement of lengths and respective diameters for each one of the three segments. The mathematical optimization method based on the Lagrange multipliers provides a strategy for finding the maximum or minimum of a function subject to certain constraints. In this case, the objective function describes the acquisition cost of pipes, and the constraints are determined from hydraulic parameters as length of irrigation laterals and total head loss permitted. The developed analytical solution provides the ideal combination of each pipe segment length and respective diameter, resulting in a decreased of the acquisition cost.

AGRICULTURAL MACHINERY AND IMPLEMENTS DESIGN PROCESS: GUIDELINES FOR SMALL AND MID-SIZED BUSINESSES

ABSTRACT This study aims at presenting the process of machine design and agricultural implements by means of a reference model, formulated with the purpose of explaining the development activities of new products, serving as a guideline to coach human resources and to assist in formalizing the process in small and medium-sized businesses (SMB), i.e. up to 500 employees. The methodology used included the process modeling, carried out from case studies in the SMB, and the study of reference models in literature. The modeling formalism used was based on the IDEF0 standard, which identifies the dimensions required for the model detailing: input information; activities; tasks; knowledge domains; mechanisms; controls and information produced. These dimensions were organized in spreadsheets and graphs. As a result, a reference model with 27 activities and 71 tasks was obtained, distributed over four phases of the design process. The evaluation of the model was carried out by the companies participating in the case studies and by experts, who concluded that the model explains the actions needed to develop new products in SMB.

SOCIAL MEDIA IN INTERNATIONAL BRAND COMMUNICATION OF SMES - A multiple case study of small Finnish design-intensive companies

Social media is a rather new phenomenon which has revolutionised the world of online communication. However, academic research on how companies can benefit from social media is lacking. The research objective of this thesis was to examine the use of social media in international brand communication of small Finnish design-intensive companies. Therefore, this research contributes also to the research gap in SME branding. The focus was on communication targeted at consumers. The research was carried out as a mixed methods research employing the questionnaire and multiple case study methods. The questionnaire was used to gather preliminary information on Finnish design-intensive companies and to provide an eligible list of companies for deeper examination. Then, four case companies were studied in more depth. The empirical evidence of the case companies was mainly gathered through theme interviews. The results of the questionnaire shed light on the internationalisation of small Finnish designintensive companies. On average, the companies had internationalised rather quickly after they had been founded. However, the share of exports was rather low in most of the companies. The results revealed also that social media was already used widely in the exporting companies and the use can be expected to grow in future. The findings of the multiple case study suggest that branding activities in small Finnish designintensive companies are constrained by limited resources and skills. In addition, the branding activities are strongly guided by the vision and values of the entrepreneur(s) rather than extensive marketing research. The brand structure was simple in all case companies and they aimed at having a standardised brand image across markets. However, all case companies had faced a need for some adaptation of their international brand communication. Internationally important brand communication channels were international fairs, the internet, word-of-mouth and social media. Social media offered a cost-effective brand communication channel for the case companies. It was used for various purposes, such as creating brand awareness and affecting how the brand is perceived. The entrepreneurs found the use of social media to be rather easy and the case companies had not faced any major challenges. However, the companies had recognised that communication in social media requires consistency and planning. The planning was rather informal and stayed on a general level. Overall, the utilisation of social media in the case companies was limited by a lack of resources. It seemed to affect especially the follow-up of brand communication in social media which stayed rather superficial.

Working capital management in the small and medium-sized enterprises Case: Project-based business environment in Flowrox Oy

This Master´s thesis illustrates how growing a business ties up the company´s working capital and what the cost of committed capital. In order to manage a company´s working capital in rapid business growth phase, the thesis suggests that by monitoring and managing the operating and cash conversion cycles of customers´ projects, a company can find ways to secure the required amount of capital. The research method of this thesis was based on literature reviews and case study research. The theoretical review presents the concepts of working capital and provides the background for understanding how to improve working capital management. The company in subject is a global small and medium-sized enterprise that manufactures pumps and valves for demanding process conditions. The company is expanding, which creates lots of challenges. This thesis concentrates to the company´s working capital management and its efficiency through the supply chain and value chain perspective. The main elements of working capital management are inventory management, accounts receivable management and accounts payable management. Prepayments also play a significant role, particularly in project-based businesses. Developing companies´ working capital management requires knowledge from different kind of key operations´ in the company, like purchasing, production, sales, logistics and financing. The perspective to develop and describe working capital management is an operational. After literature reviews the thesis present pilot projects that formed the basis of a model to monitor working capital in the case company. Based on analysis and pilot projects, the thesis introduces a rough model for monitoring capital commitments in short time period. With the model the company can more efficiently monitor and manage their customer projects.

The impact of a new partnership outsourcing arrangement: a routine-based case study in detail engineering

This thesis investigated the contemporary phenomenon of detail engineering outsourcing. The case organization had pursued a new outsourcing approach with a trusted partner. The goal of this empirical study was to examine the impact of the consequential partnership outsourcing arrangement. Particularly, the beneficence of the arrangement was evaluated based on the underlying organizational routine and the long-term economic implications of its performance outcome. The case study was needed, as the unit will likely have to rely on such distance outsourcing arrangements more and more in the future, and understanding on the impact of such operations is needed. The main findings revealed that the new outsourcing arrangement is not currently a very attractive strategic option for organizing production. The benefits which stem from the emerged, unique engineering project routine are not significant enough to make the arrangement an advantageous one, especially since increasing partnering costs are being met. This conclusion was drawn via the extended transaction cost view. Benchmarking was done in reliance to an old arrangement from which the new pursuit was a departure from. The case study then enlightened the engineering unit on the impact of its strategic maneuver by combining the routines-theory framework with contemporary methods of governance structure evaluation. Through this, it was shown that greater efforts are needed to make the new outsourcing approach a more beneficial one. However, the studied arrangement was seen to inhold potential for better results. The findings can be used to capitalize on this.

Building a creative city brand through an international mega-event : Case: Helsinki World Design Capital 2012

In order to grow, cities are increasingly competing for attention, jobs, investments, visitors, residents and significant events. Cities need to come up with creative solutions to keep up with the competition; they ought to become creative cities. Attracting talented and diverse inhabitants is a key factor in developing a creative city, which on is characterized by openness, tolerance, vibrancy and diversity. Along the need for renewed city images city brand building has become popular. Helsinki is the World Design Capital 2012 (WDC 2012) and this mega-event presents a meaningful opportunity for the city to broadcast itself globally. The purpose of this study is to evaluate how Helsinki brands itself as a creative city through an international mega-event. The sub-aims are to: 1) Map the factors behind the creative city and their relation to the city of Helsinki, 2) Describe the city branding process, 3) Evaluate the role of the Helsinki World Design Capital 2012 mega-event in Helsinki’s creative city brand building. First, the theory discusses the concept of the creative city that has gained growing attention during the past decade. Then, the city branding process is described and the benefits of hosting a mega-event are presented. Finally, co-branding a city and a mega-event in order to generate maximum benefit from the mega-event, is reviewed. This is a qualitative research for which data was collected through three face-to-face interviews, the World Design Capital 2012 bid, Helsinki’s economic development strategy, a consulting firm’s research report on the case city and web-pages. The research reveals that Helsinki has shown interest in the creative city discussion. The terminology around the concept is however approached carefully. Helsinki fits many of the creative city characteristics and recognizes its flaws for which improvement strategies have been planned. Bottlenecks keeping the city from promoting a more open mind were mainly revealed in its organizational structures. Helsinki has no official brand strategy; nonetheless pressure to develop one is present. The World Design Capital 2012 mega-event is seen as a meaningful stepping board to strengthen Helsinki’s identity and image, and start thinking about a city brand. The brand strategies of the mega-event support the values and virtues of the city itself, which enables benefits of co-branding introduces in the theory part. Helsinki has no official brand and doesn’t call itself a creative city, however this study shows signs of the city taking steps towards building a creative city brand with the help of the Helsinki World Design Capital 2012 mega-event.

The case of web based information environment in web based weight management services

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