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.

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.

Energy harvesting methods for wireless sensor nodes in heavy-duty vehicles

The number of autonomous wireless sensor and control nodes has been increasing rapidly during the last decade. Until recently, these wireless nodes have been powered with batteries, which have lead to a short life cycle and high maintenance need. Due to these battery-related problems, new energy sources have been studied to power wireless nodes. One solution is energy harvesting, i.e. extracting energy from the ambient environment. Energy harvesting can provide a long-lasting power source for sensor nodes, with no need for maintenance. In this thesis, various energy harvesting technologies are studied whilst focusing on the theory of each technology and the state-of-the-art solutions of published studies and commercial solutions. In addition to energy harvesting, energy storage and energy management solutions are also studied as a subsystem of a whole energy source solution. Wireless nodes are also used in heavy-duty vehicles. Therefore a reliable, long-lasting and maintenance-free power source is also needed in this kind of environment. A forestry harvester has been used as a case study to study the feasibility of energy harvesting in a forestry harvester’s sliding boom. The energy harvester should be able to produce few milliwatts to power the target system, an independent limit switch.

Virtual Professional Network as a Value Creator in the Dental Business

The research of virtual professional networks has been enormous but the lack of research in the dental field was obvious. This study focuses on those uses and gratifications, and motives of participants that a virtual pro-fessional network should fulfil. The aim of this study is to understand the factors behind the successful virtual professional network, and motives of participants that support a particular business network’s building up for contributing its further success. In this study the focus is on particular mo-tives, needs and benefits of participants that are significant for the net-work’s further development. The study will explore relevant scientific research and theory that is char-acteristic in networking, and theories of user’s needs and motives. Empiri-cal data was collected from dental professionals by net based question-naire that was sent by e-mail. Data analysis was done by quantitative fac-tor analysis. The findings of this study were obvious that virtual knowledge of implantology is inadequate and knowledge is rather difficult to find in the Internet. Sharing of virtual knowledge, net-learning and communication were seen to improve the quality of impolantological professionalism and also the development of these areas was experienced essential. On the grounds of this study a host of a virtual professional network can focus on those aspects that serve the users at best, can develop professionalism in implantology and can profit in its own business operations.

The Cellular Oxygen Sensor PHD2 in Cancer Growth

Adequate supply of oxygen is essential for the survival of multicellular organisms. However, in several conditions the supply of oxygen can be disturbed and the tissue oxygenation is compromised. This condition is termed hypoxia. Oxygen homeostasis is maintained by the regulation of both the use and delivery of oxygen through complex, sensitive and cell-type specific transcriptional responses to hypoxia. This is mainly achieved by one master regulator, a transcription factor called hypoxiainducible factor 1 (HIF-1). The amount of HIF-1 is under tight oxygen-dependent control by a family of oxygen-dependent prolyl hydroxylase domain proteins (PHDs) that function as the cellular oxygen sensors. Three family members (PHD1-3) are known to regulate HIF of which the PHD2 isoform is thought to be the main regulator of HIF-1. The supply of oxygen can be disturbed in pathophysiological conditions, such as ischemic disorders and cancer. Cancer cells in the hypoxic parts of the tumors exploit the ability of HIF-1 to turn on the mechanisms for their survival, resistance to treatment, and escape from the oxygen- and nutrient-deprived environment. In this study, the expression and regulation of PHD2 were studied in normal and cancerous tissues, and its significance in tumor growth. The results show that the expression of PHD2 is induced in hypoxic cells. It is overexpressed in head and neck squamous cell carcinomas and colon adenocarcinomas. Although PHD2 normally resides in the cytoplasm, nuclear translocation of PHD2 was also seen in a subset of tumor cells. Together with the overexpression, the nuclear localization correlated with the aggressiveness of the tumors. The nuclear localization of PHD2 caused an increase in the anchorage-independent growth of cancer cells. This study provides information on the role of PHD2, the main regulator of HIF expression, in cancer progression. This knowledge may prove to be valuable in targeting the HIF pathway in cancer treatment.

Implementing gateway monitoring service for infrastructure sensor networks

Wireless sensor networks and its applications have been widely researched and implemented in both commercial and non commercial areas. The usage of wireless sensor network has developed its market from military usage to daily use of human livings. Wireless sensor network applications from monitoring prospect are used in home monitoring, farm fields and habitant monitoring to buildings structural monitoring. As the usage boundaries of wireless sensor networks and its applications are emerging there are definite ongoing research, such as lifetime for wireless sensor network, security of sensor nodes and expanding the applications with modern day scenarios of applications as web services. The main focus in this thesis work is to study and implement monitoring application for infrastructure based sensor network and expand its usability as web service to facilitate mobile clients. The developed application is implemented for wireless sensor nodes information collection and monitoring purpose enabling home or office environment remote monitoring for a user.

Electrical Equivalent Circuit for Dry Bacteriorhodopsin Sensor

Bacteriorhodopsin (BR) is a photosensitive protein which functions as a light-driven proton pump. Due to its photoactivity, BR could be used in photosensing and information processing which has inspired researchers to study the photoelectric response and the appropriate measurement instrumentation for BR. In this thesis, the measurement instrumentation connected to a dry BR sensor was confirmed to affect the photovoltage response measured by using voltage amplifiers. Changing of the input impedance of the measurement instrumentation was shown to alter a part of the measured photovoltage response. The photocurrent measurements using transimpedance amplifier and the presented electrical equivalent circuit were used to show that the photocurrent measurements have no significant effect on the photoelectric response. The photocurrent was shown to be a derivate of the photovoltage response measured from the dry BR sensor when it was compared to the response measured with a voltage amplifier. This confirmed that another part of the photovoltage response was not affected by the measurement instrumentation. The time-variant behavior of the dry BR sensor was confirmed in both the photocurrent and the photovoltage measurements. This was caused by the fact that the capacitance of the dry BR sensor changes with the excitation light intensity.

Virtual Battlespace 2 Panssarikoulun opetuksessa : tapaustutkimus sotilaspedagogiikan näkökulmasta

Tutkielmani tavoitteena oli tutkia tapauksena Bohemia Interactive Simulationsin valmistaman Virtual Battlespace 2 (VBS2) -tietokonepelisimulaattorin käyttöönottoa Panssariprikaatin Panssarikoulun varusmieskoulutuksessa. Tutkimuskysymysten avulla oli tarkoituksena selvittää, mitkä tekijät ja tapahtumat vaikuttivat siihen, että VBS2 otettiin käyttöön, minkälaisin perustein koulutus suunniteltiin ja järjestelmän käyttö varusmieskoulutuksessa käynnistettiin. Lisäksi ajatuksena oli aineiston mahdollistamissa puitteissa tutkia VBS2:n käytöstä tähän mennessä kertyneitä kokemuksia kouluttajien näkökulmasta, tavoitteena tuottaa myös perustietoa tulevaisuuden VBS2-koulutuksen suunnittelua ja toteuttamista varten. Tutkimusmenetelmänä oli tapaustutkimus, jonka aineisto kerättiin toteuttamalla teemahaastatteluita. Tutkimusta varten haastateltiin kahta VBS2-järjestelmää ensimmäisenä varusmieskoulutuksessa käyttänyttä kouluttajaa. Haastatteluaineisto käsiteltiin aineistolähtöisen sisällönanalyysin menetelmin. Tuloksia tarkasteltiin sotilaspedagogiikan näkökulmasta ja suhteessa oppimisympäristöjen sekä oppimisprosessin suunnittelun teorioihin. Tutkielma rakentuu johdannosta, menetelmäluvusta, yhdistetystä teoria- ja tulosluvusta sekä johtopäätös- ja pohdintaluvusta. Tutkimuksen tuloksina ilmeni, että Virtual Battlespace 2:n käyttöönotto Panssarikoulussa oli aktiivisten ja innovatiivisten henkilöiden aikaansaannosta, jossa spontaanin, ennakkoluulottoman ja opetuksen laadun kehittämiseen tähtäävän kokeilun myötä otettiin käyttöön uudenlainen koulutusväline. Samalla saatiin aikaan myönteisiä oppimistuloksia ja kiinnostavia muutoksia yhden joukkoyksikön koulutuskulttuuriin ja totunnaisiin koulutuksen käytäntöihin. VBS2:n käyttöön liittyviä keskeisiä teemoja ovat oppimisprosessin kokonaisvaltainen hallinta, eli VBS2-koulutuksen huolellinen suunnittelu ja integrointi osaksi muuta koulutusta, koulutustapahtumien valmistelujen ja kouluttajien ammattitaidon merkitys, koulutustapahtumien johtamisen paikoin muusta sotilaskoulutuksesta poikkeavat käytännöt sekä VBS2:n aikaansaaman oppimisen ymmärtäminen. Kouluttajien kokemusten perusteella VBS2 on avoin oppimisympäristö, joka ei korvaa mitään olemassa olevista koulutusmuodoista, mutta täydentää niitä tehokkaasti tarjoten uudenlaisia ulottuvuuksia sotilaskoulutukseen. Sen avulla voidaan tehokkaasti kehittää erityisesti sotilaan henkistä ja sosiaalista toimintakykyä sekä siirtää koulutuksen painopistettä soveltaviin maastoharjoituksiin. Tutkielma avaa näkökulmia VBS2:n ja muiden virtuaalisten oppimisympäristöjen pedagogiselle pohtimiselle ja tuleville aiheeseen syventyville tutkimuksille. Lisäksi se herättää keskustelua varusmieskoulutuksemme parhaista käytänteistä ja kehitystrendeistä.

Value co-creation through virtual community participation

Consumers create a great deal of content in the Internet. As they do not get a monetary compensation for doing so, it seems apparent that other types of reward are derived from giving up one's time and other resources. The purpose of this study is to describe value creation and user participation in a virtual community. It can be broken down into three research questions. 1. What is the value creation logic of a virtual community? 2. What value is perceived by virtual community users? 3. What is the association between value perceived by virtual community users and their participation in a community? The study employs the discussion on value co-creation as well as perspectives on the notion of value for consumers to create a theoretical framework for value creation. To understand value creation in the context of virtual communities and to create a theoretical framework for user participation, existing literature and research on virtual communities is discussed. The empirical part of the study employs quantitative methodology to analyze data collected by sending a survey questionnaire to the users of a Finnish wellbeing-based virtual community. The results indicate that virtual community users perceive self-development, enjoyment, reputation-building and community commitment value when using the service and that value perceptions are associated with community participation. Moreover, it was found that different types of value are associated with different forms of participation. Based on the findings, it is suggested that the four types of value make up a considerable share of value for virtual community users. Moreover, as the results indicate that different value types are associated with different forms of participation, it suggested that virtual community organizers consider what forms of participation they want to promote and design their virtual communities to support creation of the different types of value accordingly.

Heat flux measurement inside internal combustion engine with gradient heat flux sensor.

This master’s thesis is devoted to study different heat flux measurement techniques such as differential temperature sensors, semi-infinite surface temperature methods, calorimetric sensors and gradient heat flux sensors. The possibility to use Gradient Heat Flux Sensors (GHFS) to measure heat flux in the combustion chamber of compression ignited reciprocating internal combustion engines was considered in more detail. A. Mityakov conducted an experiment, where Gradient Heat Flux Sensor was placed in four stroke diesel engine Indenor XL4D to measure heat flux in the combustion chamber. The results which were obtained from the experiment were compared with model’s numerical output. This model (a one – dimensional single zone model) was implemented with help of MathCAD and the result of this implementation is graph of heat flux in combustion chamber in relation to the crank angle. The values of heat flux throughout the cycle obtained with aid of heat flux sensor and theoretically were sufficiently similar, but not identical. Such deviation is rather common for this type of experiment.