Immobilization of Burkholderia cepacia Lipase: Kinetic Resolution in Organic Solvents, Ionic Liquids and in Their Mixtures

Immobilization of Burkholderia cepacia Lipase: Kinetic Resolution in Organic Solvents, Ionic Liquids and in Their Mixtures Biocatalysis opens the door to green and sustainable processes in synthetic chemistry allowing the preparation of single enantiomers, since the enzymes are chiral and accordingly able to catalyze chemical reactions under mild conditions. Immobilization of enzymes enhances process robustness, often stabilizes and activates the enzyme, and enables reuse of the same enzyme preparation in multiple cycles. Although hundreds of variations of immobilization methods exist, there is no universal method to yield the highly active, selective and stable enzyme catalysts. Therefore, new methods need to be developed to obtain suitable catalysts for different substrates and reaction environments. Lipases are the most widely used enzymes in synthetic organic chemistry. The literature part together with the experimental part of this thesis discusses of the effects of immobilization methods mostly used to enhance lipase activity, stability and enantioselectivity. Moreover, the use of lipases in the kinetic resolution of secondary alcohols in organic solvents and in ionic liquids is discussed. The experimental work consists of the studies of immobilization of Burkholderia cepacia lipase (lipase PS) using three different methods: encapsulation in sol-gels, cross-linked enzyme aggregates (CLEAs) and supported ionic liquids enzyme catalysts (SILEs). In addition, adsorption of lipase PS on celite was studied to compare the results obtained with sol-gels, CLEAs and SILEs. The effects of immobilization on enzyme activity, enantioselectivity and hydrolysis side reactions were studied in kinetic resolution of three secondary alcohols in organic solvents, in ionic liquids (ILs), and in their mixtures. Lipase PS sol-gels were shown to be active and stable catalysts in organic solvents and solvent:IL mixtures. CLEAs and SILEs were highly active and enantioselective in organic solvents. Sol-gels and SILEs were reusable in several cycles. Hydrolysis side reaction was suppressed in the presence of sol-gels and CLEAs.

Developing correlative Optical-Photoacustic microscopy for high-resolution in vivo imaging

PhotoAcoustic Imaging (PAI) is a branch in clinical and pre-clinical imaging, that refers to the techniques mapping acoustic signals caused by the absorption of the short laser pulse. This conversion of electromagnetic energy of the light to the mechanical (acoustic) energy is usually called photoacoustic effect. PAI, by combining optical excitation with acoustical detection, is able to preserve the diffraction limited spatial resolution. At the same time, the penetration depth is extended beyond the diffusive limit. The Laser-Scanning PhotoAcoustic Microscope system (LS-PAM) has been developed, that offers the axial resolution of 7.75 µm with the lateral resolution better than 10 µm. The first in vivo imaging experiments were carried out. Thus, in vivo label-free imaging of the mouse ear was performed. The principle possibility to image vessels located in deep layers of the mouse skin was shown. As well as that, a gold printing sample, vasculature of the Chick Chorioallantoic Membrane Assay, Drosophila larvae were imaged by PAI. During the experimental work, a totally new application of PAM was found, in which the acoustic waves, generated by incident light can be used for further imaging of another sample. In order to enhance the performance of the presented system two main recommendation can be offered. First, the current system should be transformed into reflection-mode setup system. Second, a more powerful source of light with the sufficient repetition rate should be introduced into the system.

Bioimage informatics in STED super-resolution microscopy

Optical microscopy is living its renaissance. The diffraction limit, although still physically true, plays a minor role in the achievable resolution in far-field fluorescence microscopy. Super-resolution techniques enable fluorescence microscopy at nearly molecular resolution. Modern (super-resolution) microscopy methods rely strongly on software. Software tools are needed all the way from data acquisition, data storage, image reconstruction, restoration and alignment, to quantitative image analysis and image visualization. These tools play a key role in all aspects of microscopy today – and their importance in the coming years is certainly going to increase, when microscopy little-by-little transitions from single cells into more complex and even living model systems. In this thesis, a series of bioimage informatics software tools are introduced for STED super-resolution microscopy. Tomographic reconstruction software, coupled with a novel image acquisition method STED< is shown to enable axial (3D) super-resolution imaging in a standard 2D-STED microscope. Software tools are introduced for STED super-resolution correlative imaging with transmission electron microscopes or atomic force microscopes. A novel method for automatically ranking image quality within microscope image datasets is introduced, and it is utilized to for example select the best images in a STED microscope image dataset.

Computational Analysis and Optimization of Real Gas Flow In Small Centrifugal Compressors

Small centrifugal compressors are more and more widely used in many industrialsystems because of their higher efficiency and better off-design performance comparing to piston and scroll compressors as while as higher work coefficient perstage than in axial compressors. Higher efficiency is always the aim of the designer of compressors. In the present work, the influence of four partsof a small centrifugal compressor that compresses heavy molecular weight real gas has been investigated in order to achieve higher efficiency. Two parts concern the impeller: tip clearance and the circumferential position of the splitter blade. The other two parts concern the diffuser: the pinch shape and vane shape. Computational fluid dynamics is applied in this study. The Reynolds averaged Navier-Stokes flow solver Finflo is used. The quasi-steady approach is utilized. Chien's k-e turbulence model is used to model the turbulence. A new practical real gas model is presented in this study. The real gas model is easily generated, accuracy controllable and fairly fast. The numerical results and measurements show good agreement. The influence of tip clearance on the performance of a small compressor is obvious. The pressure ratio and efficiency are decreased as the size of tip clearance is increased, while the total enthalpy rise keeps almost constant. The decrement of the pressure ratio and efficiency is larger at higher mass flow rates and smaller at lower mass flow rates. The flow angles at the inlet and outlet of the impeller are increased as the size of tip clearance is increased. The results of the detailed flow field show that leakingflow is the main reason for the performance drop. The secondary flow region becomes larger as the size of tip clearance is increased and the area of the main flow is compressed. The flow uniformity is then decreased. A detailed study shows that the leaking flow rate is higher near the exit of the impeller than that near the inlet of the impeller. Based on this phenomenon, a new partiallyshrouded impeller is used. The impeller is shrouded near the exit of the impeller. The results show that the flow field near the exit of the impeller is greatly changed by the partially shrouded impeller, and better performance is achievedthan with the unshrouded impeller. The loading distribution on the impeller blade and the flow fields in the impeller is changed by moving the splitter of the impeller in circumferential direction. Moving the splitter slightly to the suction side of the long blade can improve the performance of the compressor. The total enthalpy rise is reduced if only the leading edge of the splitter ismoved to the suction side of the long blade. The performance of the compressor is decreased if the blade is bended from the radius direction at the leading edge of the splitter. The total pressure rise and the enthalpy rise of thecompressor are increased if pinch is used at the diffuser inlet. Among the fivedifferent pinch shape configurations, at design and lower mass flow rates the efficiency of a straight line pinch is the highest, while at higher mass flow rate, the efficiency of a concave pinch is the highest. The sharp corner of the pinch is the main reason for the decrease of efficiency and should be avoided. The variation of the flow angles entering the diffuser in spanwise direction is decreased if pinch is applied. A three-dimensional low solidity twisted vaned diffuser is designed to match the flow angles entering the diffuser. The numerical results show that the pressure recovery in the twisted diffuser is higher than in a conventional low solidity vaned diffuser, which also leads to higher efficiency of the twisted diffuser. Investigation of the detailed flow fields shows that the separation at lower mass flow rate in the twisted diffuser is later than in the conventional low solidity vaned diffuser, which leads to a possible wider flow range of the twisted diffuser.

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

Thermal Stress in a Roll-to-Roll Printed Electronics Substrate

The Roll-to-Roll process makes it possible to print electronic products continuously onto a uniform substrate. Printing components on flexible surfaces can bring down the costs of simple electronic devices such as RFID tags, antennas and transistors. The possibility of quickly printing flexible electronic components opens up a wide array of novel products previously too expensive to produce on a large scale. Several different printing methods can be used in Roll-to-Roll printing, such as gravure, spray, offset, flexographic and others. Most of the methods can also be mixed in one production line. Most of them still require years of research to reach a significant commercial level. The research for this thesis was carried out at the Konkuk University Flexible Display Research Center (KU-FDRC) in Seoul, Korea. A system using Roll-to-Roll printing requires that the motion of the web can be controlled in every direction in order to align different layers of ink properly. Between printers the ink is dried with hot air. The effects of thermal expansion on the tension of the web are studied in this work, and a mathematical model was constructed on Matlab and Simulink. Simulations and experiments lead to the conclusion that the thermal expansion of the web has a great influence on the tension of the web. Also, experimental evidence was gained that the particular printing machine used for these experiments at KU-FDRC may have a problem in controlling the speeds of the cylinders which pull the web.

Machine vision methods for process measurements in pulping

The papermaking industry has been continuously developing intelligent solutions to characterize the raw materials it uses, to control the manufacturing process in a robust way, and to guarantee the desired quality of the end product. Based on the much improved imaging techniques and image-based analysis methods, it has become possible to look inside the manufacturing pipeline and propose more effective alternatives to human expertise. This study is focused on the development of image analyses methods for the pulping process of papermaking. Pulping starts with wood disintegration and forming the fiber suspension that is subsequently bleached, mixed with additives and chemicals, and finally dried and shipped to the papermaking mills. At each stage of the process it is important to analyze the properties of the raw material to guarantee the product quality. In order to evaluate properties of fibers, the main component of the pulp suspension, a framework for fiber characterization based on microscopic images is proposed in this thesis as the first contribution. The framework allows computation of fiber length and curl index correlating well with the ground truth values. The bubble detection method, the second contribution, was developed in order to estimate the gas volume at the delignification stage of the pulping process based on high-resolution in-line imaging. The gas volume was estimated accurately and the solution enabled just-in-time process termination whereas the accurate estimation of bubble size categories still remained challenging. As the third contribution of the study, optical flow computation was studied and the methods were successfully applied to pulp flow velocity estimation based on double-exposed images. Finally, a framework for classifying dirt particles in dried pulp sheets, including the semisynthetic ground truth generation, feature selection, and performance comparison of the state-of-the-art classification techniques, was proposed as the fourth contribution. The framework was successfully tested on the semisynthetic and real-world pulp sheet images. These four contributions assist in developing an integrated factory-level vision-based process control.

Characterization Of Process Efficiency Improvement In Laser Additive Manufacturing

Laser additive manufacturing (LAM), known also as 3D printing, has gained a lot of interest in past recent years within various industries, such as medical and aerospace industries. LAM enables fabrication of complex 3D geometries by melting metal powder layer by layer with laser beam. Research in laser additive manufacturing has been focused in development of new materials and new applications in past 10 years. Since this technology is on cutting edge, efficiency of manufacturing process is in center role of research of this industry. Aim of this thesis is to characterize methods for process efficiency improvements in laser additive manufacturing. The aim is also to clarify the effect of process parameters to the stability of the process and in microstructure of manufactured pieces. Experimental tests of this thesis were made with various process parameters and their effect on build pieces has been studied, when additive manufacturing was performed with a modified research machine representing EOSINT M-series and with EOS EOSINT M280. Material used was stainless steel 17-4 PH. Also, some of the methods for process efficiency improvements were tested. Literature review of this thesis presents basics of laser additive manufacturing, methods for improve the process efficiency and laser beam – material- interaction. It was observed that there are only few public studies about process efficiency of laser additive manufacturing of stainless steel. According to literature, it is possible to improve process efficiency with higher power lasers and thicker layer thicknesses. The process efficiency improvement is possible if the effect of process parameter changes in manufactured pieces is known. According to experiments carried out in this thesis, it was concluded that process parameters have major role in single track formation in laser additive manufacturing. Rough estimation equations were created to describe the effect of input parameters to output parameters. The experimental results showed that the WDA (width-depth-area of cross-sections of single track) is correlating exponentially with energy density input. The energy density input is combination of the input parameters of laser power, laser beam spot diameter and scan speed. The use of skin-core technique enables improvement of process efficiency as the core of the part is manufactured with higher laser power and thicker layer thickness and the skin with lower laser power and thinner layer thickness in order to maintain high resolution. In this technique the interface between skin and core must have overlapping in order to achieve full dense parts. It was also noticed in this thesis that keyhole can be formed in LAM process. It was noticed that the threshold intensity value of 106 W/cm2 was exceeded during the tests. This means that in these tests the keyhole formation was possible.

Towards multi bibliographic format support in Invenio

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

Vibrations in Rotating Machinery Arising from Minor Imperfections in Component Geometries

Vibrations in machines can cause noise, decrease the performance, or even damage the machine. Vibrations appear if there is a source of vibration that excites the system. In the worst case scenario, the excitation frequency coincides with the natural frequency of the machine causing resonance. Rotating machines are a machine type, where the excitation arises from the machine itself. The excitation originates from the mass imbalance in the rotating shaft, which always exists in machines that are manufactured using conventional methods. The excitation has a frequency that is dependent on the rotational speed of the machine. The rotating machines in industrial use are usually designed to rotate at a constant rotational speed, the case where the resonances can be easily avoided. However, the machines that have a varying operational speed are more problematic due to a wider range of frequencies that have to be avoided. Vibrations, which frequencies equal to rotational speed frequency of the machine are widely studied and considered in the typical machine design process. This study concentrates on vibrations, which arise from the excitations having frequencies that are multiples of the rotational speed frequency. These vibrations take place when there are two or more excitation components in a revolution of a rotating shaft. The dissertation introduces four studies where three kinds of machines are experiencing vibrations caused by different excitations. The first studied case is a directly driven permanent magnet generator used in a wind power plant. The electromagnetic properties of the generator cause harmonic excitations in the system. The dynamic responses of the generator are studied using the multibody dynamics formulation. In another study, the finite element method is used to study the vibrations of a magnetic gear due to excitations, which frequencies equal to the rotational speed frequency. The objective is to study the effects of manufacturing and assembling inaccuracies. Particularly, the eccentricity of the rotating part with respect to non-rotating part is studied since the eccentric operation causes a force component in the direction of the shortest air gap. The third machine type is a tube roll of a paper machine, which is studied while the tube roll is supported using two different structures. These cases are studied using different formulations. In the first case, the tube roll is supported by spherical roller bearings, which have some wavinesses on the rolling surfaces. Wavinesses cause excitations to the tube roll, which starts to resonate at the frequency that is a half of the first natural frequency. The frequency is in the range where the machine normally operates. The tube roll is modeled using the finite element method and the bearings are modeled as nonlinear forces between the tube roll and the pedestals. In the second case studied, the tube roll is supported by freely rotating discs, which wavinesses are also measured. The above described phenomenon is captured as well in this case, but the simulation methodology is based on the flexible multibody dynamics formulation. The simulation models that are used in both of the last two cases studied are verified by measuring the actual devices and comparing the simulated and measured results. The results show good agreement.

Hakunilan Kultsa/Urban II hanke : pohdintaa yhteisöteatterin merkityksestä alueelle

This thesis analyses what local community theatre activity means to an area and its residents, and whether this kind of activity is meaningful. The objective was to explore whether and how community art can help urban areas to move in the direction of sustainable development: whether art can be part of regional policy development work. Hakunilan Kultsa was founded in 2003. It is an Urban II, European Union project and part of the Community Iniative Programme 2001-2006, financed by the EU. Hakunilan Kultsa is also a co-operation between Vantaa city council's culture and youth services. The project encourages Hakunila residents of different ages to take part in versatile art and cultural intrests in the Hakunila youth centre. People have the opportunity to participate in theatre, expression, arts, dance, performing arts and writing groups. One of the main aims is to found a sustainable community theatre in the area. The thesis examines what effects Hakunilan Kultsa has had so far. Inquiry form and thematical interviews have been used as research methods. Interviews and questionnaires were gathered between Autumn 2004 and Spring 2005. The whole process lasted from Spring 2004 until Spring 2006. The author also made participatory observations during the research process which in turn affected the conclusions. The thesis also deals with associated topics such as urban programmes, sustainable development, Hakunila as a suburban area, resident stimulation, and community thetare work. Hakunilan Kultsa has proved its importance. Based on the enquiries and interviews, the project has effectively presented the possibility for art forms to become hobbies. There is no cultural, age or economical discrimination. The easily accessible site and the low threshold principle make it easy for people to participate. The community theatre has improved the area's public image, increased participation and initiative, and given a voice to the community.

Tuomioistuinten riidanratkaisu

English summary: Dispute resolution in Finnish courts (s.1277)

Transonic flow past on enlarged missile nose parts

Numerical computation of a viscid heat-conducting transonic flow over a generic commercial rocket profile with symmetric oversized nose part was carried out. It has been shown that at zero angle of attack for some free-streamvelocity value flow pattern loses its symmetry. This results in non-uniform pressure distribution on rocket surface in angle direction which may yield in additional oscillating stress on the rocket. Also it has been found that obtained non-symmetric flow patterns are stable for small velocity perturbations.

Design and implementation of FPGA-based LQ control of active magnetic bearings

The need for high performance, high precision, and energy saving in rotating machinery demands an alternative solution to traditional bearings. Because of the contactless operation principle, the rotating machines employing active magnetic bearings (AMBs) provide many advantages over the traditional ones. The advantages such as contamination-free operation, low maintenance costs, high rotational speeds, low parasitic losses, programmable stiffness and damping, and vibration insulation come at expense of high cost, and complex technical solution. All these properties make the use of AMBs appropriate primarily for specific and highly demanding applications. High performance and high precision control requires model-based control methods and accurate models of the flexible rotor. In turn, complex models lead to high-order controllers and feature considerable computational burden. Fortunately, in the last few years the advancements in signal processing devices provide new perspective on the real-time control of AMBs. The design and the real-time digital implementation of the high-order LQ controllers, which focus on fast execution times, are the subjects of this work. In particular, the control design and implementation in the field programmable gate array (FPGA) circuits are investigated. The optimal design is guided by the physical constraints of the system for selecting the optimal weighting matrices. The plant model is complemented by augmenting appropriate disturbance models. The compensation of the force-field nonlinearities is proposed for decreasing the uncertainty of the actuator. A disturbance-observer-based unbalance compensation for canceling the magnetic force vibrations or vibrations in the measured positions is presented. The theoretical studies are verified by the practical experiments utilizing a custom-built laboratory test rig. The test rig uses a prototyping control platform developed in the scope of this work. To sum up, the work makes a step in the direction of an embedded single-chip FPGA-based controller of AMBs.

Kohinan poisto spektrikuvista pehmeillä morfologisilla suodattimilla

Tämän diplomityön tavoitteena oli tutkia kohinan poistoa spektrikuvista käyttäen pehmeitä morfologisia suodattimia. Työssä painotettiin impulssimaisen kohinan suodattamista. Suodattimien toimintaa arvioitiin numeerisesti keskimääräisen itseisarvovirheen, neliövirheen sekä signaali-kohinasuhteen avulla ja visuaalisesti tarkastelemalla suodatettuja kuvia sekä niiden yksittäisiä spektritasoja. Käytettyjä suodatusmenetelmiä olivat suodatus kuvapisteittäin spektrin suunnassa, suodatus koko spektrissä sekä kuutiomenetelmä ja komponenteittainen suodatus. Suodatettavat kuvat sisälsivät joko suola ja pippuri- tai bittivirhekohinaa. Parhaimmat suodatustulokset sekä numeeristen virhekriteerien että visuaalisen tarkastelun perusteella saatiin komponenteittaisella sekä kuvapisteittäisellä menetelmällä. Työssä käytetyt menetelmät on esitetty algoritmimuodossa. Suodatinalgoritmien toteutukset ja suodatuskokeet tehtiin Matlab-ohjelmistolla.