Quantitative proteomics in the characterization of T helper lymphocyte differentiation

The term proteome is used to define the complete set of proteins expressed in cells or tissues of an organism at a certain timepoint. Respectively, proteomics is used to describe the methods, which are used to study such proteomes. These methods include chromatographic and electrophoretic techniques for protein or peptide fractionation, mass spectrometry for their identification, and use of computational methods to assist the complicated data analysis. A primary aim in this Ph.D. thesis was to set-up, optimize, and develop proteomics methods for analysing proteins extracted from T-helper (Th) lymphocytes. First, high-throughput LC-MS/MS and ICAT labeling methods were set-up and optimized for analysing the microsomal fraction proteins extracted from Th lymphocytes. Later, iTRAQ method was optimized to study cytokine regulated protein expression in the nuclei of Th lymphocytes. High-throughput LC-MS/MS analyses, like ICAT and iTRAQ, produce large quantities of data and robust software and data analysis pipelines are needed. Therefore, different software programs used for analysing such data were evaluated. Moreover, a pre-filtering algorithm was developed to classify good-quality and bad-quality spectra prior to the database searches. Th-lymphocytes can differentiate into Th1 or Th2 cells based on surrounding antigens, co-stimulatory molecules, and cytokines. Both subsets have individual cytokine secretion profiles and specific functions. Th1 cells participate in the cellular immunity against intracellular pathogens, while Th2 cells have important role in the humoral immunity against extracellular parasites. An abnormal response of Th1 and Th2 cells and imbalance between the subsets are charasteristic of several diseases. Th1 specific reactions and cytokines have been detected in autoimmune diseases, while Th2 specific response and cytokine profile is common in allergy and asthma. In this Ph. D. thesis mass spectrometry-based proteomics was used to study the effects of Th1 and Th2 promoting cytokines IL-12 and IL-4 on the proteome of Th lymphocytes. Characterization of microsomal fraction proteome extracted from IL-12 treated lymphobasts and IL-4 stimulated cord blood CD4+ cells resulted in finding of cytokine regulated proteins. Galectin-1 and CD7 were down-regulated in IL-12 treated cells, while IL-4 stimulation decreased the expression of STAT1, MXA, GIMAP1, and GIMAP4. Interestingly, the transcription of both GIMAP genes was up-regulated in Th1 polarized cells and down-regulated in Th2 promoting conditions.

A double madrigal

Digitoitu 12. 10. 2007.

Regulation of lymphocyte response in vitro and in vivo

CD4+ T helper (Th) cells have an important role in the defence against diverse pathogens. Th cells can differentiate into several functionally distinct subtypes including Th1 and Th2 cells. Th1 cells are important for eradicating intracellular pathogens, whereas Th2 cells pro¬tect our body against extracellular parasites. However if uncontrolled, Th cells can mediate immunopathology such as asthma or allergies, but inappropriate Th response can also lead to autoimmune diseases such as multiple sclerosis or type 1 diabetes. Deeper knowledge of the regulation of the lymphocyte response both in vitro and in vivo is important for un¬derstanding the pathogenesis of immune-mediated diseases and microbe-host interactions. In the work presented in this thesis, the first goal was to elucidate the role of novel factors, PIM kinases and c-FLIP in the regulation of human Th cell differentiation. The oncogenic serine-threonine kinases of the PIM family were shown to be preferentially expressed in Th1 cells and in addition, by using RNA interference, they were also shown to be positive regulators of Th1 differentiation. The PIM depletion experiments suggest that PIM kinases promote the expression of the hallmark cytokine of Th1 cells, IFNγ, and influence the IL12/STAT4 pathway during the early Th1 cell differentiation. In addition to cytokine and T cell receptor (TCR) induced pathways, caspase activity has been shown to regulate Th cell proliferation. In the work presented in this thesis, the two isoforms of the caspase regulator protein, c-FLIP, were shown to be differentially ex¬pressed in Th1 and Th2 cells. Both of the isoforms were up-regulated in response to TCR activation, but the expression of the short isoform was selectively induced by IL4, the Th2 inducing cytokine. Furthermore, the c-FLIP isoforms had distinct and opposite roles during the early differentiation of Th1 and Th2 cells. The knockdown of the long isoform of c-FLIP led to the induction of Th1 marker genes, such as IFNγ and TBET, whereas the depletion of c-FLIP short down-regulated Th2 marker genes IL-4 and GATA3. The third goal was to elucidate the gene expression profiles characterizing the T- and B-lymphocyte responses in vivo during experimental infection by intracellular bacte¬rium Chlamydia pneumoniae. Previously, it has been shown that CD8+ and CD4+ T cells are important for the protection against Chlamydia pneumoniae. In this study, the analysis revealed up-regulation of interferon induced genes during recurrent infection underlining the importance of IFNγ secreted by Th1 and CD8+ T cells in the protection against this pathogen. Taken together, in this study novel regulators of Th cell differ¬entiation were discovered and in addition the gene expression profiles of lymphocytes induced by Chlamydia pneumoniae infection were characterized.

Best Practices of International Double Master's Degree Programmes: Comparative Study on Finnish and Russian Universities

The purpose of this report is to disseminate the best practices of double degree programmes’ organization, implementation and development between Russian and European universities. The findings reveal good developments in the field of double degree cooperation between Russian and European universities and a high motivation from both parties. The report depicts different models of building a joint curriculum and organizing academic mobility. Foreign language skills improvement for students and university staff, involvement of international companies, and joint strategy and actions in marketing and quality assurance are some redevelopments points recommended in the report.

Modeling and Parameter Estimation of Double-Star Permanent Magnet Synchronous Machines

The power rating of wind turbines is constantly increasing; however, keeping the voltage rating at the low-voltage level results in high kilo-ampere currents. An alternative for increasing the power levels without raising the voltage level is provided by multiphase machines. Multiphase machines are used for instance in ship propulsion systems, aerospace applications, electric vehicles, and in other high-power applications including wind energy conversion systems. A machine model in an appropriate reference frame is required in order to design an efficient control for the electric drive. Modeling of multiphase machines poses a challenge because of the mutual couplings between the phases. Mutual couplings degrade the drive performance unless they are properly considered. In certain multiphase machines there is also a problem of high current harmonics, which are easily generated because of the small current path impedance of the harmonic components. However, multiphase machines provide special characteristics compared with the three-phase counterparts: Multiphase machines have a better fault tolerance, and are thus more robust. In addition, the controlled power can be divided among more inverter legs by increasing the number of phases. Moreover, the torque pulsation can be decreased and the harmonic frequency of the torque ripple increased by an appropriate multiphase configuration. By increasing the number of phases it is also possible to obtain more torque per RMS ampere for the same volume, and thus, increase the power density. In this doctoral thesis, a decoupled d–q model of double-star permanent-magnet (PM) synchronous machines is derived based on the inductance matrix diagonalization. The double-star machine is a special type of multiphase machines. Its armature consists of two three-phase winding sets, which are commonly displaced by 30 electrical degrees. In this study, the displacement angle between the sets is considered a parameter. The diagonalization of the inductance matrix results in a simplified model structure, in which the mutual couplings between the reference frames are eliminated. Moreover, the current harmonics are mapped into a reference frame, in which they can be easily controlled. The work also presents methods to determine the machine inductances by a finite-element analysis and by voltage-source inverters on-site. The derived model is validated by experimental results obtained with an example double-star interior PM (IPM) synchronous machine having the sets displaced by 30 electrical degrees. The derived transformation, and consequently, the decoupled d–q machine model, are shown to model the behavior of an actual machine with an acceptable accuracy. Thus, the proposed model is suitable to be used for the model-based control design of electric drives consisting of double-star IPM synchronous machines.

Best practices of international double degree programmes. Case of Russian and European universities

The purpose of the Master’s thesis research is to study and disseminate the best practices of international double Master’s degree programmes organization, implementation and development. The given research is focused on two main areas: motivation of higher education institutions to start double degree programmes and best practices of double degree programme design and implementation from the perspective of building joint curriculum and organizing balanced mobility and development of existing programmes in terms of increasing their quality and attractiveness. This is a case study of the double degree programmes between Russian and European universities. The study findings reveal good developments in the field of double degree cooperation between Russian and European universities and a high motivation from both parties. The research depicts different models of building a joint curriculum and organizing academic mobility. The following areas could be outlined as development points for double degree programmes: - Personal interest and commitment of organizers of double degree programmes; - Comprehensive agreement between partners on different aspects and practicalities of the double degree programme implementation; - Promotion towards more balanced student participation and two-way mobility; - Foreign language skills improvement for students and university staff; - Joint strategy and actions in marketing and quality assurance; - Involvement of international companies; - Wider usage of e-learning technology.

Double grade – rakenneputkien puristuskestävyys

Double grade S420MH/S355J2H – rakenneputki on Ruukin kylmämuovattujen rakenneputkien vakioteräslaji. Se voidaan mitoittaa joko lujuusluokan S355 tai S420 mukaisesti. Teräslajin S355 mukaisesti mitoitettaessa on suunnittelu yksinkertaista. Painonsäästöä ja pidennettyjä jännevälejä haluttaessa käytetään lujuusluokan S420 mukaista mitoitusta. Työn tavoitteena oli selvittää kylmämuovattujen teräsrakenneputkien todellinen puristuskestävyys. Eurocode 3:n mukaan kylmämuovatut teräsrakenneputket kuuluvat nurjahduskäyrälle c. Tutkimukseen valittiin viisi eri profiilia olevaa rakenneputkea, joiden poikkileikkausluokat olivat 1, 2, 3 ja 4. Käytettäessä rakenneputkia puristussauvoina, on teräksen käyttö tehokkainta poikkileikkausluokassa 3, lähellä poikkileikkausluokkaa 4. Rakenneputkista laskettiin muunnetun hoikkuuden arvoilla 0.1, 0.5, 1.0 ja 1.5 koesauvojen pituudet kaikille profiileille. Valmistettiin kolme samanlaista koesauvaa jokaisesta koosta ja puristuskokeita suoritettiin yhteensä 57 kappaletta. Koesauvojen todelliset pituudet, alkukäyryydet ja poikkileikkaukset mitattiin. Ainestodistuksista saatiin materiaalin todelliset lujuudet. Laskettiin Eurocode 3:n mukaisesti kestävyydet nurjahduskäyrille a, b ja c. Laskennallisia kestävyyksiä verrattiin puristuskokeiden tuloksiin. Puristuskokeiden tulosten perusteella voidaan b-käyrää pitää oikeana profiileille 100x100x3, 150,150x5 ja 200x200x6. Profiili 150x150x5 kuuluu poikkileikkausluokkaan 2. Profiilit 100x100x3 ja 200x200x6 kuuluvat poikkileikkausluokkaan 4. Profiili 50x50x2 kuuluu nurjahduskäyrälle c. Profiilin poikkileikkausluokka on 1 ja aiemmat tutkimukset tukevat nurjahduskäyrän c käyttöä. Profiilista 300x300x8.8 ei saatu testattua täyttä sarjaa sen suuren kapasiteetin rikottua testilaitteiston, mutta puristuskokeiden perusteella se kuuluu nurjahduskäyrälle b. Profiili kuuluu poikkileikkausluokkaan 4.

Distortion and internal warping torsion of a double symmetric hollow section

This thesis is made in cooperation with Laboratory of Steel Structures and the steel company SSAB. Maximization of the benefits of high-strength steel usually requires the usage of thin wall thicknesses. This means the failures related to buckling, distortion and warping stand out. One must be aware of these phenomena to design thin-walled structures stressed with forces such as torsional loading. It is also important to take into account small stress ranges when evaluating the accurate fatigue strength of structures. The objective of this thesis is to clarify the theory of the uniform and non-uniform torsion. This paper focuses on warping due to the non-uniform torsion in double symmetric box girder and structural hollow section. The arisen stress states are explained and researched using the finite element method. Another research target is the distortion in double symmetric box girder due to torsion, and the restraining effect of transverse diaphragms at the load end. Multiple transverse diaphragms are used to study more efficient restraining against warping and distortion than a common one end plate structure.

Modular Double-Cascade Converter

Medium-voltage motor drives extend the power rating of AC motor drives in industrial applications. Multilevel converters are gaining an ever-stronger foothold in this field. This doctoral dissertation introduces a new topology to the family of modular multilevel converters: the modular double-cascade converter. The modularity of the converter is enabled by the application of multiwinding mediumfrequency isolation transformers. Owing to the innovative transformer link, the converter presents many advantageous properties at a concept level: modularity, high input and output power quality, small footprint, and wide variety of applications, among others. Further, the research demonstrates that the transformer link also plays a key role in the disadvantages of the topology. An extensive simulation study on the new converter is performed. The focus of the simulation study is on the development of control algorithms and the feasibility of the topology. In particular, the circuit and control concepts used in the grid interface, the coupling configurations of the load inverter, and the transformer link operation are thoroughly investigated. Experimental results provide proof-of-concept results on the operation principle of the converter. This work concludes a research collaboration project on multilevel converters between LUT and Vacon Plc. The project was active from 2009 until 2014.