Molecular Characteristics of Neuroblastoma with Special Reference to Novel Prognostic Factors and Diagnostic Applications

Molecular Characteristics of Neuroblastoma with Special Reference to Novel Prognostic Factors and Diagnostic Applications Department of Medical Biochemistry and Genetics Annales Universitatis Turkuensis, Medica-Odontologica, 2009, Turku, Finland Painosalama Oy, Turku, Finland 2009 Background: Neuroblastoma, which is the most common and extensively studied childhood solid cancer, shows a great clinical and biological heterogeneity. Most of the neuroblastoma patients older than one year have poor prognosis despite intensive therapies. The hallmark of neuroblastoma, biological heterogeneity, has hindered the discovery of prognostic tumour markers. At present, few molecular markers, such as MYCN oncogene status, have been adopted into clinical practice. Aims: The aim of the study was to improve the current prognostic methodology of neuroblastoma, especially by taking cognizance of the biological heterogeneity of neuroblastoma. Furthermore, unravelling novel molecular characteristics which associate with neuroblastoma tumour progression and cell differentiation was an additional objective. Results: A new strictly defined selection of neuroblastoma tumour spots of highest proliferation activity, hotspots, appeared to be representative and reliable in an analysis of MYCN amplification status using a chromogenic in situ hybridization technique (CISH). Based on the hotspot tumour tissue microarray immunohistochemistry and high-resolution oligo-array-based comparative genomic hybridization, which was integrated with gene expression and in silico analysis of existing transcriptomics, a polysialylated neural cell adhesion molecule (NCAM) and poorly characterized amplicon at 12q24.31 were discovered to associate with outcome. In addition, we found that a previously considered new neuroblastoma treatment target, the mutated c-kit receptor, was not mutated in neuroblastoma samples. Conclusions: Our studies indicate polysialylated NCAM and 12q24.31 amplicon to be new molecular markers with important value in prognostic evaluation of neuroblastoma. Moreover, the presented hotspot tumour tissue microarray method together with the CISH technique of the MYCN oncogene copy number is directly applicable to clinical use. Key words: neuroblastoma, polysialic acid, neural cell adhesion molecule, MYCN, c-kit, chromogenic in situ hybridization, hotspot

Model-based study of a chemical-looping combustion process

Chemical-looping combustion (CLC) is a novel combustion technology with inherent separation of the greenhouse gas CO2. The technique typically employs a dual fluidized bed system where a metal oxide is used as a solid oxygen carrier that transfers the oxygen from combustion air to the fuel. The oxygen carrier is looping between the air reactor, where it is oxidized by the air, and the fuel reactor, where it is reduced by the fuel. Hence, air is not mixed with the fuel, and outgoing CO2 does not become diluted by the nitrogen, which gives a possibility to collect the CO2 from the flue gases after the water vapor is condensed. CLC is being proposed as a promising and energy efficient carbon capture technology, since it can achieve both an increase in power station efficiency simultaneously with low energy penalty from the carbon capture. The outcome of a comprehensive literature study concerning the current status of CLC development is presented in this thesis. Also, a steady state model of the CLC process, based on the conservation equations of mass and energy, was developed. The model was used to determine the process conditions and to calculate the reactor dimensions of a 100 MWth CLC system with bunsenite (NiO) as oxygen carrier and methane (CH4) as fuel. This study has been made in Oxygen Carriers and Their Industrial Applications research project (2008 – 2011), funded by the Tekes – Functional Material program. I would like to acknowledge Tekes and participating companies for funding and all project partners for good and comfortable cooperation.

Happaman hydrometallurgisen PLS-liuoksen puhdistaminen kiintoaineesta kalvosuodatustekniikalla

Tässä diplomityössä tutkittiin keraamisten mikrosuodatuskalvojen soveltuvuutta kiintoaineen erottamiseen happamasta PLS-liuoksesta eri huokoskoon omaavilla mikrosuodatuskalvoilla. Koelaitteistolla suodatettiin puhdasta vettä, kaoliinipitoista vesiliuosta sekä hapanta kuparia, kalsiumia ja kaoliinia sisältävää malliliuosta. Koeajojen tavoitteena oli saada tietoa permeaattivuon maksimimäärästä eri mikrosuodatuskalvoilla sekä tuotteen puhtaudesta. Näiden lisäksi saatiin tietoa kalvojen likaantumisesta ajon aikana. Teoriaosassa käsiteltiin yleisesti kalvosuodatusta, esitettiin yleiset kalvotekniset menetelmät ja sovellukset sekä käytiin läpi tutkimuksia samankaltaisiin kalvoihin ja sovelluksiin liittyen. Lisäksi teoriaosuudessa pohdittiin mahdollisuutta käyttää myös muita, kuin putkimoduulisia mikrosuodatuskalvoja. Myös työhön oleellisena taustana kuuluvaa hydrometallurgiaa tarkasteltiin teoreettiselta kannalta. Puhtaan veden suodatuskoetuloksista havaittiin, että kaikki kalvot jäivät selvästi valmistajan ilmoittamista arvoista. 1,0 µm CoMetas CoMem® kalvon teoreettinen vesivuo on 10 m3/(h bar) ja 3,0 µm CoMetas CoMem® teoreettinen vesivuo on yli 50 m3/(h bar). Näistä parhaimman vuon arvon sai 1,0 µm CoMetas CoMem® mikrosuodatuskalvo. Tämä kalvo oli paras sekä veden suodatuksissa että malliliuoksella tehdyillä suodatuksilla. Malliliuoksella saavutettiin n. 2000 L/(m2 h) paineen ollessa 2,0 bar ja virtausnopeuden ollessa 4,4 m/s. Vastaavat vesiajon tulokset olivat n. 1100 L/(m2 h) paineen ollessa 1,0 bar ja virtausnopeuden 2,9 m/s. Kaikki kolme käytettyä kalvoa pidättivät kaoliiniliuoksen 81–100 %:sesti. Kuparipitoista malliliuosta suodatettaessa pystyttiin vastaavasti erottamaan 77–99 % kiintoaineesta. Koeajoissa kuitenkin havaittiin huomattava vuon arvojen putoaminen, joka johtui kalvon likaantumisesta. Huomioitavaa oli kuitenkin, että hapanta malliliuosta suodatettaessa permeaattivuon arvot olivat kaoliiniliuoksen suodatuksessa saatuja vastaavia arvoja korkeammat.

Calculation of the carbon footprint of Finnish barley products - methodology and possible applications

The purpose of this thesis was to define how product carbon footprint analysis and its results can be used in company's internal development as well as in customer and interest group guidance, and how these factors are related to corporate social responsibility. From-cradle-to-gate carbon footprint was calculated for three products; Torino Whole grain barley, Torino Pearl barley, and Elovena Barley grit & oat bran, all of them made of Finnish barley. The carbon footprint of the Elovena product was used to determine carbon footprints for industrial kitchen cooked porridge portions. The basic calculation data was collected from several sources. Most of the data originated from Raisio Group's contractual farmers and Raisio Group's cultivation, processing and packaging specialists. Data from national and European literature and database sources was also used. The electricity consumption for porridge portions' carbon footprint calculations was determined with practical measurements. The carbon footprint calculations were conducted according to the ISO 14044 standard, and the PAS 2050 guide was also applied. A consequential functional unit was applied in porridge portions' carbon footprint calculations. Most of the emissions from barley products' life cycle originate from primary production. The nitrous oxide emissions from cultivated soil and the use and production of nitrogenous fertilisers contribute over 50% of products' carbon footprint. Torino Pearl barley has the highest carbon footprint due to the lowest processing output. The reductions in products' carbon footprint can be achieved with developments in cultivation and grain processing. The carbon footprint of porridge portion can be reduced by using domestically produced plant-based ingredients and by making the best possible use of the kettle. Carbon footprint calculation can be used to determine possible improvement points related to corporate environmental responsibility. Several improvement actions are related to economical and social responsibility through better raw material utilization and expense reductions.

Inversion and assimilation methods with applications in geophysical remote sensing

Stratospheric ozone can be measured accurately using a limb scatter remote sensing technique at the UV-visible spectral region of solar light. The advantages of this technique includes a good vertical resolution and a good daytime coverage of the measurements. In addition to ozone, UV-visible limb scatter measurements contain information about NO2, NO3, OClO, BrO and aerosols. There are currently several satellite instruments continuously scanning the atmosphere and measuring the UVvisible region of the spectrum, e.g., the Optical Spectrograph and Infrared Imager System (OSIRIS) launched on the Odin satellite in February 2001, and the Scanning Imaging Absorption SpectroMeter for Atmospheric CartograpHY (SCIAMACHY) launched on Envisat in March 2002. Envisat also carries the Global Ozone Monitoring by Occultation of Stars (GOMOS) instrument, which also measures limb-scattered sunlight under bright limb occultation conditions. These conditions occur during daytime occultation measurements. The global coverage of the satellite measurements is far better than any other ozone measurement technique, but still the measurements are sparse in the spatial domain. Measurements are also repeated relatively rarely over a certain area, and the composition of the Earth’s atmosphere changes dynamically. Assimilation methods are therefore needed in order to combine the information of the measurements with the atmospheric model. In recent years, the focus of assimilation algorithm research has turned towards filtering methods. The traditional Extended Kalman filter (EKF) method takes into account not only the uncertainty of the measurements, but also the uncertainty of the evolution model of the system. However, the computational cost of full blown EKF increases rapidly as the number of the model parameters increases. Therefore the EKF method cannot be applied directly to the stratospheric ozone assimilation problem. The work in this thesis is devoted to the development of inversion methods for satellite instruments and the development of assimilation methods used with atmospheric models.

Antenna Design for Contactless IC Card Applications

Contactless integrated circuit cards are one form of application of radio frequency identification. They are used in applications such as access control, identification, and payment in public transport. The contactless IC cards are passive which means that both the data and the energy are transferred to the card without contact using inductive coupling. Antenna design and optimization of the design for contactless IC cards defined by ISO/IEC14443 is studied. The basic operation principles of contactless system are presented and the structure of contactless IC card is illustrated. The structure was divided between the contactless chip and the antenna. The operation of the antenna was covered in depth and the parameters affecting to the performance of the antenna were presented. Also the different antenna technologies and connection technologies were provided. The antenna design process with the parameters and the design tools isillustrated and optimization of the design is studied. To make the design process more ideal a target of development was discovered, which was the implementation of test application. The optimization of the antenna design was presented based on the optimization criteria defined in this study. The solution for the implementation of these criteria and the effect of each criterion was found. For enhancing the performance of the antenna a focus for future study was proposed.

Separation of Gas Bubbles from Circulation Waters and Pulp Suspensions in Open Channel Flow

The objective of this thesis was to study the removal of gases from paper mill circulation waters experimentally and to provide data for CFD modeling. Flow and bubble size measurements were carried out in a laboratory scale open gas separation channel. Particle Image Velocimetry (PIV) technique was used to measure the gas and liquid flow fields, while bubble size measurements were conducted using digital imaging technique with back light illumination. Samples of paper machine waters as well as a model solution were used for the experiments. The PIV results show that the gas bubbles near the feed position have the tendency to escape from the circulation channel at a faster rate than those bubbles which are further away from the feed position. This was due to an increased rate of bubble coalescence as a result of the relatively larger bubbles near the feed position. Moreover, a close similarity between the measured slip velocities of the paper mill waters and that of literature values was obtained. It was found that due to dilution of paper mill waters, the observed average bubble size was considerably large as compared to the average bubble sizes in real industrial pulp suspension and circulation waters. Among the studied solutions, the model solution has the highest average drag coefficient value due to its relatively high viscosity. The results were compared to a 2D steady sate CFD simulation model. A standard Euler-Euler k-ε turbulence model was used in the simulations. The channel free surface was modeled as a degassing boundary. From the drag models used in the simulations, the Grace drag model gave velocity fields closest to the experimental values. In general, the results obtained from experiments and CFD simulations are in good qualitative agreement.

Engineering of Business Critical Web Applications

Research focus of this thesis is to explore options for building systems for business critical web applications. Business criticality here includes requirements for data protection and system availability. The focus is on open source software. Goals are to identify robust technologies and engineering practices to implement such systems. Research methods include experiments made with sample systems built around chosen software packages that represent certain technologies. The main research focused on finding a good method for database data replication, a key functionality for high-availability, database-driven web applications. Research included also finding engineering best practices from books written by administrators of high traffic web applications. Experiment with database replication showed, that block level synchronous replication offered by DRBD replication software offered considerably more robust data protection and high-availability functionality compared to leading open source database product MySQL, and its built-in asynchronous replication. For master-master database setups, block level replication is more recommended way to build high-availability into the system. Based on thesis research, building high-availability web applications is possible using a combination of open source software and engineering best practices for data protection, availability planning and scaling.

Applications and Markets of Linear Motors

A steady increase in practical industrial applications has secured a place for linear motors. They provide high dynamics and high positioning accuracy of the motor, high reliability and durability of all components of the system. Machines with linear motors have very big perspectives in modern industry. This thesis enables to understand what a linear motor is, where they are used and what situation there is on their market nowadays. It can help to understand reasonability of applying linear motors on manufacture and benefits of its application.

Hybrid du/dt-filter in frequency converter applications

The aim of the thesis is to investigate the hybrid LC filter behavior in modern power drives; to analyze the influence of such a du/dt filter on the control system stability. With the implementation of the inverter output RLC filter the motor control becomes more complicated. And during the design process the influence of the filter on the motor should be considered and the filter RLC parameters should be constrained.

Numerical Investigation of Flow Past a Circular Cylinder and in a Staggered Tube Bundle Using Various Turbulence Models

Transitional flow past a three-dimensional circular cylinder is a widely studied phenomenon since this problem is of interest with respect to many technical applications. In the present work, the numerical simulation of flow past a circular cylinder, performed by using a commercial CFD code (ANSYS Fluent 12.1) with large eddy simulation (LES) and RANS (κ - ε and Shear-Stress Transport (SST) κ - ω! model) approaches. The turbulent flow for ReD = 1000 & 3900 is simulated to investigate the force coefficient, Strouhal number, flow separation angle, pressure distribution on cylinder and the complex three dimensional vortex shedding of the cylinder wake region. The numerical results extracted from these simulations have good agreement with the experimental data (Zdravkovich, 1997). Moreover, grid refinement and time-step influence have been examined. Numerical calculations of turbulent cross-flow in a staggered tube bundle continues to attract interest due to its importance in the engineering application as well as the fact that this complex flow represents a challenging problem for CFD. In the present work a time dependent simulation using κ – ε, κ - ω! and SST models are performed in two dimensional for a subcritical flow through a staggered tube bundle. The predicted turbulence statistics (mean and r.m.s velocities) have good agreement with the experimental data (S. Balabani, 1996). Turbulent quantities such as turbulent kinetic energy and dissipation rate are predicted using RANS models and compared with each other. The sensitivity of grid and time-step size have been analyzed. Model constants sensitivity study have been carried out by adopting κ – ε model. It has been observed that model constants are very sensitive to turbulence statistics and turbulent quantities.

Probiotic interventions in infancy: Benefit and Safety Assessment of Extended Applications

Immaturity of the gut barrier system in the newborn has been seen to underlie a number of chronic diseases originating in infancy and manifesting later in life. The gut microbiota and breast milk provide the most important maturing signals for the gut-related immune system and reinforcement of the gut mucosal barrier function. Recently, the composition of the gut microbiota has been proposed to be instrumental in control of host body weight and metabolism as well as the inflammatory state characterizing overweight and obesity. On this basis, inflammatory Western lifestyle diseases, including overweight development, may represent a potential target for probiotic interventions beyond the well documented clinical applications. The purpose of the present undertaking was to study the efficacy and safety of perinatal probiotic intervention. The material comprised two ongoing, prospective, double-blind NAMI (Nutrition, Allergy, Mucosal immunology and Intestinal microbiota) probiotic interventions. In the mother-infant nutrition and probiotic study altogether 256 women were randomized at their first trimester of pregnancy into a dietary intervention and a control group. The intervention group received intensive dietary counselling provided by a nutritionist, and were further randomized at baseline, double-blind, to receive probiotics (Lactobacillus rhamnosus GG and Bifidobacterium lactis) or placebo. The intervention period extended from the first trimester of pregnancy to the end of exclusive breastfeeding. In the allergy prevention study altogether 159 women were randomized, double-blind, to receive probiotics (Lactobacillus rhamnosus GG) or placebo 4 weeks before expected delivery, the intervention extending for 6 months postnatally. Additionally, patient data on all premature infants with very low birth weight (VLBW) treated in the Department of Paediatrics, Turku University Hospital, during the years 1997 - 2008 were utilized. The perinatal probiotic intervention reduced the risk of gestational diabetes mellitus (GDM) in the mothers and perinatal dietary counselling reduced that of fetal overgrowth in GDM-affected pregnancies. Early gut microbiota modulation with probiotics modified the growth pattern of the child by restraining excessive weight gain during the first years of life. The colostrum adiponectin concentration was demonstrated to be dependent on maternal diet and nutritional status during pregnancy. It was also higher in the colostrum received by normal-weight compared to overweight children at the age of 10 years. The early perinatal probiotic intervention and the postnatal probiotic intervention in VLBW infants were shown to be safe. To conclude, the findings in this study provided clinical evidence supporting the involvement of the initial microbial and nutritional environment in metabolic programming of the child. The manipulation of early gut microbial communities with probiotics might offer an applicable strategy to impact individual energy homeostasis and thus to prevent excessive body-weight gain. The results add weight to the hypothesis that interventions aiming to prevent obesity and its metabolic consequences later in life should be initiated as early as during the perinatal period.

Doubly fed induction generator versus direct drive permanent magnet synchronous generator in wind power applications

The objective of this master's thesis is to compare two different generator systems for wind turbines. It is the doubly fed induction generator system with three stage gearbox and the direct drive permanent magnet generator system. The comparison of generator systems is based on annual energy production for a given wind climate. For comparison a 3 MW, 15 rpm wind turbine is used. Modelling of a turbine rotor, gearbox and converters were done. Design of two generators was done and their performance was examined.