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  • Venäläinen, Salla (Helsingin yliopisto, 2013)
    Mining of phosphorus (P) and lead (Pb) ores increases their amounts in biogeochemical cycles and, consequently, their environmental risks. Phosphorus is an important nutrient, but P loading from sewage waters and agricultural activities to watercourses may result in eutrophication, a process eventually detrimental to aquatic ecosystems. Lead, on the other hand, poses a direct risk of intoxication to all living organisms. In addition to technical applications, Pb is used in pellets and shots on shooting ranges, which accounts for a large source of Pb loading to the environment. Prevention and abatement of detrimental impacts of P and Pb require large-scale, cost-effective techniques that do not compromise the environment. This thesis was undertaken to investigate the potential of tailings from apatite ore beneficiation at the Siilinjärvi phosphate mine, Finland, in the dephosphorization of sewage and in the remediation of metal-contaminated areas. The material is a mixture of minerals, mainly phlogopite [KMg3(Si3Al)O10(OH)2] and calcite (CaCO3), accompanied by apatite [Ca5(PO4)3F] residues. Based on the versatile chemical properties, this geomaterial was hypothesized to act as a sorbent for P and Pb, rendering the tailings a potential agent for environmental remediation. A part of the original tailings material was artificially weathered by treating with a strong acid to create reaction-active aluminium (Al) and iron (Fe) (hydr)oxide sites. Some of the acidified material was further subjected to partial neutralization by treating with a strong base to precipitate any metals dissolved from the mineral structure during the acidification. Furthermore, all of the tailings materials were sieved into two particle-size fractions somewhat differing in their mineralogical composition and investigated as separate amendments. The ability of the tailings to retain P and Pb from aqueous solutions as well as the tailings-induced changes in the Pb retention capacity of a mineral soil were studied by means of an isotherm technique. A sequential fractionation procedure was undertaken to investigate (a) the distribution of inherent and added P between various chemical pools in the tailings and (b) the tailings-induced changes in the distribution of Pb between various chemical pools in a mineral soil artificially contaminated with Pb as well as in an organic shooting range soil contaminated with pellet-derived Pb. Because the toxicity of dissolved Pb depends on its chemical speciation, the tailings-induces changes in the chemical speciation of water-extractable Pb in contaminated shooting range soil was tested separately by means of a cation exchange resin. The tailings retained both P and Pb efficiently. The removal of soluble P was primarily due to specific sorption by Al and Fe (hydr)oxides and possibly to retention to calcite. Lead sorption by the untreated tailings was a combination of various sorption mechanisms taking place simultaneously, primarily through precipitation and surface complexation. All tailings materials increased the Pb sorption capacity of a mineral soil and transferred Pb from the NH4NO3-extractable pool to the more strongly bound forms. In a contaminated shooting range soil, the pellets were found to undergo continuous weathering processes that released Pb into the soil. Amending the soil with the untreated tailings (a) reduced the solubility of the pellet-derived Pb through the formation of sparingly soluble fluorpyromorphite and cerussite, (b) reduced the bioavailability of Pb by transferring it from the water-soluble and NH4NO3-extractable pools into the NaOH-extractable one and (c) transferred the most toxic cationic Pb species to the less toxic non-cationic form. The results suggest that the tailings may serve as an agent for dephosphorization of sewage and for Pb immobilization in polluted soil. The sorption properties of the material may be further optimized by chemical and physical pre-treatments. At present, the tailings material represents an uneconomic fraction of the ore deposit, but its components may render it a natural, environmentally sound and cost-effective remediation agent.
  • Wissel, Gloria (Helsingin yliopisto, 2015)
    The main goal of this dissertation is to identify novel modulators acting on ATP Binding Cassette subfamily C member 2 (ABCC2) transporters and α2-adrenoceptors subtypes. With the purpose of identifying novel modulators and their mode of action, a combination of experimental and computational approaches have been used. The first protein presented in this dissertation is the ABCC2 transporter, also known as the multidrug resistance associated protein 2 (MRP2), an efflux transporter expressed in polarized cells where it effluxes a variety of both endogenous and exogenous molecules out of the cell. The most common way to study the interactions between small molecules and ABCC2 transporter is by a vesicle transport assay. Three assays are commercially available, which use different probes to define the ABCC2- transport. With the intent to define the different assays and identify the effect that small molecules have on the ABCC2-transport, a small set of eight compounds and, subsequently a larger library of compounds were tested with the different assays. Additionally, the aim was to identify and characterise novel ABCC2 inhibitors, 16 inhibitors have been identified from the larger library and classification models were built to identify important descriptors that were able to discriminate inhibitors from inactive molecules. Instant structure-activity relationships (SAR) of four scaffolds of ABCC2 modulators are also presented. In addition, some unpublished results are presented, the homology model of ABCC2 and further insights into the SAR of ABCC2 modulators. The other proteins included in this dissertation are the three subtypes of the α2-adrenoceptors, G-protein coupled receptors, involved in the signalling pathway of adrenaline and noradrenaline. A clear subtype characterization/profile of these proteins is not available. Selective molecules could be used in treatment of high blood pressure, in the alleviation of withdrawal symptoms, and as anaesthetic with fewer side effects than the current drugs. To define the affinity of a small set of antagonists and outline the involvement of the first transmembrane helix in ligand binding, a competition binding assay has been used with chimera receptors where the first transmembrane helix has been swapped between the three subtypes. Molecular modelling has been used to explain the different binding affinities to the chimera receptors. Additionally, the aim was to identify novel α2B-adrenoceptor selective compounds, thus a mid-sized library has been screened using a miniaturized binding assay. Hierarchical classification and chemoinformatics analysis has been used to visualize and analyse the screening results.
  • Paavola, Jere (Helsingin yliopisto, 2014)
    Heart disease is the biggest killer world-wide, causing a quarter of all deaths. During the past two decades, it has also risen above infectious diseases as the leading cause of years of life lost. Heart failure, characterized by weak pump function of the heart, and disturbances in heart rhythm (arrhythmias) are common and interrelated mechanisms underlying cardiac mortality. Intracellular calcium ions are crucial to contraction and relaxation of the heart muscle, as well as to control of its rhythm. How calcium is handled and regulated is thus essential to normal cardiac function, and disturbances in these processes can have catastrophic consequences. Understanding the mechanisms of these disturbances is important for improving disease prevention, diagnosis, and management. The studies in this thesis focus on two conditions where cardiac calcium handling is impaired. Studies I - III examine the mechanisms of a genetic arrhythmia disease named catecholaminergic polymorphic ventricular tachycardia (CPVT), which is characterized by stress-induced ventricular tachycardia in a structurally normal heart. Study IV investigates cardiac function in a model of another genetic disease, autosomal dominant polycystic kidney disease (ADPKD). This systemic disease mainly affects the kidneys, and the mechanisms of the concomitant decline in cardiac function have thus far remained underinvestigated. We evaluated clinical data on cardiac function of CPVT patients, including 24h electrocardiograms, intracardiac monophasic action potential recordings, and exercise stress tests. We used cell models to study the underlying disease mechanisms in detail. During conditions of stress, CPVT cells showed increased spontaneous and irregular release of calcium from within the intracellular stores through the cardiac ryanodine receptors. These receptors, which function as intracellular calcium release channels, harbor the disease-causing mutation. The spontaneous release of calcium led to changes in the membrane potential of the cells, manifested as afterdepolarizations during the resting phase of the cardiac cycle. These afterdepolarizations were reproduced in the clinical monophasic action potential recordings of CPVT patients, and were shown to trigger arrhythmias in these patients. Changes in intracellular calcium alter the membrane potential, and these changes are reflected on the electrocardiogram. Thus, irregularities that might correspond to those observed in the cell model were then investigated in 24h electrocardiograms of CPVT patients. Increased irregularity of cardiac repolarization was found in the CPVT patients. Such irregularity was greater in the electrocardiograms of CPVT patients with a history of more severe arrhythmic events. Additionally, we found slowed depolarization in response to stress in CPVT cells and patients, suggesting reduced conduction velocity might contribute to an arrhythmic substrate in these patients. Cardiac function in ADPKD caused by mutations in polycystin-2, another intracellular calcium channel, was investigated in a zebrafish model lacking expression of the polycystin-2 protein. The zebrafish lacking polycystin-2 showed signs of heart failure, including reduced cardiac output, edema, and arrhythmias. Hearts, which were then examined in more detail ex vivo, showed impaired cycling of intracellular calcium, which is likely to underlie the cardiac dysfunction observed in vivo. The association of ADPKD with idiopathic dilated cardiomyopathy (IDCM) was examined using the Mayo ADPKD Mutation Database, which contains data on genotyped ADPKD patients. Examination of the ADPKD Database showed IDCM to be very common among ADPKD patients. IDCM was most prevalent in patients with mutations in polycystin-2, suggesting impaired calcium cycling as a potential pathomechanism. Studies I-III shed new light on mechanisms of arrhythmias in CPVT and related conditions, opening the way for future studies on arrhythmia risk and therapeutic evaluation. Furthermore, the results encourage pursuing the novel stem cell models for studying pathomechanisms and therapeutics. Study IV showed an association between ADPKD and IDCM. The zebrafish model suggested impaired calcium cycling as an underlying mechanism, highlighting the usefulness of zebrafish as a model in cardiac research.
  • Hernesniemi, Sari (Helsingin yliopisto, 2012)
    Chronic myeloid leukemia (CML) is a hematologic malignancy that originates from pluripotent hematopoietic stem cells. The genetic abnormality underlying this disease, as well as a subtype of acute lymphoblastic leukemia (ALL), is a translocation between chromosomes 9 and 22, which leads to the formation of the Philadelphia (Ph) chromosome and the oncogenic BCR-ABL1 fusion protein. Targeted inhibition of the BCR-ABL1 protein with imatinib and other specific tyrosine kinase inhibitors (TKIs) has revolutionized CML treatment and is currently regarded as the gold standard of targeted cancer therapy. In this doctoral thesis, different methodological approaches were used to characterize aberrant signaling activities in leukemic and normal cells with the ultimate aim of isolating novel prognostic markers for predicting TKI therapy outcome. First, the molecular mechanism of the disease was investigated in an ALL patient with a translocation between chromosomes 1 and 9. Cytogenetic characterization showed involvement of the ABL1 gene fused to an unknown gene. The RCSD1 gene was selected as a candidate and subsequent molecular dissection confirmed a RCSD1-ABL1 fusion. This novel fusion gene predicts sensitivity to TKI therapy in ALL patients. Second, several phosphoproteins related to immune cell function were analyzed both from the diagnostic phase CML patients and from patients under TKI therapy in order to reveal distinct signaling patterns. A single cell phosphoprotein method based on multiparameter flow cytometry was used to analyze phosphoprotein levels in different cell populations. The responsiveness of myeloid cells to ex vivo cytokine stimulation in diagnostic-phase patients was low, but was normalized in TKI-treated patients. In general, the blood leukocyte subsets responded normally to various cytokine stimulations, which indicated a non-immunosuppressive role for TKIs. This project also led to the development of a software assisted analysis program, which can conduct the whole range of flow cytometry data analysis, thereby diminishing the effort needed for manual cell population gating and interpretation. Lastly, biomarkers for therapy response were identified by analyzing aberrant signaling activities in leukemic cells collected at the time of diagnosis. The analysis was based on a phosphoproteomic array measuring phosphorylation of 46 different kinase targets. Several proteins had aberrant phosphorylation levels in patients with a poor therapy outcome − pSTAT5b being the most prominent. These biomarkers could be useful in guiding therapy selection at the time of diagnosis. In conclusion, the findings imply that TKI therapy responses can be linked to certain biological markers, which can possibly be utilized in clinical applications in the future.
  • Kalinowski, Jaroslaw (2015)
    One of the goals of modern quantum chemistry is to simulate actual chemical experiments. In order to study species closer to real life systems and bulk environments there is a need for methodological developments. There are two ways to approach large systems with a given level of accuracy: conceptual changes to quantum chemistry methods or algorithmic developments for current methods. Many scientists believe that the conceptual changes truly increase the size of the systems one can study. With more or less advanced approximations to the method it is possible to increase the efficiency of calculations orders of magnitude. The implementation and algorithms fall down in the priority list, as advanced algorithmic developments are time consuming and usually lead to lower efficiency increases than conceptual changes. In this work it is shown that algorithmic developments cannot be neglected, and that even simple changes help in utilizing the power of modern computers and can also increase the efficiency by orders of magnitude. In this work new algorithmic developments are presented and used for solving various timely chemical problems.
  • García-Matos, Marta (Helsingin yliopisto, 2005)
  • Häkkinen, Margareeta (Helsingin yliopisto, 2015)
    Opioids are the most important drugs causing fatal poisonings. Determining whether an opioid death was poisoning may, however, be difficult even if involving appropriate toxicological laboratory investigation. Apart from heroin, little statistically significant data-analysis is available for interpretation of blood concentrations of opioids from various types of post-mortem cases. Tolerance, route of administration, and delay of death after drug administration all influence postmortem drug concentrations. In this thesis, quantitative blood concentration data extracted from the high-quality Finnish postmortem toxicology database was the investigative tool to overcome this problem. Opioid deaths typically involve drug abuse, and suspected drug-abuser deaths must, by Finnish law, undergo medico-legal examination. Medico-legal autopsy in these cases includes comprehensive drug screening and, based on its results, more specific drug quantification. This thesis combined concentration data stored in the postmortem toxicology database with information from death certificates issued by forensic pathologists to allow statistical comparisons between drug poisonings and other deaths, as well as between drug abusers and other users. Concentration data mainly involved drug concentrations in postmortem femoral blood, but drug concentrations in urine and parent drug/metabolite concentration ratios also allowed assessment of buprenorphine, codeine, and tramadol deaths. Opioid poisonings proved to be mainly unintentional polydrug poisonings, regularly involving benzodiazepines, gabapentinoids, and other psycholeptics. Buprenorphine and methadone blood concentrations in fatal poisonings remained within their therapeutic ranges, and these two opioids involved mostly abuse. Concentrations of the weak opioids tramadol and codeine were above their therapeutic ranges both in abuser cases and in fatal poisonings. Tramadol abuse was common but abuse of oxycodone, fentanyl, and codeine was rather low compared to their therapeutic use. Abuse of the gabapentinoids pregabalin and gabapentin was strongly associated with opioid abuse, and compared to gabapentin abuse, pregabalin abuse was proportionally more frequent. To prevent parenteral buprenorphine abuse, opioid maintenance treatment applied a combination product of buprenorphine-naloxone. This combination product is, however, abused as well, and monitoring its abuse is challenging. In this study, urine samples collected from living patients at different phases of opioid maintenance treatment supplemented the postmortem data. Based on the criteria established with these patients, combined with postmortem data and proper background information, a urine concentration limit was estimated for suspected parenteral abuse of the buprenorphine-naloxone product in postmortem cases. Deaths and fatal poisonings due to parenteral buprenorphine-naloxone abuse occurred frequently, and abuse of the combination product was proportionally even more fatal than was abuse of buprenorphine. The results of this study will assist in medico-legal cause-of-death investigations through providing quantitative reference concentrations for the interpretation of opioid-related deaths. Further, estimating the proportion attributable to prescription opioid abuse compared to that of other opioid use and creating abuser profiles for various opioids can promote public health through proper drug policy. In a clinical context, results may be helpful in evaluating possible drug abuse and compliance among prescription-drug users. Detecting abuse of these important yet addictive medications is vital in promoting welfare and drug safety.
  • Korhonen, Silja (The Finnish Forest Research Institute, 2006)
    The purpose of this study was to extend understanding of how large firms pursuing sustained and profitable growth manage organisational renewal. A multiple-case study was conducted in 27 North American and European wood-industry companies, of which 11 were chosen for closer study. The study combined the organisational-capabilities approach to strategic management with corporate-entrepreneurship thinking. It charted the further development of an identification and classification system for capabilities comprising three dimensions: (i) the dynamism between firm-specific and industry-significant capabilities, (ii) hierarchies of capabilities and capability portfolios, and (iii) their internal structure. Capability building was analysed in the context of the organisational design, the technological systems and the type of resource-bundling process (creating new vs. entrenching existing capabilities). The thesis describes the current capability portfolios and the organisational changes in the case companies. It also clarifies the mechanisms through which companies can influence the balance between knowledge search and the efficiency of knowledge transfer and integration in their daily business activities, and consequently the diversity of their capability portfolio and the breadth and novelty of their product/service range. The largest wood-industry companies of today must develop a seemingly dual strategic focus: they have to combine leading-edge, innovative solutions with cost-efficient, large-scale production. The use of modern technology in production was no longer a primary source of competitiveness in the case companies, but rather belonged to the portfolio of basic capabilities. Knowledge and information management had become an industry imperative, on a par with cost effectiveness. Yet, during the period of this research, the case companies were better in supporting growth in volume of the existing activity than growth through new economic activities. Customer-driven, incremental innovation was preferred over firm-driven innovation through experimentation. The three main constraints on organisational renewal were the lack of slack resources, the aim for lean, centralised designs, and the inward-bound communication climate.
  • Vatanen, Anu (Helsingin yliopisto, 2016)
    Long-term ovarian function was retrospectively evaluated after allogeneic hematopoietic stem cell transplantation (HSCT) in childhood and adolescence. Cardiovascular risk factors, arterial morphology and stiffness, left ventricular (LV) mass and function, physical fitness and frailty were investigated in adult and adolescent survivors of high-risk neuroblastoma (HR NBL) after autologous HSCT in childhood. The first study population included a cohort of 92 female long-term survivors who were less than 20 years of age when treated at the Children s Hospital, Helsinki University Hospital, or Karolinska University Hospital, Huddinge, between 1978 and 2000. The follow-up data included signs of spontaneous puberty, age at menarche, the use of hormone replacement therapy, pregnancies, and information about pubertal or postpubertal serum FSH levels. The second study population included the Finnish national cohort of 19 long-term HR NBL survivors treated between 1980 and 2000, and 20 age- and sex-matched controls. Clinical examinations included 24h ambulatory blood pressure (BP), very-high-resolution vascular ultrasound, 3D echocardiography and Tissue Doppler Imaging ultrasounds, body composition, physical performance tests and interview. Older age at HSCT and total body irradiation and busulfan-based conditionings were risk factors for early ovarian aging. Leukemia survivors with previous cranial radiotherapy or transplanted after disease relapse were at high risk of premature ovarian failure. The HR NBL survivors showed increased carotid intima-media thickness, plaque formation and stiffness, increased radial artery intima thickness, and increased cardiovascular risk profile when compared to the controls. They had increased LV mass, decreased systolic and diastolic LV function when compared to the controls. Poor LV function associated with cardiac biomarkers, poor physical performance and increased BP. The survivors showed shorter telomere length and increased frequency of frailty phenotype when compared to the controls. The frailty phenotype associated with cardiovascular health and chronic inflammation. In conclusion, our study shows that the adult survivors after HSCT in young age are at risk of early reproductive and vascular aging and frailty. The survivors of pediatric HSCT require regular follow-up in adulthood and interventions for declining ovarian function, cardiovascular risk factors, high BP, subclinical signs of atherosclerosis and decreased cardiac function. Since lifestyle choices can influence cardiovascular health and frailty status, a healthy non-smoking lifestyle and physical activity should be advocated among all survivors who have received HSCT in childhood.
  • Mattsson, Teppo (Helsingin yliopisto, 2009)
    The cosmological observations of light from type Ia supernovae, the cosmic microwave background and the galaxy distribution seem to indicate that the expansion of the universe has accelerated during the latter half of its age. Within standard cosmology, this is ascribed to dark energy, a uniform fluid with large negative pressure that gives rise to repulsive gravity but also entails serious theoretical problems. Understanding the physical origin of the perceived accelerated expansion has been described as one of the greatest challenges in theoretical physics today. In this thesis, we discuss the possibility that, instead of dark energy, the acceleration would be caused by an effect of the nonlinear structure formation on light, ignored in the standard cosmology. A physical interpretation of the effect goes as follows: due to the clustering of the initially smooth matter with time as filaments of opaque galaxies, the regions where the detectable light travels get emptier and emptier relative to the average. As the developing voids begin to expand the faster the lower their matter density becomes, the expansion can then accelerate along our line of sight without local acceleration, potentially obviating the need for the mysterious dark energy. In addition to offering a natural physical interpretation to the acceleration, we have further shown that an inhomogeneous model is able to match the main cosmological observations without dark energy, resulting in a concordant picture of the universe with 90% dark matter, 10% baryonic matter and 15 billion years as the age of the universe. The model also provides a smart solution to the coincidence problem: if induced by the voids, the onset of the perceived acceleration naturally coincides with the formation of the voids. Additional future tests include quantitative predictions for angular deviations and a theoretical derivation of the model to reduce the required phenomenology. A spin-off of the research is a physical classification of the cosmic inhomogeneities according to how they could induce accelerated expansion along our line of sight. We have identified three physically distinct mechanisms: global acceleration due to spatial variations in the expansion rate, faster local expansion rate due to a large local void and biased light propagation through voids that expand faster than the average. A general conclusion is that the physical properties crucial to account for the perceived acceleration are the growth of the inhomogeneities and the inhomogeneities in the expansion rate. The existence of these properties in the real universe is supported by both observational data and theoretical calculations. However, better data and more sophisticated theoretical models are required to vindicate or disprove the conjecture that the inhomogeneities are responsible for the acceleration.
  • Palonen, Vesa (Helsingin yliopisto, 2008)
    Accelerator mass spectrometry (AMS) is an ultrasensitive technique for measuring the concentration of a single isotope. The electric and magnetic fields of an electrostatic accelerator system are used to filter out other isotopes from the ion beam. The high velocity means that molecules can be destroyed and removed from the measurement background. As a result, concentrations down to one atom in 10^16 atoms are measurable. This thesis describes the construction of the new AMS system in the Accelerator Laboratory of the University of Helsinki. The system is described in detail along with the relevant ion optics. System performance and some of the 14C measurements done with the system are described. In a second part of the thesis, a novel statistical model for the analysis of AMS data is presented. Bayesian methods are used in order to make the best use of the available information. In the new model, instrumental drift is modelled with a continuous first-order autoregressive process. This enables rigorous normalization to standards measured at different times. The Poisson statistical nature of a 14C measurement is also taken into account properly, so that uncertainty estimates are much more stable. It is shown that, overall, the new model improves both the accuracy and the precision of AMS measurements. In particular, the results can be improved for samples with very low 14C concentrations or measured only a few times.
  • Toivonen, Suvi (Helsingin yliopisto, 2002)
  • Pöyhönen, Petteri (Helsingin yliopisto, 2012)
    This dissertation introduces two new access selection strategies called the network-centric and the terminal-centric strategies. These strategies use a distributed access selection algorithm, which is designed to exploit the network cooperation to support both horizontal and vertical handovers. The algorithm development was motivated by the fact that the network cooperation hides the network boundaries and through information dissemination it enables more intelligent decision making practices to ensure better utilization of the access resources resulting in enhanced capabilities serving end-users. Two new performance metrics called the USI (User Satisfaction Index) and the OSI (Operator Satisfaction Indicator) are proposed and used to evaluate the potential performance gains of these access-selection strategies. A simulation model was developed to model how a distributed access selection algorithm in a multi-radio access technology environment including one or more operators could logically function. The technical metrics for the simulation experiments were selected to measure different aspects of the access network resource usage and end users connectivity, e.g., a number of different types of handovers and network utilization rates. The USI and OSI metrics are used to assess the non-technical performance of these access-selection strategies. The simulation results and analysis indicate that the cooperation between networks increases the network utilization, coverage and service availability when the access selection is designed to take advantage of it. For the service availability in a single operator environment, the average online time is about 10% higher when the new access selection strategies are used compared to the legacy one. For the network utilization in a multi-operator environment, the network-centric strategy results in about a 20% higher utilization rate over the legacy one when the network is not overloaded. These new strategies are also able to better benefit from the network cooperation when measured using the users disconnectivity. For the end-users, this means that they perceive better connectivity when these strategies are in use compared to the legacy one, while for the operators, this means that their network resources are utilized better. Naturally, these perceived technical benefits translate into greater satisfaction as the analysis clearly shows.
  • Makgahlela, Mahlako (Helsingin yliopisto, 2014)
    Genomic evaluations of animals in multi-breed and admixed populations tend to ignore the population structure and assume that these populations are homogeneous, which may lead to limited success in the application of this technology. The objective of this thesis was to develop approaches for accounting for the admixed structure of the Nordic Red dairy cattle (RDC) and furthermore, investigate the predictive ability of these methods in the estimation of genomic enhanced breeding values. The Nordic RDC population is a composite of the Finnish Ayrshire, Swedish Red, Norwegian Red, Danish Red, and their crosses with other breeds. The study was carried out using individual breed proportions derived from the pedigree to define the base breeds, dense marker genotypes and phenotypes of progeny tested bulls with reliabilities from traditional evaluations close to one. Two approaches were developed: (1) the multi-trait random regression model, which accounts for the interactions between marker effects and base breed origin of alleles, (2) the adjusted genomic relationship matrices by allele frequencies (AF) estimated within breeds versus across breeds, estimated from the currently genotyped versus the base (founding) population. Then, the predictive ability of genomic relationships accounted for breed composition was investigated in genomic evaluations with GBLUP of genotyped animals only, and GBLUP of both genotyped and ungenotyped animals (single-step GBLUP). Information in all evaluation models were weighted by the reliability of the phenotype (i.e., bull or cow deregressed breeding value). The validation of genomic evaluations for all models was assessed as the regression of phenotype on direct estimated genomic values or genomic enhanced breeding values. Gains in validation reliabilities were 2 and 3% for milk and protein, respectively, and -1% using the multi-trait random regression model in comparison to GBLUP model that assumed a homogeneous population. The use of AF within breeds greatly reduced differences in additive genomic relationship coefficients between populations, when assessed both across and within sub-populations. This was more evident and closer to pedigree relationships when breed-wise AF were estimated from the base population. Whereas the use of AF across breeds increased genomic relationships, especially for individuals that were originating from populations that were further from the mean population AF across breeds. Accounting for the population structure with breed-wise AF also, relaxed assumptions when incorporating pedigree-based relationships for single-step GBLUP. This advantage however, was not achieved in genomic evaluations. The validation reliabilities between GBLUP with breed-wise AF and GBLUP with AF across breed were generally similar at 33% for milk and protein and 43% for fat. The validation reliabilities increased to 37%, 40% and 47% for milk, protein and fat, respectively, but were similar irrespective of AF used to compute genomic relationships in single-step GBLUP. The improvement in at least 5% for all traits with single-step GBLUP shows the benefit of utilizing all the available information into genomic evaluations. From the methods developed, it was concluded that accounting for the population structure overall had marginal advantage in the predictive ability of genomic evaluations. However, as genomic selection is becoming a dominant tool, biased evaluations in multi-breeds from ignoring differences between breeds is clearly to be feared. Therefore, a more reasonable and cautious approach for integrating genomic information in multi-breeds would be from single-step evaluations that utilize cow performance record as phenotype and genomic relationships accounted for varying AF between the breeds founder populations.
  • Kapanen, Mika (Helsingin yliopisto, 2009)
    Radiation therapy (RT) plays currently significant role in curative treatments of several cancers. External beam RT is carried out mostly by using megavoltage beams of linear accelerators. Tumor eradication and normal tissue complications correlate to dose absorbed in tissues. Normally this dependence is steep and it is crucial that actual dose within patient accurately correspond to the planned dose. All factors in a RT procedure contain uncertainties requiring strict quality assurance. From hospital physicist´s point of a view, technical quality control (QC), dose calculations and methods for verification of correct treatment location are the most important subjects. Most important factor in technical QC is the verification that radiation production of an accelerator, called output, is within narrow acceptable limits. The output measurements are carried out according to a locally chosen dosimetric QC program defining measurement time interval and action levels. Dose calculation algorithms need to be configured for the accelerators by using measured beam data. The uncertainty of such data sets limits for best achievable calculation accuracy. All these dosimetric measurements require good experience, are workful, take up resources needed for treatments and are prone to several random and systematic sources of errors. Appropriate verification of treatment location is more important in intensity modulated radiation therapy (IMRT) than in conventional RT. This is due to steep dose gradients produced within or close to healthy tissues locating only a few millimetres from the targeted volume. The thesis was concentrated in investigation of the quality of dosimetric measurements, the efficacy of dosimetric QC programs, the verification of measured beam data and the effect of positional errors on the dose received by the major salivary glands in head and neck IMRT. A method was developed for the estimation of the effect of the use of different dosimetric QC programs on the overall uncertainty of dose. Data were provided to facilitate the choice of a sufficient QC program. The method takes into account local output stability and reproducibility of the dosimetric QC measurements. A method based on the model fitting of the results of the QC measurements was proposed for the estimation of both of these factors. The reduction of random measurement errors and optimization of QC procedure were also investigated. A method and suggestions were presented for these purposes. The accuracy of beam data was evaluated in Finnish RT centres. Sufficient accuracy level was estimated for the beam data. A method based on the use of reference beam data was developed for the QC of beam data. Dosimetric and geometric accuracy requirements were evaluated for head and neck IMRT when function of the major salivary glands is intended to be spared. These criteria are based on the dose response obtained for the glands. Random measurement errors could be reduced enabling lowering of action levels and prolongation of measurement time interval from 1 month to even 6 months simultaneously maintaining dose accuracy. The combined effect of the proposed methods, suggestions and criteria was found to facilitate the avoidance of maximal dose errors of up to even about 8 %. In addition, their use may make the strictest recommended overall dose accuracy level of 3 % (1SD) achievable.
  • Kolmonen, Marjo (Helsingin yliopisto, 2011)
    Human sport doping control analysis is a complex and challenging task for anti-doping laboratories. The List of Prohibited Substances and Methods, updated annually by World Anti-Doping Agency (WADA), consists of hundreds of chemically and pharmacologically different low and high molecular weight compounds. This poses a considerable challenge for laboratories to analyze for them all in a limited amount of time from a limited sample aliquot. The continuous expansion of the Prohibited List obliges laboratories to keep their analytical methods updated and to research new available methodologies. In this thesis, an accurate mass-based analysis employing liquid chromatography - time-of-flight mass spectrometry (LC-TOFMS) was developed and validated to improve the power of doping control analysis. New analytical methods were developed utilizing the high mass accuracy and high information content obtained by TOFMS to generate comprehensive and generic screening procedures. The suitability of LC-TOFMS for comprehensive screening was demonstrated for the first time in the field with mass accuracies better than 1 mDa. Further attention was given to generic sample preparation, an essential part of screening analysis, to rationalize the whole work flow and minimize the need for several separate sample preparation methods. Utilizing both positive and negative ionization allowed the detection of almost 200 prohibited substances. Automatic data processing produced a Microsoft Excel based report highlighting the entries fulfilling the criteria of the reverse data base search (retention time (RT), mass accuracy, isotope match). The quantitative performance of LC-TOFMS was demonstrated with morphine, codeine and their intact glucuronide conjugates. After a straightforward sample preparation the compounds were analyzed directly without the need for hydrolysis, solvent transfer, evaporation or reconstitution. The hydrophilic interaction technique (HILIC) provided good chromatographic separation, which was critical for the morphine glucuronide isomers. A wide linear range (50-5000 ng/ml) with good precision (RSD<10%) and accuracy (±10%) was obtained, showing comparable or better performance to other methods used. In-source collision-induced dissociation (ISCID) allowed confirmation analysis with three diagnostic ions with a median mass accuracy of 1.08 mDa and repeatable ion ratios fulfilling WADA s identification criteria. The suitability of LC-TOFMS for screening of high molecular weight doping agents was demonstrated with plasma volume expanders (PVE), namely dextran and hydroxyethylstarch (HES). Specificity of the assay was improved, since interfering matrix compounds were removed by size exclusion chromatography (SEC). ISCID produced three characteristic ions with an excellent mean mass accuracy of 0.82 mDa at physiological concentration levels. In summary, by combining TOFMS with a proper sample preparation and chromatographic separation, the technique can be utilized extensively in doping control laboratories for comprehensive screening of chemically different low and high molecular weight compounds, for quantification of threshold substances and even for confirmation. LC-TOFMS rationalized the work flow in doping control laboratories by simplifying the screening scheme, expediting reporting and minimizing the analysis costs. Therefore LC-TOFMS can be exploited widely in doping control, and the need for several separate analysis techniques is reduced.