Studies on the Cell Wall Structure and on the Mechanical Properties of Norway Spruce

The structure and the mechanical properties of wood of Norway spruce (Picea abies [L.] Karst.) were studied using small samples from Finland and Sweden. X-ray diffraction (XRD) was used to determine the orientation of cellulose microfibrils (microfibril angle, MFA), the dimensions of cellulose crystallites and the average shape of the cell cross-section. X-ray attenuation and x-ray fluorescence measurements were used to study the chemical composition and the trace element content. Tensile testing with in situ XRD was used to characterise the mechanical properties of wood and the deformation of crystalline cellulose within the wood cell walls. Cellulose crystallites were found to be 192 284 Å long and 28.9 33.4 Å wide in chemically untreated wood and they were longer and wider in mature wood than in juvenile wood. The MFA distribution of individual Norway spruce tracheids and larger samples was asymmetric. In individual cell walls, the mean MFA was 19 30 degrees, while the mode of the MFA distribution was 7 21 degrees. Both the mean MFA and the mode of the MFA distribution decreased as a function of the annual ring. Tangential cell walls exhibited smaller mean MFA and mode of the MFA distribution than radial cell walls. Maceration of wood material caused narrowing of the MFA distribution and removed contributions observed at around 90 degrees. In wood of both untreated and fertilised trees, the average shape of the cell cross-section changed from circular via ambiguous to rectangular as the cambial age increased. The average shape of the cell cross-section and the MFA distribution did not change as a result of fertilisation. The mass absorption coefficient for x-rays was higher in wood of fertilised trees than in that of untreated trees and wood of fertilised trees contained more of the elements S, Cl, and K, but a smaller amount of Mn. Cellulose crystallites were longer in wood of fertilised trees than in that of untreated trees. Kraft cooking caused widening and shortening of the cellulose crystallites. Tensile tests parallel to the cells showed that if the mean MFA is initially around 10 degrees or smaller, no systematic changes occur in the MFA distribution due to strain. The role of mean MFA in defining the tensile strength or the modulus of elasticity of wood was not as dominant as that reported earlier. Crystalline cellulose elongated much less than the entire samples. The Poisson ratio νca of crystalline cellulose in Norway spruce wood was shown to be largely dependent on the surroundings of crystalline cellulose in the cell wall, varying between -1.2 and 0.8. The Poisson ratio was negative in kraft cooked wood and positive in chemically untreated wood. In chemically untreated wood, νca was larger in mature wood and in latewood compared to juvenile wood and earlywood.

Factors controlling the surface energy budget over snow and ice

Polar Regions are an energy sink of the Earth system, as the Sun rays do not reach the Poles for half of the year, and hit them only at very low angles for the other half of the year. In summer, solar radiation is the dominant energy source for the Polar areas, therefore even small changes in the surface albedo strongly affect the surface energy balance and, thus, the speed and amount of snow and ice melting. In winter, the main heat sources for the atmosphere are the cyclones approaching from lower latitudes, and the atmosphere-surface heat transfer takes place through turbulent mixing and longwave radiation, the latter dominated by clouds. The aim of this thesis is to improve the knowledge about the surface and atmospheric processes that control the surface energy budget over snow and ice, with particular focus on albedo during the spring and summer seasons, on horizontal advection of heat, cloud longwave forcing, and turbulent mixing during the winter season. The critical importance of a correct albedo representation in models is illustrated through the analysis of the causes for the errors in the surface and near-surface air temperature produced in a short-range numerical weather forecast by the HIRLAM model. Then, the daily and seasonal variability of snow and ice albedo have been examined by analysing field measurements of albedo, carried out in different environments. On the basis of the data analysis, simple albedo parameterizations have been derived, which can be implemented into thermodynamic sea ice models, as well as numerical weather prediction and climate models. Field measurements of radiation and turbulent fluxes over the Bay of Bothnia (Baltic Sea) also allowed examining the impact of a large albedo change during the melting season on surface energy and ice mass budgets. When high contrasts in surface albedo are present, as in the case of snow covered areas next to open water, the effect of the surface albedo heterogeneity on the downwelling solar irradiance under overcast condition is very significant, although it is usually not accounted for in single column radiative transfer calculations. To account for this effect, an effective albedo parameterization based on three-dimensional Monte Carlo radiative transfer calculations has been developed. To test a potentially relevant application of the effective albedo parameterization, its performance in the ground-based retrieval of cloud optical depth was illustrated. Finally, the factors causing the large variations of the surface and near-surface temperatures over the Central Arctic during winter were examined. The relative importance of cloud radiative forcing, turbulent mixing, and lateral heat advection on the Arctic surface temperature were quantified through the analysis of direct observations from Russian drifting ice stations, with the lateral heat advection calculated from reanalysis products.

Accelerator Mass Spectrometry and Bayesian Data Analysis

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.

Hybrid Modelling of Titan's Interaction with the Magnetosphere of Saturn

In this dissertation we study the interaction between Saturn's moon Titan and the magnetospheric plasma and magnetic field. The method of research is a three-dimensional computer simulation model, that is used to simulate this interaction. The simulation model used is a hybrid model. Hybrid models enable individual tracking or tracing of ions and also take into account the particle motion in the propagation of the electromagnetic fields. The hybrid model has been developed at the Finnish Meteorological Institute. This thesis gives a general description of the effects that the solar wind has on Earth and other planets of our solar system. Planetary satellites can also have similar interactions with the solar wind but also with the plasma flows of planetary magnetospheres. Titan is clearly the largest among the satellites of Saturn and also the only known satellite with a dense atmosphere. It is the atmosphere that makes Titan's plasma interaction with the magnetosphere of Saturn so unique. Nevertheless, comparisons with the plasma interactions of other solar system bodies are valuable. Detecting charged plasma particles requires in situ measurements obtainable through scientific spacecraft. The Cassini mission has been one of the most remarkable international efforts in space science. Since 2004 the measurements and images obtained from instruments onboard the Cassini spacecraft have increased the scientific knowledge of Saturn as well as its satellites and magnetosphere in a way no one was probably able to predict. The current level of science on Titan is practically unthinkable without the Cassini mission. Many of the observations by Cassini instrument teams have influenced this research both the direct measurements of Titan as well as observations of its plasma environment. The theoretical principles of the hybrid modelling approach are presented in connection to the broader context of plasma simulations. The developed hybrid model is described in detail: e.g. the way the equations of the hybrid model are solved is shown explicitly. Several simulation techniques, such as the grid structure and various boundary conditions, are discussed in detail as well. The testing and monitoring of simulation runs is presented as an essential routine when running sophisticated and complex models. Several significant improvements of the model, that are in preparation, are also discussed. A main part of this dissertation are four scientific articles based on the results of the Titan model. The Titan model developed during the course of the Ph.D. research has been shown to be an important tool to understand Titan's plasma interaction. One reason for this is that the structures of the magnetic field around Titan are very much three-dimensional. The simulation results give a general picture of the magnetic fields in the vicinity of Titan. The magnetic fine structure of Titan's wake as seen in the simulations seems connected to Alfvén waves an important wave mode in space plasmas. The particle escape from Titan is also a major part of these studies. Our simulations show a bending or turning of Titan's ionotail that we have shown to be a direct result of the basic principles in plasma physics. Furthermore, the ion flux from the magnetosphere of Saturn into Titan's upper atmosphere has been studied. The modelled ion flux has asymmetries that would likely have a large impact in the heating in different parts of Titan's upper atmosphere.

Nuorten mäntyjen ulkoisen laadun kehitykseen vaikuttavat tekijät

Männyn laatuun vaikuttavista tekijöistä tässä tutkimuksessa selvitettiin, mitkä tekijät aiheuttavat nuorissa männyissä oksikkuutta, mutkaisuutta käsittäen myös lenkouden ja haaraisuutta. Jokaiselle laatuvialle laadittiin kolme eritasoista mallia. Eniten keskityttiin tutkimaan oksikkuutta aiheuttavia tekijöitä, koska oksikkuus vaikuttaa männyn sisäiseen oksaisuuteen, joka on yleisin sahatavarakappaleen laatuluokan määräävä ominaisuus. Lisäksi mutkaisuus ja erityisesti haaraisuus osoittautuivat melko sattumanvaraisesti esiintyviksi laatuvioiksi, minkä takia niiden kehittymiseen vaikuttavia tekijöitä on vaikea määritellä. Tutkimuksessa käytettiin Metsäntutkimuslaitoksen taimikoiden inventointikokeiden (TINKA-kokeet) aineiston ensimmäisen ja kolmannen mittauskerran tuloksia. Näiden mittauskertojen väli oli 15 vuotta. Tutkimuksen perustuminen useampaan kuin yhteen mittauskertaan erottaa tämän tutkimuksen monista muista mäntyjen laatua käsittelevistä tutkimuksista, jotka ovat perustuneet yhden mittauskerran poikkileikkausaineistoon. Laadittujen kolmen eritasoisen mallin perusteella voidaan todeta, että oksikkuuden ja mutkaisuuden kehittymistä mäntyihin pystytään arvioimaan kohtalaisesti jo metsikön perustietojen (syntytapa, kasvupaikka, lämpösumma) avulla, jotka metsänomistajalla on tiedossaan jo taimikkoa perustaessaan. Puutason mittauksilla pystytään selvästi tarkentamaan arviota siitä, tuleeko männystä oksikas vai ei. Sitä vastoin puutason mittaukset parantavat vain vähän arviota mutkaisuuden kehittymisestä. Haaraisuuden esiintymistä luotettavasti ennustavaa mallia ei pystytty tekemään. Oksikkuutta lisääviä tekijöitä mallien mukaan olivat mm. männyn suuri läpimitan kasvu, suuri suhteellinen pituus saman metsikön muihin puihin verrattuna, alhainen kasvatustiheys männyntaimikon alkukehitysvaiheessa ja taimikonhoidon tekemättä jättäminen. Mutkaisuutta lisääviä tekijöitä olivat mm. suuri lämpösumma eli männikön sijainti Etelä-Suomessa, männyn suuri läpimitan kasvu, pieni suhteellinen pituus, alhainen kasvatustiheys männyntaimikon alkukehitysvaiheessa ja taimikonhoidon tekemättä jättäminen. Eri uudistamistavoista kylvö osoittautui parhaimmaksi laadun kannalta sekä oksikkuutta että mutkaisuutta tarkasteltaessa. Haaraisuutta lisääviä tekijöitä olivat mm. pieni lämpösumma eli männikön sijainti Pohjois-Suomessa, männyn suuri läpimitan kasvu ja alhainen kasvatustiheys männyntaimikon alkukehitysvaiheessa.

Semi-supervised learning of WLAN radio maps

In this thesis a manifold learning method is applied to the problem of WLAN positioning and automatic radio map creation. Due to the nature of WLAN signal strength measurements, a signal map created from raw measurements results in non-linear distance relations between measurement points. These signal strength vectors reside in a high-dimensioned coordinate system. With the help of the so called Isomap-algorithm the dimensionality of this map can be reduced, and thus more easily processed. By embedding position-labeled strategic key points, we can automatically adjust the mapping to match the surveyed environment. The environment is thus learned in a semi-supervised way; gathering training points and embedding them in a two-dimensional manifold gives us a rough mapping of the measured environment. After a calibration phase, where the labeled key points in the training data are used to associate coordinates in the manifold representation with geographical locations, we can perform positioning using the adjusted map. This can be achieved through a traditional supervised learning process, which in our case is a simple nearest neighbors matching of a sampled signal strength vector. We deployed this system in two locations in the Kumpula campus in Helsinki, Finland. Results indicate that positioning based on the learned radio map can achieve good accuracy, especially in hallways or other areas in the environment where the WLAN signal is constrained by obstacles such as walls.

Metsikön rakenteen vaikutus säteilyn sammumiskertoimeen

Kasvuston G-funktio kuvaa säteilyn vähenemistä tai ”sammumista” auringon eri korkeuskulmissa varjostavan lehtialan suhteen. Sen vuoksi sitä kutsutaan sammumiskertoimeksi. Tutkimuksen tavoitteena oli selvittää vaihteleeko G-funktion muoto eri puulajien metsiköissä, ja voidaanko puulajit erottaa toisistaan G-funktion muodon avulla. Arvioin lisäksi G-funktioiden muodossa kasvukaudenaikana tapahtuvia muutoksia. Muita tutkimuksen kannalta mielenkiintoisia tutkimuskysymyksiä olivat voidaanko ryhmittymistä tai latvusmuotoa arvioida G-funktion muodon avulla. Maastomittaukset suoritettiin 3.5.2010 -30.9.2010 välisenä aikana. Tutkimusalueena oli Hyytiälän metsäaseman (68?59`N, 35?72`E) ympäristö, jonka metsät edustavat tyypillistä boreaalista havu- ja lehtimetsää. Tutkimusta varten perustettiin kuusi yhden puulajin koealaa, kaksi kutakin puulajia kohden. Tutkittavat puulajit olivat mänty (Pinus sylvestris), kuusi (Picea abies) ja rauduskoivu (Betula pendula). Koealaparit valittiin niin, että kullekin puulajille muodostui varttuneesta metsästä ja taimikosta muodostuva pari tai vaihtoehtoisesti tiheämpi ja harvempi koeala. Koealoille perustettiin 81 mittauspistettä sisältävä mittaushila, jossa kunkin pisteen aukkoisuustiedot mitattiin kahden viikon välein. Mittaukset suoritettiin kahdella LAI-2000 Plant Canopy Analyzer -laitteella. Laitteiden tulosteista koealoille saatiin aukkoisuustiedot T(?) ja LAI, joiden avulla saatiin laskettua tarkasteltavat G-funktiot. Saman puulajin G-funktiota vertailtiin toisiinsa puulajityypillisten trendien havaitsemiseksi. Keskikesällä eri puulajien G-funktioita verrattiin toisiinsa. Teoreettisten simulointien avulla tutkittiin latvuksen dimensioiden (latvuksen pituus ja säde) ja sisäisen ryhmittäisyyden vaikutusta puulajikohtaiseen G-funktioon. Simuloinneissa käytettiin hyväksi tietoa koealojen puustotunnuksista, lehtialasta sekä runkoluvusta. Puulajikohtaiset G-funktiot ovat erotettavissa toisistaan funktion minimi- ja maksimiarvojen sijoittumisen sekä suhteellisen vaihteluvälin perusteella. Havupuualojen G-funktiot eivät juuri muuttuneet kasvukauden aikana. Koivualoilla G-funktion kasvukaudenaikaiset muutokset (pelkät oksat, hiirenkorvat ja täysikasvuiset lehdet) olivat sitä vastoin helposti havaittavissa. G-funktion muodon avulla voidaan myös arvioida latvusmuotoa ja ryhmittymistä. Mäntyjen latvusmuoto on approksimoitavissa parhaiten ympyräkartion avulla. Kuusien ja koivujen latvusmuodon approksimointiin parhaana vaihtoehtona voidaan pitää ellipsoidia. Teoreettisten simulointien perusteella nuori kuusikko on muita havupuualoja ryhmittyneempi. Tutkimuksen mukaan säteily sammuu satelliittien yleisimmässä kuvaussuunnassa tehokkaammin kuin kaikkien suuntien yli laskettu keskiarvo (0,5) antaa olettaa. Puulajikohtaisten G-funktioiden avulla voidaan epäsuorasti arvioida sekä metsästä tapahtuvaa heijastusta että metsikön sisäisiä säteilyolosuhteita, sillä puulaji yhdessä metsikön rakenteen kanssa vaikuttaa metsästä heijastuvaan säteilyyn. Puulajikohtainen G-funktio on parametri, jonka avulla voidaan kalibroida malleja, joissa tarvitaan tietoa säteilyn kulusta erilaisissa kasvustoissa.

Direct detection of atmospheric particle formation using the Neutral cluster and Air Ion Spectrometer

Aerosol particles play an important role in the Earth s atmosphere and in the climate system: they scatter and absorb solar radiation, facilitate chemical processes, and serve as seeds for cloud formation. Secondary new particle formation (NPF) is a globally important source of these particles. Currently, the mechanisms of particle formation and the vapors participating in this process are, however, not truly understood. In order to fully explain atmospheric NPF and subsequent growth, we need to measure directly the very initial steps of the formation processes. This thesis investigates the possibility to study atmospheric particle formation using a recently developed Neutral cluster and Air Ion Spectrometer (NAIS). First, the NAIS was calibrated and intercompared, and found to be in good agreement with the reference instruments both in the laboratory and in the field. It was concluded that NAIS can be reliably used to measure small atmospheric ions and particles directly at the sizes where NPF begins. Second, several NAIS systems were deployed simultaneously at 12 European measurement sites to quantify the spatial and temporal distribution of particle formation events. The sites represented a variety of geographical and atmospheric conditions. The NPF events were detected using NAIS systems at all of the sites during the year-long measurement period. Various particle formation characteristics, such as formation and growth rates, were used as indicators of the relevant processes and participating compounds in the initial formation. In a case of parallel ion and neutral cluster measurements, we also estimated the relative contribution of ion-induced and neutral nucleation to the total particle formation. At most sites, the particle growth rate increased with the increasing particle size indicating that different condensing vapors are participating in the growth of different-sized particles. The results suggest that, in addition to sulfuric acid, organic vapors contribute to the initial steps of NPF and to the subsequent growth, not just later steps of the particle growth. As a significant new result, we found out that the total particle formation rate varied much more between the different sites than the formation rate of charged particles. The results infer that the ion-induced nucleation has a minor contribution to particle formation in the boundary layer in most of the environments. These results give tools to better quantify the aerosol source provided by secondary NPF in various environments. The particle formation characteristics determined in this thesis can be used in global models to assess NPF s climatic effects.

On the use of weather radar for mesoscale applications in northern conditions

Mesoscale weather phenomena, such as the sea breeze circulation or lake effect snow bands, are typically too large to be observed at one point, yet too small to be caught in a traditional network of weather stations. Hence, the weather radar is one of the best tools for observing, analyzing and understanding their behavior and development. A weather radar network is a complex system, which has many structural and technical features to be tuned, from the location of each radar to the number of pulses averaged in the signal processing. These design parameters have no universal optimal values, but their selection depends on the nature of the weather phenomena to be monitored as well as on the applications for which the data will be used. The priorities and critical values are different for forest fire forecasting, aviation weather service or the planning of snow ploughing, to name a few radar-based applications. The main objective of the work performed within this thesis has been to combine knowledge of technical properties of the radar systems and our understanding of weather conditions in order to produce better applications able to efficiently support decision making in service duties for modern society related to weather and safety in northern conditions. When a new application is developed, it must be tested against ground truth . Two new verification approaches for radar-based hail estimates are introduced in this thesis. For mesoscale applications, finding the representative reference can be challenging since these phenomena are by definition difficult to catch with surface observations. Hence, almost any valuable information, which can be distilled from unconventional data sources such as newspapers and holiday shots is welcome. However, as important as getting data is to obtain estimates of data quality, and to judge to what extent the two disparate information sources can be compared. The presented new applications do not rely on radar data alone, but ingest information from auxiliary sources such as temperature fields. The author concludes that in the future the radar will continue to be a key source of data and information especially when used together in an effective way with other meteorological data.

Physical Properties of Deep Drill Cores : Implications for Meteorite Impact Effects and Crustal Structures

Physical properties provide valuable information about the nature and behavior of rocks and minerals. The changes in rock physical properties generate petrophysical contrasts between various lithologies, for example, between shocked and unshocked rocks in meteorite impact structures or between various lithologies in the crust. These contrasts may cause distinct geophysical anomalies, which are often diagnostic to their primary cause (impact, tectonism, etc). This information is vital to understand the fundamental Earth processes, such as impact cratering and associated crustal deformations. However, most of the present day knowledge of changes in rock physical properties is limited due to a lack of petrophysical data of subsurface samples, especially for meteorite impact structures, since they are often buried under post-impact lithologies or eroded. In order to explore the uppermost crust, deep drillings are required. This dissertation is based on the deep drill core data from three impact structures: (i) the Bosumtwi impact structure (diameter 10.5 km, 1.07 Ma age; Ghana), (ii) the Chesapeake Bay impact structure (85 km, 35 Ma; Virginia, U.S.A.), and (iii) the Chicxulub impact structure (180 km, 65 Ma; Mexico). These drill cores have yielded all basic lithologies associated with impact craters such as post-impact lithologies, impact rocks including suevites and breccias, as well as fractured and unfractured target rocks. The fourth study case of this dissertation deals with the data of the Paleoproterozoic Outokumpu area (Finland), as a non-impact crustal case, where a deep drilling through an economically important ophiolite complex was carried out. The focus in all four cases was to combine results of basic petrophysical studies of relevant rocks of these crustal structures in order to identify and characterize various lithologies by their physical properties and, in this way, to provide new input data for geophysical modellings. Furthermore, the rock magnetic and paleomagnetic properties of three impact structures, combined with basic petrophysics, were used to acquire insight into the impact generated changes in rocks and their magnetic minerals, in order to better understand the influence of impact. The obtained petrophysical data outline the various lithologies and divide rocks into four domains. Based on target lithology the physical properties of the unshocked target rocks are controlled by mineral composition or fabric, particularly porosity in sedimentary rocks, while sediments result from diverse sedimentation and diagenesis processes. The impact rocks, such as breccias and suevites, strongly reflect the impact formation mechanism and are distinguishable from the other lithologies by their density, porosity and magnetic properties. The numerous shock features resulting from melting, brecciation and fracturing of the target rocks, can be seen in the changes of physical properties. These features include an increase in porosity and subsequent decrease in density in impact derived units, either an increase or a decrease in magnetic properties (depending on a specific case), as well as large heterogeneity in physical properties. In few cases a slight gradual downward decrease in porosity, as a shock-induced fracturing, was observed. Coupled with rock magnetic studies, the impact generated changes in magnetic fraction the shock-induced magnetic grain size reduction, hydrothermal- or melting-related magnetic mineral alteration, shock demagnetization and shock- or temperature-related remagnetization can be seen. The Outokumpu drill core shows varying velocities throughout the drill core depending on the microcracking and sample conditions. This is similar to observations by Kern et al., (2009), who also reported the velocity dependence on anisotropy. The physical properties are also used to explain the distinct crustal reflectors as observed in seismic reflection studies in the Outokumpu area. According to the seismic velocity data, the interfaces between the diopside-tremolite skarn layer and either serpentinite, mica schist or black schist are causing the strong seismic reflectivities.

Position-sensitive silicon strip detector characterization using particle beams

Silicon strip detectors are fast, cost-effective and have an excellent spatial resolution. They are widely used in many high-energy physics experiments. Modern high energy physics experiments impose harsh operation conditions on the detectors, e.g., of LHC experiments. The high radiation doses cause the detectors to eventually fail as a result of excessive radiation damage. This has led to a need to study radiation tolerance using various techniques. At the same time, a need to operate sensors approaching the end their lifetimes has arisen. The goal of this work is to demonstrate that novel detectors can survive the environment that is foreseen for future high-energy physics experiments. To reach this goal, measurement apparatuses are built. The devices are then used to measure the properties of irradiated detectors. The measurement data are analyzed, and conclusions are drawn. Three measurement apparatuses built as a part of this work are described: two telescopes measuring the tracks of the beam of a particle accelerator and one telescope measuring the tracks of cosmic particles. The telescopes comprise layers of reference detectors providing the reference track, slots for the devices under test, the supporting mechanics, electronics, software, and the trigger system. All three devices work. The differences between these devices are discussed. The reconstruction of the reference tracks and analysis of the device under test are presented. Traditionally, silicon detectors have produced a very clear response to the particles being measured. In the case of detectors nearing the end of their lifefimes, this is no longer true. A new method benefitting from the reference tracks to form clusters is presented. The method provides less biased results compared to the traditional analysis, especially when studying the response of heavily irradiated detectors. Means to avoid false results in demonstrating the particle-finding capabilities of a detector are also discussed. The devices and analysis methods are primarily used to study strip detectors made of Magnetic Czochralski silicon. The detectors studied were irradiated to various fluences prior to measurement. The results show that Magnetic Czochralski silicon has a good radiation tolerance and is suitable for future high-energy physics experiments.

Studies of the Human Transcriptome

Gene expression is one of the most critical factors influencing the phenotype of a cell. As a result of several technological advances, measuring gene expression levels has become one of the most common molecular biological measurements to study the behaviour of cells. The scientific community has produced enormous and constantly increasing collection of gene expression data from various human cells both from healthy and pathological conditions. However, while each of these studies is informative and enlighting in its own context and research setup, diverging methods and terminologies make it very challenging to integrate existing gene expression data to a more comprehensive view of human transcriptome function. On the other hand, bioinformatic science advances only through data integration and synthesis. The aim of this study was to develop biological and mathematical methods to overcome these challenges and to construct an integrated database of human transcriptome as well as to demonstrate its usage. Methods developed in this study can be divided in two distinct parts. First, the biological and medical annotation of the existing gene expression measurements needed to be encoded by systematic vocabularies. There was no single existing biomedical ontology or vocabulary suitable for this purpose. Thus, new annotation terminology was developed as a part of this work. Second part was to develop mathematical methods correcting the noise and systematic differences/errors in the data caused by various array generations. Additionally, there was a need to develop suitable computational methods for sample collection and archiving, unique sample identification, database structures, data retrieval and visualization. Bioinformatic methods were developed to analyze gene expression levels and putative functional associations of human genes by using the integrated gene expression data. Also a method to interpret individual gene expression profiles across all the healthy and pathological tissues of the reference database was developed. As a result of this work 9783 human gene expression samples measured by Affymetrix microarrays were integrated to form a unique human transcriptome resource GeneSapiens. This makes it possible to analyse expression levels of 17330 genes across 175 types of healthy and pathological human tissues. Application of this resource to interpret individual gene expression measurements allowed identification of tissue of origin with 92.0% accuracy among 44 healthy tissue types. Systematic analysis of transcriptional activity levels of 459 kinase genes was performed across 44 healthy and 55 pathological tissue types and a genome wide analysis of kinase gene co-expression networks was done. This analysis revealed biologically and medically interesting data on putative kinase gene functions in health and disease. Finally, we developed a method for alignment of gene expression profiles (AGEP) to perform analysis for individual patient samples to pinpoint gene- and pathway-specific changes in the test sample in relation to the reference transcriptome database. We also showed how large-scale gene expression data resources can be used to quantitatively characterize changes in the transcriptomic program of differentiating stem cells. Taken together, these studies indicate the power of systematic bioinformatic analyses to infer biological and medical insights from existing published datasets as well as to facilitate the interpretation of new molecular profiling data from individual patients.

Disordered matter studied by x-ray Raman scattering

Spectroscopy can provide valuable information on the structure of disordered matter beyond that which is available through e.g. x-ray and neutron diffraction. X-ray Raman scattering is a non-resonant element-sensitive process which allows bulk-sensitive measurements of core-excited spectra from light-element samples. In this thesis, x-ray Raman scattering is used to study the local structure of hydrogen-bonded liquids and solids, including liquid water, a series of linear and branched alcohols, and high-pressure ice phases. Connecting the spectral features to the local atomic-scale structure involves theoretical references, and in the case of hydrogen-bonded systems the interpretation of the spectra is currently actively debated. The systematic studies of the intra- and intermolecular effects in alcohols, non-hydrogen-bonded neighbors in high-pressure ices, and the effect of temperature in liquid water are used to demonstrate different aspects of the local structure that can influence the near-edge spectra. Additionally, the determination of the extended x-ray absorption fine structure is addressed in a momentum-transfer dependent study. This work demonstrates the potential of x-ray Raman scattering for unique studies of the local structure of a variety of disordered light-element systems.

Pystynävertäjän (Tomicus piniperda) vaikutus männyn (Pinus sylvestris) fotosynteesiin ja VOC-emissioihin

Pystynävertäjä on Suomessa yksi merkittävimpiä mäntyjen tuhohyönteisiä. Se syö männynversoja ontoiksi, minkä seurauksena nämä tippuvat maahan. Tästä aiheutuu puulle kasvutappioita ja metsänomistajalle tulonmenetyksiä. Pystynävertäjän ekologiaa on tutkittu paljon, mutta ei tiedetä, miten se vaikuttaa versojen fotosynteesiin ja haihtuvien orgaanisten yhdisteiden eli VOC-yhdisteiden emissioihin ennen versojen putoamista. Monissa muissa tutkimuksissa on havaittu herbivoreilla olevan vaikutusta isäntäkasviensa fotosynteesiin. Lisäksi herbivorian seurauksena isäntäkasvin VOC-emissiot ovat voineet muuttua laadultaan tai määrältään. Pystynävertäjän vaikutuksia versoihin tutkittiin kokeellisesti SMEAR II -asemalla Pirkanmaalla. Pystynävertäjän vaurioittamien ja kontrolliversojen fotosynteesiä mittattiin kahden männyn latvuksessa heinä–syyskuussa 2010. Mittaukset tehtiin kannettavalla fotosynteesimittauslaitteistolla. Samalla otettiin VOC-näytteitä neulasten emissioista adsorbenttiputkiin. Lisäksi toisesta koepuusta suljettiin pystynävertäjäja kontrolliverso raamikyvettiin, johon mahtui oksan kärkeä n. 20 cm. Raamikyvetin läpi kierrätetystä ilmasta kerättiin VOC-näytteitä SPME-kuituun ja siihen sitoutuneet yhdisteet analysoitiin enantiomeereittain. Pystynävertäjä- ja kontrolliversojen välillä ei ollut selvää eroa hiilen assimilaatiossa, transpiraatiossa, ilmarakokonduktanssissa, vedenkäytön tehokkuudessa tai fotokemiallisessa saannossa. Vain pahimmin vaurioituneissa versoissa vaurio vaikutti fotosynteesiin huomattavasti. Esimerkiksi fotokemiallinen saanto laski selvästi vasta, kun verso oli juuri katkeamaisillaan pystynävertäjän sisäänmenoreiän kohdalta. Neulaskyvettimittausten perusteella vaikuttaa siltä, että pystynävertäjä toisella koepuulla lisää monoterpeeniemissioita ja toisella vähentää niitä. Raamikyvettimittauksessa pystynävertäjä lisäsi (+)-enantiomeerin osuutta ?- ja ?-pineeni- sekä limoneeniemissioista, mutta emissioiden kokonaismäärä ei juuri eronnut kontrolliversosta. Pystynävertäjän vaikutukset versojen fotosynteesiin jäivät vähäisiksi, vaikka pystynävertäjä olikin tehnyt versoihin yhdestä neljään reikää ja niiden kohdalta poistanut suuren osan verson poikkileikkauspinta-alasta. Pystynävertäjän aiheuttamat kasvutappiot vaikuttavatkin olevan seurausta lähes yksinomaan versojen putoamisesta. Pystynävertäjä ei juuri vaikuttanut versosta haihtuvien yhdisteiden kokonaismäärään, mutta se muutti niiden keskinäisiä runsaussuhteita ja erityisesti enantiomeerien runsaussuhteita. Pystynävertäjien vaikutukset VOC-emissioihin näyttävät riippuvan suuresti kemotyypistä. Laajempien johtopäätösten tekeminen pystynävertäjän vaikutuksista männyn VOC-emissioihin vaatisi tutkimuksen toistamista suuremmalla koepuumäärällä.

Chemical Characterization of Urban Background Aerosol Using Online And Filter Methods

In order to evaluate the influence of ambient aerosol particles on cloud formation, climate and human health, detailed information about the concentration and composition of ambient aerosol particles is needed. The dura-tion of aerosol formation, growth and removal processes in the atmosphere range from minutes to hours, which highlights the need for high-time-resolution data in order to understand the underlying processes. This thesis focuses on characterization of ambient levels, size distributions and sources of water-soluble organic carbon (WSOC) in ambient aerosols. The results show that in the location of this study typically 50-60 % of organic carbon in fine particles is water-soluble. The amount of WSOC was observed to increase as aerosols age, likely due to further oxidation of organic compounds. In the boreal region the main sources of WSOC were biomass burning during the winter and secondary aerosol formation during the summer. WSOC was mainly attributed to a fine particle mode between 0.1 - 1 μm, although different size distributions were measured for different sources. The WSOC concentrations and size distributions had a clear seasonal variation. Another main focus of this thesis was to test and further develop the high-time-resolution methods for chemical characterization of ambient aerosol particles. The concentrations of the main chemical components (ions, OC, EC) of ambient aerosol particles were measured online during a year-long intensive measurement campaign conducted on the SMEAR III station in Southern Finland. The results were compared to the results of traditional filter collections in order to study sampling artifacts and limitations related to each method. To achieve better a time resolution for the WSOC and ion measurements, a particle-into-liquid sampler (PILS) was coupled with a total organic carbon analyzer (TOC) and two ion chromatographs (IC). The PILS-TOC-IC provided important data about diurnal variations and short-time plumes, which cannot be resolved from the filter samples. In summary, the measurements made for this thesis provide new information on the concentrations, size distribu-tions and sources of WSOC in ambient aerosol particles in the boreal region. The analytical and collection me-thods needed for the online characterization of aerosol chemical composition were further developed in order to provide more reliable high-time-resolution measurements.