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  • Sairanen, Samuli (2013)
    The term "botnet" has surfaced in the media in recent years, showing the complications of manipulation of massive amounts of computers. These zombie computers provide platform for many illegal or otherwise shady actions, like spam mailing and denial of service-attacks. The power of such networks is noticeable on global scale, but what is really known about these networks? Why do they exist in the first place? How are botnets being created today and how they work on a technical level? How is the emergence of mobile internet computing affecting botnet creation and what kind of possibilities does it offer? Goal of this work is to illustrate the history of botnets, understand the structure of botnets, how they are built, and how they affect the whole internet culture. Also the methods for fighting against the threat of botnets are speculated.
  • Genjang, Nevil Nuvala (2012)
    The thesis is written on the catalytic activation of carbon dioxide. It includes a literature part and an experimental part. In the literature part, a review on metal (salen) complexes in relation to their electronic and geometric properties is presented. Salicylidene-aminates are included considering similarity to the salens. Also included from literature is a selective review focusing on the mechanistic aspects in the carboxylation of epoxides by metal (salen) complexes. Some applications of iron (salen) complexes as catalyst are mentioned. In the experimental part, the bis(phenoxyiminato) chlorido iron(III)complexes are synthesized, characterized and applied on carbon dioxide/epoxide coupling reactions. Characterization is done by UV-vis, infra-red, nuclear magnetic resonance and electron impact mass spectroscopy and elemental analysis for C, H, and N. Thermogravimetric analysis for the complexes, DFT calculation for the most active species (L11)2Fe(III)Cl and X-ray for (L6)2Fe(III)Cl are also presented. X-ray crystallography reveals the space group of (L6)2Fe(III)Cl to be orthorhombic, Pbcn; a = 29.0038(14) Å, b = 8.6123(8) Å, c = 10.7843(9) Å; α = β = γ = 90 o. The ML2Cl complexes are observed to have M-O and M-N bonds involving the phenolic oxygen and azomethine nitrogen. Correlation study between spin state and the Fe-N bond length indicates a high-spin state for Fe(III) nucleus. The geometry around the metal nucleus is distorted square pyramidal. Reaction conditions for catalytic activity were fine-tuned envisaging the exclusive production of cyclic carbonates. Propylene and styrene oxides show high reactivity. The ketiminato complexes show better activity over the aldiminato complexes. Optimal result is obtained in dimethyl formamide at a temperature of 145 oC and carbon dioxide pressure of 10 bars in the presence of tetrabutylphosphonium bromide as co-catalyst. A TOF of 572/h is observed for propylene oxide. Three reaction mechanisms are proposed. Comparatively the Co(III) analogues are more active, and iodide as a halogen ligand produces a more active complex than chloride. Improving nucleophilicity of Fe(III), elimination of intramolecular H-bond and improving on solubility could yield a more active complex. Iron is a cheap and environmentally benign metal. The use of iron complexes is an attractive alternative to other transition metals which are expensive and/or toxic. The complexes are robust and show high thermal stability. Surprisingly, oligomers of styrene carbonate were noticed at the reaction temperature and pressure known to favor exclusive production of cyclic carbonates. These observations suggest the complexes for a promising study and application in future research for copolymerization. Such copolymers may have useful charateristics for diverse applications.
  • Savolainen, Talvikki (2013)
    A mining facility is planned to Hannukainen, Kolari, where iron, copper and gold will be enriched. The brown-field of Rautuvaara in the Niesajoki valley is one of the options for the tailings disposal area in the environmental assessment plan. It has been used by the Rautuvaara and Saattopora mines to dispose tailings from 1962 to 1995. The target of the study was to define groundwater table and directions, hydrostratigraphical features and water qualities as well as research groundwater – surface water interactions in order to evaluate the present state and possibility for future use as a tailings disposal area. The hydraulic gradient was delineated with ArcGIS to be towards the center part of the valley and a watershed was identified in the middle part of the northern settling pond. The hydraulic pattern was simple. Mostly, the valley is covered by till, with some alternating sand, gravel and silt units. No good aquitards were identified with permeabilities calculated from grain-size analysis and slug tests. However, the hydraulic conductivity was determined to be poor or moderate (from 10^-2 to 10^-7 m s^-1) in the till units, they dominated in the area. The surrounding surface and groundwaters followed the baseline in the area for the most and were determined to be natural waters (calcium- hydrogencarbonate) with Aquachem software. Contaminated (acid mine drainage) surface and groundwaters (sulphate-magnesium) were quite restricted in area, they were identified in surface waters and groundwater observation wells close by the abandoned tailings area. Some of these groundwater observation wells were evaluated to contain surface water by their oxygen and hydrogen ionic compositions, where others of the evaporated observations wells situated near a bog area. Groundwater seepage from the west coast was also concluded, which could have had a part in the AMD generation process. On the other hand, some of the wells contained enriched waters, in form of elevated trace element concentrations, however they were still Ca-HCO3 waters. This was the case for two artesian monitoring wells on the tailings area. It was concluded that the existing peat layer underneath the tailings is impermeable and leads to the assumption that mostly the contamination is restricted in area because of a separate tailings water body. The tailings waters had only very limited connection to the confined aquifer underneath. The thickness of the peat layer should be examined as well as the hydrostratigraphy of the aquifer, to prevent any future leaking risks to the groundwaters.
  • Chen, Xuemeng (2014)
    The study of air ions by applying air balance concept based on the Hyytiälä SMEAR II station measurement was performed in this work. Diurnal and seasonal variations in ion concentration and environmental ionizing radiation were studied by analysing data collected from long-term measurements. Total gamma radiation was the main source for ion production in the atmosphere, which can be attenuated by snow cover during winter periods.  and  emissions from radon decay process showed a share of about 20% in the production of total ion pairs, which were sensitive to variations in soil conditions. In general, more positive ions than the negative ones exist at ground level due to the earth electrode effect. Similar patterns were found in cluster ion concentration and the ion source rate derived from the total gamma radiation. On days with new particle formation (NPF), a relation was observed between cluster ion concentration, wind speed, temperature (T) as well as relative humidity (RH). A similar connection was also identified in ion source rate and ion production rate to T and RH. A high ion source rate derived from gamma dose rate was observed on non-event days and low on NPF days. The reversed case was found in the source rate derived from radon decay emissions. The ion production rate was typically higher on NPF event days than on non-event days. Two approaches were carried out in the determination of the ion production rate in the cluster size range by using an improved balance equation of air ions. The similar values obtained using these two approaches imply a balanced condition between ionizing source and the observed ion concentration. This suggests that measurement of air ions by the Balanced Scanning Mobility Analyser (BSMA) is likely to be reliable, though accurate parameterization for sub-0.8 nm ions is not available to the present knowledge. Moreover, the ion production rate and formation rate were found incomparable.
  • Heikkinen, Ari (2012)
    Turbulenssi on eräs merkittävistä ilmailun turvallisuuteen ja sujuvuuteen vaikuttavista sääilmiöistä. Viime vuosikymmeninä on keskitytty eniten lähinnä kaupalliseen ilmailuun vaikuttavan, keski- ja ylätroposfäärissä esiintyvän kirkkaan ilman turbulenssin ennustusmenetelmien kehittämiseen. Alatroposfäärin turbulenssin ennustamisesta lentoliikenteelle on julkaistu sen sijaan vain yksittäisiä tutkimustuloksia, vaikka turbulenssi onkin ollut aina tärkeässä osassa rajakerroksen perustutkimuksessa. Alatroposfäärissä esiintyvä voimakas turbulenssi voi olla kohtalokasta matalalla lentäville ilma-aluksille, ja se on myötävaikuttanut useisiin ilmailuonnettomuuksiin Suomessa. Tutkielman tavoitteena oli selvittää alustavasti erilaisten numeeristen ennustesuureiden käyttökelpoisuutta alatroposfäärin turbulenssin ennustamisessa. Ennustesuureita verifioitiin Hirlam-mallin arkistoitujen ennustekenttien ja 48:n alle 6000 jalan (n. 2 km) korkeuteen sijoittuvan lentäjien raportoiman turbulenssihavainnon avulla. Tutkittavina suureina oli tuulennopeuksia eri korkeuksilta, tuuliväänne, turbulenssin kineettinen energia (TKE) sekä erilaisia tuulennopeuden, tuuliväänteen, hydrostaattisen stabiiliuden ja TKE:n yhdistäviä suureita. Tuulennopeudet lukuun ottamatta 10 m tuulennopeutta lukeutuivat verifioinnissa parhaiten menestyneisiin suureisiin. Myös TKE:n ja tuuliväänteen yhdistävät suureet saavuttivat lupaavia tuloksia. Suurin osa havaituista turbulenssitapauksista liittyikin tuulisiin ja melko stabiilisti kerrostuneisiin tilanteisiin, ja vain kahdessa tapauksessa turbulenssi näytti olleen vapaan konvektion hallitsemaa. Verifioinnin tuloksia on pidettävä suuntaa antavina, sillä havaintojen vähäisestä määrästä voi aiheutua huomattavasti satunnaisvirhettä, ja tulokset voivat riippua huomattavastikin käytetystä verifiointimenetelmästä. Jatkossa vastaavankaltaisia verifiointeja olisi hyvä suorittaa suuremmalla havaintomäärällä. Tämän lisäksi tulisi kartoittaa turbulenssitapauksiin liittyviä synoptisia tilanteita ja tehdä tarkempia tapaustutkimuksia rajakerroksen rakenteen yksityiskohtaisemmaksi selvittämiseksi.
  • Lahdenperä, Antti (2013)
    Tutkielmassa perehdytään aldehydien asymmetrisiin hetero-Diels-Alder-reaktioihin. Hetero-Diels-Alder-reaktio on paljon käytetty menetelmä erilaisten heteroatomin sisältävien kuusirenkaiden valmistamiseen. Nämä reaktiot, joissa joko dienofiili tai dieeni sisältää heteroatomin, mahdollistavat helposti tällaisten kuusirenkaiden valmistamisen enantioselektiivisesti yhdellä reaktiolla. Hetero-Diels-Alder-reaktiot voidaan jakaa joko normaalielektronijakauman tai käänteiselektronijakauman reaktioihin, joista tutkielmassa tutustutaan tarkemmin normaalielektronijakauman reaktioihin. Näissä reaktioissa dieeni luokitellaan elektronirikkaaksi ja dienofiili elektroniköyhäksi. Reaktioiden enantioselektiivisyys saadaan usein aikaan kiraalisella Lewis-hapolla, joka ohjaa dieenin ja dienofiilin lähestymistä reaktion transitiotilassa. Tutkielman kirjallisuuskatsauksessa tutustutaan erilaisiin kiraalisiin Lewis-happoihin, joita reaktioissa on käytetty, sekä erilaisiin dieeneihin ja dienofiileihin. Tutkielman kirjallinen osuus on jaettu aktivoimattomien aldehydien ja aktivoitujen aldehydien reaktioihin. Aktivoiduilla aldehydeillä tarkoitetaan aldehydejä, jonka viereiset substituentit aktivoivat, eli vetävät karbonyylihiileltä elektronitiheyttä puoleensa. Aktivoimattomien aldehydien substituentit taas eivät vähennä karbonyylihiilen elektronitiheyttä. Kirjallisuuskatsauksessa käydään myös läpi pyridinyylialdehydeillä tehdyt hetero-Diels-Alder-reaktiot sekä muutamia luonnonaineiden kokonaissynteesejä, joissa on käytetty hetero-Diels-Alder-reaktiota. Tutkielman kokeellisesssa osuudessa kehitettiin menetelmä, jolla 2-trimetyylisiloksi-1,3-butadieenin ja 3-pyridinyylikarboksialdehydin välisen hetero-Diels-Alder-reaktion tetrahydropyranonituotteelle saatiin lopulta optimointien jälkeen 91 % eristetty saanto. Tetrahydropyranonirakenne on yleinen monissa luonnon- ja lääkeaineessa. Reaktion lopullinen saanto on tietääksemme paras saanto 2-trimetyylisiloksi-1,3-butadieenin hetero-Diels-Alder-reaktiolle ja toiseksi korkein saanto substituoimattomalle 2-alkyylisiloksi-1,3-butadieenille. Tutkielmassa kehitetty menetelmä on myös ensimmäinen aktivoimattoman aldehydin ja 2-alkyylisiloksi-1,3-butadieenin väliselle hetero-Diels-Alder-reaktiolle. Lewis-hapoista dimetyylialumiinikloridi (AlMe2Cl) katalysoi reaktiota parhaiten. Myös muut reaktio-olosuhteet, kuten lämpötila, liuotin ja reagenssien määrät, optimoitiin. Paras saanto (91 %) saatiin reaktiolle, jossa sekä dienofiiliä että dieeniä käytettiin yksi ekvivalentti.
  • Kontkanen, Jenni (2012)
    Uusien hiukkasten muodostuminen on merkittävä prosessi, jossa neutraalit klusterit ovat todennäköisesti tärkeässä roolissa. Tässä työssä tarkastellaan alle 2 nm:n kokoisten neutraalien klusterien pitoisuuksia ja niihin vaikuttaneita tekijöitä vuoden 2011 maalis-toukokuussa Hyytiälässä. Asemalla mitattiin tuolloin kaikkien klusterien kokojakaumaa hiukkaskoonsuurentajalla (PSM), varattujen klusterien kokojakaumaa ilman neutraalien klusterien ja ionien spektrometrillä (NAIS) sekä useita meteorologisia suureita ja kaasujen pitoisuuksia. Mittauksista määritettiin neutraalien, varattujen ja ioni-ioni-rekombinaatiossa muodostuneiden klusterien pitoisuudet kuudessa kokoluokassa (0,9–1,1 nm, 1,1–1,3 nm, 1,3–1,5 nm, 1,5–1,7 nm, 1,7–1,9 nm ja 1,9–2,1 nm). Klusterien kokonaispitoisuuden mediaani välillä 0,9–2,1 nm oli noin 4850 cm^-3. Eri kokoluokkia tarkastellessa pitoisuuden havaittiin laskeneen klusterikoon kasvaessa. Neutraalit klusterit dominoivat kaikkia kokoluokkia etenkin hiukkasmuodostuksen aikaan. Tämä viittaa neutraalien nukleaatiomekanismien olevan Hyytiälässä ionivälitteisiä mekanismeja tärkeämpiä. Neutraalien klusterien pitoisuus vaihteli voimakkaammin kuin ionien ja rekombinaatiotuotteiden pitoisuudet; maksimissaan se oli hiukkasmuodostus- eli eventtipäivien keskipäivällä. Pienimmässä kokoluokassa klusteripitoisuus oli ei-eventtipäivinä samansuuruinen kuin eventtipäivinä, mutta suurimmissa kokoluokissa pitoisuudet olivat ei-eventtipäivinä matalampia. Niinpä on todennäköistä, että suurimpien kokoluokkien klusterit osallistuvat hiukkasmuodostukseen, mutta pienimmän kokoluokan klusterit eivät osallistu. Hiukkasmuodostuksen aikaan UV-säteily ja lämpötila korreloivat pienimpien ja suurimpien kokoluokkien neutraalien klusterien kanssa positiivisesti ja suhteellinen kosteus ja potentiaalilämpötilan gradientti negatiivisesti. Vesihöyrypitoisuus korreloi klusteripitoisuuden kanssa positiivisesti pienimmässä kokoluokassa ja negatiivisesti suurimmissa kokoluokissa. Pienimpien kokoluokkien klusterit korreloivat positiivisesti kondensaationielun kanssa. Eri kaasuista klusteripitoisuuden kanssa voimakkaimmin korreloi rikkihappo; korrelaatio oli voimakasta etenkin hiukkasmuodostuksen aikaan suurimmissa kokoluokissa (korrelaatiokerroin oli noin 0,6–0,7). Ammoniakki- ja otsonipitoisuuden kanssa korrelaatio oli heikompaa. Metanoli- ja monoterpeenipitoisuudet korreloivat klusteripitoisuuden kanssa positiivisesti pienimmissä kokoluokissa ja kaasupitoisuuksien kertominen UV-säteilyllä vahvisti korrelaatioita.
  • Lavonen, Tiina-Leena (2012)
    In this Master’s thesis, sources of 241Am in the environment, its speciation in the environment and bioavailability are discussed. Techniques that can be used to provide 241Am speciation information in solid samples, such as TRLFS, XAFS, and fractioning techniques, such as sequential extraction or filtration are presented and discussed. In the experimental part of this study, activity concentrations and vertical distribution of 241Am were determined in sediment and soil samples collected from drainage basin area in Mercantour national park, France. Coprecipitation, ion exchange and extraction chromatography were combined to separate and purify the 241Am. Alpha sources were prepared by electrodeposition and sources were measured with alpha spectrometer. Average chemical recovery of 241Am for sediment and soil samples was 52 ± 4 %. 241Am, 239,240Pu and 238Pu activity concentrations did not correspond linearly with the organic matter content of sediment or soil. Detected inventories of 241Am, 239,240Pu, 238Pu and 241Am/239,240Pu suggested that runoff water has important contribution to the distribution and transport of americium and plutonium. 241Am/239,240Pu ratio detected in sediment and soil samples, suggest that americium has higher solubility than plutonium. Americium had migrated deeper in the soil profiles due to the runoff water filtration. Detected 241Am/239,240Pu and 238Pu/239,240Pu ratios indicated that the source of this sampling site was the global fallout from nuclear weapons tests.
  • Korpinen, Markus (2014)
    Intermolecular long-range interactions play an important role in several areas of modern research. In this thesis, van der Waals coefficients for different small coinage metal systems such as H2-H2, H2-Cu2, H2-Ag2, and H2-Au2 are determined from the results of accurate ab initio calculations. A four dimensional potential energy surface is computed with the coupled cluster method with a single, double and perturbative triple excitations (CCSD(T)) using a large augmented Dunning basis set. In the case of externally neutral molecules, the dominating long-range interactions are often van der Waals dispersion interactions. Many long-range pair potential models are using a pre-defined experimental or computational van der Waals C6 coefficients. To obtain the coefficients, the potential energy surface is modelled with spherical harmonic approximation together with bipolar spherical harmonics. It was noticed that the anisotropies of the potential energy surface can be described with terms which have similar angular dependencies as the electrostatic multipole-multipole interactions and the van der Waals interactions. These include, for example, quadrupole-quadrupole and quadrupole-hexadecapole interaction. Using the computed potential energy surfaces and least-squares fitting different long-range interaction models, C6 and C8 dispersion coefficients, and quadrupole and hexadecapole moments are obtained for hydrogen, copper, silver and gold dimers.
  • Lizcano, Raymundo (2013)
    In the literature part an introduction to emerging organic contaminants is presented as well as the subcategory of endocrine disrupting chemicals, which includes steroid hormones. An overview of liquid chromatography trends in environmental analysis as well as mass spectrometry operational conditions are discussed. Review is focused on ionization techniques and tandem mass spectrometry functionalities reported on state of the art studies of steroidal compounds in environmental samples. Experimental part presents an extensive sample preparation method and a liquid chromatography – mass spectrometry (HPLC-MS) method that were developed for the determination of concentration of eleven steroidal compounds: 4-androstene-3,17-dione (A1), trans-androsterone (A2), Corticosterone (C1), Cortisone (C2), Estrone (E1), 17-β-estradiol (E2), Estriol (E3), 17-α-ethynil estradiol (EE2), Progesterone (P), 17-hydroxy progesterone (HP) and Testosterone (T). Separation efficiency and analysis time were compared for three HPLC columns with different stationary phase: Pentafluorophenyl (PFP), C8 and C18 monolithic. Three atmospheric pressure ionization (API) techniques were tested to compare their performance: Electrospray ionization (ESI), Atmospheric Pressure Chemical Ionization (APCI) and Atmospheric Pressure Photoionization (APPI). The proposed method included the best column choice coupled with the API technique, which presented an efficient ionization for most of the target analytes. Best methodology was applied to the analysis of effluent and influent samples from the wastewater treatment plant in Viikinmäki, Helsinki.
  • Uski, Jaana (2013)
    Tässä työssä esitellään Apollonioksen ongelma. Alkuperäinen Apollonioksen ongelma oli löytää euklidisessa tasossa ympyrä, joka sivuaa kolmea annettua ympyrää. Yleensä kuitenkin sallitaan ympyröiden degeneroituminen pisteeksi tai suoraksi (ympyrä, jonka säde on nolla tai "ääretön"). Tämän takia ongelma usein laajennetaan ongelmaksi löytää ympyrä, joka sivuaa kolmea kuviota, joista kukin voi olla piste, suora tai ympyrä. Ongelmassa on näin yhteensä kymmenen eri tapausta. Apollonios Pergalainen (n. 240-190 eaa) julkaisi ja ratkaisi ongelman teoksessaan Sivuamisista lukuunottamatta vaikeinta kolmen ympyrän tapausta. Ratkaisut eivät ole säilyneet, mutta ne on voitu rekonstruoida Pappos Aleksandrialaisen kuvausten perusteella. 1500-1600-luvulla monet matemaatikot yrittivät ratkaista Apollonioksen ongelman vaikeinta tapausta euklidisen geometrian hengessä harpilla ja viivottimella. Tässä työssä perehdytään yleisimpiin menetelmiin, joilla Apollonioksen ongelma saadaan ratkaistua. Erityisesti työssä perehdytään vaikeimpaan, kolmen ympyrän, tapaukseen. Tälle esitetään algebrallinen ratkaisumenetelmä sekä inversioon eli ympyräpeilaukseen ja hyperbeleihin perustuvat ratkaisumenetelmät. Lisäksi esitellään vielä Joseph Diaz Gergonnen keksimä konstruktio.
  • Wang, Ziran (2013)
    This thesis considers the problem of finding a process that, given a collection of news, can detect significant dates and breaking news related to different themes. The themes are unsupervisedly learned from some training corpora, and they mostly have intuitive meanings, like "finance", "disaster", "wars" and so on. They are constructed only based on textual information provided in the corpora without any human intervention. To conduct this learning, the thesis use various types of component models, specifically Latent Dirichlet Allocation(LDA) and Correlated Topic Model(CTM). On top of that, to enrich the experiment, the Latent Semantic Indexing(LSA) and Multinomial Principal Component Analysis(MPCA) are also adopted for comparison. The learning produces every news coverage a relevance weight for given theme, which can be viewed as a theme distribution from statistical perspective. With the help of news time-stamp information, one can sum up and normalize these distributions from all news in day unit, and then draw the moving of accumulated relevance weights on a theme through time-line. It is natural to treat these curves as describing attention strength paid from media to different themes, and one can assume that behind every peak, there are striking events and associated news can be detected. This thesis is valuable in Media Studies research, and also can be further connected to stock or currency market for creating real value.
  • Islam, Mohammad Shafiqul (2013)
    RNA-sequencing is a high throughput sequencing technology that sequences cDNA to obtain information from a particular sample of RNA. RNA-seq has already been proven to be an important factor to research numerous incurable diseases like cancers. Like other high throughput technologies, it also produces a huge number of accurate but relatively short reads. So it remains a concerning issue for De Novo assembly tools to assemble this massive amount of short reads. Existing De Novo assembly tools to assemble RNA-seq data are developed mainly based on three different algorithms; Greedy, OLC, and Euler-path. Recent research has revealed that Euler-path approach works best for RNA-seq data. A few De Novo assembly tools are available nowadays that were developed using Euler-path approach. Most of these tools based on Euler-path can be used free of cost for non commercial purposes. However, the performance of these non-commercial usable tools varies under different criteria. Again, their performance has not been measured in all possible conditions. So, it is always a matter of concern, which tool should be used for a particular data. Main objective of this thesis work is to consider four Euler-path De Novo assembly tools available for non commercial use and find out their performance for EST data of eukaryote. Criteria of their performance would be assembly accuracy and integrity. ACM computing Classification system Applied computing Life and medical science-> Computational Biology-> Molecular Sequence Analysis
  • Basic, Marta (2015)
    Plant viruses are a prominent subject of scientific research due to their ability to annually decimate agricultural crop yields. Amongst all of the groups of plant viruses, the potyvirus group is one of the largest and therefore contributes to a large portion of all plant virus-induced economic and agricultural deficiencies. The potyvirus field has become a relevant area of research, ultimately aiming to provide a more comprehensive understanding of the infection process in the hopes of yielding virus-resistant crops, subsequently increasing food production and reducing the plant virus-related economic burden. Potato Virus A (PVA) is a positive-sense, single-stranded RNA virus of the genus Potyvirus. It has a single open reading frame that is translated into a polyprotein and latterly cleaved into 10 mature proteins: P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb, and CP. Helper component-proteinase (HC-Pro) is a multifunctional viral protein and the main subject of this study. It is involved in many stages of the virus life cycle; however, its role as a suppressor of RNA silencing, an anti-viral defense mechanism employed by the host organism, makes it a particularly interesting candidate for protein interaction studies. Because viruses are heavily dependent on the host's cellular machinery for survival, understanding the interactions between viral and host proteins is crucial for elucidating the molecular mechanisms underlying infection. The goal of this thesis was to identify potentially novel interacting partners of potyviral HC-Pro. This study utilized a Twin-Strep-tag affinity purification method for isolating HC-Pro associated binding partners from the total cell lysate of PVA-infected plant leaves. The purified macromolecular complexes were then analyzed using mass spectrometry and numerous individual proteins were identified. Gene Ontology (GO) functional annotations were generated for the obtained proteome using several R scripts and their distributions visualized as graphs. This study identified a total of 190 proteins purified from specific HC-Pro-associated complexes. Two identified host proteins were of particular interest due to their potential involvement in the RNA interference pathway and are currently being studied in more detail. Overall, this study successfully yielded numerous potentially novel protein interactions and presents an effective approach to pinpointing host binding partners of particular interest for future studies.
  • Nikunlassi, Arvi (2013)
    Internetin ja tietotekniikan yleistymisen vuoksi ohjelmistokehitys painottuu yhä enemmän yhteistyöhön ja interaktioon. Suunnitelmakeskeisyydestä ollaan siirrytty kohti ketterämpiä menetelmiä, joissa muutoksen ja kommunikaation tärkeys on tiedostettu. Asiakas ja asiakassuhde on erittäin merkittävä komponentti ohjelmistoprojektin onnistumisessa. Nykyaikaisissa ketterissä ohjelmistokehitystiimeissä asiakkaan edustaja on tiiviisti yhteydessä kehittäjiin palaverien tai muun läsnäolon kautta. Asiakkaan tiivis yhteys kehitykseen on keino tehostaa kehitystä ja saada tyydyttävämpiä tuotteita. Vähemmälle huomiolle on kuitenkin jäänyt toteutetun asiakassuhteen vaikutus kaikille projektin osapuolille. Tässä tutkielmassa tarkastellaan ohjelmistokehitystä asiakkaan ja asiakassuhteen näkökulmasta. Aluksi analysoidaan ohjelmistokehityksen peruspiirteitä ja esitellään yleisimpiä ketteriä menetelmiä. Tämän jälkeen esitellään erilaisia tutkimuksia asiakassuhteesta ja analysoidaan niiden tuloksia. Lopuksi luodaan yhteenveto havaituista ongelmista ja esitetään niihin ratkaisuehdotuksia.
  • Huttunen, Jyri-Petteri (2013)
    Opinnäytetyön tavoitteena oli tutkia modularisoidun, reaaliaikaisesti koulutettavan neuroverkkojärjestelmän toimintaa samankaltaisen, ei-modulaariseen neuroverkkojärjestelmään verrattuna. Tutkimuksen alustaksi luotiin yksinkertainen pelimaailma ja erilaisia koulutusskenaarioita, sekä toteutettiin Texasin yliopistossa kehitetyn rtNEAT-menetelmän päälle rakentuva modulaarinen kontrolliverkkojärjestelmä. Konstruoidun järjestelmän toimintaa verrattiin perus-rtNEAT -järjestelmän toimintaan, erityisesti kiinnitettiin huomiota aiemmin opitun käyttäytymisen muistamiseen. Tutkimuksen tulos osoitti, että opinnäytetyötä varten konstruoitujen järjestelmien välillä ei ollut merkittävää eroa toimintakyvyssä. Tämä johtuu todennäköisesti testiympäristönä käytetyn pelimaailman yksinkertaisuudesta. Mikäli järjestelmissä on merkittäviä eroja esimerkiksi muistiinpalauttamisen suhteen, näiden esille saamiseksi vaadittaisiin lisätutkimusta.
  • Åhlgren, Elina Harriet (2012)
    Graphene is the ultimately thin membrane composed of carbon atoms, for which future possibilities vary from desalinating sea water to fast electronics. When studying the properties of this material, molecular dynamics has proven to be a reliable way to simulate the effects of ion irradiation of graphene. As ion beam irradiation can be used to introduce defects into a membrane, it can also be used to add substitutional impurities and adatoms into the structure. In the first study introduced in this thesis, I presented results of doping graphene with boron and nitrogen. The most important message of this study was that doping of graphene with ion beam is possible and can be applied not only to bulk targets but also to a only one atomic layer thick sheet of carbon atoms. Another important result was that different defect types have characteristic energy ranges that differ from each other. Because of this, it is possible to control the defect types created during the irradiation by varying the ion energy. The optimum energy for creating a substitution for N ion is at about 50 eV (55%) and for B ion it is ca. 40% at about the same energy. Single vacancies are most probably created at an energy of about 125 eV for N (55%) and for B at ca. 180 eV (35%). For double vacancies, the maximum probabilities are roughly at 110 eV for N (16%) and at 70 eV for B (6%). The probabilities for adatoms are the highest at very small energies. A one atom thick graphene membrane is reportedly impermeable to standard gases. Hence, graphene's selectivity for gas molecules trying to pass through the membrane is determined only by the size of the defects and vacancies in the membrane. Gas separation using graphene membranes requires knowledge of the properties of defected graphene structures. In this thesis, I presented results of the accumulation of damage on graphene by ion irradiation using MD simulations. According to our results, graphene can withstand up to 35% vacancy concentrations without breakage of the material. Also, a simple model was introduced to predict the influence of the irradiation during the experiments. In addition to the specific results regarding ion irradiation manipulation of graphene, this work shows that MD is a valuable tool for material research, providing information on atomic scale rarely accessible for experimental research, e.g., during irradiation. Using realistic interatomic potentials MD provides a computational microscope helping to understand how materials behave at the atomic level.
  • Stenudd, Juho (2013)
    This Master’s Thesis describes one example on how to automatically generate tests for real-time protocol software. Automatic test generation is performed using model-based testing (MBT). In model-based testing, test cases are generated from the behaviour model of the system under test (SUT). This model expresses the requirements of the SUT. Many parameters can be varied and test sequences randomised. In this context, real-time protocol software means a system component of Nokia Siemens Networks (NSN) Long Term Evolution (LTE) base station. This component, named MAC DATA, is the system under test (SUT) in this study. 3GPP has standardised the protocol stack for the LTE eNodeB base station. MAC DATA implements most of the functionality of the Medium Access Control (MAC) and Radio Link Control (RLC) protocols, which are two protocols of the LTE eNodeB. Because complex telecommunication software is discussed here, it is challenging to implement MBT for the MAC DATA system component testing. First, the expected behaviour of a system component has to be modelled. Because it is not smart to model everything, the most relevant system component parts that need to be tested have to be discovered. Also, the most important parameters have to be defined from the huge parameter space. These parameters have to be varied and randomised. With MBT, a vast number of different kind of users can be created, which is not reasonable in manual test design. Generating a very long test case takes only a short computing time. In addition to functional testing, MBT is used in performance and worst-case testing by executing a long test case based on traffic models. MBT has been noticed to be suitable for challenging performance and worst-case testing. This study uses three traffic models: smartphone-dominant, laptop-dominant and mixed. MBT is integrated into continuous integration (CI) system, which automatically runs MBT test case generations and executions overnight. The main advantage of the MBT implementation is the possibility to create different kinds of users and simulate real-life system behaviour. This way, hidden defects can be found from test environment and SUT.
  • Puonti, Oula (2012)
    Magnetic resonance imaging (MRI) provides spatially accurate, three dimensional structural images of the human brain in a non-invasive way. This allows us to study the structure and function of the brain by analysing the shapes and sizes of different brain structures in an MRI image. Morphometric changes in different brain structures are associated with many neurological and psychiatric disorders, for example Alzheimer's disease. Tracking these changes automatically using automated segmentation methods would aid in diagnosing a particular brain disease and follow its progression. In this thesis we present a method for automatic segmentation of MRI brain scans using parametric generative models and Bayesian inference. Our method segments a given MRI scan to 41 different structures including for example hippocampus, thalamus and ventricles. In contrast to the current state-of-the-art methods in whole-brain segmentation, our method does not pose any constraints on the MRI scanning protocol used to acquire the images. Our model is based on two parts: the first part is a labeling model that models the anatomy of the brain and the second part is an imaging model that relates the label images to intensity images. Using these models and Bayesian inference we can find the most probable segmentation of a given MRI scan. We show how to train the labeling model using manual segmentations performed by experts and how to find optimal imaging model parameters using expectation-maximization (EM) optimizer. We compare our automated segmentations against expert segmentations by means of Dice scores and point out places for improvement. We then extend the labeling and imaging models and show, using a database consisting of MRI scans of 30 subjects, that the new models improve the segmentations compared to the original models. Finally we compare our method against the current state-of-the-art segmentation methods. The results show that the new models are an improvement over the old ones, and compare fairly well against other automated segmentation methods. This is encouraging, because there is still room for improvement in our models. The labeling model was trained using only nine expert segmentations, which is quite a small amount, and the automated segmentations should improve as the number of training samples grows. The upside of our method is that it is fast and generalizes straightforwardly to MRI images with varying contrast properties.
  • Xu, Tingting (2014)
    The high mortality rate among humans infected with certain types of Avian Influenza (AI) and the potential of a mutation that allows human-to-human transmission is a great concern for the public health. We formulate a mathematical model for the prevalence of AI in humans resulting from avian-to-human transmission. The model is important because the higher the prevalence, the higher the risk of a mutation that allows human-to-human transmission leading in a major epidemic. We formulate and analyse separate deterministic and stochastic versions of the model. Different time scale separation techniques are applied to the models. The influence of certain controllable parameters on the system equilibrium is interpreted from numerical results. Moreover, we also investigate the fluctuation of populations due to demographic stochasticity at the early stage of the prevalence of AI.