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The volume of data generated by high-throughput DNA sequencing has grown to a magnitude that leads to substantial computational challenges in storing and searching the data. To tackle this problem, various computational methodologies have been developed in recent years to space-efficiently index collections of data sets and enable efficient searches. One of the most recent indexing methods, Spectral Burrows-Wheeler Transform (SBWT), presents all distinct k-mers of a DNA sequence using only 4 bits and a small additional space for the rank data structures per k-mer. In addition to being space-efficient, it also enables k-mer membership queries in linear time relative to k, and constant time relative to the number of distinct k-mers in the sequence. The queries rely on rank queries over bit vectors. Experiments run on a single CPU thread have shown that in one second, hundreds of thousands of k-mer membership queries can be performed over SBWT. By parallelizing the queries on a CPU, it is possible to execute millions of queries per second. However, Graphic Processing Units (GPUs) have much more parallelization potential. The main contribution of the thesis is an implementation of the k-mer membership queries over SBWT with GPU computing. Optimizing the queries to be performed on a GPU made it possible to perform over a billion queries per second. Furthermore, the thesis presents a new enhancement for the queries over SBWT called presearching, which doubles the speed of the original SBWT search query. The rank query needed for the membership queries is implemented using space-efficient poppy rank data structures, and its derivative cumulative-poppy data structure which is one of the contributions of the thesis.

Tässä tutkielmassa on käsitelty hiilidioksidin muuntamista orgaanisiksi karbonaateiksi. Orgaanisia karbonaatteja ovat sykliset karbonaatit ja polykarbonaatit, joita saadaan hiilidioksidin reagoidessa epoksidin kanssa, sekä lineaariset karbonaatit, jotka syntyvät reaktioissa esimerkiksi metanolin kanssa. Kirjallisuuteen perustuvassa osassa on esitelty eri metallikompleksien katalysoimien karbonaatti-synteesien mekanismeja. Oleellista katalyyttisysteemin aktiivisuuden kannalta on, että se koostuu Lewisin happo-emäsparista. Kompleksin keskusmetalli toimii happona aktivoiden epoksidin tai metanolin. Lewisin emäksenä toimii useimmiten kokatalyyttinen yhdiste, joka joko avaa epoksidirenkaan tai aktivoi hiilidioksidin ennen sen insertoitumista metalli-happi-sidokseen. Kokeellisessa osassa valmistettiin syklistä propyleenikarbonaattia titaanikompleksien avulla. Karbonaattisynteesin reaktio-olosuhteet optimoitiin ja lisäksi tutkittiin reaktion kinetiikkaa, jotta kyettiin selvittämään synteesin mekanismi.

The legislation of the Paris Agreement obliges Finland to pursue actions that keep the global average temperature rise below 2°C and aim to limit the average temperature rise to 1.5°C. The current Finnish government has aligned the national goal of carbon neutrality by 2035. The role of municipalities in promoting or compensating carbon sinks has not yet been defined, although municipalities play an important role as a platform for climate work at local and regional levels. However, it is already known that the Finnish National Climate Act, which is being reformed at this moment, will be subject to an obligation to produce their own climate programs at municipal, regional or provincial level. Environmental competence and environmental development have been important in Lahti for several decades already. The City of Lahti has set its target for carbon neutrality for 2025 and it includes targets for reducing, compensating, and increasing carbon sinks. This work focused on the examination of carbon sequestration and sinks in an urban environment in Lahti, in the example area of approximately 82 hectares, through which a wider understanding of the city's potential to grow coal stocks and sinks in a tight urban structure within different land use classes and different ground cover between them. Based on the Finnish Environment Agency's CORINE land cover classification, the current potential of carbon sequestration for urban land use classes were calculated in this work and the actions to increase carbon sequestration capacity were identified. The work examined the availability of the finished spatial data and to supplement incomplete information, existing literature on the topic was used, as well as other existing spatial records of the city of Lahti and previously made surveys. The largest carbon sink was observed in forest areas, of which in mixed forests representing the largest forest type in the area. Through the calculations and literature carbon sinks and stocks in residential areas were also found to be significant in terms of vegetation, as well as in terms of soil based on the literature review. In planting street and park trees for the purpose of increasing the carbon sink, the most important thing was found to be the long lifetime of trees and securing it. Growing of carbon sinks is most effective in areas where carbon sequestration is already at a high level but increasing vegetation cover in all urban land covers will increase the carbon sink in the long run. One major conclusion of the work was that Lahti's current method of determining carbon sinks and stocks has been inadequate at least for the determining them in built areas, and future measures to maintain, preserve and increase carbon stocks and sinks would not be seen by the same calculation method in the computing. In general, the research data and methods are still largely based on observations and results from the operational processes of natural ecosystems, and these are utilized in urban planning, construction, and maintenance of urban green areas. An incomplete knowledge of the ecological processes in urban areas is a problem that produced challenges in this work as well. More research data is needed on carbon sinks in urban land use classes to gain a more secure understanding of carbon sinks and stocks, although the common importance of vegetation in urban areas is already clear. Although the work focused on carbon in an urban environment, it is necessary to remember the diversity of the urban environment and the other ecosystem services it produces. Land use planning, as well as the management of green spaces in the urban environment, can enhance both the size of carbon storages and sinks and biodiversity and they do not have to be entirely separate from each other.

Tutkielmassa esitetään kolme erilaista keinoa todistaa Hilbertin Nullstellensatzin heikko muoto ja tarkastellaan lähestysmistapojen eroavaisuuksia. Tämän jälkeen Nullstellensatzin vahva muoto johdetaan heikosta muodosta käyttäen radikaaleja ja Rabinowitschin keinoa. Lopuksi esitellään joitakin algebrallisen geometrian peruskäsitteitä, joihin Nullstellensatz kytkeytyy ja käydään läpi esimerkkejä tuloksen soveltamisesta.

Tässä tutkielmassa muotoillaan Hiltonin ja Milnorin lause, joka sanoo, että yhtenäisten CW-kompleksien yhden pisteen yhdisteen redusoidun suspension silmukka-avaruudella on sama homotopiatyyppi kuin näiden CW-kompleksien eräiden iteroitujen nitistysten (smash product) redusoitujen suspensioden silmukka-avaruuksien äärettömällä heikolla tulolla. Työssä käydään läpi lauseen muotoilussa ja todistuksessa tarvittavia käsitteitä ja aputuloksia. Keskeisimpiä näistä ovat Ioan Jamesin redusoidut tulot ja Wittin kaavat. Lausetta ei todisteta.

Computation offloading can be used to leverage the resources of nearby computers to ease the computational burden of mobile devices. Cloudlets are an approach, where the client's tasks are executed inside a virtual machine (VM) on a nearby computing element, while the client orchestrates the deployment of the VM and the remote execution in it. Mobile devices tend to move, and while moving between networks, their address is prone to change. Should a user bring their device close to a better performing Cloudlet host, migration of the original Cloudlet VM might also be desired, but their address is then prone to change as well. Communication with Cloudlets relies on the TCP/IP networking stack, which resolves address changes by terminating connections, and this seriously impairs the usefulness of Cloudlets in presence of mobility events. We surveyed a number of mobility management protocols, and decided to focus on Host Identity Protocol (HIP). We ported an implementation, HIP for Linux (HIPL), to the Android operating system, and assessed its performance by benchmarking throughput and delay for connection recovery during network migration scenarios. We found that as long as the HIPL hipfw-module, and especially the Local Scope Identifier (LSI) support was not used, the implementation performed adequately in terms of throughput. On the average, the connection recovery delays were tolerable, with an average recovery time of about 8 seconds when roaming between networks. We also found that with highly optimized VM synthesis methods, the recovery time of 8 seconds alone does not make live migration favourable over synthesizing a new VM. We found HIP to be an adequate protocol to support both client mobility and server migration with Cloudlets. Our survey suggests that HIP avoids some of the limitations found in competing protocols. We also found that the HIPL implementation could benefit from architectural changes, for improving the performance of the LSI support.

HIV and AIDS epidemic remains an issue burdening most severely developing countries of the Global South and especially Sub-Saharan Africa. Globally 37 million people are living with AIDS and from these more than half in SSA. In Namibia, estimated HIV prevalence is 13.8% compared to the average 7.1% in East and Southern Africa and global average 0.8%. Until recently, representative data of HIV prevalence has not been available in developing countries. Currently HIV testing is included in Demographic and Health Surveys which are conducted in more than 90 developing countries around the world with the support of the DHS Program funded by USAID. These data also often include georeference, which enables also spatial analysis of the HIV epidemic. In this study, HIV epidemic in Namibia has been studied using traditional methods utilised in population studies, which have been complemented with methods of spatial approach. Sub-regional estimates for HIV prevalence inside administrative regions have been modelled using Kernel density estimation. Factors driving the epidemic have been assessed with a logistic regression model that estimates individual’s HIV risk. In Namibia, HIV prevalence is highest in North-Central Namibia and Caprivi strip. However, according to sub-regional estimates for HIV prevalence there exist variation also inside these areas. In North-Central Namibia, high rates of HIV prevalence depended more on proximity to urban centre than population density alone. Presence of urban centres did not increase HIV prevalence everywhere in Namibia. Also inside urban areas, for example Windhoek, sub-regional estimates for HIV prevalence differed considerably. In the logistic regression model, the following results were found: Women have 1.8 times higher odds for being HIV positive. 30-39-year olds had highest odds for being HIV positive. For men only, odds ratio was highest among 40-49-year olds. Higher educational attainment and higher wealth quintile decreased individual’s HIV risk. Formerly married had higher risk for HIV. Certain language groups had higher odds for being HIV positive, these included especially Lozi and Oshiwambo. Increasing number of lifetime number of sexual partners increased individual’s HIV risk. From regional factors, strong migration inflow and average HIV prevalence in the area increased individual’s HIV risk. The DHS data is available free of charge for academic purposes. Other data and all software used in this study are open source. These data and software were utilised partly in order to demonstrate that spatial approach on the HIV epidemic is possible even without vast resources. Especially in developing countries utilisation of open source opens up possibilities that would otherwise be limited. The results of this study confirm to a large extent findings from other developing countries of the Global South where DHS data have been used in HIV studies. However, characteristics unique for the epidemic in Namibia were also found. The dynamics of the HIV epidemic are difficult to grasp and it is important that even though the situation is improving these complexities are challenged and the phenomenon further investigated.

Tutkielmassa perehdyttiin hajautetun HLA-simulointiarkkitehtuurin suorituskykyyn reaaliaikaisen simulaattorin toteutuksen kannalta. Aluksi esitellään erilaisia simulaation tyyppejä ja niihin liittyviä simulaattorijärjestelmien toteutuksia. Sen jälkeen kuvataan tarkemmin tähän tutkielmaan valitun HLA-simulointiarkkitehtuurin toimintamallia sekä sen erityispiirteitä. Työssä kerrotaan minkälaisia vaatimuksia reaaliaikaisuus ja hajautettavuus simulointijärjestelmälle aiheuttavat ja miten HLA pystyy näihin kohtiin vastaamaan. Koska HLA ei tarjoa yksiselitteisiä vastauksia moniin kohtiin, tutkielma esittelee vaihtoehtoja ja syitä valita mitäkin niistä. Joihinkin kohtiin etsitään myös kiertoteitä tai perustellaan miksi ongelma voidaan jopa jättää ratkaisematta tietynlaisissa käyttötapauksissa. Tutkielmassa esitellään myös suorituskykymittauksia, joita voi hyödyntää valitessa toteutusmalleja ja etsiessä olemassa olevan simulaattorin pullonkauloja. Case-tapauksena esitellään merenkulkusimulaattori, jossa kehitystyössä hyödynnetään tutkielmassa selvitettyjä ongelmakohtia ja hyödynnetään joitain toteuttamismalleja. ACM Computing Classification System (CCS): C.2.4 [Distributed Systems], I.6.3 [Applications], I.6.7 [Simulation Support Systems], I.6.8 [Types of Simulation]

Monsuuni-ilmastoa luonnehtivat vuodenaikojen mukaan suuntaansa vaihtavat ilmamassojen liikkeet sekä niihin liittyvät sadekaudet. Aasian monsuunisysteemi on yksi maapallon merkittävimmistä ilmastosysteemeistä ja sen vaikutusalue ulottuu Arabian meren länsiosista Itä-Aasiaan sekä Australian pohjoisosiin. Se jaetaan kahteen ala-systeemiin: Intian monsuuniin ja Itä-Aasian monsuuniin. Monsuunialueella asuu yli puolet maapallon ihmisistä ja näiden yhteiskuntien hyvinvointi on täysin riippuvainen kesämonsuuni sateiden maantieteellisestä jakautumisesta sekä voimakkuudesta. On esitetty, että käynnissä oleva ilmastonmuutos on jo vaikuttanut monsuunisysteemeihin. Tässä tutkimuksessa perehdyin holoseenin aikaisiin monsuunivaihteluihin. Omia tuloksiani vertasin muualta monsuuni alueelta peräisin oleviin monsuuni-ilmastoa käsitteleviin tuloksiin sekä myös Pohjois-Atlantin alueen ilmastorekonstruktioihin. Tutkimuskohteeni on Kumphawapi järvi, joka sijaitsee Koillis-Thaimaassa. Thaimaa on ihanteellinen kohde monsuunitutkimuksille, koska se sijaitsee molempien monsuunin ala-systeemien vaikutusalueella. Järven syvimmästä kohdasta noudettiin 3.81 metriä pitkä sedimenttisarja, josta määritin orgaanisen aineksen määrän sekä analysoin kasvimakrofossiili koostumuksen. Sedimenttisarja ajoitettiin radiohiili menetelmällä suhteellisen tiheällä näytevälillä ja ajoitusten perusteella luotiin ikä-syvyys malli. Tätä aineistoa käytin menneiden vedenpintojen vaihteluiden eli holoseenin aikaisen monsuunin voimakkuuden rekonstruoimiseen. Laskin näytteistä myös makroskooppiset hiilipartikkelit. Näiden avulla arvioin ihmistoiminnan mahdollista vaikutusta ympäristöön. Omaa aineistoani tukemaan minulla oli käytettävissäni aiempaa paleoekologista aineistoa samasta järvestä. Tutkimustulokseni paljastivat, että järven hydrologiset olosuhteet olivat holoseenin aikana vaihdelleet huomattavasti. Holoseenin alussa järvi oli suhteellisen syvä, ja tämä viittaa kosteisiin olosuhteisiin eli voimakkaaseen kesämonsuuniin. Keski holoseenin aikana veden syvyys oli matala, joka taas viittaa heikkoon kesämonsuuniin. Myöhäisholoseenin aikana veden syvyys vaihteli. Tämä viittaa monsuuni-ilmastossa tapahtuneisiin lyhyempikestoisiin vaihteluihin. Omat tulokseni vertautuvat hyvin muihin ilmasto rekonstruktioihin Aasiasta. Kumphawapi-järven aineisto myös viittaa siihen, että alueellinen monsuuni-ilmasto on ollut yhteydessä pohjoisten leveysasteiden ilmastoon. Lisäksi Aasian monsuuni-ilmasto näyttäisi kytkeytyvän trooppiseen nk. ENSO systeemiin. Kumphawapi-järven sedimentaatiossa esiintyi usean tuhannen vuoden katkos, joka ajoittuu keski holoseeniin, Siksi tulkinta siitä oliko keski holoseenin veden pinnan lasku ilmaston vai ihmisen aiheuttama, jää tässä tutkimuksessa selvittämättä. Joka tapauksessa aineistoni viittaa siihen, että myöhäisholoseenin vaihtelut veden pinnoissa oli ilmaston eikä ihmistoiminnan aiheuttamaa. Kasvimakrofossiilimenetelmä yhdistettynä hyvään kronologiaan ja litologiseen analyysiin, muulla paleoekologisella aineistolla tuettuna, osoittautui hyväksi tavaksi tutkia holoseenin aikaisia kosteusolosuhteita. Eri tutkimusten tulkintojen välillä esiintyi kuitenkin epäyhtenäisyyttä ja siksi lisätutkimukset ovat tarpeellisia; ja näissä tutkimuksissa kannattaa hyödyntää myös kasvimakrofossiili menetelmää.

To date, Turkey has one of the highest refugee populations in the world. The Syrian conflict has played a major role in this as over 2,5 million Syrians have taken refuge in Turkey. Most of Syrian refugees are residing in the largest city of Turkey, Istanbul. Turkey is a signatory member of the Convention relating to the Status of Refugees, however has an exception for permanent residency granted only for European refugees. Thus, under Turkish refugee policy, Syrians are merely granted temporary protection that guarantees them a temporary residency permit. However, the policy does not cover; at the time of this research; the right to work. Syrian refugees, undocumented Syrians and Syrian Palestinians are especially vulnerable in Turkish society due to the lack of permanent residency and legal work. This research identifies how Syrian refugees create home as well as the factors that influence their home-making process in Istanbul. The factors are evaluated through the conditions under which Syrian refugees are residing in Istanbul including the right to work, housing and residency. The research also evaluates the refugees home-making in retrospective to their living conditions, feeling of home, legal position, access to a dwelling place as well as cultural identification. Although, this research focuses on the individual experience of home-making for Syrian refugees, it considers and examines Syrian refugees in a context of politicised bodies. As international refugees, Syrian refugees are highly politicized bodies, whose lives are affected by international politics as well as the domopolitics of the country in which they reside. Subsequently, their home and their home-making processes are also politicised. Beyond politics, refugeeness alters one's relationship to home and place, making home a complex concept attached with emotions and potential pain and loss. Literacy identifies that refugees displace their home through space and time. Hence, this research treats home as a socially and culturally produced metaphor that describes a person's belonging within socio-spatial narratives, but of which content is individually chosen to describe or to support a person's identity and psychological environment. The method of this research was a combination of two field trips to Istanbul, Turkey, fourteen in-depth interviews and qualitative analysis. The main reference of the research are the fourteen in-depth interviews that included ten men and four women; aged from 20 to 40 years old; Syrians residing in Istanbul. The interviewees were selected through social media online connections and face-to-face acquaintances during the field trips. The interviewees time of residence in Istanbul varied from two months to over four years. The eleven influencing factors identified in this research can be more commonly divided into two categories: the common factors and the personal factors. Common factors related to the responder's habitation environment; such as the city of Istanbul and the Turkish society. These common factors included: the city itself, the Turkish culture and society, the legislation, working life, housing, discrimination and relationships with their family and friends as well as with the Turkish people. The interviewees considered these factors as the ones that impacted everyday life and which they could not 'escape'. Personal factors that were identified are related to interviewees personality, world views and emotions. The interviewees could be divided into four main categories of personal factor denominators: their relationship to Syria, sense of belonging, definition of home and views of the future. This research concludes that displacement has an impact on how home is perceived and reflected by the interviewees. Its findings are in accordance to previous research literature on home-making among refugees, but it questions refugee policies that emphasis on repatriation as the most favourable long term solution for refugees as well as the position of housing as a most influential factor in refugees' home-making, by stating that other factors such as relationship to family and friends and earning a living, are higher in importance for those who have arrived into a new country less than two years ago.