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As the virtual world grows more complex, finding a standard way for storing data becomes increasingly important. Ideally, each data item would be brought into the computer system only once. References for data items need to be cryptographically verifiable, so the data can maintain its identity while being passed around. This way there will be only one copy of the users family photo album, while the user can use multiple tools to show or manipulate the album. Copies of users data could be stored on some of his family members computer, some of his computers, but also at some online services which he uses. When all actors operate over one replicated copy of the data, the system automatically avoids a single point of failure. Thus the data will not disappear with one computer breaking, or one service provider going out of business. One shared copy also makes it possible to delete a piece of data from all systems at once, on users request. In our research we tried to find a model that would make data manageable to users, and make it possible to have the same data stored at various locations. We studied three systems, Persona, Freenet, and GNUnet, that suggest different models for protecting user data. The main application areas of the systems studied include securing online social networks, providing anonymous web, and preventing censorship in file-sharing. Each of the systems studied store user data on machines belonging to third parties. The systems differ in measures they take to protect their users from data loss, forged information, censorship, and being monitored. All of the systems use cryptography to secure names used for the content, and to protect the data from outsiders. Based on the gained knowledge, we built a prototype platform called Peerscape, which stores user data in a synchronized, protected database. Data items themselves are protected with cryptography against forgery, but not encrypted as the focus has been disseminating the data directly among family and friends instead of letting third parties store the information. We turned the synchronizing database into peer-to-peer web by revealing its contents through an integrated http server. The REST-like http API supports development of applications in javascript. To evaluate the platform s suitability for application development we wrote some simple applications, including a public chat room, bittorrent site, and a flower growing game. During our early tests we came to the conclusion that using the platform for simple applications works well. As web standards develop further, writing applications for the platform should become easier. Any system this complex will have its problems, and we are not expecting our platform to replace the existing web, but are fairly impressed with the results and consider our work important from the perspective of managing user data.

The literature part of this thesis contains the review of development of portable gas chromatograph (GC) and its application in gas analysis. The scope includes portable capillary GC and chip-based GC. Gas chromatography is a separation technique based on different retention behavior of compounds in stationary phase. The use of portable GC enables chemists to carry out rapid on-site chemical analysis. Rapid, on-site analyses are valuable in fields such as air quality monitoring, emergency reaction and forensic application. Studies have shown that performance of portable GC analysis in these fields was as promising as conventional, bench-top GC analysis. The aims of portable GC development were mainly improved separation efficiency, faster analysis, greater portability, reduced power consumption, increased autonomous time and lower detection limit. Different components of portable GC are reviewed: they are separating channels/columns and stationary phases, temperature programming system, pre-concentrator, injector and detector. Semi-packed column and materials with great surface-area-to-volume ratio as stationary phase support were researched to increase surface area of retention. An improved separation efficiency was observed. Multi-channel capillary chips were fabricated to increase sample capacity of the column. Resistive heating was used in portable GC to provide high heating rate. This enables high efficiency separation in fast GC analysis. Efforts were made to reduce power consumption of the heating system to increase portable time. Using ambient air as the carrier gas eliminate the need of helium gas tank in the portable GC system. Researches were done to overcome the limitations of using ambient air. Vacuum-outlet GC technique was used to speed up the analysis. Air purification method was discussed to provide stable supply of clean air. Stability of stationary phase in ambient air was compared. A pre-concentrator is always used to lower the detection limit of gas analysis. Solid-phase microextraction (SPME) devices were commonly used. Micro-fabricated pre-concentrators were designed to enrich the analyte on-line prior to sample injection. The type of adsorbent in pre-concentrator and methods to achieve selectivity were discussed. Miniaturized detectors reported in portable GC were reviewed. Changes in the detector design were made to enhance signal quality and sensitivity in various detectors. They were made very small and light to increase portability of the GC. At last, portable GCxGC system is also mentioned. GCxGC has higher separation power than one-dimensional GC system. It allows chemist to separate analytes from complicated matrixes. Pneumatic and thermal modulation that transfer analyte bands from column to column was described. The advantages of adaptive GCxGC were also explained. The experimental part of this thesis describes a standard gas generation system of volatile organic compounds (VOCs) and its use in VOCs quantitation with internal standard, using SPME arrow as the sampler. The standard generation system was based on diffusion of analyte vapour through a deactivated capillary out of a GC vial. The vapour was carried away by nitrogen gas then diluted in various mixing ratio with nitrogen gas. The standard gas generation system can produce gas standard from any compound with high vapour pressure. The concentration of gas standard generated was validated with liquid standard. After choosing the appropriate sampling time with SPME arrow, calibration curves were constructed with conventional GC-MS and portable capillary GC-MS. Internal standard, octanal in this experiment, was generated using similar method. At various dilution factor of VOC standard, the peak area of internal standard was similar despite fluctuations. It showed the mass of internal standard extracted on the SPME arrow was relatively constant in different points on the calibration curves. Calibration curves of the VOCs with internal standard showed an improved correlation coefficient compared to calibration curves of the same VOCs without internal standard. It showed the use of internal standard in the can compensate the errors during sampling procedures. For real sample analysis, VOCs emitted from lemon sample was analyzed using the system to estimate emission rate of VOCs from lemon sample. Possible add-ons to the system were also discussed to make the system portable and reduce the uncertainty arising from variation of temperature and humidity in air during air sampling.

Single-cell RNA sequencing (scRNA-seq) allows the analysis of differences in the RNA expression between individual cells. While this is usually performed by short read sequencing, long read sequencing like Pacific Biosciences (PacBio) and Oxford Nanopore (ONT) is also applied by researchers. As long read technologies allow to capture entire RNA molecules, combined with single-cell sequencing, this enables the exploration of cell-specific isoform expression patterns. In single-cell sequencing each cell is tagged by a different oligonucleotide, called barcode, during sequencing, to enable the identification of the origin of each read. With short reads, these are straighforward to identify and correct. However, with the higher error rate of long reads, the identification of the barcodes becomes more challenging. Tools exist for the identification and correction of barcodes in short reads and for combinations of long and short reads, but only few tools work with long reads exclusively. Additionally, most tools are focused on one specific scRNA-seq protocol. While most protocols work in a similar way, the location, length or other characteristics of the barcodes might differ, meaning not all tools work for all protocols. This thesis introduces a novel barcode calling algorithm for long reads called BArcoDe callinG via Edit distance gRaph, or Badger, which can accomodate for different scRNAseq protocols. The algorithm uses a novel data structure called edit distance graph, which is based on the Hamming distance graph. Within the graph, every distinct barcode is represented by a node. Edges are added between nodes where the represented barcodes have an edit distance below a certain threshold between them. As calculating the edit distance is computationally expensive, a filter is used to find similar barcodes, and only between those the edit distance is calculated. Additionally, the algorithm is implemented and its performance evaluated, both on its own and in comparison to the existing method scTagger, where Badger outperforms scTagger in both precision and recall.

Particle Induced X-ray Emission (PIXE) is an ion beam analysis technique. In PIXE, atoms in the sample are excited when the sample is bombarded with protons, alpha particles, or heavy ions. X-rays are emitted when atoms in the sample de-excite. Each element has unique characteristic x-rays. In the spectrum, area of each peak is proportional to the elemental concentration in the sample. The existing PIXE set-up in the accelerator laboratory was upgraded to external beam PIXE to do in air measurements, because of need to analyse large amounts of archaeological samples. Different exit window set-ups were constructed and tested. The goal was to get maximum beam spot area with minimum beam energy loss in the exit window. The set-up enables the use of 100 nm thick Si3N4 exit window membranes and 4-mm-diameter beam spot area. For the measurements in the current work, a 500 nm thick Si3N4 membrane was used due to its higher durability. Current measurement can be difficult when doing PIXE in air because of ionization of air molecules in the beam's path and charge collection differences at sample surface. The set-up utilizes a beam profile monitor (BPM), which measures the current in vacuum prior to the exit window, and therefore is not affected by the current measurement difficulties in air. Along with the BPM, a current integrator was also used in the current measurements. Current integrator was used to collect the charge from the sample holder. These two methods together provided reliable way of current measurement. With the developed set-up, 166 pottery pieces from the neolithic stone age from different parts of Finland, Sweden and Estonia, were measured to determine their elemental concentrations for provenance research. AXIL software was used to analyse the spectra.

Interatomic potentials are used to describe the motion of the individual atoms in atomistic simulations. An accurate treatment of the interatomic forces in a system of atoms requires heavy quantum mechanical calculations, which are not computationally feasible in large-scale simulations. Interatomic potentials are computationally more efficient analytical functions used for calculating the potential energy of a system of atoms, allowing simulations of larger systems or longer time scales than in quantum mechanical simulations. The interatomic potential functions must be fitted to known properties of the material the potential describes. Developing a potential for a specific material typically involves fitting a number of parameters included in the functional form, against a database of important material properties, such as cohesive, structural, and elastic properties of the relevant crystal structures. In the Tersoff-Albe formalism, the fitting is performed with a coordination-based approach, where structures in a wide range of coordination numbers are used in the fitting process. Including many differently coordinated structures in the fitting database is important to get good transferability to structures not considered in the fitting process. In this thesis, we review different types of widely used interatomic potentials, and develop an iron-oxygen potential in the Tersoff-Albe formalism. We discuss the strengths and weaknesses of the developed potential, as well the challenges faced in the fitting process. The potential was showed to successfully predict the energetics of various oxygen-vacancy defect clusters in iron, and the basic properties of the common iron oxide wüstite. The potential might therefore mainly be applicable to atomistic simulations involving oxygen-based defects in solid iron, such as irradiation or diffusion simulations.

Stimuli-responsive polymers have emerged as appealing compounds for the development of high-tech and functional materials. In particular, thermoresponsive polymers have been investigated for a variety of applications. Among these, hydrogel production for additive manufacturing is especially attractive. In fact, hydrogels obtained from synthetic and thermoresponsive polymers can be tailored to obtain biocompatible scaffolds for employment in the biomedical field. Poly(2-oxazolines) and poly(2-oxazines) stand out as promising starting materials for the production of novel hydrogels. In this work, a thermoresponsive and amphiphilic triblock copolymer composed of 2-methyl-2-oxazoline and 2-phenyl-2-oxazine was investigated to determine whether a suitable candidate for biofabrication purposes could be obtained. The copolymer was firstly synthetised, before partial hydrolysis and post-polymerization modification could be carried out. These further manipulations allowed to alter the substituent in position 2 of the 2-methyl-2-oxazoline unit and yield crosslinkable units. The mechanical properties of the triblock were investigated with numerous rheological studies before 3D printing and crosslinking were performed. Crosslinked hydrogels were obtained by using a photoinitiator (Irgacure 2959) and UV radiation. Lastly, swelling behaviour was investigated to determine the capacity of the hydrogels to absorb water and test their durability over time. Overall, this study provided results on specific conditions and parameters required for the fabrication of chemically crosslinked hydrogels, that can be optimised in the future to produce functional materials for additive manufacturing applications.

Prostate cancer remains one of the most frequently diagnosed cancers in men. While its localized form is typically slowly advancing, the aggressive and metastasized forms are responsible for a significant amount of deaths in men in developed countries. Thus, more reliable methods of diagnosis are currently highly sought-after. Prostate Specific Membrane Antigen (PSMA) remains a highly-researched receptor of choice, which has been found to be overexpressed in majority of prostate cancers. Several PSMA-targeting inhibitors with suitable radioisotopes are already being utilized for PET imaging (18F, 68Ga) and treatment (177Lu) of prostate cancer, with new radiotracers possessing improved characteristics being highly sought-after. Fluoroglycosylation is a typical method of altering the properties of radiotracers, leading into more desirable tracer characteristics, such as increased renal excretion due to the compound’s increased hydrophilicity. This can be achieved with chemical reactions, such as oxime formation, where the molecule is conjugated with a fluorine-containing carbohydrate. The aim of this study was to develop two 18F-labeled PSMA inhibitors via oxime formation by utilizing two 18F-labeled carbohydrates: 5-[18F]fluoro-5-deoxyribose ([18F]9) and 2-[18F]fluoro-2-deoxy-D-glucose ([18F]12). The precursor 3 moiety was successfully synthesized by utilizing an amide coupling reaction (yield 56%), followed by acid-catalyzed deprotection. The purification of precursor 3 was achieved by high-performance liquid chromatography (HPLC) with a yield of 29%. The precursor moiety was conjugated with [18F]9 and [18F]12 via oxime formation to yield compounds [19F]4 (yield 39%) and [19F]5 (yield 39%), respectively. This was followed by the synthesis of their respective radioisotopes, [18F]4 and [18F]5. [18F]9 exhibited more favorable labeling characteristics with precursor 3 compared to those of [18F]12, likely due to its readily-available aldehydic form, and milder reaction conditions. Conjugation of [18F]9 with precursor 3 moiety was successfully achieved in 15 minutes at room temperature in the presence of 0.3 M anilinium acetate buffer, with a radiolabeling yield up to 91% (1.5 mM peptide concentration). Comparably, conjugation with [18F]12 was achieved in 30 minutes at 85 ℃ in the presence of aniline, with a radiolabeling yield of 57% (9.8 mM peptide concentration). Minor by-product formation was also evident with [18F]5 while the reaction appeared more specific with [18F]4. Purification of [18F]4 was achieved by HPLC, yielding the radiotracer with 98% radiochemical purity. Similarly, purification of [18F]5 was demonstrated with HLPC using a smaller batch, yielding the product with a radiochemical purity of 88%. Minor degradation of the oxime ether bond into free [18F]9 or [18F]12 was evident as a function of time in an acidic environment, especially with [18F]5. The lipophilicity of the compounds was also demonstrated by the shake-flask method. Both compounds were found to be highly hydrophilic, with LogD7.4 values of –2.8±0.3 and -3.1±0.2 for [18F]5 and [18F]4, respectively. Further experiments should be made to optimize the radiosynthesis protocols for higher activities, and to determine the minimum peptide concentration and reaction time needed for the oxime ether formation. Additionally, the molar activities of the compounds should be determined. Also, the IC50 inhibition potency of PSMA with [18F]4 should be evaluated prior to any in vivo trials to better evaluate its potential as a possible PSMA inhibitor.

DevOps software development methodologies have steadily gained ground over the past 15 years. Properly implemented DevOps enables the software to be integrated and deployed at a rapid pace. The implementation of DevOps practices create pressure for software testing. In the world of fast-paced integrations and deployments, software testing must perform its quality assurance function quickly and efficiently. The goal of this thesis was to identify the most relevant DevOps software testing practices and their impact on software testing. Software testing in general is a widely studied topic. This thesis looks into the recent develop- ments of software testing in DevOps. The primary sources of this study consist of 15 academic papers, which were collected with the systematic literature review source collection methodolo- gies. The study combines both systematic literature review and rapid review methodologies. The DevOps software testing practices associated with high level of automation, continuous testing and DevOps culture adoption stood out in the results. These were followed by the practices highlighting the need for flexible and versatile test tooling and test infrastructures. DevOps adoption requires the team composition and responsibilities to be carefully planned. The selected testing practices should be carefully chosen. Software testing should be primarily organized in highly automated DevOps pipelines. Manual testing should be utilized to validate the results of the automatic tests. Continuous testing, multiple testing levels and versatile test tooling should be utilized. Integration and regression testing should be run on all code changes. Application monitoring and the collection of telemetry data should be utilized to improve the tests.

Tämän työn tarkoituksena oli kehittää työkalut verkkokeskustelun auki purkamiseen. Työkalut mahdollistaisivat verkkokeskustelun nopean analysoimisen, jolloin sitä voitaisiin käyttää mm. verkko-oppimisen sosiaalisten ulottuvuuksien ymmärtämiseksi, kun dialogirakennetta verrataan teorioihin sosiaalisista rakenteista ja vuorovaikutuksista. Lisäksi työkaluja voidaan käyttää opetuksen tutkimuksen tukena ja verkkopohjaisen opetuksen kehittämisessä. Teoriataustana toimii tutkimus verkko-oppimisesta ja erityisenä aihealueena toimii tietokoneavusteinen kollaboratiivinen oppiminen. Termin alle jää laaja joukko eri opetustoimintaa, mutta tässä työssä termillä tarkoitetaan verkon välityksellä toteutettua ryhmäkeskustelua, jossa tavoitteena on oppiminen. Materiaalina toimi yhteensä 16 verkkokeskustelua, joissa neljä eri neljän hengen ryhmää keskustelivat neljästä eri kvanttifysiikkaan liittyvästä aiheesta. Tutkimusmenetelmänä käytettiin temaattista analyysiä keskustelun sisällön ja rakenteen varmistamiseksi. Tätä seurasi sosiaalinen verkostoanalyysi keskustelun rakenteen kautta. Tähän käytettiin erityisesti McDonnell at. al (2014) kehittämää tapaa käyttää triadisia, eli kolmikoista muodostuneita, rooleja verkon analysoimiseksi. Analyysejä varten keskustelut taulukoitiin s.e. jokaisesta viestistä merkittiin lähettäjän ja lähetysajan lisäksi kenelle viesti oli suunnattu ja mitä teemoja viesti piti sisällään. Tämän jälkeen kirjoitettiin Python-kieliset skriptit dialogirakenteen visualisoimiseksi ja niissä esiintyneiden roolien laskemiseksi. Tuloksiksi saatiin, että ryhmät keskustelivat tehtävänannon mukaisesti ja että verkkokeskustelun dialogirakenne voidaan esittää graafisesti niin sanottuna asynkronisena temporaalisena verkkona. Lisäksi keskusteluissa esiintyneet roolit voidaan laskea helposti ja esittää ns. lämpökartta-kuvana. Työn tavoitteet toteutuivat ja työssä kirjoitetut Python-skriptit lyhentävät merkittävästi verkkokeskustelun rakenteen analysoimista. Lisäksi tuloksia voidaan mahdollisesti käyttää ymmärtämään ryhmän sisäisiä sosiaalisia rakenteita. Tämä vaatii kuitenkin lisää työtä tässä käytetyn laskentamallin ja teorioiden yhdistämiseksi.

Significant changes in sea-ice variability have occurred in the northern North Atlantic since the last deglaciation, resulting in global scale shifts in climate. By inferring the dynamic changes of palaeo seaice to past changes in climate, it is possible to predict future changes in response to anthropogenic climate change. Diatoms allow for detailed reconstructions of palaeoceanographic and sea-ice conditions, both qualitatively, using information of species ecologies and quantitatively, via a transfer function based upon diatom species optima and tolerances of the variable to be reconstructed. Three diatom species comprising a large portion of the training set are proxies for the presence of sea ice: Fragilariopsis oceanica, Fragilariopsis reginae-jahniae and Fossula arctica, have currently been grouped into one species – F. oceanica – in the large diatom training set of the northern North Atlantic region. The clustering of the species may result in an imprecise reconstruction of sea ice that does not take into account all the available ecological information. The proportions of the three species were recounted from the original surface sediment slides alongside the additional chrysophyte cyst Archaeomonas sp. and statistically analysed using Canoco and the R software package eHOF. A core from Kangerlussuaq Trough comprising the Late Holocene (~690–1498 Common Era) was also recounted and analysed using C2. The separated diatom species and chrysophyte cyst Archaeomonas sp. exhibited different relationships to both sea-ice concentration (aSIC) and sea surface temperature (aSST). The separated F. oceanica is a ‘cold-mixed’ water species occurring at cold aSST and both low and high aSIC. High abundances occur in the marginal ice zone (MIZ) where surficial meltwater is high during the spring bloom, with additional inputs from glacial meltwaters nearshore. F. reginae-jahniae is a sea-ice associated species related to cold aSST and high aSIC. High abundances occur in the low salinity Arctic Water dominated MIZ which experiences significant aSIC. F. arctica is a sea-ice associated species related to cold aSST and high aSIC. High abundances occur in the low salinity Arctic Water dominated MIZ which experiences high aSIC, particularly in polynya conditions. F. arctica can be considered a characteristic polynya species at high abundances. Archaeomonas sp. is a ‘cold-mixed’ water species related to both cold and relatively warm aSST and low and high aSIC. High abundances occur in both relatively warm ice-free Atlantic Water and also in cold high aSIC Arctic Water conditions rendering it a more complex indicator for aSST or aSIC proxy. However, the aversion to MIZ conditions indicates that Archaeomonas sp. is associated with a relatively saline unstratified water column. This is the first time that the distribution and ecology of Archaeomonas sp. has been presented. As such, the ecology described here can be used in future studies. The separation of the three diatom species is crucial for the ecological interpretation of downcore assemblage changes. It is also crucial for the application of transfer functions in order to have greater precision in reconstructing aSIC and assessing the influence of Arctic Water or Atlantic Water, even at low abundances.