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Pattern-based Understanding and Learning System (PULS) can be considered as one key component of a large distributed news surveillance system. It is formed by the following three parts, 1. an Information Extraction (IE) system running on the back-end, which receives news articles as plain text in RSS feeds arriving continuously in real-time from several partner systems, processes and extracts information from these feeds and stores the information into the database; 2. a Web-based decision support (DS) system running on the front-end, which visualizes the information for decision-making and user evaluation; 3. both of them share the central database, which stores the structured information extracted by IE system and visualized by decision support system. In the IE system, there is an increasing need to extend the capability of extracting information from only English articles in medical and business domain to be able to handle articles in other languages like French, Russian and in other domains. In the decision support system, several new ways of Information Visualization and user evaluation interfaces are required by users for getting better decision support. In order to achieve these new features, a number of approaches including Information Extraction, machine learning, Information Visualization, evolutionary delivery model, requirements elicitation, modelling, database design approach and a variety of evaluation approaches have been investigated and adopted. Besides, various programming languages such as Lisp, Java, Python, JavaScript/Jquery, etc. have been used. More importantly, appropriate development process has been followed. This thesis reports on the whole process followed to achieve the required improvements made to PULS.

The Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated protein (Cas9) (CRISPR-Cas9) system is a widely used gene editing technology due to its potential to alter the genome precisely in desired locations. Due to the potential of the CRISPR-Cas9 system, the objective of the thesis is to improve the precise editing of genes by modifying the CRISPR-Cas9 platform. Ultimately, the aim is to develop a platform that can edit any mutation and repair it to a normal, functional gene in patient cells. In general, CRISPR-Cas9 provides opportunities in treating monogenic diseases, for example by modifying long-term hematopoietic stem cells in immunodeficiencies. CRISPR-Cas9 can target disease-causing mutation sites and introduce double-strand breaks. Afterwards, the native DNA repair machinery of a cell repairs the cut site either by more efficient, error-prone non-homologous end joining (NHEJ) or precise homology-directed recombination (HDR). In most clinically oriented genome editing studies, the desired repair outcome is the latter because it allows precise repair of the mutation according to the exogenous repair template. Despite all its positive features, the optimization of CRISPR-based editing system is crucial before medical use; CRISPR-Cas9 induces a p53-mediated DNA damage response, which leads to a transient G1 cell cycle arrest and hampers HDR-based precision genome editing. Other problems include the repair pathway depending on the cell cycle phase, repair template proximity, and off-target activity. This thesis demonstrates that Cas9 fusions allow addressing the problems mentioned above. Cas9 fusions with DNA repair proteins ensure improved editing efficiency at the close proximity to the target site in HEK293T, BJ5-ta and RPE reporter cell lines. In addition, Cas9 coupled with the engineered cell cycle timer, AcrⅡA2-cdt1, favors the editing at the S/G2 cell cycle phases avoiding the p53-mediated response. AcrⅡA2-cdt1 is a reversible, phage-derived CRISPR inhibitor that selectively inhibit CRISPR-Cas9 at the G1 cell cycle phase and releasing it at the S phase. This thesis provides extensive look on the CRISPR-Cas9 editing and its challenges in immortalized cell lines and primary cells. In the thesis, the generation of reporter cell lines is prior to the validation of the novel Cas9-fusions. Furthermore, the optimization of primary T cell and CD34+ hematopoietic stem cell electroporation with different electroporation systems brings the study closer to clinical applications. The thesis provides insights about the effect of the target site and the cell type for genome editing outcomes. The editing efficiencies depend on the Cas9 fusion protein, cell type and its proliferation rate. The editing efficiency in primary T cells and CD34+ hematopoietic stem cells can significantly improve by optimizing transfection and culturing conditions, such as concentration of the CRISPR-Cas9 complex, cell culturing time and electroporation program. Cas9 fusions improve the safety and efficiency of the CRISPR-Cas9 system depending the cell type and the proliferation rate of the cell. Timing the induction of double-strand breaks also improves the editing efficiency. Overall, the methods used in the thesis give useful tools for eventual translational applications.

Blood glucose monitoring (BGM) is an essential part of diabetes management. Currently available BGM technologies are invasive by nature, and require either sampling blood or an invasive needlelike sensor to be inserted under the skin. Extraction of interstitial fluid using magnetohydrodynamics is proposed as a technology to enable truly non-invasive glucose monitoring. Presently, only direct current (DC) has been investigated to be employed for magnetohydrodynamic extraction of interstitial fluid. In this study we studied in a skin model whether the extraction rate of magnetohydrodynamic extraction can be increased by using a unipolar square wave, with same time-averaged current as DC extraction used as a control. The results indicate a 2.3-fold increase in the average extraction rate, when unipolar square wave of double intensity is applied, as compared to DC. The results serve towards reducing the measurement time in non-invasive glucose monitoring systems utilizing magnetohydrodynamic extraction.

Cancer is a worldwide health problem; in 2018 9.6 million people died of cancer, meaning that about 1 in 6 deaths was caused by it. The challenge with cancer drug therapy has been the development of cancer drugs that are effective against cancer but are not harmful to the healthy cells. One of the solutions to this has been antibody-drug conjugates (ADCs), where a cytotoxic drug is bound to an antibody. The antibody binds to specific antigen present on the surface of the cancer cell, thus working as a vessel to carry the drug specifically to the cancer cells. Monomethyl auristatin E (MMAE) and monomethyl auristatin F (MMAF) are mitosis preventing cancer drugs. The auristatins are pentapeptides that were developed from dolastatin 10. MMAE consist of monomethyl valine (MeVal), valine (Val), dolaisoleiune (Dil), dolaproine (Dap) and norephedrine (PPA). MMAF has otherwise similar structure, but norephedrine is replaced by phenylalanine (Phe). They prevent cell division and cancer cell proliferation by binding to microtubules and are thus able to kill any kind of cell. By attaching the auristatin to an antibody that targets cancer cells, they can effectively be used in the treatment of cancer. MMAE and MMAF exist as two conformers in solution, namely as cis- and trans-conformers. The trans-conformer resembles the biologically active conformer. It was recently noted that in solution 50-60 % of the MMAE and MMAF-molecules exist in the biologically inactive cis-conformer. The molecule changes from one conformer to the other by the rotation of an amide bond. However, this takes several hours in body temperature. As the amount of the cis-conformer is significant, the efficacy of the drug is decreased, and the possibility of side effects is increased. It is possible that the molecule leaves the cancer cell in its inactive form, migrates to healthy cells and tissue, and transforms to the active form there, damaging the healthy cell. The goal of this study was to modify the structure of the auristatins so that the cis/trans-equilibrium would change to favor the biologically active trans-conformer. The modifications were done virtually, and the relative energies were computed using high-level quantum chemical methods, at density functional theory (DFT), 2nd order perturbation theory (MP2) and coupled cluster levels. Intramolecular interactions were analyzed computationally, employing symmetry-adapted perturbation theory and the non-covalent interactions analysis. The results suggest that simple halogenation of the benzene ring para-position is able to significantly shift the cis/trans-equilibrium to favor the trans-conformer. This is due to changes in intramolecular interactions that favor the trans-conformer after halogenation. For example, the NCI analysis shows that the halogen atom invokes stabilizing intramolecular interactions with the Dil amino acid; there is no such interaction between the para-position hydrogen and Dil in the original molecules. We also performed docking studies that show that the halogenated molecules can bind to microtubules, thus confirming that the modified structures have potential to be developed into new, more efficient and safe cancer drugs. The most promising drug candidates are Cl-MMAF, F-MMAF, and F-MMAE where 94, 90, and 79 % of the molecule is predicted to exist in the biologically active trans-conformer, respectively.

Studies have consistently shown that regular consumption of wholegrain or cereal dietary fibre can prevent and reduce risk of chronic diseases. Despite the extensive worldwide efforts to encourage wholegrain consumption, most cereals in Africa are still mainly consumed in their refined form. Ogi-porridge, which is a traditional fermented cereal based food, for example, serves as a vital source of energy for infants and adults in west Africa, but its nutritional quality is low, particularly in dietary fibre and protein contents. Unfortunately, poor nutrition quality and in some cases microbiologically unsafe fermented foods in Africa not only lead to gastrointestinal disorders, but also contributes to the development of chronic diseases, with long term consumption. Therefore, improving the safety and nutritional quality of cereal-based fermented foods and increasing their dietary fibre content would be an essential step towards reducing the occurrence of these diseases in Africa. This study aimed at evaluating the use of starter cultures, pearl millet wholegrain flour and egusi to improve safety and nutritional quality of pearl millet ogi-porridge. The traditional ogi was prepared in a process that involved soaking, wet-milling, wet-sieving and spontaneous fermentation. Modified ogi was prepared by inoculating pearl millet wholegrain flour (0.5 mm) with Lactobacillus plantarum (previously isolated from pearl millet) and Saccharomyces cerevisiae. Changes in cell density of microbial groups and acidity was followed during production of ogi. Ogi-porridge was prepared from each type of ogi, by adding boiling water to ogi, with minimal stirring. Proximate composition and bioavailability of starch and protein were analyzed for the ogi-porridges. Finally, sensory quality of the traditional and modified ogi-porridges and their egusi milk supplemented forms, were compared by west Africans living in Finland who were familiar with ogi-porridge. At the end of ogi production, only a slight reduction in Enterobacteriaceae cell density was observed in the traditional ogi, while, 2 log cycle reduction in Enterobacteriaceae was obtained for modified ogi. Modified ogi contained 60% higher total titratable acidity than traditional ogi. In the case of nutritional quality, modified ogi-porridge had 10.09% higher protein content than the traditional ogi-porridge. Starch and protein digestibility were also higher for modified ogi-porridge. Sensory evaluation indicated that an organoleptically acceptable ogi-porridge can be prepared from pearl millet wholegrain flour and starter cultures. Supplementation of traditional and modified ogi-porridges with up to 25% egusi milk (8.81% protein content) was acceptable. As percentage of egusi milk increased from 0-25%, protein content of supplemented ogi-porridges increased. In conclusion, a microbiologically safer, nutritionally superior, and an acceptable ogi-porridge was obtained using the modified method of ogi-porridge production employed in this study.

Biological populations arise, develop and evolve under a series of well-studied laws and fairly regular mechanisms. Population genetics is a field of science, that aims to study and model these laws and the genetic composition and diversity of populations of various types of species and life. At best, population genetic models can be of use in verifying past events of a population and eventually reconstructing unknown population histories in light of multidisciplinary evidence. An example case of this is the research concerning human population prehistory of Finland. Population simulations are a sub-branch of the rapidly developing field of bioinformatics and can be divided into two pipelines: forward-in-time and backward-in-time (coalescent). The methodologies enable in silico testing of the development of genetic composition of individuals in a well-defined population. This thesis focuses on the forward-in-time approach. Multiple pieces of software exist today for forward population simulations, and simuPOP [http://simupop.sourceforge.net] probably is the single most flexible one of them. Being able to incorporate transmission of genomes and arbitrary individual information between generations, simuPOP has potential applications even beyond population genetics. However, simuPOP tends to use an enormous amount of computer random access memory when simulating large population sizes. This thesis introduces three approaches to improve the throughput of simuPOP. These are i) introducing scripting guidelines, ii) approximating a complex simulation using the inbuilt biallelic mode of simuPOP and iii) changes in the source code of simuPOP that would enable improved throughput. A previous simuPOP script designed to simulate past demographic events of Finnish population history is used as an example. A batch of 100 simulation runs is run on three versions of the previous script: standard, modified and biallelic. As compared to the standard mode, the modified simulation script performs marginally faster. Despite doubling the user time of a single simulation run, the biallelic approximation method proves to consume three times less random access memory still being compatible from the population genetic point of view. This suggests that built-in support for the biallelic approximation could be a valuable supplement to simuPOP. Evidently, simuPOP can be applied to very complex forward population simulations. The use of individual information fields enables the user to set up arbitrary simulation scenarios. Data structure changes at source code level are likely to improve throughput even further. Besides introducing improvements and guidelines to the simulation workflow, this thesis is a standalone case study concerning the use and development of a bioinformatics software. Furthermore, an individual development version of simuPOP called simuPOP-rev is founded with the goal of implementing the source code changes suggested in this thesis. ACM Computing Classification System (CCS): D.1 [Programming techniques], G.1.6 [Optimization], H.3 [Information storage and retrieval]

Web development is in great demand these days. Constantly developing technologies enables to create impressive websites and mitigates the amount of development work. However, it is useful to consider the performance aspect, which affects directly to user experience. Performance in this context means website’s load times. Front end web development typically involves using Cascading Style Sheets (CSS) which is a style sheet language and a web technology that is used to describe the visual presentation of a website. This research consist of a literature review part, which contains background knowledge about how web browsers work, performance in general, performance metrics along with CSS performance optimization and an empirical part, which includes different benchmarks presented in major software industry conferences for testing the performance of a certain CSS feature, that have a possibility to improve the performance of the website. The loading times obtained from the benchmarks are reviewed and compared with each other. In addition, a few techniques are presented that do not have their own benchmark, but which may have an effect on performance. To highlight the results, CSS performance is usually not the biggest bottleneck of performance on a website, since the overall style calculation takes about a quarter of the total runtime calculation on average. However, utilizing some particular techniques and managing to shrink the style calculation costs can be valuable. Based on the benchmarks on this research, using shadow DOM and scoped styles have a positive effect on style performance. For layout, performance benefits can be achieved by utilizing CSS containment and concurrent rendering. From other practices, it can be concluded that removing unused CSS, avoiding reflow and repaint along with complex selectors and considering the usage of web fonts a better results can be achieved in terms of performance.

In pig breeding many important traits are measurable only on females or after slaughter, which makes it difficult to observe these traits for the estimation of traditional estimated breeding values (EBVs). Genomic selection is expected to overcome these difficulties, since it makes use of large number of genetic markers called single nucleotide polymorphisms (SNPs). Dense genotyping of SNPs is needed for sufficient accuracy, but the costs increase with the density of the panel. It is possible to reduce the costs by genotyping some animals with a low-density SNP panels. Missing genotypes can then be imputed to correspond to the information of the denser SNP panel. The choice of optimal imputation program is dependent on structure of the population. The aim of this study was to compare performance of two imputation programs (BEAGLE and fastPHASE) to impute genotypes in the Finnish Yorkshire pig population. Data consisted of 809 boars. In data set 1 imputation was performed for all boars born after 2007 and in data set 2 for all boars born after 2005. Genotypes of the remaining boars were used as a reference population. Performance of these programs was evaluated by the allele error rate and computing time. The effect of SNP location, average distance between adjacent SNPs, size of the chromosome and MAF on the allele error rate was also studied. The average allele error rate using BEAGLE for the data set 1 was 2,88 % and time required for imputation was 8min 38s. Results using BEAGLE for the data set 2 were 2,58 % and 11min 50s. The average allele error rate using fastPHASE for the data set 1 was 4,02 % and time required for imputation for chromosome 1 was 1d 16h 11min 4s. Results using fastPHASE for the data set 2 were 3,71 % and 11d 11h 2min 31s. Allele error rates were highest at the end of the chromosome and lowest at the centre of the chromosomes. The average distance between adjacent SNPs did not have a notable effect on error rates. Error rates tended to be lower in large chromosomes than in small chromosomes. Error rates increased with increasing MAF. According to this study, BEAGLE is recommendable program for genotype imputation because of its good accuracy and short computational time.

Tässä tutkielmassa tarkastellaan särkikaloja väli-isäntinä hyödyntävien imumatolajien esiintyvyyttä, niiden tunnistamista ja merkitystä. Tutkielmassa keskitytään lähinnä imumatolajeihin, joiden pääisäntäeläimiä ovat nisäkkäitä, ja joilla on havaittu olevan kliinistä merkitystä myös ihmisille. Tutkielma sisältää kirjallisuuskatsauksen lisäksi alkuperäistutkimuksen, jossa selvitettiin Itämerestä pyydetyissä särjissä loisivien imumatojen esiintymistä. Tutkimuksen aikana tavoitteena oli myös selvittää, löydetäänkö särjistä Pseudamphistomum truncatum -lajin metacercarioita, sillä kyseisestä lajista oli tehty aiemmin havaintoja Kaakkois-Suomen alueella elävistä ketuista. Imumatojen esiintymisen selvittämisen lisäksi tutkielmassa perehdytään kalojen iänmääritykseen, joka voidaan tehdä esimerkiksi laskemalla hartian lukkoluun (cleithrum) kasvuvyöhykkeiden lukumäärä. Tutkimuksessa hyödynnettiin WHO:n vuonna 1995 julkaisemassa raportissa esiteltyä digestiomenetelmää, jolla imumatojen metacercaria-muotoja vapautettiin särkien lihaskudoksesta. Näytteinä olivat joitakin päiviä aiemmin preparoidut särkifileet, joita tutkittiin yhteensä 85 kappaletta. Fileet käsiteltiin loiskystien vapauttamiseksi mekaanisesti sauvasekoittimella ja kemiallisesti pepsiiniliuoksella. Syntynyt seos laskeutettiin suppilossa, ja selkeytysten jälkeen sedimentti kerättiin mikroskoopin avulla tarkasteltavaksi. Iänmääritykseen satunnaisesti valikoiduilta 20 särjeltä irrotettiin hartian lukkoluu. Keittämällä suoritetun puhdistuksen jälkeen luusta laskettiin mikroskoopin avulla kasvuvyöhykkeet, joiden lukumäärä vastaa kalan ikää vuosissa. Aineistossa havaittiin imumatojen metacercaria-muotoja 98 %:ssa tutkituista näytteistä. Valtaosan löydöksistä muodostivat kolme ulkonäöltään toisistaan erottuvaa metacercaria-tyyppiä. Lisäksi erotettiin silmämääräisesti ainakin kolmenlaisia digestion aikana vapautuneita imumatoja. Metacercarioita ja vapautuneita imumatoja kerättiin joiltakin laskentamaljoilta (noin 10 %:sta) erilleen ja lähetettiin PCR-menetelmällä suoritettavaan lajinmääritykseen. PCR-tulosten perusteella 46 %:ssa tutkituista särjistä tehtiin silmämääräisen morfologisen tunnistuksen perusteella P. truncatum -löydös. Iänmäärityksessä havaittiin kokonaisuutena positiivinen korrelaatio iän ja pituuden välillä. Tutkimuksessa löydettiin särjistä nisäkkäisiin tarttuvia imumatoja. Tämän tuloksen ja aiempien Euroopassa ja Venäjällä tehtyjen selvitysten perusteella voidaan olettaa, että kalaa ravintonaan käyttävillä nisäkkäillä on riski saada imumatoinfektio särjenlihasta. Ihmisiin ja kalaa syöviin lemmikkieläimiin kohdistuvaa riskiä voidaan kuitenkin pienentää etenkin, jos kalanliha kuumennetaan valmistuksen yhteydessä kauttaaltaan. Muita särkikaloja ei sisällytetty tutkimukseen, mutta myös niistä aiheutuva imumatoinfektioriski on todennäköisesti alueella suuri, koska monen lajin ekologinen lokero on jossakin elämänvaiheessa samankaltainen särjen kanssa.

Human norovirus (HuNoV) is the leading cause of foodborne illness globally. Especially minimally processed goods such as berries and shellfish are common sources of HuNoV outbreaks. High pressure processing (HPP) is a relatively novel food processing technology that can both inactivate foodborne pathogens and extend the shelf-life of food items in cold temperatures. HPP is especially suitable for fresh purees, juices and sauces. In this study, we used murine norovirus strain MNV-1 to model the inactivation of HuNoV by HPP in three berry puree matrices and phosphate-buffered saline (PBS). We assessed the effect of HPP by cell-based TCID50 infectivity assay and real-time reverse transcription quantitative PCR (RT-qPCR) with RNase and porcine gastric mucin (PGM) binding assay. We strived to find if there were differences between distinct pressures (4500 and 6000 bars) and hold times (3, 6, and 9 minutes) to efficiently inactivate MNV-1 in berry purees. We observed that the matrix type affected the survival of MNV-1 significantly both during HPP and transportation. During transportation, MNV-1 survived better in PBS than in berry purees. MNV-1 was efficiently inactivated in PBS leading to >3-log10 reductions in the number of infectious particles (TCID50/ml) at both 4500 and 6000 bars. In berry puree matrices, MNV-1 was most efficiently inactivated in blackcurrant puree resulting in ≈3-log10 reductions in genome equivalents. The efficacy of pressures and hold-times could not be differentiated in any of the used matrices. MNV-1 in raspberry puree showed no infectivity in RAW 264.7 cells but displayed ≈2-log10 reductions in genome equivalents. MNV-1 in strawberry puree displayed <1-log10 reductions in RAW 264.7 cells. Our results imply that PGM binding assay and RNase as pre-RT-qPCR treatments have problems in selecting infectious MNV-1 particles for amplification. Hence when using these pre-treatments, concluding on MNV-1 infectivity should be done cautiously.