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Clostridium botulinum on gram-positiivinen, ehdottoman anaerobi, itiöitä muodostava sauvamainen bakteeri, joka tuottaa vegetatiivisen kasvun aikana voimakkainta tunnettua myrkkyä, botulinumtoksiinia. C. botulinum jaetaan seitsemään erilaiseen tyyppiin, jotka merkitään kirjaimin A, B, C, D, E, F ja G. Eri tyyppien tuottamat toksiinit eroavat serologisesti toisistaan. Botulismia tunnetaan neljä eri muotoa ja näitä kaikkia muotoja tavataan myös hevosilla. Hevoset ovat botulinumtoksiinille erittäin herkkiä. Niillä sairastumiset johtuvat usein saastuneen rehun syömisestä. Tutkimuksen tarkoituksena on selvittää esiintyykö terveiden hevosten ulosteessa C. botulinum tyyppien A, B, E ja F itiöitä ja voivatko ympäristötekijät ja ruokinta vaikuttaa itiöiden esiintyvyyteen. Syventävät opintoni liittyvät osatyönä tutkimukseen C. botulinumin esiintyvyydestä hunajassa. Mehiläisten tiedetään hakevan vettä ravinnokseen sekä pesän lämmön säätelyyn erityisesti lantakasojen ja lantaloiden reunoilta. Hevosen uloste voisi siten toimita potentiaalisena itiölähteenä. Näytteet kerättiin eläinlääkäreiden ja tallinomistajien avustuksella 19 tallilta eri puolilta Suomea. Tutkimuksen osana tehdyssä kyselyssä kerättiin lisäksi tietoa hevosten ruokinnasta, kuivituksesta ja vedensaannista. Näytteiden esikäsittelyn jälkeen C. botulinumin esiintyminen osoitettiin käyttäen Multiplex-PCR-menetelmää. Kvantitatiivinen määritys suoritettiin modifioidulla MPN (Most Probable Number) -menetelmällä. Tutkituista näytteistä todettiin 11 %:lla kliinisesti terveitä hevosia C. botulinumin itiöitä ulosteessa. Todetut tyypit olivat B ja F. Tulos korreloi elintarvike- ja ympäristöhygienian laitoksella meneillään olevan maaperätutkimuksen kanssa. Kyselytutkimuksen perusteella todettiin säilörehun syötön sekä laiduntamisen olevan suhteellisen yleistä positiiviseksi havaittujen hevosten ryhmässä. Tutkimuksen perusteella hevosen uloste saattaa toimia kontaminaatiolähteenä C. botulinumin itiöiden siirtymiselle hunajaan.

Clostridium botulinum on gram-positiivinen, anaerobinen bakteeri, jota esiintyy maaperässä ja vesistöjen sedimenteissä maailmanlaajuisesti. Epäsuotuisissa olosuhteissa se tuottaa kestävän itiön. Ympäristön itiöt voivat kontaminoida sekä elintarvikkeita että eläinten rehuja. C. botulinumin tuottama botulinumtoksiini on yksi vahvimmista tunnetuista myrkyistä ja se sairastuttaa niin ihmisiä kuin eläimiäkin. Myös nauta on botulinumtoksiinille herkkä. Maailmalla on raportoitu useita tapauksia, joissa karja on sairastunut ja menehtynyt botulismin aiheuttamiin halvausoireisiin. Suomessa on ollut naudan botulismiepäilyjä, mutta tapauksia ei ole raportoitu. Yleisesti tapaukset liittyvät pilaantuneen säilörehun syöttämiseen. Osalta sairastuneista naudoista on pystytty eristämään C. botulinumin itiöitä tai toksiinia ruoansulatuskanavasta tai ulosteesta. Tässä työssä tutkittiin C. botulinum -itiöiden mahdollista esiintymistä naudan ulosteessa laidunkaudella. Tutkimuksen tarkoituksena oli selvittää onko naudan uloste mahdollinen kontaminaatiolähde hunajassa esiintyville C. botulinumin itiöille. Mehiläiset käyttävät vettä sekä pesän lämmönsäätelyyn että omaksi ravinnokseen. Lantaloiden vedestä ne saavat tarvitsemiaan kivennäisaineita. Suomessa ei ole aikaisemmin tutkittu C. botulinumin itiöiden esiintymistä naudan ulosteessa. Näytteet kerättiin keinosiementäjien avustuksella sadalta eri naudalta eri puolilta Suomea. Näytteenottotiloilla karjanhoitaja täytti kyselykaavakkeen, jonka avulla selvitettiin mm. nautojen ruokintaa, vedensaantia ja laidunolosuhteita. C. botulinumin detektio tehtiin rikastuksen jälkeen multiplex-PCR-menetelmällä. Itiöiden määrä määritettiin MPN (Most Probable Number) -menetelmää käyttäen. Näytteistä punnittiin 1 g:n erissä kymmenen putken sarjat, joista positiivisen tuloksen antaneiden putkien lukumäärästä MPN-luku laskettiin. Käytetyllä menetelmällä naudan ulostenäytteistä todettiin C. botulinumin suhteen positiiviseksi kaksi (2 %) näytettä. Niiden itiöiden määrä oli vähäinen, ka. 11 kpl itiöitä/ 100 g näytettä. Vähäisen itiöiden esiintyvyyden takia tulosta ei voida käsitellä tilastollisesti ja siten ei voida sanoa onko positiivisten eläinten esiintymisellä alueellista vaihtelua. Tutkimuksen perusteella voidaan olettaa, että uloste ei olisi merkittävä hunajan kontaminaatiolähde.

Clostridium botulinum is a gram-positive, strictly anaerobic, sporeforming rod which produces botulinum neurotoxin during its vegetative growth phase. Botulinum toxins are divided into seven different serotypes (A to G) depending on their antigenic properties. They are the most potent toxins known and are responsible for botulism in human and animals. Botulism is a disease that causes flaccid paralysis and is often fatal. A preformed botulinum toxin in food or forage causes food or forage poisoning when ingested. In wound botulism a wound is contaminated by C. botulinum spores and the toxin is produced as the spores germinate and grow in anaerobic conditions in the wound. Infant botulism is a disease of children aged less than 1 year. The spores of C. botulinum are able to germinate in the intestine of an infant and produce toxin. There is also another type of botulism where the bacterium colonizes an adult intestine. In comparison with other species swine is more resistant to botulism. Though the exact reasons are not known it is probably due to several factors such as components of the intestinal normal flora of swine, permeability of the swine intestine mucosa to botulinum toxin and the affinity of toxin to the nervous tissue of swine. Swine intestine may, however carry botulinal spores. As bees are more likely to collect water from contaminated than from clean sources, spores of C. botulinum from swine intestine can potentially contaminate honey. Honey is known to be a risk factor for infant botulism. The aim of the advanced studies was to determine whether fecal samples from finnish swine contain spores of C. botulinum and whether some environmental factors have influence on the incidence of the spores in swine intestine. The studies are associated with a research project conducted in the department of food and environmental hygiene on the contamination routes of C. botulinum in the production environments of honey. A total of 100 fecal samples from 20 piggerys from different parts of Finland were collected. A questionnaire was filled regarding each piggery. A proportion of 10 g of each fecal sample was incubated anaerobically divided in 10 tubes containing 10 ml of TPGY-broth (Tryptone-Peptone-Glucose-Yeast). The aim was to determine the concentration of the spores in the fecal samples using a Most Probable Number-technique (MPN). The method for detection of the toxin genes A, B, E, and F was multiplex-PCR. In this study there were found no fecal samples positive for BoNT genes A, B, E or F. No conclusions on the influence of different environmental factors of the piggery could drawn based on this study.

Patients with inflammatory bowel disease (IBD) are at increased risk for developing symptomatic Clostridium difficile infection (CDI) with worse clinical outcomes, including mortality, as compared with the general population. IBD-patients are also more susceptible to have recurrences of CDI. At present, predisposing factors for CDI in IBD-patients are poorly established. To characterize IBD-related CDI, a retrospective cohort from HUS register was gathered. Patient characteristics were compared with two control groups: IBD-patients with CDI and CDI-patients. According to our results, there was no statistically significant difference in mortality rate between IBD- and CDI-patients in contrary to previous reports. We detected corticosteroid consumption in IBD patients with CDI to be greater than in patient with IBD alone. It could be considered as a risk factor for CDI. Clarifying risk factors for CDI could lead to better understanding of optimal treatment for CDI in IBD patients.

Imbalance of intestinal microbiota is called dysbiosis. Signs of dysbiosis are altered abundance of different bacterial species and reduced diversity together with altered interactions between bacterial species and microbiota and the host. Dysbiosis of intestinal microbiota is connected to many intestinal diseases and today many studies are focused to find so called “next generation” probiotics to be used for the alleviation of dysbiosis instead of traditional antibiotic treatments. The study was made in the Human Microbiome Research Program, Faculty of Medicine, University of Helsinki. Aim of the study was to isolate spore-forming bacterial species for the treatment of intestinal inflammation and infections with bacterial therapy. For this purpose, feces from a healthy adult who had acted as a donor for fecal microbiota transplantation was used to isolate spore-forming commensal bacteria. The isolated bacteria were identified and their ability to adhere into intestinal epithelium and strengthen it was investigated. Also anti-inflammatory potential of these isolated bacterial strains was investigated. For isolating bacteria three different heat treatments and ethanol and methanol treatments were used as a pre-treatment step. Pre-treated samples were cultivated on YCFA-media and isolates were picked from plates at different growth points for further cultivation. Selected isolates were purified, their DNA was isolated and they were identified by partial 16S rRNA -gene sequencing. From these identified isolates four isolates were chosen for further investigation and their full length 16S rRNA -gene was sequenced. These isolates were studied also by using API and aerotolerance tests. Potential anti-inflammatory and adhesion properties of the isolates were investigated by attenuation, adhesion and TER-experiments. In the isolation, the effect of different pre-treatments on the recovery of isolates was clear and based on sequencing isolates that were spore-forming anaerobic bacteria were selected for further investigation. Three of the isolates were Clostridium butyricum and one Blautia wexlerae species. Anti- and pro-inflammatory properties of these isolates were very different depending on isolate and one of them was potentially anti-inflammatory. Isolates also adhered differentially and two of them possibly strengthened gut epithelial barrier so they are promising for further research and in the future investigation with these isolates continues. Experience and results with different cultivation methods can be used to for further development of cultivation for anaerobic intestinal bacteria.

Embedded systems are everywhere. The variety of different types of embedded systems and purposes are wide. Yet, many of these systems are islands in an age where more and more systems are being connected to the Internet. The ability to connect to the Internet can be taken advantage in multiple ways. One is to take advantage of the resources cloud computing can offer. Currently, there are no comprehensive overviews how embedded systems could be enhanced by cloud computing. In this thesis we study what cloud enhanced embedded systems are and what their benefits, risks, typical implementation methods, and platforms are. This study is executed as an extended systematic mapping study. The study shows that the interest from academia and practice in cloud enhanced embedded systems has been growing significantly in recent years. The most prevalent research area is wireless sensor networks followed by the more recent research area Internet of things. Most of the technology is available for implementing cloud enhanced embedded systems but comprehensive development tools such as frameworks or middlewares are scarce. Results of the study indicate that existing embedded systems and other non-computing devices would benefit from connectivity and cloud resources. This enables the development of new applications for consumers and industry that would not be possible without cloud resources. As an indication of this we see several systems developed for consumers such as remotely controlled thermostats, media players that depend on cloud resources, and network attached storage systems that integrate with cloud access and discovery. The academic literature is full of use cases for cloud enhanced embedded systems and model implementations. However, the actual integration process as well as specific engineering techniques are rarely explained or scrutinized. Currently, the typical integration process is very custom to the application. There are few examples of efforts to create specific development tools, more transparent protocols, and open hardware to support the development of ecosystems for cloud enhanced embedded systems.

As the data traffic, as well as the speed demands, increases, the mobile networks require means for economically fulfil these demands. The solution comes from the cloud. In order to move the processing to the cloud, it must be carefully dimensioned to know how much resources each situation requires. This means there must be a way to calculate from the traffic the virtual machines required and the hardware resources the virtual machines need, when the cloud infrastructure used is OpenStack. This thesis provides two methods for calculating the virtual machines from the traffic profile. The first one is based on performance testing of the virtual network functions and the second one is based on machine learning technique called multiple linear regression analysis. Furthermore in this work, approximation algorithms are being used in order to solve multidimensional variates of classical optimization problems such as bin packing problem and subset sum problem. These algorithms are used to dimension required resources from the virtual machines to hardware and vice versa. The algorithms are bundled to a program with a graphical user interface to make as user friendly as possible.

In the world of globalization immigration processes represent consequence of the search for better life. Every year more immigrants are coming to stay and live in Finland. Understanding patterns of living, spatial locations and clustering of this specific population becomes important and integral step towards integration of immigration population in society. Studies of immigration population conducted in Finland and Helsinki Metropolitan Area are mostly done with descriptive statistical methods mostly employed for describing social patterns and participation of immigrant population within the whole population. Employment of inferential statistical methods, spatial statistical methods, precisely Exploratory Spatial Data Analysis (ESDA methods), specifically Global and Local Moran's Index is becoming extremely important because of the quantitative and qualitative results which can be gained. This thesis is consisted of analysis of immigrant population patterns, conducted by Global and Local Moran's Index used by ArcGIS and GeoDa software. ArcGIS is a market leading, commercial GIS package for computation, analysis and production of different sorts of GIS analysis and results. Spatial statistic toolbox, as integral part of ArcGIS software package is used for interpretation of spatial statistics results (maps, graphs, reports etc.), which can be obtained, by use of several different methods. GeoDa is non-commercial software, relatively new in GIS practice in Finland, focusing specifically in spatial statistics analysis. It is used for manipulation and operationalization of spatial data analysis, designed for implementation of different and unique (Bivariate Moran's I, etc.) ESDA techniques. Both software are computing comparable but different results, quantitatively and visually. For global measurements of spatial autocorrelation and presence of clustering within analyzed area Global Moran's Index is employed. Local measurements and for mapping of possible cluster and outlier occurrences (Anselin Local Moran's Index) is being used. Employment of weight matrix produced in ArcGIS and GeoDa is allowing creation of conceptualization of spatial weight matrix on the same principles in ArcGIS and GeoDa. Conceptualization of weight matrix in the case of lattice data with shared border is contiguity concept. Contiguity concept is using queen concept for defining neighbors, because it allows bigger analyzing capacity. Both software are using same statistical equations but outcome results are showing variety of differences, because of the differences in computing, presenting and visual displaying of the results. GeoDa is producing more significant statistical and visual results. The task is to test and compare computational, visual and analytical capabilities and possibilities of both software and analyze quality of outcome results (maps, diagrams, box plots, etc.) Data on immigration population is provided by HSY (Helsingin Seudun Ympäristö) with the lattice grid level size (1x1km, 500x500m, 250x250m). Purpose of my thesis is also to analyze lattice data with new square grid sizes (50x50m), which are inputting more specific local area inputs for location of local spatial autocorrelation and hot spot activities. Creation of new lattice size is motivated by conceptualizing of the data which is aggregated on the building level (Pks_vaki). Main motive is to try to detect new trends in development of clustering and clusters of immigrant population in Greater Helsinki, formulate and impose scale and area size from a different perspective. Results are informing about undetected process of clustering in the central areas of Helsinki not noticed in the previous studies of immigration population. They are offering different perspective on the problem of clustering of immigration population in Helsinki Metropolitan area.

Programming courses often receive large quantities of program code submissions to exercises which, due to their large number, are graded and students provided feedback automatically. Teachers might never review these submissions therefore losing a valuable source of insight into student programming patterns. This thesis researches how these submissions could be reviewed efficiently using a software system, and a prototype, CodeClusters, was developed as an additional contribution of this thesis. CodeClusters' design goals are to allow the exploration of the submissions and specifically finding higher-level patterns that could be used to provide feedback to students. Its main features are full-text search and n-grams similarity detection model that can be used to cluster the submissions. Design science research is applied to evaluate CodeClusters' design and to guide the next iteration of the artifact and qualitative analysis, namely thematic synthesis, to evaluate the problem context as well as the ideas of using software for reviewing and providing clustered feedback. The used study method was interviews conducted with teachers who had experience teaching programming courses. Teachers were intrigued by the ability to review submitted student code and to provide more tailored feedback to students. The system, while still a prototype, is considered worthwhile to experiment on programming courses. A tool for analyzing and exploring submissions seems important to enable teachers to better understand how students have solved the exercises. Providing additional feedback can be beneficial to students, yet the feedback should be valuable and the students incentivized to read it.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder caused by degeneration of motor neurons in brain and spinal cord. The degeneration of motor neurons leads to muscle atrophy and paralysis. Currently there is no cure for ALS. Available drugs for ALS can lengthen the survival time by a couple of months. Several factors involve the pathophysiology of ALS, such as endoplasmic reticulum stress and neuroinflammation. Mesencephalic astrocyte-derived neurotrophic factor (MANF) is a protein which has shown neuroprotective effects on animal models of Parkinson disease and brain ischemia. C-terminal fragment of MANF can cross the blood-brain barrier, allowing it to be administered subcutaneously instead of injected directly into the brain. The experimental part consists of two parts. The aim of the first part was to study the pharmacokinetic properties of next generation MANF (C-MANF). The aim of the second part was to elucidate the effect of twice a week administered subcutaneous injection of C-MANF in genetic SOD1-G93A mouse model and its neuroprotective effects by assessing protection of lumbar motor neurons. Pharmacokinetic properties of C-MANF were determined in wild type mice after a single subcutaneous injection of C-MANF at different time points by using indirect ELISA assay. The effects of C-MANF in SOD1-G93A mouse model were assessed by subcutaneous injection of either C-MANF or PBS twice a week and by monitoring clinical score and motor behavior of mice from 10 weeks of age to clinical endpoint. Hematoxylin eosin staining was used to study neuroprotective effects of C-MANF. C-MANF administered subcutaneously is absorbed into the blood circulation and the highest serum concentration of C-MANF is after 60 minutes of dosing. Subcutaneously injected C-MANF also crosses the blood-brain barrier and reach the brain in 120 minutes. C-MANF did not preserve motor function or ameliorated ALS symptoms in SOD1-G93A mouse model. In this study C-MANF did not increase the survival of SOD1-G93A mice. C-MANF did not significantly protect motor neurons from degeneration even though there was a slight trend between the groups. No beneficial effects were observed with C-MANF in SOD1-G93A mouse model and therefore the dose and frequency of administration of C-MANF were not optimal. Subcutaneously injected C-MANF provides a safer dosing option for neurodegenerative disorders.