Adopting the Vaadin Java framework to rebuild VTT’s Web Interfaces and Database Applications

With the growth in new technologies, using online tools have become an everyday lifestyle. It has a greater impact on researchers as the data obtained from various experiments needs to be analyzed and knowledge of programming has become mandatory even for pure biologists. Hence, VTT came up with a new tool, R Executables (REX) which is a web application designed to provide a graphical interface for biological data functions like Image analysis, Gene expression data analysis, plotting, disease and control studies etc., which employs R functions to provide results. REX provides a user interactive application for the biologists to directly enter the values and run the required analysis with a single click. The program processes the given data in the background and prints results rapidly. Due to growth of data and load on server, the interface has gained problems concerning time consumption, poor GUI, data storage issues, security, minimal user interactive experience and crashes with large amount of data. This thesis handles the methods by which these problems were resolved and made REX a better application for the future. The old REX was developed using Python Django and now, a new programming language, Vaadin has been implemented. Vaadin is a Java framework for developing web applications and the programming language is extremely similar to Java with new rich components. Vaadin provides better security, better speed, good and interactive interface. In this thesis, subset functionalities of REX was selected which includes IST bulk plotting and image segmentation and implemented those using Vaadin. A code of 662 lines was programmed by me which included Vaadin as the front-end handler while R language was used for back-end data retrieval, computing and plotting. The application is optimized to allow further functionalities to be migrated with ease from old REX. Future development is focused on including Hight throughput screening functions along with gene expression database handling

Models to study intermediate filament dynamics and functions

Intermediate filaments are part of the cytoskeleton and nucleoskeleton; they provide cells with structure and have important roles in cell signalling. The IFs are a large protein family with more than 70 members; each tightly regulated and expressed in a cell type-specific manner. Although the IFs have been known and studied for decades, our knowledge about their specific functions is still limited, despite the fact that mutations in IF genes cause numerous severe human diseases. In this work, three IF proteins are examined more closely; the nuclear lamin A/C and the cytoplasmic nestin and vimentin. In particular the regulation of lamin A/C dynamics, the role of nestin in muscle and body homeostasis as well as the functions and evolutionary aspects of vimentin are investigated. Together this data highlights some less well understood functions of these IFs. We used mass-spectrometry to identify inter-phase specific phosphorylation sites on lamin A. With the use of genetically engineered lamin A protein in combination with high resolution microscopy and biochemical methods we discovered novel roles for this phosphorylation in regulation of lamin dynamics. More specifically, our data suggests that the phosphorylation of certain amino acids in lamin A determines the localization and dynamics of the protein. In addition, we present results demonstrating that lamin A regulates Cdk5-activity. In the second study we use mice lacking nestin to gain more knowledge of this seldom studied protein. Our results show that nestin is essential for muscle regeneration; mice lacking nestin recover more slowly from muscle injury and show signs of spontaneous muscle regeneration, indicating that their muscles are more sensitive to stresses and injury. The absence of nestin also leads to decreased over-all muscle mass and slower body growth. Furthermore, nestin has a role in controlling testicle homeostasis as nestin-/- male mice show a greater variation in testicle size. The common fruit fly Drosophila melanogaster lacks cytoplasmic IFs as most insects do. By creating a fly that expresses human vimentin we establish a new research platform for vimentin studies, as well as provide a new tool for the studies of IF evolution.

Discerning Cultural Depictions and Mistakes in Kafe Piter, a Russian Language Textbook for Finnish Students

This thesis presents the results of an analysis of the content in the series of Russian textbooks Kafe Piter, which is widely used in Finnish educational institutions for adult learners at the time that the research is conducted. The purpose of this study is to determine and describe how a textbook may purvey an image of a foreign country (in this case, Russia). Mixed-methods research with a focus on the qualitative content analysis of Kafe Piter is performed. The guidelines for textbook evaluation of cultural content proposed by Byram (1993) are used in this study as the basis for creating a qualitative analysis checklist, which is adopted according to the needs of the current research. The selection of the categories in the checklist is based on major themes where direct statements about Russia, Russian people and culture appear in the textbook. The cultural content and the way in which it is presented in Kafe Piter are also compared to the intercultural competence objectives of the Common European Framework of Reference for Languages. Because the textbook was not written by a native Russian speaker, it was also important to investigate the types of mistakes found in the books. A simple quantitative analysis in the form of descriptive statistics was done, which consisted of counting the mistakes and inaccuracies in Kafe Piter. The mistakes were categorized into several different groups: factual or cultural, lexicosemantic, grammatical, spelling and punctuation mistakes. Based on the results, the cultural content of Kafe Piter provides a rich variety of cultural information that allows for a good understanding of the Russian language and Russian culture. A sufficient number of cross-cultural elements also appear in the textbook, including cultural images and information describing and comparing Russian and Finnish ways of life. Based on the cultural topics covered in Kafe Piter, we conclude that the textbook is in line with the intercultural competence objectives set out in the Common European Framework of Reference for Languages. The results of the study also make it clear that a thorough proofreading of Kafe Piter is needed in order to correct mistakes - more than 130 cultural and linguistic mistakes and inaccuracies appear in the textbook.

English L2 Learners’ Speech – And How the Spoken Language Course Affects Its Lexical Richness

Tässä sivuaineen tutkielmassa tarkasteltiin englannin kielen sanaston kehitystä lukion vieraan kielen syventävän suullisen kurssin aikana. Tutkimuksessa selvitettiin, miten oppilaiden sanastollinen rikkaus muuttuu puhutussa kielessä. Sanastollista rikkautta analysoitiin sanastollisen variaation ja sanastollisen tiheyden mittareilla. Työssä hyödynnettiin pitkittäistutkimusasetelmaa eli verrattiin yhden oppilasryhmän puhetta sekä ennen lukion englannin kielen suullista kurssia että sen jälkeen. Osanottajia oli yhteensä yhdeksän, jotka kaikki olivat lukion toisella vuosikurssilla. Osallistujien tekemät suulliset testit olivat osa Turun yliopiston keräämää tutkimuskäyttöön tarkoitettua materiaalia. Äänitteistä tehdyt transkriptiot muokattiin tätä tutkimusta varten sopiviksi, jonka jälkeen niistä mitattiin sanastollista rikkautta erilaisilla mittareilla. Aineistoa tutkittiin määrällisin menetelmin. Tulokset osoittavat, että keskimääräisesti sekä puheen sanastollinen variaatio että sanastollinen tiheys kehittyivät kurssin aikana hiukan. Toisin sanoen oppilaat käyttivät kurssin jälkeen tehdyssä testissä aavistuksen verran monipuolisempaa sanastoa, ja sisältösanojen osuus kieliopillisiin sanoihin nähden oli hieman suurempi kuin ennen kurssia. Kurssin aikana oppilaiden aktiivisessa sanavarastossa tapahtunut kehitys ei kuitenkaan ollut tilastollisesti merkitsevää. Lisäksi tutkimus osoitti, että osallistujien väliset erot olivat suuria, mutta erot tasoittuivat jonkin verran kurssin jälkeen. Tutkimustulosten perusteella voidaan olettaa englannin kielen suullisen kurssin sekä lisänneen oppilaiden sanastollista rikkautta että tasoittaneen yksilöllisiä eroja, yhdessä monien muiden mahdollisten tekijöiden kanssa. Tutkimusotoksen pienuuden vuoksi tuloksia ei kuitenkaan voida yleistää. Jatkossa olisi mielenkiintoista laajentaa tutkimusnäkökulmaa koskemaan muitakin sanastollisen rikkauden osa-alueita kuten sanastollista sofistikaatiota. Olisi myös mielenkiintoista sisällyttää tutkimukseen oppilaiden passsiivisen sanavaraston mittaaminen ja mahdollisesti tutkia englannin kielen suullisen kurssin vaikutuksia oppilaiden suullisen kielitaidon kehittymiseen laajemminkin kuin vain sanavaraston osalta.