Study of ligand-based virtual screening tools in computer-aided drug design

Virtual screening is a central technique in drug discovery today. Millions of molecules can be tested in silico with the aim to only select the most promising and test them experimentally. The topic of this thesis is ligand-based virtual screening tools which take existing active molecules as starting point for finding new drug candidates. One goal of this thesis was to build a model that gives the probability that two molecules are biologically similar as function of one or more chemical similarity scores. Another important goal was to evaluate how well different ligand-based virtual screening tools are able to distinguish active molecules from inactives. One more criterion set for the virtual screening tools was their applicability in scaffold-hopping, i.e. finding new active chemotypes. In the first part of the work, a link was defined between the abstract chemical similarity score given by a screening tool and the probability that the two molecules are biologically similar. These results help to decide objectively which virtual screening hits to test experimentally. The work also resulted in a new type of data fusion method when using two or more tools. In the second part, five ligand-based virtual screening tools were evaluated and their performance was found to be generally poor. Three reasons for this were proposed: false negatives in the benchmark sets, active molecules that do not share the binding mode, and activity cliffs. In the third part of the study, a novel visualization and quantification method is presented for evaluation of the scaffold-hopping ability of virtual screening tools.

Fraktioinnin tehostaminen lajittelussa

Painelajittimet ovat yleisimpiä hiokkeen lajitteluun käytettyjä lajittimia. Painelajittimien suorituskyky on parantunut viimeisten vuosikymmenien aikana niin paljon, että pyörrepuhdistuksesta on pääosin voitu luopua osana hiokkeen lajittelua. Painelajittimen erinomaisuus perustuu siihen, että sillä voidaan erottaa massasta hyvinkin erilaisia epäpuhtauksia. Nykyään vallitsevia painelajittelun trendejä ovat sakeuden nosto, energiankulutuksen vähentäminen sekä eri fraktioiden erottumisen tehostuminen. Kaikilla pyritään vähentämään vedenkäyttöä ja parantamaan massan ominaisuuksia jatkoprosesseja silmälläpitäen. Tässä työssä tarkasteltiin painelajittimen roottorin kierrosnopeuden vaikutusta akseptimassan laatuun. Luodaan malli freeness-pudotukselle lajittimen yli. Sekä tarkastellaan myös automaatioon pohjautuvan säädön käyttöönottoa lajittimen akseptimassan freenesvaihteluiden tasaamiseksi. Toisaalta tehdään myös suppea selvitys lajittimien energiankulutuksista erilaisilla roottorin pyörimisnopeuksilla. Tuotantokäytössä oleviin lajittimiin asennettujen invertterisäätöjen ja koepisteistä saatujen tulosten avulla voidaan todeta, että laskemalla roottorin pyörimisnopeutta voidaan lajittimessa tapahtuvaa freenespudotusta kasvattaa. Samalla saavutetaan hyötyjä myös muissa massan ominaisuuksissa, kuten vetolujuudessa. Automaattisäädön käyttöönotolla saavutetaan huomattavasti pienempi hajonta akseptimassan freeneksessä. Rejektilinjan lajittimissa hajonta lähes puolittui ja päälinjan lajittimissa päästiin noin kolmanneksen parannukseen. Energian kulutuksia tutkittaessa huomataan, että roottorin kierrosnopeutta alentamalla voidaan merkittävästi vähentää lajittimien energian kulutusta. Parhaassa tapauksessa voidaan säästää neljännes lajittelun energiakustannuksissa.

Country Risk and Market Reactions to Earnings Announcements: Evidence from Finnish Stock Markets

The objective of this thesis is to examine the market reaction around earnings announcements in Finnish stock markets. The aim is to find out whether the extreme market conditions during the financial crisis are reflected in stock prices as a stronger reaction. In addition to this, the purpose is to investigate how extensively Finnish listed companies report the country segmentation of revenues in their interim reports and whether the country risk is having a significant impact on perceived market reaction. The sample covers all companies listed in Helsinki stock exchange at 1.1.2010 and these companies’ interim reports from the first quarter of 2008 to last quarter of 2009. Final sample consists of 81 companies and 630 firm-quarter observations. The data sample has been divided in two parts, of which country risk sample contains 17 companies and 127 observations and comparison sample covers 66 companies and 503 observations. Research methodologies applied in this thesis are event study and cross-sectional regression analysis. Empirical results indicate that the market reaction occurs mainly during the announcement day and is slightly stronger in case of positive earnings surprises than the reactions observed in previous studies. In case of negative earnings surprises no significant differences can be observed. In case of country risk sample and negative earnings surprise market reaction is negative already in advance of the disclosure contrary to comparison sample. In case of positive surprise no differences can be observed. Country risk variable developed during this study seems to explain only minor part of the market reaction.

Effects of stock splits on stock returns: An event study of Finnish companies

Tämän kandidaatintyön tavoitteena on tutkia osakkeen nimellisarvon jakamisen vaikutusta osakkeen markkina-arvoon Suomessa vuosina 1996-2007. Ilmiötä tarkastellaan tapahtumatutkimusmenetelmän avulla ja lopullinen tutkittavien osakesplittien määrä on 38. Tutkimuksessa ei löydetty epänormaaleja tuottoja splittien julkistushetkellä, joten tämän aineiston mukaan sijoittajat eivät pitäneet sitä johdolta tulevana positiivisena signaalina. Sitä vastoin tutkimuksessa löydettiin positiivinen kurssimuutos niiden osakkeiden kohdalla, jolloin pörssiyhtiö ilmoitti splitin ohella myös osingonjaostaan.

The Effect of Dividend Yield to Stocks’ Performance on Bullish and Bearish Finnish Stock Market

This study examines the relationship between dividend yield and stock return over bullish and bearish Finnish stock market by testing for alpha and beta shifts across bull and bear markets. In addition, this study examines if various factors, such as a standard deviation of dividends, firm size and profitability have an effect on the size, of the firms’ dividends and systematic risk of the stocks. We divide stocks into five portfolios on the basis of their past average dividend yields and investigate if the highest yielding portfolios outperform the lowest yielding portfolios during the different market conditions. As a result, high yielding stocks were most stable during the examination period and offered downside protection on bear markets. However, a strategy of forming portfolios with past dividend yields led to negative alphas even in bull markets. Standard deviation of dividends, firm size and profitability were found to have no effect on the size of dividends and systematic risk of the stocks.

Identifying first graders at risk of reading and writing difficulties : creating a group-based screening tool in kiswahili in Tanzania

Early identification of beginning readers at risk of developing reading and writing difficulties plays an important role in the prevention and provision of appropriate intervention. In Tanzania, as in other countries, there are children in schools who are at risk of developing reading and writing difficulties. Many of these children complete school without being identified and without proper and relevant support. The main language in Tanzania is Kiswahili, a transparent language. Contextually relevant, reliable and valid instruments of identification are needed in Tanzanian schools. This study aimed at the construction and validation of a group-based screening instrument in the Kiswahili language for identifying beginning readers at risk of reading and writing difficulties. In studying the function of the test there was special interest in analyzing the explanatory power of certain contextual factors related to the home and school. Halfway through grade one, 337 children from four purposively selected primary schools in Morogoro municipality were screened with a group test consisting of 7 subscales measuring phonological awareness, word and letter knowledge and spelling. A questionnaire about background factors and the home and school environments related to literacy was also used. The schools were chosen based on performance status (i.e. high, good, average and low performing schools) in order to include variation. For validation, 64 children were chosen from the original sample to take an individual test measuring nonsense word reading, word reading, actual text reading, one-minute reading and writing. School marks from grade one and a follow-up test half way through grade two were also used for validation. The correlations between the results from the group test and the three measures used for validation were very high (.83-.95). Content validity of the group test was established by using items drawn from authorized text books for reading in grade one. Construct validity was analyzed through item analysis and principal component analysis. The difficulty level of most items in both the group test and the follow-up test was good. The items also discriminated well. Principal component analysis revealed one powerful latent dimension (initial literacy factor), accounting for 93% of the variance. This implies that it could be possible to use any set of the subtests of the group test for screening and prediction. The K-Means cluster analysis revealed four clusters: at-risk children, strugglers, readers and good readers. The main concern in this study was with the groups of at-risk children (24%) and strugglers (22%), who need the most assistance. The predictive validity of the group test was analyzed by correlating the measures from the two school years and by cross tabulating grade one and grade two clusters. All the correlations were positive and very high, and 94% of the at-risk children in grade two were already identified in the group test in grade one. The explanatory power of some of the home and school factors was very strong. The number of books at home accounted for 38% of the variance in reading and writing ability measured by the group test. Parents´ reading ability and the support children received at home for schoolwork were also influential factors. Among the studied school factors school attendance had the strongest explanatory power, accounting for 21% of the variance in reading and writing ability. Having been in nursery school was also of importance. Based on the findings in the study a short version of the group test was created. It is suggested for use in the screening processes in grade one aiming at identifying children at risk of reading and writing difficulties in the Tanzanian context. Suggestions for further research as well as for actions for improving the literacy skills of Tanzanian children are presented.

High-Throughput Screening for Novel Prostate Cancer Drug Targets –Getting Personal

Prostate cancers form a heterogeneous group of diseases and there is a need for novel biomarkers, and for more efficient and targeted methods of treatment. In this thesis, the potential of microarray data, RNA interference (RNAi) and compound screens were utilized in order to identify novel biomarkers, drug targets and drugs for future personalized prostate cancer therapeutics. First, a bioinformatic mRNA expression analysis covering 9873 human tissue and cell samples, including 349 prostate cancer and 147 normal prostate samples, was used to distinguish in silico prevalidated putative prostate cancer biomarkers and drug targets. Second, RNAi based high-throughput (HT) functional profiling of 295 prostate and prostate cancer tissue specific genes was performed in cultured prostate cancer cells. Third, a HT compound screen approach using a library of 4910 drugs and drug-like molecules was exploited to identify potential drugs inhibiting prostate cancer cell growth. Nine candidate drug targets, with biomarker potential, and one cancer selective compound were validated in vitro and in vivo. In addition to androgen receptor (AR) signaling, endoplasmic reticulum (ER) function, arachidonic acid (AA) pathway, redox homeostasis and mitosis were identified as vital processes in prostate cancer cells. ERG oncogene positive cancer cells exhibited sensitivity to induction of oxidative and ER stress, whereas advanced and castrate-resistant prostate cancer (CRPC) could be potentially targeted through AR signaling and mitosis. In conclusion, this thesis illustrates the power of systems biological data analysis in the discovery of potential vulnerabilities present in prostate cancer cells, as well as novel options for personalized cancer management.

Added Value of Combining Value and Momentum Indicators in the Swiss Stock Market

The purpose of the thesis is to examine the added value of combining value and momentum indicators in the Swiss stock exchange. Value indicators employed are P/E, EV/EBITDA, P/CF, P/B ja P/S. Momentum indicators examined are 52-week high, acceleration rate, 12-month past return and 6-month past return. The thesis examines whether the composite value measures based on the above mentioned ratios can add value and whether the inclusion of momentum can further improve the risk return profile of the value portfolios. The data is gathered from the Swiss equity market during the sample period from May 2001 to May 2011. Previous studies have shown that composite value measures can somewhat add value to the value portfolio strategy. Similarly, recent academic literature have found evidence that momentum works well as a timing indicator for time to entry to value stocks. This study indicates that the added value of composite value measures exists. It also shows that momentum combined to acceleration rate can significantly improve the risk adjusted performance of value-only portfolios.

Stock Repurchase Authorizations - Finnish Companies

The aim of this study is to examine the abnormal market reaction caused by share repurchase authorizations. We study this abnormal reaction from five different angles. First four concentrate on average abnormal returns while the fifth concentrates on cumulative abnormal return. Data consists of 508 share repurchase authorization from Finnish stock market. Event study methodology is used to examine the stock price reaction and regression analysis is used to find correlation between actual buybacks and abnormal returns. The empirical results show that markets do usually react positively to share repurchase authorizations. There are some differences depending which of the five angles the abnormal returns are being examined. Statistically we can confirm that some authorization give positive reaction while others do not. Also we didn’t find a statistically significant positive correlation between actual buybacks and abnormal returns.

Performance Comparison of Behavioral Finance -based Investment Strategies in the Finnish Stock Market 1996-2010

In this thesis traditional investment strategies (value and growth) are compared to modern investment strategies (momentum, contrarian and GARP) in terms of risk, performance and cumulative returns. Strategies are compared during time period reaching from 1996 to 2010 in the Finnish stock market. Used data includes all listed main list stocks, dividends and is adjusted in case of splits, and mergers and acquisitions. Strategies are tested using different holding periods (6, 12 and 36 months) and data is divided into tercile portfolios based on different ranking criteria. Contrarian and growth strategies are the only strategies with improved cumulative returns when longer holding periods are used. Momentum (52-week high price1) and GARP strategies based on short holding period have the best performance and contrarian and growth strategies the worst. Momentum strategies (52-week high price) along with short holding period contrarian strategies (52-week low price2) have the lowest risk. Strategies with the highest risk are both growth strategies and two momentum strategies (52-week low price). The empirical results support the efficiency of momentum, GARP and value strategies. The least efficient strategies are contrarian and growth strategies in terms of risk, performance and cumulative returns. Most strategies outperform the market portfolio in all three measures. 1 Stock ranking criterion (current price/52-week highest price) 2 Stock ranking criterion (current price/52-week lowest price)