Data analysis tools and methods for DNA microarray and high-throughput sequencing data

The recent rapid development of biotechnological approaches has enabled the production of large whole genome level biological data sets. In order to handle thesedata sets, reliable and efficient automated tools and methods for data processingand result interpretation are required. Bioinformatics, as the field of studying andprocessing biological data, tries to answer this need by combining methods and approaches across computer science, statistics, mathematics and engineering to studyand process biological data. The need is also increasing for tools that can be used by the biological researchers themselves who may not have a strong statistical or computational background, which requires creating tools and pipelines with intuitive user interfaces, robust analysis workflows and strong emphasis on result reportingand visualization. Within this thesis, several data analysis tools and methods have been developed for analyzing high-throughput biological data sets. These approaches, coveringseveral aspects of high-throughput data analysis, are specifically aimed for gene expression and genotyping data although in principle they are suitable for analyzing other data types as well. Coherent handling of the data across the various data analysis steps is highly important in order to ensure robust and reliable results. Thus,robust data analysis workflows are also described, putting the developed tools andmethods into a wider context. The choice of the correct analysis method may also depend on the properties of the specific data setandthereforeguidelinesforchoosing an optimal method are given. The data analysis tools, methods and workflows developed within this thesis have been applied to several research studies, of which two representative examplesare included in the thesis. The first study focuses on spermatogenesis in murinetestis and the second one examines cell lineage specification in mouse embryonicstem cells.

Remembering the War and Aggression: A Discourse Analysis of Japan’s State Apologies and Commemoration Speeches on August 15th 1995-2015

Memories of historical injustices affect contemporary politics from local to global level. In East Asia, questions of commemoration and historical responsibility have turned into international and domestic controversies. The main focus has been and still is in apologies conducted by Japanese prime ministers in regards to the war, aggression and colonialism during the era of Imperial Japan. Although it is granted that state apologies are not a crucial part of reconciliation, they can be analysed as a linked but separate process within the context of memory and international relations. The purpose of this study is to examine the discourses of history in Japanese prime ministers’ commemoration speeches on Memorial Ceremony for the War Dead from 1995 to 2015 in order to analyse how the Japanese government is reflecting on its past. In particular, attention is paid on what is being commemorated and how, whether it is the war and its victims or Japan’s post-war era of peace. As an apology is a reciprocal activity, responses from Japan’s most vocal former victims, South Korea and China, were also examined. Discourse analysis was used to identify and examine the different representations of the past. In addition, the apology statements of Japanese prime ministers were analysed in the Many to Many apology framework developed by Tavuchis (1991). Primary material consisted of 21 prime ministers’ speeches from the annual Memorial Ceremony for the War Dead on August 15th and from three apology statements made in 1995, 2005 and 2015. Further international context was primarily collected from newspaper articles of The New York Times and The Times throughout the examined period. It can be concluded from the findings that in the official Japanese remembrance of the past war from 1985’s annexation of Taiwan to the atomic bombings in 1945, both discourses that reinforce apology and remorse over Japan’s past aggressions and discourses that consciously avoid doing so are used. The commemoration speeches and apology statements consistently assert that Japan has acknowledged its past and expresses regret over the acts of aggression. At the same time, the speeches and statements strengthen the narrative that Japan was a victim of circumstances as well as turn the focus on post-war peace-making or on Japan’s own victimhood.

Opportunity Analysis and Category Management as a Base for Effective Indirect Sourcing

Hankintojen johtamisen kirjallisuus korostaa tehokkaan hankinnan olevan käypä keino tehostaa organisaation tulosta kokonaisvaltaisesti. Myös kasvava tietoisuus erityisesti epäsuorista hankintamenetelmistä ja työkaluista toimivat kannustimina tälle tutkimukselle. Tämän Pro Gradu -tutkimuksen päätarkoituksena on rakentaa kokonaisvaltainen ymmärrys epäsuorasta hankinnasta sekä löytää keinoja sen tehostamiseksi. Tutkimuksen tavoitteena on selvittää, miten globaali, monikansal- linen organisaatio voi parantaa kannattavuuttaan epäsuorissa hankinnoissa, sekä mitkä tekijät hankintastrategiassa vaikuttavat siihen. Tutkimus toteutettiin yksittäisenä tapaustutkimuksena suuren globaalin, monikan- sallisen yrityksen työntekijän näkökulmasta, Pääosa datasta pohjautuu vuonna 2015 toteutettuun Opportunity -analyysi projektiin, joka toteutettiin yhteistyössä ulkoisen konsulttifirman kanssa. Osa datasta pohjautuu puolistrukturoituihin haas- tatteluihin organisaation hankintajohtajan kanssa. Datan keruussa hyödynnettiin lisäksi henkilökohtaista havainnointia ja sekundääristä aineistoa organisaatiosta. Tämä Pro Gradu tutkimus on toteutettu kvalitatiivisella otteella, sisältäen joitakin kvantitatiivisia metodin piirteitä.