Multi-source ingestion of publisher articles - The SCOAP3 repository experience

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Open Repository Theseus – Success Story of 24 Finnish Universities of Applied Sciences

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Repository sustainability

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Practical Data Curation and Management for Institutional Repositories

Workshop at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

HIMALDOC: A Tool for a Regional Open Repository on Sustainable Mountain Development Issues in the Hindu Kush Himalaya

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Let's do data research work: the creation of a portal with research information from Catalan Universities

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Managing open access workflows at the University of St Andrews: challenges and Pathfinder solutions

Presentation of Janet Aucock, at the FinELib Consortium Seminar (Aineistopäivä), April 16, 2015 in Helsinki.

Cardiovascular health from childhood to adulthood – with special reference to early vascular changes. The Cardiovascular Risk in Young Finns Study

Background: Recent recommendations aim to improve cardiovascular health (CVH) by encouraging the general population to meet positive and modifiable ideal CVH metrics: not smoking, being physically active, and maintaining normal weight, blood pressure, blood glucose and total cholesterol levels and a healthy diet. Aims: The aim of the present study was to report the prevalence of ideal CVH in children and young adults and study the associations of CVH metrics with markers of subclinical atherosclerosis. Participants and methods: The present thesis is part of the Cardiovascular Risk in Young Finns Study (Young Finns Study). Data on associations of CVH metrics and subclinical atherosclerosis were available from 1,898 Young Finns Study participants. In addition, joint analyses were performed combining data from the International Childhood Cardiovascular Cohort (i3C) Consortium member studies from Australia and the USA. Results: None of the participants met all 7 CVH metrics and thus had ideal CVH in childhood and only 1% had ideal CVH as young adults. The number of CVH metrics present in childhood and adulthood predicted lower carotid artery intima-media thickness, improved carotid artery distensibility and lower risk of coronary artery calcification. Those who improved their CVH status from childhood to adulthood had a comparable risk of subclinical atherosclerosis to participants who had always had a high CVH status. Conclusions: Ideal CVH proved to be rare among children and young adults. A higher number of ideal CVH metrics and improvement of CVH status between childhood and adulthood predicted a lower risk of subclinical atherosclerosis.

Identification of characteristics for successful university-company partnership development

The importance of university-company collaboration has increased during the last decades. The drivers for that are, on the one hand, changes in business logic of companies and on the other hand the decreased state funding of universities. Many companies emphasize joint research with universities as an enabling input to their development processes, which aim at creating new innovations, products and wealth. These factors have changed universities’ operations and they have adopted several practices of dynamic business organizations, such as strategic planning, monitoring and controlling methods of internal processes etc. The objective of this thesis is to combine different characteristics of successful university-company partnership and its development. The development process starts with identifying potential partners in the university’s interest group, which requires understanding the role of different partners in the innovation system. Next, in order to find a common development basis, matching the policy and strategy between partners is needed. The third phase is to combine the academic and industrial objectives of a joint project, which is a typical form of university-company collaboration. The optimum is a win-win situation where both partners, universities and companies, can get addedvalue. For the companies added value typically means access to new research results before their competitors. For the universities added value offers a possibility to carry on high level scientific work. The research output in the form of published scientific articles is evaluated by the international science community. Because the university-company partnership is often executed by joint projects, the different forms of this kind of projects is discussed in this study. The most challenging form of collaboration is a semi-open project model, which is not based on bilateral activities between universities and companies but on a consortium of several universities, research institutes and companies. The universities and companies are core actors in the innovation system. Thus the discussion of their roles and relations to public operators like publicly funded financiers is important. In the Finnish innovation system there are at least the following doers executing strategies and policies: EU, Academy of Finland and TEKES. In addition to these, Strategic Centres for Science, Technology and Innovation which are owned jointly by companies, universities and research organizations have a very important role in their fields of business. They transfer research results into commercial actions to generate wealth. The thesis comprises two parts. The first part consists of an overview of the study including introduction, literature review, research design, synthesis of findings and conclusions. The second part introduces four original research publications.

Expression of neuronal nitric oxide synthase in the hippocampal formation in affective disorders

Hippocampal output is increased in affective disorders and is mediated by increased glutamatergic input via N-methyl-D-aspartate (NMDA) receptor and moderated by antidepressant treatment. Activation of NMDA receptors by glutamate evokes the release of nitric oxide (NO) by the activation of neuronal nitric oxide synthase (nNOS). The human hippocampus contains a high density of NMDA receptors and nNOS-expressing neurons suggesting the existence of an NMDA-NO transduction pathway which can be involved in the pathogenesis of affective disorders. We tested the hypothesis that nNOS expression is increased in the human hippocampus from affectively ill patients. Immunocytochemistry was used to demonstrate nNOS-expressing neurons in sections obtained from the Stanley Consortium postmortem brain collection from patients with major depression (MD, N = 15), bipolar disorder (BD, N = 15), and schizophrenia (N = 15) and from controls (N = 15). nNOS-immunoreactive (nNOS-IR) and Nissl-stained neurons were counted in entorhinal cortex, hippocampal CA1, CA2, CA3, and CA4 subfields, and subiculum. The numbers of Nissl-stained neurons were very similar in different diagnostic groups and correlated significantly with the number of nNOS-IR neurons. Both the MD and the BD groups had greater number of nNOS-IR neurons/400 µm² in CA1 (mean ± SEM: MD = 9.2 ± 0.6 and BD = 8.4 ± 0.6) and subiculum (BD = 6.7 ± 0.4) when compared to control group (6.6 ± 0.5) and this was significantly more marked in samples from the right hemisphere. These changes were specific to affective disorders since no changes were seen in the schizophrenic group (6.7 ± 0.8). The results support the current view of the NMDA-NO pathway as a target for the pathophysiology of affective disorders and antidepressant drug development.

Isolation and characterization of bacterial strains with a hydrolytic profile with potential use in bioconversion of agroindustial by-products and waste

There is a trend towards the use of novel technologies nowadays, mainly focused on biological processes, for recycling and the efficient utilization of organic residues that can be metabolized by different microorganisms as a source of energy. In the present study the isolation of bacterial strains from six different agro-industrial by-products and waste was performed with the objective of evaluating their hydrolytic capacities and suitability for use in bioconversion of specific substrates. The 34 isolated strains were screened in specific culture media for the production of various hydrolytic enzymes (lipase, protease, cellulase, and amylase). It was found that 28 strains exhibited proteolytic activity, 18 had lipolytic activity, 13 had caseinolytic activity, 15 had amylolytic activity, and 11 strains exhibited cellulolytic activity. The strains that showed the highest hydrolytic capacities with biotechnological potential were selected, characterized genotipically, and identified as Bacillus, Serratia, Enterococcus, Klebsiella, Stenotrophomonas, Lactococcus, and Escherichia genera. It was concluded that the strain isolates have a high potential for use in the bioconversion of agro-industrial waste, both as a pure culture and as a microbial consortium.

Lohkoketjuteknologian soveltaminen finanssisektorille

Tämän kandidaatintutkielman tarkoituksena on tutkia, miten lohkoketjuteknologiaa voi soveltaa finanssisektorille. Tutkimus tarjoaa yleiskuvan lohkoketjuteknologista, sekä sen sovelluskohteista finanssisektorilla. Tutkimusmenetelmä on kvalitatiivinen ja se toteutettiin haastattelemalla pankkeja, jotka osallistuvat Distributed Ledger Group (DLG)-konsortioon. Kyseinen konsortio pyrkii 42 pankin ja R3cev nimisen yrityksen välisessä yhteistyössä soveltamaan lohkoketjuteknologiaa pankkisektorille. Haastattelujen perusteella pankit pitävät lohkoketjuteknologian potentiaalia pitkällä aikavälillä suurena. Erityisesti lohkoketjuteknologian odotetaan laskevan kustannuksia, sekä nopeuttavan toimintoja useiden eri tuotteiden kohdalla. Pelkästään pankkisektorilla tutkitaan tällä hetkellä kymmeniä eri sovelluskohteita. Ennen kuin lohkoketjulla voidaan nähdä kaupallista toimintaa, tulee haasteita ylittää sekä teknisellä, että säädännöllisellä puolella. Vielä on liian varhaista arvioida, milloin lohkoketjuteknologiaa tullaan soveltamaan laajemmin finanssisektorilla. Pankkien oma tutkimus aiheesta oli vielä suhteellisen varhaisessa vaiheessa. Lohkoketjuteknologian potentiaali voidaan nähdä tutkimuksen perusteella valtavan suurena. Vielä on kuitenkin vaikea arvioida tullaanko tähän potentiaaliin tulevaisuudessa yltämään. Finanssisektorilla on monia toimijoita, jotka tutkivat lohkoketjuteknologiaa ja se vauhdittaa kehitystä. Lohkoketjuteknologia saattaa tulevaisuudessa mullistaa monia finanssisektorin osa-alueita tai jopa korvata ne kokonaan.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

Proteolytic processing of the CUX1 transcription factor generates an isoform, p110 that accelerates entry into S phase. To identify targets of p110 CUX1 that are involved in cell cycle progression, we performed genome-wide location analysis using a promoter microarray. Since there are no antibodies that specifically recognize p110, but not the full-length protein, we expressed physiological levels of a p110 isoform with two tags and purified chromatin by tandem affinity purification (ChAP). Conventional ChIP performed on synchronized populations of cells confirmed that p110 CUX1 is recruited to the promoter of cell cycle-related targets preferentially during S phase. Multiple approaches including silencing RNA (siRNA), transient infection with retroviral vectors, constitutive expression and reporter assays demonstrated that most cell cycle targets are activated whereas a few are repressed or not affected by p110 CUX1. Functional classes that were over-represented among targets included DNA replication initiation. Consistent with this finding, constitutive expression of p110 CUX1 led to a premature and more robust induction of replication genes during cell cycle progression, and stimulated the long-term replication of a plasmid bearing the oriP replicator of Epstein Barr virus (EBV).

Encapsulation de Dehalococcoides: avantage pour la déhalogénation des solvants chlorés en sites contaminés

Le tétrachloroéthène (PCE) et les éthènes chlorés qui lui sont apparentés ont été abondamment utilisés pour plusieurs applications en industrie dès le début du 20e siècle. Ils sont cependant comptés parmi les polluants les plus communs des sols et de l’eau et beaucoup d’efforts sont déployés afin de les éliminer. Nous croyons que la conversion des éthènes chlorés en éthènes par des microorganismes est une solution prometteuse. Le premier aspect du projet visait donc à établir les conditions pour lesquelles un consortium enrichi en Dehalococcoides ethenogenes permettrait la conversion complète de PCE en éthène. Les expériences réalisées nous ont permis de souligner le rôle de l’acide lactique ajouté aux cultures comme source de carbone et source indirecte d’électrons pour la déhalorespiration. Nous avons également pu établir l’effet de la concentration initiale de biomasse dans les cultures sur le profil de déhalogénation du PCE. Le deuxième aspect du projet visait à développer un protocole d’encapsulation du consortium dans une matrice polymérique afin de profiter des nombreux avantages potentiels de l’encapsulation. Nous avons testé trois montages d’encapsulation différents : atomisation avec jet d’air, atomisation avec vibrations ultrasoniques et « drop-wise ». Le dernier montage prévoyait l’encapsulation des cultures dans des billes d’alginate enrobées de chitosane gélifié par du lignosulfonate. C’est le seul montage qui nous a permis d’encapsuler le consortium de façon efficace sans effet significatifs négatifs sur son activité de déchlorination. Aussi, la comparaison des profils de déhalogénation du PCE de cellules encapsulées et cellules libres a montré une plus faible accumulation de TCE, 1,2-DCE et VC dans les échantillons de cellules encapsulée et, par conséquent, une conversion plus rapide et plus complète du PCE en éthène. Finalement, nous avons observé une tendance favorable à l’idée que les microorganismes encapsulés bénéficient d’un effet de protection contre de faibles concentrations d’oxygène.

Performances de la puce exon et son application dans l’analyse de l’épissage alternatif associé à la métastase du cancer de sein

Nous montrons l’utilisation de la puce exon d’Affymetrix pour l’analyse simultanée de l’expression des gènes et de la variation d’isoformes. Nous avons utilisé les échantillons d’ARN du cerveau et des tissus de référence qui ont été antérieurement utilisés dans l’étude du consortium MicroArray Quality Control (MAQC). Nous démontrons une forte concordance de la quantification de l’expression des gènes entre trois plateformes d’expression populaires à savoir la puce exon d’Affymetrix, la puce Illumina et la puce U133A d’Affymetrix. Plus intéressant nous montrons que la majorité des discordances entre les trois plateformes résulterait des positions différentes des sondes à travers les plateformes et que les variations d’isoforme exactes ne peuvent être identifiées que par la puce exon. Nous avons détecté avec succès, entre les tissus de référence et ceux du cerveau, une centaine de cas d’évènements d’épissage alternatif. La puce exon est requise dans l’analyse de l’épissage alternatif associé aux pathologies telles que les cancers et les troubles neurologiques. Comme application de cette technologie, nous avons analysé les variations d’épissage dans la métastase du cancer de sein développé dans le model de la souris. Nous avons utilisé une gamme bien définie de trois lignées de tumeur mammaire ayant différents potentiels métastatiques. Par des analyses statistiques, nous avons répertorié 2623 transcripts présentant des variations d’expression et d’isoformes entre les types de tumeur. Une analyse du réseau de gènes montre qu’environ la moitié d’entre eux est impliquée dans plusieurs activités cellulaires, ainsi que dans nombreux cancers et désordres génétiques.