Grey literature, green open access: the BLDS Digital Library

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

Leveraging open access for integrating repository data at Indiana University Libraries

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

Open Access Button Workshop

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

Open Access Button

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

Open access and e-infrastructure

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

User-generated experiences: how automated platforms for content creation and sharing has transformed information access

Esitys KDK-käytettävyystyöryhmän järjestämässä seminaarissa: Miten käyttäjien toiveet haastavat metatietokäytäntöjämme? / How users' expectations challenge our metadata practices? 30.9.2014.

Open Access Subject Repositories – an Overview

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

Extended hydrogen photoproduction by nitrogen-fixing cyanobacteria

Cyanobacteria are the only prokaryotic organisms performing oxygenic photosynthesis. They comprise a diverse and versatile group of organisms in aquatic and terrestrial environments. Increasing genomic and proteomic data launches wide possibilities for their employment in various biotechnical applications. For example, cyanobacteria can use solar energy to produce H2. There are three different enzymes that are directly involved in cyanobacterial H2 metabolism: nitrogenase (nif) which produces hydrogen as a byproduct in nitrogen fixation; bidirectional hydrogenase (hox) which functions both in uptake and in production of H2; and uptake hydrogenase (hup) which recycles the H2 produced by nitrogenase back for the utilization of the cell. Cyanobacterial strains from University of Helsinki Cyanobacteria Collection (UHCC), isolated from the Baltic Sea and Finnish lakes were screened for efficient H2 producers. Screening about 400 strains revealed several promising candidates producing similar amounts of H2 (during light) as the ΔhupL mutant of Anabaena PCC 7120, which is specifically engineered to produce higher amounts of H2 by the interruption of uptake hydrogenase. The optimal environmental conditions for H2 photoproduction were significantly different between various cyanobacterial strains. All suitable strains revealed during screening were N2-fixing, filamentous and heterocystous. The top ten H2 producers were characterized for the presence and activity of the enzymes involved in H2 metabolism. They all possess the genes encoding the conventional nitrogenase (nifHDK1). However, the high H2 photoproduction rates of these strains were shown not to be directly associated with the maximum capacities of highly active nitrogenase or bidirectional hydrogenase. Most of the good producers possessed a highly active uptake hydrogenase, which has been considered as an obstacle for efficient H2 production. Among the newly revealed best H2 producing strains, Calothrix 336/3 was chosen for further, detailed characterization. Comparative analysis of the structure of the nif and hup operons encoding the nitrogenase and uptake hydrogenase enzymes respectively showed minor differences between Calothrix 336/3 and other N2-fixing model cyanobacteria. Calothrix 336/3 is a filamentous, N2-fixing cyanobacterium with ellipsoidal, terminal heterocysts. A common feature of Calothrix 336/3 is that the cells readily adhere to substrates. To make use of this feature, and to additionally improve H2 photoproduction capacity of the Calothrix 336/3 strain, an immobilization technique was applied. The effects of immobilization within thin alginate films were evaluated by examining the photoproduction of H2 of immobilized Calothrix 336/3 in comparison to model strains, the Anabaena PCC 7120 and its ΔhupL mutant. In order to achieve optimal H2 photoproduction, cells were kept under nitrogen starved conditions (Ar atmosphere) to ensure the selective function of nitrogenase in reducing protons to H2. For extended H2 photoproduction, cells require CO2 for maintenance of photosynthetic activity and recovery cycles to fix N2. Application of regular H2 production and recovery cycles, Ar or air atmospheres respectively, resulted in prolongation of H2 photoproduction in both Calothrix 336/3 and the ΔhupL mutant of Anabaena PCC 7120. However, recovery cycles, consisting of air supplemented with CO2, induced a strong C/N unbalance in the ΔhupL mutant leading to a decrease in photosynthetic activity, although total H2 yield was still higher compared to the wild-type strain. My findings provide information about the diversity of cyanobacterial H2 capacities and mechanisms and provide knowledge of the possibilities of further enhancing cyanobacterial H2 production.

Liber & Open Access

Seminaariesitys Avoimen tieteen kansainvälinen tilannekuva 2015 -seminaarissa Helsingissä 13.4.2015.

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.

Initialization of Continuous Nonlinear Models Using Extended Kalman Filter

The two main objectives of Bayesian inference are to estimate parameters and states. In this thesis, we are interested in how this can be done in the framework of state-space models when there is a complete or partial lack of knowledge of the initial state of a continuous nonlinear dynamical system. In literature, similar problems have been referred to as diffuse initialization problems. This is achieved first by extending the previously developed diffuse initialization Kalman filtering techniques for discrete systems to continuous systems. The second objective is to estimate parameters using MCMC methods with a likelihood function obtained from the diffuse filtering. These methods are tried on the data collected from the 1995 Ebola outbreak in Kikwit, DRC in order to estimate the parameters of the system.

Making it viable - enabling Open Access for Finnish scholarly journals

Poster at the CERN Workshop on Innovations in Scholarly Communication (OAI9), Geneva, June 17-19, 2015.