Bridge over troubled water - using the CRIS in building Open Access infrastructures

Presentation at the Nordic Perspectives on Open Access and Open Science seminar, Helsinki, October 15, 2013

Open Access at the Nordic Council of Ministers

Presentation at the Nordic Perspectives on Open Access and Open Science seminar, Helsinki, October 15, 2013

Do Open Access journals qualify?

Presentation at the Nordic Perspectives on Open Access and Open Science seminar, Helsinki, October 15, 2013

Identification of research trends in the field of separation processes. Application of epidemiological model, citation analysis, text mining, and technical analysis of the financial markets

Choice of industrial development options and the relevant allocation of the research funds become more and more difficult because of the increasing R&D costs and pressure for shorter development period. Forecast of the research progress is based on the analysis of the publications activity in the field of interest as well as on the dynamics of its change. Moreover, allocation of funds is hindered by exponential growth in the number of publications and patents. Thematic clusters become more and more difficult to identify, and their evolution hard to follow. The existing approaches of research field structuring and identification of its development are very limited. They do not identify the thematic clusters with adequate precision while the identified trends are often ambiguous. Therefore, there is a clear need to develop methods and tools, which are able to identify developing fields of research. The main objective of this Thesis is to develop tools and methods helping in the identification of the promising research topics in the field of separation processes. Two structuring methods as well as three approaches for identification of the development trends have been proposed. The proposed methods have been applied to the analysis of the research on distillation and filtration. The results show that the developed methods are universal and could be used to study of the various fields of research. The identified thematic clusters and the forecasted trends of their development have been confirmed in almost all tested cases. It proves the universality of the proposed methods. The results allow for identification of the fast-growing scientific fields as well as the topics characterized by stagnant or diminishing research activity.

Genetic variability among Commelina weed species from the states of Paraná and São Paulo, Brazil

This work aims to carry out a comparative analysis using RAPD molecular markers in four Commelina weed species from the state of Paraná and C. benghalensis populations from the states of Paraná and São Paulo, Brazil. The genomic plant DNA sample was extracted from the leaves, separated, randomly fragmented and amplified by PCR. Random amplified polymorphic DNA fragments (RAPD markers) were analyzed by using POPGENE statistical program. Eighty-five primer sequences were tested but only three were suitable as molecular markers producing 37 DNA polymorphic fragments for comparisons among four Commelina species and 22 polymorphic fragments for comparisons among C. benghalensis populations. The results showed that there were inter-specific and intra-specific genetic variabilities among Commelina plant genera. Genetic diversity analysis between species indicated four mono-specific clusters and it was suggested to keep C. villosa as one species. Regarding the intra-specific genetic variability of C. benghalensis alone, three groups were verified, although there were 13 populations from two geographical areas. However, these clusters do not correspond to the distinct characteristics verified.

Growth of the crabgrass species Digitaria ciliaris and Digitaria nuda

The aim of this research paper was to compare the growth of D. ciliaris and D. nuda crabgrass species under non-competitive conditions. To this end, two experiments were conducted, one from March - July 2010 and the other from February - June 2011. The experimental design of both trials was completely randomized making a factorial (2 seasons x 2 species crabgrass x 12 evaluation periods) with four replications. Assessments began at 15 days after sowing (DAS), and repeated weekly until 92 DAS. The variables evaluated were total dry matter (roots+leaves+stems), leaf area, leaf number and tiller. The results were submitted to analysis of variance and the absolute growth rate, relative growth rate and leaf area ratio were calculated using the means, which were adjusted regression models. The crabgrass species were significantly different in leaf area, leaf number, tiller number and dry matter per plant. D. ciliaris for all variables was statistically higher than D. nuda. Regarding the speed at which the growth of the species occurred, the absolute growth rate and relative growth rate of D. ciliaris was also greater than D. nuda. In addition, D. ciliaris also had a lower leaf area ratio indicating greater efficiency in converting light energy into carbohydrates. It can be concluded that D. ciliaris has a higher growth rate in conditions where there is no limitation of nutrients and water availability in relation to D. nuda, mainly due to D. ciliaris have greater leaf area, number of leaves and dry matter accumulation per plant.

Making the impact on research and society : a case study: crowdsourcing solutions developed for the linguistic research and citizen science

Can crowdsourcing solutions serve many masters? Can they be beneficial for both, for the layman or native speakers of minority languages on the one hand and serious linguistic research on the other? How did an infrastructure that was designed to support linguistics turn out to be a solution for raising awareness of native languages? Since 2012 the National Library of Finland has been developing the Digitisation Project for Kindred Languages, in which the key objective is to support a culture of openness and interaction in linguistic research, but also to promote crowdsourcing as a tool for participation of the language community in research. In the course of the project, over 1,200 monographs and nearly 111,000 pages of newspapers in Finno-Ugric languages will be digitised and made available in the Fenno-Ugrica digital collection. This material was published in the Soviet Union in the 1920s and 1930s, and users have had only sporadic access to the material. The publication of open-access and searchable materials from this period is a goldmine for researchers. Historians, social scientists and laymen with an interest in specific local publications can now find text materials pertinent to their studies. The linguistically-oriented population can also find writings to delight them: (1) lexical items specific to a given publication, and (2) orthographically-documented specifics of phonetics. In addition to the open access collection, we developed an open source code OCR editor that enables the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary since these rare and peripheral prints often include already archaic characters, which are neglected by modern OCR software developers but belong to the historical context of kindred languages, and are thus an essential part of the linguistic heritage. When modelling the OCR editor, it was essential to consider both the needs of researchers and the capabilities of lay citizens, and to have them participate in the planning and execution of the project from the very beginning. By implementing the feedback iteratively from both groups, it was possible to transform the requested changes as tools for research that not only supported the work of linguistics but also encouraged the citizen scientists to face the challenge and work with the crowdsourcing tools for the benefit of research. This presentation will not only deal with the technical aspects, developments and achievements of the infrastructure but will highlight the way in which user groups, researchers and lay citizens were engaged in a process as an active and communicative group of users and how their contributions were made to mutual benefit.

Repository and its place at the University of Pardubice

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

‘Just how (re)usable is Research Data? A legal perspective’ - A poster summarizing the recommendations of the OpenAIRE legal and licensing study.

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

Implementing Widely-used Vocabularies to Produce Linked Open Data in the Context of Open Repositories

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

Open innovation model for a large company in the ICT industry: Case Ericsson LMF

Open innovation paradigm states that the boundaries of the firm have become permeable, allowing knowledge to flow inwards and outwards to accelerate internal innovations and take unused knowledge to the external environment; respectively. The successful implementation of open innovation practices in firms like Procter & Gamble, IBM, and Xerox, among others; suggest that it is a sustainable trend which could provide basis for achieving competitive advantage. However, implementing open innovation could be a complex process which involves several domains of management; and whose term, classification, and practices have not totally been agreed upon. Thus, with many possible ways to address open innovation, the following research question was formulated: How could Ericsson LMF assess which open innovation mode to select depending on the attributes of the project at hand? The research followed the constructive research approach which has the following steps: find a practical relevant problem, obtain general understanding of the topic, innovate the solution, demonstrate the solution works, show theoretical contributions, and examine the scope of applicability of the solution. The research involved three phases of data collection and analysis: Extensive literature review of open innovation, strategy, business model, innovation, and knowledge management; direct observation of the environment of the case company through participative observation; and semi-structured interviews based of six cases involving multiple and heterogeneous open innovation initiatives. Results from the cases suggest that the selection of modes depend on multiple reasons, with a stronger influence of factors related to strategy, business models, and resources gaps. Based on these and others factors found in the literature review and observations; it was possible to construct a model that supports approaching open innovation. The model integrates perspectives from multiple domains of the literature review, observations inside the case company, and factors from the six open innovation cases. It provides steps, guidelines, and tools to approach open innovation and assess the selection of modes. Measuring the impact of open innovation could take years; thus, implementing and testing entirely the model was not possible due time limitation. Nevertheless, it was possible to validate the core elements of the model with empirical data gathered from the cases. In addition to constructing the model, this research contributed to the literature by increasing the understanding of open innovation, providing suggestions to the case company, and proposing future steps.

Holstein white coat color and performance: phenotypic, genetic and environmental correlations

Correlations of measures of percentages of white coat color, five measures of production and two measures of reproduction were obtained from 4293 first lactation Holsteins from eight Florida dairy farms. Percentages of white coat color were analyzed as recorded and transformed by an extension of Box-Cox procedures. Statistical analyses were by derivative-free restricted maximum likelihood (DFREML) with an animal model. Phenotypic and genetic correlations of white percentage (not transformed) were with milk yield, 0.047 and 0.097; fat yield, 0.002 and 0.004; fat percentage, -0.047 and -0.090; protein yield, 0.024 and 0.048; protein percentage, -0.070 and -0.116; days open, -0.012 and -0.065; and calving interval, -0.007 and -0.029. Changes in magnitude of correlations were very small for all variables except days open. Genetic and phenotypic correlations of transformed values with days open were -0.027 and -0.140. Modest positive correlated responses would be expected for white coat color percentage following direct selection for milk, fat, and protein yields, but selection for fat and protein percentages, days open, or calving interval would lead to small decreases.

Flavonoids and other phenolic compounds: characterization and interactions with lepidopteran and sawfly larvae

This thesis focuses on flavonoids, a subgroup of phenolic compounds produced by plants, and how they affect the herbivorous larvae of lepidopterans and sawflies. The first part of the literature review examines different techniques to analyze the chemical structures of flavonoids and their concentrations in biological samples. These techniques include, for example, ultraviolet-visible spectroscopy, mass spectrometry, and nuclear magnetic resonance spectroscopy. The second part of the literature review studies how phenolic compounds function in the metabolism of larvae. The harmful oxidation reactions of phenolic compounds in insect guts are also emphasized. In addition to the negative effects, many insect species have evolved the use of phenolic compounds for their own benefit. In the experimental part of the thesis, high concentrations of complex flavonoid oligoglycosides were found in the hemolymph (the circulatory fluid of insects) of birch and pine sawflies. The larvae produced these compounds from simple flavonoid precursors present in the birch leaves and pine needles. Flavonoid glycosides were also found in the cocoon walls of sawflies, which suggested that flavonoids were used in the construction of cocoons. The second part of the experimental work studied the modifications of phenolic compounds in conditions that mimicked the alkaline guts of lepidopteran larvae. It was found that the 24 plant species studied and their individual phenolic compounds had variable capacities to function as oxidative defenses in alkaline conditions. The excrements of lepidopteran and sawfly species were studied to see how different types of phenolics were processed by the larvae. These results suggested that phenolic compounds were oxidized, hydrolyzed, or modified in other ways during their passage through the digestive tract of the larvae.

Influence of lactation on motor activity and elevated plus maze behavior

Lactating rats show less noise-induced freezing and fewer inhibitory responses on the 6th day post-delivery when submitted to water and food deprivation in a classical conflict paradigm. Lactating mice go more often to the illuminated chamber in a light-dark cage and stay longer in it than virgin females. The present study was designed to assess the influence of this physiological state, i.e. lactation, on the elevated plus maze (EPM) and open-field behavior in adult female rats. Total (TL) and central (CL) locomotion and rearing (RF) frequencies were measured in an open-field. Number of entries into the open and closed arms as well as the time spent in each of these arms were measured in the EPM. Percent time spent and number of entries into the open arms were calculated and compared. In the open-field, TL was significantly decreased (115 ± 10.6 vs 150 ± 11.6) while CL and RF did not differ from those presented by virgin rats. In the EPM, lactating rats displayed a significant reduction in percent time spent (10.9 ± 1.5 vs 17.4 ± 2.3) in the open arms as well as a tendency to a reduction in percent entries into the open arms (35.7 ± 4.7 vs 45.7 ± 4.3). These results show that the physiological state of lactation modulates the open-field and EPM behaviors in rats

Signaled two-way avoidance learning using electrical stimulation of the inferior colliculus as negative reinforcement: effects of visual and auditory cues as warning stimuli

The inferior colliculus is a primary relay for the processing of auditory information in the brainstem. The inferior colliculus is also part of the so-called brain aversion system as animals learn to switch off the electrical stimulation of this structure. The purpose of the present study was to determine whether associative learning occurs between aversion induced by electrical stimulation of the inferior colliculus and visual and auditory warning stimuli. Rats implanted with electrodes into the central nucleus of the inferior colliculus were placed inside an open-field and thresholds for the escape response to electrical stimulation of the inferior colliculus were determined. The rats were then placed inside a shuttle-box and submitted to a two-way avoidance paradigm. Electrical stimulation of the inferior colliculus at the escape threshold (98.12 ± 6.15 (A, peak-to-peak) was used as negative reinforcement and light or tone as the warning stimulus. Each session consisted of 50 trials and was divided into two segments of 25 trials in order to determine the learning rate of the animals during the sessions. The rats learned to avoid the inferior colliculus stimulation when light was used as the warning stimulus (13.25 ± 0.60 s and 8.63 ± 0.93 s for latencies and 12.5 ± 2.04 and 19.62 ± 1.65 for frequencies in the first and second halves of the sessions, respectively, P<0.01 in both cases). No significant changes in latencies (14.75 ± 1.63 and 12.75 ± 1.44 s) or frequencies of responses (8.75 ± 1.20 and 11.25 ± 1.13) were seen when tone was used as the warning stimulus (P>0.05 in both cases). Taken together, the present results suggest that rats learn to avoid the inferior colliculus stimulation when light is used as the warning stimulus. However, this learning process does not occur when the neutral stimulus used is an acoustic one. Electrical stimulation of the inferior colliculus may disturb the signal transmission of the stimulus to be conditioned from the inferior colliculus to higher brain structures such as amygdala