DSpace REST API: an Interface for Reusing DSpace Content, and Practical Applications

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

Mirage 2: A responsive user interface for DSpace

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

SimpleREST -RESTful DSpace API

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

Sinningia allagophylla(Gesneriaceae): in vitro cultivation of a native plant of the Brazilian cerrado

We used axillary buds as initial explants for hormone interaction studies required for in vitro cultivation of S. allagophylla. Callus production was achieved on gelled Murashige & Skoog medium (MS) supplemented with indole-3-acetic acid (IAA= 0.1 and 0.5 mg.l­1 alone or combined with 6 benzylaminopurine) (BA= 0.01 and 0.1 mg.l-1). A hormone balance between IAA and BA that would encourage shoot bud development was not found. Nodal segments from axenic cultures grown in the presence of cytokinin (0.1 mg.1­1 of BA) without any auxin on MS medium with half-strength macronutrients were used as a standard explant source for subsequent experiments on optimum mineral culture media composition for S. allagophylla in vitro cultivation. We found that explants kept in vitro on gelled Gamborg et al. (B5) mineral composition culture medium showed better shoot and specially root growth than on MS medium. Comparisons of the ammonium and nitrate ratios of MS and B5 media indicate that B5 medium has a substantial reduced ammonium ion when compared to MS medium, as well as a lower total nitrogen level. The growth response pattern obtained in vitro may be evidence of the adaptation of this species to soils of poor mineral composition as found in the Brazilian cerrado, as well as an indication that nitrogen levels play a key role for S. allagophylla growth.

Design and evaluation of web interface signs to improve web usability : a semiotic framework

Technological innovations, the development of the internet, and globalization have increased the number and complexity of web applications. As a result, keeping web user interfaces understandable and usable (in terms of ease-of-use, effectiveness, and satisfaction) is a challenge. As part of this, designing userintuitive interface signs (i.e., the small elements of web user interface, e.g., navigational link, command buttons, icons, small images, thumbnails, etc.) is an issue for designers. Interface signs are key elements of web user interfaces because ‘interface signs’ act as a communication artefact to convey web content and system functionality, and because users interact with systems by means of interface signs. In the light of the above, applying semiotic (i.e., the study of signs) concepts on web interface signs will contribute to discover new and important perspectives on web user interface design and evaluation. The thesis mainly focuses on web interface signs and uses the theory of semiotic as a background theory. The underlying aim of this thesis is to provide valuable insights to design and evaluate web user interfaces from a semiotic perspective in order to improve overall web usability. The fundamental research question is formulated as What do practitioners and researchers need to be aware of from a semiotic perspective when designing or evaluating web user interfaces to improve web usability? From a methodological perspective, the thesis follows a design science research (DSR) approach. A systematic literature review and six empirical studies are carried out in this thesis. The empirical studies are carried out with a total of 74 participants in Finland. The steps of a design science research process are followed while the studies were designed and conducted; that includes (a) problem identification and motivation, (b) definition of objectives of a solution, (c) design and development, (d) demonstration, (e) evaluation, and (f) communication. The data is collected using observations in a usability testing lab, by analytical (expert) inspection, with questionnaires, and in structured and semi-structured interviews. User behaviour analysis, qualitative analysis and statistics are used to analyze the study data. The results are summarized as follows and have lead to the following contributions. Firstly, the results present the current status of semiotic research in UI design and evaluation and highlight the importance of considering semiotic concepts in UI design and evaluation. Secondly, the thesis explores interface sign ontologies (i.e., sets of concepts and skills that a user should know to interpret the meaning of interface signs) by providing a set of ontologies used to interpret the meaning of interface signs, and by providing a set of features related to ontology mapping in interpreting the meaning of interface signs. Thirdly, the thesis explores the value of integrating semiotic concepts in usability testing. Fourthly, the thesis proposes a semiotic framework (Semiotic Interface sign Design and Evaluation – SIDE) for interface sign design and evaluation in order to make them intuitive for end users and to improve web usability. The SIDE framework includes a set of determinants and attributes of user-intuitive interface signs, and a set of semiotic heuristics to design and evaluate interface signs. Finally, the thesis assesses (a) the quality of the SIDE framework in terms of performance metrics (e.g., thoroughness, validity, effectiveness, reliability, etc.) and (b) the contributions of the SIDE framework from the evaluators’ perspective.

Making the impact on research and society : nichesourcing of Uralic language material for the benefit of linguistic research and native-speakers

Presentation at the 12th Bibliotheca Baltica Symposium at Södertörn University Library

Multivariate analysis of pollen frequency of the native species Escallonia pulverulenta (Saxifragaceae) in Chilean honeys

The aim of this work was the identification of geographic zones suitable for the production of honeys in which pollen grains of Escallonia pulverulenta (Ruiz & Pav.) Pers. (Saxifragaceae) can be detected. The analysis of botanical origin of 240 honey samples produced between La Serena and Puerto Mont (the IV and X Administrative Regions of Chile), allowed the detection of pollen grains of E. pulverulenta in 46 Chilean honeys. The geographic distribution of the honeys studied is presented together with their affinities, through factor analysis and frequency tables. The study was based on the presence of E. pulverulenta pollen. Escallonia pulverulenta pollen percentages oscillated between 0.24% and 78.5%. Seventeen of the studied samples were designated as unifloral - i.e. samples showing more than 45% pollen of a determined plant species. Two of these corresponded to E. pulverulenta (corontillo, madroño or barraco) honeys. The remaining unifloral honeys correspond to 8 samples of Lotus uliginosus Schkuhr (birdsfoot trefoil), 2 samples of Aristotelia chilensis (Molina) Stuntz (maqui) and 1 sample of Escallonia rubra (Ruiz & Pav.) Pers. (siete camisas), Eucryphia cordifolia Cav. (ulmo or muemo), Weinmannia trichosperma Cav. (tineo), Rubus ulmifolius Schott (blackberry) and Brassica rapa L. (turnip). Honeys with different percentages of E. pulverulenta pollen - statistically analyzed through correspondence analysis - could be associated and assigned to one of three geographic types, defined on the basis of this analysis. The geographical type areas defined were the Northern Mediterranean Zone (samples from the IV Region), Central Mediterranean Zone (samples from the V to the VIII regions including two samples of unifloral Escallonia pulverulenta honey), and Southern Mediterranean Zone (samples from the IX Region).

Germination, initial growth, and biomass allocation in three native Cerrado species

The parameters of germination, initial growth, and biomass allocation of three native plant species of Cerrado (Copaifera langsdorffii, Dipteryx alata and Kielmeyera coriacea) were established. The species had germination percentages above 88% and average germination times longer than 139 hours. The average time for the opening of the first leaf pair was more than 538 hours for all three species. The average root length of C. langsdorffii and D. alata seedlings after 80 days of growth was around 40cm, four times larger than the average shoot length (<10cm), although the root and shoot biomasses were similar for both species. The average root length (>20cm) of K. coriacea seedlings was four times larger than the average shoot length (<5cm), and the root biomass was 243% greater than the shoot biomass. Increase in seedling biomass was sustained primarily by the cotyledons in C. langsdorffii and D. alata, which acted as reserve organs and showed progressive weight reductions. Increase in seedling biomass in K. coriacea was sustained primarily by photosynthesis, since the cotyledons showed no significant weight reduction, acting primarily as photosynthetic organs. The length of the root systems was at least four times larger than the length of the shoots parts in all three species. Higher investment in root length rather than in root biomass suggest that the initial growth of these species is primarily to ensure access to water resources, apparently putting off the function of the radicular system as storage organ.

pH titration of native and unfolded ß-trypsin: evaluation of the D D G0 titration and the carboxyl pK values

The stabilizing free energy of ß-trypsin was determined by hydrogen ion titration. In the pH range from 3.0 to 7.0, the change in free energy difference for the stabilization of the native protein relative to the unfolded one (D D G0 titration) was 9.51 ± 0.06 kcal/mol. An isoelectric point of 10.0 was determined, allowing us to calculate the Tanford and Kirkwood electrostatic factor w. This factor presented a nonlinear behavior and indicated more than one type of titratable carboxyl groups in ß-trypsin. In fact, one class of carboxyl group with a pK = 3.91 ± 0.01 and another one with a pK = 4.63 ± 0.03 were also found by hydrogen ion titration of the protein in the folded state

[Carte marine depuis le Cap de Bonne-Espérance jusqu'à Java]

Kartta kuuluu A. E. Nordenskiöldin kokoelmaan

Evidence for the expression of native Mycobacterium tuberculosis phospholipase C: recognition by immune sera and detection of promoter activity

The genome of Mycobacterium tuberculosis H37Rv contains three contiguous genes (plc-a, plc-b and plc-c) which are similar to the Pseudomonas aeruginosa phospholipase C (PLC) genes. Expression of mycobacterial PLC-a and PLC-b in E. coli and M. smegmatis has been reported, whereas expression of the native proteins in M. tuberculosis H37Rv has not been demonstrated. The objective of the present study was to demonstrate that native PLC-a is expressed in M. tuberculosis H37Rv. Sera from mice immunized with recombinant PLC-a expressed in E. coli were used in immunoblots to evaluate PLC-a expression. The immune serum recognized a 49-kDa protein in immunoblots against M. tuberculosis extracts. No bands were visible in M. tuberculosis culture supernatants or extracts from M. avium, M. bovis and M. smegmatis. A 550-bp DNA fragment upstream of plc-a was cloned in the pJEM12 vector and the existence of a functional promoter was evaluated by detection of ß-galactosidase activity. ß-Galactosidase activity was detected in M. smegmatis transformed with recombinant pJEM12 grown in vitro and inside macrophages. The putative promoter was active both in vitro and in vivo, suggesting that expression is constitutive. In conclusion, expression of non-secreted native PLC-a was demonstrated in M. tuberculosis.

Screening of antibacterial extracts from plants native to the Brazilian Amazon Rain Forest and Atlantic Forest

More than 20% of the world's biodiversity is located in Brazilian forests and only a few plant extracts have been evaluated for potential antibacterial activity. In the present study, 705 organic and aqueous extracts of plants obtained from different Amazon Rain Forest and Atlantic Forest plants were screened for antibacterial activity at 100 µg/ml, using a microdilution broth assay against Staphylococcus aureus, Enterococcus faecalis, Pseudomonas aeruginosa and Escherichia coli. One extract, VO581, was active against S. aureus (minimum inhibitory concentration (MIC) = 140 µg/ml and minimal bactericidal concentration (MBC) = 160 µg/ml, organic extract obtained from stems) and two extracts were active against E. faecalis, SM053 (MIC = 80 µg/ml and MBC = 90 µg/ml, organic extract obtained from aerial parts), and MY841 (MIC = 30 µg/ml and MBC = 50 µg/ml, organic extract obtained from stems). The most active fractions are being fractionated to identify their active substances. Higher concentrations of other extracts are currently being evaluated against the same microorganisms.

Evaluation by blue native polyacrylamide electrophoresis colorimetric staining of the effects of physical exercise on the activities of mitochondrial complexes in rat muscle

Blue native polyacrylamide electrophoresis (BN-PAGE) is a technique developed for the analysis of membrane complexes. Combined with histochemical staining, it permits the analysis and quantification of the activities of mitochondrial oxidative phosphorylation enzymes using whole muscle homogenates, without the need to isolate muscle mitochondria. Mitochondrial complex activities were measured by emerging gels in a solution containing all specific substrates for NADH dehydrogenase and cytochrome c oxidase enzymes (complexes I and IV, respectively) and the colored bands obtained were measured by optique densitometry. The objective of the present study was the application of BN-PAGE colorimetric staining for enzymatic characterization of mitochondrial complexes I and IV in rat muscles with different morphological and biochemical properties. We also investigated these activities at different times after acute exercise of rat soleus muscle. Although having fewer mitochondria than oxidative muscles, white gastrocnemius muscle presented a significantly higher activity (26.7 ± 9.5) in terms of complex I/V ratio compared to the red gastrocnemius (3.8 ± 0.65, P < 0.05) and soleus (9.8 ± 0.9, P < 0.001) muscles. Furthermore, the complex IV/V ratio of white gastrocnemius muscle was always significantly higher when compared to the other muscles. Ninety-five minutes of exhaustive physical exercise induced a decrease in complex I/V and complex IV/V ratios after all resting times (0, 3 and 6 h) compared to control (P < 0.05), probably reflecting the oxidative damage due to increasing free radical production in mitochondria. These results demonstrate the possible and useful application of BN-PAGE-histochemical staining to physical exercise studies.

Scientist-friendly policies for non-native English-speaking authors: timely and welcome

That English is the lingua franca of today's science is an indisputable fact. Publication in English in international journals is a pre-requisite for a research paper to gain visibility in academia. However, English proficiency appears to be taken for granted in the scientific community, though this language can be a hurdle for a number of authors, particularly from non-native English-speaking countries. The influence of English proficiency on the publication output of Brazilian authors has never been assessed. We report our preliminary data on the relationship between the English proficiency of 51,223 researchers registered in the CNPq database and their publication output in international journals. We have found that publication rates are higher for those authors with good command of English, particularly written English. Although our research is still underway and our results are preliminary, they suggest that the correlation between written English proficiency and research productivity should not be underestimated. We also present the comments of some Brazilian scientists with high publication records on the relevance of communication skills to the scientific enterprise.

Nichesourcing for the benefit of linguistic research and native speakers

The National Library of Finland is implementing the Digitization Project of Kindred Languages in 2012–16. Within the project we will digitize materials in the Uralic languages as well as develop tools to support linguistic research and citizen science. Through this project, researchers will gain access to new corpora 329 and to which all users will have open access regardless of their place of residence. Our objective is to make sure that the new corpora are made available for the open and interactive use of both the academic community and the language societies as a whole. The project seeks to digitize and publish approximately 1200 monograph titles and more than 100 newspapers titles in various Uralic languages. The digitization will be completed by the early of 2015, when the Fenno-Ugrica collection would contain around 200 000 pages of editable text. The researchers cannot spend so much time with the material that they could retrieve a satisfactory amount of edited words, so the participation of a crowd in editing work is needed. Often the targets in crowdsourcing have been split into several microtasks that do not require any special skills from the anonymous people, a faceless crowd. This way of crowdsourcing may produce quantitative results, but from the research’s point of view, there is a danger that the needs of linguistic research are not necessarily met. Also, the number of pages is too high to deal with. The remarkable downside is the lack of shared goal or social affinity. There is no reward in traditional methods of crowdsourcing. Nichesourcing is a specific type of crowdsourcing where tasks are distributed amongst a small crowd of citizen scientists (communities). Although communities provide smaller pools to draw resources, their specific richness in skill is suited for the complex tasks with high-quality product expectations found in nichesourcing. Communities have purpose, identity and their regular interactions engenders social trust and reputation. These communities can correspond to research more precisely. Instead of repetitive and rather trivial tasks, we are trying to utilize the knowledge and skills of citizen scientists to provide qualitative results. Some selection must be made, since we are not aiming to correct all 200,000 pages which we have digitized, but give such assignments to citizen scientists that would precisely fill the gaps in linguistic research. A typical task would editing and collecting the words in such fields of vocabularies, where the researchers do require more information. For instance, there’s a lack of Hill Mari words in anatomy. We have digitized the books in medicine and we could try to track the words related to human organs by assigning the citizen scientists to edit and collect words with OCR editor. From the nichesourcing’s perspective, it is essential that the altruism plays a central role, when the language communities involve. Upon the nichesourcing, our goal is to reach a certain level of interplay, where the language communities would benefit on the results. For instance, the corrected words in Ingrian will be added onto the online dictionary, which is made freely available for the public and the society can benefit too. This objective of interplay can be understood as an aspiration to support the endangered languages and the maintenance of lingual diversity, but also as a servant of “two masters”, the research and the society.