Hands-On: Interlinking Institutional Repositories and Europe PubMed Central

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

Bye, ContentDM: Another one bites the dust

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

How can we agree on some product agnostic repository function fundamentals?

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

EPrints Imports via DOI and ORCID

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

ORCiD – Membership and implementation at Chalmers University of Technology

Poster 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

The Human Communication Science Virtual Lab (HCS vLab): A repository microclimate in a rapidly evolving research-ecosystem

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

Itä-Suomen solmupysäkit : Joukkoliikenteen pysäkkisolmut Etelä-Savon, Pohjois-Savon ja Pohjois-Karjalan maakunnissa

Joukkoliikenteen toimivuuden ja palvelutason kannalta hyvällä pysäkki-infrastruktuurilla on merkittävä vaikutus. Itä-Suomen kolmen maakunnan alueella on noin 12 000 linja-autopysäkkiä, yli 30 rautatieseisaketta ja neljä lentoasemaa. Näistä pieni osa on tässä selvityksessä inventoitu alueen solmupysäkkeinä. Solmupysäkeillä on suuri merkitys paikallisen, alueellisen ja valtakunnallisen kulkumuotoriippumattoman joukkoliikenneverkoston kannalta. Solmupysäkit sijaitsevat keskeisillä paikoilla ja suurimman lähietäisyydellä on tiheää asutusta. Keskeisten solmupysäkkien valinnan jälkeen seuraava kehitysaskel tulisi ottaa solmupysäkkistatuksen viemisenä käytäntöön, pysäkeille ja asiakasinformaatioon. Valitut pysäkit toimivat vaihtopaikkoina, liityntäpysäkkeinä, taajamasolmuina ja matkakeskuksina. Parannustoimenpiteitä tulisi ohjata niin tieympäri stön,pysäkkivarustuksen, opastuksen, pysäkkikohtaisen informaation ja nettipohjaisen tiedon kehittämiseen. Itä-Suomen solmupysäkit työssä valittiin Pohjois-Savon, Etelä-Savon ja Pohjois-Karjalan alueelta 125 solmupysäkkiä, jotka ovat monien eri tahojen kehittämis- ja ylläpitovastuulla. Yksittäisistä kehittämiskohteista suurin ovat kuntataajamissa sijaitsevien pysäkkisolmut. Joukkoliikenteen informaatio on taajamasolmujen osalta puutteellista. Pysäkin tarkka paikantaminen hankalaa ja usein myös fyysiset opasteet ovat puutteellisia. Aikatauluja ja tärkeimpien matkakohteiden vuorotarjontaa on vaikeaa selvittää. Lyhyen suunnitelmaraportin lisäksi selvityksen toteuttanut Sito on tuottanut Pohjois-Savon ELY-keskukselle pysäkkeihin liittyvän inventointiaineiston. Paikkatietoaineisto on saatavilla sekä ArcGis että Google-yhteensopivana. Google yhteensopiva aineisto mahdollistaa pysäkkien paikantamisen Google Streetview palvelun avulla.

Median digitalisoituminen ja yhdistetty tieto

Esitys Kansalliskirjaston Finto-palvelun ja arkistosektorin KDK-yhteistyöverkoston järjestämässä seminaarissa: Linkity! Kohti yhteentoimivaa metatietoa 3.9.2014.

Nichesourcing The Uralic Languages For The Benefit Of Linguistic Research And Lingual Societies

The emerging technologies have recently challenged the libraries to reconsider their role as a mere mediator between the collections, researchers, and wider audiences (Sula, 2013), and libraries, especially the nationwide institutions like national libraries, haven’t always managed to face the challenge (Nygren et al., 2014). In the Digitization Project of Kindred Languages, the National Library of Finland has become a node that connects the partners to interplay and work for shared goals and objectives. In this paper, I will be drawing a picture of the crowdsourcing methods that have been established during the project to support both linguistic research and lingual diversity. The National Library of Finland has been executing the Digitization Project of Kindred Languages since 2012. The project seeks to digitize and publish approximately 1,200 monograph titles and more than 100 newspapers titles in various, and in some cases endangered Uralic languages. Once the digitization has been completed in 2015, the Fenno-Ugrica online collection will consist of 110,000 monograph pages and around 90,000 newspaper pages to which all users will have open access regardless of their place of residence. The majority of the digitized literature was originally published in the 1920s and 1930s in the Soviet Union, and it was the genesis and consolidation period of literary languages. This was the era when many Uralic languages were converted into media of popular education, enlightenment, and dissemination of information pertinent to the developing political agenda of the Soviet state. The ‘deluge’ of popular literature in the 1920s to 1930s suddenly challenged the lexical orthographic norms of the limited ecclesiastical publications from the 1880s onward. Newspapers were now written in orthographies and in word forms that the locals would understand. Textbooks were written to address the separate needs of both adults and children. New concepts were introduced in the language. This was the beginning of a renaissance and period of enlightenment (Rueter, 2013). The linguistically oriented population can also find writings to their delight, especially lexical items specific to a given publication, and orthographically documented specifics of phonetics. The project is financially supported by the Kone Foundation in Helsinki and is part of the Foundation’s Language Programme. One of the key objectives of the Kone Foundation Language Programme is to support a culture of openness and interaction in linguistic research, but also to promote citizen science as a tool for the participation of the language community in research. In addition to sharing this aspiration, our objective within the Language Programme is to make sure that old and new corpora in Uralic languages are made available for the open and interactive use of the academic community as well as the language societies. Wordlists are available in 17 languages, but without tokenization, lemmatization, and so on. This approach was verified with the scholars, and we consider the wordlists as raw data for linguists. Our data is used for creating the morphological analyzers and online dictionaries at the Helsinki and Tromsø Universities, for instance. In order to reach the targets, we will produce not only the digitized materials but also their development tools for supporting linguistic research and citizen science. The Digitization Project of Kindred Languages is thus linked with the research of language technology. The mission is to improve the usage and usability of digitized content. During the project, we have advanced methods that will refine the raw data for further use, especially in the linguistic research. How does the library meet the objectives, which appears to be beyond its traditional playground? The written materials from this period are a gold mine, so how could we retrieve these hidden treasures of languages out of the stack that contains more than 200,000 pages of literature in various Uralic languages? The problem is that the machined-encoded text (OCR) contains often too many mistakes to be used as such in research. The mistakes in OCRed texts must be corrected. For enhancing the OCRed texts, the National Library of Finland developed an open-source code OCR editor that enabled the editing of machine-encoded text for the benefit of linguistic research. This tool was necessary to implement, since these rare and peripheral prints did often include already perished characters, which are sadly neglected by the modern OCR software developers, but belong to the historical context of kindred languages and thus are an essential part of the linguistic heritage (van Hemel, 2014). Our crowdsourcing tool application is essentially an editor of Alto XML format. It consists of a back-end for managing users, permissions, and files, communicating through a REST API with a front-end interface—that is, the actual editor for correcting the OCRed text. The enhanced XML files can be retrieved from the Fenno-Ugrica collection for further purposes. Could the crowd do this work to support the academic research? The challenge in crowdsourcing lies in its nature. The targets in the traditional crowdsourcing have often 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 linguists are not necessarily met. Also, the remarkable downside is the lack of shared goal or the social affinity. There is no reward in the traditional methods of crowdsourcing (de Boer et al., 2012). Also, there has been criticism that digital humanities makes the humanities too data-driven and oriented towards quantitative methods, losing the values of critical qualitative methods (Fish, 2012). And on top of that, the downsides of the traditional crowdsourcing become more imminent when you leave the Anglophone world. Our potential crowd is geographically scattered in Russia. This crowd is linguistically heterogeneous, speaking 17 different languages. In many cases languages are close to extinction or longing for language revitalization, and the native speakers do not always have Internet access, so an open call for crowdsourcing would not have produced appeasing results for linguists. Thus, one has to identify carefully the potential niches to complete the needed tasks. When using the help of a crowd in a project that is aiming to support both linguistic research and survival of endangered languages, the approach has to be a different one. In nichesourcing, the 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 complex tasks with high-quality product expectations found in nichesourcing. Communities have a purpose and identity, and their regular interaction engenders social trust and reputation. These communities can correspond to research more precisely (de Boer et al., 2012). Instead of repetitive and rather trivial tasks, we are trying to utilize the knowledge and skills of citizen scientists to provide qualitative results. In nichesourcing, we hand in such assignments that would precisely fill the gaps in linguistic research. A typical task would be editing and collecting the words in such fields of vocabularies where the researchers do require more information. For instance, there is lack of Hill Mari words and terminology 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 the OCR editor. From the nichesourcing’s perspective, it is essential that altruism play a central role when the language communities are involved. In nichesourcing, our goal is to reach a certain level of interplay, where the language communities would benefit from the results. For instance, the corrected words in Ingrian will be added to an online dictionary, which is made freely available for the public, so 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’: research and society.

Isolamento de coliformes, estafilococos e enterococos de leite cru provenientes de tanques de refrigeração por expansão comunitários: identificação, ação lipolítica e proteolítica

O isolamento e a identificação de microrganismos em leite cru se tornam interessantes do ponto de vista de saúde pública, pois dependendo das espécies isoladas, ações direcionadas podem ser tomadas visando a melhoria de sua qualidade. A deterioração do leite é conseqüência sobretudo do crescimento de microrganismos psicrotróficos, que produzem lipases e proteases termoestáveis que não são desnaturadas durante o processo de pasteurização, conferindo sabores e odores rançoso e amargo, respectivamente. Assim, o objetivo deste trabalho foi isolar e identificar os principais gêneros de bactérias pertencentes à família Enterobacteriaceae, Gram-negativas oxidase positiva, gêneros Staphylococcus e Enterococcus, bem como atividade de lipases e proteases de 16 propriedades rurais do município de Boa Esperança-MG. As bactérias Gram-negativas foram isoladas em ágar eosina azul de metileno (EMB) e ágar Entérico Hektoen. Estafilococos foram isolados em ágar Baird-Parker e Enterococcus em ágar KF. Colônias de interesse foram coletadas e submetidas à coloração de Gram, e às provas de catalase e oxidase. Após esses procedimentos, os isolados selecionados foram identificados utilizando-se Bactray I, II e III; Api 20 Strep; e provas sugeridas pelo Bergey's Manual of Determinative Bacteriology. A identificação sorológica de Enterococcus foi realizada utilizando-se Prolex. O leite oriundo das 16 propriedades continha cepas de microrganismos fecais como Escherichia coli e Enterococcus do grupo D de Lancefield. Bactérias Gram-negativas oxidase positiva foram identificadas em cinco propriedades. Staphylococcus foram encontrados em 10 propriedades. O leite coletado nas fazendas investigadas possui microrganismos que comprometem sua qualidade. Todos os grupos de microrganismos testados revelaram atividades de lipase e protease.

Microbial profile of a kefir sample preparations: grains in natura and lyophilized and fermented suspension

Probiotics are supplementary foods developed by microbial strains that improve animal health beyond basic nutrition. Probiotics are consumed orally, regardless of being considered as normal inhabitants of the intestines, able to survive in enzimatic and biliary secretions. Kefir is a probiotic originated from the old continent, fermented by several bacteria and yeasts, encapsulated in a polyssacharide matrix, and resembles jelly grains. Kefir is also presented as its sourish product both in sugary or milky suspensions containing vitamins, aminoacids, peptides, carbohydrates, ethanol, and volatile compounds. Kefir is known to have a diverse microbial content depending on the country and fermentative substrates, which cause distinct probiotic effects. In this sense, the purpose of this work was to isolate, identify, and quantify the microbial content of a native sugary kefir sample (fermented suspension and lyophilized natural grains). Serial dilutions were plated on Rogosa agar (AR) and De Man, Rogosa and Sharpe (MRS), for Lactobacillus; Brain Heart Infusion (BHI), for total bacteria; Sabouraud-Dextrose-Agar (SDA), for yeasts and filamentous fungi; Thioglycolate Agar (TA), for Streptococcus, Acetobacteria and Leuconostoc; and Coconut Water Agar (CWA), and CWA supplemented with yeast extract (CWAY), for various genera. Genera and species for all strains were identified through biochemical reactions and specific API systems. The microbial profile of kefir was different from other sources of grains despite the presence of similar microorganisms and others which have not been reported yet. The data obtained with the CWA and CWAE media suggest that both substrates are alternative and salutary media for culture of kefir strains.

Influence of physical damage and freezing on histamine concentration and microbiological quality of yellowfin tuna during processing

Yellowfin tuna has a high level of free histidine in their muscle, which can lead to histamine formation by microorganisms if temperature abuse occurs during handling and further processing. The objective of this study was to measure levels of histamine in damaged and undamaged thawed muscle to determine the effect of physical damage on the microbial count and histamine formation during the initial steps of canning processing and to isolate and identify the main histamine-forming microorganisms present in the flesh of yellowfin tuna. Total mesophilic and psicrophilic microorganisms were determined using the standard plate method. The presence of histamine-forming microorganisms was determined in a modified Niven's agar. Strains were further identified using the API 20E kit for enterobacteriaceae and Gram-negative bacilli. Physically damaged tuna did not show higher microbiological contamination than that of undamaged muscle tuna. The most active histamine-forming microorganism present in tuna flesh was Morganella morganii. Other decarboxylating microorganisms present were Enterobacter agglomerans and Enterobacter cloacae. Physical damage of tune during catching and handling did not increase the level of histamine or the amount of microorganisms present in tuna meat during frozen transportation, but they showed a higher risk of histamine-forming microorganism growth during processing.

Verkkosivujen grafiikkatyökalut

Tutkielman tarkoituksena on vertailla verkkosivujen grafiikkatyökaluja. Tutkielmassa käsitellään kahta 2D-grafiikkaan liittyvää web-tekniikkaa: SVG:tä ja HTML5:n canvas-elementtiä. Ensin esitellään molemmat teknologiat, sitten käydään läpi molempien käyttöä esimerkkien ja kuvien avulla. Työssä esitetään myös eri tapoja toteuttaa animaatioita. Lopuksi teknologioita ja niiden käyttömahdollisuuksia vertaillaan. Tutkielmassa pyritään vastaamaan seuraaviin kysymyksiin: Mitä ovat SVG ja HTML5:n canvas-elementti? Miten niitä käytetään? Miten ne eroavat toisistaan? Mihin käyttötarkoituksiin ne sopivat? SVG on skaalautuvan vektorigrafiikan formaatti kaksiulotteisen grafiikan esittämiseen. SVG perustuu vektoreihin ja se kuvataan XML-tyylisellä kielellä. SVG soveltuu tilanteisiin, joissa kuviota halutaan suurentaa ja pienentää laadun kärsimättä. HTML5:n uutuus canvas-elementti luo verkkosivulle piirtoalustan, johon voidaan piirtää JavaScriptillä Canvas API:n kautta. Canvas-alustalle piirretyt kuvat perustuvat bittikarttaan, joten teknologia soveltuu parhaiten pikseleiden tasolla tehtyihin operaatioihin ja esimerkiksi web-ohjelmien toteuttamiseen.

Aspects of spatial and habitat ecology of multiple Anopheles species (Diptera: Culicidae): malaria vectors in the highlands and foothills of Ecuador

The resurgence of malaria in highland regions of Africa, Oceania and recently in South America underlines the importance of the study of the ecology of highland mosquito vectors of malaria. Since the incidence of malaria is limited by the distribution of its vectors, the purpose of this PhD thesis was to examine aspects of the ecology of Anopheles mosquitoes in the Andes of Ecuador, South America. A historical literature and archival data review (Chapter 2) indicated that Anopheles pseudopunctipennis transmitted malaria in highland valleys of Ecuador prior to 1950, although it was eliminated through habitat removal and the use of chemical insecticides. Other anopheline species were previously limited to low-altitude regions, except in a few unconfirmed cases. A thorough larval collection effort (n=438 attempted collection sites) in all road-accessible parts of Ecuador except for the lowland Amazon basin was undertaken between 2008 - 2010 (Chapter 3). Larvae were identified morphologically and using molecular techniques (mitochondrial COl gene), and distribution maps indicated that all five species collected (Anopheles albimanus, An. pseudopunctipennis, Anopheles punctimacula, Anopheles oswaldoi s.l. and Anopheles eiseni) were more widespread throughout highland regions than previously recorded during the 1940s, with higher maximum altitudes for all except An. pseudopunctipennis (1541 m, 1930 m, 1906 m, 1233 m and 1873 m, respectively). During larval collections, to characterize species-specific larval habitat, a variety of abiotic and biotic habitat parameters were measured and compared between species-present and species-absent sites using chi-square tests and stepwise binary logistic regression analyses (Chapter 4). An. albimanus was significantly associated with permanent pools with sand substrates and An. pseudopunctipennis with gravel and boulder substrates. Both species were significantly associated with floating cyanobacterial mats and warmer temperatures, which may limit their presence in cooler highland regions. Anopheles punctimacula was collected more often than expected from algae-free, shaded pools with higher-than-average calculated dissolved oxygen. Anopheles oswaldoi s.l., the species occurring on the Amazonian side of the Andes, was associated with permanent, anthropogenic habitats such as roadside ditches and ponds. To address the hypothesis that human land use change is responsible for the emergence of multiple highland Anopheles species by creating larval habitat, common land uses in the western Andes were surveyed for standing water and potential larval habitat suitability (Chapter 5). Rivers and road edges provided large amounts of potentially suitable anopheline habitat in the western Andes, while cattle pasture also created potentially suitable habitat in irrigation canals and watering ponds. Other common land uses surveyed (banana farms, sugarcane plantations, mixed tree plantations, and empty lots) were usually established on steep slopes and had very little standing water present. Using distribution and larval habitat data, a GIS-based larval habitat distribution model for the common western species was constructed in ArcGIS v.l 0 (ESRI 2010) using derived data layers from field measurements and other sources (Chapter 6). The additive model predicted 76.4 - 97.9% of the field-observed collection localities of An. albimanus, An. pseudopunctipennis and An. punctimacula, although it could not accurately distinguish between species-absent and speciespresent sites due to its coarse scale. The model predicted distributional expansion and/or shift of one or more anopheline species into the following highland valleys with climate warming: Mira/Chota, Imbabura province, Tumbaco, Pichincha province, Pallatanga and Sibambe, Chimborazo province, and Yungilla, Azuay province. These valleys may serve as targeted sites of future monitoring to prevent highland epidemics of malaria. The human perceptions of malaria and mosquitoes in relation to land management practices were assessed through an interview-based survey (n=262) in both highlands and lowlands, of male and female land owners and managers of five property types (Chapter 7). Although respondents had a strong understanding of where the disease occurs in their own country and of the basic relationship among standing water, mosquitoes and malaria, about half of respondents in potential risk areas denied the current possibility of malaria infection on their own property. As well, about half of respondents with potential anopheline larval habitat did not report its presence, likely due to a highly specific definition of suitable mosquito habitat. Most respondents who are considered at risk of malaria currently use at least one type of mosquito bite prevention, most commonly bed nets. In conclusion, this interdisciplinary thesis examines the occurrence of Anopheles species in the lowland transition area and highlands in Ecuador, from a historic, geographic, ecological and sociological perspective.