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

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

Onomástica, ecología y territorio. La toponimia de La Rioja como indicador biogeográfico y de la dinámica del paisaje forestal

Se presenta un trabajo de investigación toponímica en La Rioja con enfoque geobotánico. La premisa de partida es que la toponimia relacionada con especies y agrupaciones vegetales, productos forestales y usos del suelo proporciona información valiosa sobre la corología y la dinámica de la vegetación al ser clasificada y analizada con criterios biogeográficos y ecológicos. Se ha elegido la región riojana como zona piloto, al concurrir distintos tipos fisonómicos de vegetación y un conjunto muy diverso de comunidades vegetales representativas del paisaje peninsular. Se añade una larga historia de usos agrícolas en la llanura del Ebro que contrasta con la predominante actividad forestal en las zonas montañosas, en particular la potenciación de los pastos para ganadería trashumante. La Rioja tiene carácter de encrucijada no sólo fitocorológica: es también tierra de fronteras políticas y transiciones lingüísticas. En el léxico y la toponimia conviven variantes puras del castellano, rasgos del romance navarro-aragonés, elementos genuinos de una variante medieval riojana, palabras mozárabes y un numeroso y significativo elenco de topónimos de origen vasco. El trabajo se inicia con unas consideraciones epistemológicas. Se establece un planteamiento de la Toponimia como ciencia interdisciplinar, la etiología de los nombres geográficos, así como su valor apelativo descriptor de los atributos del paisaje. Se enumeran los condicionantes metodológicos de la investigación toponímica y se desarrolla una reflexión sobre las particularidades de la toponimia geobotánica. Se dedica un epígrafe a reseñar estudios precedentes de toponimia botánica y ecológica y el estado actual de conocimientos sobre la toponimia de La Rioja. La delimitación superficial de los parajes designados por los nombres geográficos es clave para un análisis orientado a detectar la correspondencia entre los elementos aludidos por el topónimo y las especies y comunidades vegetales. Las áreas de distribución y presencia, así como las transformaciones del paisaje, quedan definidas en superficies acotadas territorialmente. La metodología seguida se basa en la revisión exhaustiva de fuentes toponímicas ya existentes; destacadamente, los datos procedentes de la cartografía del Castro de Rústica, adscritos a polígonos con dimensión espacial. Las denominaciones de las parcelas catastrales se han complementado con los nombres geográficos del Diccionario de Toponimia Actual de La Rioja (DTALR) (González Blanco, 1987), el nomenclátor NomGeo del IGN, y algunas recopilaciones toponímicas municipales. De la base de datos conjunta se han seleccionado los topónimos con significado geobotánico. Se propone una taxonomía de grupos semánticos basada en categorías de estructura (arbolado, matorral, cubiertas herbáceas y áreas de vegetación escasa o rala) y en la adscripción a tipos de vegetación potencialmente dominantes, ordenados según una escala de higrofilia decreciente). También se reseñan topónimos referentes a usos y aprovechamientos en el medio rural: dehesas, ganadería, productos forestales y algunos cultivos agrícolas. El trabajo reúne en un repertorio sistemático los datos toponímicos, acopiados por comarcas y términos municipales. Se incluye la relación de nombres geográficos encontrados por campos nocionales y se comentan los nombres vernáculos que les han dado origen y su etimología. Quedan señalados los topónimos georreferenciados y asignados a entidades superficiales en la cartografía digital catastral, que se ha superpuesto a mapas forestales a escalas 1:200.000 y 1:50.000, en cuya elaboración participamos. El análisis ha permitido definir “topónimo externo” como el recinto catastral en que la especie o agrupación aludida no tiene presencia en la vegetación actual, al menos como dominante. Los topónimos externos más significativos de cada grupo han sido analizados describiendo la cubierta vegetal actual correspondiente, lo que permite interpretar, junto con las características fisiográficas del paraje, las causas posibles de ausencia del elemento aludido, teniendo en cuenta criterios generales de mesología, de dinámica de la vegetación y de la historia de la acción humana. El trabajo se cierra con un capítulo de conclusiones generales, conceptuales y metodológicas, así como una relación de líneas de profundización de la investigación que quedan apuntadas. Se completa con una relación de fuentes y referencias bibliográficas fundamentales. ABSTRACT This paper presents a study of the toponymy of La Rioja with a specific focus on place names reflecting the region’s geobotany. Its underlying premise is that the toponymy associated with plant species and communities, forest products and land uses can provide valuable information about the chorology and vegetation dynamics when classified and analysed using biogeographical and ecological criteria. La Rioja has been chosen for this pilot study because it concentrates vegetation types of distinct physiognomy and a highly diverse set of plant communities that can be considered representative of the vegetation of the peninsula’s landscapes. This combines with a long history of different agricultural uses on the Ebro plain that contrast with the predominance of forestry activity in the more mountainous areas, in particular the promotion of pasture for livestock transhumance. Indeed, La Rioja is not only a crossroads in terms of its phytochorology, but it is also a land of political boundaries and language transitions. Coexisting in its lexicon and toponymy, we find pure Castilian variants, features from the Romance language of Navarro-Aragonese, genuine elements of the medieval variant of the Riojan dialect, words of Mozarabic and a large and significant list of place names of Basque origin. The paper begins by outlining a number of epistemological considerations and establishes an interdisciplinary approach to toponymy, the aetiology of geographical names, and their value in the descriptive naming of the features of a landscape. It continues by enumerating the methodological determinants of toponymic research and reflects on the specific characteristics of geobotanical toponyms. The next section is dedicated to examining previous studies of botanical and ecological place names and providing a state-of-the-art review of the toponymy of La Rioja. Delimiting the sites designated by the geographical names is essential to any analysis designed to detect the correspondence between the elements alluded to by the toponyms and plant species and communities. These areas of distribution and presence, as well as the landscape changes, are defined in terms of spatially delimited surface areas. The methodology adopted involves an exhaustive review of existing toponymic sources; in particular, data obtained from the maps of the Rustic Cadastre, assigned to spatial polygons. The names of these cadastral parcels are complemented by the geographical names taken from the Diccionario de Toponimia Actual de La Rioja (DTALR) (González Blanco, 1987); the gazetteer – NomGeo, published by Spain’s Instituto Geográfico Nacional; and, various municipal list of toponyms. Place names with a geobotanical meaning were then selected from this joint database. The paper proposes a taxonomy of semantic groups based on structural categories (namely wooded areas, brushland, grassy areas and areas of scanty or sparse vegetation) and assignment to the potentially dominant type of vegetation (ordered on a scale of decreasing hygrophilic trends). Place names referring to land uses and practices in rural areas – including, pasture, livestock, forest products and some agricultural crops – are also described. The study produces a systematic list of toponyms ordered by counties and municipalities. The geographical names are organised by notional fields and the vernacular names that have given rise to them and their etymology are discussed. The toponyms are georeferenced and assigned to surface elements on the digital cadastral map, superimposed on forest maps at scales of 1:200,000 and 1:50,000, in the production of which the authors participated. The analysis has allowed us to define “external toponyms” as those cadastral parcels in which the plant species or group alluded to is no longer present in the vegetation, at least as the dominant type. The most significant external toponyms in each group have been analysed by describing the corresponding, present-day vegetation cover, which allows us to interpret, along with the physiographic features of the site, the possible causes of the absence of the aforementioned element, bearing in mind general criteria of mesology, vegetation dynamics and the history of human action. The paper finishes by offering a number of general conceptual and methodological conclusions, and a list of areas that future research can usefully examine. The study is supplemented with a list of sources and key references.

The Alps Vegetation Database - a geo-referenced community-level archive of all terrestrial plants occurring in the Alps.

Mountain ranges are biodiversity hotspots worldwide and provide refuge to many organisms under contemporary climate change. Gathering field information on mountain biodiversity over time is of primary importance to understand the response of biotic communities to climate changes. For plants, several long-term observation sites and networks of mountain biodiversity are emerging worldwide to gather field data and monitor altitudinal range shifts and community composition changes under contemporary climate change. Most of these monitoring sites, however, focus on alpine ecosystems and mountain summits, such as the global observation research initiative in alpine environments (GLORIA). Here we describe the Alps Vegetation Database, a comprehensive community level archive (GIVD ID EU-00-014) which aims at compiling all available geo-referenced vegetation plots from lowland forests to alpine grasslands across the greatest mountain range in Europe: the Alps. This research initiative was funded between 2008 and 2011 by the Danish Council for Independent Research and was part of a larger project to compare cross-scale plant community structure between the Alps and the Scandes. The Alps Vegetation Database currently harbours 35,731 geo-referenced vegetation plots and 5,023 valid taxa across Mediterranean, temperate and alpine environments. The data are mainly used by the main contributors of the Alps Vegetation Database in an ecoinformatics approach to test hypotheses related to plant macroecology and biogeography, but external proposals for joint collaborations are welcome.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature.

The main goal of CleanEx is to provide access to public gene expression data via unique gene names. A second objective is to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-data set comparisons. A consistent and up-to-date gene nomenclature is achieved by associating each single experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of human genes and genes from model organisms. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing cross-references to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resource, such as cDNA clones or Affymetrix probe sets. The web-based query interfaces offer access to individual entries via text string searches or quantitative expression criteria. CleanEx is accessible at: http://www.cleanex.isb-sib.ch/.

CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature and linked to an improved annotation system

Résumé: L'automatisation du séquençage et de l'annotation des génomes, ainsi que l'application à large échelle de méthodes de mesure de l'expression génique, génèrent une quantité phénoménale de données pour des organismes modèles tels que l'homme ou la souris. Dans ce déluge de données, il devient très difficile d'obtenir des informations spécifiques à un organisme ou à un gène, et une telle recherche aboutit fréquemment à des réponses fragmentées, voir incomplètes. La création d'une base de données capable de gérer et d'intégrer aussi bien les données génomiques que les données transcriptomiques peut grandement améliorer la vitesse de recherche ainsi que la qualité des résultats obtenus, en permettant une comparaison directe de mesures d'expression des gènes provenant d'expériences réalisées grâce à des techniques différentes. L'objectif principal de ce projet, appelé CleanEx, est de fournir un accès direct aux données d'expression publiques par le biais de noms de gènes officiels, et de représenter des données d'expression produites selon des protocoles différents de manière à faciliter une analyse générale et une comparaison entre plusieurs jeux de données. Une mise à jour cohérente et régulière de la nomenclature des gènes est assurée en associant chaque expérience d'expression de gène à un identificateur permanent de la séquence-cible, donnant une description physique de la population d'ARN visée par l'expérience. Ces identificateurs sont ensuite associés à intervalles réguliers aux catalogues, en constante évolution, des gènes d'organismes modèles. Cette procédure automatique de traçage se fonde en partie sur des ressources externes d'information génomique, telles que UniGene et RefSeq. La partie centrale de CleanEx consiste en un index de gènes établi de manière hebdomadaire et qui contient les liens à toutes les données publiques d'expression déjà incorporées au système. En outre, la base de données des séquences-cible fournit un lien sur le gène correspondant ainsi qu'un contrôle de qualité de ce lien pour différents types de ressources expérimentales, telles que des clones ou des sondes Affymetrix. Le système de recherche en ligne de CleanEx offre un accès aux entrées individuelles ainsi qu'à des outils d'analyse croisée de jeux de donnnées. Ces outils se sont avérés très efficaces dans le cadre de la comparaison de l'expression de gènes, ainsi que, dans une certaine mesure, dans la détection d'une variation de cette expression liée au phénomène d'épissage alternatif. Les fichiers et les outils de CleanEx sont accessibles en ligne (http://www.cleanex.isb-sib.ch/). Abstract: The automatic genome sequencing and annotation, as well as the large-scale gene expression measurements methods, generate a massive amount of data for model organisms. Searching for genespecific or organism-specific information througout all the different databases has become a very difficult task, and often results in fragmented and unrelated answers. The generation of a database which will federate and integrate genomic and transcriptomic data together will greatly improve the search speed as well as the quality of the results by allowing a direct comparison of expression results obtained by different techniques. The main goal of this project, called the CleanEx database, is thus to provide access to public gene expression data via unique gene names and to represent heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and crossdataset comparisons. A consistent and uptodate gene nomenclature is achieved by associating each single gene expression experiment with a permanent target identifier consisting of a physical description of the targeted RNA population or the hybridization reagent used. These targets are then mapped at regular intervals to the growing and evolving catalogues of genes from model organisms, such as human and mouse. The completely automatic mapping procedure relies partly on external genome information resources such as UniGene and RefSeq. The central part of CleanEx is a weekly built gene index containing crossreferences to all public expression data already incorporated into the system. In addition, the expression target database of CleanEx provides gene mapping and quality control information for various types of experimental resources, such as cDNA clones or Affymetrix probe sets. The Affymetrix mapping files are accessible as text files, for further use in external applications, and as individual entries, via the webbased interfaces . The CleanEx webbased query interfaces offer access to individual entries via text string searches or quantitative expression criteria, as well as crossdataset analysis tools, and crosschip gene comparison. These tools have proven to be very efficient in expression data comparison and even, to a certain extent, in detection of differentially expressed splice variants. The CleanEx flat files and tools are available online at: http://www.cleanex.isbsib. ch/.

The joint influence of personal achievement goals and classroom goal structures on achievement-relevant outcomes

The authors provide an analytic framework for studying the joint influence of personal achievement goals and classroom goal structures on achievement-relevant outcomes. This framework encompasses 3 models (the direct effect model, indirect effect model, and interaction effect model), each of which addresses a different aspect of the joint influence of the 2 goal levels. These 3 models were examined together with a sample of 1,578 Japanese junior high and high school students from 47 classrooms. Results provided support for each of the 3 models: Classroom goal structures were not only direct, but also indirect predictors of intrinsic motivation and academic self-concept, and some cross-level interactions between personal achievement goals and classroom goal structures were observed (indicating both goal match and goal mismatch effects). A call is made for more research that takes into consideration achievement goals at both personal and structural levels of representation. (PsycINFO Database Record (c) 2012 APA, all rights reserved)(journal abstract)

A Fast Large Scale Iris Database Classification with Optimum-Path Forest Technique: A Case Study

Majority of biometric researchers focus on the accuracy of matching using biometrics databases, including iris databases, while the scalability and speed issues have been neglected. In the applications such as identification in airports and borders, it is critical for the identification system to have low-time response. In this paper, a graph-based framework for pattern recognition, called Optimum-Path Forest (OPF), is utilized as a classifier in a pre-developed iris recognition system. The aim of this paper is to verify the effectiveness of OPF in the field of iris recognition, and its performance for various scale iris databases. This paper investigates several classifiers, which are widely used in iris recognition papers, and the response time along with accuracy. The existing Gauss-Laguerre Wavelet based iris coding scheme, which shows perfect discrimination with rotary Hamming distance classifier, is used for iris coding. The performance of classifiers is compared using small, medium, and large scale databases. Such comparison shows that OPF has faster response for large scale database, thus performing better than more accurate but slower Bayesian classifier.

Simultaneous bilateral hip replacement reveals superior outcome and fewer complications than two-stage procedures: a prospective study including 1819 patients and 5801 follow-ups from a total joint replacement registry

Background Total joint replacements represent a considerable part of day-to-day orthopaedic routine and a substantial proportion of patients undergoing unilateral total hip arthroplasty require a contralateral treatment after the first operation. This report compares complications and functional outcome of simultaneous versus early and delayed two-stage bilateral THA over a five-year follow-up period. Methods The study is a post hoc analysis of prospectively collected data in the framework of the European IDES hip registry. The database query resulted in 1819 patients with 5801 follow-ups treated with bilateral THA between 1965 and 2002. According to the timing of the two operations the sample was divided into three groups: I) 247 patients with simultaneous bilateral THA, II) 737 patients with two-stage bilateral THA within six months, III) 835 patients with two-stage bilateral THA between six months and five years. Results Whereas postoperative hip pain and flexion did not differ between the groups, the best walking capacity was observed in group I and the worst in group III. The rate of intraoperative complications in the first group was comparable to that of the second. The frequency of postoperative local and systemic complication in group I was the lowest of the three groups. The highest rate of complications was observed in group III. Conclusions From the point of view of possible intra- and postoperative complications, one-stage bilateral THA is equally safe or safer than two-stage interventions. Additionally, from an outcome perspective the one-stage procedure can be considered to be advantageous.

Joint lavage for osteoarthritis of the knee

Background Osteoarthritis is the most common form of joint disorder and a leading cause of pain and physical disability. Observational studies suggested a benefit for joint lavage, but recent, sham-controlled trials yielded conflicting results, suggesting joint lavage not to be effective. Objectives To compare joint lavage with sham intervention, placebo or non-intervention control in terms of effects on pain, function and safety outcomes in patients with knee osteoarthritis. Search methods We searched CENTRAL, MEDLINE, EMBASE, and CINAHL up to 3 August 2009, checked conference proceedings, reference lists, and contacted authors. Selection criteria We included studies if they were randomised or quasi-randomised trials that compared arthroscopic and non-arthroscopic joint lavage with a control intervention in patients with osteoarthritis of the knee. We did not apply any language restrictions. Data collection and analysis Two independent review authors extracted data using standardised forms. We contacted investigators to obtain missing outcome information. We calculated standardised mean differences (SMDs) for pain and function, and risk ratios for safety outcomes. We combined trials using inverse-variance random-effects meta-analysis. Main results We included seven trials with 567 patients. Three trials examined arthroscopic joint lavage, two non-arthroscopic joint lavage and two tidal irrigation. The methodological quality and the quality of reporting was poor and we identified a moderate to large degree of heterogeneity among the trials (I2 = 65%). We found little evidence for a benefit of joint lavage in terms of pain relief at three months (SMD -0.11, 95% CI -0.42 to 0.21), corresponding to a difference in pain scores between joint lavage and control of 0.3 cm on a 10-cm visual analogue scale (VAS). Results for improvement in function at three months were similar (SMD -0.10, 95% CI -0.30 to 0.11), corresponding to a difference in function scores between joint lavage and control of 0.2 cm on a WOMAC disability sub-scale from 0 to 10. For pain, estimates of effect sizes varied to some degree depending on the type of lavage, but this variation was likely to be explained by differences in the credibility of control interventions: trials using sham interventions to closely mimic the process of joint lavage showed a null-effect. Reporting on adverse events and drop out rates was unsatisfactory, and we were unable to draw conclusions for these secondary outcomes. Authors' conclusions Joint lavage does not result in a relevant benefit for patients with knee osteoarthritis in terms of pain relief or improvement of function.

A new universal, standardized implant database for product identification: a unique tool for arthroplasty registries.

INTRODUCTION Every joint registry aims to improve patient care by identifying implants that have an inferior performance. For this reason, each registry records the implant name that has been used in the individual patient. In most registries, a paper-based approach has been utilized for this purpose. However, in addition to being time-consuming, this approach does not account for the fact that failure patterns are not necessarily implant specific but can be associated with design features that are used in a number of implants. Therefore, we aimed to develop and evaluate an implant product library that allows both time saving barcode scanning on site in the hospital for the registration of the implant components and a detailed description of implant specifications. MATERIALS AND METHODS A task force consisting of representatives of the German Arthroplasty Registry, industry, and computer specialists agreed on a solution that allows barcode scanning of implant components and that also uses a detailed standardized classification describing arthroplasty components. The manufacturers classified all their components that are sold in Germany according to this classification. The implant database was analyzed regarding the completeness of components by algorithms and real-time data. RESULTS The implant library could be set up successfully. At this point, the implant database includes more than 38,000 items, of which all were classified by the manufacturers according to the predefined scheme. Using patient data from the German Arthroplasty Registry, several errors in the database were detected, all of which were corrected by the respective implant manufacturers. CONCLUSIONS The implant library that was developed for the German Arthroplasty Registry allows not only on-site barcode scanning for the registration of the implant components but also its classification tree allows a sophisticated analysis regarding implant characteristics, regardless of brand or manufacturer. The database is maintained by the implant manufacturers, thereby allowing registries to focus their resources on other areas of research. The database might represent a possible global model, which might encourage harmonization between joint replacement registries enabling comparisons between joint replacement registries.

Effect of chin-cup treatment on the temporomandibular joint: a systematic review

AIM To systematically search the literature and assess the available evidence for the influence of chin-cup therapy on the temporomandibular joint regarding morphological adaptations and appearance of temporomandibular disorders (TMD). MATERIALS AND METHODS Electronic database searches of published and unpublished literature were performed. The following electronic databases with no language and publication date restrictions were searched: MEDLINE (via Ovid and PubMed), EMBASE (via Ovid), the Cochrane Oral Health Group's Trials Register, and CENTRAL. Unpublished literature was searched on ClinicalTrials.gov, the National Research Register, and Pro-Quest Dissertation Abstracts and Thesis database. The reference lists of all eligible studies were checked for additional studies. Two review authors performed data extraction independently and in duplicate using data collection forms. Disagreements were resolved by discussion or the involvement of an arbiter. RESULTS From the 209 articles identified, 55 papers were considered eligible for inclusion in the review. Following the full text reading stage, 12 studies qualified for the final review analysis. No randomized clinical trial was identified. Eight of the included studies were of prospective and four of retrospective design. All studies were assessed for their quality and graded eventually from low to medium level of evidence. Based on the reported evidence, chin-cup therapy affects the condylar growth pattern, even though two studies reported no significance changes in disc position and arthrosis configuration. Concerning the incidence of TMD, it can be concluded from the available evidence that chin-cup therapy constitutes no risk factor for TMD. CONCLUSION Based on the available evidence, chin-cup therapy for Class III orthodontic anomaly seems to induce craniofacial adaptations. Nevertheless, there are insufficient or low-quality data in the orthodontic literature to allow the formulation of clear statements regarding the influence of chin-cup treatment on the temporomandibular joint.

HUNT: launch of a full-length cDNA database from the Helix Research Institute

The Helix Research Institute (HRI) in Japan is releasing 4356 HUman Novel Transcripts and related information in the newly established HUNT database. The institute is a joint research project principally funded by the Japanese Ministry of International Trade and Industry, and the clones were sequenced in the governmental New Energy and Industrial Technology Development Organization (NEDO) Human cDNA Sequencing Project. The HUNT database contains an extensive amount of annotation from advanced analysis and represents an essential bioinformatics contribution towards understanding of the gene function. The HRI human cDNA clones were obtained from full-length enriched cDNA libraries constructed with the oligo-capping method and have resulted in novel full-length cDNA sequences. A large fraction has little similarity to any proteins of known function and to obtain clues about possible function we have developed original analysis procedures. Any putative function deduced here can be validated or refuted by complementary analysis results. The user can also extract information from specific categories like PROSITE patterns, PFAM domains, PSORT localization, transmembrane helices and clones with GENIUS structure assignments. The HUNT database can be accessed at http://www.hri.co.jp/HUNT.

Analysis of the moisture effect on the mechanical behaviour of an adhesively bonded joint under proportional multi-axial loads

The objective of the study is to identify the 3D behaviour of an adhesive in an assembly, and to take into account the effect of ageing in a marine environment. To that end, three different tests were employed. Gravimetric analyses were used to determine the water diffusion kinetics in the adhesive. Bulk tensile tests were performed to highlight the effects of humid ageing on the adhesive behaviour. Modified Arcan tests were performed for several ageing times to obtain the experimental database which was necessary to identify constitutive models. A Mahnken-Schlimmer type model was determined for the unaged state according to a procedure developed in a previous study. This identification used inverse techniques. It was based on the unaged modified Arcan results and on a coupling between an optimisation routine and finite-element analysis. Then, a global inverse identification procedure was developed. Its aim was to relate the unaged parameters to the moisture concentration and overcome the difficulties usually associated with ageing of bonded assemblies in a humid environment: a non-uniformity of the stress state and a gradient of mechanical properties in the adhesive. This procedure was similar to the one used in the first part but needed modified Arcan results for several ageing times. It also required an initial assumption for the evolution of the Mahnken-Schlimmer parameters with the moisture concentration.