Avoimet julkaisuarkistot ja niiden tekniikka

Open Access -liike pyrkii vapauttamaan tieteellisen tiedon kaupallisuuden rajoitteista edesauttamalla artikkeleiden rinnakkaisversioiden avointa ja esteetöntä verkkotallennusta. Sen mahdollistamiseksi verkkoon perustetaan julkaisuarkistoja, joiden toiminta-ajatuksena on säilöä taustayhteisönsä tieteellinen tuotanto avoimesti ja keskitetysti yhteen paikkaan. Avoimen lähdekoodin arkistosovellukset jakavat sisältönsä OAI-protokollan avulla ja muodostavat näin globaalin virtuaalisen tietoverkon. Suurten tietomäärien käsittelyssä on huomioitava erityisesti kuvailutiedon rooli tehokkaiden hakujen toteuttamisessa sekä tiedon yksilöiminen verkossa erilaisten pysyvien tunnisteiden, kuten Handle:n tai URN:n avulla. Tieteellisen tiedon avoimella saatavuudella on merkittävä vaikutus myös oppimisen näkökulmasta. Julkaisuarkistot tarjoavat oppimateriaalin lisäksi uusia mahdollisuuksia julkaisukanavan ja oppimisymp äristön integroimiseen. Työssä esitellään avoimen saatavuuden keskeisiä teemoja sekä sen käytännön toteutusta varten kehitettyjä teknisiä ratkaisuja. Näiden pohjalta toteutetaan Meilahden kampuksen avoin julkaisuarkisto. Työssä pohditaan myös julkaisuarkistojen soveltuvuutta oppimisprosessin tukemiseen tutkivan- ja sulautuvan oppimisen viitekehyksessä. ACM Computing Classification System (CCS): H.3 [INFORMATION STORAGE AND RETRIEVAL], H.3.7 [Digital Libraries], H.3.3 [Information Search and Retrieval], H.3.5 [Online Information Services], K.3 [COMPUTERS AND EDUCATION], K.3.1 [Computer Uses in Education]

Integrating CDS/ISIS Databases with Greenstone Digital Library Software (GSDL)

CDS/ISIS is an advanced non-numerical information storage and retrieval software developed by UNESCO since 1985 to satisfy the need expressed by many institutions, especially in developing countries, to be able to streamline their information processing activities by using modern (and relatively inexpensive) technologies [1]. CDS/ISIS is available for MS-DOS, Windows and Unix operating system platforms. The formatting language of CDS/ISIS is one of its several strengths. It is not only used for formatting records for display but is also used for creating customized indexes. CDS/ISIS by itself does not facilitate in publishing its databases on the Internet nor does it facilitate in publishing on CD-ROMs. However, numbers of open source tools are now available, which enables in publishing CDS/ISIS databases on the Internet and also on CD-ROMs. In this paper, we have discussed the ways and means of integrating CDS/ISIS databases with GSDL, an open source digital library (DL) software.

Implementing WWWISIS for Providing Web Access to Bibliographic Databases

CDS/ISIS, an advanced non-numerical information storage and retrieval software was developed by UNESCO. With the emergence of WWW technology, most of the information activities are becoming Web-centric. Libraries and information providers are taking advantage of these Internet developments to provide access to their resources/information on the Web. A number of tools are now available for publishing CDS/ISIS databases on the Internet. One such tool is the WWWISIS Web gateway software, developed by BIREME, Brazil. This paper illustrates porting of sample records from a bibliographic database into CDS/ISIS, and then publishing this database on the Internet using WWWISIS.

The absolute orientation of a molecule in space: Extension of the 'CIP' system

A scheme for denoting the absolute spatial orientation of molecules and molecular fragments is presented; this is based on three angular deviations - one for each spatial dimension - with respect to a reference orientation, which is itself defined with the help of certain features of the Cahn-Ingold-Prelog stereochemical notation. The new scheme helps in reconstructing the three-dimensional characteristics of molecules from purely verbal descriptors, and may thus find application in various information storage and retrieval processes (e.,-. encrypting holograms, etc.).

Dual Confocal Laser-Induced Fluorescence/Moveable Contactless Conductivity Detector For Capillary Electrophoresis Microchip

A new dual simultaneous detector was developed for capillary electrophoresis microchip. Confocal laser-induced fluorescence (LIF) and moveable contactless conductivity detection (MCCD) were combined together for the first time. The two detection systems shared a common detection cell and could respond simultaneously. They were mutually independent and advantageous in analyses of mixtures containing organic and inorganic ions. The confocal LIF had high sensitivity and the MCCD could move along the separation channel and detect in different positions of the channel. The detection conditions of the dual detector were optimized. Rhodamine B was used to evaluate the performance of the dual detector. The limit of detection of the confocal LIF was < 5 nM, and that of the MCCD was 0.1 mu M. The dual detector had highly sensitivity and could offer response easily, rapidly and simultaneously. 

Micromachining Of Passive Planar Micromixer On Poly (Methyl Methacrylate) Substrate With Excimer Laser Ablation

Excimer laser ablation technique was introduced into this work to fabricate a passive planar micromixer on the PMMA substrate. T-junction shaped and width-changed S-shaped microchannels were both designed in this micromixer to enhance mixing effect. The mixing experiment of distilled water and Rhodamine B with injection flow rate of 500 and 1,500 mu m/s validates the mixing effectivity of this micromixer, and indicates the feasibility of excimer laser ablation in the microfabrication of mu-TAS device.

Analytical method of predicating the instabilities of a micro arch-shaped beam under electrostatic loading

An arch-shaped beam with different configurations under electrostatic loading experiences either the direct pull-in instability or the snap-through first and then the pull-in instability. When the pull-in instability occurs, the system collides with the electrode and adheres to it, which usually causes the system failure. When the snap-through instability occurs, the system experiences a discontinuous displacement to flip over without colliding with the electrode. The snap-through instability is an ideal actuation mechanism because of the following reasons: (1) after snap-through the system regains the stability and capability of withstanding further loading; (2) the system flips back when the loading is reduced, i.e. the system can be used repetitively; and (3) when approaching snap-through instability the system effective stiffness reduces toward zero, which leads to a fast flipping-over response. To differentiate these two types of instability responses for an arch-shaped beam is vital for the actuator design. For an arch-shaped beam under electrostatic loading, the nonlinear terms of the mid-plane stretching and the electrostatic loading make the analytical solution extremely difficult if not impossible and the related numerical solution is rather complex. Using the one mode expansion approximation and the truncation of the higher-order terms of the Taylor series, we present an analytical solution here. However, the one mode approximation and the truncation error of the Taylor series can cause serious error in the solution. Therefore, an error-compensating mechanism is also proposed. The analytical results are compared with both the experimental data and the numerical multi-mode analysis. The analytical method presented here offers a simple yet efficient solution approach by retaining good accuracy to analyze the instability of an arch-shaped beam under electrostatic loading.

Modeling sequencing errors by combining Hidden Markov models.

Among the largest resources for biological sequence data is the large amount of expressed sequence tags (ESTs) available in public and proprietary databases. ESTs provide information on transcripts but for technical reasons they often contain sequencing errors. Therefore, when analyzing EST sequences computationally, such errors must be taken into account. Earlier attempts to model error prone coding regions have shown good performance in detecting and predicting these while correcting sequencing errors using codon usage frequencies. In the research presented here, we improve the detection of translation start and stop sites by integrating a more complex mRNA model with codon usage bias based error correction into one hidden Markov model (HMM), thus generalizing this error correction approach to more complex HMMs. We show that our method maintains the performance in detecting coding sequences.

Toward interoperable bioscience data.

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

La veille bibliographique. Partie 4, Un élément de surveillance

Voici la quatrième et dernière partie des résultats d'une veille bibliographique sur la surveillance biologique de l'exposition aux produits chimiques en milieu de travail (SBEPCMT) mise en place par un réseau francophone multidisciplinaire.

Construction et validation de filtres de recherche bibliographique pour soutenir la prise de décisions basée sur les évidences : le cas de la sécurité des patients.

Les filtres de recherche bibliographique optimisés visent à faciliter le repérage de l’information dans les bases de données bibliographiques qui sont presque toujours la source la plus abondante d’évidences scientifiques. Ils contribuent à soutenir la prise de décisions basée sur les évidences. La majorité des filtres disponibles dans la littérature sont des filtres méthodologiques. Mais pour donner tout leur potentiel, ils doivent être combinés à des filtres permettant de repérer les études couvrant un sujet particulier. Dans le champ de la sécurité des patients, il a été démontré qu’un repérage déficient de l’information peut avoir des conséquences tragiques. Des filtres de recherche optimisés couvrant le champ pourraient s’avérer très utiles. La présente étude a pour but de proposer des filtres de recherche bibliographique optimisés pour le champ de la sécurité des patients, d’évaluer leur validité, et de proposer un guide pour l’élaboration de filtres de recherche. Nous proposons des filtres optimisés permettant de repérer des articles portant sur la sécurité des patients dans les organisations de santé dans les bases de données Medline, Embase et CINAHL. Ces filtres réalisent de très bonnes performances et sont spécialement construits pour les articles dont le contenu est lié de façon explicite au champ de la sécurité des patients par leurs auteurs. La mesure dans laquelle on peut généraliser leur utilisation à d’autres contextes est liée à la définition des frontières du champ de la sécurité des patients.

Testing search strategies for systematic reviews in the Medline literature database through PubMed

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

UNSUPERVISED INDEXING OF MEDLINE ARTICLES THROUGH GRAPH-BASED RANKING

The biomedical literature is extensively catalogued and indexed in MEDLINE. MEDLINE indexing is done by trained human indexers, who identify the most important concepts in each article, and is expensive and inconsistent. Automating the indexing task is difficult: the National Library of Medicine produces the Medical Text Indexer (MTI), which suggests potential indexing terms to the indexers. MTI’s output is not good enough to work unattended. In my thesis, I propose a different way to approach the indexing task called MEDRank. MEDRank creates graphs representing the concepts in biomedical articles and their relationships within the text, and applies graph-based ranking algorithms to identify the most important concepts in each article. I evaluate the performance of several automated indexing solutions, including my own, by comparing their output to the indexing terms selected by the human indexers. MEDRank outperformed all other evaluated indexing solutions, including MTI, in general indexing performance and precision. MEDRank can be used to cluster documents, index any kind of biomedical text with standard vocabularies, or could become part of MTI itself.

Using incomplete citation data for MEDLINE results ranking.

Information overload is a significant problem for modern medicine. Searching MEDLINE for common topics often retrieves more relevant documents than users can review. Therefore, we must identify documents that are not only relevant, but also important. Our system ranks articles using citation counts and the PageRank algorithm, incorporating data from the Science Citation Index. However, citation data is usually incomplete. Therefore, we explore the relationship between the quantity of citation information available to the system and the quality of the result ranking. Specifically, we test the ability of citation count and PageRank to identify "important articles" as defined by experts from large result sets with decreasing citation information. We found that PageRank performs better than simple citation counts, but both algorithms are surprisingly robust to information loss. We conclude that even an incomplete citation database is likely to be effective for importance ranking.