Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

Human dermal fibroblasts, keratinocytes and adipose stem cells behaviour on patterned electrospun nanofiber meshes

Natural extracellular Matrix (ECM) creates a unique cellular microenvironment. It acts as a support to organize cells in tissues, maintains their structure and works also as a reservoir for cytokines, thus controlling cell growth and differentiation. A well-defined biomaterial surface topography is believed to be adequate to mimic native ECM for guiding cell growth or tissue regeneration. This structure can be achieved by using an electrospinning technique, which allows producing a non-woven nanofibrous structure with topographic features mimicking the natural ECM. [...]info:eu-repo/semantics/publishedVersio

Expression, purification and bioactivity of recombinant human bone morphogenetic protein-4,-9,-10,-11 and-14 produced in Escherichia coli for tissue engineering applications

[Excerpt] Bone morphogenetic proteins (BMPs) are cytokines from the TGFb superfamily, with important roles during embryonic development and in inducing bone and cartilage in the adult body. In this contribution, we report the expression of recombinant human BMP-4, BMP-9, BMP-10, BMP-11 (or growth differentiation factor-11, GDF-11) and BMP-14 (GDF-5), using Escherichia coli pET-25b expression system. The BMPs were purified by affinity chromatography and its bioactivity accessed in C2C12 cell line, by screening the expression of osteogenic markers with RT-PCR. [...]Fundação para a Ciência e Tecnologia for PhD grant SFRH/BD/17049/2004 and project ElastM POCI/CTM/ 57177/2004 supported by FEDER and the Fundação para a Ciência e Tecnologia; European STREP Project HIPPOCRATES (NMP3-CT-2003-505758). The work was carried out under the scope of the European NoE EXPERTISSUES (NMP3-CT-2004-500283).info:eu-repo/semantics/publishedVersio

Expertise-based peer selection in Peer-to-Peer networks

Peer-to-Peer systems have proven to be an effective way of sharing data. Modern protocols are able to efficiently route a message to a given peer. However, determining the destination peer in the first place is not always trivial. We propose a a message to a given peer. However, determining the destination peer in the first place is not always trivial. We propose a model in which peers advertise their expertise in the Peer-to-Peer network. The knowledge about the expertise of other peers forms a semantic topology. Based on the semantic similarity between the subject of a query and the expertise of other peers, a peer can select appropriate peers to forward queries to, instead of broadcasting the query or sending it to a random set of peers. To calculate our semantic similarity measure, we make the simplifying assumption that the peers share the same ontology. We evaluate the model in a bibliographic scenario, where peers share bibliographic descriptions of publications among each other. In simulation experiments complemented with a real-world field experiment, we show how expertise-based peer selection improves the performance of a Peer-to-Peer system with respect to precision, recall and the number of messages

Expression, purification and osteogenic bioactivity of recombinant human BMP-4, -9, -10, -11 and -14

Bone morphogenetic proteins (BMPs) are cytokines from the TGF-b superfamily, with important roles during embryonic development and in the induction of bone and cartilage tissue differentiation in the adult body. In this contribution, we report the expression of recombinant human BMP-4, BMP-9, BMP-10, BMP-11 (or growth differentiation factor- 11, GDF-11) and BMP-14 (GDF-5), using Escherichia coli pET-25b vector. BMPs were overexpressed, purified by affinity his-tag chromatography and shown to induce the expression of early markers of bone differentiation (e.g. smad-1, smad-5, runx2/cbfa1, dlx5, osterix, osteopontin, bone sialoprotein and alkaline phosphatase) in C2C12 cells and in human adipose stem cells. The described approach is a promising method for producing large amounts of different recombinant BMPs that show potential for novel biomedical applications.The author wishes to acknowledge the Sanger Institute for kindly offering the bacterial clones for cloning of human BMP-9 to -14. This work was supported by Fundacao para a Ciencia e Tecnologia (PhD grant SFRH/BD/17049/2004, project ElastM POCI/CTM/57177/2004 funded by FEDER and the Fundacao para a Ciencia e Tecnologia; and European STREP Project HIPPOCRATES (NMP3-CT-2003-505758). This work was carried out under the scope of the European NoE EXPERTISSUES (NMP3-CT-2004-500283)

Silk nanoparticles for delivery of human BMP-2 in bone regenerative medicine applications

[Excerpt] A tissue engineering approach combines the use of scaffold biomaterials, stem cells and growth factors. Bone morphogenetic proteins (BMPs) are growth factors that have sparked a great interest in tissue engineering due to their strong ability to promote new bone formation. Herein, we report the use of silk derived nanoparticles as carriers for delivery of human BMP-2. Silks are attractive biomaterials for tissue engineering due to its biocompatibility, slow biodegradability and excellent mechanical properties. Recombinant human BMP-2 was expressed in Escherichia coli and purified by affinity chromatography, showing bioactivity in human adipose stem cells. BMP2-containing silk particles were then prepared by a water-in-oil emulsion method. [...]info:eu-repo/semantics/publishedVersio

Associative and spatial relationships in thesaurus-based retrieval

The OASIS (Ontologically Augmented Spatial Information System) project explores terminology systems for thematic and spatial access in digital library applications. A prototype implementation uses data from the Royal Commission on the Ancient and Historical Monuments of Scotland, together with the Getty AAT and TGN thesauri. This paper describes its integrated spatial and thematic schema and discusses novel approaches to the application of thesauri in spatial and thematic semantic distance measures. Semantic distance measures can underpin interactive and automatic query expansion techniques by ranking lists of candidate terms. We first illustrate how hierarchical spatial relationships can be used to provide more flexible retrieval for queries incorporating place names in applications employing online gazetteers and geographical thesauri. We then employ a set of experimental scenarios to investigate key issues affecting use of the associative (RT) thesaurus relationships in semantic distance measures. Previous work has noted the potential of RTs in thesaurus search aids but the problem of increased noise in result sets has been emphasised. Specialising RTs allows the possibility of dynamically linking RT type to query context. Results presented in this paper demonstrate the potential for filtering on the context of the RT link and on subtypes of RT relationships

Producing Cochrane systematic reviews—a qualitative study of current approaches and opportunities for innovation and improvement

Background: Producing high-quality, relevant systematic reviews and keeping them up to date is challenging. Cochrane is a leading provider of systematic reviews in health. For Cochrane to continue to contribute to improvements in heath, Cochrane Reviews must be rigorous, reliable and up to date. We aimed to explore existing models of Cochrane Review production and emerging opportunities to improve the efficiency and sustainability of these processes. Methods: To inform discussions about how to best achieve this, we conducted 26 interviews and an online survey with 106 respondents. Results: Respondents highlighted the importance and challenge of creating reliable, timely systematic reviews. They described the challenges and opportunities presented by current production models, and they shared what they are doing to improve review production. They particularly highlighted significant challenges with increasing complexity of review methods; difficulty keeping authors on board and on track; and the length of time required to complete the process. Strong themes emerged about the roles of authors and Review Groups, the central actors in the review production process. The results suggest that improvements to Cochrane's systematic review production models could come from improving clarity of roles and expectations, ensuring continuity and consistency of input, enabling active management of the review process, centralising some review production steps; breaking reviews into smaller "chunks", and improving approaches to building capacity of and sharing information between authors and Review Groups. Respondents noted the important role new technologies have to play in enabling these improvements. Conclusions: The findings of this study will inform the development of new Cochrane Review production models and may provide valuable data for other systematic review producers as they consider how best to produce rigorous, reliable, up-to-date reviews

Thermal neutron background at Laboratorio Subterráneo de Canfranc (LSC)

The thermal neutron background at Laboratorio Subterráneo de Canfranc (LSC) has been determined using several He proportional counter detectors. Bare and Cd shielded counters were used in a series of long measurements. Pulse shape discrimination techniques were applied to discriminate between neutron and gamma signals as well as other intrinsic contributions. Montecarlo simulations allowed us to estimate the sensitivity of the detectors and calculate values for the background flux of thermal neutrons inside Hall-A of LSC. The obtained value is (3.5±0.8)×10 n/cms, and is within an order of magnitude compared to similar facilities.This work was supported partially by the Spanish Ministerio de Ciencia e Innovación and its Plan Nacional de I+D+i de Física de Partículas projects: FPA2016-76765-P and FPA2018-096717-B-C21. The authors want to acknowledge the help provided by the staff at LSC in the preparation and support for this work