Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Entwicklung eines Dienstleistungssystems fuer kostenguenstiges Bauen mit hoher Qualitaet auf der Basis dezentraler Produktion marktueblicher Bauteile und modernster Informations- und Kommunikationssysteme. Teilprojekt: Planung und Koordinierung des Verbundvorhabens; Entwicklung eines CAD/CAM Systems fuer Wand-Decke-Dach, Ausbausysteme, Aussenanlagen und der Tragwerksplanung Abschlussbericht

SIGLEAvailable from TIB Hannover: F03B917 / FIZ - Fachinformationszzentrum Karlsruhe / TIB - Technische InformationsbibliothekBundesministerium fuer Bildung und Forschung, Berlin (Germany)DEGerman

Use of flow cytometry for characterization and fractionation of cell populations based on their expression of heparan sulfate epitopes

Item does not contain fulltextThe ability to characterize alterations in heparan sulfate (HS) structure during development or as a result of loss or mutation of one or more components of the HS biosynthetic pathway is essential for broad understanding of the effects these changes may have on cell/tissue function. The use of anti-HS antibodies provides an opportunity to study HS chain composition in situ, with a multitude of different antibodies having been generated that recognize subtle differences in HS patterning, with the number and positioning of sulfate groups influencing antibody binding affinity. Flow cytometry is a valuable technique to enable the rapid characterization of the changes in HS-specific antibody binding in situ, allowing multiple cell types to be directly compared. Additionally fluorescent-activated cell sorting (FACS) allows fractionation of cells based on their HS-epitope expression

A developmentally regulated heparan sulfate epitope defines a subpopulation with increased blood potential during mesodermal differentiation.

Contains fulltext : 69422.pdf (publisher's version ) (Closed access)Heparan sulfate (HS) is a mandatory coreceptor for many growth factors and morphogens involved in embryonic development; its bioactivity is dictated by complex sulfation motifs embedded within the polymer chain. Using a panel of HS-specific antibodies we have identified a unique HS epitope recognized by antibody HS4C3 that is selectively expressed during differentiation of embryonic stem (ES) cells along the mesodermal lineage to the hemangioblast stage. The appearance of this high-affinity HS4C3-binding (HS4C3(high)) epitope is transient; the epitope is specifically expressed within the emerging Brachyury(+) (Bry(+)) population and marks those cells that will become fetal liver kinase 1 (Flk1)(+). Fluorescence-activated cell sorting (FACS) separation and colony forming assays revealed that HS4C3(high)/Flk1(+) cells have a dramatically increased potential to form both blast and endothelial colonies, both of which depend upon the HS-binding growth factor vascular endothelial growth factor. Critically, expression of this HS epitope is tightly regulated, disappearing from the cell surface as the resultant hematopoietic lineages mature, in a similar manner to protein markers Bry and Flk1. In vivo studies showed a remarkable correlation with in vitro findings, with expression of HS4C3-binding epitopes restricted to newly formed mesodermal tissues during gastrulation. We believe this is the first time a defined HS epitope has been implicated in a specific developmental pathway and that this provides, in addition, a novel enrichment technique for the isolation of hemangioblasts from mixed differentiated ES cell cultures