78 research outputs found
A “textbook” view of the metastatic progression of a malignant tumor.
No full text<p>Figure 1 from:</p>
<p><strong> </strong>Divoli A, Mendonça EA, Evans JA, Rzhetsky A (2011) Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis. PLoS Comput Biol 7(10): e1002132. doi:10.1371/journal.pcbi.1002132</p>
<p> </p>
<p><strong>A “textbook” view of the metastatic progression of a malignant tumor.</strong></p>
<p>The tumor's development starts with its growth at the primary location (<em>primary tumor</em>). In metastatic progression, some cells from the primary tumor detach from the colony (<em>detachment</em>), enter blood or lymph vessels (<em>intravasation</em>) and travel within the body (<em>migration/transport</em>). Next, the traveling cells exit blood or lymph vessels (<em>extravasation</em>) and colonize new sites in the body. There, they divide and form tiny colonies at first (<em>micrometastasis</em>), followed by further cell proliferation, recruitment of blood vessels (<em>angiogenesis</em>) that provide small colonies with sufficient nutrients to develop into large tumors (<em>macrometastasis</em>). It is currently unclear if secondary colonies can re-metastasize to form tertiary and quaternary colonies (dotted line indicating a cyclic process).</p>
<p>doi:10.1371/journal.pcbi.1002132.g001</p
Do Peers See More in a Paper Than Its Authors?
No full textRecent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances
BiolE: Extracting informative sentences from the biomedical literature
No full textSummary: BiolE is a rule-based system that extracts informative sentences relating to protein families, their structures, functions and diseases from the biomedical literature. Based on manual definition of templates and rules, it aims at precise sentence extraction rather than wide recall. After uploading source text or retrieving abstracts from MEDLINE, users can extract sentences based on predefined or user-defined template categories. BiolE also provides a brief insight into the syntactic and semantic context of the source-text by looking at word, N-gram and MeSH-term distributions. Important applications of BiolE are in, for example, annotation of microarray data and of protein databases. © The Author 2005. Published by Oxford University Press. All rights reserved
Full text and figure display improves bioscience literature search.
No full textWhen reading bioscience journal articles, many researchers focus attention on the figures and their captions. This observation led to the development of the BioText literature search engine, a freely available Web-based application that allows biologists to search over the contents of Open Access Journals, and see figures from the articles displayed directly in the search results. This article presents a qualitative assessment of this system in the form of a usability study with 20 biologist participants using and commenting on the system. 19 out of 20 participants expressed a desire to use a bioscience literature search engine that displays articles' figures alongside the full text search results. 15 out of 20 participants said they would use a caption search and figure display interface either frequently or sometimes, while 4 said rarely and 1 said undecided. 10 out of 20 participants said they would use a tool for searching the text of tables and their captions either frequently or sometimes, while 7 said they would use it rarely if at all, 2 said they would never use it, and 1 was undecided. This study found evidence, supporting results of an earlier study, that bioscience literature search systems such as PubMed should show figures from articles alongside search results. It also found evidence that full text and captions should be searched along with the article title, metadata, and abstract. Finally, for a subset of users and information needs, allowing for explicit search within captions for figures and tables is a useful function, but it is not entirely clear how to cleanly integrate this within a more general literature search interface. Such a facility supports Open Access publishing efforts, as it requires access to full text of documents and the lifting of restrictions in order to show figures in the search interface
- …
