eGIFT: Mining Gene Information from the Literature

<p>Abstract</p> <p>Background</p> <p>With the biomedical literature continually expanding, searching PubMed for information about specific genes becomes increasingly difficult. Not only can thousands of results be returned, but gene name ambiguity leads to many irrelevant hits. As a result, it is difficult for life scientists and gene curators to rapidly get an overall picture about a specific gene from documents that mention its names and synonyms.</p> <p>Results</p> <p>In this paper, we present eGIFT (<url>http://biotm.cis.udel.edu/eGIFT</url>), a web-based tool that associates informative terms, called <it>i</it>Terms, and sentences containing them, with genes. To associate <it>i</it>Terms with a gene, eGIFT ranks <it>i</it>Terms about the gene, based on a score which compares the frequency of occurrence of a term in the gene's literature to its frequency of occurrence in documents about genes in general. To retrieve a gene's documents (Medline abstracts), eGIFT considers all gene names, aliases, and synonyms. Since many of the gene names can be ambiguous, eGIFT applies a disambiguation step to remove matches that do not correspond to this gene. Another additional filtering process is applied to retain those abstracts that focus on the gene rather than mention it in passing. eGIFT's information for a gene is pre-computed and users of eGIFT can search for genes by using a name or an EntrezGene identifier. <it>i</it>Terms are grouped into different categories to facilitate a quick inspection. eGIFT also links an <it>i</it>Term to sentences mentioning the term to allow users to see the relation between the <it>i</it>Term and the gene. We evaluated the precision and recall of eGIFT's <it>i</it>Terms for 40 genes; between 88% and 94% of the <it>i</it>Terms were marked as salient by our evaluators, and 94% of the UniProtKB keywords for these genes were also identified by eGIFT as <it>i</it>Terms.</p> <p>Conclusions</p> <p>Our evaluations suggest that <it>i</it>Terms capture highly-relevant aspects of genes. Furthermore, by showing sentences containing these terms, eGIFT can provide a quick description of a specific gene. eGIFT helps not only life scientists survey results of high-throughput experiments, but also annotators to find articles describing gene aspects and functions.</p

Cox-Maze III procedure with valvular surgery in an autopneumonectomized patient

<p>Abstract</p> <p>Destructive pulmonary inflammation can leave patients with only a single functional lung, resulting in anatomical and physiological changes that may interfere with subsequent cardiac surgeries. Such patients are vulnerable to perioperative cardiopulmonary complications. Herein, we report the first case, to our knowledge, of an autopneumonectomized patient who successfully underwent a modified Cox-Maze III procedure combined with valvular repairs. The three major findings in this case can be summarized as follows: (1) a median sternotomy with peripheral cannulations, such as femoral cannulations, can provide an optimal exposure and prevent the obstruction of vision that may occur as a result of multiple cannulations through a median sternotomy; (2) a modified septal incision combined with biatrial incisions facilitate adequate exposure of the mitral valve; and (3) the aggressive use of intraoperative ultrafiltration may be helpful for the perioperative managements as decreasing pulmonary water contents, thereby avoiding the pulmonary edema associated with secretion of inflammatory cytokines during a cardiopulmonary bypass. We also provide several suggestions for achieving similar satisfactory surgical outcomes in patients with a comparable condition.</p