Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

Objective:

This paper examines the development and evaluation of an automatic summarization system in the domain of molecular genetics. The system is a potential component of an advanced biomedical information management application called Semantic MEDLINE and could assist librarians in developing secondary databases of genetic information extracted from the primary literature.

Methods:

An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease. The summarization system was evaluated on the task of identifying data describing genes associated with bladder cancer in MEDLINE citations. A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard. Recall, precision, and F-measure were calculated.

Results:

The system achieved recall of 46%, and precision of 88% (F-measure = 0.61) by taking Gene References into Function (GeneRIFs) into account.

Conclusion:

The new summarization schema for genetic etiology has potential as a component in Semantic MEDLINE to support the work of data curators.

Highlights

• Semantic MEDLINE streamlines information retrieval by succinctly expressing the meaning of sometimes complicated text and summarizing output according to a user''s needs.
• Semantic MEDLINE identifies genes noted in biomedical text as associated with a disease process.
• Semantic MEDLINE can potentially simplify secondary database curation.

Implications

• Library information retrieval services can potentially benefit from automated applications such as Semantic MEDLINE.
• Use of such automated applications can facilitate the library''s work in interdepartmental collaborative endeavors, thus reinforcing the library''s core value in its parent institution.

     

Bowels control brain: gut hormones and obesity

Peptide hormones are released from the gastrointestinal tract in response to nutrients and communicate information regarding the current state of energy balance to the brain. These hormones regulate appetite, energy expenditure and glucose homeostasis. They can act either via the circulation at target peripheral tissues, by activation of the vagus nerve or by acting on key brain regions implicated in energy homeostasis such as the hypothalamus and brainstem. This review gives an overview of the main gut hormones implicated in the regulation of food intake and how some of these are being targeted to develop anti obesity treatments.     

Peak muscle activation, joint kinematics, and kinetics during elliptical and stepping movement pattern on a Precor Adaptive Motion Trainer

Kinematic, kinetic, and electromyography data were collected from the biceps femoris, rectus femoris (RF), gluteus maximus, and erector spinae (ES) during a step and elliptical exercise at a standardized workload with no hand use. Findings depicted 95% greater ankle plantar flexion (p = .01), 29% more knee extension (p = .003), 101% higher peak knee flexor moments (p < .001) 54% greater hip extensor moments (p < .001), 268% greater anterior joint reaction force (p = .009), 37% more RF activation (p < .001), and 200 % more ES activation (p <. 001) for the elliptical motion. Sixteen percent more hip flexion (p < .001), 42% higher knee extensor moments (p < .001), and 54% greater hip flexor moments (p = .041) occurred during the step motion. Biomechanical differences between motions should be considered when planning an exercise regimen.     

Best performances by men and women open-water swimmers during the 'English Channel Swim' from 1900 to 2010

Abstract Little research has examined ultra-endurance swimming performances. The 'English Channel Swim', where swimmers have to cover a distance of 32?km between England and France represents a unique long-distance, open-water, sea-swimming challenge, and each year swimmers from all over the world try to succeed in this challenge. The best times in minutes and the nationality of successful men and women swimmers were analysed from 1900 to 2010. A total of 1,533 swimmers (455 women and 1,078 men) from more than 40 countries have successfully completed the 'English Channel Swim'. Great Britain was the country most represented, with 38% of the total, followed by the United States with 20%. Swim speed has increased progressively for both sexes (P??0.05). The results suggest that the performance of women open-water ultra-distance swimmers may be similar to that of men. Further studies investigating anthropometrical and physiological characteristics of open-water ultra-swimmers are needed to compare men's and women's open-water ultra-swim performances.     

Startups by recent university graduates and their faculty: Implications for university entrepreneurship policy

Earlier research on the role of universities in fostering entrepreneurial economic development almost exclusively covers spin-offs by faculty and staff. In contrast, we provide general evidence from the U.S. showing that the gross flow of start-ups by recently graduated students with an undergraduate degree in science or engineering is at least an order of magnitude larger than the spin-offs by their faculty, that a recent graduate is twice as likely as her Professor to start a business within three years of graduation, and that the graduates’ spin-offs are not of low quality. Three case studies illustrate how universities may stimulate science and engineering students and recent graduates to create new firms of high quality. We conclude that transforming university goals and practices toward increasing start-ups led by faculty might not be the most effective way for universities to stimulate entrepreneurial economic development.     

Children's reasoning about disclosing adult transgressions: effects of maltreatment, child age, and adult identity

A total of two hundred ninety-nine 4- to 9-year-old maltreated and nonmaltreated children of comparable socioeconomic status and ethnicity judged whether children should or would disclose unspecified transgressions of adults (instigators) to other adults (recipients) in scenarios varying the identity of the instigator (stranger or parent), the identity of the recipient (parent, police, or teacher), and the severity of the transgression ("something really bad" or "something just a little bad"). Children endorsed more disclosure against stranger than parent instigators and less disclosure to teacher than parent and police recipients. The youngest maltreated children endorsed less disclosure than nonmaltreated children, but the opposite was true among the oldest children. Older maltreated children distinguished less than nonmaltreated children between parents and other types of instigators and recipients.     

Fetal Genotype for the Xenobiotic Metabolizing Enzyme NQO1 Influences Intrauterine Growth Among Infants Whose Mothers Smoked During Pregnancy

Maternal smoking during pregnancy retards fetal growth and depresses infant birth weight. The magnitude of these effects may be moderated by fetal genotype. The current study investigated maternal smoking, fetal genotype, and fetal growth in a large population sample of dizygotic twins. Maternal smoking retarded fetal growth in a dose-dependent fashion. In a subsample of 497 twin pairs whose mothers smoked during pregnancy, a functional polymorphism in the NAD(P)H:quinone oxidoreductase gene ( NQO1 Pro187Ser; rs1800566) was significantly associated with fetal growth within families. The effect was strongest among moderate smokers. This is the first demonstration that fetal genotype for an enzyme involved in tobacco smoke metabolism influences intrauterine growth independent of maternal genotype. Future studies should conduct formal tests of Fetal Genotype × Maternal Smoking interactions.     

Beyond Giving: Political Advocacy and Volunteer Behaviors of Public University Alumni

College and university leaders have paid an enormous level of attention to one domain of alumni involvement: charitable giving. In light of the decline of state support for higher education and the shrinking ability of families to pay for college, such emphasis is understandable. However, this emphasis has blinded scholars and practitioners to understanding the important non-monetary support roles played by college alumni. Drawing on data from a research extensive university, this study employs a sequential mixed method design (focus groups and confirmatory factor analysis) to demonstrate that non-monetary support behaviors are best understood through the distinct, but interrelated domains of political advocacy and volunteerism. Political advocacy behaviors include contacting legislators, the governor’s office, local politicians and serving on a political action team, while volunteer behaviors include mentoring new alumni, recruiting students, and participating in special events. The study breaks ground for future research on alumni support for higher education, including strategies to recruit alumni volunteers and advocates.