An evaluation of human protein-protein interaction data in the public domain.
(17/48)
BACKGROUND: Protein-protein interaction (PPI) databases have become a major resource for investigating biological networks and pathways in cells. A number of publicly available repositories for human PPIs are currently available. Each of these databases has their own unique features with a large variation in the type and depth of their annotations. RESULTS: We analyzed the major publicly available primary databases that contain literature curated PPI information for human proteins. This included BIND, DIP, HPRD, IntAct, MINT, MIPS, PDZBase and Reactome databases. The number of binary non-redundant human PPIs ranged from 101 in PDZBase and 346 in MIPS to 11,367 in MINT and 36,617 in HPRD. The number of genes annotated with at least one interactor was 9,427 in HPRD, 4,975 in MINT, 4,614 in IntAct, 3,887 in BIND and <1,000 in the remaining databases. The number of literature citations for the PPIs included in the databases was 43,634 in HPRD, 11,480 in MINT, 10,331 in IntAct, 8,020 in BIND and <2,100 in the remaining databases. CONCLUSION: Given the importance of PPIs, we suggest that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date. We hope that our analysis will help guide biomedical scientists in selecting the most appropriate database for their needs especially in light of the dramatic differences in their content. (+info)
Representations of sound in american deaf literature.
(18/48)
Sound plays a prominent role in narrative description of characters and environs in mainstream American literature. A review of American Deaf literature shows that the representations of sound held for deaf writers are in extensional and oppositional terms. American deaf writers, in their descriptions of entities, characters, functions, and settings, have created different representations of sound. In American Deaf literature, the representations of sound are filled with altered-acoustic and extra-acoustic images of sounds. The representations reflect psychophysiological experiences that presume the existence of an acoustic world by American deaf and hard-of-hearing writers, independent of the age when their hearing was lost, and changes in American Deaf culture. (+info)
A rubric to assess critical literature evaluation skills.
(19/48)
OBJECTIVE: To develop and describe the use of a rubric for reinforcing critical literature evaluation skills and assessing journal article critiques presented by pharmacy students during journal club exercises. DESIGN: A rubric was developed, tested, and revised as needed to guide students in presenting a published study critique during the second through fourth years of a first-professional doctor of pharmacy degree curriculum and to help faculty members assess student performance and provide formative feedback. Through each rubric iteration, the ease of use and clarity for both evaluators and students were determined with modifications made as indicated. Student feedback was obtained after using the rubric for journal article exercises, and interrater reliability of the rubric was determined. ASSESSMENT: Student feedback regarding rubric use for preparing a clinical study critique was positive across years. Intraclass correlation coefficients were high for each rubric section. The rubric was modified a total of 5 times based upon student feedback and faculty discussions. CONCLUSION: A properly designed and tested rubric can be a useful tool for evaluating student performance during a journal article presentation; however, a rubric can take considerable time to develop. A rubric can also be a valuable student learning aid for applying literature evaluation concepts to the critique of a published study. (+info)
Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor.
(20/48)
Today, digitization of legacy literature is a big issue. This also applies to the domain of biosystematics, where this process has just started. Digitized biosystematics literature requires a very precise and fine grained markup in order to be useful for detailed search, data linkage and mining. However, manual markup on sentence level and below is cumbersome and time consuming. In this paper, we present and evaluate the GoldenGATE editor, which is designed for the special needs of marking up OCR output with XML. It is built in order to support the user in this process as far as possible: Its functionality ranges from easy, intuitive tagging through markup conversion to dynamic binding of configurable plug-ins provided by third parties. Our evaluation shows that marking up an OCR document using GoldenGATE is three to four times faster than with an off-the-shelf XML editor like XML-Spy. Using domain-specific NLP-based plug-ins, these numbers are even higher. (+info)
Grappling with the literature of education research and practice.
(21/48)
The absence of a central database and use of specialized language hinder nonexperts in becoming familiar with the science teaching and learning literature and using it to inform their work. The challenge of locating articles related to a specific question or problem, coupled with the difficulty of comprehending findings based on a variety of different perspectives and practices, can be prohibitively difficult. As I have transitioned from bench to classroom-based research, I have become familiar with how to locate, decipher, and evaluate the education research literature. In this essay, I point out analogies to the literature of science research and practice, and I reference some of the literature that I have found useful in becoming an education researcher. I also introduce a new regular feature, "Current Insights: Recent Research in Science Teaching and Learning," which is designed to point CBE--Life Sciences Education (CBE-LSE) readers to current articles of interest in life sciences education, as well as more general and noteworthy publications in education research. (+info)
Ancient Chinese literature reveals pathways of eggplant domestication.
(22/48)
The evolution in the use of MIBG in more than 25 years of experimental and clinical applications.
(24/48)
Radioiodinated metaiodobenzylguanidine (MIBG), or Iobenguane, was developed in the late 1970s at the Michigan University Medical Center for imaging the adrenal medulla and its diseases, and was rapidly extended to depict a wide range of tumors of neural crest origin. Because of its high and selective uptake and retention by these tumors, careful consideration was also given to the therapeutic potential of [(131)I]MIBG. Beside imaging and therapy of neuroendocrine tumors, the possibility of in vivo assessment of cardiac sympathetic neuronal activity led recently to a renewed interest for MIBG scintigraphy and this application is still expanding. In this paper, we review the evolution in the use of MIBG in more than 25 years of experimental and clinical applications, with attention also to the developments in radiochemistry and instrumentation. A literature search in PubMed based on ''metaiodobenzylguanidine or MIBG'' was conducted; from this analysis, it appears that the use of MIBG evolved from nearly exclusively oncology (both for diagnosis and therapy) to new applications mainly aimed to study the sympathetic neuronal integrity of the heart. Those currently exceed those about imaging of tumor diseases. We also report the geographic distribution of published papers. (+info)