Quantitative assessment of dictionary-based protein named entity tagging.
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OBJECTIVE: Natural language processing (NLP) approaches have been explored to manage and mine information recorded in biological literature. A critical step for biological literature mining is biological named entity tagging (BNET) that identifies names mentioned in text and normalizes them with entries in biological databases. The aim of this study was to provide quantitative assessment of the complexity of BNET on protein entities through BioThesaurus, a thesaurus of gene/protein names for UniProt knowledgebase (UniProtKB) entries that was acquired using online resources. METHODS: We evaluated the complexity through several perspectives: ambiguity (i.e., the number of genes/proteins represented by one name), synonymy (i.e., the number of names associated with the same gene/protein), and coverage (i.e., the percentage of gene/protein names in text included in the thesaurus). We also normalized names in BioThesaurus and measures were obtained twice, once before normalization and once after. RESULTS: The current version of BioThesaurus has over 2.6 million names or 2.1 million normalized names covering more than 1.8 million UniProtKB entries. The average synonymy is 3.53 (2.86 after normalization), ambiguity is 2.31 before normalization and 2.32 after, while the coverage is 94.0% based on the BioCreAtive data set comprising MEDLINE abstracts containing genes/proteins. CONCLUSION: The study indicated that names for genes/proteins are highly ambiguous and there are usually multiple names for the same gene or protein. It also demonstrated that most gene/protein names appearing in text can be found in BioThesaurus. (+info)
An evaluation of computer-based programmed instruction for promoting teachers' greetings of parents by name.
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Although greeting parents by name facilitates subsequent parent-teacher communication, baseline measures revealed that 4 preschool teachers never or rarely greeted parents by name during morning check-in. To promote frequent and accurate use of parents' names by teachers, the effects of a fully automated computerized assessment and programmed instruction (CAPI) intervention were evaluated in a multiple baseline design. The CAPI intervention involved assessment and training of relations among parents' and children's pictures and names, and produced rapid learning of parent names. The CAPI intervention also resulted in substantial improvements in the classroom use of parents' names for 3 of the 4 teachers; however, a supervisor-mediated feedback package (consisting of instructions, differential reinforcement, and error correction) was necessary to maintain name use for 2 of those teachers. The practical strengths and limitations of computer-based teacher training are discussed. (+info)
Using a Spanish surname match to improve identification of Hispanic women in Medicare administrative data.
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OBJECTIVE: To assess the effectiveness of a Spanish surname match for improving the identification of Hispanic women in Medicare administrative data in which Hispanics are historically underrepresented. DATA SOURCES: We collected self-identified race/ethnicity data (N=2,997) from a mailed survey sent to elderly Medicare beneficiaries who resided in 11 geographic areas consisting of eight metropolitan counties and three nonmetropolitan areas (171 counties) in the fall of 2004. The 1990 Census Spanish Surname list was used to identify Hispanics in the Medicare data. In addition, we used data published on the U.S. Census Bureau website to obtain estimates of elderly Hispanics. STUDY DESIGN: We used self-identified race/ethnicity as the gold standard to examine the agreement with Medicare race code alone, and with Medicare race code+Spanish surname match. Additionally, we estimated the proportions of Hispanic women and men, in each of the 11 geographic areas in our survey, using the Medicare race code alone and the Medicare race code+Spanish surname match, and compared those estimates with estimates derived from U.S. Census 2000 data. PRINCIPAL FINDINGS: The Spanish surname match dramatically increased the accuracy of the Medicare race code for identifying both Hispanic and white women, producing improvements comparable with those seen for men. CONCLUSIONS: We recommend the addition of a proxy race code in the Medicare data using the Spanish surname match to improve the accuracy of racial/ethnic representation.To assess the effectiveness of a Spanish surname match for improving the identification of Hispanic women in Medicare administrative data in which Hispanics are historically underrepresented. We collected self-identified race/ethnicity data (N=2,997) from a mailed survey sent to elderly Medicare beneficiaries who resided in 11 geographic areas consisting of eight metropolitan counties and three nonmetropolitan areas (171 counties) in the fall of 2004. The 1990 Census Spanish Surname list was used to identify Hispanics in the Medicare data. In addition, we used data published on the U.S. Census Bureau website to obtain estimates of elderly Hispanics. We used self-identified race/ethnicity as the gold standard to examine the agreement with Medicare race code alone, and with Medicare race code+Spanish surname match. Additionally, we estimated the proportions of Hispanic women and men, in each of the 11 geographic areas in our survey, using the Medicare race code alone and the Medicare race code+Spanish surname match, and compared those estimates with estimates derived from U.S. Census 2000 data. The Spanish surname match dramatically increased the accuracy of the Medicare race code for identifying both Hispanic and white women, producing improvements comparable with those seen for men. We recommend the addition of a proxy race code in the Medicare data using the Spanish surname match to improve the accuracy of racial/ethnic representation. (+info)
Use of geocoding and surname analysis to estimate race and ethnicity.
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OBJECTIVE: To review two indirect methods, geocoding and surname analysis, for estimating race/ethnicity as a means for health plans to assess disparities in care. STUDY DESIGN: Review of published articles and unpublished data on the use of geocoding and surname analyses. PRINCIPAL FINDINGS: Few published studies have evaluated use of geocoding to estimate racial and ethnic characteristics of a patient population or to assess disparities in health care. Three of four studies showed similar estimates of the proportion of blacks and one showed nearly identical estimates of racial disparities, regardless of whether indirect or more direct measures (e.g., death certificate or CMS data) were used. However, accuracy depended on racial segregation levels in the population and region assessed and geocoding was unreliable for identifying Hispanics and Asians/Pacific Islanders. Similarly, several studies suggest surname analyses produces reasonable estimates of whether an enrollee is Hispanic or Asian/Pacific Islander and can identify disparities in care. However, accuracy depends on the concentrations of Asians or Hispanics in areas assessed. It is less accurate for women and more acculturated and higher SES persons due intermarriage, name changes, and adoption. Surname analysis is not accurate for identifying African Americans. Recent unpublished analyses suggest plans can successfully use a combined geocoding/surname analyses approach to identify disparities in care in most regions. Refinements based on Bayesian methods may make geocoding/surname analyses appropriate for use in areas where the accuracy is currently poor, but validation of these preliminary results is needed. CONCLUSIONS: Geocoding and surname analysis show promise for estimating racial/ethnic health plan composition of enrollees when direct data on major racial and ethnic groups are lacking. These data can be used to assess disparities in care, pending availability of self-reported race/ethnicity data. (+info)
Notification that new names and new combinations have appeared in volume 56, part 5, of the IJSEM.
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This listing of names published in a previous issue of the IJSEM is provided as a service to bacteriology to assist in the recognition of new names and new combinations. This procedure was proposed by the Judicial Commission [Minute 11(ii), Int J Syst Bacteriol 41 (1991), p. 185]. The names given herein are listed according to the Rules of priority (i.e. page number and order of valid publication of names in the original articles). Taxonomic opinions included in this List (i.e. the creation of synonyms or the emendation of circumscriptions) cannot be considered as validly published nor, in any other way, approved by the International Committee on Systematics of Prokaryotes and its Judicial Commission. (+info)
The influence of personal familiarity on object naming, knowledge, and use in dementia.
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Reports of semantic dementia patients have shown more accurate identification and use for personal objects than unfamiliar analogs of the same objects (e.g., personal comb versus experimenter's comb) [Bozeat, S., Lambon Ralph, M. A., Patterson, K., & Hodges, J. R. (2002). The influence of personal familiarity and context on object use in semantic dementia. Neurocase, 8, 127-134; Snowden, J. S., Griffiths, H., & Neary, D. (1994). Semantic dementia: Autobiographical contribution to preservation of meaning. Cognitive Neuropsychology, 11, 265-288]. Despite potential clinical implications, the personal object advantage has not been explored in various dementia populations. Sixteen mild to moderate dementia patients were tested with 12-15 of their personal objects and laboratory analog objects. Four tasks were administered: Naming, Gesture, Semantic/Script Generation, and Personal Object Decision (i.e., Is this yours?). Although 25% of the sample performed at chance in identifying personal objects as their own, participants generated more specific information (t=2.3, p=.03) and more accurate gestures (t=2.4, p=.03) for personal objects. Thus, the personal object advantage was observed for script/semantic knowledge and movement sequences, and should be considered in residential planning for various dementia patients. (+info)
Personally addressed hand-signed letters increase questionnaire response: a meta-analysis of randomised controlled trials.
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BACKGROUND: Postal questionnaires are commonly used to collect data for health studies, but non-response reduces study sample sizes and can introduce bias. Finding ways to increase the proportion of questionnaires returned would improve research quality. We sought to quantify the effect on response when researchers address participants personally by name on letters that accompany questionnaires. METHODS: All randomised controlled trials in a published systematic review that evaluated the effect on response of including participants' names on letters that accompany questionnaires were included. Odds ratios for response were pooled in a random effects meta-analysis and evidence for changes in effects over time was assessed using random effects meta-regression. RESULTS: Fourteen randomised controlled trials were included covering a wide range of topics. Most topics were unrelated to health or social care. The odds of response when including participants' names on letters were increased by one-fifth (pooled OR 1.18, 95% CI 1.03 to 1.34; p = 0.015). When participants' names and hand-written signatures were used in combination, the effect was a more substantial increase in response (OR 1.45, 95% CI 1.27 to 1.66; p < 0.001), corresponding to an absolute increase in the proportion of questionnaires returned of between 4% and 10%, depending on the baseline response rate. There was no evidence that the magnitude of these effects had declined over time. CONCLUSION: This meta-analysis of the best available evidence indicates that researchers using postal questionnaires can increase response by addressing participants by name on cover letters. The effect appears to be enhanced by including hand-written signatures. (+info)
List of new names and new combinations previously effectively, but not validly, published.
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The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination. (+info)