Collocation analysis for UMLS knowledge-based word sense disambiguation

BACKGROUND: The effectiveness of knowledge-based word sense disambiguation (WSD) approaches depends in part on the information available in the reference knowledge resource. Off the shelf, these resources are not optimized for WSD and might lack terms to model the context properly. In addition, they might include noisy terms which contribute to false positives in the disambiguation results. METHODS: We analyzed some collocation types which could improve the performance of knowledge-based disambiguation methods. Collocations are obtained by extracting candidate collocations from MEDLINE and then assigning them to one of the senses of an ambiguous word. We performed this assignment either using semantic group profiles or a knowledge-based disambiguation method. In addition to collocations, we used second-order features from a previously implemented approach.Specifically, we measured the effect of these collocations in two knowledge-based WSD methods. The first method, AEC, uses the knowledge from the UMLS to collect examples from MEDLINE which are used to train a Naïve Bayes approach. The second method, MRD, builds a profile for each candidate sense based on the UMLS and compares the profile to the context of the ambiguous word.We have used two WSD test sets which contain disambiguation cases which are mapped to UMLS concepts. The first one, the NLM WSD set, was developed manually by several domain experts and contains words with high frequency occurrence in MEDLINE. The second one, the MSH WSD set, was developed automatically using the MeSH indexing in MEDLINE. It contains a larger set of words and covers a larger number of UMLS semantic types. RESULTS: The results indicate an improvement after the use of collocations, although the approaches have different performance depending on the data set. In the NLM WSD set, the improvement is larger for the MRD disambiguation method using second-order features. Assignment of collocations to a candidate sense based on UMLS semantic group profiles is more effective in the AEC method.In the MSH WSD set, the increment in performance is modest for all the methods. Collocations combined with the MRD disambiguation method have the best performance. The MRD disambiguation method and second-order features provide an insignificant change in performance. The AEC disambiguation method gives a modest improvement in performance. Assignment of collocations to a candidate sense based on knowledge-based methods has better performance. CONCLUSIONS: Collocations improve the performance of knowledge-based disambiguation methods, although results vary depending on the test set and method used. Generally, the AEC method is sensitive to query drift. Using AEC, just a few selected terms provide a large improvement in disambiguation performance. The MRD method handles noisy terms better but requires a larger set of terms to improve performance

Suplementación de raciones para cebo intensivo de terneros con aceites vegetales: rendimientos productivos, calidad de la canal, de la grasa y de la carne

Se han estudiado los efectos de la incorporación de aceites de origen vegetal sobre los rendimientos productivos, calidad de la canal y de la grasa en el ganado vacuno. Se utilizaron 240 terneros agrupados en 24 lotes de 10 terneros cada uno. Las raciones experimentales fueron: Tratamiento Control (4% de aceite de palma), Oliva (4,8% de jabón cálcico de aceite de oliva), Soja (4% de aceite de soja). De cada lote se seleccionó al azar un ternero (8 terneros por tratamiento) para diseccionar su 6ª costilla. No se han observado diferencias significativas entre tratamientos para ningún parámetro productivo ni de calidad de la canal. Los animales que consumieron aceite de oliva presentaron un mayor contenido (P=0,09) en C18:2 cis-9, trans-11 CLA en la grasa intramuscular que los que consumieron palma

Suplementación de raciones para cebo intensivo de terneros con aceites vegetales: calidad de carne

Se han estudiado los efectos de la incorporación de aceites de origen vegetal sobre la calidad de carne en el ganado vacuno. Se utilizaron 240 terneros agrupados en 24 lotes de 10 terneros cada uno. Las raciones experimentales fueron: Tratamiento Control (4% de aceite de palma), Oliva (4,8% de jabón cálcico de aceite de oliva), Soja (4% de aceite de soja). De cada lote se seleccionó al azar un ternero (8 terneros por tratamiento) para diseccionar su 6ª costilla. Se tomaron medidas de pH, color y textura del músculo Longissimus dorsi. Por último se realizó un análisis sensorial mediante un panel de catadores en el que se analizaron los parámetros de olor, textura y flavor de la carne. La carne de los animales alimentados con aceite de palma (Control) presentó el valor más alto (P0,05). En el análisis sensorial de la carne no se han observado diferencias significativas en los parámetros estudiados

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

<p>Abstract</p> <p>Background</p> <p>Evaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD.</p> <p>Methods</p> <p>In our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set.</p> <p>Results</p> <p>The resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE.</p> <p>We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods.</p> <p>Conclusions</p> <p>The MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions.</p

Employment Expectations and Gross Flows by Type of Work Contract

There is growing interest in understanding firms’ temporary and permanent employment practices and how institutional changes shape them. Using data on Spanish establishments, we examine: (a) how employers adjust temporary and permanent job and worker flows to prior employment expectations, and (b) how the 1994 and 1997 labour reforms promoting permanent employment affected establishments’ employment practices. Generally, establishments’ prior employment expectations are realized through changes in all job and worker flows. However, establishments uniquely rely on temporary hires as a buffer to confront diminishing long-run employment expectations. None of the reforms significantly affected establishments’ net temporary or permanent employment flows.http://deepblue.lib.umich.edu/bitstream/2027.42/40032/3/wp646.pd

Multitasking Compensatory Saccadic Training Program for Hemianopia Patients: A New Approach With 3-Dimensional Real-World Objects

Producción CientíficaPurpose: To examinewhether a noncomputerized multitasking compensatory saccadic training program (MCSTP) for patients with hemianopia, based on a reading regimen and eight exercises that recreate everyday visuomotor activities using threedimensional (3D) real-world objects, improves the visual ability/function, quality of life (QL), and functional independence (FI). Methods: The 3D-MCSTP included four in-office visits and two customized homebased daily training sessions over 12weeks. A quasiexperimental, pretest/posttest study designwas carried out with an intervention group (IG) (n = 20) and a no-training group (NTG) (n = 20) matched for age, hemianopia type, and brain injury duration. Results: The groups were comparable for the main baseline variables and all participants (n = 40) completed the study. The IGmainly showed significant improvements in visual-processing speed (57.34% ± 19.28%; P < 0.0001) and visual attention/retention ability (26.67% ± 19.21%; P < 0.0001), which also were significantly greater (P < 0.05) than in the NTG. Moreover, the IG showed large effect sizes (Cohen’s d) in 75% of the totalQL and FI dimensions analyzed; in contrast to the NTGthat showed negligiblemean effect sizes in 96% of these dimensions. Conclusions: The customized 3D-MCSTP was associated with a satisfactory response in the IG for improving complex visual processing, QL, and FI. Translational Relevance: Neurovisual rehabilitation of patientswith hemianopia seems more efficient when programs combine in-office visits and customized home-based training sessions based on real objects and simulating real-life conditions, than no treatment or previously reported computer-screen approaches, probably because of better stimulation of patients´ motivation and visual-processing speed brain mechanisms

Knowledge-based biomedical word sense disambiguation: comparison of approaches

<p>Abstract</p> <p>Background</p> <p>Word sense disambiguation (WSD) algorithms attempt to select the proper sense of ambiguous terms in text. Resources like the UMLS provide a reference thesaurus to be used to annotate the biomedical literature. Statistical learning approaches have produced good results, but the size of the UMLS makes the production of training data infeasible to cover all the domain.</p> <p>Methods</p> <p>We present research on existing WSD approaches based on knowledge bases, which complement the studies performed on statistical learning. We compare four approaches which rely on the UMLS Metathesaurus as the source of knowledge. The first approach compares the overlap of the context of the ambiguous word to the candidate senses based on a representation built out of the definitions, synonyms and related terms. The second approach collects training data for each of the candidate senses to perform WSD based on queries built using monosemous synonyms and related terms. These queries are used to retrieve MEDLINE citations. Then, a machine learning approach is trained on this corpus. The third approach is a graph-based method which exploits the structure of the Metathesaurus network of relations to perform unsupervised WSD. This approach ranks nodes in the graph according to their relative structural importance. The last approach uses the semantic types assigned to the concepts in the Metathesaurus to perform WSD. The context of the ambiguous word and semantic types of the candidate concepts are mapped to Journal Descriptors. These mappings are compared to decide among the candidate concepts. Results are provided estimating accuracy of the different methods on the WSD test collection available from the NLM.</p> <p>Conclusions</p> <p>We have found that the last approach achieves better results compared to the other methods. The graph-based approach, using the structure of the Metathesaurus network to estimate the relevance of the Metathesaurus concepts, does not perform well compared to the first two methods. In addition, the combination of methods improves the performance over the individual approaches. On the other hand, the performance is still below statistical learning trained on manually produced data and below the maximum frequency sense baseline. Finally, we propose several directions to improve the existing methods and to improve the Metathesaurus to be more effective in WSD.</p

Measurement of tt̅ spin correlation in pp̅ collisions using the CDF II detector at the Tevatron

7 páginas, 2 figuras, 1 tabla.-- PACS numbers: 12.38.Qk, 13.85.-t, 14.65.Ha.-- CDF Collaboration: et al.The tt̅ spin correlation at production is a fundamental prediction of QCD and a potentially incisive test of new physics coupled to top quarks. We measure the tt̅ spin state in pp̅ collisions at √s=1.96  TeV using 1001 candidate events in the lepton plus jets decay channel reconstructed in the CDF II detector. In the helicity basis, for a top-quark mass of 172.5  GeV/c2, we find a spin correlation coefficient κ=0.60±0.50  (stat)±0.16  (syst), consistent with the QCD prediction, κ≈0.40.This work was supported by the U.S. Department of Energy and National Science Foundation; the Italian Istituto Nazionale di Fisica Nucleare; the Ministry of Education, Culture, Sports, Science and Technology of Japan; the Natural Sciences and Engineering Research Council of Canada; the National Science Council of the Republic of China; the Swiss National Science Foundation; the A. P. Sloan Foundation; the Bundesministerium für Bildung und Forschung, Germany; the World Class University Program, the National Research Foundation of Korea; the Science and Technology Facilities Council and the Royal Society, UK; the Institut National de Physique Nucleaire et Physique des Particules/CNRS; the Russian Foundation for Basic Research; the Ministerio de Ciencia e Innovación, and Programa Consolider-Ingenio 2010, Spain; the Slovak R & D Agency; and the Academy of Finland.Peer reviewe

Physiological stress does not increase with urbanization in European blackbirds:Evidence from hormonal, immunological and cellular indicators

Urbanization changes the landscape structure and ecological processes of natural habitats. While urban areas expose animal communities to novel challenges, they may also provide more stable environments in which environmental fluctuations are buffered. Species´ ecology and physiology may determine their capacity to cope with the city life. However, the physiological mechanisms underlying organismal responses to urbanization, and whether different physiological systems are equally affected by urban environments remain poorly understood. This severely limits our capacity to predict the impact of anthropogenic habitats on wild populations. In this study, we measured indicators of physiological stress at the endocrine, immune and cellular level (feather corticosterone levels, heterophil to lymphocyte ratio, and heat-shock proteins) in urban and non-urban European blackbirds (Turdus merula) across 10 European populations. Among the three variables, we found consistent differences in feather corticosterone, which was higher in non-urban habitats. This effect seems to bedependent on sex, being greater in males. In contrast, we found no significant differences between urban and non-urban habitats in the two other physiological indicators. The discrepancy between these different measurements of physiological stress highlights the importance of including multiple physiological variables to understand the impact of urbanization on species' physiology. Overall, our findings suggest that adult European blackbirds living in urban and non-urban habitats do not differ in terms of physiological stress at an organismal level. Furthermore, we found large differences among populations on the strength and direction of the urbanization effect, which illustrates the relevance of spatial replication when investigating urban-induced physiological responses

Search for the standard model Higgs boson decaying to a bb̄ pair in events with one charged lepton and large missing transverse energy using the full CDF data set

We present a search for the standard model Higgs boson produced in association with a W boson in √s=1.96TeV pp̄ collision data collected with the CDFA II detector at the Tevatron corresponding to an integrated luminosity of 9.45fb -1. In events consistent with the decay of the Higgs boson to a bottom-quark pair and the W boson to an electron or muon and a neutrino, we set 95% credibility level upper limits on the WH production cross section times the H→bb̄ branching ratio as a function of Higgs boson mass. At a Higgs boson mass of 125GeV/c2, we observe (expect) a limit of 4.9 (2.8) times the standard model value. © 2012 American Physical Society.Department of Energy (US); National Science Foundation (US); Istituto Nazionale di Fisica Nucleare (Italia); Ministry of Education, Culture, Sports, Science and Technology (Japan); National Research Council of Canada; Swiss National Science Foundation; Alfred P. Sloan Foundation; Bundesministerium für Bildung und Forschung (Deutschland); National Research Foundation of Korea; Science and Technology Facilities Council (UK); The Royal Society (UK); Russian Foundation for Basic Research; Ministerio de Ciencia e Innovación (España); Slovak Research and Development Agency; Academy of Finland; Australian Research Council.Peer Reviewe