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Jun'ichi Tsujii - One of the best experts on this subject based on the ideXlab platform.
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building a high quality sense inventory for improved abbreviation disambiguation
Bioinformatics, 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org
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Building a high-quality sense inventory for improved abbreviation disambiguation
Bioinformatics (Oxford England), 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.
N Okazaki - One of the best experts on this subject based on the ideXlab platform.
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building a high quality sense inventory for improved abbreviation disambiguation
Bioinformatics, 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org
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Building a high-quality sense inventory for improved abbreviation disambiguation
Bioinformatics (Oxford England), 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.
Sophia Ananiadou - One of the best experts on this subject based on the ideXlab platform.
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building a high quality sense inventory for improved abbreviation disambiguation
Bioinformatics, 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/ Contact: okazaki@chokkan.org
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Building a high-quality sense inventory for improved abbreviation disambiguation
Bioinformatics (Oxford England), 2010Co-Authors: N Okazaki, Sophia Ananiadou, Jun'ichi TsujiiAbstract:The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation. A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts. The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/.
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building an abbreviation dictionary using a term recognition approach
Bioinformatics, 2006Co-Authors: Naoaki Okazaki, Sophia AnaniadouAbstract:Motivation: Acronyms result from a highly productive type of term variation and trigger the need for an acronym dictionary to establish associations between acronyms and their expanded forms. Results: We propose a novel method for recognizing acronym definitions in a text collection. Assuming a word sequence co-occurring frequently with a parenthetical expression to be a potential expanded form, our method identifies acronym definitions in a similar manner to the statistical term recognition task. Applied to the whole MEDLINE (7 811 582 abstracts), the implemented system extracted 886 755 acronym candidates and recognized 300 954 expanded forms in reasonable time. Our method outperformed base-line systems, achieving 99% precision and 82--95% recall on our evaluation corpus that roughly emulates the whole MEDLINE. Availability and Supplementary information: The implementations and supplementary information are available at our web site: http://www.chokkan.org/research/acromine/ Contact: okazaki@mi.ci.i.u-tokyo.ac.jp
Yulin Feng - One of the best experts on this subject based on the ideXlab platform.
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Effect of peroxisome proliferators activated receptor gamma and its ligand on airway mucus hypersecretion in rats
Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases, 2009Co-Authors: Wei-jia Liu, Yulin FengAbstract:To explore the effect and the molecular mechanisms of peroxisome proliferators activated receptor gamma (PPAR-gamma) and its ligand on airway mucus hypersecretion. Thirty-six Sprague-Dawley rats were randomized into the following groups: (1) Rats in the saline control group (n = 6) received normal saline inhalation; (2) Rats in the rosiglitazone control group (n = 6) received inhaled saline and oral rosiglitazone 8 mg/kg simultaneously; (3) Rats in the acrolein group (n = 6) received inhaled Acronine 3.0 mg/L, 6 h/day, for 12 days; (4) Rats in the rosiglitazone intervention group (n = 18) received inhaled acrolein and oral rosiglitazone 2 mg/kg, 4 mg/kg, 8 mg/kg, respectively, as the low dose, the moderate dose and the high dose intervention groups (n = 6 each). The lung tissue sections were stained with HE for histopathological examination. The changes of airway mucus were examined with AB-PAS. Expressions of MUC5AC and PPAR-gamma protein in the bronchial epithelium were detected by immunohistochemistry. The expression of mRNA was measured with real time RT-PCR. The data were analyzed with SPSS 10.0 software. Variables were compared with One-Way ANOVA and q test. The correlations between variables were analyzed using Pearson's correlation coefficient. The levels of airway mucus were (60.2 +/- 9.3)%, (4.9 +/- 1.0)%, (53.3 +/- 8.5)%, (26.5 +/- 7.4)%, (12.5 +/- 3.7)% respectively in the acrolein group, the saline control group, the low dose rosiglitazone intervention group, the moderate dose rosiglitazone intervention group, and the high dose rosiglitazone intervention group, the difference being significant among groups (F = 93.80, P < 0.01). The protein expressions of MUC5AC in the bronchial epithelium examined by immunohistochemistry were 4339 +/- 453, 1636 +/- 282, 3996 +/- 346, 3048 +/- 331, 2376 +/- 343 respectively in the acrolein group, the saline control group, the low dose rosiglitazone intervention group, the moderate dose rosiglitazone intervention group, and the high dose rosiglitazone intervention group, the difference being significant among groups (F = 67.74, P < 0.01). The protein expressions of PPAR-gamma were 1159 +/- 184, 838 +/- 151, 1272 +/- 189, 1568 +/- 282, 1872 +/- 270 respectively in the acrolein group, the saline control group, the low dose rosiglitazone intervention group, the moderate dose rosiglitazone intervention group, and the high dose rosiglitazone intervention group, the difference being significant among groups (F = 21.53, P < 0.01). The mRNA expressions of MUC5AC (the relative copies) were 35.3 +/- 10.0, 2.2 +/- 0.7, 30.5 +/- 10.2, 18.6 +/- 5.3, 10.8 +/- 2.6 respectively in the acrolein group, the saline control group, the low dose rosiglitazone intervention group, the moderate dose rosiglitazone intervention group, and the high dose rosiglitazone intervention group, the difference being significant among groups (F = 29.67, P < 0.01). The mRNA expressions of PPAR-gamma (the relative copies) were 7.8 +/- 1.9, 2.0 +/- 0.6, 9.8 +/- 2.8, 18.6 +/- 5.3, 31.6 +/- 8.9 in the acrolein group, the saline control group, the low dose rosiglitazone intervention group, the moderate dose rosiglitazone intervention group, and the high dose rosiglitazone intervention group, the difference being significant among groups (F = 39.47, P < 0.01). The expression of MUC5AC mRNA was negatively correlated with the protein expression of PPAR-gamma in the acrolein group (r = -0.880, P < 0.01). PPAR-gamma was involved in airway mucus hypersecretion induced by acrolein. PPAR-gamma and its ligand rosiglitazone inhibited acrolein-induced airway mucus hypersecretion, possibly through downregulation of MUC5AC.
José Walkimar De M. Carneiro - One of the best experts on this subject based on the ideXlab platform.
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Structure-Activity Relationship Studies of New Acronine Analogues as Suggested by Molecular Descriptors
Arzneimittel-Forschung, 2011Co-Authors: Miguel Rascado F. Neto, João Batista Neves Dacosta, Carlos Mauricio R. Sant'anna, José Walkimar De M. CarneiroAbstract:This work describes the results of an investigation on the structure-activity relationships of a series of Acronine (CAS 7008-42-6) analogues which possess cytotoxic and antitumor activity. The results were obtained employing a commercially available software, which correlates structure and activity through calculations with different descriptors. The best results, obtained with electrostatic descriptors, led to propose new structures which present higher calculated activity than that of Acronine.