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Items 1 to 10 of about 7459
1. Lu Z, Hunter L: Go molecular function terms are predictive of subcellular localization. Pac Symp Biocomput; 2005;:151-61
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Go molecular function terms are predictive of subcellular localization.
  • A protein's function is closely linked to its subcellular localization.
  • Use of Gene Ontology (GO) molecular function terms to extend sequence-based subcellular localization prediction has been previously shown to improve predictive performance.
  • Here, we explore directly the relationship between GO function annotations and localization information, identifying both highly predictive single terms, and terms with large information gain with respect to location.
  • The results identify a number of predictive and informative GO terms with respect to subcellular location, particularly nucleus, extracellular space, membrane, mitochondrion, endoplasmic reticulum and Golgi.
  • There are several clear examples illustrating why the addition of function information provides additional predictive power over sequence alone.
  • Other interesting phenomena can also be seen in the results.
  • Most predictive or informative terms are imperfect, and incorrect prediction may often call out significant biological phenomena.
  • Finally, these results may be useful in the GO annotation process.

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  • (PMID = 15759622.001).
  • [ISSN] 2335-6936
  • [Journal-full-title] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
  • [ISO-abbreviation] Pac Symp Biocomput
  • [Language] ENG
  • [Grant] United States / NIAAA NIH HHS / AA / AA013524-05; United States / NIGMS NIH HHS / GM / T32 GM07635-25; United States / NIAAA NIH HHS / AA / U01 AA013524; United States / NIAAA NIH HHS / AA / 5U01 AA13524-03; United States / NIGMS NIH HHS / GM / T32 GM007635; United States / NIAAA NIH HHS / AA / U01 AA013524-05; United States / NIAAA NIH HHS / AA / AA013524-03; United States / NIAAA NIH HHS / AA / U01 AA013524-03
  • [Publication-type] Journal Article; Research Support, U.S. Gov't, P.H.S.
  • [Publication-country] United States
  • [Chemical-registry-number] 0 / Proteins
  • [Other-IDs] NLM/ NIHMS91740; NLM/ PMC2652875
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2. Kwon D, Kim S, Shin SY, Chatr-aryamontri A, Wilbur WJ: Assisting manual literature curation for protein-protein interactions using BioQRator. Database (Oxford); 2014;2014
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Assisting manual literature curation for protein-protein interactions using BioQRator.
  • The time-consuming nature of manual curation and the rapid growth of biomedical literature severely limit the number of articles that database curators can scrutinize and annotate.
  • Hence, semi-automatic tools can be a valid support to increase annotation throughput.
  • Although a handful of curation assistant tools are already available, to date, little has been done to formally evaluate their benefit to biocuration.
  • Moreover, most curation tools are designed for specific problems.
  • Thus, it is not easy to apply an annotation tool for multiple tasks.
  • BioQRator is a publicly available web-based tool for annotating biomedical literature.
  • It was designed to support general tasks, i.e. any task annotating entities and relationships.
  • In the BioCreative IV edition, BioQRator was tailored for protein- protein interaction (PPI) annotation by migrating information from PIE the search.
  • The results obtained from six curators showed that the precision on the top 10 documents doubled with PIE the search compared with PubMed search results.
  • It was also observed that the annotation time for a full PPI annotation task decreased for a beginner-intermediate level annotator.
  • This finding is encouraging because text-mining techniques were not directly involved in the full annotation task and BioQRator can be easily integrated with any text-mining resources.
  • Database URL: http://www.bioqrator.org/.

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  • [Copyright] © The Author(s) 2014. Published by Oxford University Press.
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  • (PMID = 25052701.001).
  • [ISSN] 1758-0463
  • [Journal-full-title] Database : the journal of biological databases and curation
  • [ISO-abbreviation] Database (Oxford)
  • [Language] ENG
  • [Grant] United States / Intramural NIH HHS / /
  • [Publication-type] Journal Article; Research Support, N.I.H., Intramural; Research Support, Non-U.S. Gov't
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC4105708
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3. Qi J, Xu M, Lu Z: [An investigation of the effect of rostral ventrolateral medulla lesion on pressor response induced by electrical stimulation of hypothalamic paraventricular nucleus in the cat]. Hua Xi Yi Ke Da Xue Xue Bao; 1993 Mar;24(1):31-5
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] [An investigation of the effect of rostral ventrolateral medulla lesion on pressor response induced by electrical stimulation of hypothalamic paraventricular nucleus in the cat].
  • The experiments were performed on 20 adult cats anesthetized with chloralose and urethane, paralyzed and artificially ventilated.
  • The rostral ventrolateral medulla (RVL) was explored by electrical stimulation.
  • We found that an area, 3-5 mm rostral to the obex, 3-4 mm lateral to the midline, and 0-1 mm from the ventral surface of the medulla, was the most effective region for producing a pressor response.
  • After bilateral microinjection of kainic acid into or electrolytic lesion of the above-mentioned active RVL area, a large decrease in arterial blood pressure was elicited, and the pressor response induced by electrical stimulation of the hypothalamic paraventricular nucleus (PA) was nearly eliminated.
  • The results suggest that the RVL mediates the PA pressor response.

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  • (PMID = 8340088.001).
  • [ISSN] 0257-7712
  • [Journal-full-title] Hua xi yi ke da xue xue bao = Journal of West China University of Medical Sciences = Huaxi yike daxue xuebao
  • [ISO-abbreviation] Hua Xi Yi Ke Da Xue Xue Bao
  • [Language] CHI
  • [Publication-type] English Abstract; Journal Article
  • [Publication-country] China
  • [Chemical-registry-number] SIV03811UC / Kainic Acid
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4. Kilaru P, Kim W, Sequeira W: Cocaine and scleroderma: is there an association? J Rheumatol; 1991 Nov;18(11):1753-5
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Cocaine and scleroderma: is there an association?
  • Scleroderma is a multisystem disease of unknown etiology.
  • A disease predominantly of women, it is distinctly rare in young men.
  • A case of scleroderma in a young male cocaine user is presented, and the possibility that cocaine may play a part in its etiology is explored.
  • [MeSH-major] Cocaine. Scleroderma, Systemic / chemically induced. Substance-Related Disorders / complications
  • [MeSH-minor] Adult. Humans. Male. Recurrence


5. Kim S, Wilbur WJ: Thematic clustering of text documents using an EM-based approach. J Biomed Semantics; 2012 Oct 5;3 Suppl 3:S6
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Thematic clustering of text documents using an EM-based approach.
  • Clustering textual contents is an important step in mining useful information on the web or other text-based resources.
  • The common task in text clustering is to handle text in a multi-dimensional space, and to partition documents into groups, where each group contains documents that are similar to each other.
  • However, this strategy lacks a comprehensive view for humans in general since it cannot explain the main subject of each cluster.
  • Utilizing semantic information can solve this problem, but it needs a well-defined ontology or pre-labeled gold standard set.
  • In this paper, we present a thematic clustering algorithm for text documents.
  • Given text, subject terms are extracted and used for clustering documents in a probabilistic framework.
  • An EM approach is used to ensure documents are assigned to correct subjects, hence it converges to a locally optimal solution.
  • The proposed method is distinctive because its results are sufficiently explanatory for human understanding as well as efficient for clustering performance.
  • The experimental results show that the proposed method provides a competitive performance compared to other state-of-the-art approaches.
  • We also show that the extracted themes from the MEDLINE® dataset represent the subjects of clusters reasonably well.

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  • (PMID = 23046528.001).
  • [ISSN] 2041-1480
  • [Journal-full-title] Journal of biomedical semantics
  • [ISO-abbreviation] J Biomed Semantics
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3465205
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6. Yeganova L, Comeau DC, Wilbur WJ: Machine learning with naturally labeled data for identifying abbreviation definitions. BMC Bioinformatics; 2011 Jun 09;12 Suppl 3:S6
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Machine learning with naturally labeled data for identifying abbreviation definitions.
  • BACKGROUND: The rapid growth of biomedical literature requires accurate text analysis and text processing tools.
  • Detecting abbreviations and identifying their definitions is an important component of such tools.
  • Most existing approaches for the abbreviation definition identification task employ rule-based methods.
  • While achieving high precision, rule-based methods are limited to the rules defined and fail to capture many uncommon definition patterns.
  • Supervised learning techniques, which offer more flexibility in detecting abbreviation definitions, have also been applied to the problem.
  • However, they require manually labeled training data.
  • METHODS: In this work, we develop a machine learning algorithm for abbreviation definition identification in text which makes use of what we term naturally labeled data.
  • Positive training examples are naturally occurring potential abbreviation-definition pairs in text.
  • Negative training examples are generated by randomly mixing potential abbreviations with unrelated potential definitions.
  • The machine learner is trained to distinguish between these two sets of examples.
  • Then, the learned feature weights are used to identify the abbreviation full form.
  • This approach does not require manually labeled training data.
  • RESULTS: We evaluate the performance of our algorithm on the Ab3P, BIOADI and Medstract corpora.
  • Our system demonstrated results that compare favourably to the existing Ab3P and BIOADI systems.
  • We achieve an F-measure of 91.36% on Ab3P corpus, and an F-measure of 87.13% on BIOADI corpus which are superior to the results reported by Ab3P and BIOADI systems.
  • Moreover, we outperform these systems in terms of recall, which is one of our goals.

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  • (PMID = 21658293.001).
  • [ISSN] 1471-2105
  • [Journal-full-title] BMC bioinformatics
  • [ISO-abbreviation] BMC Bioinformatics
  • [Language] ENG
  • [Grant] United States / Intramural NIH HHS / /
  • [Publication-type] Journal Article; Research Support, N.I.H., Intramural
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3111592
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7. Spassova M, Lu Z: Tuning the voltage dependence of tetraethylammonium block with permeant ions in an inward-rectifier K+ channel. J Gen Physiol; 1999 Sep;114(3):415-26
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  • [Title] Tuning the voltage dependence of tetraethylammonium block with permeant ions in an inward-rectifier K+ channel.
  • To understand the role of permeating ions in determining blocking ion-induced rectification, we examined block of the ROMK1 inward-rectifier K+ channel by intracellular tetraethylammonium in the presence of various alkali metal ions in both the extra- and intracellular solutions.
  • We found that the channel exhibits different degrees of rectification when different alkali metal ions (all at 100 mM) are present in the extra- and intracellular solution.
  • A quantitative analysis shows that an external ion site in the ROMK1 pore binds various alkali metal ions (Na+, K+, Rb+, and Cs+) with different affinities, which can in turn be altered by the binding of different permeating ions at an internal site through a nonelectrostatic mechanism.
  • Consequently, the external site is saturated to a different level under the various ionic conditions.
  • Since rectification is determined by the movement of all energetically coupled ions in the transmembrane electrical field along the pore, different degrees of rectification are observed in various combinations of extra- and intracellular permeant ions.
  • Furthermore, the external and internal ion-binding sites in the ROMK1 pore appear to have different ion selectivity: the external site selects strongly against the smaller Na+, but only modestly among the three larger ions, whereas the internal site interacts quite differently with the larger K+ and Rb+ ions.

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  • (PMID = 10469731.001).
  • [ISSN] 0022-1295
  • [Journal-full-title] The Journal of general physiology
  • [ISO-abbreviation] J. Gen. Physiol.
  • [Language] ENG
  • [Grant] United States / NIGMS NIH HHS / GM / F32 GM019215; United States / NIGMS NIH HHS / GM / R01 GM055560; United States / NIGMS NIH HHS / GM / GM19215; United States / NHLBI NIH HHS / HL / HL03814; United States / NIGMS NIH HHS / GM / GM55560
  • [Publication-type] Journal Article; Research Support, U.S. Gov't, P.H.S.
  • [Publication-country] United States
  • [Chemical-registry-number] 0 / Kcnj1 protein, rat; 0 / Metals, Alkaline Earth; 0 / Potassium Channel Blockers; 0 / Potassium Channels; 0 / Potassium Channels, Inwardly Rectifying; 66-40-0 / Tetraethylammonium; RWP5GA015D / Potassium
  • [Other-IDs] NLM/ PMC2229458
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8. Fröhlich A, Lu Z: The "rosette-like" structures in the cuticle of Petrobius brevistylis are the openings of epidermal glands. Arthropod Struct Dev; 2013 Jan;42(1):89-94
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] The "rosette-like" structures in the cuticle of Petrobius brevistylis are the openings of epidermal glands.
  • We examined the "rosette-like" structures (RS), found in Archaeognatha and Thysanura, in the compound eyes and the antennae of the machilid Petrobius brevistylis using SEM and TEM.
  • The nature of the RS was unknown until now, and hypothesized to be either a sensillum or the opening of a gland.
  • Our studies show that RS are the orifices of epidermal glands.
  • A gland consists of a single glandular unit of 4 cells: a duct cell, a secretory cell, a ciliary cell and an enveloping cell.
  • The glands are class 3 epidermal glands as defined by Noirot and Quennedey (1974).
  • [MeSH-major] Insects / ultrastructure
  • [MeSH-minor] Animals. Arthropod Antennae / ultrastructure. Compound Eye, Arthropod / ultrastructure. Epidermis / ultrastructure. Microscopy, Electron, Scanning. Microscopy, Electron, Transmission

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  • [Copyright] Copyright © 2012 Elsevier Ltd. All rights reserved.
  • (PMID = 23064145.001).
  • [ISSN] 1873-5495
  • [Journal-full-title] Arthropod structure & development
  • [ISO-abbreviation] Arthropod Struct Dev
  • [Language] eng
  • [Publication-type] Journal Article
  • [Publication-country] England
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9. Liu Y, Hu Y, Lu Z: [Cells culture of human lumbar disc and its morphological observation]. Zhonghua Yi Xue Za Zhi; 1999 Feb;79(2):109-11
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] [Cells culture of human lumbar disc and its morphological observation].
  • OBJECTIVE: To observe the continuous changes of disc cells, and explore the degeneration influenced by the cell effects.
  • METHODS: Three discs were obtained from three human embryos and one was from a healthy adult.
  • They were dissected and were digested with trypsin and collagenase.
  • The isolated cells were cultured in HAM F-12 medium and 10% fetal bovine serum.
  • The cultured cells were refrigerated and revived for observation under light microscope and TEM.
  • RESULTS: The biological characteristics of the primary and the second generation of the disc cells were similar to those of the cells in vivo.
  • After subculture, notochordal cells and chondrocytes were shown the characteristics of dedifferentiation.
  • The metabolism of the revived cells after refrigeration was normal.
  • The structures of the organellae in disc cells varied with the changes of cell biological characteristics.
  • CONCLUSION: This successful model is useful for the study of biology and pharmacology of human disc cells.
  • [MeSH-major] Intervertebral Disc / cytology
  • [MeSH-minor] Adult. Cells, Cultured. Chondrocytes / ultrastructure. Fetus. Humans

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  • (PMID = 11601015.001).
  • [ISSN] 0376-2491
  • [Journal-full-title] Zhonghua yi xue za zhi
  • [ISO-abbreviation] Zhonghua Yi Xue Za Zhi
  • [Language] chi
  • [Publication-type] English Abstract; Journal Article
  • [Publication-country] China
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10. Li L, Lu Z, Han O: [Epidemiology of melioidosis in China]. Zhonghua Liu Xing Bing Xue Za Zhi; 1994 Oct;15(5):292-5
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] [Epidemiology of melioidosis in China].
  • From 1975 to 1989, a total of 73 strains of P. pseudomallei was isolated from the water samples and the pathological samples of human and domestic animals in 13 counties and cities located different latitude from four provinces Qiong, Yue, Gui and Xiang in China.
  • Serological investigation demonstrated that the geographical distribution of the organism had a significant correlation with the positive rate of antibodies against P. pseudomallei and the native foci of the organisms distributed over the southern subtropical zone and the edge of tropical zone in Qiong, Yue and Gui.
  • In endemic areas, the positive rates of antibodies against P. pseudomallei in human-beings, horses, oxen and pigs are 3.8%-15.2%, 9.1%-18.4%, 6.6%-33.0% and 35% respectively.
  • The investigation results showed the horses and mules infected by the organism would interfere with quarantine of the animals, meanwhile, the meat contaminated by the bacterium would endanger the public health.
  • In Sept. and Oct. of 1989, three cases in Zhanjiang and Sanya of Hainan were reported, two cases died of acute melioidosis with septicemia, another case was the chronic leg ulcers.
  • So, it was predicated that there could have some cases of melioidosis which were misdiagnosed or missed out.
  • [MeSH-major] Antibodies, Bacterial / blood. Burkholderia pseudomallei / isolation & purification. Horses / microbiology. Melioidosis / epidemiology. Swine / microbiology
  • [MeSH-minor] Animals. Cattle. China / epidemiology. Horse Diseases / epidemiology. Humans. Seroepidemiologic Studies. Swine Diseases / epidemiology. Water Microbiology

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  • (PMID = 7532109.001).
  • [ISSN] 0254-6450
  • [Journal-full-title] Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi
  • [ISO-abbreviation] Zhonghua Liu Xing Bing Xue Za Zhi
  • [Language] chi
  • [Publication-type] English Abstract; Journal Article
  • [Publication-country] CHINA
  • [Chemical-registry-number] 0 / Antibodies, Bacterial
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