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an example of parsing PubMed XML file using the
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| # from requirements.txt | |
| ## Nice PubMed XML file parser; @42c8ccc is at version 0.3.0 | |
| #git+git://github.com/titipata/pubmed_parser.git@42c8ccc | |
| ## library for processing XML and HTML in the Python language, https://lxml.de/ | |
| #lxml | |
| from info import ArticleInfo | |
| from info import AuthorInfo | |
| from pprint import pprint | |
| import pmid_importer | |
| import os | |
| import pprint | |
| def test_parse_detail_xml(): | |
| parsed_articles = pmid_importer.parse_detail_xml( | |
| os.path.join("data", "pubmed-set1.xml")) | |
| assert len(parsed_articles) == 4, "Expect to have 4 articles" | |
| assert parsed_articles == expect_parsed_articles1(), "Expected parsed return this list of dictionary #1" | |
| parsed_articles2 = pmid_importer.parse_detail_xml( | |
| os.path.join("data", "pubmed-set2.xml")) | |
| assert len(parsed_articles2) == 27, "Expect to have 27 articles" | |
| assert parsed_articles2 == expect_parsed_articles2(), "Expected parsed return this list of dictionary #2" | |
| def expect_parsed_articles1(): | |
| return [ | |
| (ArticleInfo( | |
| pmid='1760380', | |
| abstract='Risk factors for cancer have been found in the past to act synergistically in a number of studies.\nHowever, these studies were not always designed to test the hypothesis of synergism, and have sometimes failed to equate for important variables, which might influence the results.\nThe present study tests the hypothesis that psychosocial variables and physical ones (personality/stress, smoking, and genetic predisposition) interact in a synergistic fashion in the causation of lung cancer and coronary heart disease (CHD).', | |
| pubdate='1991', | |
| journal='Integrative physiological and behavioral science : the official journal of the Pavlovian Society', | |
| affiliations='University of London.', | |
| mesh_terms='D000328:Adult|D000368:Aged|D003327:Coronary Disease|D006801:Humans|D006973:Hypertension|D016015:Logistic Models|D008297:Male|D008875:Middle Aged|D009369:Neoplasms|D010553:Personality Development|D012307:Risk Factors|D012907:Smoking|D013315:Stress, Psychological|D014434:Type A Personality', | |
| pub_types='D016428:Journal Article; D016441:Retracted Publication', | |
| doi='10.1007/BF02691067', | |
| title='Personality, stress, smoking, and genetic predisposition as synergistic risk factors for cancer and coronary heart disease.'), | |
| 'Eysenck HJ, Grossarth-Maticek R, Everitt B (1991). Personality, stress, smoking, and genetic predisposition as synergistic risk factors for cancer and coronary heart disease. Integrative physiological and behavioral science : the official journal of the Pavlovian Society, 26(4), 309-22.', | |
| [ | |
| AuthorInfo( | |
| pmid='1760380', | |
| firstname='H J', | |
| lastname='Eysenck', | |
| initials='HJ', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country='University of London'), | |
| AuthorInfo( | |
| pmid='1760380', | |
| firstname='R', | |
| lastname='Grossarth-Maticek', | |
| initials='R', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country='University of London'), | |
| AuthorInfo( | |
| pmid='1760380', | |
| firstname='B', | |
| lastname='Everitt', | |
| initials='B', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country='University of London')]), | |
| (ArticleInfo( | |
| pmid='2999142', | |
| abstract='We have studied the effects of tunicamycin and inhibitors of the processing of N-linked glycans including N-methyl-1-deoxynojirimycin, castanospermine, mannodeoxynojirimycin, and swainsonine on the transport of glycoprotein E2 and the intracellular maturation of the coronavirus mouse hepatitis virus A59.\nIndirect immunofluorescence staining with monoclonal antibodies revealed that glycoprotein E2 exhibits different antigenic properties depending on the presence and on the structure of the N-linked oligosaccharides and that efficient transport of glycoprotein E2 to the plasma membrane requires the removal of glucose residues.\nIn the presence of tunicamycin in the nonglycosylated E2 apoprotein was synthesized in normal amounts and readily acylated throughout the infectious cycle.\nThis E2-species could not be detected on the surface of mouse hepatitis virus A59-infected cells with indirect immunofluorescence staining or lactoperoxidase labeling.\nN-Methyl-1-deoxynojirimycin and castanospermine, both of which selectively inhibited the processing glucosidases, caused a drop in virion formation by two log steps and a drastic delay in the surface expression of glycoprotein E2.\nThe E2 species synthesized under such conditions was acylated but accumulated intracellularly in a compartment distinct from the Golgi.\nConcomitantly, synthesis of the matrix glycoprotein E1 of mouse hepatitis virus A59 was drastically impaired.\nMannodeoxynojirimycin and swainsonine, which block later stages of the processing pathway, had less or no effect on the transport of glycoprotein E2 and the formation of virus particles.', | |
| pubdate='1985-12-15', | |
| journal='The Journal of biological chemistry', | |
| affiliations='', | |
| mesh_terms='D017485:1-Deoxynojirimycin|D000215:Acylation|D000470:Alkaloids|D000818:Animals|D000911:Antibodies, Monoclonal|D002451:Cell Compartmentation|D003332:Coronaviridae|D004591:Electrophoresis, Polyacrylamide Gel|D005455:Fluorescent Antibody Technique|D005944:Glucosamine|D005959:Glucosidases|D007212:Indolizines|D007784:Lactoperoxidase|D051379:Mice|D008807:Mice, Inbred BALB C|D008854:Microscopy, Electron|D006517:Murine hepatitis virus|D009844:Oligosaccharides|D017026:Swainsonine|D014415:Tunicamycin|D014759:Viral Envelope Proteins', | |
| pub_types="D016428:Journal Article; D013485:Research Support, Non-U.S. Gov't", | |
| doi='', | |
| title='The effects of processing inhibitors of N-linked oligosaccharides on the intracellular migration of glycoprotein E2 of mouse hepatitis virus and the maturation of coronavirus particles.'), | |
| 'Repp R, Tamura T, Boschek CB, Wege H, Schwarz RT, Niemann H (1985). The effects of processing inhibitors of N-linked oligosaccharides on the intracellular migration of glycoprotein E2 of mouse hepatitis virus and the maturation of coronavirus particles. The Journal of biological chemistry, 260(29), 15873-9.', | |
| [ | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='R', | |
| lastname='Repp', | |
| initials='R', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country=''), | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='T', | |
| lastname='Tamura', | |
| initials='T', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country=''), | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='C B', | |
| lastname='Boschek', | |
| initials='CB', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country=''), | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='H', | |
| lastname='Wege', | |
| initials='H', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country=''), | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='R T', | |
| lastname='Schwarz', | |
| initials='RT', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country=''), | |
| AuthorInfo( | |
| pmid='2999142', | |
| firstname='H', | |
| lastname='Niemann', | |
| initials='H', | |
| authorid='', | |
| affiliation='', | |
| email='', | |
| country='')]), | |
| (ArticleInfo( | |
| pmid='7524255', | |
| abstract="A variety of hydroxyethyl starch HES preparations with different molecular weight average (Mw) and molar substitution (MS) is available for volume replacement during acute normovolemic haemodilution (ANH).\nParticularly with regard to microcirculation, the ideal solution for volume therapy has not been found.\nThe influence of four different HES preparations on macro- and microcirculation was investigated in 40 patients scheduled for elective aorto-coronary bypass grafting and undergoing ANH (preoperative withdrawn blood: 10 ml.kg-1): 1) 6% HES with Mw of 450,000 dalton and MS of 0.7; 2) 6% HES with Mw of 200,000 dalton and MS of 0.5; 3) 6% HES with Mw of 200,000 dalton and MS of 0.62; 4) 6% HES with Mw of 40,000 dalton and MS of 0.5.\nA 5th group without ANH served as a control (10 patients in each group).\nIn addition to systemic haemodynamics and various laboratory parameters, skin capillary blood flow was measured by laser Doppler flowmetry.\nLaser Doppler flow (LDF) was monitored simultaneously at the patient's forehead and forearm.\nChanges in systemic haemodynamics were similar in all ANH-patients.\nSystemic vascular resistance (SVR) was lowest after infusion of HES 200/0.5.\nThe most pronounced increase in plasma viscosity was in patients of group 1 (450/0.7) (P < 0.05) and plasma viscosity remained highest during the entire investigation period in these patients.\nAfter ANH, skin capillary blood flow measured at the forehead decreased in all patients except in patients of group 2 (200/0.5: max.\n+18%).\nGroup 3 (200/0.62) showed the highest decrease in forehead-LDF.\nDuring CPB, forehead-LDF decreased significantly in groups 3 (200/0.62) and 4 (40/0.5).(ABSTRACT TRUNCATED AT 250 WORDS)", | |
| pubdate='1994-07', | |
| journal='Acta anaesthesiologica Scandinavica', | |
| affiliations='Department of Anesthesiology and Intensive Care Medicine, Justus-Liebig-University Giessen, Germany.', | |
| mesh_terms='D001775:Blood Circulation|D001809:Blood Viscosity|D001810:Blood Volume|D001026:Coronary Artery Bypass|D005542:Forearm|D005546:Forehead|D006438:Hemodilution|D006801:Humans|D006895:Hydroxyethyl Starch Derivatives|D017078:Laser-Doppler Flowmetry|D008297:Male|D008833:Microcirculation|D008970:Molecular Weight|D009994:Osmolar Concentration|D010101:Oxygen Consumption|D010952:Plasma Substitutes|D012039:Regional Blood Flow|D012867:Skin|D014655:Vascular Resistance', | |
| pub_types='D016430:Clinical Trial; D016428:Journal Article; D016449:Randomized Controlled Trial', | |
| doi='10.1111/j.1399-6576.1994.tb03924.x', | |
| title='Retracted: Influence of volume replacement with different HES-solutions on microcirculatory blood flow in cardiac surgery.'), | |
| 'Boldt J, Zickmann B, Rapin J, Hammermann H, Dapper F, Hempelmann G (1994). Retracted: Influence of volume replacement with different HES-solutions on microcirculatory blood flow in cardiac surgery. Acta anaesthesiologica Scandinavica, 38(5), 432-8.', | |
| [ | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='J', | |
| lastname='Boldt', | |
| initials='J', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany'), | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='B', | |
| lastname='Zickmann', | |
| initials='B', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany'), | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='J', | |
| lastname='Rapin', | |
| initials='J', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany'), | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='H', | |
| lastname='Hammermann', | |
| initials='H', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany'), | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='F', | |
| lastname='Dapper', | |
| initials='F', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany'), | |
| AuthorInfo( | |
| pmid='7524255', | |
| firstname='G', | |
| lastname='Hempelmann', | |
| initials='G', | |
| authorid='', | |
| affiliation='Department of Anesthesiology and Intensive Care Medicine Justus-Liebig-University Giessen', | |
| email='', | |
| country='Germany')]), | |
| (ArticleInfo( | |
| pmid='9083040', | |
| abstract='Genomic imprinting refers to the parental allele-specific expression of genes.\nThe precise mechanism underlying this phenomenon, which may involve DNA methylation, is not yet known.\nU2af1-rs1(SP2) is an imprinted gene expressed from the paternal allele and is methylated on the maternal allele.\nHere we report an artificial system in which expression and methylation of the endogenous imprinted gene U2af1-rs1 can be affected by interaction with its own transgene in the testis.\nWe suggest that there is a mechanism in male gametogenesis by which the U2af1-rs1 gene is kept unmethylated to be expressed in the offspring in addition to a mechanism in female gametogenesis by which the U2af1-rs1 gene is methylated and is not expressed in the offspring.', | |
| pubdate='1997-04-04', | |
| journal='The Journal of biological chemistry', | |
| affiliations='Department of Bioscience, National Cardiovascular Center Research Institute, 5-7-1, Fujishiro-dai, Suita, Osaka 565, Japan. hatada@ri.ncvc.go.jp', | |
| mesh_terms='D000483:Alleles|D000818:Animals|D019175:DNA Methylation|D005260:Female|D018392:Genomic Imprinting|D008297:Male|D051379:Mice|D008810:Mice, Inbred C57BL|D009419:Nerve Tissue Proteins|D009687:Nuclear Proteins|D011506:Proteins|D015183:Restriction Mapping|D012261:Ribonucleoproteins|D013094:Spermatozoa|D013737:Testis|D019076:Transgenes', | |
| pub_types="D016428:Journal Article; D013485:Research Support, Non-U.S. Gov't", | |
| doi='10.1074/jbc.272.14.9120', | |
| title='Aberrant methylation of an imprinted gene U2af1-rs1(SP2) caused by its own transgene.'), | |
| 'Hatada I, Nabetani A, Arai Y, Ohishi S, Suzuki M, Miyabara S, Nishimune Y, Mukai T (1997). Aberrant methylation of an imprinted gene U2af1-rs1(SP2) caused by its own transgene. The Journal of biological chemistry, 272(14), 9120-2.', | |
| [ | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='I', | |
| lastname='Hatada', | |
| initials='I', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='A', | |
| lastname='Nabetani', | |
| initials='A', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='Y', | |
| lastname='Arai', | |
| initials='Y', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='S', | |
| lastname='Ohishi', | |
| initials='S', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='M', | |
| lastname='Suzuki', | |
| initials='M', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='S', | |
| lastname='Miyabara', | |
| initials='S', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='Y', | |
| lastname='Nishimune', | |
| initials='Y', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan'), | |
| AuthorInfo( | |
| pmid='9083040', | |
| firstname='T', | |
| lastname='Mukai', | |
| initials='T', | |
| authorid='', | |
| affiliation='Department of Bioscience National Cardiovascular Center Research Institute 5-7-1 Fujishiro-dai Suita Osaka 565', | |
| email='hatada@ri.ncvc.go.jp', | |
| country='Japan')])] | |
| def expect_parsed_articles2(): | |
| return [(ArticleInfo(pmid='10704411', | |
| abstract='BACKGROUND\nDrugs of abuse have a common property in mammals, which is their ability to facilitate the release of the neurotransmitter and neuromodulator dopamine in specific brain regions involved in reward and motivation.\nThis increase in synaptic dopamine levels is believed to act as a positive reinforcer and to mediate some of the acute responses to drugs.\nThe mechanisms by which dopamine regulates acute drug responses and addiction remain unknown.\n\n\n\nRESULTS\n\nWe present evidence that dopamine plays a role in the responses of Drosophila to cocaine, nicotine or ethanol.\nWe used a startle-induced negative geotaxis assay and a locomotor tracking system to measure the effect of psychostimulants on fly behavior.\nUsing these assays, we show that acute responses to cocaine and nicotine are blunted by pharmacologically induced reductions in dopamine levels.\nCocaine and nicotine showed a high degree of synergy in their effects, which is consistent with an action through convergent pathways.\nIn addition, we found that dopamine is involved in the acute locomotor-activating effect, but not the sedating effect, of ethanol.\n\n\n\n\nCONCLUSIONS\nWe show that in Drosophila, as in mammals, dopaminergic pathways play a role in modulating specific behavioral responses to cocaine, nicotine or ethanol.\nWe therefore suggest that Drosophila can be used as a genetically tractable model system in which to study the mechanisms underlying behavioral responses to multiple drugs of abuse.', | |
| pubdate='2000-02-24', | |
| journal='Current biology : CB', | |
| affiliations='Department of Anesthesia, University of California San Francisco, California 94143-0452, USA.', | |
| mesh_terms='D000818:Animals|D001522:Behavior, Animal|D003042:Cocaine|D004298:Dopamine|D004330:Drosophila|D000431:Ethanol|D008297:Male|D009538:Nicotine', | |
| pub_types="D016428:Journal Article; D013486:Research Support, U.S. Gov't, Non-P.H.S.; D013487:Research Support, U.S. Gov't, P.H.S.", | |
| doi='10.1016/s0960-9822(00)00336-5', | |
| title='Dopamine modulates acute responses to cocaine, nicotine and ethanol in Drosophila.'), | |
| 'Bainton RJ, Tsai LT, Singh CM, Moore MS, Neckameyer WS, Heberlein U (2000). Dopamine modulates acute responses to cocaine, nicotine and ethanol in Drosophila. Current biology : CB, 10(4), 187-94.', | |
| [AuthorInfo(pmid='10704411', | |
| firstname='R J', | |
| lastname='Bainton', | |
| initials='RJ', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='10704411', | |
| firstname='L T', | |
| lastname='Tsai', | |
| initials='LT', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='10704411', | |
| firstname='C M', | |
| lastname='Singh', | |
| initials='CM', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='10704411', | |
| firstname='M S', | |
| lastname='Moore', | |
| initials='MS', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='10704411', | |
| firstname='W S', | |
| lastname='Neckameyer', | |
| initials='WS', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='10704411', | |
| firstname='U', | |
| lastname='Heberlein', | |
| initials='U', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco California 94143-0452', | |
| email='', | |
| country='USA')]), | |
| (ArticleInfo(pmid='8454279', | |
| abstract='A 67-year-old white man with a remote history of a chordoma of the clivus presented with myasthenia gravis.\nWe investigated the possibility that these conditions were related immunologically.\nTissue sections of various chordoma specimens were reacted with dilutions of patient serum and control serum by an indirect immunoperoxidase method.\nIn addition, sections were reacted with antibodies to muscle antigens.\nOf six chordomas\n, five reacted positively to patient serum.\nNone reacted to control serum.\nOne chordoma reacted positively to desmin, and all six reacted positively to myoglobin.\nWe propose that the patient may have produced antibody to muscle-like antigens of the chordoma that subsequently cross-reacted with acetylcholine receptor and led to clinical myasthenia gravis.', | |
| pubdate='1993-03', | |
| journal='Human pathology', | |
| affiliations="Department of Pathology, Lutheran General Hospital, Park Ridge, IL, USA; Department of Neurology, St Luke's Medical Center, Cedar Rapids, IA, USA.;Department of Pathology, Lutheran General Hospital, Park Ridge, IL, USA; Department of Neurology, St Luke's Medical Center, Cedar Rapids, IA, USA.", | |
| mesh_terms='D000199:Actins|D000368:Aged|D000941:Antigens|D001859:Bone Neoplasms|D002817:Chordoma|D003893:Desmin|D006801:Humans|D008297:Male|D009132:Muscles|D009157:Myasthenia Gravis|D009211:Myoglobin|D011950:Receptors, Cholinergic', | |
| pub_types='D002363:Case Reports; D016428:Journal Article', | |
| doi='10.1016/0046-8177(93)90047-K', | |
| title='Myasthenia gravis in a man with a history of chordoma: observations of muscle-like antigens in carcinoma.'), | |
| 'Carson HJ, Streib EW (1993). Myasthenia gravis in a man with a history of chordoma: observations of muscle-like antigens in carcinoma. Human pathology, 24(3), 339-342.', | |
| [AuthorInfo(pmid='8454279', | |
| firstname='Henry J', | |
| lastname='Carson', | |
| initials='HJ', | |
| authorid='', | |
| affiliation='Department of Pathology Lutheran General Hospital Park Ridge IL', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='8454279', | |
| firstname='Erich W', | |
| lastname='Streib', | |
| initials='EW', | |
| authorid='', | |
| affiliation="Department of Neurology St Luke's Medical Center Cedar Rapids IA", | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='8454279', | |
| firstname='', | |
| lastname='Department of Pathology, Lutheran General Hospital, Park Ridge, IL, USA', | |
| initials='', | |
| authorid='', | |
| affiliation='Department of Pathology Lutheran General Hospital Park Ridge IL', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='8454279', | |
| firstname='', | |
| lastname='Department of Pathology, Lutheran General Hospital, Park Ridge, IL, USA', | |
| initials='', | |
| authorid='', | |
| affiliation="Department of Neurology St Luke's Medical Center Cedar Rapids IA", | |
| email='', | |
| country='USA')]), | |
| (ArticleInfo(pmid='15320745', | |
| abstract='The article has been retracted by the Editorial office of the journal Current Pharmaceutical Design, due to some inconsistencies in the article [1].\nThe article appeared to be copied verbatim from published papers.\nUpon checking these facts, we have established that considerable portions of this review are made up of text copied verbatim from other published material.\nThe Publisher has retracted this article in accordance with good ethical practices.\n\n\n\nREFERENCE\n[1] Vasanthi HR, Parameswari RP and Das DK.\nTocotrienols and its Role in Cardiovascular Health- a Lead for Drug Design.\nCurr Pharm Des 2011; 17(21): 2170-5.\n\n\n\n\nBentham Science apologizes to the readers of the journal for any inconvenience this may have caused.\nThe Bentham Editorial Policy on Article Retraction can be found at https://benthamscience.com/editorial-policies-main.php\n\n\n\nBENTHAM SCIENCE DISCLAIMER\n\nIt is a condition of publication that manuscripts submitted to this journal have not been published and will not be simultaneously submitted or published elsewhere.\nFurthermore, any data, illustration, structure or table that has been published elsewhere must be reported, and copyright permission for reproduction must be obtained.\nPlagiarism is strictly forbidden, and by submitting the article for publication the authors agree that the publishers have the legal right to take appropriate action against the authors, if plagiarism or fabricated information is discovered.\nBy submitting a manuscript, the authors agree that the copyright of their article is transferred to the publishers if and when the article is accepted for publication.', | |
| pubdate='2004', | |
| journal='Current pharmaceutical design', | |
| affiliations='Department of Sports Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan. jiwamoto@sc.itc.keio.ac.jp', | |
| mesh_terms='D000818:Animals|D002118:Calcium|D002762:Cholecalciferol|D004359:Drug Therapy, Combination|D005260:Female|D006620:Hip Fractures|D006801:Humans|D008107:Liver Diseases|D008297:Male|D015675:Osteocalcin|D010024:Osteoporosis|D015663:Osteoporosis, Postmenopausal|D013026:Space Flight|D024482:Vitamin K 2|D014893:Weightlessness', | |
| pub_types='D016428:Journal Article; D016454:Review', | |
| doi='10.2174/1381612043383782', | |
| title='Retracted: Effects of Vitamin K2 on Osteoporosis'), | |
| 'Iwamoto J, Takeda T, Sato Y (2004). Retracted: Effects of Vitamin K2 on Osteoporosis Current pharmaceutical design, 10(21), 2557-76.', | |
| [AuthorInfo(pmid='15320745', | |
| firstname='Jun', | |
| lastname='Iwamoto', | |
| initials='J', | |
| authorid='', | |
| affiliation='Department of Sports Medicine Keio University School of Medicine 35 Shinanomachi Shinjuku-ku Tokyo 160-8582', | |
| email='jiwamoto@sc.itc.keio.ac.jp', | |
| country='Japan'), | |
| AuthorInfo(pmid='15320745', | |
| firstname='Tsuyoshi', | |
| lastname='Takeda', | |
| initials='T', | |
| authorid='', | |
| affiliation='Department of Sports Medicine Keio University School of Medicine 35 Shinanomachi Shinjuku-ku Tokyo 160-8582', | |
| email='jiwamoto@sc.itc.keio.ac.jp', | |
| country='Japan'), | |
| AuthorInfo(pmid='15320745', | |
| firstname='Yoshihiro', | |
| lastname='Sato', | |
| initials='Y', | |
| authorid='', | |
| affiliation='Department of Sports Medicine Keio University School of Medicine 35 Shinanomachi Shinjuku-ku Tokyo 160-8582', | |
| email='jiwamoto@sc.itc.keio.ac.jp', | |
| country='Japan')]), | |
| (ArticleInfo(pmid='12486199', | |
| abstract='Understanding how ethanol influences behavior is key to deciphering the mechanisms of ethanol action and alcoholism.\nIn mammals, low doses of ethanol stimulate locomotion, whereas high doses depress it.\nThe acute stimulant effect of ethanol has been proposed to be a manifestation of its rewarding effects.\nIn Drosophila, ethanol exposure transiently potentiates locomotor activity in a biphasic dose- and time-dependent manner.\nAn initial short-lived peak of activity corresponds to an olfactory response to ethanol.\nA second, longer-lasting period of increased activity coincides with rising internal ethanol concentrations; these closely parallel concentrations that stimulate locomotion in mammals.\nHigh-resolution analysis of the walking pattern of individual flies revealed that locomotion consists of bouts of activity; bout structure can be quantified by bout frequency, bout length, and the time spent walking at high speeds.\nEthanol exposure induces both dramatic and dynamic changes in bout structure.\nMutants with increased ethanol sensitivity show distinct changes in ethanol-induced locomotor behavior, as well as genotype-specific changes in activity bout structure.\nThus, the overall effect of ethanol on locomotor behavior in Drosophila is caused by changes in discrete quantifiable parameters of walking pattern.\nThe effects of ethanol on locomotion are comparable in flies and mammals, suggesting that Drosophila is a suitable model system to study the underlying mechanisms.', | |
| pubdate='2002-12-15', | |
| journal='The Journal of neuroscience : the official journal of the Society for Neuroscience', | |
| affiliations='Department of Anatomy, University of California at San Francisco, San Francisco, California 94143, USA.', | |
| mesh_terms='D000344:Afferent Pathways|D000818:Animals|D001331:Automation|D001522:Behavior, Animal|D000242:Cyclic AMP|D004305:Dose-Response Relationship, Drug|D004330:Drosophila|D000431:Ethanol|D007700:Kinetics|D008124:Locomotion|D008297:Male|D009154:Mutation|D012680:Sensitivity and Specificity', | |
| pub_types="D016428:Journal Article; D013485:Research Support, Non-U.S. Gov't", | |
| doi='', | |
| title='High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila.'), | |
| 'Wolf FW, Rodan AR, Tsai LT, Heberlein U (2002). High-resolution analysis of ethanol-induced locomotor stimulation in Drosophila. The Journal of neuroscience : the official journal of the Society for Neuroscience, 22(24), 11035-44.', | |
| [AuthorInfo(pmid='12486199', | |
| firstname='Fred W', | |
| lastname='Wolf', | |
| initials='FW', | |
| authorid='', | |
| affiliation='Department of Anatomy University of California at San Francisco San Francisco California 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='12486199', | |
| firstname='Aylin R', | |
| lastname='Rodan', | |
| initials='AR', | |
| authorid='', | |
| affiliation='Department of Anatomy University of California at San Francisco San Francisco California 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='12486199', | |
| firstname='Linus T-Y', | |
| lastname='Tsai', | |
| initials='LT', | |
| authorid='', | |
| affiliation='Department of Anatomy University of California at San Francisco San Francisco California 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='12486199', | |
| firstname='Ulrike', | |
| lastname='Heberlein', | |
| initials='U', | |
| authorid='', | |
| affiliation='Department of Anatomy University of California at San Francisco San Francisco California 94143', | |
| email='', | |
| country='USA')]), | |
| (ArticleInfo(pmid='16213219', | |
| abstract='We identified moody in a genetic screen for Drosophila mutants with altered cocaine sensitivity.\nHypomorphic mutations in moody cause an increased sensitivity to cocaine and nicotine exposure.\nIn contrast, sensitivity to the acute intoxicating effects of ethanol is reduced.\nThe moody locus encodes two novel GPCRs, Moody-alpha and Moody-beta.\nWhile identical in their membrane-spanning domains, the two Moody proteins differ in their long carboxy-terminal domains, which are generated by use of alternative reading frames.\nBoth Moody forms are required for normal cocaine sensitivity, suggesting that they carry out distinct but complementary functions.\nMoody-alpha and Moody-beta are coexpressed in surface glia that surround the nervous system, where they are actively required to maintain the integrity of the blood-brain barrier in the adult fly.\nWe propose that a Moody-mediated signaling pathway functions in glia to regulate nervous system insulation and drug-related behaviors.', | |
| pubdate='2005-10-07', | |
| journal='Cell', | |
| affiliations='Department of Anesthesia, University of California, San Francisco, CA 94143, USA.', | |
| mesh_terms='D017398:Alternative Splicing|D000818:Animals|D001522:Behavior, Animal|D001812:Blood-Brain Barrier|D001921:Brain|D003042:Cocaine|D019970:Cocaine-Related Disorders|D004195:Disease Models, Animal|D018765:Dopamine Uptake Inhibitors|D029721:Drosophila Proteins|D004331:Drosophila melanogaster|D004361:Drug Tolerance|D008297:Male|D009043:Motor Activity|D009457:Neuroglia|D009538:Nicotine|D017434:Protein Structure, Tertiary|D043562:Receptors, G-Protein-Coupled|D019966:Substance-Related Disorders', | |
| pub_types="D016428:Journal Article; D052061:Research Support, N.I.H., Extramural; D013487:Research Support, U.S. Gov't, P.H.S.", | |
| doi='10.1016/j.cell.2005.07.029', | |
| title='moody encodes two GPCRs that regulate cocaine behaviors and blood-brain barrier permeability in Drosophila.'), | |
| 'Bainton RJ, Tsai LT, Schwabe T, DeSalvo M, Gaul U, Heberlein U (2005). moody encodes two GPCRs that regulate cocaine behaviors and blood-brain barrier permeability in Drosophila. Cell, 123(1), 145-56.', | |
| [AuthorInfo(pmid='16213219', | |
| firstname='Roland J', | |
| lastname='Bainton', | |
| initials='RJ', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='16213219', | |
| firstname='Linus T-Y', | |
| lastname='Tsai', | |
| initials='LT', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='16213219', | |
| firstname='Tina', | |
| lastname='Schwabe', | |
| initials='T', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='16213219', | |
| firstname='Michael', | |
| lastname='DeSalvo', | |
| initials='M', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='16213219', | |
| firstname='Ulrike', | |
| lastname='Gaul', | |
| initials='U', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='16213219', | |
| firstname='Ulrike', | |
| lastname='Heberlein', | |
| initials='U', | |
| authorid='', | |
| affiliation='Department of Anesthesia University of California San Francisco CA 94143', | |
| email='', | |
| country='USA')]), | |
| (ArticleInfo(pmid='16384580', | |
| abstract='Lipoyl-lysine swinging arms are crucial to the reactions catalysed by the 2-oxo acid dehydrogenase multienzyme complexes.\nA gene encoding a putative lipoate protein ligase (LplA) of Thermoplasma acidophilum was cloned and expressed in Escherichia coli.\nThe recombinant protein, a monomer of molecular mass 29 kDa, was catalytically inactive.\nCrystal structures in the absence and presence of bound lipoic acid were solved at 2.1 A resolution.\nThe protein was found to fall into the alpha/beta class and to be structurally homologous to the catalytic domains of class II aminoacyl-tRNA synthases and biotin protein ligase, BirA.\nLipoic acid in LplA was bound in the same position as biotin in BirA. The structure of the T.acidophilum LplA and limited proteolysis of E.coli LplA together highlighted some key features of the post-translational modification.\nA loop comprising residues 71-79 in the T.acidophilum ligase is proposed as interacting with the dithiolane ring of lipoic acid and discriminating against the entry of biotin.\nA second loop comprising residues 179-193 was disordered in the T.acidophilum structure; tryptic cleavage of the corresponding loop in the E.coli LplA under non-denaturing conditions rendered the enzyme catalytically inactive, emphasizing its importance.\nThe putative LplA of T.acidophilum lacks a C-terminal domain found in its counterparts in E.coli (Gram-negative) or Streptococcus pneumoniae (Gram-positive).\nA gene encoding a protein that appears to have structural homology to the additional domain in the E.coli and S.pneumoniae enzymes was detected alongside the structural gene encoding the putative LplA in the T.acidophilum genome.\nIt is likely that this protein is required to confer activity on the LplA as currently purified, one protein perhaps catalysing the formation of the obligatory lipoyl-AMP intermediate, and the other transferring the lipoyl group from it to the specific lysine residue in the target protein.', | |
| pubdate='2006-02-24', | |
| journal='Journal of molecular biology', | |
| affiliations="Department of Biochemistry, University of Cambridge, Old Addenbrooke's Site, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK.", | |
| mesh_terms='D000595:Amino Acid Sequence|D019843:Archaeal Proteins|D001710:Biotin|D019731:Carbon-Nitrogen Ligases|D018360:Crystallography, X-Ray|D004926:Escherichia coli|D029968:Escherichia coli Proteins|D008969:Molecular Sequence Data|D010453:Peptide Synthases|D011485:Protein Binding|D011499:Protein Processing, Post-Translational|D017434:Protein Structure, Tertiary|D012097:Repressor Proteins|D013379:Substrate Specificity|D013822:Thermoplasma|D008063:Thioctic Acid|D014157:Transcription Factors|D014357:Trypsin', | |
| pub_types="D003160:Comparative Study; D016428:Journal Article; D013485:Research Support, Non-U.S. Gov't", | |
| doi='10.1016/j.jmb.2005.11.057', | |
| title='Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification.'), | |
| 'McManus E, Luisi BF, Perham RN (2006). Structure of a putative lipoate protein ligase from Thermoplasma acidophilum and the mechanism of target selection for post-translational modification. Journal of molecular biology, 356(3), 625-37.', | |
| [AuthorInfo(pmid='16384580', | |
| firstname='Edward', | |
| lastname='McManus', | |
| initials='E', | |
| authorid='', | |
| affiliation="Department of Biochemistry University of Cambridge Old Addenbrooke's Site Sanger Building 80 Tennis Court Road Cambridge CB2 1GA", | |
| email='', | |
| country='UK'), | |
| AuthorInfo(pmid='16384580', | |
| firstname='Ben F', | |
| lastname='Luisi', | |
| initials='BF', | |
| authorid='', | |
| affiliation="Department of Biochemistry University of Cambridge Old Addenbrooke's Site Sanger Building 80 Tennis Court Road Cambridge CB2 1GA", | |
| email='', | |
| country='UK'), | |
| AuthorInfo(pmid='16384580', | |
| firstname='Richard N', | |
| lastname='Perham', | |
| initials='RN', | |
| authorid='', | |
| affiliation="Department of Biochemistry University of Cambridge Old Addenbrooke's Site Sanger Building 80 Tennis Court Road Cambridge CB2 1GA", | |
| email='', | |
| country='UK')]), | |
| (ArticleInfo(pmid='15550987', | |
| abstract="Drosophila has been developed recently as a model system to investigate the molecular and neural mechanisms underlying responses to drugs of abuse.\nGenetic screens for mutants with altered drug-induced behaviors thus provide an unbiased approach to define novel molecules involved in the process.\nWe identified mutations in the Drosophila LIM-only (LMO) gene, encoding a regulator of LIM-homeodomain proteins, in a genetic screen for mutants with altered cocaine sensitivity.\nReduced Lmo function increases behavioral responses to cocaine, while Lmo overexpression causes the opposite effect, reduced cocaine responsiveness.\nExpression of Lmo in the principal Drosophila circadian pacemaker cells, the PDF-expressing ventral lateral neurons (LN(v)s), is sufficient to confer normal cocaine sensitivity.\nConsistent with a role for Lmo in LN(v)function,Lmomutants also show defects in circadian rhythms of behavior.\nHowever, the role for LN(v)s in modulating cocaine responses is separable from their role as pacemaker neurons: ablation or functional silencing of the LN(v)s reduces cocaine sensitivity, while loss of the principal circadian neurotransmitter PDF has no effect.\nTogether, these results reveal a novel role for Lmo in modulating acute cocaine sensitivity and circadian locomotor rhythmicity, and add to growing evidence that these behaviors are regulated by shared molecular mechanisms.\nThe finding that the degree of cocaine responsiveness is controlled by the Drosophila pacemaker neurons provides a neuroanatomical basis for this overlap.\nWe propose that Lmo controls the responsiveness of LN(v)s to cocaine, which in turn regulate the flies' behavioral sensitivity to the drug.", | |
| pubdate='2004-12', | |
| journal='PLoS biology', | |
| affiliations='Department of Anatomy, Program in Neuroscience and Medical Science Training Program, University of California, San Francisco, USA.', | |
| mesh_terms='D000483:Alleles|D000818:Animals|D001522:Behavior, Animal|D001683:Biological Clocks|D002940:Circadian Rhythm|D003042:Cocaine|D029721:Drosophila Proteins|D004331:Drosophila melanogaster|D005786:Gene Expression Regulation|D020868:Gene Silencing|D018398:Homeodomain Proteins|D008954:Models, Biological|D008957:Models, Genetic|D009154:Mutation|D009474:Neurons|D009479:Neuropeptides|D018377:Neurotransmitter Agents|D017434:Protein Structure, Tertiary|D020133:Reverse Transcriptase Polymerase Chain Reaction', | |
| pub_types="D016428:Journal Article; D052061:Research Support, N.I.H., Extramural; D013487:Research Support, U.S. Gov't, P.H.S.", | |
| doi='10.1371/journal.pbio.0020408', | |
| title='Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors.'), | |
| 'Tsai LT, Bainton RJ, Blau J, Heberlein U (2004). Lmo mutants reveal a novel role for circadian pacemaker neurons in cocaine-induced behaviors. PLoS biology, 2(12), e408.', | |
| [AuthorInfo(pmid='15550987', | |
| firstname='Linus T-Y', | |
| lastname='Tsai', | |
| initials='LT', | |
| authorid='', | |
| affiliation='Department of Anatomy Program in Neuroscience and Medical Science Training Program University of California San Francisco', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='15550987', | |
| firstname='Roland J', | |
| lastname='Bainton', | |
| initials='RJ', | |
| authorid='', | |
| affiliation='Department of Anatomy Program in Neuroscience and Medical Science Training Program University of California San Francisco', | |
| email='', | |
| country='USA'), | |
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| firstname='Justin', | |
| lastname='Blau', | |
| initials='J', | |
| authorid='', | |
| affiliation='Department of Anatomy Program in Neuroscience and Medical Science Training Program University of California San Francisco', | |
| email='', | |
| country='USA'), | |
| AuthorInfo(pmid='15550987', | |
| firstname='Ulrike', | |
| lastname='Heberlein', | |
| initials='U', | |
| authorid='', | |
| affiliation='Department of Anatomy Program in Neuroscience and Medical Science Training Program University of California San Francisco', | |
| email='', | |
| country='USA')]), | |
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