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Article ; Online: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates.

Kavitha, Kuppuswamy / Sivakumar, Subramaniam / Ramesh, Balasubramanian

2020 Volume 267, Page(s) 106478

Abstract: Discovery of a potent SARS-CoV-2 main protease ( ... ...

Abstract	Discovery of a potent SARS-CoV-2 main protease (M
MeSH term(s)	Amino Acid Sequence ; Binding Sites ; COVID-19/drug therapy ; COVID-19/pathology ; COVID-19/virology ; Catalytic Domain ; Coronavirus M Proteins/chemistry ; Coronavirus M Proteins/metabolism ; Crystallography, X-Ray ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Prodrugs/chemistry ; Prodrugs/metabolism ; Protease Inhibitors/chemistry ; Protease Inhibitors/metabolism ; Protein Binding ; Pyrimidines/chemistry ; Pyrimidines/metabolism ; SARS-CoV-2/enzymology ; SARS-CoV-2/isolation & purification ; Sequence Alignment ; Thermodynamics ; Triazoles/chemistry ; Triazoles/metabolism
Chemical Substances	Coronavirus M Proteins ; Prodrugs ; Protease Inhibitors ; Pyrimidines ; Triazoles ; triazolo(1,5-a)pyrimidine
Keywords	covid19
Language	English
Publishing date	2020-09-22
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2020.106478
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Article: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors: In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates

Kavitha, Kuppuswamy / Sivakumar, Subramaniam / Ramesh, Balasubramanian

Biophys Chem

Abstract: Discovery of a potent SARS-CoV-2 main protease (Mpro) inhibitor is the need of the hour to combat COVID-19. A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 Mpro and the ... ...

Abstract	Discovery of a potent SARS-CoV-2 main protease (Mpro) inhibitor is the need of the hour to combat COVID-19. A total of 1000 protease-inhibitor-like compounds available in the ZINC database were screened by molecular docking with SARS-CoV-2 Mpro and the top 2 lead compounds based on binding affinity were found to be 1,2,4 triazolo[1,5-a] pyrimidin-7-one compounds. We report these two compounds (ZINC000621278586 and ZINC000621285995) as potent SARS-CoV-2 Mpro inhibitors with high affinity (<-9 kCal/mol) and less toxicity than Lopinavir and Nelfinavir positive controls. Both the lead compounds effectively interacted with the crucial active site amino acid residues His41, Cys145 and Glu166. The lead compounds satisfied all of the druglikeness rules and devoid of toxicity or mutagenicity. Molecular dynamics simulations showed that both lead 1 and lead 2 formed stable complexes with SARS-CoV-2 Mpro as evidenced by the highly stable root mean square deviation (<0.23 nm), root mean square fluctuations (0.12 nm) and radius of gyration (2.2 nm) values. Molecular mechanics Poisson-Boltzmann surface area calculation revealed thermodynamically stable binding energies of -129.266 ± 2.428 kJ/mol and - 116.478 ± 3.502 kJ/mol for lead1 and lead2 with SARS-CoV-2 Mpro, respectively.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #778539
Database	COVID19

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Article ; Online: 1,2,4 triazolo[1,5-a] pyrimidin-7-ones as novel SARS-CoV-2 Main protease inhibitors

Kavitha, Kuppuswamy / Sivakumar, Subramaniam / Ramesh, Balasubramanian

Biophysical Chemistry

In silico screening and molecular dynamics simulation of potential COVID-19 drug candidates

2020 Volume 267, Page(s) 106478

Keywords	Biophysics ; Organic Chemistry ; Biochemistry ; covid19
Language	English
Publisher	Elsevier BV
Publishing country	us
Document type	Article ; Online
ZDB-ID	185052-0
ISSN	1873-4200 ; 0301-4622
ISSN (online)	1873-4200
ISSN	0301-4622
DOI	10.1016/j.bpc.2020.106478
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Article: Tertiary structure prediction and identification of druggable pocket in the cancer biomarker - Osteopontin-c.

Sivakumar, Subramaniam / Niranjali Devaraj, Sivasitambaram

Journal of diabetes and metabolic disorders

2014 Volume 13, Issue 1, Page(s) 13

Abstract: Background: Osteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature ...

Abstract	Background: Osteopontin (Eta, secreted sialoprotein 1, opn) is secreted from different cell types including cancer cells. Three splice variant forms namely osteopontin-a, osteopontin-b and osteopontin-c have been identified. The main astonishing feature is that osteopontin-c is found to be elevated in almost all types of cancer cells. This was the vital point to consider it for sequence analysis and structure predictions which provide ample chances for prognostic, therapeutic and preventive cancer research. Methods: Osteopontin-c gene sequence was determined from Breast Cancer sample and was translated to protein sequence. It was then analyzed using various software and web tools for binding pockets, docking and druggability analysis. Due to the lack of homological templates, tertiary structure was predicted using ab-initio method server - I-TASSER and was evaluated after refinement using web tools. Refined structure was compared with known bone sialoprotein electron microscopic structure and docked with CD44 for binding analysis and binding pockets were identified for drug designing. Results: Signal sequence of about sixteen amino acid residues was identified using signal sequence prediction servers. Due to the absence of known structures of similar proteins, three dimensional structure of osteopontin-c was predicted using I-TASSER server. The predicted structure was refined with the help of SUMMA server and was validated using SAVES server. Molecular dynamic analysis was carried out using GROMACS software. The final model was built and was used for docking with CD44. Druggable pockets were identified using pocket energies. Conclusions: The tertiary structure of osteopontin-c was predicted successfully using the ab-initio method and the predictions showed that osteopontin-c is of fibrous nature comparable to firbronectin. Docking studies showed the significant similarities of QSAET motif in the interaction of CD44 and osteopontins between the normal and splice variant forms of osteopontins and binding pockets analyses revealed several pockets which paved the way to the identification of a druggable pocket.
Language	English
Publishing date	2014-01-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2680289-2
ISSN	2251-6581
ISSN	2251-6581
DOI	10.1186/2251-6581-13-13
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Article: Analysis of EAWAG-BBD pathway prediction system for the identification of malathion degrading microbes.

Sivakumar, Subramaniam / Anitha, Palanivel / Ramesh, Balsubramanian / Suresh, Gopal

Bioinformation

2017 Volume 13, Issue 3, Page(s) 73–77

Abstract: Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and ... ...

Abstract	Insecticides are the toxic substances that are used to kill insects. The use of insecticides is believed to be one of the major factors behind the increase in agricultural productivity in the 20th century. The organophosphates are now the largest and most versatile class of insecticide used and Malathion is the predominant type utilized. The accumulation of Malathion in environment is the biggest threat to the environment because of its toxicity. Malathion is lethal to beneficial insects, snails, micro crustaceans, fish, birds, amphibians, and soil microorganisms. Chronic exposure of non-diabetic farmers to organophosphorus Malathion pesticides may induce insulin resistance, which might ultimately results in diabetes mellitus. Given the potential carcinogenic risk from the pesticides there is serious need to develop remediation processes to eliminate or minimize contamination in the environment. Biodegradation could be a reliable and cost effective technique for pesticide abatement. Since today as there were no metabolic pathway predicted for the degradation of organophosphates pesticide Malathion in KEGG database or in any of the other pathway databases. Thus in the present study, an attempt has been made to predict the microbial biodegradation pathway of Malathion using bioinformatics tools. The present study predicted the degradation pathway for Malathion. The present study also identifies, Streptomyces sp. and E.coli are capable of degrading Malathion through pathway prediction system.
Language	English
Publishing date	2017-03-31
Publishing country	Singapore
Document type	Journal Article
ZDB-ID	2203786-X
ISSN	0973-2063
ISSN	0973-2063
DOI	10.6026/97320630013073
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Article ; Online: Author Correction: Cancer Testis Antigen Promotes Triple Negative Breast Cancer Metastasis and is Traceable in the Circulating Extracellular Vesicles.

Kannan, Anbarasu / Philley, Julie V / Hertweck, Kate L / Ndetan, Harrison / Singh, Karan P / Sivakumar, Subramaniam / Wells, Robert B / Vadlamudi, Ratna K / Dasgupta, Santanu

Scientific reports

2020 Volume 10, Issue 1, Page(s) 1907

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Language	English
Publishing date	2020-01-31
Publishing country	England
Document type	Published Erratum
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-58045-z
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Article ; Online: Cancer Testis Antigen Promotes Triple Negative Breast Cancer Metastasis and is Traceable in the Circulating Extracellular Vesicles.

Kannan, Anbarasu / Philley, Julie V / Hertweck, Kate L / Ndetan, Harrison / Singh, Karan P / Sivakumar, Subramaniam / Wells, Robert B / Vadlamudi, Ratna K / Dasgupta, Santanu

Scientific reports

2019 Volume 9, Issue 1, Page(s) 11632

Abstract: Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a ... ...

Abstract	Triple negative breast cancer (TNBC) has poor survival, exhibits rapid metastases, lacks targeted therapies and reliable prognostic markers. Here, we examined metastasis promoting role of cancer testis antigen SPANXB1 in TNBC and its utility as a therapeutic target and prognostic biomarker. Expression pattern of SPANXB1 was determined using matched primary cancer, lymph node metastatic tissues and circulating small extracellular vesicles (sEVs). cDNA microarray analysis of TNBC cells stably integrated with a metastasis suppressor SH3GL2 identified SPANXB1 as a potential target gene. TNBC cells overexpressing SH3GL2 exhibited decreased levels of both SPANXB1 mRNA and protein. Silencing of SPANXB1 reduced migration, invasion and reactive oxygen species production of TNBC cells. SPANXB1 depletion augmented SH3GL2 expression and decreased RAC-1, FAK, A-Actinin and Vinculin expression. Phenotypic and molecular changes were reversed upon SPANXB1 re-expression. SPANXB1 overexpressing breast cancer cells with an enhanced SPANXB1:SH3GL2 ratio achieved pulmonary metastasis within 5 weeks, whereas controls cells failed to do so. Altered expression of SPANXB1 was detected in the sEVs of SPANXB1 transduced cells. Exclusive expression of SPANXB1 was traceable in circulating sEVs, which was associated with TNBC progression. SPANXB1 represents a novel and ideal therapeutic target for blocking TNBC metastases due to its unique expression pattern and may function as an EV based prognostic marker to improve TNBC survival. Uniquely restricted expression of SPANXB1 in TNBCs, makes it an ideal candidate for targeted therapeutics and prognostication.
MeSH term(s)	Adaptor Proteins, Signal Transducing/metabolism ; Animals ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Biomarkers, Tumor/antagonists & inhibitors ; Biomarkers, Tumor/blood ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Breast/pathology ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Proliferation/genetics ; Cell-Derived Microparticles/metabolism ; Disease Progression ; Female ; Gene Expression Profiling ; Gene Knockdown Techniques ; Humans ; Kaplan-Meier Estimate ; Liver/pathology ; Liver Neoplasms/blood ; Liver Neoplasms/diagnosis ; Liver Neoplasms/prevention & control ; Liver Neoplasms/secondary ; Lung/pathology ; Lung Neoplasms/blood ; Lung Neoplasms/diagnosis ; Lung Neoplasms/prevention & control ; Lung Neoplasms/secondary ; Mice ; Neoplasm Invasiveness/pathology ; Nuclear Proteins/antagonists & inhibitors ; Nuclear Proteins/blood ; Nuclear Proteins/genetics ; Nuclear Proteins/metabolism ; Oligonucleotide Array Sequence Analysis ; Prognosis ; RNA, Small Interfering/metabolism ; Reactive Oxygen Species/metabolism ; Triple Negative Breast Neoplasms/blood ; Triple Negative Breast Neoplasms/drug therapy ; Triple Negative Breast Neoplasms/mortality ; Triple Negative Breast Neoplasms/pathology ; Xenograft Model Antitumor Assays
Chemical Substances	Adaptor Proteins, Signal Transducing ; Antineoplastic Agents ; Biomarkers, Tumor ; Nuclear Proteins ; RNA, Small Interfering ; Reactive Oxygen Species ; SH3GL2 protein, human ; SPANXB1 protein, human
Language	English
Publishing date	2019-08-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-48064-w
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Article ; Online: The relationship between measurement method and corneal structure on apparent intraocular pressure in glaucoma and ocular hypertension.

Nessim, Maged / Mollan, Susan P / Wolffsohn, James S / Laiquzzaman, Mohammad / Sivakumar, Subramaniam / Hartley, Stephanie / Shah, Sunil

Contact lens & anterior eye : the journal of the British Contact Lens Association

2013 Volume 36, Issue 2, Page(s) 57–61

Abstract: Purpose: To analyse the relationship between measured intraocular pressure (IOP) and central corneal thickness (CCT), corneal hysteresis (CH) and corneal resistance factor (CRF) in ocular hypertension (OHT), primary open-angle (POAG) and normal tension ... ...

Abstract	Purpose: To analyse the relationship between measured intraocular pressure (IOP) and central corneal thickness (CCT), corneal hysteresis (CH) and corneal resistance factor (CRF) in ocular hypertension (OHT), primary open-angle (POAG) and normal tension glaucoma (NTG) eyes using multiple tonometry devices. Methods: Right eyes of patients diagnosed with OHT (n=47), normal tension glaucoma (n=17) and POAG (n=50) were assessed. IOP was measured in random order with four devices: Goldmann applanation tonometry (GAT); Pascal dynamic contour tonometer (DCT); Reichert ocular response analyser (ORA); and Tono-Pen XL. CCT was then measured using a hand-held ultrasonic pachymeter. CH and CRF were derived from the air pressure to corneal reflectance relationship of the ORA data. Results: Compared to the GAT, the Tonopen and ORA Goldmann equivalent (IOPg) and corneal compensated (IOPcc) measured higher IOP readings (F=19.351, p<0.001), particularly in NTG (F=12.604, p<0.001). DCT was closest to Goldmann IOP and had the lowest variance. CCT was significantly different (F=8.305, p<0.001) between the 3 conditions as was CH (F=6.854, p=0.002) and CRF (F=19.653, p<0.001). IOPcc measures were not affected by CCT. The DCT was generally not affected by corneal biomechanical factors. Conclusion: This study suggests that as the true pressure of the eye cannot be determined non-invasively, measurements from any tonometer should be interpreted with care, particularly when alterations in the corneal tissue are suspected.
MeSH term(s)	Aged ; Cornea/diagnostic imaging ; Cross-Sectional Studies ; Female ; Follow-Up Studies ; Glaucoma/diagnosis ; Glaucoma/physiopathology ; Humans ; Intraocular Pressure ; Male ; Microscopy, Acoustic ; Middle Aged ; Ocular Hypertension/diagnosis ; Ocular Hypertension/physiopathology ; Prospective Studies ; Reproducibility of Results ; Tonometry, Ocular/methods
Language	English
Publishing date	2013-04
Publishing country	England
Document type	Comparative Study ; Journal Article
ZDB-ID	2004847-6
ISSN	1476-5411 ; 1367-0484
ISSN (online)	1476-5411
ISSN	1367-0484
DOI	10.1016/j.clae.2012.11.001
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Article: Mitochondrial Reprogramming Regulates Breast Cancer Progression.

Kannan, Anbarasu / Wells, Robert B / Sivakumar, Subramaniam / Komatsu, Satoshi / Singh, Karan P / Samten, Buka / Philley, Julie V / Sauter, Edward R / Ikebe, Mitsuo / Idell, Steven / Gupta, Sudeep / Dasgupta, Santanu

Clinical cancer research : an official journal of the American Association for Cancer Research

2016 Volume 22, Issue 13, Page(s) 3348–3360

Abstract: Purpose: The goal of this study was to understand the role of altered mitochondrial function in breast cancer progression and determine the potential of the molecular alteration signature in developing exosome-based biomarkers.: Experimental design: ... ...

Abstract	Purpose: The goal of this study was to understand the role of altered mitochondrial function in breast cancer progression and determine the potential of the molecular alteration signature in developing exosome-based biomarkers. Experimental design: This study was designed to characterize the critical components regulating mitochondrial function in breast tumorigenesis. Experiments were conducted to assess the potential of these molecules for exosome-based biomarker development. Results: We observed a remarkable reduction in spontaneous metastases through the interplay in mitochondria by SH3GL2, vesicular endocytosis-associated protein and MFN2, an important regulator of mitochondrial fusion. Following its overexpression in breast cancer cells, SH3GL2 translocated to mitochondria and induced the production of superoxide and release of cytochrome C from mitochondria to the cytoplasm. These molecular changes were accompanied by decreased lung and liver metastases and primary tumor growth. SH3GL2 depletion reversed the above phenotypic and associated molecular changes in nontumorigenic and tumorigenic breast epithelial cells. Loss of SH3GL2 and MFN2 expression was evident in primary human breast cancer tissues and their positive lymph nodes, which was associated with disease progression. SH3GL2 and MFN2 expression was detected in sera exosomes of normal healthy women, but barely detectable in the majority of the women with breast cancer exhibiting SH3GL2 and MFN2 loss in their primary tumors. Conclusions: This study identified a new mitochondria reprogramming pathway influencing breast cancer progression through SH3GL2 and MFN2. These proteins were frequently lost in breast cancer, which was traceable in the circulating exosomes. Clin Cancer Res; 22(13); 3348-60. ©2016 AACR.
MeSH term(s)	Adaptor Proteins, Signal Transducing/genetics ; Adaptor Proteins, Signal Transducing/metabolism ; Apoptosis/genetics ; Breast Neoplasms/diagnosis ; Breast Neoplasms/pathology ; Cell Line, Tumor ; Cell Proliferation ; Cytochromes c/secretion ; Disease Progression ; Exosomes/metabolism ; Female ; GTP Phosphohydrolases/genetics ; GTP Phosphohydrolases/metabolism ; Humans ; Liver Neoplasms/secondary ; Lung Neoplasms/secondary ; MCF-7 Cells ; Mitochondria/metabolism ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Superoxides/metabolism ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism
Chemical Substances	Adaptor Proteins, Signal Transducing ; Mitochondrial Proteins ; SH3GL2 protein, human ; Tumor Suppressor Proteins ; Superoxides (11062-77-4) ; Cytochromes c (9007-43-6) ; GTP Phosphohydrolases (EC 3.6.1.-) ; MFN2 protein, human (EC 3.6.1.-)
Language	English
Publishing date	2016-02-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1225457-5
ISSN	1557-3265 ; 1078-0432
ISSN (online)	1557-3265
ISSN	1078-0432
DOI	10.1158/1078-0432.CCR-15-2456
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Article: Preventing intraocular pressure increase after phacoemulsification and the role of perioperative apraclonidine.

Kasetti, Savitha R / Desai, Shrivatsa P / Sivakumar, Subramaniam / Sunderraj, Palaniswamy

Journal of cataract and refractive surgery

2002 Volume 28, Issue 12, Page(s) 2177–2180

Abstract: Purpose: To evaluate the effectiveness of prophylactic topical apraclonidine 1% in preventing an intraocular pressure (IOP) rise in the early period after uneventful phacoemulsification with intraocular lens (IOL) implantation.: Setting: District ... ...

Abstract	Purpose: To evaluate the effectiveness of prophylactic topical apraclonidine 1% in preventing an intraocular pressure (IOP) rise in the early period after uneventful phacoemulsification with intraocular lens (IOL) implantation. Setting: District general hospital, United Kingdom. Methods: In this prospective masked randomized trial, 61 patients had elective, routine, corneal tunnel, sutureless phacoemulsification with in-the-bag foldable IOL implantation. A single surgeon operated on all the patients. Patients were randomized to receive topical apraclonidine 1% eyedrops (n = 31) or artificial tears (control group, n = 30) 1 hour preoperatively and at the end of the surgery. An observer masked to the perioperative drops used measured the IOP preoperatively and 3 to 6 hours and 16 to 24 hours postoperatively. The primary outcome was the change in IOP between the baseline and the 2 postoperative intervals. The IOP changes within and between the groups were analyzed using the t test and chi-square test. Results: The changes between the postoperative and preoperative IOPs in the study groups were statistically significant (apraclonidine, P = 0.018 and P = 0.007, respectively; artificial tears, P = 0.028 and P = 0.023, respectively; paired t test). There was no significant difference in the postoperative IOP between the apraclonidine and control groups 3 to 6 hours and 16 to 24 hours postoperatively (P = 0.717 and P = 0.497, respectively; independent t test). The mean difference was 0.2 mm Hg (95% confidence interval [CI], -3.4 to 3.1) in the apraclonidine group and 2.2 mm Hg (95% CI, -2.5 to 7.0) in the control group. In each group, a few patients had an IOP greater than 30 mm Hg in the first 24 hours. Conclusion: Prophylactic topical perioperative apraclonidine 1% did not cause a significant reduction in the postoperative IOP when compared with a control group.
MeSH term(s)	Administration, Topical ; Adrenergic alpha-Agonists/administration & dosage ; Adrenergic alpha-Agonists/therapeutic use ; Aged ; Aged, 80 and over ; Clonidine/administration & dosage ; Clonidine/analogs & derivatives ; Clonidine/therapeutic use ; Double-Blind Method ; Female ; Humans ; Intraocular Pressure/drug effects ; Lens Implantation, Intraocular ; Male ; Middle Aged ; Ocular Hypertension/etiology ; Ocular Hypertension/prevention & control ; Ophthalmic Solutions ; Phacoemulsification ; Postoperative Complications/prevention & control ; Prospective Studies
Chemical Substances	Adrenergic alpha-Agonists ; Ophthalmic Solutions ; apraclonidine (843CEN85DI) ; Clonidine (MN3L5RMN02)
Language	English
Publishing date	2002-08-16
Publishing country	United States
Document type	Clinical Trial ; Journal Article ; Randomized Controlled Trial
ZDB-ID	632744-8
ISSN	1873-4502 ; 0886-3350
ISSN (online)	1873-4502
ISSN	0886-3350
DOI	10.1016/s0886-3350(02)01454-2
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