12 results on '"MOLECULAR models"'
Search Results
2. Molecular modelling analysis of T219A mutant envelope protein revealed novel virulence enhancing factors in Dengue virus isolated from Kerala state, India.
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Kumar, Y. Nanda, Jeyakodi, G., Kumar, N. Pradeep, Gunasekaran, K., and Jambulingam, P.
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DENGUE viruses , *MUTANT proteins , *MOLECULAR models , *MEMBRANE fusion , *VIRAL envelope proteins , *MOLECULAR docking , *GLYCOPROTEINS - Abstract
• T219A mutation identified in E-protein of DENV from Kerala state, India was characterised by computational methods. • The T219A mutation was observed to cause poor antibody neutralisation. • The T219A mutation observed to induce fusion mechanisms responsible for the increased virulence of DENV. Dengue virus (DENV) is an emerging health threat and its envelope glycoprotein E, is involved in the anchoring and fusion mechanisms. Anchoring followed by conformational changes of E-protein are responsible for the fusion and entry of DENV into host. The variation in the conformation of the E-protein due to mutations, results in its altered binding with antibodies (Abs) and also its receptors. This leads to failure of neutralization of DENV and enhance the infection. In our earlier studies we have identified T219A mutation in the E-protein of DENV and the present study is focused on the impact of this mutation on the conformation of E-protein and also its binding variation with Abs and Fc-γ receptor. A comparative molecular modelling studies of wild type and T219A mutant E-proteins revealed that, the mutation induced several conformational variations in the E-protein and resulted in the variable binding orientation with altered affinities. Further, the mutation was also observed to enhance the fusion mechanism by Fc-γ receptors that mediate the efficient entry of DENV into host cell through altered membrane fusion mechanism. Such conformational variations of E-protein could be the responsible factors for enhanced virulence of DENV infections. Image, graphical abstract [ABSTRACT FROM AUTHOR]
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- 2020
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3. First principles modelling of the ion binding capacity of finger millet.
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Yong, Wei Cong Matthew, Devi, Apramita, Lin, Tsair-Fuh, and Chappell, Helen F.
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RAGI ,GLUCURONIC acid ,DENSITY functional theory ,IONIC structure ,TRACE elements - Abstract
Finger millet, a cereal grain widely consumed in India and Africa, has gained more attention in recent years due to its high dietary fibre (arabinoxylan) and trace mineral content, and its climate resilience. The aim of this study was to understand the interactions between potassium (K
+ ), calcium (Ca2+ ) and zinc (Zn2+ ) ions and the arabinoxylan structure and determine its ion-binding capacity. Three variations of a proposed model of the arabinoxylan structure were constructed and first principles Density Functional Theory calculations were carried out to determine the cation-binding capacity of the arabinoxylan complexes. Zn2+ -arabinoxylan complexes were highly unstable and thermodynamically unfavourable in all three models. Ca2+ and K+ ions, however, form thermodynamically stable complexes, particularly involving two glucuronic acid residues as a binding pocket. Glucuronic acid residues are found to play a key role in stabilising the cation-arabinoxylan complex, and steric effects are more important to the stability than charge density. Our results highlight the most important structural features of the millet fibre regarding ion-storage capacity, and provide valuable preliminary data for confirmatory experimental studies and for the planning of clinical trials where the bioavailability of bound ions following digestion may be tested. [ABSTRACT FROM AUTHOR]- Published
- 2024
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4. Molecular surveillance of Kelch-13 gene in Plasmodium falciparum field isolates from Mayurbhanj District, Odisha, India, and in silico artemisinin-Kelch-13 protein interaction study.
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Murmu, Laxman Kumar, Panda, Madhusmita, Meher, Biswa Ranjan, Purohit, Prasant, Behera, Jayantiprava, and Barik, Tapan Kumar
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PLASMODIUM falciparum ,PROTEIN-protein interactions ,NATURAL selection ,MOLECULAR dynamics ,CRYSTALLOIDS (Botany) - Abstract
The global malaria control and elimination program faces major threats due to the emergence and transmission of the anti-malarial drug-resistant strain of Plasmodium falciparum. Monitoring of artemisinin (ART) resistance marker Kelch-13 in the malaria-endemic region is essential in mitigating the disease's morbidity and mortality. The current study aimed to generate baseline information for further surveillance in the future. The current research was designed and conducted from July 2019 to June 2021 to monitor Pfkelch13 mutation at the molecular level in the eastern region of India. We also conducted an in silico study to understand the drug-protein interactions between ART and the protein crystal of PfKelch13 (KELCH) with PDB id:4ZGC. The kelch-13 gene was amplified by nested polymerase chain reaction (PCR) and sequenced through the Sanger sequencing method. Reference 3D7 clone (PF3D7_1343700) was used to align and probe all the sequences. The sequence analysis showed the absence of validated or associated mutation in the Kelch-13 propeller domain. The absence of natural selection in drug resistance was confirmed by the Tajima test. Further, in silico interaction studies between the drug ART and the Kelch propeller domain of P. falciparum were evaluated by structure predictions, molecular docking, molecular dynamics (MD) simulations, and estimations of binding free energies for the KELCH-ART complex. The results were compared with the apoprotein (KELCH-APO). The study confirmed the favorable binding of ART with the Kelch-13 propeller domain. [ABSTRACT FROM AUTHOR]
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- 2023
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5. Nitration of Jharia basin coals, India: a study of structural modifications by XRD and FTIR techniques.
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Boral, Prabal, Varma, Atul K., and Maity, Sudip
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NITRATION ,COAL basins ,FOURIER transform infrared spectroscopy ,LIQUID waste - Abstract
Four coal samples from Jharia basin, India are treated with nitric acid in glacial acetic acid and aqueous media to find out the chemical, petrographic and spatial structure of the organic mass by X-ray diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FTIR) techniques. X-ray parameters of coal like interlayer spacing (d
002 ), crystallite size (Lc ), aroamticity (fa ), average number of aromatic layers (Nc ), and coal rank (I26 /I20 ) have been determined using profile-fitting software. Considerable variation is observed in treated coals in comparison to the demineralized coals. The d002 values of treated coals have increased in both the media showing increase in disordering of organic moieties. A linear relationship has been observed between d002 values with the volatile matter of the coals. Similarly, the d002 values show linear relationship with Cdmf contents for demineralized as well as for the treated coals in both the media. The Lc and Nc values have decreased in treated coals corresponding to demineralized coals. The present study shows that nitration in both the media is capable of removing the aliphatic side chains from the coals and aromaticity (fa ) increases with increase in rank and shows a linear relationship with the vitrinite reflectance. The corresponding I26 /I20 values are least for treated coals in glacial acetic acid medium followed by raw and then to treated coals in aqueous medium. FTIR studies show that coal arenes of the raw coals are converted into nitro-arenes in structurally modified coals (SMCs) in both the media, the corresponding bands at 1550–1490 and 1355–1315 cm−1 respectively. FTIR study confirms that nitration is the predominant phenomenon, though, oxidation and nitration phenomena takes place simultaneously during treatment with nitric acid to form SMCs. In comparison to raw coals, the SMCs show higher aromaticity and may be easily converted to coal derived products like activated carbon and specialty carbon materials. [ABSTRACT FROM AUTHOR]- Published
- 2021
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6. Ethnological validation of Ashwagandha (Withania somnifera L. Dunal) ghrita as 'Vajikarana Rasayana': In-silico, in-vitro and in-vivoapproach.
- Author
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Gurav, Shailendra, Wanjari, Manish, Bhole, Ritesh, Raut, Nishikant, Prasad, Satyendra, Saoji, Suprit, Chikhale, Rupesh, Khanal, Pukar, Pant, Amit, Ayyanar, Muniappan, and Gurav, Nilambari
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DRUG efficacy , *COMPUTER simulation , *IN vitro studies , *AYURVEDIC medicine , *IN vivo studies , *MOLECULAR models , *APHRODISIACS , *BIOINFORMATICS , *ETHNOLOGY , *PLANT extracts , *GINSENG , *DRUG toxicity , *PHARMACODYNAMICS - Abstract
Processing cow ghee (clarified butterfat) with therapeutic herbs, i.e. ghrita, is recognized for augmenting the therapeutic efficacy of plant materials. Ashwagandha ghrita (AG) is an effective Ayurvedic formulation consisting of Indian ginseng, i.e., Withania somnifera (L.) Dunal, the main constituent used to treat infertility, weakness, gynaecological disorders, and general debility. The present investigation was undertaken to corroborate the ethnopharmacological claim of AG as ' Vajikarana Rasayana' for its aphrodisiac potential using bioinformatics (in-silico) and experimental (in-vitro and in-vivo) approaches. AG was formulated as per the methods reported in Ayurved sarsangraha. AG was further subjected to HPLC, GCMS analysis, and biological (acute toxicity and aphrodisiac) assessment per the standard procedures. Thirty-eight bioactives of Indian ginseng were subjected to computational studies (molecular docking and network pharmacology) to confirm the plausible mechanism. AG was found to be safe up to 2000 mg/kg body wt., and it showed dose-dependent upsurge (p < 0.01 and p < 0.05, wherever necessary) in mount and intromission frequency, genital grooming, and anogenital sniffing at 150 and 300 mg/kg body weight suggesting aphrodisiac activity. In-vitro studies demonstrated significant relaxation of the Corpus Cavernosal Smooth Muscle at all concentrations in a dose-dependent manner. Furthermore, the results of molecular modelling studies were in agreement with the biological activity and showed interaction with phosphodiesterase-5 as a possible target. AG exhibited an aphrodisiac effect and substantiated the traditional claim of Indian ginseng-based ghrita formulation as 'Vajikarana Rasayana'. [Display omitted] • In Ayurveda , Withania somnifera (L.) Dunal (Ashwagandha) is revered as Rasayana. • The medicinal efficacy of plant components is known to be increased when processed with ghee. • Ashwagandha ghrita is a cow ghee-based traditional herbal preparation used to treat infertility. • It is the first scientific confirmation of the aphrodisiac claims made for Ashwagandha ghrita. [ABSTRACT FROM AUTHOR]
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- 2023
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7. Contribution and Citation Impact of Panjab University in Chemistry Research during 2008-15.
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Singh, Neeraj Kumar, Gupta, Ritu, Bansal, Jivesh, and Saini, Harinder Singh
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CHEMICAL research ,SCHOLARLY publishing ,PANJAB University (Chandigarh, India) - Abstract
This paper analyzes 833 research publications of the Panjab University in chemistry during eight years (2008-15), as covered in Scopus International database. The study quantifies publication data in various aspects of performance, such as the publication growth, research impact and quality, national and international collaboration, contribution and impact of authors, major areas of research and preferred channels of research communications and characteristics of higher cited papers. The findings reveal that Panjab University total publications in chemistry has increased at an annual average growth rate of 17.04% and registered an average citation impact per paper of 6.38 during 2008-15. Of its total publications (833), 22.33% publications of Panjab University did not get any citations as against 77.67% getting 1 or more citations. The 28.69% and 25.81% of the Panjab University publications in chemistry were involved in national and international collaboration during 2008-15. th Among its performance in top 20 most productive Indian universities, Punjab University stood at 16 th rank in terms of publications output (833) and h-index (27), 13 rank in average citation per paper th (6.38) and share of high cited papers (0.12%) and 8 rank in terms of international collaborative papers (25.81%) during 2008-15. Of the 1140 authors involved in 833 papers, the top 15 most productive authors of Punjab University in chemistry together contributed 70.83% and 70.65% share of total publications and citations of Panjab University in chemistry during 2008-15. Of the 221 journals contributing to Panjab University in chemistry research output, the top 30 journals together accounted for 48.37% share of the Panjab University output in chemistry during 2008-15.The top 22 comparatively higher cited papers individually received 31 to 123 citations and together got 12198 citations, with average citation per paper of 55.41. Among 22 higher cited papers, 9 had the participation of single institution (zero collaboration), 9 involve national collaboration and 4 involve international collaboration. These 22 higher cited papers involve 88 authors and 45 organizations and were published in 18 journals. [ABSTRACT FROM AUTHOR]
- Published
- 2016
8. Effect of phosphate status and pH on sulphate sorption and desorption.
- Author
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Barrow, N. J. and Debnath, Abhijit
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SOILS ,PHOSPHATE fertilizers ,SULFATE minerals ,SORPTION - Abstract
For soils from tea estates in northern India, sulphate sorption was of a similar magnitude to, and sometimes exceeded, phosphate sorption. Only a small part of this relatively large sulphate sorption was caused by the low pH of these soils. Most was caused by increased negative charge as a result of prior reaction over many decades with phosphate fertilizers. This decreased sorption of both phosphate and sulphate, but the effect on phosphate was larger. This is compatible with a model in which the mean location of the charge on the adsorbed phosphate ions is closer to the surface than for sulphate. On soils of low phosphate status, sulphate desorption curves showed hysteresis; on soils of high phosphate status, they did not. Further, on soils of high phosphate status, displacement of sulphate by phosphate solutions was faster. We interpret these observations as showing that, for low phosphate status soils, sulphate ions penetrated the surface, but for high phosphate status soils it did not because the pathways by which sulphate diffuses into the adsorbing material were blocked. We also show that, with increasing soil phosphate status, phosphate solutions were less effective in displacing sorbed sulphate. We think this also occurred because reaction with phosphate had decreased the affinity for phosphate more than it decreased the affinity for sulphate. [ABSTRACT FROM AUTHOR]
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- 2015
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9. Potential energy landscapes for anion Frenkel-pair formation in ceria and india
- Author
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Walsh, Aron, Woodley, Scott M., Catlow, C. Richard A., and Sokol, Alexey A.
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POTENTIAL energy surfaces , *ANIONS , *CERIUM oxides , *OPTOELECTRONICS , *DIELECTRIC devices , *CHEMICAL reactions , *LATTICE theory , *ELECTRONIC excitation , *METALLIC oxides , *RADIATION injuries , *MOLECULAR models - Abstract
Abstract: Ceria (CeO2) and india (In2O3) represent two of the most important metal oxide systems for catalytic and optoelectronic applications, respectively. Here, we report analytical interatomic potential models for these two materials, which reproduce the materials structural, elastic and dielectric properties. The potential models are then applied to study the fundamental defect reactions occurring in these materials. Further, we focus on the mechanisms of oxygen diffusion through the lattice, arising from anion Frenkel-pair formation, which is of particular interest for understanding the processes involved in radiation damage and catalysis. The thermodynamic barriers associated with the formation of the first stable anion Frenkel-pairs are 5.80eV and 4.81eV in cerium dioxide and indium sesquioxide, respectively; while for recombination, we calculate barriers of 0.78eV and 0.23eV. The threshold displacement energy for radiation damage in ceria is found to be 35.4eV, in excellent agreement with recent experimental measurements, while for india we predict a value of 14.2eV. [Copyright &y& Elsevier]
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- 2011
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10. Mutagenic, Genotoxic and Immunomodulatory effects of Hydroxychloroquine and Chloroquine: a review to evaluate its potential to use as a prophylactic drug against COVID-19.
- Author
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Giri, Allan, Das, Ankita, Sarkar, Ajoy K., and Giri, Ashok K.
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DRUG side effects ,COVID-19 ,ANTIMALARIALS ,HYDROXYCHLOROQUINE ,CHLOROQUINE ,PHARMACOLOGY ,CYTOCHROME P-450 - Abstract
Hydroxychloroquine (HCQ) and Chloroquine (CQ) are two anti-malarial drugs that are now being extensively used by front-line healthcare workers and other common people as a prophylactic drug against the Corona Virus Disease − 19 (COVID-19) in India and as well as in many parts of the world. While only a few in vitro studies have pointed to some efficacy of these drugs as a prophylactic against COVID-19, to date, there are no clinical studies that have established any clinical efficacy of these drugs as a prophylactic. These drugs are commonly used for the treatment of Rheumatoid Arthritis (RA) and Systemic Lupus Erythematosus (SLE) because of its immunomodulatory effects. Previously, we have evaluated the genetic toxicology of different drugs and chemicals including antimalarial drug CQ both in vitro and in vivo. Thus, we recognize the need to critically review the mutagenic, genotoxic, and immunomodulatory effects of these drugs, to find out whether it is safe to use as a prophylactic drug against COVID-19. Existing literature suggests that CQ can induce mutagenic and genotoxic effects in multiple test systems and both the drugs have immunomodulatory effects. There was no data available to evaluate the mutagenicity and genotoxicity for HCQ. However, during metabolism about 60% of both the drugs remain unchanged and about 40% of the drugs are metabolized into two metabolites, desethylchloroquine and bisdesethylchloroquine by the action of the cytochrome P450 (CYP) enzymes in the liver. Both HCQ and CQ are immunomodulatory drugs and have the potential to suppress normal immune system activation. In this review, we have elucidated the mechanism of immunomodulation by both HCQ and CQ and highlighted the mutagenic and genotoxic effects from the available literature. This article is written with the sole objective that the reader will be able to recognize the adverse effects of these drugs when consumed by healthy individuals as a prophylactic. Current literature indicates that healthy individuals should refrain from the use of these drugs until further investigation. [ABSTRACT FROM AUTHOR]
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- 2020
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11. Frequency Of Egfr And Alk Mutations In Patients Of Lung Carcinoma Of Indian Origin.
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Reddy, Sarath chandra, Sasiakala, Praveen, Anuradha, Amrithanshu, and Bilimagga, Ramesh S.
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LUNGS ,CARCINOMA ,LUNG cancer - Abstract
INTRODUCTION: Lung cancer accounts for 13 per cent of all new cancer cases and 19 per cent of cancer related deaths worldwide whereas in India, lung cancer constitutes 6.9 per cent of all new cancer cases and 9.3 per cent of all cancer related deaths. EGFR mutations are commonly present in Non-Small cell Lung Carcinoma and they have a predictive role in the therapy with TKIs in Lung carcinomas. MATERIALS AND METHODS: A total of 3112 patients were registered between august of 2010 and 2017 .These patients' data was reviewed and patients with EGFR and ALK mutation study done were included in the study. RESULTS: A total of 1147 patients underwent EGFR and ALK mutation studies. Among these, 802 patients underwent EGFR and 345 patients underwent ALK mutation studies respectively. Among the patients, the mean age was 61.9 years and the incidence of EGFR and ALK mutation overall was 39.1% (313) and 8.1 % (28) respectively. With exon 19 being the commonest at 20% positivity, the distribution of other exon mutations among EGFR positive patients were exon 21(14%), exon 18 (4.7%), exon 20 (1.6%) and dual exon mutations (1.8%). CONCLUSION: Compared to the Western prevalence rate in the range of 14-24% of EGFR positivity and 3% of ALK positivity, this study demonstrated higher incidence of EGFR and ALK positivity. So, any effort to obtain a tissue sample for mutation study should be encouraged. [ABSTRACT FROM AUTHOR]
- Published
- 2017
12. Study Of Copper, Zinc And Selenium Associated With Superoxide Dismutase, Catalase And Glutathione Peroxidase Level In Serum Of Breast Cancer Patients Of North India.
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Jain, Vinod and Singh, Gitika Nanda
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GLUTATHIONE peroxidase ,SUPEROXIDE dismutase ,BREAST cancer ,BREAST self-examination ,SELENIUM ,CATALASE - Abstract
Study of Copper, Zinc and Selenium associated with Superoxide Dismutase, Catalase and Glutathione Peroxidase level in serum of Breast cancer patients of North India A. K. Singh, V. Jain, G. N. Singh 1Department of Surgery, King George's Medical University, 2Surgery, King Georg's Medical University, Lucknow, India I declare that my presentation : will not include discussion of unapproved or "off-label" usage of a commercial product or device. Introduction: Breast cancer in women is most common cancer world wide and second most common cancer overall. Trace elements and antioxidant enzymes have been found involved in development and prevention of malignancies including breast cancer. This study aims to find out association between trace elements: copper, zinc and selenium along with antioxidant enzymes: SOD, Catalase, Glutathione peroxidise levels in breast cancer patients of various clinical stages. Materials & Methods: This Prospective observational cohort study is conducted in department of general surgery, King George's Medical University, Lucknow, U.P., India. Blood sample of 152 breast cancer patients were analysed and age matched with 152 controls. Unpaired t-test is used to compare the antioxidant enzymesand trace elements between cases and controls. The plasma level of copper, zinc, selenium and antioxidant enzymes (SOD, Catalase, Glutathione peroxidase) were analysed in both groups to find out any statistically significant correlation. Results: Plasma copper levels (μgm/dl) are higher in cases with mean of 132.43±6.10 vs controls 113.58±11.70 with p<0.0001. Plasma zinc levels (μgm/dl) (case: 88.25±6.30, control: 109.92±8.33, p<0.0001)) and selenium (μmol/dl) (case:3.27±0.18, control: 3.33±0.22 (p<0.0001)) are lower in breast cancer patients. Mean levels of Superoxide dismutase (IU/ ml) (case: 9.49±6.25, control: 27.04±4.39, p<0.0001), Catalase (IU/ ml) (case:0.09±0.08, control: 0.29±0.24, p<0.0001) and Glutathione peroxidise (nanomolNADPH oxidase/min/mg protein) (case: 16.96±10.20, control; 46.70±14.18, p<0.0001) are observed to be lower in breast cancer patients. Blood level of selenium, Superoxide dismutase, Catalase and Glutathione peroxidase are found to have a direct correlation while Plasma levels of Copper has inverse correlation with advanced stages of breast cancer Conclusion: Lower levels of antioxidant enzymes (Superoxide dismutase, Catalase and Glutathione peroxidase) and selenium found in breast cancer patients along with higher copper levels suggest that these metals and antioxidant enzymes play role in etiopathogenesis and aggressiveness of disease. This gives insight to initiate research for additive therapy of antioxidants and selenium in patients of breast cancer to achieve better outcome. Disclosure of Interest: None Declared. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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