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Vaidya P, Bera K, Wang X, Patil P, Velcheti V, Madabhushi A. P2.17-35 Integrating CT Radiomic & Quantitative Histomorphometric Whole Slide Image Features Predicts Disease Free Survival in ES-NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Bera K, Vaidya P, Velu P, Choi H, Fu P, Gupta A, Velcheti V, Madabhushi A. P2.17-34 Integrated Clinico-Radiomic Nomogram for Predicting Disease-Free Survival (DFS) in Stage I and II Non-Small Cell Lung Cancer. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Patil P, Khorrami M, Zagouras A, Bera K, Fu P, Gupta A, Velcheti V, Pennell N, Madabhushi A. P2.04-16 Novel CT Based Radiomic Features are Prognostic and Predictive of Benefit of Chemoimmunotherapy in Advanced Non-Squamous NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Velcheti V, Lu C, Bera K, Wang X, Fu P, Yang M, Rimm D, Schalper K, Madabhushi A. MA15.05 Computerized Measurements of Cellular Diversity on H&E Tissue Are Prognostic of OS and Associated with Mutational Status in NSCLC. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Alilou M, Patil P, Fu P, Bera K, Velcheti V, Madabhushi A, Vaidya P. P1.04-25 CT Based Vessel Tortuosity Features Are Prognostic of Overall Survival and Predictive of Immunotherapy Response in NSCLC Patients. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Maher J, Lucas A, Zezoff D, Crawford E, Chang J, Ziogas A, Runge A, Chinn J, Cooper E, Dinicu A, Naaseh A, White K, Bera K, Bernstein M, Hari A, Tewari S, Pearre D, Tewari K. Towards eliminating cervical cancer in East Africa: Feasibility of visual inspection with acetic acid (VIA) screening and immediate cryotherapy in rural and urban Tanzania. Gynecol Oncol 2019. [DOI: 10.1016/j.ygyno.2019.04.259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Millan S, Satish L, Bera K, Sahoo H. Binding and inhibitory effect of the food colorants Sunset Yellow and Ponceau 4R on amyloid fibrillation of lysozyme. NEW J CHEM 2019. [DOI: 10.1039/c8nj05827j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Amyloid fibrillogenesis of proteins is known to be the root cause of a large number of diseases like Parkinson's, Alzheimer's, and Huntington's disease, spongiform encephalopathy, amyloid polyneuropathy, type-II diabetes, etc.
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Ismail M, Hill V, Statsevych V, Huang R, Prasanna P, Correa R, Singh G, Bera K, Beig N, Thawani R, Madabhushi A, Aahluwalia M, Tiwari P. Shape Features of the Lesion Habitat to Differentiate Brain Tumor Progression from Pseudoprogression on Routine Multiparametric MRI: A Multisite Study. AJNR Am J Neuroradiol 2018; 39:2187-2193. [PMID: 30385468 DOI: 10.3174/ajnr.a5858] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/06/2018] [Indexed: 11/07/2022]
Abstract
BACKGROUND AND PURPOSE Differentiating pseudoprogression, a radiation-induced treatment effect, from tumor progression on imaging is a substantial challenge in glioblastoma management. Unfortunately, guidelines set by the Response Assessment in Neuro-Oncology criteria are based solely on bidirectional diametric measurements of enhancement observed on T1WI and T2WI/FLAIR scans. We hypothesized that quantitative 3D shape features of the enhancing lesion on T1WI, and T2WI/FLAIR hyperintensities (together called the lesion habitat) can more comprehensively capture pathophysiologic differences across pseudoprogression and tumor recurrence, not appreciable on diametric measurements alone. MATERIALS AND METHODS A total of 105 glioblastoma studies from 2 institutions were analyzed, consisting of a training (n = 59) and an independent test (n = 46) cohort. For every study, expert delineation of the lesion habitat (T1WI enhancing lesion and T2WI/FLAIR hyperintense perilesional region) was obtained, followed by extraction of 30 shape features capturing 14 "global" contour characteristics and 16 "local" curvature measures for every habitat region. Feature selection was used to identify most discriminative features on the training cohort, which were evaluated on the test cohort using a support vector machine classifier. RESULTS The top 2 most discriminative features were identified as local features capturing total curvature of the enhancing lesion and curvedness of the T2WI/FLAIR hyperintense perilesional region. Using top features from the training cohort (training accuracy = 91.5%), we obtained an accuracy of 90.2% on the test set in distinguishing pseudoprogression from tumor progression. CONCLUSIONS Our preliminary results suggest that 3D shape attributes from the lesion habitat can differentially express across pseudoprogression and tumor progression and could be used to distinguish these radiographically similar pathologies.
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Vaidya P, Bera K, Fu P, Ganesan S, Khunger A, Patil P, Velcheti V, Madabhushi A. P3.16-10 Radiomic Features on CT are Prognostic of Recurrence as well as Predictive of Added Benefit of Adjuvant Chemotherapy in ES-NSCLC. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Patil P, Bera K, Vaidya P, Khorrami M, Jain P, Madabhushi A, Velcheti V. P2.04-17 Pre-Therapy Radiomic Features Can Distinguish Hyperprogression from Other Response Patterns to PD1/PD-L1 Inhibitors in NSCLC. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Bera K, Rani P, Kishor G, Agarwal S, Kumar A, Singh DV. Structural elucidation of transmembrane domain zero (TMD0) of EcdL: A multidrug resistance-associated protein (MRP) family of ATP-binding cassette transporter protein revealed by atomistic simulation. J Biomol Struct Dyn 2017; 36:2938-2950. [DOI: 10.1080/07391102.2017.1372311] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Mahapatra MK, Bera K, Singh DV, Kumar R, Kumar M. In silico modelling and molecular dynamics simulation studies of thiazolidine based PTP1B inhibitors. J Biomol Struct Dyn 2017; 36:1195-1211. [PMID: 28393626 DOI: 10.1080/07391102.2017.1317026] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has been identified as a negative regulator of insulin and leptin signalling pathway; hence, it can be considered as a new therapeutic target of intervention for the treatment of type 2 diabetes. Inhibition of this molecular target takes care of both diabetes and obesity, i.e. diabestiy. In order to get more information on identification and optimization of lead, pharmacophore modelling, atom-based 3D QSAR, docking and molecular dynamics studies were carried out on a set of ligands containing thiazolidine scaffold. A six-point pharmacophore model consisting of three hydrogen bond acceptor (A), one negative ionic (N) and two aromatic rings (R) with discrete geometries as pharmacophoric features were developed for a predictive 3D QSAR model. The probable binding conformation of the ligands within the active site was studied through molecular docking. The molecular interactions and the structural features responsible for PTP1B inhibition and selectivity were further supplemented by molecular dynamics simulation study for a time scale of 30 ns. The present investigation has identified some of the indispensible structural features of thiazolidine analogues which can further be explored to optimize PTP1B inhibitors.
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Millan S, Satish L, Bera K, Susrisweta B, Singh DV, Sahoo H. A Spectroscopic and Molecular Simulation Approach toward the Binding Affinity between Lysozyme and Phenazinium Dyes: An Effect on Protein Conformation. J Phys Chem B 2017; 121:1475-1484. [DOI: 10.1021/acs.jpcb.6b10991] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Satish L, Millan S, Bera K, Mohapatra S, Sahoo H. A spectroscopic and molecular dynamics simulation approach towards the stabilizing effect of ammonium-based ionic liquids on bovine serum albumin. NEW J CHEM 2017. [DOI: 10.1039/c7nj02900d] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Experimental and theoretical evidence in support of the stabilizing effect of ammonium-based ionic liquids on thermal unfolding/refolding of bovine serum albumin is provided in this article.
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Bera K, Nosalova G, Sivova V, Ray B. Structural Elements and Cough Suppressing Activity of Polysaccharides from Zingiber officinale Rhizome. Phytother Res 2016; 30:105-11. [PMID: 26522239 DOI: 10.1002/ptr.5508] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 09/24/2015] [Accepted: 10/12/2015] [Indexed: 12/21/2022]
Abstract
Zingiber officinale is used for the management of fever, bronchial asthma and cough for thousands of years. While the link to a particular indication has been established in human, the active principle of the formulation remains unknown. Herein, we have investigated a water extracted polysaccharides (WEP) containing fraction from its rhizome. Utilizing a traditional aqueous extraction protocol and using chemical, chromatographic and spectroscopic methods a fraction containing a branched glucan and polygalaturonan in a ratio of 59:1 was characterized. This glucan, which has a molecular mass of 36 kDa, is made up of terminal-, (1,4)- and (1,4,6)-linked α-Glcp residues. Oral administration of WEP in doses of 25 and 50 mg/kg body weight significantly inhibited the number of citric acid-induced cough efforts in guinea pigs. It does not alter the specific airway smooth muscle reactivity significantly. Thus, traditional aqueous extraction method provides molecular entities, which induces antitussive activity without addiction.
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Bera K, Sarkar S, Jana U. Iron-catalyzed tandem carbon–carbon/carbon–oxygen bond formation/aromatization of 2′-alkynyl-biphenyl-2-carbinols: a new approach to the synthesis of substituted phenanthrenes. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Paul K, Bera K, Jalal S, Sarkar S, Jana U. Fe-Catalyzed Novel Domino Isomerization/Cyclodehydration of Substituted 2-[(Indoline-3-ylidene)(methyl)]benzaldehyde Derivatives: An Efficient Approach toward Benzo[b]carbazole Derivatives. Org Lett 2014; 16:2166-9. [PMID: 24742160 DOI: 10.1021/ol500505k] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Jalal S, Bera K, Sarkar S, Paul K, Jana U. Efficient synthesis of functionalized dihydroquinolines, quinolines and dihydrobenzo[b]azepine via an iron(iii) chloride-catalyzed intramolecular alkyne–carbonyl metathesis of alkyne tethered 2-amino benzaldehyde/acetophenone derivatives. Org Biomol Chem 2014; 12:1759-70. [DOI: 10.1039/c3ob42292e] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-catalyzed synthesis of dihydroquinolines, quinolines and dihydrobenzo[b]azepine.
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Bera K, Jalal S, Sarkar S, Jana U. FeCl3-catalyzed synthesis of functionally diverse dibenzo[b,f]oxepines and benzo[b]oxepines via alkyne–aldehyde metathesis. Org Biomol Chem 2014; 12:57-61. [DOI: 10.1039/c3ob41624k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Bera K, Khanam J, Mohanraj KP, Mazumder B. Design and evaluation of mucoadhesive beads of glipizide as a controlled release drug delivery system. J Microencapsul 2013; 31:220-9. [DOI: 10.3109/02652048.2013.834989] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Sarkar S, Bera K, Jalal S, Jana U. Synthesis of Structurally Diverse Polyfunctional Pyrrolo[1,2-a]quinolines by Sequential Iron-Catalyzed Three-Component Coupling and Gold-Catalyzed Hydroarylation Reactions. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300659] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jalal S, Sarkar S, Bera K, Maiti S, Jana U. Synthesis of Nitroalkenes Involving a Cooperative Catalytic Action of Iron(III) and Piperidine: A One-Pot Synthetic Strategy to 3-Alkylindoles, 2H-Chromenes andN-Arylpyrrole. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300172] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sarkar S, Bera K, Maiti S, Biswas S, Jana U. Three-Component Coupling Synthesis of Diversely Substituted N-Aryl Pyrroles Catalyzed by Iron(III) Chloride. SYNTHETIC COMMUN 2013. [DOI: 10.1080/00397911.2011.650273] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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49
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Sarkar S, Maiti S, Bera K, Jalal S, Jana U. Highly efficient synthesis of polysubstituted fluorene via iron-catalyzed intramolecular Friedel–Crafts alkylation of biaryl alcohols. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bera K, Sarkar S, Jalal S, Jana U. Synthesis of Substituted Phenanthrene by Iron(III)-Catalyzed Intramolecular Alkyne–Carbonyl Metathesis. J Org Chem 2012; 77:8780-6. [PMID: 22954237 DOI: 10.1021/jo301371n] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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