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Accelerating Least Squares Imaging Using Deep Learning Techniques [article]

Janaki Vamaraju, Jeremy Vila, Mauricio Araya-Polo, Debanjan Datta, Mohamed Sidahmed, Mrinal Sen
2019 arXiv   pre-print
Wave equation techniques have been an integral part of geophysical imaging workflows to investigate the Earth's subsurface. Least-squares reverse time migration (LSRTM) is a linearized inversion problem that iteratively minimizes a misfit functional as a function of the model perturbation. The success of the inversion largely depends on our ability to handle large systems of equations given the massive computation costs. The size of the system almost exponentially increases with the demand for
more » ... igher resolution images in complicated subsurface media. We propose an unsupervised deep learning approach that leverages the existing physics-based models and machine learning optimizers to achieve more accurate and cheaper solutions. We compare different optimizers and demonstrate their efficacy in mitigating imaging artifacts. Further, minimizing the Huber loss with mini-batch gradients and Adam optimizer is not only less memory-intensive but is also more robust. Our empirical results on synthetic, densely sampled datasets suggest faster convergence to an accurate LSRTM result than a traditional approach.
arXiv:1911.06027v2 fatcat:o4sibaygmfhdzf4lhecddrjraq

Colloidal Gels with Tunable Mechanomorphology Regulate Endothelial Morphogenesis

Smruti K. Nair, Sukanya Basu, Ballari Sen, Meng-Hsuan Lin, Arati N. Kumar, Yuan Yuan, Paul J. Cullen, Debanjan Sarkar
2019 Scientific Reports  
Endothelial morphogenesis into capillary networks is dependent on the matrix morphology and mechanical properties. In current 3D gels, these two matrix features are interdependent and their distinct roles in endothelial organization are not known. Thus, it is important to decouple these parameters in the matrix design. Colloidal gels can be engineered to regulate the microstructural morphology and mechanics in an independent manner because colloidal gels are formed by the aggregation of
more » ... s into a self-similar 3D network. In this work, gelatin based colloidal gels with distinct mechanomorphology were developed by engineering the electrostatic interaction mediated aggregation of particles. By altering the mode of aggregation, colloidal gels showed either compact dense microstructure or tenuous strand-like networks, and the matrix stiffness was controlled independently by varying the particle fraction. Endothelial Cell (EC) networks were favored in tenuous strand-like microstructure through increased cell-matrix and cell-cell interactions, while compact dense microstructure inhibited the networks. For a given microstructure, as the gel stiffness was increased, the extent of EC network was reduced. This result demonstrates that 3D matrix morphology and mechanics provide distinct signals in a bidirectional manner during EC network formation. Colloidal gels can be used to interrogate the angiogenic responses of ECs and can be developed as a biomaterial for vascularization.
doi:10.1038/s41598-018-37788-w pmid:30705322 pmcid:PMC6355882 fatcat:owl7ztvtarfazdfs2esleautyi

Virtual screening assisted identification of small molecule against 2019 novel coronavirus protease enzyme

Arkadeep Sarkar, Deepak Shilkar, Arindam Maity, Sarmi Sardar, Sudhan Debnath, Debanjan Sen, Venkatesan Jayaprakash
2020 JOURNAL OF PHARMACEUTICAL CHEMISTRY  
The 2019 novel coronavirus infection or COVID-19 can be designated as a global threat. Till date, there is a lack of dedicated therapeutics available against this fatal infection. In the present work, we performed structure-based drug design studies in order to identify clinically used molecules exhibiting crucial binding with 2019-coronavirus main protease enzyme. Based on ligand binding energy and interaction with essential amino acids, two molecules were selected. The stability of the
more » ... ed molecules with main protease enzyme was further studied by performing molecular dynamics simulation.
doi:10.14805/jphchem.2020.art116 fatcat:exzdizze7vdzlbjefiocsbn22i

PROPAB: Computation of Propensities and Other Properties from Segments of 3D structure of Proteins

Rifat Nawaz UL Islam, Chittran Roy, Parth Sarthi Sen Gupta, Shyamashree Banerjee, Debanjan Mitra, Sahini Banerjee, Amal Kumar Bandyopadhyay
2018 Bioinformation  
Residues in allelic positions, in the local segment of aligned sequences of proteins show wide variations. Here, we describe PROPAB that computes the propensity tables for helix, strand and coil types from multiple 3D structure files following ab initio statistical procedure. It also classifies them in range specific and chain specific manners. It further computes percentage composition and physicochemical properties along with residues propensities. It also prepares FASTA files for different
more » ... gments (helix, strand and coil) in the exact order that they follow in the sequence. Representative analyses on orthologous (homologous across species) proteins demonstrate wide segmental variations of physicochemical properties. Such variations provide insights to relate the adaptation of these proteins in a given functional constraint under diverse environmental conditions. Thus, the program finds applications in the structural and evolutionary analysis of proteins. Availability: PROPAB is freely available at http://sourceforge.net/projects/propab/ for worldwide user.
doi:10.6026/97320630014190 pmid:30108414 pmcid:PMC6077827 fatcat:rgk4aycyqbhpdbejn3ytvr5tci

Increased Toll-like Receptor-2 Expression on Nonclassic CD16+Monocytes from Patients with Inflammatory Stage of Eales' Disease

Aditi Sen, Imran Hussain Chowdhury, Debanjan Mukhopadhyay, Suman Kalyan Paine, Amrita Mukherjee, Lakshmi Kanta Mondal, Mitali Chatterjee, Basudev Bhattacharya
2011 Investigative Ophthalmology and Visual Science  
PURPOSE. To identify the distribution, differential Toll-like receptor (TLR) expression, and functional contribution of monocyte subpopulations in the inflammatory stage of Eales' disease (ED). METHODS. Peripheral blood mononuclear cells were isolated from nine patients during the inflammatory stage of ED and nine age-and sex-matched healthy controls. The expression of CD14, CD16, TLR-2, and TLR-4 on monocytes was measured by flow cytometry. The CD14 ϩ , CD16 Ϫ , and CD16 ϩ monocyte populations
more » ... were sorted on the basis of magnetic-activated cell-sorting methodology, and levels of cytokines were measured by ELISA. RESULTS. In ED patients, the number of circulating monocytes was significantly expanded compared with that in controls (P ϭ 0.01), with a marked increase in the nonclassic CD16 ϩ subset, which showed an activated phenotype in patients that correlated with levels of serum proinflammatory cytokines and clinical progression. A higher expression of cell surface TLR-2 (P ϭ 0.02), but not TLR-4, was found in monocytes of patients with ED. Furthermore, TLR-2 was expressed at higher levels on CD16 ϩ monocytes than on CD16 Ϫ monocytes in patients, whereas no significant variation was found in TLR-4 expression on different monocyte subsets. Peptidoglycan-induced TNF-␣ expression correlated with TLR-2 expression in monocytes isolated from controls (r ϭ 0.85, P ϭ 0.0061), but not in monocytes isolated from ED patients (r ϭ 0.553, P ϭ 0.1328). CONCLUSIONS. These results indicate that in the pathogenesis of ED, TLR activation and increased numbers of nonclassic CD16 ϩ monocytes are crucial regulators, along with the secretion of proinflammatory cytokines that perpetuate the inflammatory process in the retina. (Invest Ophthalmol Vis Sci. 2011; 52:6940 -6948)
doi:10.1167/iovs.11-7834 pmid:21791592 fatcat:dopx2up6izfnpbiymfgjaczufe

Using complex networks towards information retrieval and diagnostics in multidimensional imaging

Soumya Jyoti Banerjee, Mohammad Azharuddin, Debanjan Sen, Smruti Savale, Himadri Datta, Anjan Kr Dasgupta, Soumen Roy
2015 Scientific Reports  
We present a fresh and broad yet simple approach towards information retrieval in general and diagnostics in particular by applying the theory of complex networks on multidimensional, dynamic images. We demonstrate a successful use of our method with the time series generated from high content thermal imaging videos of patients suffering from the aqueous deficient dry eye (ADDE) disease. Remarkably, network analyses of thermal imaging time series of contact lens users and patients upon whom
more » ... r-Assisted in situ Keratomileusis (Lasik) surgery has been conducted, exhibit pronounced similarity with results obtained from ADDE patients. We also propose a general framework for the transformation of multidimensional images to networks for futuristic biometry. Our approach is general and scalable to other fluctuation-based devices where network parameters derived from fluctuations, act as effective discriminators and diagnostic markers.
doi:10.1038/srep17271 pmid:26626047 pmcid:PMC4667282 fatcat:i74vu5ml7zggvpg7eyodxivxsa

Is Cartridge Based Nucleic Acid Amplification Test (CBNAAT) Better Than Conventional Tests in Diagnosing Childhood Tuberculosis? Evidence from a Tertiary Care Hospital in Eastern India

Sandip Sen, Anjan Kumar Das, Debanjan Sinha
2019 Saudi Journal of Medical and Pharmaceutical Sciences  
Tuberculosis is one of the major causes of mortality and morbidity in childhood. It is challenging to diagnose in childhood population due to difficulty in collection of sample and paucibacillary nature. Despite of considering mycobacterium culture as gold-standard test, it is time consuming (4-8 weeks) while traditional ZN stain is poorly sensitive or specific. In 2013, WHO endorsed Cartridge Based Nucleic Acid Amplification Test (CBNAAT) for diagnosis of TB. Still, there is lack of adequate
more » ... search on TB detection efficacy of CBNAAT over ZN stain or culture. Aims & Objective: Comparison of CBNAAT over ZN stain & mycobacterium culture, in terms of Sensitivity, Specificity, Positive Predictive Value, Negative predictive value. Materials & Methods: Total of 565 patients admitted to Paediatric Medicine department over 2 years from July 2017 to July 2019 with clinical signs (radiological) and symptoms of local & disseminated tuberculosis and history of close contact were selected and grouped under pulmonary and extrapulmonary categories. Each sample was analyzed by CBNAAT, ZN smear and culture. Results: In the pulmonary group, CBNAAT detected 43 out of 185 sputum samples (23.2%), 110 out of 308 gastric lavage samples (35.7%), 0 out of 4 BAL samples. Besides, in extrapulmonary group-6 out of 41 CSF samples, 3 out of 15 pleural fluid, 0 out of 7 ascitic fluid and 3 out of 5 LN biopsy samples were detected by CBNAAT. Sensitivity, specificity, positive predictive value, negative predictive value of CBNAAT in reference to ZN stain was 100%, 92.1%, 70.6% and 100% while in reference to culture was 93.2%, 99.1%, 96.2% and 97.2% respectively. Conclusion: CBNAAT assay is highly sensitive and specific to detect tuberculosis rapidly comparing to the traditional tests with rifampicin resistance associated with mutation of rpoB gene in a single test. It also helps in avoiding injudicious use of anti-tubercular drugs.
doi:10.36348/sjmps.2019.v05i11.013 fatcat:hykii2bm2fgwpgjs3fhfl67bia

POWAINDv1.0: A Program for Protein-Water Interactions Determination

Sahini Banerjee, Department of Biological Sciences, ISI, Kolkata, West Bengal, India, Buddhadev Mondal, Rifat Nawaz Ul Islam, Parth Sarthi Sen Gupta, Debanjan Mitra, Amal Kumar Bandyopadhyay, Department of Zoology, Burdwan Raj Collage, East Burdwan, West Bengal, India, Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India, Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India, Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India, Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India
2018 Bioinformation  
Protein is the most exposed biomolecule in the aqueous environment of the cell. Its structure maintains a delicate balance between the rigidity and the flexibility that imparts binding specificity to its substrate/ligand, etc. Intramolecular interactions of polar and non-polar groups of amino acid residues and intermolecular weak interactions between these groups and shell-waters may contribute to the overall stability of the tertiary structure. However, the question as to what are the dynamics
more » ... of interactions of shell-water with respect to weak forces and atom-groups of protein (AGP), requires systematic investigations. In this end, we have developed a procedure POWAINDv1.0 that analyzes interactions of crystallographic shell-waters (CSH) in residues and AGP specific manner. The shell-water and AGP specific bridge-interactions are also extracted. Further, the program analyzes favorable and unfavorable nature of each interaction based on the actual and 75% of the sum of van der Waals (vdW) radii of interacting atoms. The EXCEL-outputs are useful in understanding the profile for AGP-CSH interactions and contribution of each component in AGP. Taken together, the program provides intricate details on CSHprotein interactions and finds application in the structural Bioinformatics.
doi:10.6026/97320630014530 pmid:31223212 pmcid:PMC6563665 fatcat:cd4iqhr5erfwvdtfyftq7ltscu

AUTOMINv1.0: an automation for minimization of Protein Data Bank files and its usage

Rifat Nawaz Ul Islam, Department of Zoology, The University of Burdwan, East Burdwan, West Bengal, India, Debanjan Mitra, Parth Sarthi Sen Gupta, Sahini Banerjee, Buddhadev Mondal, Amal Kumar Bandyopadhyay, Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India, Department of Chemistry, IISER Berhampur, Ganjam, Odisha, India, Department of Biological Sciences, ISI, Kolkata, West Bengal, India, Department of Zoology, Burdwan Raj College, East Burdwan, West Bengal, India, Department of Biotechnology, The University of Burdwan, East Burdwan, West Bengal, India
2018 Bioinformation  
Global minimal structure of protein/enzyme is energetically compromised that maintains an intricate balance between the rigidity and the flexibility. Such a state makes it interactive to its ligand molecules. Although protein data bank files (PDB) may have achieved the state, in many situations minimization has been crucial to overcome unwanted steric clashes, and other conformational strains. It is more so, when orthologous PDB structures that are intended in a given study, show variations in
more » ... esolution, R-factor, shell-water contents, loop characteristics etc. Here, a fully automated procedure of minimization would be highly useful. AUTOMINv1.0 is such an automation of minimization that runs on any number of structure files with any number of chains in them along with the inclusion of selective/non-selective shell-waters interacting with polar and or non-polar atom-types of protein. Comparison of the mean binaryitems of salt-bridges of minimized and un-minimized structures (chains > 100) of nucleoside diphosphate kinase from mimi virus shows dramatic improvements in the earlier. Again, the mean steric clashes of 2AZ3.pdb are reduced upon minimization. Remarkably, the observed steric clashes between shell-waters and atom-types of protein are seen to be removed upon minimization. Taken together, AUTOMINv1.0 is an automation of minimization that finds applications in structural bioinformatics.
doi:10.6026/97320630014525 pmid:31435151 pmcid:PMC6681769 fatcat:z5zynkyrabenhabvruebjjvhna

Implementing efficient global optimization methods in full waveform inversion

Debanjan Datta, 0000-0002-7800-228X, Austin, The University Of Texas At, Mrinal K. Sen
2020
The modeling and inversion codes were written by Debanjan Datta and the Schur subroutine was written by Debanjan Datta & Piyoosh Jaysaval. certain parts of the model.  ...  This work was done by Debanjan Datta under his advisor's guidance. to represent the entire velocity model.  ... 
doi:10.26153/tsw/9514 fatcat:yziwegyq4fbt3mczy3sb2is32a

I-VIVO ATIMALARIAL STUDY OF PITC2 of Pluchea indica (L.) Less AGAIST Plasmodium berghei AD Plasmodium yolli MODEL

Abhishek Kundu, Debanjan Sen, Tapan Chatterjee
unpublished
The antimalarial properties of crude extract and PITC-2 a compound isolated from tissue cultured plant Pluchea indica traditionally used medicine in various regions of India was evaluated for antimalarial property. The air-dried powdered plant part (roots) was extracted, sequentially with solvents of increased polarity (methanol, butanol, petroleum-ether, and ethyl-acetate). The extract was then administrated orally into albino mice infected with malarial parasites at dose of 100 and 300
more » ... ay keeping Chloroquine and Sodium artisunate as standard. Ethyl acetate insoluble fraction and isolated compound PITC2 prove significant antimalarial effects.
fatcat:5tjw6wrrf5g6hpci3lpqpyg63u

BigMM 2020 Opinion

2020 2020 IEEE Sixth International Conference on Multimedia Big Data (BigMM)  
Chair Mukesh Saini and Dinesh Vishwakarma; Registration and Local Arrangements Chair A V Subramanyam, Ayesha Choudhary, and Mukesh Kumar Giluka; Proceeding Co-Chairs Anirban Chakraborty and Debashis Sen  ...  Co-Chairs Mayurakshi Chaudhuri and Naimul Khan; Best Paper Award Committee Co-Chairs Jianquan Liu and Ramesh Agrawal; Demonstration Co-Chairs Chiranjoy Chattopadhyay and Junjun Jiang; Publicity Co-Chairs Debanjan  ... 
doi:10.1109/bigmm50055.2020.00005 fatcat:gjkltfr2ebhrdmdo44qtvpmofa

ACTS 2020 TOC

2020 2020 Advanced Communication Technologies and Signal Processing (ACTS)  
Debarati Sen Indian Instutute of Technology Kharagpur debarati@gssst.iitkgp.ac.in Prof. Navid Shaghaghi Santa Clara University nshaghaghi@scu.edu Dr.  ...  Debanjan Sadhya ABV-Indian Institute of Information Technology Gwalior debanjan.sadhya@gmail.com Dr. Sudarsan Sahoo NIT Silchar sura.cuttack@gmail.com Dr.  ... 
doi:10.1109/acts49415.2020.9350402 fatcat:h5cc6htkpbbjpj6u2oiwctctz4

Table of Contents

2021 2021 IEEE Congress on Evolutionary Computation (CEC)  
Mappings for UMAP Embeddings 704 Finn Schofield and Andrew Lensen Victoria University of Wellington, New Zealand Mersmann, Dessislava Peeva, Lennard Reese, Frederik Rehbach, Nicolas Rehbach, Amrita Sen  ...  Warchulski and Jaroslaw Arabas Warsaw University of Technology, Institute of Computer Science, Poland Improving Differential Evolution through Bayesian Hyperparameter Optimization 832 Subhodip Biswas, Debanjan  ... 
doi:10.1109/cec45853.2021.9504744 fatcat:gnwg3ppxbbga3ceypy5sc666xi

Table of Contents

2021 2021 Devices for Integrated Circuit (DevIC)  
Design of a Modified 8-bit Semiflash Analog to Digital Converter Pranati Ghoshal, Chanchal Dey and Sunit Kumar Sen 311-315 70.  ...  Autonomous Remote -monitoring Low -cost Agricultural System Udayan Bhattacharyya, Debanjan Mandal, Nikita Agarwal, Sayantika Sanyal, Sohom Basak, Shnouli Mukherjee, Anisha Karmakar, Saurav Sarkar and  ... 
doi:10.1109/devic50843.2021.9455830 fatcat:rcbgrlyelff63bwlbohfsytsyi
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