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PHYSICS INFORMED NEURAL NETWORKS (PINNs) FOR APPROXIMATING NONLINEAR DISPERSIVE PDEs

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Journal of Computational Mathematics 2021年第6期39卷 816-847页

作者： Genming Bai Ujjwal Koley siddhartha mishra Roberto Molinaro Seminar for Applied Mathematics(SAM) D-Math ETH ZurichRamistrasse 101 Centre for Applicable Mathematics Tata Institute of Fundamental Research P.O.Box 6503GKVK Post OfficeBangalore 560065India

We propose a novel algorithm,based on physics-informed neural networks(PINNs)to efficiently approximate solutions of nonlinear dispersive PDEs such as the KdV-Kawahara,Camassa-Holm and Benjamin-Ono *** stability of solutions of these dispersive PDEs is leveraged to prove rigorous bounds on the resulting *** present several numerical experiments to demonstrate that PINNs can approximate solutions of these dispersive PDEs very accurately.

关键词： Nonlinear dispersive PDEs Deep learning Physics Informed Neural Networks

The phytochemical, biological, and medicinal attributes of phytoecdysteroids: An updated review

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Acta Pharmaceutica Sinica B 2021年第7期11卷 1740-1766页

作者： Niranjan Das siddhartha Kumar mishra Anusha Bishayee Eunüs S.Ali Anupam Bishayee Department of Chemistry Iswar Chandra Vidyasagar CollegeBelonia-799155TripuraIndia Cancer Biology Laboratory Department of ZoologySchool of Biological SciencesDr.Harisingh Gour Central UniversitySagar-470003Madhya PradeshIndia Pine View School OspreyFL 34229USA Department of Biochemistry and Molecular Genetics Feinberg School of MedicineNorthwestern UniversityChicagoIL 60611USA Lake Erie College of Osteopathic Medicine BradentonFL 34211USA

The phytoecdysteroids(PEs)comprise a large group of biologically-active plant steroids,which have structures similar to those of insect-molting *** are distributed in plants as secondary metabolites that offer protection against phytophagus(plant-eating)*** insects consume the plants containing these chemicals,they promptly molt and undergo metabolic destruction;the insects eventually ***,ecdysteroids are a group of polyhydroxylated ketosteroids that are structurally similar to *** carbon skeleton of ecdysteroids is termed as cyclopentanoperhydro-phenanthrene with aβ-side chain at *** essential characteristics of ecdysteroids are a cis-(5β-H)junction of rings A and B,a 7-en-6-one chromophore,and a trans(14α-OH)junction of rings C and *** only synthesize PEs from mevalonic acid in the mevalonate pathway of the plant cell using acetyl-CoA as a precursor;the most common PE is *** far,over 400 PEs have been identified and reported,and a compilation of 166 PEs originating from 1998 has been previously *** the present review,we have summarized 212 new PEs reported between 1999 and *** have also critically analyzed the biological,pharmacological,and medicinal properties of PEs to understand the full impact of these phytoconstituents in health and disease.

关键词： Phytoecdysteroids Secondary metabolites Antioxidant Anti-inflammatory Antimicrobial Antidiabetic Anticancer activity

Finite Volume Methods for Wave Propagation in Stratified Magneto-Atmospheres

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Communications in Computational Physics 2010年第3期7卷 473-509页

作者： Franz Georg Fuchs Andrew D.McMurry siddhartha mishra Nils Henrik Risebro Knut Waagan Centre of Mathematics for Applications(CMA) University of OsloP.O.Box 1053BlindernN-0316 OsloNorway High Altitude Observatory(HAO) National Center of Atmospheric ResearchP.O.Box 3000Boulder80307-3000 ColoradoUSA

We present a model for simulating wave propagation in stratified magnetoatmospheres. The model is based on equations of ideal MHD together with gravitational source terms. In addition, we present suitable boundary data and steady statesto model wave propagation. A finite volume framework is developed to simulate thewaves. The framework is based on HLL and Roe type approximate Riemann solversfor numerical fluxes, a positivity preserving fractional steps method for discretizingthe source and modified characteristic and Neumann type numerical boundary conditions. Second-order spatial and temporal accuracy is obtained by using an ENO piecewise linear reconstruction and a stability preserving Runge-Kutta method *** boundary closures are suitably modified to ensure mass balance. The numericalframework is tested on a variety of test problems both for hydrodynamic as well asmagnetohydrodynamic configurations. It is observed that only suitable choices of HLLsolvers for the numerical fluxes and balanced Neumann type boundary closures yieldstable results for numerical wave propagation in the presence of complex magneticfields.

关键词： Solar atmospheres MHD equations finite volume methods non-reflecting boundary conditions

Approximate Riemann Solvers and Robust High-Order Finite Volume Schemes for Multi-Dimensional Ideal MHD Equations

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Communications in Computational Physics 2011年第2期9卷 324-362页

作者： Franz Georg Fuchs Andrew D.McMurry siddhartha mishra Nils Henrik Risebro Knut Waagan Centre of Mathematics for Applications University of OsloP.O.Box 1053Blindern N-0316 OsloNorway Seminar for Applied Mathematics D-MathETH ZürichHG G.57.2Rämistrasse 101Zürich-8092Switzerland Center for Scientific Computation and Mathematical Modeling The University of MarylandCSCAMM 4146CSIC Building#406Paint Branch Drive College ParkMD 20742-3289USA

We design stable and high-order accurate finite volume schemes for the ideal MHD equations in *** obtain excellent numerical stability due to some new elements in the *** schemes are based on three-and five-wave approximate Riemann solvers of the HLL-type,with the novelty that we allow a varying normal magnetic *** is achieved by considering the semiconservative Godunov-Powell form of the MHD *** show that it is important to discretize the Godunov-Powell source term in the right way,and that the HLL-type solvers naturally provide a stable upwind ***-order versions of the ENO-and WENO-type reconstructions are proposed,together with precise modifications necessary to preserve positive pressure and *** the discrete source term to second order while maintaining stability requires non-standard techniques,which we *** first-and second-order schemes are tested on a suite of numerical experiments demonstrating impressive numerical resolution as well as stability,even on very fine meshes.

关键词： Conservation laws MHD divergence constraint Godunov-Powell source terms upwinded source terms high-order schemes

KINETIC FUNCTIONS IN MAGNETOHYDRODYNAMICS WITH RESISTIVITY AND HALL EFFECT

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Acta Mathematica Scientia 2009年第6期29卷 1684-1702页

作者： Philippe G. Le siddhartha mishra FlochLaboratoire Jacques-Louis Lions Centre National de la Recherche ScientifiqueUniversit Pierre et Marie Curie (Paris 6) 4 Place Jussieu 75258 Paris France Seminar for Applied Mathematics D-Math ETH HG Raemistrasse Zürich-8092 Switzerland

We consider a nonlinear hyperbolic system of two conservation laws which arises in ideal magnetohydrodynamics and includes second-order terms accounting for magnetic resistivity and Hall effect. We show that the initial value problem for this model may lead to solutions exhibiting complex wave structures, including undercompressive nonclassical shock waves. We investigate numerically the subtle competition that takes place between the hyperbolic, diffusive, and dispersive parts of the system. Following Abeyratne, Knowles, LeFloch, and Truskinovsky, who studied similar questions arising in fluid and solid flows, we determine the associated kinetic function which characterizes the dynamics of undereompressive shocks driven by resistivity and Hall effect. To this end, we design a new class of ＂schemes with eontroled dissipation＂, following recent work by LeFloch and Mohammadian. It is now recognized that the equivalent equation associated with a scheme provides a guideline to design schemes that capture physically relevant, nonclassical shocks. We propose a new class of schemes based on high-order entropy conservative, finite differences for the hyperbolic flux, and high-order central differences for the resistivity and Hall terms. These schemes are tested for several regimes of （co-planar or not） initial data and parameter values, and allow us to analyze the properties of nonclassical shocks and establish the existence of monotone kinetic functions in magnetohydrodynamics.

关键词： hyperbolic conservation law magnetohydrodynamics magnetic resistivity Hall effect undercompressive shock kinetic function

Automatic area estimation of algal blooms in water bodies from UAV images using texture analysis

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Water Science and Engineering 2024年第1期17卷 62-71页

作者： Ajmeria Rahul Gundu Lokesh siddhartha Goswami R.N.Ponnalagu Radhika Sudha Department of Electrical and Electronics Engineering Birla Institute of Technology&SciencePilani Hyderabad CampusTelangana 500078India

Algal blooms,the spread of algae on the surface of water bodies,have adverse effects not only on aquatic ecosystems but also on human *** adverse effects of harmful algal blooms(HABs)necessitate a convenient solution for detection and *** aerial vehicles(UAVs)have recently emerged as a tool for algal bloom detection,efficiently providing on-demand images at high spatiotemporal *** study developed an image processing method for algal bloom area estimation from the aerial images(obtained from the internet)captured using *** a remote sensing method of HAB detection,analysis,and monitoring,a combination of histogram and texture analyses was used to efficiently estimate the area of *** features like entropy(using the Kullback-Leibler method)were emphasized with the aid of a gray-level co-occurrence *** results showed that the orthogonal images demonstrated fewer errors,and the morphological filter best detected algal blooms in real time,with a precision of 80%.This study provided efficient image processing approaches using on-board UAVs for HAB monitoring.

关键词： Algal bloom Image processing Texture analysis Histogram analysis Unmanned aerial vehicles

Niche breadth and overlap of spotted deer and domestic cattle with swamp deer in tropical region of Nepal

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Ecological Processes 2022年第1期11卷 238-247页

作者： siddhartha Regmi Bijaya Neupane Bijaya Dhami Deepak Gautam Saroj Panthi Megharaj Poudel Institute of Forestry Tribhuvan University44107 HetaudaNepal Institute of Forestry Tribhuvan University33700 PokharaNepal School of Ecology and Nature Conservation Beijing Forestry UniversityBeijing 100083China Ministry of Forest Environment and Soil ConservationPokhara 33700GandakiNepal Ministry of Forests and Environment Forest Research and Training CenterKathmandu 44600Nepal Faculty of Agriculture and Forestry University of Helsinki00014 HelsinkiFinland

Background:Knowledge about the niche overlap among wild species and domestic cattle is helpful to conserve and manage *** assessed the habitat niche breadth and overlap of sympatrically living spotted deer(Axis axis)and domestic cattle with swamp deer(Cervus duvaucelii)in Shuklaphanta National Park,Nepal during the dry season to explore the possibility of interspecific competition by studying the habitat use by these *** assumption was made that the presence of pellets is proof of habitat used by ***:Grids of 2 km×2 km have four subgrids,each with four sample plots,making a total of 16 plots(20 m×20 m)in each *** size of each sub-grid was 200 m×200 m and they were placed randomly inside the grid but at least 1 km apart from one *** data was collected in a 96 plots in ***’s niche breadth and Morisita’s overlap index were calculated to determine the niche breadth and the habitat overlap,***:The Levin’s measure of niche breadth suggested that spotted deer had the highest acclimatization with an index value of 0.94,followed by domestic cattle at 0.50,and swamp deer at 0.33 in our study ***,our findings supported the evidence that spotted deer are habitat generalists,whereas swamp deer are habitat *** swamp deer had lower niche breadth and more overlap with domestic ***:Our study showed the least niche breadth of swamp deer in comparison to spotted deer and domestic *** domestic cattle had the highest and least niche overlap with spotted deer and swamp deer,respectively,in terms of habitat *** study suggests that domestic cattle grazing should be stopped,and grassland management should be carried out for the benefit of *** studies should be conducted,including different seasons and places,prior to appropriate habitat *** addition,further studies are needed to quantify the extent of interspecific competition by incorporating more species.

关键词： Generalist Levin’s niche breadth Morisita’s overlap index Spatial overlap Habitat specialist

Non-small Cell Lung Cancer Epigenomes Exhibit Altered DNA Methylation in Smokers and Neversmokers

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 991-1013页

作者： Jennifer A.Karlow Erica C.Pehrsson Xiaoyun Xing Mark Watson siddhartha Devarakonda Ramaswamy Govindan Ting Wang Department of Genetics Washington University School of MedicineSt.LouisMO 63110USA The Edison Family Center for Genome Sciences and Systems Biology Washington University School of MedicineSt.LouisMO 63110USA Department of Pathology and Immunology Washington University School of MedicineSt.LouisMO 63110USA Department of Medicine Washington University School of MedicineSt.LouisMO 63110USA McDonnell Genome Institute Washington University School of MedicineSt.LouisMO 63108USA

Epigenetic alterations are widespread in cancer and can complement genetic alterations to influence cancer progression and treatment *** determine the potential contribution of DNA methylation alterations to tumor phenotype in non-small cell lung cancer(NSCLC)in both smoker and never-smoker patients,we performed genome-wide profiling of DNA methylation in 17 primary NSCLC tumors and 10 matched normal lung samples using the complementary assays,methylated DNA immunoprecipitation sequencing(MeDIP-seq)and methylation sensitive restric-tion enzyme sequencing(MRE-seq).We reported recurrent methylation changes in the promoters of several genes,many previously implicated in cancer,including FAM83A and SEPT9(hy-pomethylation),as well as PCDH7,NKX2-1,and SOX17(hypermethylation).Although many methylation changes between tumors and their paired normal samples were shared across patients,several were specific to a particular smoking *** example,never-smokers displayed a greater proportion of hypomethylated differentially methylated regions(hypoDMRs)and a greater number of recurrently hypomethylated promoters,including those of ASPSCRI,TOP2A,DPP9,and USP39,all previously linked to *** outside of promoters were also widespread and often recurrent,particularly methylation loss over repetitive elements,highly enriched for ERV1 *** hypoDMRs were enriched for several transcription factor binding motifs,often for genes involved in signaling and cell *** example,71%of recurrent promoter hypoDMRs contained a motif for ***,the majority of DMRs were located within an active chromatin state in tissues profiled using the Roadmap Epigenomics data,suggesting that methylation changes may contribute to altered regulatory programs through the adaptation of cell type-specific expression programs.

关键词： Non-small cell lung cancer Epigenomics M&M methylCRF DNA methylation

Stand structure and species diversity regulate biomass carbon stock under major Central Himalayan forest types of India

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Ecological Processes 2021年第1期10卷 195-212页

作者： siddhartha Kaushal Ratul Baishya Ecology&Ecosystem Research Laboratory Department of BotanyUniversity of DelhiDelhi 110007India

Background:Data on the impact of species diversity on biomass in the Central Himalayas,along with stand structural attributes is sparse and ***,few studies in the region have related population structure and the influence of large trees on *** data is crucial for maintaining Himalayan biodiversity and carbon ***,we investigated these relationships in major Central Himalayan forest types using nondestructive methodologies to determine key factors and underlying ***:Tropical Shorea robusta dominant forest has the highest total biomass density(1280.79 Mg ha^(−1))and total carbon density(577.77 Mg C ha^(−1))along with the highest total species richness(21 species).The stem density ranged between 153 and 457 trees ha^(−1) with large trees(>70 cm diameter)contributing 0–22%.Conifer dominant forest types had higher median diameter and Cedrus deodara forest had the highest growing stock(718.87 m^(3) ha^(−1));furthermore,*** contributed maximally toward total carbon density(14.6%)among all the 53 species *** semecarpifolia–Rhododendron arboreum association forest had the highest total basal area(94.75 m^(2) ha^(−1)).We found large trees to contribute up to 65%of the growing *** percent of the species contributed more than 50%of the carbon *** dominance regulated the growing stock significantly(R^(2)=0.707,p<0.001).Temperate forest types had heterogeneous biomass distribution within the forest *** found total basal area,large tree density,maximum diameter,species richness,and species diversity as the predominant variables with a significant positive influence on biomass carbon *** structural attributes and diversity influenced the ordination of study sites under PCA *** showed no significant correlation with either biomass or species diversity ***:The results suggest biomass hyperdominance with both selection effects and niche complementarit

关键词： Biomass hyperdominance Elevational gradient Growing stock Large trees Carbon allocation Forest management