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Use of methylation filtration and Cot fractionation for analysis of genome composition and comparative genomics in bread wheat

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Journal of Genetics and Genomics 2011年第7期38卷 315-325页

作者： Rajib Bandopadhyay Sachin Rustgi Rajat Kanti Chaudhuri Paramjit Khuran Jitendra Paul Khurana akhilesh kumar tyagi Harindra Singh Balyan Andreas Houben Pushpendra kumar Gupta Department of Genetics & Plant Breeding Ch. Charan Singh University Meerut 250004 India Department of Biotechnology Birla Institute of Technology Mesra 835215 Ranchi India Department of Crop & Soil Sciences Washington State University Pullman 99163 USA Department of Botany University of Calcutta Kolkata 700019 India Department of Plant Molecular Biology University of Delhi South Campus New Delhi 110021 India Leibniz Institute of Plant Genetics and Crop Plant Research Corrensstrasse-03 Gatersleben 06466 Germany

We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and Cot fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences （e.g., transposable elements and simple sequence repeats）, protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/ exclusion in methylation-filtered （MF） library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags （ESTs） available in the public domain. Only a limited overlap among ME high Cot （HC）, and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.

关键词： Methylation--filtration Cot fractionation Transposable elements Gene-rich regions

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Ameliorative Effects of Paclobutrazol via Physio-Biochemical and Molecular Manifestation in Rice under Water Deficit Stress

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Rice science 2024年第5期31卷 603-616,I0065页

作者： Chirag MAHESHWARI Nitin kumar GARG Archana SINGH Aruna tyagi Indian Council of Agricultural Research-Indian Agricultural Research Institute New Delhi 110012India Sri Karan Narendra Agricultural University JobnerRajasthan 303329India

To comprehensively explore the physio-biochemical and molecular changes of paclobutrazol(PBZ) at the ideal dose under water deficit stress(WDS) conditions, we investigated the effects of 100 mg/kg PBZ applied via drenching on various physio-biochemical and molecular parameters in three rice varieties(N22, IR64, and IR64 DTY1.1) under both mild [75%-80% relative water content(RWC)] and severe(60%-65% RWC) WDS conditions. The results showed that PBZ treatment positively influenced the physio-biochemical parameters, significantly increasing dry matter(16.27%-61.91%), RWC(6.48%-16.34%), membrane stability index(4.37%-10.35%), and total chlorophyll content(8.97%-29.09%) in the rice varieties under both mild and severe WDS. Moreover, PBZ treatment reduced drought susceptibility(0.83-0.95) and enhanced drought tolerance efficiency(60.92%-86.78%), indicating its potential as a stress-mitigating agent. Global methylation analysis revealed changes in DNA methylation patterns, indicating the regulatory influence of PBZ on gene expression. The expression analysis of genes involved in the diversification of geranylgeranyl pyrophosphate towards the biosynthesis of abscisic acid, gibberellin acid, and chlorophyll showed alterations in their expression levels, suggesting the involvement of PBZ in the isoprenoid pathway. Overall, this study provides valuable insights into the potential mechanisms by which PBZ modulates physiological and molecular responses in rice plants under WDS. The findings highlight the importance of PBZ as a promising agent for enhancing drought tolerance in rice and offer valuable information for future research in crop stress management.

关键词： rice paclobutrazol drought stress abscisic acid gibberellic acid

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On the Zeros of a Special Class of Polynomials

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Journal of Mathematical Research with Applications 2024年第4期44卷 470-474页

作者： Mahnaz Shafi CHISHTI Vipin kumar tyagi Mohammad Ibrahim MIR School of Basic and Applied Sciences Shobhit Institute of Engineering and Technology (Deemed to be University) Department of Mathematics University of KashmirSouth Campus

Let P be a complex polynomial of the form P （z）=（λz-a）mΠj=1n-m（z-zj）,where|zj|≥1,1≤j≤*** aim of this paper is to obtain generalisation of a result due to Zargar and Manzoor and a result due to Mir,Nazir and... 详细信息

关键词： bound coefficient polynomial zeros

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Deep Learning-Based Speech Emotion Recognition: Leveraging Diverse Datasets and Augmentation Techniques for Robust Modeling

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Journal of Harbin Institute of Technology(New series) 2024年

作者： Ayush Porwal Praveen kumar tyagi Ajay Sharma Dheeraj kumar Agarwal Department of Electronics and Instrumentation Engineering， Shri G.S.Institute of Technology and Science Department of Electronics and Communication Engineering， Maulana Azad National Institute of Technology School of Computing Science and Engineering， VIT Bhopal University

In recent years， Speech Emotion Recognition (SER) has developed into an essential instrument for interpreting human emotions from auditory data. The proposed research focused on the development of a SER system employing deep learning and multiple datasets containing samples of emotive speech. The primary objective of this research endeavor is to investigate the utilization of Convolutional Neural Networks (CNNs) in the process of sound feature extraction. Stretching， pitch manipulation， and noise injection are a few of the techniques utilized in this study to improve the data quality. The investigation includes coverage of these methods. Feature extraction methods including Zero Crossing Rate， Chroma＿stft， MFCC， RMS， and MelSpectogram are used to train a model. By using these techniques， audio signals can be transformed into recognized features that can be utilized to train the model. Ultimately， the study will produce a thorough evaluation of the model’s performance. When this method was applied， the model achieved an impressive accuracy of 94.57% on the test dataset. Proposed work also validated on EMO-BD and IEMOCAP dataset. These consist of further data augmentation， feature engineering， and hyperparameter optimization. By following these development paths， SER systems will be able to be implemented in real-world scenarios with greater accuracy and resilience.

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The Receptor-Like Cytoplasmic Kinase （OsRLCK） Gene Family in Rice： Organization, Phylogenetic Relationship, and Expression during Development and Stress

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Molecular Plant 2008年第5期1卷 732-750页

作者： Shubha Vij Jitender Giri Prasant kumar Dansana Sanjay Kapoor akhilesh K. tyagi Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology University of Delhi South Campus Benito Juarez Road New Delhi 110021 India

Receptor-like cytoplasmic kinases （RLCKs） in plants belong to the super family of receptor-like kinases （RLKs）. These proteins show homology to RLKs in kinase domain but lack the transmembrane domain. Some of the functionally characterized RLCKs from plants have been shown to play roles in development and stress responses. Previously, 149 and 187 RLCK encoding genes were identified from Arabidopsis and rice, respectively. By using HMM-based domain structure and phylogenetic relationships, we have identified 379 OsRLCKs from rice. OsRLCKs are distributed on all 12 chromosomes of rice and some members are located on duplicated chromosomal segments. Several OsRLCKs probably also undergo alternative splicing, some having evidence only in the form of gene models. To understand their possible functions, expression patterns during landmark stages of vegetative and reproductive development as well as abiotic and biotic stress using microarray and MPSS-based data were analyzed. Real-time PCR-based expression profiling for a selected few genes confirmed the outcome of microarray analysis. Differential expression patterns observed for majority of OsRLCKs during development and stress suggest their involvement in diverse functions in rice. Majority of the stress-responsive OsRLCKs were also found to be localized within mapped regions of abiotic stress QTLs. Outcome of this study would help in selecting organ/development stage specific OsRLCK genes/targets for functional validation studies.

关键词： abiotic stress biotic stress genome-wide analysis kinase rice RLCK.

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Long noncoding RNA: TRIMming the viral load

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Cellular & Molecular Immunology 2019年第11期16卷 843-845页

作者： akhilesh kumar Himanshu kumar Laboratory of Immunology and Infectious Disease Biology Department of Biological SciencesIndian Institute of Science Education and Research BhopalBhopal By-pass roadBhauriBhopalMadhya Pradesh 462066India Laboratory of Host Defense WPI Immunology Frontier Research CenterOsaka University3-1 Yamada-okaSuitaOsaka 565-0871Japan

Viruses are obligate intracellular entities that require a living host and its machinery for *** replication,viral components known as pathogen-associated molecular patterns(PAMPs)are sensed by a family of innate immune sensors or pattern recognition receptors(PRRs)and promote an antiviral *** nucleic acids are one of the key PAMPs sensed by cytosolic RIG-I-like receptors(RLRs),Cyclic GMP-AMP Synthase(cGAS),Absent In Melanoma 2(AIM2),Interferon Gamma Inducible Protein 16(IFI16),and Z-DNA Binding Protein 1(ZBP1 or DAI)and endosome-localized Toll-like receptors(TLR3,7,8,and 9).1 Recognition of viral RNA by Retinoic acid-inducible gene I(RIG-I),Melanoma differentiation associated gene 5(MDA5),and TLR3,7,and 8 or viral DNA by TLR9,cGAS,AIM2,IFI16,and DAI triggers a cascade of signaling events to recruit transcription factors,interferon regulatory factors and NF-κ*** IRF3/7 and NF-κB translocate to the nucleus and induce expression of type I and III interferons and proinflammatory cytokines,respectively.1 The production of these interferons is further enhanced in an autocrine and paracrine manner through the JAK-STAT signaling *** I and III interferons further induce interferoninducible genes,and together with proinflammatory cytokines,they develop an antiviral *** antiviral state is characterized by by apoptosis of virally infected cells and inhibition of the cellular protein synthesis machinery,making the uninfected cells resistant to viral infection and initiates virus-specific adaptive immune responses(Fig.1a).

关键词： interferon load viral

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Fractional Wavelet Packet Transformations Involving Hankel–Clifford Integral Transformations

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Acta Mathematica Sinica,English Series 2016年第7期32卷 783-796页

作者： akhilesh PRASAD Sumant kumar Department of Applied Mathematics Indian School of Mines

In this paper, we introduce the fractional wavelet transformations （FrWT） involving Han- kel-Clifford integral transformation （HCIIT） on the positive half line and studied some of its basic properties. Also we obtain Parseval＇s relation and an inversion formula. Examples of fractional powers of Hankel-Clifford integral transformation （FrHClIT） and FrWT are given. Then, we introduce the concept of fractional wavelet packet transformations FrBWPT and FrWPIT, and investigate their properties.

关键词： Wavelet packet transformation fractional Hankel-Clifford integral transformation frac-tional Hankel-Clifford integral convolution wavelet

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Synthetic and biological studies on a cyclopolypeptide of plant origin

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2008年第5期9卷 391-400页

作者： Rajiv DAHIYA akhilesh kumar Department of Pharmaceutical Chemistry Rajiv Academy for Pharmacy

Objective:A natural cyclic peptide previously isolated from Citrus medica was synthesized by coupling of tetrapep-tide units Boc-Leu-Pro-Trp-Leu-OMe and Boc-Ile-Ala-Ala-Gly-OMe after proper deprotection at carboxyl and amino terminals followed by cyclization of linear octapeptide segment. Methods:Solution phase technique was adopted for the synthesis of cyclooctapeptide-sarcodactylamide. Required tetrapeptide units were prepared by coupling of Boc-protected dipeptides viz. Boc-Leu-Pro-OH and Boc-Ile-Ala-OH with respective dipeptide methyl esters Trp-Leu-OMe and Ala-Gly-OMe. Cyclization of linear octapeptide unit was done by p-nitrophenyl ester method. The structure of synthesized cyclopolypeptide was elucidated by FTIR,1H NMR,13C NMR,FABMS spectral data and elemental analysis. The newly synthesized peptide was evaluated for dif-ferent pharmacological activities including antimicrobial,anthelmintic and cytotoxic activities. Results:Synthesis of sarcodac-tylamide was accomplished with >78% yield utilizing dicyclohexylcarbodiimide(DCC) as coupling agent. Newly synthesized peptide possessed potent cytotoxic activity against Dalton's lymphoma ascites(DLA) and Ehrlich's ascites carcinoma(EAC) cell lines,in addition to moderate anthelmintic activity against earthworms Megascoplex konkanensis,Pontoscotex corethruses and Eudrilus sp. Moreover,cyclopolypeptide displayed good antimicrobial activity against pathogenic fungi Candida albicans and Gram-negative bacteria Pseudomonas aeruginosa,in comparison to standard drugs griseofulvin and ciprofloxacin. Conclusion:Solution phase technique employing DCC and triethylamine(TEA) as base proved to be effective for the synthesis of natural cyclooctapeptide. N-methyl morpholine(NMM) was found to be a better base for the cyclization of linear octapeptide unit in comparison to TEA and pyridine.

关键词： Cyclic octapeptide Citrus medica var. sarcodactylis Sarcodactylamide Peptide synthesis Anthelmintic activity Antimicrobial activity Cytotoxicity

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Application of Fractional Order PID Controller for AGC Under Deregulated Environment

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International Journal of Automation and computing 2018年第1期15卷 84-93页

作者： Nagendra kumar Barjeev tyagi Vishal kumar Department of Electrical Engineering Indian Institute of Technology

In this paper, a fractional order proportional integral derivative （FOPID） controller for multiarea automatic generation control （AGC） scheme has been designed. FOPID controller has five parameters and provides two additional degrees of flexibility in comparison to a proportional integral derivative （PID） controller. The optimal values of parameters of FOPID controller have been determined using Big Bang Big Crunch （BBBC） search algorithm. The designed controller regulates real power output of generators to achieve the best dynamic response of frequency and tie-line power on a load perturbation. The complete scheme for designing of the controllers has been developed and demonstrated on multiarea deregulated power system. The performance of the designed FOPID controllers has been compared with the optimally tuned PID controllers. It is observed from the results that the FOPID controller shows a considerable improvement in the performance as compared to the conventional PID controller.

关键词： Automatic generation control (AGC) deregulation Big Bang Big Brunch (BBBC) algorithm fractional order propor-tional integral derivative (FOPID) controller optimization.

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Potential of roots and shoots of Napier grass for arresting soil erosion and runoff of mollisols soils of Himalayas

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International Soil and Water Conservation Research 2023年第3期11卷 538-548页

作者： Sushma Tamta akhilesh kumar Daniel Prakash Kushwaha Krishi Vigyan Kendra Khodawandpur848202BegusaraiBiharIndia Department of Soiland Water Conservation Engineering G.B.Pant University of Agriculture and TechnologyPantnagar263145India

In this study, a soil filled Hydraulic Tilting Flume (HTF) was used as a test plot under simulated rainfallconditions. This flume was flled with mollisols soils (sandy loam in texture) collected from tarai regionof Himalayas. The effects of root and shoot characteristics of Napier grass in terms of leaf area index (LAI),shoot length (SL), number of leaves (NL), number of tillers (NT), shoot biomass (SB), root density (RD),root length (RL), root biomass (RB), and total biomass (TB) were investigated on runoff and sedimentoutflow at 90, 120 and 150 days after planting (DAP). Four simulated rainfall intensities namely 4.0, 6.5,8.3 and 9.4 cm/h over three land slopes of 1, 2 and 3% were selected. Runoff samples collected fromwhole plant plot and only root plot were analyzed for runoff and sediment outflow. Findings revealedthat Napier grasses were very effective to reduce runoff and sediment outflow and its efficacy increasedwith the extended growth stages. The reduction in runoff and sediment outflow at 90, 120 and 150 DAPwas obtained as 56% and 85%, 68% and 90%, and 74% and 96%, respectively, as compared to bare plotconditions. It was observed that the comparative contribution of shoots in runoff rate reduction washigher than the roots. On the contrary, the root part of the plant showed more contribution in sedimentrate reduction as compared to the shoot part. Step wise regression was attempted for the selection ofeffective input parameters to establish authentic runoff and sediment outflow models. Power form ofmultiple non-linear regression (MNLR) showed very satisfactory results for predicting runoff and sedimentoutflow with coefficient of determination (R^(2)) as 97.4% and 99.0%, respectively, root mean squareerror (RMSE) as 38.8 cc/m^(2)/min and 0.126 g/m^(2)/min, respectively, and coefficient of efficiency (CE) as93.9% and 96.7%, respectively, during testing period.

关键词： Rootand shoot characteristics Runoff and sedimentreduction Simulated rainfall conditions Hydraulic tilting flume Step wise regression analysis

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