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Advances in DNA methylation and its role in cytoplasmic male sterility in higher plants

Journal of Integrative Agriculture 2024年第1期23卷 1-19页

作者： Atiqur Rahman Hasan Sofiur Rahman Shakil Uddin Naima Sultana Shirin Akhter Ujjal Kumar Nath Shamsun Nahar Begum Mazadul Islam Afroz Naznin Nurul Amin Sharif Ahmed Akbar Hossain Department of Genetics and Plant Breeding Bangladesh Agricultural UniversityMymensingh 2202Bangladesh Plant Breeding Division Bangladesh Institute of Nuclear AgricultureMymensingh 2202Bangladesh Tuber Crop Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Horticulture Research Centre Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh Biotechnology Division Bangladesh Agricultural Research Institute(BARI)Joydebpur 1701Bangladesh international Rice Research Institute Bangladesh OfficeDhaka 1213Bangladesh Division of Soil Science Bangladesh Wheat and Maize Research InstituteDinajpur 5200Bangladesh

The impact of epigenetic modifications like DNA methylation on plant phenotypes has expanded the possibilities for crop *** methylation plays a part in the regulation of both the chromatin structure and gene expression,and the enzyme involved,DNA methyltransferase,executes the methylation process within the plant *** regulating crucial biological pathways,epigenetic changes actively contribute to the creation of the ***,epigenome editing may assist in overcoming some of the drawbacks of genome editing,which can have minor off-target consequences and merely facilitate the loss of a gene’s *** drawbacks include gene knockout,which can have such off-target *** review provides examples of several molecular characteristics of DNA methylation,as well as some plant physiological processes that are impacted by these epigenetic changes in the *** also discuss how DNA alterations might be used to improve crops and meet the demands of sustainable and environmentally-friendly farming.

关键词： DNA methylation epigenetics CMS male sterility chromatin architecture gene expression higher plants

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GliomaCNN: An Effective Lightweight CNN Model in Assessment of Classifying Brain Tumor from Magnetic Resonance Images Using Explainable AI

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Computer Modeling in Engineering & Sciences 2024年第9期140卷 2425-2448页

作者： Md.Atiqur Rahman Mustavi Ibne Masum Khan Md Hasib M.F.Mridha Sultan Alfarhood Mejdl Safran Dunren Che Department of Computer Science and Engineering Ahsanullah University of Science and TechnologyDhaka1208Bangladesh Department of Computer Science and Software Engineering The University of Western AustraliaPerthWA 6009Australia Department of Computer Science American International University-BangladeshDhaka1229Bangladesh Department of Computer Science College of Computer and Information SciencesKing Saud UniversityP.O.Box 51178Riyadh11543Saudi Arabia School of Computing Southern Illinois UniversityCarbondale62901USA

Brain tumors pose a significant threat to human lives and have gained increasing attention as the tenth leading cause of global *** study addresses the pressing issue of brain tumor classification using Magnetic resonance imaging(MRI).It focuses on distinguishing between Low-Grade Gliomas(LGG)and High-Grade Gliomas(HGG).LGGs are benign and typically manageable with surgical resection,while HGGs are malignant and more *** research introduces an innovative custom convolutional neural network(CNN)model,*** stands out as a lightweight CNN model compared to its *** research utilized the BraTS 2020 dataset for its *** with the gradient-boosting algorithm,GliomaCNN has achieved an impressive accuracy of 99.1569%.The model’s interpretability is ensured through SHapley Additive exPlanations(SHAP)and Gradient-weighted Class Activation Mapping(Grad-CAM++).They provide insights into critical decision-making regions for classification *** challenges in identifying tumors in images without visible signs,the model demonstrates remarkable performance in this critical medical application,offering a promising tool for accurate brain tumor diagnosis which paves the way for enhanced early detection and treatment of brain tumors.

关键词： Deep learning magnetic resonance imaging convolutional neural networks explainable AI boosting algorithm ablation

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Ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry-characterized extract of Aerides odorata Lour alleviates paracetamol-induced hepatotoxicity in animal model evidenced by biochemical,molecular,and computational studies

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Animal Models and Experimental Medicine 2024年第4期7卷 497-522页

作者： A.M.Abu Ahmed Md.Atiar Rahman Farjana Sharmen A.S.M.Ali Reza Md.Shahidul Islam Md.Mamunur Rashid Md.Khalid Juhani Rafi Tanvir Ahmed Siddiqui Md.Muzahid Ahmed Ezaj Srabonti Saha Md.Nazim Uddin Walla Alelwani Department of Genetic Engineering and Biotechnology University of ChittagongChittagongBangladesh Department of Biochemistry and Molecular Biology University of ChittagongChittagongBangladesh Department of Pharmacy International Islami University ChittagongChittagongBangladesh Institute of Food Science and Technology Bangladesh Council of Scientific and Industrial ResearchDhakaBangladesh Department of Biochemistry College of ScienceUniversity of JeddahJeddahSaudi Arabia

Background:Many kinds of orchids have significant health benefits although ade-quate research on their biological functions is yet to be carried *** study inves-tigated the paracetamol-induced liver damage-protecting effect of epiphytic Aerides odorata methanol extract(AODE).Methods:The protective effects of AODE were studied by analyzing its effect on liver function parameters,messenger RNA(mRNA)expression,and tissue histopatho-logical *** results were confirmed by ligand-receptor interaction of molecular docking and multitarget interaction of network pharmacological ***:AODE significantly(p<0.05)minimized the dose-dependent increase in acid phosphatase,aspartate aminotransferase,alanine aminotransferase,alkaline phos-phatase,γ-glutamyl transferase,lactate dehydrogenase,and total bilirubin compared to the reference drug *** level decreased,and the antioxidant genes catalase(CAT),superoxide dismutase(SOD),β-actin,paraoxonase-1(PON1),and phosphofructokinase-1(PFK-1)were upregulated in AODE-treated paracetamol-intoxicated rats.A total of 376 compounds comprising phenols and flavonoids were identified using ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry(UPLC-qTOF-MS).The online toxicity assessment using SwissADME and admetSAR exhibited drug-like,nontoxic,and potential pharmaco-logical ***,in silico analysis showed that isoacteoside,one of the identified compounds,exhibited the best docking score(−11.42)with the liver pro-tein human pituitary adenylate cyclase-1(Protein Data Bank ID:3N94).Furthermore,network pharmacology analysis identified the top 10 hub genes,namely AKT1(protein kinase B),CTNNB1(catenin beta-1),SRC(proto-oncogene c-Src),TNF(tumor necrosis factor),EGFR(epidermal growth factor receptor),HSP90AA1(heat shock protein 90α),MAPK3(mitogen-activated protein kinase 3),STAT3(signal transducer and activator of transcription 3),CASP3(caspase protein),

关键词： Aerides odorata animal model mRNA expression PCM-induced hepatotoxicity UPLC-qTOF-MS

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Are gender inclusiveness and rural transformation interlinked?The case of bangladesh

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Journal of Integrative Agriculture 2024年第6期23卷 2112-2126页

作者： Maria Fay Rola-Rubzen Mohammad Jahangir Alam Jon Marx Sarmiento Ismat Ara Begum Al Amin Al Abbasi Subrata Saha UWA School of Agriculture and Environment The University of Western AustraliaPerth 6009Australia Department of Agribusiness and Marketing Bangladesh Agricultural UniversityMymensingh-2202Bangladesh Department of Agricultural Economics Bangladesh Agricultural UniversityMymensingh-2202Bangladesh

Gender inclusiveness is important in the rural transformation process of bangladesh as rural women play key roles in both agricultural and non-agricultural *** inclusiveness also leads to gender *** empirically evaluate relationships between rural transformation and gender inclusiveness in *** consider three rural transformation indicators:high-value commodities’share in agricultural output values,non-farm employment’s share in rural labor employment,and non-agricultural GDP’s share in total *** capturing gender inclusiveness include the per capita rural income of males and females,ratio of investments into gender programs,female access to education,access to healthcare,employment participation,land ownership,and asset *** test the effect of the difference in per capita rural income of males and females and the ratio of their incomes and check for the robustness of the gender variables across different model *** 128 district-level observations from 32 districts of bangladesh across four time periods(2000,2005,2010 and 2016),we use both ordinary least squares and fixed effects panel regression *** find that female land and asset ownership and access to education and healthcare are robust determinants of various stages of rural ***,our results suggest that improving women’s ownership of land and assets and investing in women’s education and healthcare will likely contribute to a more inclusive rural transformation.

关键词： rural transformation bangladesh gender inclusiveness investments on women

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Review of coastal land transformation:Factors,impacts,adaptation strategies,and future scopes

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Geography and Sustainability 2024年第2期5卷 167-178页

作者： Md.Abubakkor Siddik Abu Reza Md.Towfiqul Islam Dr.Wazed Research and Training Institute Begum Rokeya UniversityRangpur 5404Bangladesh Department of Emergency Management Patuakhali Science and Technology UniversityPatuakhali-8602Bangladesh Department of Disaster Management Begum Rokeya UniversityRangpur 5404Bangladesh Department of Development Studies Daffodil International UniversityDhaka 1216Bangladesh

Coastal land transformation has been identified as a topic of research in many countries around the *** studies have been conducted to determine the causes and impacts of land ***,much less is understood about coupling change detection,factors,impacts,and adaptation strategies for coastal land transformation at a global *** review aims to present a systematic review of global coastal land transformation and its leading research *** 1,741 documents of Scopus and Web of Science,60 studies have been selected using the PRISMA-2020 *** revealed that existing literature included four leading focus areas regarding coastal land transformation:change detection,driving factors,impacts,and adaptation *** focus areas were further analyzed,and it was found that more than 80%of studies used Landsat imagery to detect land *** growth and urbanization were among the major driving factors *** review further identified that about 37%of studies included impact *** studies identified impacts on ecosystems,land surface temperature,migration,water quality,and occupational effects as significant ***,only four studies included adaptation *** review explored the scope of comprehensive research in coastal land transformation,addressing change detection,factor and impact analysis,and mitigation-adaptation *** research also proposes a conceptual framework for comprehensive coastal land transformation *** framework can provide potential decision-making guidance for future studies in coastal land transformation.

关键词： Coastal land transformation Land use and land cover Landsat Population PRISMA

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Relationship between Seed Priming Mediated Seedling Vigor and Yield Performance of Spring Wheat

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Phyton-international Journal of Experimental Botany 2024年第6期93卷 1159-1177页

作者： Md.Parvez Anwar Masuma Akhter Sharmin Aktar Sinthia Afsana Kheya A.K.M.Mominul Islam Sabina Yeasmin Ahmed Khairul Hasan Md.Harun Or Rashid Department of Agronomy Bangladesh Agricultural UniversityMymensingh2202Bangladesh

Seed priming is a pre-germinated technique that can enhance seed germination percentage,faster and synchro-nized germination,better seedling growth,and yield under stress *** ascertain the most effective seed priming method that would ensure the potential yield of wheat in bangladesh,two experiments were carried out from December 2021 to March 2022 at the Department of Agronomy,bangladesh Agricultural *** wheat varieties namely BARI Gom-28 and BWMRI Gom-1 were subjected to a range of priming chemicals in both lab and pot *** compounds included the following:control(no priming),hydropriming(distilled water),10000 ppm KNO_(3),15000 ppm KNO_(3),40000 ppm Mannitol,60000 ppm Mannitol,10000 ppm NaCl,20000 ppm NaCl,100 ppm PEG,150 ppm PEG,500 ppm NaOCl,1000 ppm NaOCl,10000 ppm CaCl_(2),20000 ppm CaCl_(2),10000 ppm KCl and 20000 ppm KCl.A complete randomized design(CRD)with three repli-cations was used to set up the *** results showed that BARI Gom-28 and BWMRI Gom-1 responded best to KCl priming in terms of rapid seed germination and strong seedling *** the other hand,the best priming agents for plant growth and productivity turned out to be CaCl_(2) and *** results of this study support the possibility of using seed priming as a technique to improve wheat plant development and output by raising seed emergence and survival rates.

关键词： Priming seedling percentage germination growth yield wheat

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Detecting anomalies in blockchain transactions using machine learning classifiers and explainability analysis

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Blockchain(Research and Applications) 2024年第3期5卷 106-122页

作者： Mohammad Hasan Mohammad Shahriar Rahman Helge Janicke Iqbal H.Sarker Department of Computer Science and Engineering Premier University4000 ChitagongBangladesh Department of Computer Science and Engineering United International University1212 DhakaBangladesh Cyber Security Cooperative Research Centre 6027 PerthAustralia Centre for Securing Digital Futures Edith Cowan University6027 PerthAustralia

As the use of blockchain for digital payments continues to rise,it becomes susceptible to various malicious *** detecting anomalies within blockchain transactions is essential for bolstering trust in digital ***,the task of anomaly detection in blockchain transaction data is challenging due to the infrequent occurrence of illicit *** several studies have been conducted in the field,a limitation persists:the lack of explanations for the model’s *** study seeks to overcome this limitation by integrating explainable artificial intelligence(XAI)techniques and anomaly rules into tree-based ensemble classifiers for detecting anomalous Bitcoin *** shapley additive explanation(SHAP)method is employed to measure the contribution of each feature,and it is compatible with ensemble ***,we present rules for interpreting whether a Bitcoin transaction is anomalous or ***,we introduce an under-sampling algorithm named XGBCLUS,designed to balance anomalous and non-anomalous transaction *** algorithm is compared against other commonly used under-sampling and over-sampling ***,the outcomes of various tree-based single classifiers are compared with those of stacking and voting ensemble *** experimental results demonstrate that:(i)XGBCLUS enhances true positive rate(TPR)and receiver operating characteristic-area under curve(ROC-AUC)scores compared to state-of-the-art under-sampling and over-sampling techniques,and(ii)our proposed ensemble classifiers outperform traditional single tree-based machine learning classifiers in terms of accuracy,TPR,and false positive rate(FPR)scores.

关键词： Anomaly detection Blockchain Bitcoin transactions Data imbalance Data sampling Explainable AI Machine learning Decision tree Anomaly rules

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Fractional order prey-predator model incorporating immigration on prey:Complexity analysis and its control

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international Journal of Biomathematics 2024年第5期17卷 285-317页

作者： Md.Jasim Uddin Chandra Nath Podder Departmentof Mathematics university of Dhaka Dhaka-1000Bangladesh

In this paper,the Caputo fractional derivative is assumed to be the prey-predator *** order to create Caputo fractional differential equations for the prey-predator model,a discretization process is first *** fixed points of the model are categorized *** identify requirements for the fixed points of the suggested prey-predator model's local asymptotic *** demonstrate analytically that,under specific parametric conditions,a fractional order prey-predator model supports both a Neimark-Sacker(NS)bifurcation and a Flip *** present evidence for NS and Flip bifurcations using central manifold and bifurcation *** parameter values and the initial conditions have been found to have a profound impact on the dynamical behavior of the fractional order prey-predator *** the bifurcation parameter is increased,the system displays chaotic *** simulations are shown to demonstrate chaotic behaviors like bifurcations,phase portraits,invariant closed cycles,and attractive chaotic sets in addition to validating analytical *** suggested prey-predator dynamical system's chaotic behavior will be controlled by the OGY and hybrid control methodology,which will also visualize the chaotic state for various biological parameters.

关键词： Prey-predator model Caputo fractional derivative Flip and Neimark-Sacker(NS)bifurcations immigration chaos control numerical simulation

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Genome-Wide Analysis for Yield-Related Agronomic and Biochemical Traits of Chinese and bangladeshi Grass Pea Genotypes Using SSR Markers

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Phyton-international Journal of Experimental Botany 2024年第8期93卷 1781-1804页

作者： Md.Mosiur Rahman Md.Ruhul Quddus Quanle Xu Muhammad Malek Hossain Rong Liu Mengwei Li Xin Yan Guan Li Yishan Ji Chenyu Wang Ashutosh Sarker Tao Yang Xuxiao Zong Md.Monoar Hossain Saleh Alfarraj Mohammad Javed Ansari Sagar Maitra Akbar Hossain Institute of Crop Sciences Chinese Academy of Agricultural Sciences(CAAS)Beijing100081China Pulses Research Center Bangladesh Agricultural Research Institute(BARI)Gazipur1701Bangladesh Hybrid Rice Division Bangladesh Rice Research Institute(BRRI)Gazipur1701Bangladesh Northwest Agriculture&Forestry university Yangling712199China international Center for Agricultural Research in the Dry Areas(ICARDA) New Delhi110012India Wheat Breeding Division Bangladesh Wheat and Maize Research InstituteDinajpur5200Bangladesh Zoology Department College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Department of Botany Hindu College Moradabad(Mahatma Jyotiba Phule Rohilkhand UniversityBareilly)Moradabad244001India Department of Agronomy and Agroforestry Centurion University of Technology and ManagementOdisha761211India Soil Science Division Bangladesh Wheat and Maize Research InstituteDinajpur5200Bangladesh

Grass pea(Lathyrus sativus L.)is an imperative food crop cultured in dryland agricultural *** is a vital source of dietary protein to millions of populaces living in low-income countries in South-East Asia and *** study highlights the improvement of genomic properties and their application in marker-trait relationships for 17 yield-related characters in 400 grass pea genotypes from China and *** characters were assessed via 56 polymorphic markers using general linear model(GLM)(P+G+Q)and mixed linear model(MLM)(P+G+Q+K)in the tassel software based on the linkage disequilibrium and population structure *** structure analysis showed two major groups and one admixed group in the *** significant loci pairs of linkage disequilibrium(LD)mean value(D′)was 0.479.A total of 99 and 61 marker-trait associations in GLM and MLM models allied to the 17 traits were accepted at a 5%level of *** these markers,21 markers were associated with more than one trait;12 marker-trait associations passed the Bonferroni correction *** models found six markers C41936,C39067,C34100,C47146,C47638,and C43047 significantly associated with days to maturity,flower color,plant height,and seed per pod were detected in the Hebei and Liaoyang location(p≤0.01),and the interpretation rate(R^(2)value)11.2%to 43.6%.Conferring to the consequences,the association analysis methodology may operative system for quantitative,qualitative,and biochemical traits related to gene position mapping and support breeders in improving novel approaches for advancing the grass pea quality.

关键词： Grass pea dryland agriculture genome-wide association yield contributing traits SSR markers

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The Global Energy and Water Exchanges(GEWEX)Project in Central Asia:The Case for a Regional Hydroclimate Project

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Advances in Atmospheric Sciences 2024年第5期41卷 777-783页

作者： Michael BRODY Maksim KULIKOV Sagynbek ORUNBAEV Peter J.VAN OEVELEN international Agricultural university Tashkent 111200Uzbekistan George Mason university FairfaxVirginia 22030USA university of Central Asia Bishkek 720001Kyrgyz Republic american university of Central Asia Bishkek 720060Kyrgyz Republic international GEWEX project George Mason UniversityFairfaxVirginia 22030USA

Central Asia consists of the former Soviet Republics,Kazakhstan,Kyrgyz Republic,Tajikistan,Turkmenistan,and *** region’s climate is continental,mostly semi-arid to *** is a significant part of the region’s *** its nature of intensive water use,agriculture is extremely vulnerable to climate *** growth and irrigation development have significantly increased the demand for water in the *** climate change issues include melting glaciers and a shrinking snowpack,which are the foundation of the region’s water resources,and a changing precipitation *** glaciers are located in Kyrgyzstan and Tajikistan,leading to transboundary water resource *** already has extremely high *** indicate that Central Asia has been warming and precipitation might be *** warming is expected to increase,but its spatial and temporal distribution depends upon specific global *** of future precipitation show significant uncertainties in type,amount,and *** Hydroclimate Projects(RHPs)are an approach to studying these *** steps to develop an RHP began in 2021 with a widely distributed online survey about these climate *** was followed up with an online workshop and then,in 2023,an in-person workshop,held in Tashkent,*** for the Global Energy and Water Exchanges(GEWEX)project for the region include both observations and modeling,as well as development of better and additional precipitation observations,all of which are topics for the next workshop.A well-designed RHP should lead to reductions in critical climate uncertainties in policy-relevant timeframes that can influence decisions on necessary investments in climate adaptation.

关键词： GEWEX Central Asia climate change agriculture

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