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Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits

Phyton-International Journal of Experimental Botany 2024年第8期93卷 2075-2093页

作者： abdul karim amin Yan He Xianglong Wang Pengwei Li Muhammad Ahmad Hassan Mohammad Yousof Soltani Yiling Zhang Mohammad Alem amin Ahmad Shah Ahmadzai Yajing Liu Songhu Wang Anhui Province Key Laboratory of Horticultural Crop Quality Biology School of HorticultureAnhui Agricultural UniversityHefei230036China Anhui Academy of Agricultural Sciences Hefei230001China Anhui Province Key Laboratory of Soybean Molecular Breeding and Crop Quality Biology School of AgronomyAnhui Agricultural UniversityHefei230036China Department of Horticulture Ghazni UniversityGhazni2301Afghanistan State Key Laboratory of Crop Genetics and Germplasm Enhancement College of HorticultureNanjing Agricultural UniversityNanjing210095China

Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every *** this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,***,shelf-life analysis was carried out for both cultivars at room *** exhibited that Riogrand showed higher firmness and less weight loss than *** ethylene production was higher in SalarF1,compared with Riogrand during post-harvest *** performed transcriptomic analysis of both cultivars in different storage *** discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),*** genes are enriched in ethylene biosynthesis and response,as well as cell wall-related *** response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in *** cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of *** quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome *** findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.

关键词： Shelf life transcriptome analysis tomato differentially expressed genes(DEGs) ethylene

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Determination of hemoglobin adduct of a musk xylene metabolite in trout as biomarker of exposure by gas chromatography mass spectrometry

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Journal of Environmental Sciences 2005年第6期17卷 989-992页

作者： Mohammad abdul karim Mohammad Rezaul Department of Chemistry and Biochemistry Baylor University P.O. Box 97348 Waco TX 76798-7348 USADepartment of Biochemistry and Molecular Biology University of Rajshahi Rajshahi 6205 Bangladesh

Musk xylene（MX） is frequently used as fragrances in formulation of personal care products. Quantification of a bound 4-amino- MX（4-AMX） as cysteine adducts in trout hemoglobin（Hb） was made by gas chromatography-ion trap-mass spectrometry（GC/MS）. The Hb samples were collected from trout after 24 h exposure to MX at 10μg/g, and or menhaden oil（control）. The formation of cysteine-Hb adduct was observed from nitroso derivative of MX, released by alkaline hydrolysis. The released 4-AMX metabolite was extracted in n- hexane. The extract was then reduced by evaporation, and analyzed by GC/MS. When similar agreement of mass spectral features and retention time of 4-AMX were obtained in both standard and sample solutions, the presence of 4-AMX metabolite in the Hb was confirmed. The concentration of 4-AMX was found to be 3.1 × 10^-6 6.9 × 10^-6 mg/g in the Hb solution. Quantitation was made based on an internal standard, a calibration plot, and response factor. In the non-hydrolyzed and laboratory blank extracts, the 4-AMX metabolite was not detected. Additionally, coeluting and interfefing ions were observed in the biological samples.

关键词： biomarkers musk xylene metabolite Hb adducts fish exposure

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FSPAM:A Feature Construction Method to Identifying Cell Populations in ScRNA-seq Data

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Computer Modeling in Engineering & Sciences 2020年第1期122卷 377-397页

作者： amin Einipour Mohammad Mosleh karim Ansari-Asl Department of Computer Engineering Dezful BranchIslamic Azad UniversityDezfulIran Department of Electrical Engineering Faculty of EngineeringShahid Chamran University of AhvazAhvazIran

The emergence of single-cell RNA-sequencing(scRNA-seq)technology has introduced new information about the structure of cells,diseases,and their associated biological *** of the main uses of scRNA-seq is identifying cell populations,which sometimes leads to the detection of rare cell ***,the new method is still in its infancy and with its advantages comes computational challenges that are just beginning to *** important tool in the analysis is dimensionality reduction,which transforms high dimensional data into a meaningful reduced *** technique allows noise removal,visualization and compression of high-dimensional *** paper presents a new dimensionality reduction approach where,during an unsupervised multistage process,a feature set including high valuable markers is created which can facilitate the isolation of cell *** proposed method,called fusion of the Spearman and Pearson affinity matrices(FSPAM),is based on a graph-based Gaussian *** of the graph theory can be effective to overcome the challenge of the nonlinear relations between cellular markers in scRNA-seq ***,with a proper fusion of the Pearson and Spearman correlation coefficient criteria,it extracts a set of the most important features in a new *** fact,the FSPAM aggregates the various aspects of cell-to-cell similarity derived from the Pearson and Spearman metrics,and reveals new aspects of cell-to-cell similarity,which can be used to extract new *** results of the identification of cell populations via k-means++clustering method based on the features extracted from the FSPAM and different datasets of scRNA-seq suggested that the proposed method,regardless of the characteristics that govern each dataset,enjoys greater accuracy and better quality compared to previous methods.

关键词： Single cell RNA sequencing cell population feature extraction fusion

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Countermeasure of river bend scour using a combination of submerged vanes and riprap

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International Journal of Sediment Research 2018年第4期33卷 478-492页

作者： Piya Biswas abdul karim Barbhuiya Department of Civil Engineering National Institute of Technology

A series of laboratory flume experiments were done in a large-scale 180° bend with non-cohesive sediment to find optimal or effective protection works at a bend. Detailed study of the scour and flow field dynamics with and without protection works was done. Spatially dense, high frequency velocity data were collected and analyzed to describe the pattern and magnitude of three-dimensional(3 D)velocity throughout the bend. Characterizing the role of flow field dynamics on the pattern of deposition and erosion through experimental measurements provided valuable data about how such flow features contribute to scour and about the performance of the protection works. From the experimental results, it is revealed that for a perennial river it is not possible to protect from scour either with riprap or with submerged vanes alone. Protection from scour at a bend can be achieved with proper combination of these two works. First, submerged vanes can protect the toe, and, second, riprap can protect the upper part of the slope if it is not damaged through toe erosion. The experiments convincingly demonstrate the efficiency of this bank protection technique.

关键词： River bend erosion Three-dimensional flow Vanes Riprap Open channel Sedimentation

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Time gap for temporal cloak based on spectral hole burning in atomic medium

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Chinese Physics B 2016年第8期25卷 175-180页

作者： abdul Jabar M S Bakht amin Bacha Iftikhar Ahmad Department of Physics University of Malakand

We demonstrate the possibility of creating a time gap in the slow light based on spectral hole burning in a fourlevel Doppler broadened sodium atomic system. A time gap is also observed between the slow and the fast light in the hole burning region and near the burnt hole region, respectively. A cloaking time gap is attained in microseconds and no distortion is observed in the transmitted pulse. The width of the time gap is observed to vary with the inverse Doppler effect in this system. Our results may provide a way to create multiple time gaps for a temporal cloak.

关键词： temporal cloak susceptibility slow and fast light spectral holes

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Biodegradation of natural and synthetic estrogens in moving bed bioreactor

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Chinese Journal of Chemical Engineering 2018年第2期26卷 393-399页

作者： Mohammad Mehdi amin Bijan Bina karim Ebrahim Zeynab Yavari Farzaneh Mohammadi Environment Research Center Research Institute for Primordial Prevention of Non-communicable Disease Isfahan University of Medical Sciences Department of Environmental Health Engineering School of Health Isfahan University of Medical Sciences Student Research Committee Isfahan University of Medical Sciences

Estrogen hormones as a group of endocrine disruptive compounds （EDC） can interfere with endocrine system in humans and animals. The goal of this study was to investigate the elimination rate of Estrone （El）, 17β-estradiol （E2） and 17α-ethinyl estradiol （EE2） in Moving Bed Bioreactor （MBBR）. These analytes extracted by Dispersive Liquid-Liquid Microextraction （DLLME） technique, followed by derivatization, and detected by GC/MS. Estrogen removal efficiency in MBBR improved at high solid retention times （SRTs）, which notion is owing to development ofnitrification. Estrogenspecificremovalratewasbetween 0,22-1.45μg.（gVSS） 1.d -1 for natural and synthetic hormones. The adsorption rate was 0.9%-3.2% 0-1.3%, and 0.7%-5.7% for E1, E2, and EE2, respectively. In addition, the biodegradation rates were more than 95% for these compounds. These results illustrated that in MBBR, the hiodegradation and the adsorption to biomass are considered as two significant routes for elimination of estrogenic compounds. As a whole, the deterioration rate of estrogens enhanced by MBBR compared to other biological wastewater treatment processes such as conventional activated sludge.

关键词： Estrogen hormones Adsorption Biodegradation Nitrification

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Charged Noncommutative Wormhole Solutions via Power-Law f(T) Models

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Communications in Theoretical Physics 2016年第10期65卷 411-422页

作者： Shamaila Rani abdul Jawad M.Bilal amin Department of Mathematics COMSATS Institute of Information Technology

In this paper,we explore static spherically symmetric charged wormhole solutions in extended teleparallel gravity taking power-law f(T) *** consider noncommutative geometry under Lorentzian *** order to obtain matter components,we develop field equations using effective energy-momentum tensor for non-diagonal *** explore solutions by considering various viable power-law f(T) models,which also include teleparallel gravity *** violation of energy conditions obtain by exotic matter to form wormhole solutions in teleparallel case while,physical acceptable wormhole solutions exist for charged noncommutative wormhole solutions for some cases of power-law *** effective energy-momentum tensor and charge are responsible for the violation of the energy ***,we check the equilibrium condition for these *** equilibrium condition meets for the teleparallel case and some power-law solutions while remaining solutions are either in less equilibrium or in disequilibrium situation.

关键词： f(T) gravity wormhole Lorentzian distribution noncommutative geometry

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Dynamical Comparison of Several Third-Order Iterative Methods for Nonlinear Equations

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Computers, Materials & Continua 2021年第5期67卷 1951-1962页

作者： Obadah Said Solaiman Samsul Ariffin abdul karim Ishak Hashim Department of Mathematical Sciences Faculty of Science&TechnologyUniversiti Kebangsaan MalaysiaBangi Selangor43600Malaysia Department of Fundamental and Applied Sciences Center for Smart Grid Energy Research(CSMER)Institute of Autonomous SystemUniversiti Teknologi PETRONASBandar Seri IskandarSeri IskandarPerak DR32610Malaysia

There are several ways that can be used to classify or compare iterative methods for nonlinear equations,for instance;order of convergence,informational efficiency,and efficiency *** this work,we use another way,namely the basins of attraction of the *** purpose of this study is to compare several iterative schemes for nonlinear *** the selected schemes are of the third-order of convergence and most of them have the same efficiency *** comparison depends on the basins of attraction of the iterative techniques when applied on several polynomials of different *** a comparison,we determine the CPU time(in seconds)needed by each scheme to obtain the basins of attraction,besides,we illustrate the area of convergence of these schemes by finding the number of convergent and divergent points in a selected range for all *** confirm the fact that basins of attraction differ for iterative methods of different orders,furthermore,they vary for iterative methods of the same order even if they have the same efficiency ***,this leads to the need for a new index that reflects the real efficiency of the iterative scheme instead of the commonly used efficiency index.

关键词： Nonlinear equations iterative methods basins of attraction order of convergence

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Modification of Oil Palm Empty Fruit Bunch and Sugarcane Bagasse Biomass as Potential Reinforcement for Composites Panel and Thermal Insulation Materials

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Journal of Bionic Engineering 2019年第1期16卷 175-188页

作者： Nor Azlina Ramlee Mohammad Jawaid Edi Syams Zainudin Shaikh abdul karim Yamani Department of Biocomposite Laboratory Institute of Tropical Forestry and Forest Products (INTROP)Universiti Putra Malaysia 43400 SerdangSelangorMalaysia Department of Mechanical and Manufacturing Engineering Faculty of EngineeringUniversiti Putra Malaysia 43400 SerdangSelangorMalaysia Faculty of Applied Science Wood Industry Universiti Teknologi MARA Campus of Jengka 26400 Bandar Tun Abdul Razak JengkaPahangMalaysia

This paper focuses on the study of the effect of modification of Oil Palm Empty Fruit Bunch(OPEFB)and sugarcane bagasse(SCB)biomass as potential reinforcement for composites panel and thermal *** fibres were treated with three types of chemicals:2%silane,4%H2O2 and 4%H2O2-2%silane for 3 *** influence of modified fibres content in composites was examined by structural changes using image analyser,Fourier transform infrared(FTIR),Scanning Electron Microscopy(SEM),tensile,interracial shear strength(IFSS)and thermal *** diameter of both fibres was reduced after treatment and showed decreasing of lignin and hemi-cellulose in *** strength has been increased by 2%silane treatment for both fibres and 4%H2O2 treatment displays higher result for *** properties of treated SCB fibre with silane display higher residual content and better thermal *** charac-terization showed that 2%silane treatment removed silica bodies of OPEFB fibre while 4%H2O2 treatment uniformly filled porosity of SCB ***,results revealed that treated OPEFB fibre is enough to improve compatibility and mechanical properties,while treated SCB fibre was effective in thermal stability for fabrication of composite materials.

关键词： oil palm empty fruit bunch sugarcane bagasse fibre treatment tensile properties thermal properties interracial shear strength

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LDSVM: Leukemia Cancer Classification Using Machine Learning

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Computers, Materials & Continua 2022年第5期71卷 3887-3903页

作者： abdul karim Azhari Azhari Mobeen Shahroz Samir Brahim Belhaouri Khabib Mustofa Department of Computer Science&Electronics Universitas Gadjah MadaYogyakarta55281Indonesia Department of Artificial Intelligence The Islamia University of BahawalpurBahawalpur63100Pakistan Division of Information&Computer Technology College of Science&EngineeringHamad Bin Khalifa UniversityDoha5825Qatar

Leukemia is blood cancer, including bone marrow and lymphatictissues, typically involving white blood cells. Leukemia produces an abnormalamount of white blood cells compared to normal blood. Deoxyribonucleicacid (DNA) microarrays provide reliable medical diagnostic services to helpmore patients find the proposed treatment for infections. DNA microarraysare also known as biochips that consist of microscopic DNA spots attachedto a solid glass surface. Currently, it is difficult to classify cancers usingmicroarray data. Nearly many data mining techniques have failed becauseof the small sample size, which has become more critical for ***, they are not highly effective in improving results and are frequently employed by doctors for cancer diagnosis. This study proposes a novelmethod using machine learning algorithms based on microarrays of leukemiaGSE9476 cells. The main aim was to predict the initial leukemia *** learning algorithms such as decision tree (DT), naive bayes (NB),random forest (RF), gradient boosting machine (GBM), linear regression(LinR), support vector machine (SVM), and novel approach based on thecombination of Logistic Regression (LR), DT and SVM named as ensembleLDSVM model. The k-fold cross-validation and grid search optimizationmethods were used with the LDSVM model to classify leukemia in patientsand comparatively analyze their impacts. The proposed approach evaluatedbetter accuracy, precision, recall, and f1 scores than the other ***, the results were relatively assessed, which showed LDSVMperformance. This study aims to successfully predict leukemia in patientsand enhance prediction accuracy in minimum time. Moreover, a Syntheticminority oversampling technique (SMOTE) and Principal compenent analysis(PCA) approaches were implemented. This makes the records generalized andevaluates the outcomes well. PCA reduces the feature count without losing anyinformation and deals with class imbalanced dataset

关键词： Leukemia GSE9476 cancer genes classification machine learning ensemble LDSVM classifier

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