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Prediction of promiscuous T cell epitopes in RNA dependent RNA polymerase of Chikungunya virus

Asian Pacific Journal of Tropical Medicine 2017年第8期10卷 825-829页

作者： yasir Waheed Sher Zaman Safi Muzammil Hasan Najmi Hafsa Aziz muhammad Imran Foundation University Medical College Foundation University IslamabadDHA-I Islamabad(44000)Pakistan Interdisciplinary Research Centre in Biomedical Materials(IRCBM) COMSATS Institute of Information TechnologyLahore CampusLahorePakistan Nuclear Medicine Oncology and Radiotherapy Institute Islamabad Islamabad(44000)Pakistan Department of Medical Laboratory Sciences(DMLS) Faculty of Health and Allied Sciences(FHAS)Imperial College of Business Studies(ICBS)LahorePakistan Department of Microbiology University of Health SciencesLahorePakistan

Objective: To explore RNA dependent RNA polymerase of Chikungunya virus(CHIKV) and develop T cell based epitopes with high antigenicity and good binding affinity for the human leukocyte antigen(HLA) classes as targets for epitopes based CHIKV vaccine. Methods: In this study we downloaded 371 non-structural protein 4 protein sequences of CHIKV belonging to different regions of the world from the US National Institute of Allergy and Infectious Diseases(NIAID) virus pathogen resource database. All the sequences were aligned by using CLUSTALW software and a consensus sequence was developed by using Uni Pro U Gene Software version 1.2.1. PropredⅠand Propred software were used to predict HLAⅠ and HLAⅡ binding promiscuous epitopes from the consensus sequence of non-structural protein 4 protein. The predicted epitopes were analyzed to determine their antigenicity through Vaxijen server version 2.0. All the HLAⅠ binding epitopes were scanned to determine their immunogenic potential through the Immune Epitope Database(IEDB). All the predicted epitopes of our study were fed to IEDB database to determine whether they had been tested earlier. Results: Twenty two HLA class Ⅱ epitopes and eight HLA classⅠepitopes were predicted. The promiscuous epitopes WMNMEVKII at position 486–494 and VRRLNAVLL at 331–339 were found to bind with 37 and 36 of the 51 HLA class Ⅱ alleles respectively. Epitope MANRSRYQS at position 58–66 and epitopes YQSRKVENM at positions 64–72 were predicted to bind with 12 and 9 HLAⅠI alleles with antigenicity scores of 0.754 9 and 1.013 0 respectively. Epitope YSPPINVRL was predicted to bind 18 HLAⅠ alleles and its antigenicity score was 1.425 9 and immunogenicity score was 0.173 83. This epitope is very useful in the preparation of a universal vaccine against CHIKV infection. Conclusions: Epitopes reported in this study showed promiscuity, antigenicity as well as good binding affinity for the HLA classes. These epitopes will provide the baseline for development

关键词： Chikungunya virus Epitope vaccine HLA binding T cell epitopes

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Feasibility-Guided Constraint-Handling Techniques for Engineering Optimization Problems

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Computers, Materials & Continua 2021年第6期67卷 2845-2862页

作者： muhammad Asif Jan yasir Mahmood Hidayat Ullah Khan Wali Khan Mashwani muhammad Irfan Uddin Marwan Mahmoud Rashida Adeeb Khanum Ikramullah Noor Mast Institute of Numerical Sciences Kohat University of Science&TechnologyKohatPakistan Department of Economics Abbottabad University of Science&TechnologyAbbottabadPakistan Institute of Computing Kohat University of Science&TechnologyKohatPakistan Faculty of Applied Studies King Abdulaziz UniversityJeddahSaudi Arabia Jinnah College for Women University of PeshawarPeshawarPakistan Department of Physics Kohat University of Science&TechnologyKohatPakistan

The particle swarm optimization(PSO)algorithm is an established nature-inspired population-based meta-heuristic that replicates the synchronizing movements of birds and *** is essentially an unconstrained algorithm and requires constraint handling techniques(CHTs)to solve constrained optimization problems(COPs).For this purpose,we integrate two CHTs,the superiority of feasibility(SF)and the violation constraint-handling(VCH),with a *** CHTs distinguish feasible solutions from infeasible ***,in SF,the selection of infeasible solutions is based on their degree of constraint violations,whereas in VCH,the number of constraint violations by an infeasible solution is of more ***,a PSO is adapted for constrained optimization,yielding two constrained variants,denoted SF-PSO and *** SF-PSO and VCH-PSO are evaluated with respect to ve engineering problems:the Himmelblau’s nonlinear optimization,the welded beam design,the spring design,the pressure vessel design,and the three-bar truss *** simulation results show that both algorithms are consistent in terms of their solutions to these problems,including their different available *** of the SF-PSO and the VCHPSO with other existing algorithms on the tested problems shows that the proposed algorithms have lower computational cost in terms of the number of function evaluations *** also report our disagreement with some unjust comparisons made by other researchers regarding the tested problems and their different variants.

关键词： Constrained evolutionary optimization constraint handling techniques superiority of feasibility violation constraint-handling technique swarm based evolutionary algorithms particle swarm optimization engineering optimization proble

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Plant extract-loaded bacterial cellulose composite membrane for potential biomedical applications

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Journal of Bioresources and Bioproducts 2021年第1期6卷 26-32页

作者： Atiya Fatima Sumayia yasir MohdShariq Khan Sehrish Manan muhammad Wajid Ullah Mazhar Ul-Islam Department of Chemical Engineering College of EngineeringDhofar UniversitySalalahSultanate of Oman Department of Biomedical Engineering Huazhong University of Science and TechnologyWuhan 430074China

Bacterial cellulose(BC)has been extensively explored as biomaterial for various biomedical applications owing to its non-toxic nature and unique structural morphology and impressive physicochemical and mechanical ***,its high production cost and lack of antimicrobial activity have restricted its large-scale production and therapeutic ***,the current study is aimed to devise a strategy for low-cost BC production and develop its composite with bioactive materials to bless it with antimicrobial ***,5 mm thick reticulated fibrous and highly porous BC was produced by utilizing the wasted rotten tomatoes as the production *** produced bacterial cellulose waste(BCW)(i.e.,produced from wastes)was ex-situ modified with bioactive plant extract(PE)obtained from Euclea schimperi,and the bactericidal activity of the developed BCW/PE was evaluated against Gram-positive Staphylococcus aureus and Gram-negative Escherichia coli through disc diffusion and colony forming unit(CFU)count *** BCW/PE composite showed high bactericidal activities against *** and produced clear inhibition zone whereas negligible activity was observed against ***,indicating its bactericidal activity mainly against the Gram-positive ***,this study illustrates that there is a huge potential for developing valuable biomaterials from food wastes and utilizing their liquid holding capabilities for value-added applications in medical and pharmaceutical fields.

关键词： Bacterial cellulose Food waste Plant extract Bactericidal activity Biomedical application

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Spatiotemporal Changes in NDVI and Its Driving Factors in the Kherlen River Basin

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中国地理科学：英文版 2023年第2期33卷 377-392页

作者： muhammad Naveed HE Hongshi ZONG Shengwei DU Haibo SATTI Zulqarnain TAN Xinyuan QAZI muhammad yasir Key Laboratory of Geographical Processes and Ecological Security in Changbai Mountains Ministry of EducationSchool of Geographical SciencesNortheast Normal UniversityChangchun 130024China School of Natural Resources University of MissouriColumbia 65211USA Xinjiang Institute of Ecology and Geography Chinese Academy of SciencesUrumqi 830011China

Vegetation is an important factor linking the atmosphere,water,soil,and biological functions,and it plays a specific role in the climate change response and sustainable development of regional ***,little information is available on vegetation vulnerability and its driving ***,studying temporal and spatial change characteristics of vegetation and their corresponding mechanisms is important for assessing ecosystem stability and formulating ecological policies in the Kherlen River *** used Moderate-resolution Imaging Spectroradiometer(MODIS)normalized difference vegetation index(NDVI)remote sensing images from 2000 to 2020 to analyse temporal changes in NDVI with the autoregressive moving average model(ARMA)and the breaks for additive season trend(BFAST)in the basin and to assess natural,anthropogenic and topographic factors with the Geodetector *** results show that:1)the long NDVI time series remained stable in the Kherlen River Basin from 2000 to 2020,with a certain significant mutation period from 2013 to 2017;2)the coefficient of variation(CV)in the analysis of the spatial NDVI was generally constant,mainly at the level of 0.01–0.07,and the spatial NDVI change was minimally impacted by external interference;and 3)temperature and precipitation are the key factors affecting the NDVI in the basin,and changes in local hydrothermal conditions directly affect the local *** results of this study could provide a scientific basis for the effective protection of the ecological environment and will aid in understanding the influence of vegetation change mechanisms and the corresponding factors.

关键词： normalized difference vegetation index(NDVI) spatial stability vegetation ecology Geodetector Kherlen River Basin

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Overview of Strain Characterization in Relation to Serological and Molecular Detection of Citrus tristeza Closterovirus

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Phyton-International Journal of Experimental Botany 2021年第4期90卷 1063-1074页

作者： yasir Iftikhar Mazhar Abbas Mustansar Mubeen muhammad Zafar-ul-Hye Faheema Bakhtawar Sonum Bashir Ashara Sajid muhammad Asif Shabbir Department of Plant Pathology College of AgricultureUniversity of SargodhaSargodha40100Pakistan Institute of Horticultural Sciences University of Agriculture FaisalabadFaisalabad38000Pakistan State Key Laboratory of Agricultural Microbiology and Provincial Key Laboratory of Plant Pathology of Hubei Province College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan430070China Department of Soil Science Faculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultan60800Pakistan

Tristeza is a devastating viral disease in all the citrus growing countries throughout the world and has killed millions of citrus trees in severely affected *** citrus species grafted on sour orange rootstock are affected by this ***,the sweet orange,grapefruit and lime trees grafted on sour orange exhibit severe symptoms like quick decline,vein clearing,pin holing,bark scaling and degeneration leading to variable *** expression of Citrus tristeza virus(CTV)in different hosts has been attributed to virus isolates which are from severe to *** serological and molecular assays have been deployed to differentiate the strains of *** tristeza virus is diversified towards its strains on the basis of biological,serological and molecular *** expression is due to genetic alteration and different molecular basis have now been adopted for strain *** review will give a brief idea about the different CTV isolates,their characterization based on nucleic acid and serological *** methods along with salient features for strain characterization has also been *** review will also open the new aspects towards formulation of management strategies through different detection techniques.

关键词： Citrus tristeza virus symptomology detection serology isolates and host rang

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Physiological and Biochemical Characteristics and Response Patterns of Salinity Stress Responsive Genes (SSRGs) in Wild Quinoa (Chenopodium quinoa L.)

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Phyton-International Journal of Experimental Botany 2023年第2期92卷 399-410页

作者： Yurong Jiang muhammad yasir Yuefen Cao Lejia Hu Tongli Yan Shuijin Zhu Guoquan Lu The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province College of Advanced Agricultural SciencesZhejiang A&F UniversityHangzhou311300China College of Agriculture and Biotechnology Zhejiang UniversityHangzhou310058China

Cultivating salt-tolerant crops is a feasible way to effectively utilize saline-alkali land and solve the problem of underutilization of saline ***,a protein-comprehensive cereal in the plant kingdom,is an exceptional crop in terms of salt stress tolerance *** seems an excellent model for the exploration of salt-tolerance mechanisms and cultivation of salt-tolerant *** this study,the seeds and seedlings of the quinoa cultivar Shelly were treated with different concentrations of NaCl *** physiological,biochemical characteristics and agronomic traits were investigated,and the response patterns of three salt stress-responsive genes(SSRGs)in quinoa were determined by real-time *** optimum level of stress tolerance of quinoa cultivar Shelly was found in the range of 250–350 mM concentration of *** stress significantly induced expression of superoxide dismutase(SOD),peroxidase(POD),and particularly betaine aldehyde dehydrogenase(BADH).BADH was discovered to be more sensitive to salt stress and played an important role in the salt stress tolerance of quinoa seedlings,particularly at high NaCl concentrations,as it displayed upregulation until 24 h under 100 mM salt ***,it showed upregulation until 12 h under 250 mM salt *** together,these results suggest that BADH played an essential role in the salt-tolerance mechanism of *** on the expression level and prompt response induced by NaCl,we suggest that the BADH can be considered as a molecular marker for screening salt-tolerant quinoa germplasm at the early stages of crop *** treatment at different plant ontogeny or at different concentrations had a significant impact on quinoa ***,an appropriate treatment approach needs to be chosen rationally in the process of screening salt-tolerant quinoa germplasm,which is useful to the utilization of saline *** study provides a fundamental information to deepen knowledge of the s

关键词： Salt tolerant NaCl stress stress-responsive genes

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Assessment of sunflower germplasm for phytoremediation of lead-polluted soil and production of seed oil and seed meal for human and animal consumption

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Journal of Environmental Sciences 2020年第1期32卷 24-38页

作者： Afsheen Zehra Zulfiqar Ali Sahito Wenbin Tong Lin Tang yasir Hamid muhammad Bilal Khan Zarina Ali Beena Naqui Xiaoe Yang Ministry of Education(MOE)Key Laboratory of Environmental Remediation and Ecosystem Health College of Environmental and Resources ScienceZhejiang UniversityHangzhou 310058China Department of Botany Federal Urdu University of ArtsScience and TechnologyKarachi 75300Pakistan Technical Extension Station of Soil Fertilizer and Rural Energy QujiangQuzhou 324000China PCSIR Laboratories Complex KarachiDr Salimuzzaman RoadKarachi 75280Pakistan

Phytoremediation is a valuable technology for mitigating soil contamination in agricultural lands,but phytoremediation without economic revenue is unfeasible for land owners and *** use of crops with high biomass and bioenergy for phytoremediation is a unique strategy to derive supplementary benefits along with remediation ***(Helianthus annuus L.)is a high-biomass crop that can be used for the phytoremediation of polluted lands with additional advantages(biomass and oil).In this study,40 germplasms of sunflower were screened in field conditions for phytoremediation with the possibility for oil and meal *** study was carried out to the physiological maturity *** studied germplasms mopped up substantial concentrations of Pb,with maximum amounts in shoot>root>seed *** phytoextraction efficiency of the germplasm was assessed in terms of the Transfer factor(TF),Metal removal efficiency(MRE)and Metal extraction ratio(MER).Among all assessed criteria,GP.8585 was found to be most appropriate for restoring moderately Pb-contaminated soil accompanied with providing high biomass and high yield *** Pb content in the oil of GP.8585 was below the Food safety standard of China,with 59.5% oleic acid and 32.1% linoleic ***,amino acid analysis in meal illustrated significant differences among essential and nonessential amino *** acid was found in the highest percentage(22.4%),whereas cysteine in the lowest percentage(1.3%).Therefore,its efficient phytoextraction ability and good quality edible oil and meal production makes GP.8585 the most convenient sunflower germplasm for phytoremediation of moderately Pb-contaminated soil,with fringe benefits to farmers and landowners.

关键词： Heavy metal Soil contamination Metal removal efficiency(MRE) Germplasm(GP) Phytoextraction Edible oil Fatty acids(FA) Amino acids(AAs)

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Antagonistic Potential of Bacterial Species against Fungal Plant Pathogens(FPP)and Their Role in Plant Growth Promotion(PGP):A Review

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Phyton-International Journal of Experimental Botany 2022年第9期91卷 1859-1877页

作者： Amjad Ali yasir Iftikhar Mustansar Mubeen Haider Ali muhammad Ahmad Zeshan Zohaib Asad muhammad Zafar-ul-Hye Malik Abdul Rehman Mazhar Abbas muhammad Rafique muhammad Usman Ghani Department of Plant Protection Sivas University of Science and TechnologySivas58140Turkey Department of Plant Pathology College of AgricultureUniversity of SargodhaSargodha40100Pakistan College of Bioscience University of BirminghamBirminghamB152TTUK Department of Plant Pathology PMAS University of Arid AgricultureRawalpindi43490Pakistan Department of Soil Science Faculty of Agricultural Sciences and TechnologyBahauddin Zakariya UniversityMultan60800Pakistan Citrus Research Institute Sargodha40100Pakistan Department of Agriculture and Agribusiness Management University of Karachi75270KarachiPakistan Pest warning&Quality Control of Pesticides SahiwalPunjab40210Pakistan Institute of Soil and Environmental Sciences University of AgricultureFaisalabad38000Pakistan

Since the 19th century to date,the fungal pathogens have been involved in causing devastating diseases in *** types of fungal pathogens have been observed in important agricultural crops that lead to significant pre and postharvest *** application of synthetic fungicide against the fungal plant pathogens(FPP)is a traditional management practice but at the same time these fungicides kill other beneficial microbes,insects,animal,and humans and are harmful to *** antagonistic microorganism such as bacteria are being used as an alternate strategy to control the *** antagonistic species are cost-effective and eco-friendly in *** biocontrol bacteria have a broad mechanism against fungal pathogens present in the phyllosphere and rhizosphere of the *** antagonistic bacteria have different strategies against the FPP,by producing siderophore,biofilm,volatile organic compounds(VOCs),through parasitism,antibiosis,competition for limited resources and induce systemic resistance(ISR)in the host plant by activating the immune *** commercial bio-products synthesized by the major bacterial species Pseudomonas syringae,Burkholderia cepacia,Streptomyces griseoviridis,Pseudomonas fluorescens and Bacillus subtilis are used to control Fusarium,Pythium,Rhizoctonia,Penicillium,Alternaria,and *** commercial bio-formulations of bacteria act as both antifungal and plant growth *** Plant growth-promoting rhizobacteria(PGPR)played a significant role in improving plant health by nitrogen-fixing,phosphorus solubilization,phytohormones production,minimizing soil metal contamination,and by ACC deaminase antifungal *** articles are available on the specific antifungal activity of bacteria in plant ***,this review article has summarized the information on biocontrol activity of bacteria against the FPP and the role of PGPR in plant growth *** review also provided a complete picture

关键词： Fungi plant pathogens synthetic fungicide antagonism bio-products PGPR

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A Hierarchal Clustered Based Proactive Caching in NDN-Based Vehicular Network

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Computer Systems Science & Engineering 2023年第10期47卷 1185-1208页

作者： muhammad yasir Khan muhammad Adnan Jawaid Iqbal Noor ul Amin Byeong-Hee Roh Jehad Ali Department of Computer Science&Information Technology Hazara University Mansehra21120Pakistan Department of Electronics Engineering Kookmin University Seoul Korea Faculty of Computing Riphah International University Islamabad Pakistan Department of AI Convergence Network Ajou UniversitySuwon16499Korea

An Information-Centric Network(ICN)provides a promising paradigm for the upcoming internet architecture,which will struggle with steady growth in data and changes in *** ICN architectures have been designed,including Named Data Networking(NDN),which is designed around content delivery instead of *** data is the central part of the ***,NDN was developed to get rid of the dependency on IP addresses and provide content *** is one of the major research dimensions for this upcoming internet *** research has been carried out to solve the mobility issues,but it still has problems like handover delay and packet loss ratio during real-time video streaming in the case of consumer and producer *** solve this issue,an efficient hierarchical Cluster Base Proactive Caching for Device Mobility Management(CB-PC-DMM)in NDN Vehicular Networks(NDN-VN)is proposed,through which the consumer receives the contents proactively after handover during the mobility of the *** a consumer moves to the next destination,a handover interest is sent to the connected router,then the router multicasts the consumer’s desired data packet to the next hop of neighboring ***,once the handover process is completed,consumers can easily get the content to the newly connected router.A CB-PCDMM in NDN-VN is proposed that improves the packet delivery ratio and reduces the handover delay aswell as cluster ***,the intra and inter-domain handover handling procedures in CB-PC-DMM for NDN-VN have been *** the validation of our proposed scheme,MATLAB simulations are *** simulation results show that our proposed scheme reduces the handover delay and increases the consumer’s interest satisfaction *** proposed scheme is compared with the existing stateof-the-art schemes,and the total percentage of handover delays is decreased by up to 0.1632%,0.3267%,2.3437%,2.3255%,and 3.7313%at the mobil

关键词： Vehicular network named data networking caching hierarchical architecture

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Fuzzy Logic Control of a Head-movement Based Semi-autonomous Human–machine Interface

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Journal of Bionic Engineering 2023年第2期20卷 645-655页

作者： yasirÖzlük Eda Akman Aydin Institute of Sciences Selçuk UniversityAlaaddin Keykubad CampusSelçukluKonya42130Turkey Faculty of Technology Electrical and Electronics EngineeringGazi University06500 Teknikokullar BesevlerAnkara06500Turkey

Quadriplegia is a neuromuscular disease that may cause varying degrees of functional loss in trunk and *** such cases,head movements can be used as an alternative communication *** this study,a human–machine interface which is controlled by human head movements is designed and *** proposed system enables users to steer the desired movement direction and to control the speed of an output device by using head *** movements of the users are detected using a 6 DOF IMUs measuring three-axis accelerometer and three-axis *** head movement axes and the Euler angles have been associated with movement direction and speed,*** ensure driving safety,the speed of the system is determined by considering the speed requested by the user and the obstacle distance on the *** this context,fuzzy logic algorithm is employed for closed-loop speed control according to distance sensors and reference speed data.A car model was used as the output device on the machine ***,the wireless communication between human and machine interfaces provides to adapt this system to any remote device or *** implemented system was tested by five *** of the system was evaluated in terms of task completion times and feedback from the subjects about their experience with the *** indicate that the proposed system is easy to use;and the control capability and usage speed increase with user *** control speed is improved with the increase in user experience.

关键词： Human-machine interface(HMI) Head-movement Obstacle avoidance Inertial measurement unit(IMU) Fuzzy logic

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