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Artificial Fish Swarm for Multi Protein Sequences Alignment in Bioinformatics

Computers, Materials & Continua 2022年第9期72卷 6091-6106页

作者： Medhat A.Tawfeek saad Alanazi A.A.Abd El-Aziz Department of Computer Science College of Computer and Information SciencesJouf UniversitySaudi Arabia(KSA Department of Computer Science Faculty of Computers and InformationMenoufia UniversityEgypt Department of Information Systems College of Computer and Information SciencesJouf UniversitySaudi Arabia(KSA) Department of Information Systems and Technology Faculty of Graduates Studies and ResearchCairo UniversityEgypt

The alignment operation between many protein sequences or DNAsequences related to the scientific bioinformatics application is very *** is a trade-off in the objectives in the existing techniques of MultipleSequence Alignment (MSA). The techniques that concern with speed ignoreaccuracy, whereas techniques that concern with accuracy ignore speed. Theterm alignment means to get the similarity in different sequences with highaccuracy. The more growing number of sequences leads to a very complexand complicated problem. Because of the emergence;rapid development;anddependence on gene sequencing, sequence alignment has become importantin every biological relationship analysis process. Calculating the numberof similar amino acids is the primary method for proving that there is arelationship between two sequences. The time is a main issue in any alignmenttechnique. In this paper, a more effective MSA method for handling themassive multiple protein sequences alignment maintaining the highest accuracy with less time consumption is proposed. The proposed method dependson Artificial Fish Swarm (AFS) algorithm that can break down the mostchallenges of MSA problems. The AFS is exploited to obtain high accuracyin adequate time. ASF has been increasing popularly in various applicationssuch as artificial intelligence, computer vision, machine learning, and dataintensive application. It basically mimics the behavior of fish trying to getthe food in nature. The proposed mechanisms of AFS that is like preying,swarming, following, moving, and leaping help in increasing the accuracy andconcerning the speed by decreasing execution time. The sense organs that aidthe artificial fishes to collect information and vision from the environmenthelp in concerning the accuracy. These features of the proposed AFS make thealignment operation more efficient and are suitable especially for large-scaledata. The implementation and experimental results put the proposed AFS as afirst choice in th

关键词： Multiple sequence alignment swarm intelligence artificial fish swarm protein sequences

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Fusarium pseudograminearum and *** affect the root system architecture of bread wheat

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作物学报：英文版 2023年第1期11卷 316-321页

作者： Ahmed saad Jack Christopher Anke Martin Stephen McDonald Cassandra Percy Centre for Crop Health University of Southern QueenslandToowoombaQLD 4350Australia University of Queensland Queensland Alliance for Agriculture and Food Innovation(QAAFI)Leslie Research FacilityToowoombaQLD 4350Australia

Yield losses of bread wheat due to crown rot can be more severe when drought conditions occur during the grain-filling *** architecture characteristics are important for soil exploration and belowground resource acquisition and are essential for adaptation to water-limited *** such as root angle,length and density have been strongly associated with acquisition efficiency and contribute to yield stability of the *** impact of crown rot pathogens on wheat root architecture is poorly *** examined differences in root angle,length and number,as well as dry root weight of the crown rot-susceptible bread wheat cultivar,Livingston inoculated with one of two crown rot pathogens Fusarium culmorum or Fusarium pseudograminearum in a transparent-sided root observation *** adverse impacts on plant health and growth were revealed by visual discolouration of the leaf sheaths;fresh and dry shoot weight;leaf area of the oldest and the youngest fully expanded leaf and leaf *** of most recorded root system measurements were reduced when inoculated with either *** or *** contrast,root angle was increased in the presence of *** but was not significantly changed by *** development of whiteheads and grain losses in bread wheat caused by crown rot have previously been associated with blockages of the vascular *** method employed here was able to identify differences in the pathogen impacts on roots,which were not detected using previous *** research indicates that in the presence of *** and *** infection,not only reductions in the size and biomass of the shoot system but also changes in the length,biomass and architecture of the root system could play an important role in yield loss.

关键词： Crown rot Root characteristics Livingston Wheat

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A Review on Primary and Secondary Controls of Inverter-interfaced Microgrid

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Journal of Modern Power Systems and Clean Energy 2021年第5期9卷 969-985页

作者： Kafeel Ahmed Mehdi Seyedmahmoudian saad Mekhilef N.M.Mubarak Alex Stojcevski School of Software and Electrical Engineering Swinburne University of TechnologyVIC 3122VictoriaAustralia Power Electronics and Renewable Energy Research Laboratory Department of Electrical EngineeringUniversity of Malaya50603 Kuala LumpurMalaysia Department of Chemical Engineering Faculty of Engineering and ScienceCurtin University of Technology98009 SarawakMalaysia

The demand of electricity and environmental issues associated with conventional power generation plants are increasing *** technology has transformed the conventional power system through the integration of distributed generation(DG).With the help of modern power electronic technology,the conventional power system is able to support the integration of DGs based on renewable energy sources(RESs).The systematic combination of DGs with energy storage system forms a microgrid(MG),which can operate in islanded mode or grid-connected *** intermittent nature of RES and varying load pose substantial obstacles such as voltage and frequency instability,and the unreliability of *** feeder impedances and non-linear loads are considered as present challenges in MG *** control has been useful in undertaking solutions to these *** paper covers the deep insight of different control methods applied at the primary and secondary control levels in hierarchical *** primary control,the classification based on droop and non-droop controls is *** virtual synchronization machine(VSM)based control method is *** and frequency restoration control and economical operations at decentralized and centralized secondary control are analyzed in *** on the existing literature,critical discussion on MG control and future trends are also presented to provide future research perspectives.

关键词： Distributed generation(DG) hierarchical control droop control non-droop control inverter

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Sparse Approximations of the Schur Complement for Parallel Algebraic Hybrid Solvers in 3D

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Numerical Mathematics(Theory,Methods and Applications) 2010年第3期3卷 276-294页

作者： L.Giraud A.Haidar Y.saad Joint INRIA-CERFACS Lab-42 AV.Coriolis 31057ToulouseFrance Department of Computer Science University of TennesseeKnoxvilleTN37996USA. Department of Computer Science and Engineering University of MinnesotaMinneapolisMN55455USA

In this paper we study the computational performance of variants of an algebraic additive Schwarz preconditioner for the Schur complement for the solution of large sparse linear *** earlier works,the local Schur complements were computed exactly using a sparse direct *** robustness of the preconditioner comes at the price of this memory and time intensive computation that is the main bottleneck of the approach for tackling huge *** this work we investigate the use of sparse approximation of the dense local Schur *** approximations are computed using a partial incomplete LU *** a numerical calculation is the core of the multi-level incomplete factorization such as the one implemented in pARMS. The numerical and computing performance of the new numerical scheme is illustrated on a set of large 3D convection-diffusion problems;preliminary experiments on linear systems arising from structural mechanics are also reported.

关键词： Hybrid direct/iterative solver domain decomposition incomplete/partial factorization Schur approximation scalable preconditioner convection-diffusion large 3D problems parallelscientific computing High Performance Computing.

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Creeper:a tool for detecting permission creep in file system access controls

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Cybersecurity 2019年第1期2卷 239-252页

作者： Simon Parkinson saad Khan James Bray Daiyaan Shreef Department of Computer Science School of Computing and EngineeringUniversity of HuddersfieldQueensgateHD13DHHuddersfieldUK

Access control mechanisms are widely used in multi-user IT systems where it is necessary to restrict access to computing *** is certainly true of file systems whereby information needs to be protected against unintended *** permissions often evolve over time,and changes are often made in an ad hoc manner and do not follow any rigorous *** is largely due to the fact that the structure of the implemented permissions are often determined by experts during initial system configuration and documentation is rarely ***,permissions are often not audited due to the volume of information,the requirement of expert knowledge,and the time required to perform manual *** paper presents a novel,unsupervised technique whereby a statistical analysis technique is developed and applied to detect instances of permission *** system(herein refereed to as Creeper)has initially been developed for Microsoft systems;however,it is easily extensible and can be applied to other access control *** analysis has demonstrated good performance and applicability on synthetic file system permissions with an average accuracy of 96%.Empirical analysis is subsequently performed on five real-world systems where an average accuracy of 98%is established.

关键词： Permission creep Access control Auditing χ^2 statistics

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On a new modified fractional analysis of Nagumo equation

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International Journal of Biomathematics 2019年第3期12卷 191-205页

作者： Khaled M.saad Sinan Deniz Dumitru Baleanu Department of Mathematics College of Science and Arts Najran University P.O. Box 1988 Najran Saudi Arabia Department of Mathematics Faculty of Applied Science Taiz University P.O. Box 6169 Taiz Yemen Department of Mathematics Faculty of Art and Sciences Manisa Celal Bayar University 45140 Manisa Turkey Department of Mathematics Faculty of Sciences Cankaya University 06530 Ankara Turkey Institute of Space Sciences Magurele-Bucharest Romania

In this work, a new modified fractional form of the Nagumo equation has been presented and deeply analyzed. Using the Caputo–Fabrizio and Atangana–Baleanu time-fractional derivatives, classical Nagumo model is transformed to a new fractional version. The modified equation has been solved by using the homotopy analysis transform method. The convergence analysis has been also examined with the help of the so-called hh-curves and average residual error. Comparing the obtained approximate solution with the exact solution leaves no doubt believing that the proposed technique is very efficient and converges toward the exact solution very rapidly.

关键词： Nagumo equation nonlinear diffusion and convection homotopy analysis transform method Caputo-Fabrizio-Caputo derivative Atangana-Baleanu-Caputo time-fractional derivatives

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Effect of Zn/Mg ratio on cathodic protection of carbon steel using Al-Zn-Mg sacrificial anodes

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Transactions of Nonferrous Metals Society of China 2020年第8期30卷 2067-2078页

作者： Mosaad SADAWY saad saad Randa ABDEL-KARIM Department of Mining and Petroleum Engineering Faculty of EngineeringNasr CityAl-Azhar UniversityCairo 11371Egypt Department of Metallurgy Faculty of EngineeringCairo UniversityGiza 12613Egypt

Al-Zn-Mg alloys with different Zn/Mg mass ratios were evaluated as sacrificial anodes for cathodic protection of carbon steel in 3.5 wt.%Na Cl *** anodes were fabricated from pure Al,Zn and Mg metals using casting *** microscopy,SEM-EDS,XRD and electrochemical techniques were *** results indicated that with decreasing Zn/Mg mass ratio,the grain size ofα(Al)and the particle size of the precipitates decreased while the volume fraction of the precipitates *** anode with Zn/Mg mass ratio>4.0 exhibited the lowest corrosion rate,while the anode with Zn/Mg mass ratio<0.62 gave the highest corrosion rate and provided the highest cathodic protection efficiency for carbon steel(AISI 1018).Furthermore,the results showed that the anode with Zn/Mg mass ratio<0.62 exhibited a porous corrosion product compared to the other anodes.

关键词： cathodic protection Al-Zn-Mg sacrificial anode current capacity passive film precipitate grain size

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End-to-End 2D Convolutional Neural Network Architecture for Lung Nodule Identification and Abnormal Detection in Cloud

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Computers, Materials & Continua 2023年第4期75卷 461-475页

作者： Safdar Ali saad Asad Zeeshan Asghar Atif Ali Dohyeun Kim Department of Software Engineering the University of LahoreDefence Road CampusLahore55150Pakistan Department of Computer Engineering Jeju National UniversityAra CampusJeju City63243Korea

The extent of the peril associated with cancer can be perceivedfrom the lack of treatment, ineffective early diagnosis techniques, and mostimportantly its fatality rate. Globally, cancer is the second leading cause ofdeath and among over a hundred types of cancer;lung cancer is the secondmost common type of cancer as well as the leading cause of cancer-relateddeaths. Anyhow, an accurate lung cancer diagnosis in a timely manner canelevate the likelihood of survival by a noticeable margin and medical imagingis a prevalent manner of cancer diagnosis since it is easily accessible to peoplearound the globe. Nonetheless, this is not eminently efficacious consideringhuman inspection of medical images can yield a high false positive rate. Ineffectiveand inefficient diagnosis is a crucial reason for such a high mortalityrate for this malady. However, the conspicuous advancements in deep learningand artificial intelligence have stimulated the development of exceedinglyprecise diagnosis systems. The development and performance of these systemsrely prominently on the data that is used to train these systems. A standardproblem witnessed in publicly available medical image datasets is the severeimbalance of data between different classes. This grave imbalance of data canmake a deep learning model biased towards the dominant class and unableto generalize. This study aims to present an end-to-end convolutional neuralnetwork that can accurately differentiate lung nodules from non-nodules andreduce the false positive rate to a bare minimum. To tackle the problem ofdata imbalance, we oversampled the data by transforming available images inthe minority class. The average false positive rate in the proposed method isa mere 1.5 percent. However, the average false negative rate is 31.76 *** proposed neural network has 68.66 percent sensitivity and 98.42 percentspecificity.

关键词： Convolutional neural networks medical image processing lung nodule identification data imbalance deep learning

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Plasma adrenomedullin level in children with obesity: relationship to left ventricular function

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World Journal of Pediatrics 2018年第1期14卷 84-91页

作者： Kotb Abbass Metwalley Hekma saad Farghaly Tahra Sherief Pediatric Endocrinology Unit Department of PediatricsFaculty of MedicineAssiut UniversityB.OAssiut71111Egypt Department of Clinical Pathology Faculty of MedicineAssiut UniversityAssiutEgypt

Background Obese children are at increased risk for abnormal cardiac structure and function. Little is known about adre-nomedullin (AM), a cytokine produced in various organs and tissues, as a biomarker of cardiac hypertrophy in obese children. This study aimed to assess the plasma AM levels in a cohort of obese children and its relationship to left ventricular (LV) functions. Methods The study included 60 obese children and 60 non-obese children matched for age and gender as control group. Blood pressure, serum lipid profile, fasting glucose, insulin and plasma AM and the homeostatic model assessment of insulin resistance (HOMA-IR) were measured. Cardiac dimensions and LV functions were assessed using conventional echocardiography. Results Compared to control subjects, obese children had higher blood pressure (P = 0.01), insulin (P = 0.001), HOMA-IR (P = 0.001), and AM (P = 0.001). Moreover, obese children had higher LV mass index (LVMI) (P = 0.001), indicating LV hypertrophy;prolonged isovolumic relaxation times (P = 0.01), prolonged mitral deceleration time (DcT) (P = 0.01) and reduced ratio of mitralE-to-mitralA-wave peak velocity (P = 0.01), indicating LV diastolic dysfunction. Laboratory abnor-malities were only present in children with LV hypertrophy. In multivariate analysis in obese children with LV hypertrophy, AM levels were positively correlated with LVMI [odds ratio (OR) 1.14, 95% confidence interval (Cl) 1.08–1.13,P = 0.0001] and mitral DcT (OR 2.25, 95% CI 1.15–2.05,P = 0.01) in the presence of higher blood pressure and HOMA-IR. A cut-offvalue of AM at 52 pg/mL could differentiate obese children with and without left ventricular hypertrophy at a sensitivity of 94.32% and specificity of 92.45%. Conclusions Plasma AM levels may be elevated in obese children particularly those with LV hypertrophy and is correlated with higher blood pressure and insulin resistance. Measurement of plasma AM levels in obese children may help to identify those at high risk o

关键词： Adrenomedullin Left ventricular function Obesity

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A Note on the Generalized and Universal Associated Legendre Equations

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Communications in Theoretical Physics 2018年第7期69卷 19-24页

作者： Keegan L.A.Kirk Kyle R.Bryenton Nasser saad School of Mathematical & Computational Sciences University of Prince Edward Island

A class of second-order differential equations commonly arising in physics applications are considered,and their explicit hypergeometric solutions are provided. Further, the relationship with the Generalized and Universal Associated Legendre Equations are examined and established. The hypergeometric solutions, presented in this work,will promote future investigations of their mathematical properties and applications to problems in theoretical physics.

关键词： universal associated Legendre polynomials generalized associated Legendre equation hypergeo-metric series exact solutions

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