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Metabologenomics and network pharmacology to understand the molecular mechanism of cancer research

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World Journal of Clinical Cases 2024年第3期12卷 474-478页

作者： (yusuf) Tutar Department of Basic Pharmaceutical Sciences Faculty of PharmacyDivision of BiochemistryUniversity of Health SciencesIstanbul 34668Turkey Health Sciences Faculty Recep Tayyip Erdogan UniversityRize 53350Turkey Molecular Oncology Division Health Sciences InstitutesUniversity of Health SciencesIstanbul 34668Turkey Molecular Medicine Division Health Sciences InstitutesUniversity of Health SciencesIstanbul 34668Turkey

In this editorial I comment on the article“Network pharmacological and molecular docking study of the effect of Liu-Wei-Bu-Qi capsule on lung cancer”published in the recent issue of the World Journal of Clinical Cases 2023 November 6;11(31):*** all living forms are able to manufacture particular chemicals-metabolites that enable them to differentiate themselves from one another and to overcome the unique obstacles they encounter in their natural *** methods for chemical warfare,communication,nutrition acquisition,and stress prevention are made possible by these specialized *** is a popular technique for collecting direct mea-surements of metabolic activity from many biological ***,con-fusing metabolite identification is a typical issue,and biochemical interpretation is frequently constrained by imprecise and erroneous genome-based estimates of enzyme *** annotation and gene integration uses a biochemical reaction network to obtain a metabolite-gene association so called *** network uses an approach that emphasizes metabolite-gene consensus via biochemical *** metabolomics and genomics data is ***,computer networking proposes that using meta-bolomics data may improve annotations in sequenced species and provide testable hypotheses for specific biochemical *** The genome and metabolites of biological organisms are not fully characterized with current ***,increasing high-throughput metabolomics and genomics data provide promising generation of paired data sets to understand the molecular mechanism of biochemical processes as well as determining targets for pharmaceutical drug *** network infrastructures to integrate omics analysis can provide molecular mechanism of biochemical ***,clinical data may be integrated to gene expression–metabolite expression by system genetics appr

关键词： Network pharmacology Metabologenomics Genome Pathways Cancer

Decoding 17-Beta-hydroxysteroid Dehydrogenase 13:A Multifaceted Perspective on Its Role in Hepatic Steatosis and Associated Disorders

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Journal of Clinical and Translational Hepatology 2024年第10期12卷 857-864页

作者： Coskun Ozer Demirtas (yusuf) Yilmaz Department of Gastroenterology School of MedicineMarmara UniversityIstanbulTurkiye Institute of Gastroenterol-ogy Marmara UniversityistanbulTurkiye Department of Gastroenterology School of MedicineRecep Tayyip Erdogan UniversityRizeTurkiye The Global NASH Council WashingtonDCUSA

Chronic liver disease(CLD)represents a significant global health burden,with hepatic steatosis-associated disorders—such as metabolic dysfunction-associated steatohepatitis(MASH),alcoholic liver disease,and hepatitis C virus infection—being major *** genome-wide association studies have identified the rs72613567:TA variant in the 17-beta-hydroxysteroid dehydrogenase 13(HSD17B13)gene as a protective factor against the development and progression of these *** this review,we summarized the current evidence surrounding the HSD17B13 rs72613567 variant,aiming to elucidate its impact on CLD risk and outcomes,and to explore the potential mechanisms behind its hepatoprotective *** rs72613567:TA variant induces a splice donor site mutation,resulting in a truncated,nonfunctional HSD17B13 *** studies have demonstrated that this loss-of-function mutation confers protection against the development of cirrhosis and hepatocellular carcinoma(HCC)in patients with MASH,alcoholic liver disease,and hepatitis C virus ***,the rs72613567:TA variant has been associated with reduced liver enzyme levels and improved survival in HCC *** this variant into genetic risk scores has shown promise in predicting the progression of fatty liver disease to cirrhosis and ***,inhibiting HSD17B13 expression through RNA interference and small molecule inhibitors has emerged as a potential therapeutic strategy for ***,the precise molecular mechanisms underlying the hepatoprotective effects of the HSD17B13 rs72613567 variant remain to be fully *** research should focus on clarifying the structure-function relationship of HSD17B13 and its role in liver pathophysiology to facilitate the development of targeted therapies for CLD associated with hepatic steatosis.

关键词： 17-Beta-hydroxysteroid dehydrogenase 13 Chronic liver disease Polymorphism Genetics Risk factor Hepatocellular carcinoma Metabolic dysfunction-associated steatohepatitis

A Comparative Study of Metaheuristic Optimization Algorithms for Solving Real-World Engineering Design Problems

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Computer Modeling in Engineering & Sciences 2024年第4期139卷 1039-1094页

作者： Elif Varol Altay Osman Altay (yusuf) Ovik Department of Software Engineering Manisa Celal Bayar UniversityManisa45400Turkey

Real-world engineering design problems with complex objective functions under some constraints are relatively difficult problems to *** design problems are widely experienced in many engineering fields,such as industry,automotive,construction,machinery,and interdisciplinary ***,there are established optimization techniques that have shown effectiveness in addressing these types of *** research paper gives a comparative study of the implementation of seventeen new metaheuristic methods in order to optimize twelve distinct engineering design *** algorithms used in the study are listed as:transient search optimization(TSO),equilibrium optimizer(EO),grey wolf optimizer(GWO),moth-flame optimization(MFO),whale optimization algorithm(WOA),slimemould algorithm(SMA),harris hawks optimization(HHO),chimp optimization algorithm(COA),coot optimization algorithm(COOT),multi-verse optimization(MVO),arithmetic optimization algorithm(AOA),aquila optimizer(AO),sine cosine algorithm(SCA),smell agent optimization(SAO),and seagull optimization algorithm(SOA),pelican optimization algorithm(POA),and coati optimization algorithm(CA).As far as we know,there is no comparative analysis of recent and popular methods against the concrete conditions of real-world engineering ***,a remarkable research guideline is presented in the study for researchersworking in the fields of engineering and artificial intelligence,especiallywhen applying the optimization methods that have emerged *** research can rely on this work for a literature search on comparisons of metaheuristic optimization methods in real-world problems under similar conditions.

关键词： Metaheuristic optimization algorithms real-world engineering design problems multidisciplinary design optimization problems

On the interaction phenomena to the nonlinear generalized Hietarinta-type equation

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Journal of Ocean Engineering and Science 2024年第1期9卷 89-97页

作者： Usman Younas T.A.Sulaiman Jingli Ren A.(yusuf) State Key Laboratory of Power Grid Environmental Protection/Henan Academy of Big Data Zhengzhou UniversityZhengzhou 450001China Faculty of Science Federal University DutseJigawaNigeria Department of Computer Engineering Biruni University IstanbulTurkey

In this paper,we describe the nonlinear behavior of a generalized fourth-order Hietarinta-type equa-tion for dispersive waves in(2+1)*** various wave formations are retrieved by using Hirota’s bilinear method(HBM)and various test function *** Hirota method is a widely used and robust mathematical tool for finding soliton solutions of nonlinear partial differential equa-tions(NLPDEs)in a variety of disciplines like mathematical physics,nonlinear dynamics,oceanography,engineering sciences,and others requires bilinearization of nonlinear *** different wave structures in the forms of new breather,lump-periodic,rogue waves,and two-wave solutions are *** addi-tion,the physical behavior of the acquired solutions is illustrated in three-dimensional,two-dimensional,density,and contour profiles by the assistance of suitable *** on the obtained results,we can assert that the employed methodology is straightforward,dynamic,highly efficient,and will serve as a valuable tool for discussing complex issues in a diversity of domains specifically ocean and coastal *** have also made an important first step in understanding the structure and physical be-havior of complex structures with our findings *** believe this research is timely and relevant to a wide range of engineering *** results obtained are useful for comprehending the fundamental scenarios of nonlinear sciences.

关键词： Hirota’s bilinear method Lump-periodic solutions Breather waves Rouge waves Multi-waves

New lump interaction complexitons to the(2+1)-dimensional Korteweg-de Vries equation with electrostatic wave potential in plasmas

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Journal of Ocean Engineering and Science 2024年第2期9卷 173-177页

作者： Tukur Abdulkadir Sulaiman Abdullahi (yusuf) Alrazi Abdeljabbar Mustafa Bayram Department of Computer Engineering Biruni UniversityIstanbulTurkey Department of Mathematics Federal University DutseJigawaNigeria Department of Mathematics Near East University TRNCMersin 10Turkey Department of Mathematics Khalifa University for Science and TechnologyAbu DhabiUAE

A soliton is a packet of self-reinforcing waves that maintains its structure when moving at a constant *** are caused by the cancellation of the medium’s nonlinear and dispersive *** plas-mas,the bilinear form of Hirota will be utilized to investigate the(2+1)-dimensional Korteweg-de Vries equation with electrostatic wave *** for complexiton lump interaction have been *** throw further light on the physical qualities of the recorded data,certain 3-dimensional and contour plots are presented to illustrate the interaction elements of these solutions.

关键词： (2+1)-dimensional Korteweg-de Vries equation Multi waves solutions Brether waves solutions Numerical simulations

Global black soil distribution

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Frontiers of Agricultural Science and Engineering 2024年第2期11卷 271-281页

作者： Yuxin TONG Marcos E.ANGELINI (yusuf) YIGINI Isabel LUOTTO Global Soil Partnership Land and Water DivisionFood and Agriculture Organization of the United NationsRome 00153Italy

Black soils, characterized by their thick, dark horizons enriched with organic matter, epitomize highly fertile soils. However, their fertility precipitates intense land use, engendering challenges such as soil erosion, nutrient depletion, pollution, compaction, salinization, and acidification. Notably, these soils are significant contributors to global greenhouse gas emissions, primarily due to substantial losses in soil organic carbon. Despite these challenges, black soils are pivotal for global food production. This paper delineates the implementation of digital soil mapping for the global cartography of black soils and human interference on these soils. Predominantly distributed in Eastern Europe, Central and Eastern Asia, and North and South America, black soils cover an approximate area of 725 Mha, with the Russian Federation,Kazakhstan, and China collectively have over half of this area. Agriculturally,these soils underpin significant proportions of global crop yields, producing 66% of sunflower, 30% of wheat, and 26% of potato outputs. The organic carbon content in the upper 30 cm of these soils is estimated at 56 *** management of black soils is imperative for ensuring food security and addressing climate change on a global scale.

关键词： Black soils distribution map food security soil organic carbon

Dynamic Forecasting of Traffic Event Duration in Istanbul:A Classification Approach with Real-Time Data Integration

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Computers, Materials & Continua 2024年第8期80卷 2259-2281页

作者： Mesut Ulu (yusuf) Sait Türkan Kenan Menguc Ersin Namlı Tarık Kucukdeniz Occupational Health and Safety Department Bandirma Onyedi Eylul UniversityBalikesir10200Türkiye Department of Industrial Engineering Istanbul University-CerrahpasaIstanbul34320Türkiye Department of Industrial Engineering Istanbul Technical UniversityIstanbul34467Türkiye

Today,urban traffic,growing populations,and dense transportation networks are contributing to an increase in traffic *** incidents include traffic accidents,vehicle breakdowns,fires,and traffic disputes,resulting in long waiting times,high carbon emissions,and other undesirable *** is vital to estimate incident response times quickly and accurately after traffic incidents occur for the success of incident-related planning and response *** study presents a model for forecasting the traffic incident duration of traffic events with high *** proposed model goes through a 4-stage process using various features to predict the duration of four different traffic events and presents a feature reduction approach to enable real-time data collection and *** the first stage,the dataset consisting of 24,431 data points and 75 variables is prepared by data collection,merging,missing data processing and data *** the second stage,models such as Decision Trees(DT),K-Nearest Neighbour(KNN),Random Forest(RF)and Support Vector Machines(SVM)are used and hyperparameter optimisation is performed with *** the third stage,feature selection and reduction are performed and real-time data are *** the last stage,model performance with 14 variables is evaluated with metrics such as accuracy,precision,recall,F1-score,MCC,confusion matrix and *** RF model outperforms other models with an accuracy of 98.5%.The study’s prediction results demonstrate that the proposed dynamic prediction model can achieve a high level of success.

关键词： Traffic event duration forecasting machine learning feature reduction shapley additive explanations(SHAP)

Deciphering the implications of MAFLD and MASLD definitions in the NAFLD population:results from a single-center biopsy study

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Chinese Medical Journal 2024年第5期137卷 616-618页

作者： Eda Kaya (yusuf) Yilmaz Department of Internal Medicine Ruhr University BochumUniversity Hospital Knappschaftskrankenhaus BochumBochum 44892Germany Institute of Gastroenterology Marmara Universityİstanbul 34840Turkey Department of Gastroenterology School of MedicineRecep Tayyip Erdoğan UniversityRize 53100Turkey

To the Editor:The nomenclature for steatotic liver disease has been a topic of debate since *** conventional expression,non-alcoholic fatty liver disease(NAFLD),was introduced in 1980 to describe the occurrence of steatosis in the absence of other hepatic ***,in recent years,there has been a growing movement to phase out and retire this *** 2020,Eslam et al^([1])proposed a new definition—metabolic(dysfunction)associated fatty liver disease(MAFLD)—redefining the disease to include hepatic steatosis along with other factors such as diabetes,obesity,overweight,or meeting the criteria for metabolic dysfunction.

关键词： NAFLD liver MAF

An evaluation of ureteral diameter ratio and vesicoureteral reflux index in the treatment of primary vesicoureteral reflux

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Asian Journal of Urology 2024年第3期11卷 437-442页

作者： (yusuf) Atakan Baltrak Nebil Akdogan Mutlu Deger Volkan Izol Ibrahim Atilla Aridogan Nihat Satar Division Pediatric Urology Department of UrologyMedical FacultyCukurova UniversityAdanaTurkey

Objective:Vesicoureteral reflux(VUR)index is a simple,validated tool that reliably predicts significant improvement and spontaneous resolution of primary reflux in *** aim of this study was to evaluate and compare the ureter diameter ratio(UDR)and VUR index(VURx)of patients treated with endoscopic injection(EI)and ureteroneocystostomy(UNC)methods in the pediatric age group due to primary ***:Patients under the age of 18 years old who underwent EI and UNC with the diagnosis of primary VUR between January 2011 and September 2021 were determined as the *** UDR was assessed using voiding cystourethrography,and the VURx score was determined prior to treatment based on hospital records included in the ***:A total of 255 patients,60(23.5%)boys and 195(76.5%)girls,with a mean age of 76.5(range 13.0e204.0)months,were included in the *** was applied to 130(51.0%)patients and UNC was applied to 125(49.0%)patients due to primary *** optimum cut-off for the distal UDR was obtained as 0.17 with sensitivity and specificity of 73.0%and 63.0%,*** positive and negative predictive values were 66.0%and 70.0%,***:When the UDR and VURx score are evaluated together for the surgical treatment of primary VUR in the pediatric age group,it is thought that it may be useful in predicting the clinical course of the disease and evaluating surgical treatment options.

关键词： Distalureter diameter ratio Vesicoureteral reflux Vesicoureteral reflux index management Vesicoureteral reflux index