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finDr:A web server for in silico D-peptide ligand identification

Synthetic and Systems Biotechnology 2021年第4期6卷 402-413页

作者： Helena Engel Felix Guischard Fabian Krause Janina Nandy Paulina Kaas Nico Hofflin Maja Kohn Normann Kilb Karsten Voigt Steffen Wolf Tahira Aslan Fabian Baezner Salom´e Hahne Carolin Ruckes Joshua Weygant alisa Zinina Emir Bora Akmeriç Enoch B.Antwi Dennis Dombrovskij Philipp Franke Klara L.Lesch Niklas Vesper Daniel Weis Nicole Gensch Barbara Di Ventura mehmet ali oztürk Signalling Research Centres BIOSS and CIBSS University of FreiburgSchanzlestr.1879104FreiburgGermany Institute of Biology III Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany Institute of Biology II Faculty of BiologyUniversity of FreiburgSchanzlestr.179104FreiburgGermany AG Roth-Lab for MicroarrayCopying ZBSA-Centre for Biological Systems AnalysisUniversity of FreiburgHabsburgerstrasse 4979104FreiburgGermany Biomolecular Dynamics Institute of PhysicsUniversity of FreiburgHermann-Herder-Strasse 3a79104FreiburgGermany Core Facility Signalling Factory Centre for Biological Signaling Studies(BIOSS)University of FreiburgSchanzlestr.1879104FreiburgGermany Spemann Graduate School of Biology and Medicine(SGBM) University of FreiburgAlbertstraße 19A79104FreiburgGermany Internal Medicine IV Department of MedicineMedical CenterUniversity of FreiburgHugstetter Straße 5579106FreiburgGermany Institute for Biochemistry University of FreiburgAlbertstr.2179104FreiburgGermany

In the rapidly expanding field of peptide therapeutics,the short in vivo half-life of peptides represents a considerable limitation for drug action.D-peptides,consisting entirely of the dextrorotatory enantiomers of naturally occurring levorotatory amino acids(AAs),do not suffer from these shortcomings as they are intrinsically resistant to proteolytic degradation,resulting in a favourable pharmacokinetic *** experimentally identify D-peptide binders to interesting therapeutic targets,so-called mirror-image phage display is typically performed,whereby the target is synthesized in D-form and L-peptide binders are screened as in conventional phage *** technique is extremely powerful,but it requires the synthesis of the target in D-form,which is challenging for large *** we present finDr,a novel web server for the computational identification and optimization of D-peptide ligands to any protein structure(https://***/).finDr performs molecular docking to virtually screen a library of helical 12-mer peptides extracted from the RCSB Protein Data Bank(PDB)for their ability to bind to the *** a separate,heuristic approach to search the chemical space of 12-mer peptides,finDr executes a customizable evolutionary algorithm(EA)for the de novo identification or optimization of D-peptide *** a proof of principle,we demonstrate the validity of our approach to predict optimal binders to the pharmacologically relevant target phenol soluble modulin alpha 3(PSMα3),a toxin of methicillin-resistant Staphylococcus aureus(MRSA).We validate the predictions using in vitro binding assays,supporting the success of this *** to conventional methods,finDr provides a low cost and easy-to-use alternative for the identification of D-peptide ligands against protein targets of choice without size *** believe finDr will facilitate D-peptide discovery with implications in biotechnology and biomedicine.

关键词： D-peptide Web server Evolutionary algorithm Peptide design Molecular docking Mirror-image phage display

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Evolutionary Safe Padé Approximation Scheme for Dynamical Study of Nonlinear Cervical Human Papilloma Virus Infection Model

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Computer Modeling in Engineering & Sciences 2024年第9期140卷 2275-2296页

作者： Javaid ali Armando Ciancio Kashif ali Khan Nauman Raza Haci mehmet Baskonus Muhammad Luqman Zafar-Ullah Khan Department of Mathematics Govt.Graduate College TownshipLahore54770Pakistan Universitàdegli Studi di Messina Dipartimento di Scienze BiomedicheOdontoiatriche e delle Immagini Morfologiche e FunzionaliMessina98122Italy Department of Mathematics University of Engineering and TechnologyLahore54890Pakistan Department of Mathematics University of the PunjabLahore54590Pakistan Mathematics Research Center Near East University TRNCMersin 10Nicosia99138Turkey Department of Mathematics and Science Education Faculty of EducationHarran UniversitySanliurfa63190Turkey Department of Dermatology Rashid Latif Medical CollegeLahore54600Pakistan

This study proposes a structure-preserving evolutionary framework to find a semi-analytical approximate solution for a nonlinear cervical cancer epidemic(CCE)*** underlying CCE model lacks a closed-form exact *** solutions obtained through traditional finite difference schemes do not ensure the preservation of the model’s necessary properties,such as positivity,boundedness,and ***,the development of structure-preserving semi-analytical approaches is always *** research introduces an intelligently supervised computational paradigm to solve the underlying CCE model’s physical properties by formulating an equivalent unconstrained optimization ***-free safe Padérational functions approximate the mathematical shape of state variables,while the model’s physical requirements are treated as problem *** primary model of the governing differential equations is imposed to minimize the error between approximate *** evolutionary algorithm,the Genetic Algorithm with Multi-Parent Crossover(GA-MPC),executes the optimization *** resulting method is the Evolutionary Safe PadéApproximation(ESPA)*** proof of unconditional convergence of the ESPA scheme on the CCE model is supported by numerical *** performance of the ESPA scheme on the CCE model is thoroughly investigated by considering various orders of non-singular Padéapproximants.

关键词： Nonlinear cervical cancer epidemic non-singular Padéapproximants approximate solutions computational biology

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Assessment of the implementation status of best available techniques for cleaner production in the textile industry

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Frontiers of Environmental Science & Engineering 2024年第8期18卷 133-148页

作者： mehmet Eren Yaman Emrah ozturk Ulku Yetis mehmet Kitis Department of Environmental Engineering Suleyman Demirel UniversityIsparta 32260Turkey Department of Environmental Protection Technologies Isparta University of Applied SciencesIsparta 32200Turkey Department of Environmental Engineering Middle East Technical UniversityAnkara 06800Turkey

The draft Integrated Pollution Prevention and Control(IPPC)regulation mandates compliance with best available techniques(BATs)for textile manufacturers.A study in Turkish textile facilities,covering 56 units across four sub-sectors,assessed the status of 488 BATs through on-site visits and *** aim was to gauge the sector’s adherence to *** findings revealed that 37% of surveyed BATs were fully implemented,rising to 88% when considering potential future *** suggests a strong industry inclination toward adopting BATs for cleaner production and *** study highlighted significant BAT-related investments in the textile sector,driven by environmental concerns,regulations,customer demands,resource efficiency,competition,and cost-benefit ***,the study results also indicated that there is still much work to do for the implementation of some *** was found that 60 BATs had lower implementation ratios(IR:0%-43%).Lower IR values for these BATs are mainly due to factors like specificity,high costs,long payback periods,operational difficulties,limited expertise,space constraints,customer requirements,quality concerns,operational issues,and sector-specific *** study recommends similar assessments in other European industrial sectors to evaluate compliance with mandatory BATs outlined in the Industrial Emissions *** insights from this study on the Turkish textile sector can serve as a valuable guide for future evaluations.

关键词： Best available techniques(BAT) Cleaner production Green Deal Integrated Pollution Prevention and Control(IPPC) Textile sector

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A geochemical perspective on the genesis of Cenozoic basic volcanism in northeastern Turkey:an overview of metasomatism and heterogeneity of the sub-continental lithospheric mantle in a post-collisional setting

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Acta Geochimica 2024年第3期43卷 489-506页

作者： mehmet Arslan Irfan Temizel Department of Geological Engineering Karadeniz Technical University61080 TrabzonTurkey

The post-collisional Cenozoic basic volcanic rocks in NE Turkey show temporal variations in whole-rock lithophile element and highly siderophile element(HSE)systematics that are mainly associated with the nature of sub-continental lithospheric mantle(SCLM)sources and parental melt *** far,the traditional whole-rock lithophile geochemical data of these basic volcanic rocks have provided important constraints on the nature of SCLM *** lithophile element and HSE geochemical data of these basic volcanic rocks also reveal the heterogeneity of the SCLM source,which is principally related to variable metasomatism resulting from previous subduction(s)and post-collisional mantle-crust interactions in an extensional *** element geochemical features suggest that the parental magmas have derived from metasomatized spinel-to garnet-bearing SCLM sources for Eocene and Miocene basic volcanic rocks with subduction signatures whereas originated from spinel-to garnet-bearing SCLM sources for Mio-Pliocene and Plio-Quaternary basaltic volcanic rocks without the subduction *** element and HSE geo-chemistry also reveal that Eocene and Miocene basic vol-canic rocks were affected by more pronounced crustal contamination than the basaltic volcanic rocks of Mio-Pliocene and ***,the integrated lithophile element and HSE compositions of these basic volcanic rocks,together with the regional asymmetric lithospheric delamination model,reveal that the compositional variation(especially due to metasomatism)was significant temporally in the heterogeneity of the SCLM sources from which parental magmas formed during the Cenozoic era.

关键词： Basalt Lithospheric mantle Metasomatism Mantle heterogeneity Cenozoic volcanics NE Turkey

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A machine learning-guided design and manufacturing of wearable nanofibrous acoustic energy harvesters

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Nano Research 2024年第10期17卷 9181-9192页

作者： Negar Hosseinzadeh Kouchehbaghi Maryam Yousefzadeh aliakbar Gharehaghaji Safoora Khosravi Danial Khorsandi Reihaneh Haghniaz Ke Cao mehmet R.Dokmeci Mohammad Rostami ali Khademhosseini Yangzhi Zhu Terasaki Institute for Biomedical Innovation Los AngelesCA 91367USA Department of Textile Engineering Amirkabir University of Technology(Tehran Polytechnic)Hafez Avenue*** TehranIran Department of Electrical and Computer Engineering University of British ColumbiaVancouverBC V6T1Z4Canada Chemical Sciences Division Oak Ridge National LaboratoryOak RidgeTN 37831USA Department of Computer Science University of Southern CaliforniaLos AngelesCA 90007USA

Nanofibrous acoustic energy harvesters(NAEHs)have emerged as promising wearable platforms for efficient noise-to-electricity conversion in distributed power energy systems and wearable sound amplifiers for assistive listening ***,their reallife efficacy is hampered by low power output,particularly in the low-frequency range(rk along with solving an optimization problem to find the optimal input values of the electrospinning(applied voltage,nozzle-collector distance,electrospinning time,and drum rotation speed)to generate maximum output performance(acoustic-to-electricity conversion efficiency).We first prepared a dataset to train the network to predict the output power given the input variables with high *** introducing the neural network,we fix the network and then solve an optimization problem using a genetic algorithm to search for the input values that lead to the maximum energy harvesting *** ML-guided wearable PVDF/PU NAEH platform can deliver a maximal acoustoelectric power density output of 829μW/cm^(3) within the surrounding noise *** addition,our system can function stably in a broad frequency(0.1-2 kHz)with a high energy conversion efficiency of 66%.Sound recognition analysis reveals a robust correlation exceeding 0.85 among lexically akin terms with varying sound intensities,contrasting with a diminished correlation below 0.27 for words with disparate semantic ***,this work provides a previously unexplored route to utilize ML in advancing wearable NAEHs with excellent practicability.

关键词： wearable electronics acoustic energy harvester machine learning piezoelectric nanogenerator electrospun nanofiber

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A robust optimization method for label noisy datasets based on adaptive threshold: Adaptive-k

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Frontiers of Computer Science 2024年第4期18卷 49-60页

作者： Enes DEDEOGLU Himmet Toprak KESGIN mehmet Fatih AMASYali Department of Computer Engineering Yildiz Technical UniversityIstanbul 34220Turkey

The use of all samples in the optimization process does not produce robust results in datasets with label *** the gradients calculated according to the losses of the noisy samples cause the optimization process to go in the wrong *** this paper,we recommend using samples with loss less than a threshold determined during the optimization,instead of using all samples in the *** proposed method,Adaptive-k,aims to exclude label noise samples from the optimization process and make the process *** noisy datasets,we found that using a threshold-based approach,such as Adaptive-k,produces better results than using all samples or a fixed number of low-loss samples in the *** the basis of our theoretical analysis and experimental results,we show that the Adaptive-k method is closest to the performance of the Oracle,in which noisy samples are entirely removed from the ***-k is a simple but effective *** does not require prior knowledge of the noise ratio of the dataset,does not require additional model training,and does not increase training time *** the experiments,we also show that Adaptive-k is compatible with different optimizers such as SGD,SGDM,and *** code for Adaptive-k is available at GitHub.

关键词： robust optimization label noise noisy label deep learning noisy datasets noise ratio estimation robust training

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New solutions for four novel generalized nonlinear fractional fifth-order equations

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Journal of Ocean Engineering and Science 2024年第1期9卷 59-65页

作者： mehmet Senol Lanre Akinyemi Henrietta Nkansah Waleed Adel Nevsehir HacıBekta¸s Veli University Department of MathematicsNevsehirTurkey Department of Mathematics Lafayette CollegeEastonPennsylvaniaUSA Department of Mathematics University of Cape CoastCape CoastGhana Department of Mathematics and Engineering Physics Faculty of EngineeringMansoura UniversityEgypt UniversitéFrançaise dÉgypte Ismailia Desert RoadEl ShoroukCairoEgypt

In this paper,new four fifth-order fractional nonlinear equations are derived and *** frac-tional terms are defined in the conformable sense and these equations are then solved using two effective methods,namely,the sub-equation and the generalized Kudryashov *** methods were tested on the proposed models and succeeded in finding new solutions with different values of parameters.A graphical representation of some results is provided and proves the efficiency and applicability of the proposed methods for providing solutions with known physical *** methods are good candi-dates for solving other similar problems in the future.

关键词： Conformable derivative Generalized Kudryashov method Sub-equation method Riccati equation Solitons

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Introduction to the Special Issue on Recent Developments on Computational Biology-I

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Computer Modeling in Engineering & Sciences 2024年第6期139卷 2261-2264页

作者： Carlo Cattani Haci mehmet Baskonus Armando Ciancio Engineering School(DEIM) University of TusciaViterbo01100Italy Department of Mathematics and Science Education Faculty of EducationHarran UniversitySanliurfa63190Turkey Universitàdegli Studi di Messina Dipartimento di Scienze BiomedicheOdontoiatriche e delle Immagini Morfologiche e FunzionaliMessina98122Italy

In modern time,experts started to use interdisciplinary properties with the development of technology and ***,these disciplines provide more sophisticated properties of real-world *** this sense,some models need to be investigated by using revised and modified traditional *** first discipline is the applied sciences such as physics,engineering,mechanics,electricity,biology,economy and mathematical applications[1-5].In this stage,many methods[5-10]are developed and *** uncover the deep properties of problems is to use the main properties of such interdisciplinary ***,works conducted on such mathematical models including non-local operators,partial,ordinary and integer order have introduced a deeper investigation of problems for *** using technological tools,expertsmay observe more realistic and exact results of models.

关键词： properties. integer operators

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Subsequent pregnancy outcomes and fertility rates in the case series that underwent bilateral hypogastric artery ligation(BHGAL)due to severe postpartum hemorrhage

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Asian pacific Journal of Reproduction 2024年第1期13卷 28-33页

作者： OKUTUCU Gulcan EVSEN mehmet S PEKER Nurullah YAMAN TUNC Senem ICEN mehmet S Department of Obstetrics and Gynecology Division of PerinatologyTurkish Ministry of Health Ankara City HospitalAnkaraTurkey Department of Obstetrics and Gynecology Dicle UniversitySchool of MedicineDiyarbakirTurkey

Objective:To evaluate the effect of bilateral hypogastric artery ligation(BHGAL)on women's pregnancy outcomes and fertility rates in cases with severe postpartum ***:Patients hospitalized in a tertiary care center between 2007 and 2018 were included in the *** records of cases were obtained from the hospital database,*** demographic data,morbidities or complications associated with BHGAL surgery,any additional haemostatic interventional or surgical procedures,preoperative admission and lowest postoperative haematocrit-hemoglobin values,blood products given,type of anaesthesia,intensive care unit(ICU)and length of hospital stay were *** cases without surgical sterilization,future fertility and subsequent pregnancy outcomes were assessed for at least two years after *** was obtained through face-to-face or telephone interviews with patients whose long-term fertility and subsequent pregnancy outcomes were ***:Sixty-eight patients with BHGAL surgery history were included in the study.26 Of 37 cases(70%)that did not undergo surgical sterilization had a desire for pregnancy after the *** of these cases(23%)were diagnosed with secondary *** fertility rate of these cases was 77%,and subsequent pregnancy was detected in 20 women.A total of 25 pregnancies,including first and second pregnancies,developed,and 15 of these pregnancies resulted in term delivery,six preterm births,one stillbirth,and three ***:The postoperative pregnancy rate was found to be higher than the rate of women with infertility problems,and this surgery does not seem to adversely affect pregnancy *** is a tertiary center experience and cohort studies with large patient series are needed.

关键词： Fertility Iliac artery Ligations Postpartum hemorrhage Pregnancy outcomes

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Detecting early changes in choroidal vascularity and thickness using optical coherence tomography in patients with corneal crosslinking for keratoconus

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International Journal of Ophthalmology(English edition) 2024年第7期17卷 1267-1272页

作者： Selim Doganay mehmet Omer Kiristioglu Derya Doganay Elif Kacmaz Department of Ophthalmology Bursa Uludag University School of MedicineBursa 16059Turkey Department of Ophthalmology University of Health Sciences Bursa Yuksek Ihtisas Training and Research HospitalBursa 16310Turkey

AIM:To investigate changes in choroidal thickness and vascularity in keratoconus patients treated with corneal ***:This study evaluated 28 eyes of 22 patients with keratoconus who underwent corneal *** choroidal thicknesses were evaluated on enhanced depth imaging optical coherence tomography at the preoperative and postoperative 3d,1,and *** thickness in the four cardinal quadrants and the fovea were *** choroidal vascularity index was also ***:There was no significant difference in central choroidal thickness between the preoperative and postoperative 3d,1mo(P>0.05).There was a significant increase in the 3mo(P=0.034)and a significant decrease in the horizontal choroidal vascularity index on the postoperative 3d(P=0.014),there was no statistically significant change in vertical axes and other visits in horizontal sections(P>0.05).CONCLUSION:This study sheds light on choroidal changes in postoperative corneal crosslinking for *** it suggests the procedure’s relative safety for submacular choroid,more extensive research is necessary to confirm these findings and their clinical significance.

关键词： keratoconus corneal crosslinking choroidal vascularity index enhanced depth imaging optical coherence tomography

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