PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collections

Permanent URI for this collectionhttps://hdl.handle.net/20.500.13091/5

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Now showing 1 - 16 of 16

Citation - WoS: 2
Citation - Scopus: 2
Adrenal Lesion Classification With Abdomen Caps and the Effect of Roi Size
(Springer, 2023) Solak, Ahmet; Ceylan, Rahime; Bozkurt, Mustafa Alper; Cebeci, Hakan; Koplay, Mustafa
Accurate classification of adrenal lesions on magnetic resonance (MR) images are very important for diagnosis and treatment planning. The detection and classification of lesions in medical imaging heavily rely on several key factors, including the specialist's level of experience, work intensity, and fatigue of the clinician. These factors are critical determinants of the accuracy and effectiveness of the diagnostic process, which in turn has a direct impact on patient health outcomes. With the spread of artificial intelligence, the use of computer-aided diagnosis (CAD) systems in disease diagnosis has also increased. In this study, adrenal lesion classification was performed using deep learning on MR images. The data set used was obtained from the Department of Radiology, Faculty of Medicine, Selcuk University, and all adrenal lesions were identified and reviewed in consensus by two radiologists experienced with abdominal MR. Studies were carried out on two different data sets created by T1- and T2-weighted MR images. The data set consisted of 112 benign and 10 malignant lesions for each mode. Experiments were performed with regions of interest (ROIs) of different sizes to increase the working performance. Thus, the effect of the selected ROI size on the classification performance was assessed. In addition, instead of the convolutional neural network (CNN) models used in deep learning, a unique classification model structure called Abdomen Caps was proposed. When the data sets used in classification studies are manually separated for training, validation, and testing, different results are obtained with different data sets for each stage. To eliminate this imbalance, tenfold cross-validation was used in this study. The best results obtained were 0.982, 0.999, 0.969, 0.983, 0.998, and 0.964 for accuracy, precision, recall, F1-score, area under the curve (AUC) score, and kappa score, respectively.
Citation - WoS: 1
Citation - Scopus: 1
Analysis of Fluid Forces Impacting on the Impeller of a Mixed Flow Blood Pump With Computational Fluid Dynamics
(Sage Publications Ltd, 2024) Diallo, Abdoulaye Billo; Cinar, Hasan; Yapici, Rafet
This study presents four different impeller designs to compare hydrodynamic forces. Numerical simulation studies are performed via computational fluid dynamics to specify and investigate the hydraulic forces impacting the impeller of the mixed-flow blood pump with a volute. The design point of this pump is that the flow rate is 5 L/min, the rotational speed is 8000 rpm, and the manometric head is 100 mmHg. The designed impellers are placed in the same volute and simulation studies are performed with the same mesh size (17.3 million cells) of the pumps. The simulation studies have been conducted in setting 1050 kg/m3 blood density, 35 cP fluid viscosity, and SST-k omega turbulence model. Additionally, this study examines the changes in hydraulic forces and hydraulic efficiency with fluid viscosity. As a result of experimental simulation studies, the highest hydraulic efficiencies of 40.87% and 39.5% are achieved in the case of the shaftless-grooveless and shafted-grooveless impeller, respectively. The maximum axial forces are obtained from the pump with the shaftless-grooveless impeller. Whereas radial forces, maximum values are calculated in the pump with the shaftless-outer groove impeller for all flow rates. Finally, the wall shear stresses, which are important for blood pump designs, are evaluated and the maximum value of 227 Pa is observed in the pump impeller with a shaftless-grooved.
Citation - WoS: 1
Citation - Scopus: 2
Computational Fluid Dynamics Simulating of the Fda Benchmark Blood Pump With Different Coefficient Sets and Scaler Shear Stress Models Used in the Power-Law Hemolysis Model
(Springer Japan Kk, 2025) Önder, Ahmet; İncebay, Ömer; Yapıcı, Rafet
Hemolysis is the most important issue to consider in the design and optimization of blood-contacting devices. Although the use of Computational Fluid Dynamics (CFD) in hemolysis prediction studies provides convenience and has promising potential, it is an extremely challenging process. Hemolysis predictions with CFD depend on the mesh, implementation method, coefficient set, and scalar-shear-stress model. To this end, an attempt was made to find the combination that would provide the most accurate result in hemolysis prediction with the commonly cited power-law based hemolysis model. In the hemolysis predictions conducted using CFD on the Food and Drug Administration (FDA) benchmark blood pump, 3 different scalar-shear-stress models, and 5 different coefficient sets with the power-law based hemolysis model were used. Also, a mesh independence test based on hemolysis and pressure head was performed. The pressure head results of CFD simulations were compared with published pressure head of the FDA benchmark blood pump and a good agreement was observed. In addition, results of CFD-hemolysis predictions which are conducted with scalar-shear-stress model and coefficient set combinations were compared with experimental hemolysis data at three operating conditions such as 6-7 L/min flow rates at 3500 rpm rotational speeds and 6 L/min at 2500 rpm. One of the combinations of the scalar-shear-stress model and the coefficient set was found to be within the error limits of the experimental measurements, while all other combinations overestimated hemolysis.
Citation - WoS: 10
Citation - Scopus: 14
Heuristic Optimization of Impeller Sidewall Gaps-Based on the Bees Algorithm for a Centrifugal Blood Pump by Cfd
(SAGE PUBLICATIONS LTD, 2021) Önder, Ahmet; İncebay, Ömer; Şen, Muhammed Arif; Yapıcı, Rafet; Kalyoncu, Mete
Optimization studies on blood pumps that require complex designs are gradually increasing in number. The essential design criteria of centrifugal blood pump are minimum shear stress with maximal efficiency. The geometry design of impeller sidewall gaps (blade tip clearance, axial gap, radial gap) is highly effective with regard to these two criteria. Therefore, unlike methods such as trial and error, the optimal dimensions of these gaps should be adjusted via a heuristic method, giving more effective results. In this study, the optimal gaps that can ensure these two design criteria with The Bees Algorithm (BA), which is a population-based heuristic method, are investigated. Firstly, a Computational Fluid Dynamics (CFD) analysis of sample pump models, which are selected according to the orthogonal array and pre-designed with different gaps, are performed. The dimensions of the gaps are optimized through this mathematical model. The simulation results for the improved pump model are nearly identical to those predicted by the BA. The improved pump model, as designed with the optimal gap dimensions so obtained, is able to meet the design criteria better than all existing sample pumps. Thanks to the optimal gap dimensions, it has been observed that compared to average values, it has provided a 42% reduction in aWSS and a 20% increase in efficiency. Moreover, original an approach to the design of impeller sidewall gaps was developed. The results show that computational costs have been significantly reduced by using the BA in blood pump geometry design.
Citation - WoS: 3
Citation - Scopus: 3
Hyperspectral Imaging-Based Cutaneous Wound Classification Using Neighbourhood Extraction 3d Convolutional Neural Network
(Walter De Gruyter Gmbh, 2023) Cihan, Mucahit; Ceylan, Murat
Objectives: Hyperspectral imaging is an emerging imaging modality that beginning to gain attention for medical research and has an important potential in clinical applications. Nowadays, spectral imaging modalities such as multispectral and hyperspectral have proven their ability to provide important information that can help to better characterize the wound. Oxygenation changes in the wounded tissue differ from normal tissue. This causes the spectral characteristics to be different. In this study, it is classified cutaneous wounds with neighbourhood extraction 3-dimensional convolutional neural network method.Methods: The methodology of hyperspectral imaging performed to obtain the most useful information about the wounded and normal tissue is explained in detail. When the hyperspectral signatures of wounded and normal tissues are compared on the hyperspectral image, it is revealed that there is a relative difference between them. By taking advantage of these differences, cuboids that also consider neighbouring pixels are generated, and a uniquely designed 3-dimensional convolutional neural network model is trained with the cuboids to extract both spatial and spectral information.Results: The effectiveness of the proposed method was evaluated for different cuboid spatial dimensions and training/testing rates. The best result with 99.69% was achieved when the training/testing rate was 0.9/0.1 and the cuboid spatial dimension was 17. It is observed that the proposed method outperforms the 2-dimensional convolutional neural network method and achieves high accuracy even with much less training data. The obtained results using the neighbourhood extraction 3-dimensional convolutional neural network method show that the proposed method highly classifies the wounded area. In addition, the classification performance and the2computation time of the neighbourhood extraction 3-dimensional convolutional neural network methodology were analyzed and compared with existing 2-dimensional convolutional neural network.Conclusions: As a clinical diagnostic tool, hyperspectral imaging, with neighbourhood extraction 3-dimensional convolutional neural network, has yielded remarkable results for the classification of wounded and normal tissues. Skin color does not play any role in the success of the proposed method. Since only the reflectance values of the spectral signatures are different for various skin colors. For different ethnic groups, The spectral signatures of wounded tissue and the spectral signatures of normal tissue show similar spectral characteristics among themselves.
Citation - WoS: 4
Citation - Scopus: 6
A New Approach Based on Collective Intelligence To Solve Traveling Salesman Problems
(MDPI, 2024) Kıran, Mustafa Servet; Beşkirli, Mehmet
This paper presents a novel approach based on the ant system algorithm for solving discrete optimization problems. The proposed method is based on path construction, path improvement techniques, and the footprint mechanism. Some information about the optimization problem and collective intelligence is used in order to create solutions in the path construction phase. In the path improvement phase, neighborhood operations are applied to the solution, which is the best of the population and is obtained from the path construction phase. The collective intelligence in the path construction phase is based on a footprint mechanism, and more footprints on the arc improve the selection chance of this arc. A selection probability is also balanced by using information about the problem (e.g., the distance between nodes for a traveling salesman problem). The performance of the proposed method has been investigated on 25 traveling salesman problems and compared with state-of-the-art algorithms. The experimental comparisons show that the proposed method produced comparable results for the problems dealt with in this study.
Citation - WoS: 1
Citation - Scopus: 3
A New Breakpoint To Classify 3d Voxels in Mri: A Space Transform Strategy With 3t2fts-V2 and Its Application for Resnet50-Based Categorization of Brain Tumors
(MDPI, 2023) Koyuncu, Hasan; Barstugan, Muecahid
Three-dimensional (3D) image analyses are frequently applied to perform classification tasks. Herein, 3D-based machine learning systems are generally used/generated by examining two designs: a 3D-based deep learning model or a 3D-based task-specific framework. However, except for a new approach named 3t2FTS, a promising feature transform operating from 3D to two-dimensional (2D) space has not been efficiently investigated for classification applications in 3D magnetic resonance imaging (3D MRI). In other words, a state-of-the-art feature transform strategy is not available that achieves high accuracy and provides the adaptation of 2D-based deep learning models for 3D MRI-based classification. With this aim, this paper presents a new version of the 3t2FTS approach (3t2FTS-v2) to apply a transfer learning model for tumor categorization of 3D MRI data. For performance evaluation, the BraTS 2017/2018 dataset is handled that involves high-grade glioma (HGG) and low-grade glioma (LGG) samples in four different sequences/phases. 3t2FTS-v2 is proposed to effectively transform the features from 3D to 2D space by using two textural features: first-order statistics (FOS) and gray level run length matrix (GLRLM). In 3t2FTS-v2, normalization analyses are assessed to be different from 3t2FTS to accurately transform the space information apart from the usage of GLRLM features. The ResNet50 architecture is preferred to fulfill the HGG/LGG classification due to its remarkable performance in tumor grading. As a result, for the classification of 3D data, the proposed model achieves a 99.64% accuracy by guiding the literature about the importance of 3t2FTS-v2 that can be utilized not only for tumor grading but also for whole brain tissue-based disease classification.
Citation - WoS: 14
Citation - Scopus: 15
Optimization of Butterworth and Bessel Filter Parameters With Improved Tree-Seed Algorithm
(Mdpi, 2023) Beşkirli, Mehmet; Kıran, Mustafa Servet
Filters are electrical circuits or networks that filter out unwanted signals. In these circuits, signals are permeable in a certain frequency range. Attenuation occurs in signals outside this frequency range. There are two types of filters: passive and active. Active filters consist of passive and active components, including transistors and operational amplifiers, but also require a power supply. In contrast, passive filters only consist of resistors and capacitors. Therefore, active filters are capable of generating signal gain and possess the benefit of high-input and low-output impedance. In order for active filters to be more functional, the parameters of the resistors and capacitors in the circuit must be at optimum values. Therefore, the active filter is discussed in this study. In this study, the tree seed algorithm (TSA), a plant-based optimization algorithm, is used to optimize the parameters of filters with tenth-order Butterworth and Bessel topology. In order to improve the performance of the TSA for filter parameter optimization, opposition-based learning (OBL) is added to TSA to form an improved TSA (I-TSA). The results obtained are compared with both basic TSA and some algorithms. The experimental results show that the I-TSA method is applicable to this problem by performing a successful prediction process.
Citation - WoS: 6
Citation - Scopus: 8
Pan-Based Activated Carbon Nanofiber/Metal Oxide Composites for Co2 and Ch4 Adsorption: Influence of Metal Oxide
(SCIENTIFIC TECHNICAL RESEARCH COUNCIL TURKEY-TUBITAK, 2021) Kırbıyık Kurukavak, Çisem; Büyükbekar, Burak Zafer; Ersöz, Mustafa
In the present study, we successfully prepared two different electrospun polyacrylonitrile (PAN) based-activated carbon nanofiber (ACNF) composites by incorporation of well-distributed Fe2O3 and Co3O4, nanoparticles (NPs). The influence of metal oxide on the structural, morphological, and textural properties of final composites was thoroughly investigated. The results showed that the morphological and textural properties could be easily tuned by changing the metal oxide NPs. Even though, the ACNE composites were not chemically activated by any activation agent, they presented relatively high surface areas (S-BET) calculated by Brunauer-Emmett-Thller (BET) equation as 212.21 and 185.12 m(2)/g for ACNE/Fe2O3 and ACNF/Co3O4 composites, respectively. Furthermore, the ACNE composites were utilized as candidate adsorbents for CO2 and CH4 adsorption. The ACNF/Fe2O3 and ACNF/Co3O4 composites resulted the highest CO2 adsorption capacities of 1.502 and 2.166 mmol/g at 0 degrees C, respectively, whereas the highest CH4 adsorption capacities were obtained to be 0.516 and 0.661 mmol/g at 0 degrees C by ACNF/Fe2O3 and ACNE/Co3O4 composites, respectively. The isosteric heats calculated lower than 80 kJ/mol showed that the adsorption processes of CO2 and CH4 were mainly dominated by physical adsorption for both ACNE composites. Our findings indicated that ACNF-metal oxide composites are useful materials for designing of CO2 and CH4 adsorption systems.
Citation - WoS: 1
Citation - Scopus: 1
Paramagnetic Characterization of Fossil Mollusc Shells at Eastern Part of the Old Konya Lake: Its Importance for Epr Dating
(Oxford Univ Press, 2023) Ekici, Gamze; Sayın, Ülkü; Işık, Mesut; Kapan, Sevinc; Demir, Ahmet; Aydın Karaaslan, Hülya; Delikan, Arif
Fossil mollusc shells are used for dating geological materials because they are well preserved throughout geological time. In this study, the radicals in the structure of fossil mollusc shells (Dreissena iconica, Valvata piscinalis, Bithynia tentaculate, Unio pictorum) collected from the Eastern Part of Old Konya Lake in Turkiye were investigated by EPR technique. For all fossil shells, microwave and temperature dependence of the signals were examined, and the signals suitable for dating are discussed. Characteristic features of intrinsic and impurity-related radicals were identified and the importance of paleontological evaluation of molluscs to get a reliable equivalent dose in EPR dating studies was emphasised.
Citation - WoS: 25
Citation - Scopus: 22
A Phenyl Glycinol Appended Calix[4]arene Film for Chiral Detection of Ascorbic Acid on Gold Surface
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019) Akpınar, Merve; Temel, Farabi; Tabakcı, Begüm; Özçelik, Egemen; Tabakcı, Mustafa
This paper describes the synthesis of new chiral calix [4]arene derivative having (R)-2-phenylglycinol moiety (compound 6), and its chiral recognition studies for ascorbic acid (AA) enantiomers by using Quartz Crystal Microbalance (QCM). Initial experiments indicated that the outstanding selective chiral recognition (alpha) was observed as 2.61 for L-enantiomer of AA. The sensitivity (S) and the limit of detection (LOD) values for L-AA were calculated as 0.0226 Hz/mu M and 0.63 mu M, respectively. Furthermore, the sorption behavior and mechanism of AA onto compound 6 film were evaluated and the sorption data exhibited a good correlation with the Freundlich isotherm models. The maximum uptake of L-AA by the sensor was found as 5895.76 mg/g. In conclusion, chiral recognition of AA enantiomers as real-time, sensitive, selective and effective was performed by a calixarene derivative coated QCM sensor.
Radon Anomalies in Water Sources in Hatay Region After the 2023 Kahramanmaras, Earthquake
(Elsevier Sci Ltd, 2025) Erdogan, Mehmet; Atav, Ulfet; Manisa, Kaan; Acar, Merve; Satilmis, Halimenur; Bozdag, Ayla
In this study, we have investigated possible radon anomalies caused by the Pazarc & imath;k and Elbistan earthquakes (7.7 and 7.6 Mw) and their aftershocks that occurred on February 6, 2023 in Turkey. Radon activity measurements of groundwater samples taken from 9 water sources between March 17 and June 25, 2023 were carried out in certain periods with the AlphaGUARD radon detector. During this measurement period, the radon activity observed in two water sources changed by approximately 5-times between the measurements. These significant changes in the radon activity may be related to the seismic activity in the region. The radon anomalies observed in these water sources may be of use in predicting possible future earthquakes to occur in the region.
Citation - WoS: 1
Citation - Scopus: 1
Structural Properties and Electron Spin Resonance (esr) Dose Estimations of Fossil Cow Tooth Enamel From Kosk Hoyuk, Turkey
(Springer, 2023) Karataş, Özgül; Kayalı, Refik; Ünal Ercan, Hatice
In this work, two cow teeth collected from the Nigde-Kosk Hoyuk excavation site in Turkey were studied for characterization and dosimetric purposes. Each tooth sample was prepared by applying mechanical and chemical methods to obtain the enamel fractions. To do this, mineralogical and elemental concentration properties of the tooth enamels were investigated by performing X-ray diffraction (XRD) and scanning electron microscopy coupled with energy-dispersive X-ray measurements (SEM-EDX). It was found that the enamel structures contained a highly hydroxyapatite crystalline without any characteristic impurities. The dose response of the tooth enamels was determined by using the electron spin resonance (ESR) method. Absorbed radiation doses were calculated as (26.05 & PLUSMN; 0.15) Gy and (25.48 & PLUSMN; 0.18) Gy by the additive dose method using both natural radiation doses and artificial irradiation doses of the enamel samples. It is concluded that these samples could be used to reconstruct radiation doses. This result can be considered as a precursor for future ESR dosimetry/dating studies of other fossil teeth at this excavation site.
Citation - WoS: 3
Citation - Scopus: 5
Study on Phenolic and Organic Acid Compositions and Antioxidant and Enzyme Inhibition Activities of Agaricomycetes Mushroom Species From Turkey
(Begell House Inc., 2023) Tel-çayan, G.; Deveci, E.; Çayan, F.
Mushrooms stand out as one of nature’s best gifts among the natural product sources with their diversity, therapeutic values and increasing popularity. In this study, antioxidant (ABTS•+ scavenging, β-carotene-bleaching, cupric-reducing antioxidant capacity (CUPRAC), DPPH• scavenging, and metal chelating assays), and enzyme (butyrylcholinesterase (BChE) and acetylcholinesterase (AChE), α-amylase and α-glucosidase) inhibition activities of the extracts obtained from Coprinus comatus (O.F. Müll.) Pers., Cerrena unicolor (Bull.) Murrill, Inocutis rheades (Pers.) Fiasson & Niemelä and Leptoporus mollis (Pers.) Quél. mushroom species were investigated. The presence of phenolic and organic acid compounds associated with the bioactive properties of the mushroom species was determined by HPLC-DAD. Fumaric acid was found to be prominent compound in C. comatus (43.90 µg/g dw) and C. unicolor (659.9 µg/g dw), vanillin in L. mollis (19.48 µg/g dw), and p-coumaric acid in I. rheades (21.32 µg/g dw). L. mollis methanol extract, as well as higher antioxidant activity than the standards in CUPRAC and β-carotene-bleaching assays, was noted as superior antioxidant active in all assays (except metal chelating). C. comatus possessed the highest inhibition activity on α-amylase (IC50: 0.23 mg/mL for methanol extract), AChE (IC50: 125.50 µg/mL for hexane extract), and BChE (IC50: 61.03 µg/mL for methanol extract). Also, C. comatus methanol (IC50: 0.09 mg/mL) and L. mollis hexane (IC50: 0.11 mg/ mL) extracts were better α-glucosidase inhibition active than the acarbose (IC50: 0.37 mg/mL). Our study ascertained that the studied mushroom species are particularly sources of biochemically active compounds with therapeutic potential. © 2023 by Begell House, Inc. www.begellhouse.com.
Citation - WoS: 3
Citation - Scopus: 3
Synthesis of Glucose/Fructose Sensitive Poly(ethylene Glycol) Methyl Ether Methacrylate Particles With Novel Boronate Ester Bridge Crosslinker and Their Dye Release Applications
(Slovensko Kemijsko Drustvo, 2022) Yıldırım, Şeküre; Akyıldız, Hasan; Çetinkaya, Zeynep
In this study, it is aimed to develop glucose/fructose sensitive poly(ethylene glycol) methyl ether methacrylate (PEGMA) particles which can be employed in controlled drug delivery applications. For this purpose, a boric acid based crosslinker was synthesized using 4-vinylphenylboronic acid (VPBA) and its formation was confirmed by H-1-NMR and FT-IR analyses. Sugar-sensitive polymeric particles were then achieved using this crosslinker and PEGMA monomer in single step and surfactant free emulsion polymerization technique. Polymeric particles were characterized by DLS, SEM, and TEM in terms of size and morphology. In order to determine the sensitivity of the particles to sugar molecules, first Rhodamine B dye (as a model drug) loading experiments were performed. Then, the particles were subjected to glucose/fructose rich media and dye release was monitored as a function of time using UV-Vis spectrophotometry. The results of the current study revealed that the PEGMA particles were more sensitive to fructose (similar to 39% release) compared to glucose (similar to 25% release) at pH 7.4 and 310 K.
Citation - WoS: 19
Citation - Scopus: 22
Urease Immobilized Electrospun Pva/Chitosan Nanofibers With Improved Stability and Reusability Characteristics: an Application for Removal of Urea From Artificial Blood Serum
(TAYLOR & FRANCIS INC, 2020) Kutlu, Nur; Doğaç, Yasemin İspirli; Deveci, İlyas; Teke, Mustafa
Electrospun polyvinyl alcohol (PVA)/Chitosan nanofibers were successfully prepared and were used as carriers for the first time in urease immobilization. Also, urease immobilized electrospun PVA/Chitosan nanofibers were applied for the removal of urea from artificial blood serum by recycled reactor. The nanofibers were optimized and synthesized by electrospinning technique according to the operational parameters. The morphology and structure of the nanofibers were characterized by scanning electron microscopy (SEM), attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and thermogravimetric analysis (TGA). Urease was immobilized on the nanofibers by adsorption and crosslinking methods. According to immobilization results, nanofiber enhanced urease stability properties like thermal stability, pH stability, and reusability. Urease immobilized electrospun PVA/Chitosan nanofiber protected its activity by 85% after 10 uses and 45% after 20 uses. Urea removal rates of artificial blood serum were as follows: 100% at 1st cycle, 95% at 2nd, 3rd and 4th cycles; 85% at the 5th cycle; 76% at the 6th cycle, and 65% at the last three cycles.

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