WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 9Citation - Scopus: 11Size, Material Type, and Concentration Estimation for Micro-Particles in Liquid Samples(Elsevier Science SA, 2024-05) Genc, Sinan; Erdem, Talha; Icoz, KutayThe on -site examination and characterization of microparticles are becoming crucial due to the significant rise in plastic pollution in natural resources. Hence, identifying the specific microplastic composition and quantity would enable the implementation of preventive measures. This paper presents a cost-effective setup that utilizes the Random Forest algorithm to detect the size and refractive index of micro particles, hence facilitating the identification of the material type. The system utilizes the scattering patterns of laser light from the dispersion of microparticles, namely within the concentration range of 0.05 fM to 3.00 fM. The refractive indices and particle sizes of melamine (Me8) spheres with a size of 8 mu m, as well as polystyrene (PS8) spheres with a size of 8 mu m and (PS10) 10 mu m, were estimated using the Random Forest algorithm and recorded scattering patterns. The proposed method may deliver findings with an average deviation of 0.23 mu m for particle size and 0.015 for particle refractive index. The statistical analysis indicated that there was no notable disparity between the experimental findings and the predictions derived from the machine learning system. The existing configuration can be readily converted into a point -of -use system that can be employed on -site for the purpose of monitoring and identifying microplastic contamination.Article Citation - WoS: 18Citation - Scopus: 20Respiration Monitoring Using a Paper-Based Wearable Humidity Sensor, a Step Forward to Clinical Tests(Elsevier Science SA, 2023-06) Solak, Irfan; Gencer, Serife; Yildirim, Beyza; Oznur, Emine; Hah, Dooyoung; Icoz, KutayMonitoring respiratory variables can provide valuable information for clinical applications and sport activities. Paper-based wearable respiration monitoring systems have great advantages and potential, they are low-cost, easily disposable, non-invasive and can provide real-time, reliable data. Despite some examples presented for exhaled breath analysis using paper-based sensors exist, none of them have been validated yet in a study involving many patients. In this work, we present a novel paper-based platform for exhaled breath sensors and validate it on 101 subjects including 41 patients to demonstrate its clinical applicability. By using the paperbased wearable capacitive sensors, we collected respiration data from different groups of people, namely, smokers, non-smokers and patients diagnosed with pneumonia, or chronic obstructive pulmonary disease (COPD). The change in humidity during inhale and exhale was converted to capacitance change and thus an electrical signal was obtained. The electrical signal was transmitted to a nearby computer and capacitance versus time data was post-processed. Four ratio parameters were defined on the recorded data; area, rate, maximum amplitude, and average maximum-minimum difference, all of which were compared between deep breathing and normal breathing. The collected data was statistically analyzed, and the humidity changes were compared among different groups. The results show that the developed sensor and the proposed analysis method can be used to detect the humidity changes in breathing, and to differentiate between smokers and non-smokers, and between non-smokers and patients with pulmonary disease.Article Citation - WoS: 15Citation - Scopus: 16Quartz-Crystal Microbalance Measurements of Cd19 Antibody Immobilization on Gold Surface and Capturing B Lymphoblast Cells: Effect of Surface Functionalization(Wiley-VCH Verlag GmbH, 2018-02-05) Icoz, Kutay; Soylu, Mehmet Cagri; Canikara, Zeynep; Unal, EkremWe have investigated different surface functionalization methods to immobilize CD19 antibody on gold surface to capture B lymphoblast cells associated with the acute lymphoblastic leukemia disease. Quartz Crystal Microbalance measurements were performed to analyze the binding kinetics of each layer and determine the optimum method, which results in higher cell capture rates. The random orientation of antibody and oriented antibody through protein G was investigated and protein G presence resulted in 15,2Hz frequency shift for 10(4)cells/mL. The 3-mercaptopropyltrimethoxysilane (MPS) and 11-Mercaptoundecanoic acid (MUA) coatings of gold surface together with 4-(N-Maleimidomethyl)cyclohexane-1-carboxylic acid 3-sulfo-N-hydroxysuccinimide ester sodium salt (Sulfo-SMCC) and N-Ethyl-N'-(3-dimethylaminopropyl) carbodiimide hydrochloride (EDC)/N-hydroxysulfosuccinimide (NHS) linker layers were tested on QCM for protein G and antibody binding. The results indicate that MUA, EDC/NHS, protein G, antibody CD19 is the optimum surface modification among the tested combinations. By using the optimum surface functionalization method, minimum 10(3) cell per mL was measured as 1.9Hz frequency shift.Article Citation - WoS: 18Citation - Scopus: 21Parameter Investigation of Topological Data Analysis for EEG Signals(Elsevier Sci Ltd, 2021-01) Altindis, Fatih; Yilmaz, Bulent; Borisenok, Sergey; Icoz, KutayTopological data analysis (TDA) methods have become appealing in EEG signal processing, because they may help the scientists explore new features of complex and large amount of data by simplifying the process from a geometrical perspective. Time delay embedding is a common approach to embed EEG signals into the state space. Parameters of this embedding method are variable and the structure of the state space can be entirely different depending on their selection. Additionally, extracted persistent homologies of the state spaces depend on filtration level and the number of points used. In this study, we showed how to adapt false nearest neighbor (FNN) test to find out the suitable/optimal time embedding parameters (i.e., time delay and embedding dimension) for EEG signals, and compared their effects on different types of artefacts and motor intention waves that are commonly used in brain-computer interfaces. We extracted and compared persistent homologies of state spaces that were reconstructed with four different sets of parameters. Later, the effect of filtration level on extracted persistent homologies was compared, and statistical significance levels were computed between leftand right-hand movement imaginations. Finally, computational cost of the discussed methods was found, and the adaptability of this method to a real-time application was evaluated. We demonstrated that the discussed parameters of the TDA approach were highly crucial to extract true topological features of the EEG signals, and the adapted testing approaches depicted the applicability of this approach on real-time analysis of EEG signals.Article Citation - WoS: 50Citation - Scopus: 63Optical Detection of Microplastics in Water(Springer Heidelberg, 2021-01-19) Iri, Ahmet H.; Shahrah, Malek H. A.; Ali, Ali M.; Qadri, Sayed A.; Erdem, Talha; Ozdur, Ibrahim T.; Icoz, KutayUnfortunately, the plastic pollution increases at an exponential rate and drastically endangers the marine ecosystem. According to World Health Organization (WHO), microplastics in drinking water have become a concern and may be a risk to human health. One of the major efforts to fight against this problem is developing easy-to-use, low-cost, portable microplastic detection systems. To address this issue, here, we present our prototype device based on an optical system that can help detect the microplastics in water. This system that costs less than $370 is essentially a low-cost Raman spectrometer. It includes a collimated laser (5 mW), a sample holder, a notch filter, a diffraction grating, and a CCD sensor all integrated in a 3D printed case. Our experiments show that our system is capable of detecting microplastics in water having a concentration less than 0.015% w/v. We believe that the designed portable device can find a widespread use all over the world to monitor the microplastic content in an easier and cost-effective manner.Article Citation - WoS: 16Citation - Scopus: 19On-Demand Weighing of Single Dry Biological Particles Over a 5-Order Dynamic Range(Royal Soc Chemistry, 2014) Chan, Bin-Da; Icoz, Kutay; Huang, Wanfeng; Chang, Chun-Li; Savran, Cagri A.We report a simple and highly versatile system to select and weigh individual dry biological particles. The system is composed of a microtweezer to pick and place individual particles and a cantilever-based resonator to weigh them. The system can weigh entities that vary from a red blood cell (similar to 10(-11) g) to the eye-brain complex of an insect (similar to 10(-6) g), covering a 5-order-of-magnitude mass range. Due to its versatility and ease of use, this weighing method is highly compatible with established laboratory practices. The system can provide complementary mass information for a wide variety of individual particles imaged using scanning electron microscopy and determine comparative weights of individual biological entities that are attached to microparticles as well as weigh fractions of individual biological entities that have been subjected to focused ion beam milling.Article Citation - WoS: 16Citation - Scopus: 18Microfluidic Chip Based Direct Triple Antibody Immunoassay for Monitoring Patient Comparative Response to Leukemia Treatment(Springer, 2020-07-13) Icoz, Kutay; Akar, Unal; Unal, EkremWe report a time and cost-efficient microfluidic chip for screening the leukemia cells having three specific antigens. In this method, the target blast cells are double sorted with immunomagnetic beads and captured by the 3rd antibody immobilized on the gold surface in a microfluidic chip. The captured blast cells in the chip were imaged using a bright-field optical microscope and images were analyzed to quantify the cells. First sorting was performed with nano size immunomagnetic beads and followed by 2nd sorting where micron size immunomagnetic beads were used. The low-cost microfluidic platform is made of PMMA and glass including micro size gold pads. The developed microfluidic platform was optimized with cultured B type lymphoblast cells and tested with the samples of leukemia patients. The 8 bone marrow samples of 4 leukemia patients on the initial diagnosis and on the 15th day after the start of the chemotherapy treatment were tested both with the developed microfluidic platform and the flow cytometry. A 99% statistical agreement between the two methods shows that the microfluidic chip is able to monitor the decrease in the number of blast cells due to the chemotherapy. The experiments with the patient samples demonstrate that the developed system can perform relative measurements and have a potential to monitor the patient response to the applied therapy and to enable personalized dose adjustment.Article Citation - WoS: 7Citation - Scopus: 9Immunomagnetic Separation of B Type Acute Lymphoblastic Leukemia Cells from Bone Marrow With Flow Cytometry Validation and Microfluidic Chip Measurements(Taylor & Francis inc, 2020-10-22) Icoz, Kutay; Eken, Ahmet; Cinar, Suzan; Murat, Aysegul; Ozcan, Servet; Unal, Ekrem; Deniz, GunnurIn order to detect the blast cells from bone marrow of patients, one strategy is to first isolate the cells using immunomagnetic beads. The aim of this study was to report the experimental results of the immunomagnetic separation efficiency of the blast cells from bone marrow of pediatric leukemia patients. To test the efficiency of immunomagnetic separation, flow cytometry measurements at critical steps were performed. We here reported 94.5% capture efficiency for CD10 nano beads. Patients samples were also analyzed with a microfluidic chip to test the feasibility for further developments.Article Citation - WoS: 14Citation - Scopus: 15Image-Analysis Based Readout Method for Biochip: Automated Quantification of Immunomagnetic Beads, Micropads and Patient Leukemia Cell(Pergamon-Elsevier Science Ltd, 2020-06) Uslu, Fatma; Icoz, Kutay; Tasdemir, Kasim; Dogan, Refika S.; Yilmaz, BulentFor diagnosing and monitoring the progress of cancer, detection and quantification of tumor cells is utmost important. Beside standard bench top instruments, several biochip-based methods have been developed for this purpose. Our biochip design incorporates micron size immunomagnetic beads together with micropad arrays, thus requires automated detection and quantification of not only cells but also the micropads and the immunomagnetic beads. The main purpose of the biochip is to capture target cells having different antigens simultaneously. In this proposed study, a digital image processing-based method to quantify the leukemia cells, immunomagnetic beads and micropads was developed as a readout method for the biochip. Color, size-based object detection and object segmentation methods were implemented to detect structures in the images acquired from the biochip by a bright field optical microscope. It has been shown that manual counting and flow cytometry results are in good agreement with the developed automated counting. Average precision is 85 % and average error rate is 13 % for all images of patient samples, average precision is 99 % and average error rate is 1% for cell culture images. With the optimized micropad size, proposed method can reach up to 95 % precision rate for patient samples with an execution time of 90 s per image.Article Citation - WoS: 3Citation - Scopus: 6High Spatial Resolution IoT Based Air PM Measurement System(Springer, 2021-04-12) Icoz, Ebru; Malik, Fasih M.; Icoz, KutayAir pollution is one of the global problems of the current era. According to World Health Organization more than 80% of the people living in metropolitan areas breathe air which exceeds the guideline limits. Particulate matter, the mixture of liquid and solid particles having diameters less than 10 mu m, is one of the important pollutants in the air. The main source of the Particulate matter is mostly burning reactions associated with industry, vehicles and homes. Several studies have shown the lethal impact of particulate matter to public health and environment. The rise of particulate matter amount in air has been linked to several health problems such as not only respiratory diseases but also mortality in infants and heart attacks. Currently, bulky stations which are high-cost and have limited spatial resolution are used to monitor the air quality. In this study we developed an alternative particulate matter measurement system which is portable and low-cost (less than 200 USD) and also integrated with cloud computing. The system allows real time distant monitoring of PM particles with high spatial resolution (meter range). The developed sensor system is able to provide air quality data in correlation with the existing stations (R-2 = 0.87). The statistical comparison between the developed system and the reference methods revealed that two systems produced statistically equal results in detecting the variations of the particulate matter.