WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 7Citation - Scopus: 8Using Students' Performance to Improve Ontologies for Intelligent E-Learning System(Edam, 2015) Icoz, Kutay; Sanalan, Vehbi A.; Cakar, Mehmet Akif; Ozdemir, Esra Benli; Kaya, SukruOntologies have often been recommended for E-learning systems, but few efforts have successfully incorporated student data to represent knowledge conceptualizations. Defining key concepts and their relations between each other establishes the backbone of our E-learning system. The system guides an individual student through his/her course by evaluating their progress and suggesting instructional material to review based upon their answers. Three main tasks are performed within this framework: building ontologies for the course, measuring a student's understanding level for the concepts, and making personal suggestions to create an individualized learning environment. This paper presents: the integration of ontologies, assisted with student data, together with an intelligent Recommendation Module for the development of an E-learning system; the comparison and correction adaption of ontology from students' mind maps; and the assessment of students' actual weaknesses in comparison to what Recommendation Module suggests. The sample of 127 students, five classrooms, was conveniently selected among seventh grade students of a demographically average school in a major city in Turkey. The students' achievement was assessed and the scores for different questions were investigated for associations with concepts made in the students' minds. The results provided significant correlations among scores, and a fit model for the concepts represented by questions. The student suggested model slightly differed from the ontology map from the experts. Based on the data-supported model, the Recommendation Module more accurately determined the students' learning deficiencies and suggested concepts to be reviewed.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: 3Citation - Scopus: 6Simple Staining of Cells on a Chip(MDPI, 2022-11-13) Kosker, Fatma Betul; Aydin, Omer; Icoz, KutaySimple staining of cells is a widely used method in basic medical diagnostics, education, and research laboratories. The stains are low-cost, but the extensive consumption results in excessive toxic waste generation. Thus, to decrease the amount of toxic waste resulting from the cell staining procedure is a need. In this study, we developed a magnetically driven and compartmentalized passive microfluidic chip to perform simple staining of human eukaryotic cells, K562 cells, and lymphocyte cells derived from patients. We demonstrated simple staining on cells with trypan blue, methylene blue, crystal violet, and safranin for high, medium, and low cell densities. The stained cells were imaged using a bright field optical microscope and a cell phone to count cells on the focal plane. The staining improved the color signal of the cell by 25-135-pixel intensity changes for the microscopic images. The validity of the protocol was determined using Jurkat and MDA-MB-231 cell lines as negative controls. In order to demonstrate the practicality of the system, lymphocyte cells derived from human blood samples were stained with trypan blue. The color intensity changes in the first and last compartments were analyzed to evaluate the performance of the chip. The developed method is ultra-low cost, significantly reduces the waste generated, and can be integrated with mobile imaging devices in terms of portability. By combining microfabrication technology with cell staining, this study reported a novel contribution to the field of microfluidic biosensors. In the future, we expect to demonstrate the detection of pathogens using this method.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: 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: 12Citation - Scopus: 13Numerical Analysis and Experimental Verification of Optical Scattering From Microplastics(Royal Soc, 2023-08) Genc, Sinan; Icoz, Kutay; Erdem, TalhaAccurate and fast characterization of the micron-sized plastic particles in aqueous media requires an in-depth understanding of light interaction with these particles. Due to the complexity of Mie scattering theory, the features of the scattered light have rarely been related to the physical properties of these tiny objects. To address this problem, we reveal the relation of the wavelength-dependent optical scattering patterns with the size and refractive index of the particles by numerically studying the angular scattering features. We subsequently present a low-cost setup to measure the optical scattering of the particles. Theoretical investigation shows that the angular distribution of the scattered light by microplastics carries distinct signatures of the particle size and the refractive index. The results can be used to develop a portable, low-cost setup to detect microplastics in water.Article Citation - WoS: 36Citation - Scopus: 43Molecular Separation by Using Active and Passive Microfluidic Chip Designs: A Comprehensive Review(Wiley, 2023-10-27) Ebrahimi, Aliakbar; Icoz, Kutay; Didarian, Reza; Shih, Chih-Hsin; Tarim, E. Alperay; Nasseri, Behzad; Avci, HuseyinSeparation and identification of molecules and biomolecules such as nucleic acids, proteins, and polysaccharides from complex fluids are known to be important due to unmet needs in various applications. Generally, many different separation techniques, including chromatography, electrophoresis, and magnetophoresis, have been developed to identify the target molecules precisely. However, these techniques are expensive and time consuming. "Lab-on-a-chip" systems with low cost per device, quick analysis capabilities, and minimal sample consumption seem to be ideal candidates for separating particles, cells, blood samples, and molecules. From this perspective, different microfluidic-based techniques have been extensively developed in the past two decades to separate samples with different origins. In this review, "lab-on-a-chip" methods by passive, active, and hybrid approaches for the separation of biomolecules developed in the past decade are comprehensively discussed. Due to the wide variety in the field, it will be impossible to cover every facet of the subject. Therefore, this review paper covers passive and active methods generally used for biomolecule separation. Then, an investigation of the combined sophisticated methods is highlighted. The spotlight also will be shined on the elegance of separation successes in recent years, and the remainder of the article explores how these permit the development of novel techniques. This review is about the microfludic-based methods that have been used in the past two decades for the separation of different biomolecules like protein, DNA, and RNA. In this regard, passive, active, and hybrid microfludic methods that are used for biomolecules separation are disscused and reviewed in this paper.imageArticle Citation - WoS: 28Citation - Scopus: 34Micro- and Nanodevices Integrated With Biomolecular Probes(Pergamon-Elsevier Science Ltd, 2015-12) Alapan, Yunus; Icoz, Kutay; Gurkan, Umut A.Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities. (C) 2015 Elsevier Inc. All rights reserved.