Browsing by Author "Kocak, Onur"

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Automatic Brain Tumor Detection and Volume Estimation in Multimodal MRI Scans via a Symmetry Analysis
(2023) Ficici, Cansel; Erogul, Osman; Telatar, Ziya; Kocak, Onur; 0000-0002-8240-4046
In this study, an automated medical decision support system is presented to assist physicians with accurate and immediate brain tumor detection, segmentation, and volume estimation from MRI which is very important in the success of surgical operations and treatment of brain tumor patients. In the proposed approach, first, tumor regions on MR images are labeled by an expert radiologist. Then, an automated medical decision support system is developed to extract brain tumor boundaries and to calculate their volumes by using multimodal MR images. One advantage of this study is that it provides an automated brain tumor detection and volume estimation algorithm that does not require user interactions by determining threshold values adaptively. Another advantage is that, because of the unsupervised approach, the proposed study realized tumor detection, segmentation, and volume estimation without using very large labeled training data. A brain tumor detection and segmentation algorithm is introduced that is based on the fact that the brain consists of two symmetrical hemispheres. Two main analyses, i.e., histogram and symmetry, were performed to automatically estimate tumor volume. The threshold values used for skull stripping were computed adaptively by examining the histogram distances between T1- and T1C-weighted brain MR images. Then, a symmetry analysis between the left and right brain lobes on FLAIR images was performed for whole tumor detection. The experiments were conducted on two brain MRI datasets, i.e., TCIA and BRATS. The experimental results were compared with the labeled expert results, which is known as the gold standard, to demonstrate the efficacy of the presented method. The performance evaluation results achieved accuracy values of 89.7% and 99.0%, and a Dice similarity coefficient value of 93.0% for whole tumor detection, active core detection, and volume estimation, respectively.
City Hospitals Model in Biomedical Calibration Service
(2015) Kocak, Onur; Budak, Erdem I.; Beytar, Faruk; Ozgode, Busra; Coruh, Baris; Kocoglu, Arif; Erogul, Osman
Clinical engineering comprise of management of medical technology, medical device maintenance, repair, and calibration which they are bought according to capacity of health institution. In this study, entirely using principles have been given about medical device maintenance, repair, and calibration. A model has been designed which is biomedical calibration production service to new vast city hospitals. The hospitals have high bed capacity and because of that there are more different types of medical devices in their inventory. According to the model has been depicted about separating medical devices too. Besides, process planning has been materialized in biomedical calibration. A new work flow model has been suggested result of evaluating both of calibration and preventive maintenance. Moreover in this study mentioned about laboratory accreditation to international traceability need. Furthermore an offset investment model has been examined to medical device calibrators which they will have bought city hospitals. Urgent actions have detected for all consider authority to the investment model success.
A Clinical Engineering Approach for Design and Management of Central Sterilization Units
(2015) Kocak, Onur; Ozgode, Busra; Kocoglu, Arif; Erogul, Osman; 0000-0002-4640-6570; 0000-0003-4803-5504; AAW-3005-2021; AAF-8122-2020
Central Sterilization Unit (CSU) are the units that performs sterilization of medical devices, instruments and consumables which used in hospitals and these units are planned to provide services within a quality management system and traceability. The numbers of sterilization procedures are carried out in medium and large scale hospitals, this situation can lead to reduced efficiency of the sterilization process have become critical. In this study, using a medium scale hospital as base, planning to work in coordination with the clinical engineering unit the structure of a central sterilization unit that coordinated to work with clinical engineering unit is recommended. The following issues are discussed in detail: architecture of the CSU, departments, staff, process of monitoring, validation and quality cycles. In addition, contributions to the technical efficiency of the sterilization process from biomedical engineers and technicians which are appointed by the clinical engineering units were examined.
Comparison of Non - Parametric PSD Detection Methods in the Anaylsis of EEG Signals in Sleep Apnea
(2015) Kocak, Onur; Beytar, Faruk; Firat, Hikmet; Telatar, Ziya; Erogul, Osman
Sleep apnea is characterized by complete cessation of airflowin the mouth and nose for at least 10 seconds and it is a disease that causes significant disruption of sleep patterns. In the absence of treatment, it can lead to serious health problems such as heart attack and stroke. Polysomnography is the gold standard examination methods used in the diagnosis of the disease. In this study, EEG signals obtained from the polysomnography recording are divided into sub-bands and their epochs in pre apnea, intra apnea and post apnea were analyzed. Non-parametric power spectral density (PSD) detection methods (Periodogram, Welch and Multi Taper) applied to the EEG signals were compared.
Controllable Tension Adjustment Design in Kinesio Taping
(2019) Evren, Elif; Zaim, Zeynep Ezgi; Oter, Seckin; Kocak, Onur
In this study, two different devices were designed to enable the kinesio banding to reach the desired tension level for correct treatment and the data obtained from these two different systems were compared and recorded. The first designed measuring device is based on software processing of optical permeability. Depending on the increase and decrease in the force applied to the belt, the pores on the belt expand or contract. Intense light is sent over the band. The light reaching the receiver below the band varies depending on the pore width of the band. The information received simultaneously is divided into levels by the software and notified to the user. Another planned performance design is tension detection via pressure sensor. In this method, the pressure sensor between the kinesio tape and the platform changes value due to the pressure force applied to it as the belt tensiones. In both designs, the desired tension levels for the tape were obtained and verification was performed by expert physiotherapists.
Design and Analysis of an Autoclave Simulation Using MATLAB/Simulink
(2015) Altinsu, Betul; Kocak, Onur; Akpek, Ali; ABI-1247-2020
The aim of this study is to make simulations with Matlab/Simulink to be used in the production phase of the autoclave in the sterilization unit. Sterilization unit is very important in terms of hospital employees and patients for protecting from infections and accidents. The study examined autoclave equipments that are fabricated based on the EN standards, then mathematical calculations were performed by (1)the references obtained from these calculations. These references transferred as the necessary characteristics for MATLAB/Simulink modelling. By analyzing these characteristics, the impact of the variations throughout the production or development pahese can be predicted by investigating the changes in these characteristics. After this study, it is anticipated to convet this model into prototypes and obtain more tangible result. In this study, embedded sytems are used and the data is transferred to an electronic media. Later, the system will be tested on one of the autoclaves that is currently available on the market. It is planned that by exchanging the mainboard of the autoclave with another mainbored which the new software has installed and inspected on the device, afterwards.
Electronic Pillbox Design for Demantia Patients
(2015) Cebeci, Semih Ahmet; Ciftcioglu, Caglar; Kocak, Onur; Akpek, Ali; ABI-1247-2020
In this study, dementia and Alzheimer patients that suffer from frequently forgeting the names and timing of their medications are considered and a new arduino based electronic pillbox is designed. This system is also found convenient for nursing homes and houses for aged people where mainly dementia patients live together. At the same time, it is possible that this system may provide great ease for pharmacies.
Evaluation of the Methods Used for the Vital Signs Measurement in Hospitalized Patients
(2018) Numanoglu, Rukiye; Kocak, Onur; Malhan, Simten; Oksuz, Ergun; 0000-0002-5723-5965; K-8238-2012
In general, vital signs measurements which includes measurement of blood pressure, body temperature, pulse and oxygen levels provide very important information about the health status of the hospitalized patients and the effects of treatment. Measurements and documentation of the vital signs carried out by nurses at hospitals. In this study, the methods used in vital signs measurements of hospitalized patients were evaluated by observations and interviews at a foundation university hospital and the advantages and disadvantages of the existing technologies were determined. As a result of interviews with healthcare providers and observations, it was determined that vital signs measurements of hospitalized patients were performed by 2 different methods. The mean time of vital signs measurements were determined as 3 minutes and 4 seconds (SD: 00:31) in medical treatment patients, 2 minutes and 11 seconds (SD: 00:18) in surgical patients, and 2 minutes and 37 seconds (SD: 00:37) in all patients. It was determined that the measurement results were recorded in the patient physical file in an average of 1 minute 2 seconds (SD: 00:52) and it was revealed that 15% of the measurement records were wrong, 26.9% were delayed and 10.6% were not recorded which performed by the nurses. It was also determined that the measurement results were not included in the hospital information system. It is thought that vital findings will provide important data for artificial intelligence studies in the following period with the recording of the results of the measurement to the electronic environment.
A Low Cost Design Non-invasive Glucose Monitoring Experimental Setup
(2018) Evren, Elif; Kocak, Onur
In this non-interventional study, infrared glucose measurement, a non-invasive method of blood glucose measurement that is painless, hygienic and more practical, was investigated and a data supporting the feasibility of this method was obtained using a low-cost assay. Another goal of this study is to demonstrate that the infrared transceiver array can measure optical changes due to different solvents and different glucose concentrations. The data are obtained and compared based on the concentration of glucose in each solution and solution. The closed system we use for this study is completely isolated from the outside environment and the 950nm infrared receiver transmitter installed with arduino is prevented from being influenced by different light sources. In our study, water, isopropyl alcohol and glycerol were used as solvent for glucose determination. Our receiver-transmitter is the most commonly used infrared transceiver in the 950-nm wavelength range. The data received from the receiver was converted to volt value with Arduino software and significant values were created. As a result of the measurements, it was observed that the voltage value changed due to the concentration of the solution. As the glucose concentration in the solution increased, the voltage value decreased.
A Medical Waste Management Model for Public Private Partnership Hospitals
(2015) Kocak, Onur; Kurtuldu, Huseyin; Akpek, Ali; Kocoglu, Arif; Erogul, Osman; JMC-5224-2023
Today, with developing technologies and expanding health care system, medical waste has reached a fairly large volume. Particularly, the extensive use of disposable medical devices and supplies are among the factors that increase the production of medical waste. Monitoring the processes involving the separation, temporary storage, disposal, and transfer of medical waste is critical in terms of the environment and human health. In this study, the implementation of medical waste collection, separation and classification processes were surveyed in new city hospitals constructed with public-private partnership. The standards for temporarily holding wastes were also discussed. Furthermore, the cost analysis required for the handling and disposal of medical waste was provided. By means of studying the medical waste disposal methods, few suggestions regarding the most appropriate methods and models of offset technology investments for the city hospitals were proposed.
New Concept Design of an Insulin Pen for Visually Impaired or Blind Diabetius Mellitus Patients
(2015) Ucar, Tuba; Kocak, Onur; Akpek, Ali; ABI-1247-2020
Today, diabetes mellitus (diabetes) emerges as an increasingly important health problem because of the problems and frequency that it cause all over the world. Especially type 2 diabetes mellitus is increasing rapidly in all of the developed and developing society with the rapid changes in lifestyle. As of the year 2013, the number of the diabetes patients are 382 million. And this number is expected to reach 592 million increased by %55 in 2035. The main reason of this population growth due to the obesity and physical inactivity is increasing beacuse of urbanization and aging. In our country, according to result of the studies of Turkey diabetes apidemiology (TURDEP-I), type 2 diabetes mellitus %7.2, frequency of impaired glucose tolerance (IGT) %6.7 was found. In the studies of TURDEP-II that is published recently has been seen significantly increase of 2 type diabetes mellitus at age of 20 and over. Uncontrolled diabetes leading to hypoglycemia causes development of complications that affect all systems of the body. (cardiovascular system-eyes-kidney-nervous system) The risk of lower extremity amputation in diabetes patients is 25 times higher than without diabetes. Especaially in developed countries, the most common cause is visual loss and blindness. Under the light of these information, the form of insulin pen was designed that can be used more comfortable for visually handicapped people and blinds
Novel Concept On In Situ Syntheses And Investigation Of Photon Energy Effect On Agnp Size With A Custom Build Device For Enhanced Antimicrobial Efficiency
(2022) Bunyatova, Ulviye; Kocum, Ismail Cengiz; Turkmen, Kubra Erkan; Haberal, Orhan Erdem; Kocak, Onur; Koca, Helin Cikmaz; 10.1007/s11051-022-05612-2
The objectives of the present study were to examine the influence of visible light photons on photoreduction of the silver nanoparticles (AgNPs), detect optoelectronic feedback, and observe the antimicrobial activity. For this purpose, an optoelectronic device was designed and successfully tested. The finding shows that identical nanocomplexes with silver salt express various responses to the LEDs with different wavelengths by scattering different portions of light. It is the first time to discuss the effect of visible light photons on nanosized particles in detail based on the quantitative optical/voltage analysis. The photoreduction of the AgNPs is in good agreement with photon energy and the AgNPs occur in nanocomplex in a wavelength versus time-dependent mariner. The blue LED having photon energy 7.04 eV reduces the average size of AgNPs down to the range 4-6 nm in 12 min, while AgNPs obtained under influence of green (6.11 eV) and red (5.04 eV) LEDs have average sizes 6-8 nm and 12-14 nm respectively. The successful synthesis of AgNPs was additionally examined using UV-Vis, SEM, XPS, XRD, FTIR, and TEM techniques. AgNPs proved for antimicrobial activity against Escherichia coli 25922, Enterococcus faecalis 29212, Pseudomonas aeruginosa 27853, and Candida albicans 10231 at four different concentrations. The antibacterial test for all selected bacteria showed that AgNPs which have an average size of 4-6 nm synthesized by blue LED revealed the largest inhibition zone around 16-11 mm, while the antifungal test shows that the maximum inhibition zone was exposed by AgNPs which have an average size of 6-8 nm synthesized by red LED.
Remote Control of Centrifuge and Injection Systems via MATLAB and ARDUINO
(2015) Ciftcioglu, Caglar; Kocak, Onur; Akpek, Ali; ABI-1247-2020
In this study, types of centrifuges, dc motor structures, MATLAB and ARDUINO sytems that are used to control these structures remotely have been described concisely. The aim of this study is to ensure ease-of-use for centrifuge systems and lower the workload for the users. At the end of the study, It has been observed that it is very easy to control the centrifuge systems even the control unit is far away than the centrifuge systems. In future, it will be possible to integrate the remotely controlled centrifuge systems with biochemical or hormone devices. Blood samples can be placed into the centrifuge systems, the centrifuged blood sample can be analyzed by biochemical and hormome devices and results can be provided by the assistance of a robotic hand that is jointed to this integrated centrifuge system,
Remote Monitoring System For Incubator Data
(2018) Tan, Kubilay; Kavsaoglu, Ahmet Resit; Kocak, Onur; Akbay, Cansu; 0000-0002-4380-9075; GYE-1783-2022
In this study, an electronic system. has been developed to collect data from the incubator devices in the neonatal intensive care services to allow the remote monitoring and control of authorized personnel via the internet interface. Temperature and humidity values of the environment obtained from the designed system are calculated and displayed instantly on the user panel. Pulse, body weight, body temperature and blood-oxygen saturation values which are critically important are detected by high-precision sensors placed on the body surface and transferred to the internet interface screen. In this way, it is expected that this system and the staff working in hospitals and obstetrics clinics will he able to solve the workload and medical data losses.
Smartphones and Programmable Shunts: Are These Indispensable Phones Safe and Smart?
(2017) Ozturk, Sait; Cakin, Hakan; Kurtuldu, Huseyin; Kocak, Onur; Erol, Fatih S.; Kaplan, Metin; https://orcid.org/0000-0003-0876-4999; 28342922
OBJECTIVE: This study aimed to determine whether smartphones affect programmable shunts. METHODS: iPhone 5S (Apple Inc., Cupertino, CA, USA) and Samsung Galaxy S5 (Samsung Electronics, Gumi, South Korea) smartphones were chosen for this study. For both phones, magnetic field mapping was performed with 3-dimensional magnetic scanning systems constructed with high-precision motorized stages, and a Hall effect sensor was used to measure the flux density on the smartphone surface. The distance (h) between the distal outlet of the reservoir and the rugby ball of the Strata valve (Medtronic Inc., Minneapolis, MN, USA) was measured using highly sensitive microanalysis optical method. During optical microanalysis, while keeping a 3-cm distance between the valve and the magnetic generator, the h value (mm) was recorded for different magnetic flux densities (MFDs). Then, direct x-ray radiography was performed for radiologic assessment after each process under different magnetic fields. For analysis of the Codman Certas valve (Codman Neuro, Raynham, MA, USA), the magnet orientation and the angle between the magnet with the tantalum ball were measured with the same optical analysis. RESULTS: Maximum MFDs found 62 G for iPhone 5S and 61 G for Samsung Galaxy S5. When the magnetic generator formed a current at 0, 30, 60, and 90 G, the h values of the Strata valve adjusted to 100 mm H2O opening pressure were 320, 280, 190, and 175 mm, respectively. When the magnetic generator was removed from the environment, the h value returned to 320 mm. In direct graphs taken after each optical analysis at different Gauss values, substitution was not observed at the indicator. The angle in the Codman Certas valve was 123.9 degrees, 112.5 degrees, and 103.6 degrees at the magnetic flux densities of 0, 60, and 90 G, respectively. When the magnetic field was removed (0 G), the angle was still 103.6 degrees, suggesting an irreversible effect in the shunt construct. CONCLUSIONS: Smartphones exert reversible effects on Strata programmable valves without producing remarkable radiologic findings and irreversible effects on Codman Certas valves.
Structural EEG Signal Analysis For Sleep Apnea Classification
(Başkent Üniversitesi Mühendislik Fakültesi, 2024-03-27) Kocak, Onur; Ficici, Cansel; Firat, Hikmet; Telatar, Ziya
Objectives: Diagnosing the sleep apnea can be critical in preventing the person having sleep disorder from unhealthy results. The aim of this study is to obtain a sleep apnea scoring approach by comparing parametric and non-parametric power spectral density (PSD) estimation methods from EEG signals recorded from different brain regions (C4-M1 and O2-M1) for transient signal analysis of sleep apnea patients. Methods: Power Spectral Density (PSD) methods (Burg, Yule-Walker, periodogram, Welch and multi-taper) are examined for the detection of apnea transition states including pre-apnea, intra-apnea and post-apnea together with statistical methods. Results: In the experimental studies, EEG recordings available in the database were analyzed with PSD methods. Results showed that there are statistically significant differences between parametric and non-parametric methods applied for PSD analysis of apnea transition states in delta, theta, alpha and beta bands. Moreover, it was also revealed that PSD of EEG signals obtained from C4-M1 and O2-M1 channels were also found statistically different as proved by classification using the K-nearest neighbour (KNN) method. Conclusions: It was concluded that not only applying different PSD methods, but also EEG signals from different brain regions provided different statistical results in terms of apnea transition states as obtained from KNN classification.
Temporal Lobe Epilepsy Focus Detection Based on the Correlation Between Brain MR Images and EEG Recordings with a Decision Tree
(DIAGNOSTICS, 2024-11) Ficici, Canse; Telatar, Ziya; Erogul, Osman; Kocak, Onur
Background/Objectives: In this study, a medical decision support system is presented to assist physicians in epileptic focus detection by correlating MRI and EEG data of temporal lobe epilepsy patients. Methods: By exploiting the asymmetry in the hippocampus in MRI images and using voxel-based morphometry analysis, gray matter reduction in the temporal and limbic lobes is detected, and epileptic focus prediction is realized. In addition, an epileptic focus is also determined by calculating the asymmetry score from EEG channels. Finally, epileptic focus detection was performed by associating MRI and EEG data with a decision tree. Results: The results obtained from the proposed algorithm provide 100% overlap with the physician's finding on the EEG data. Conclusions: MRI and EEG correlation in epileptic focus detection was improved compared with physicians. The proposed algorithm can be used as a medical decision support system for epilepsy diagnosis, treatment, and surgery planning.
Vibrational Viscosimeter Design for Biomedical Purposes
(2018) Akbay, Cansu; Kocak, Onur
In this study, a vibrational viscosimeter design used in biomedical applications, especially dialysis systems were performed. Differently from existing systems, it has larger sample container in size. Considering the effect of temperature on viscosity, to obtain more sensitive measurements, homogeneous distribution of the temperature in container was provided and the temperature was controlled via temperature sensors placed in many sides of container. Following the design of system, it was tested by using water and glycerol which has different viscosity. The results obtained with the measurements showed that the viscosity decreased with temperature.