Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Review Citation - WoS: 30Citation - Scopus: 33Molecular Separation by Using Active and Passive Microfluidic Chip Designs: a Comprehensive Review(Wiley, 2023) Ebrahimi, Aliakbar; Didarian, Reza; Shih, Chih-Hsin; Nasseri, Behzad; Ethan Li, Yi-Chen; Shih, Steven; İçöz, Kutay; Tarım, Ergün Alperay; Akpek, Ali; Çeçen, Berivan; Bal Öztürk, Ayça; Güleç, Kadri; Tarım, Burcu Sırma; Tekin, Hüseyin CumhurSeparation 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. © 2023 The Authors. Advanced Materials Interfaces published by Wiley-VCH GmbH.Review Citation - WoS: 23Citation - Scopus: 24Microfluidic-Based Technologies for Diagnosis, Prevention, and Treatment of Covid-19: Recent Advances and Future Directions(Springer, 2023) Tarım, Ergün Alperay; Anıl İnevi, Müge; Özkan, İlayda; Keçili, Seren; Bilgi, Eyüp; Başlar, Muhammet Semih; Özçivici, Engin; Öksel Karakuş, Ceyda; Tekin, Hüseyin CumhurThe COVID-19 pandemic has posed significant challenges to existing healthcare systems around the world. The urgent need for the development of diagnostic and therapeutic strategies for COVID-19 has boomed the demand for new technologies that can improve current healthcare approaches, moving towards more advanced, digitalized, personalized, and patient-oriented systems. Microfluidic-based technologies involve the miniaturization of large-scale devices and laboratory-based procedures, enabling complex chemical and biological operations that are conventionally performed at the macro-scale to be carried out on the microscale or less. The advantages microfluidic systems offer such as rapid, low-cost, accurate, and on-site solutions make these tools extremely useful and effective in the fight against COVID-19. In particular, microfluidic-assisted systems are of great interest in different COVID-19-related domains, varying from direct and indirect detection of COVID-19 infections to drug and vaccine discovery and their targeted delivery. Here, we review recent advances in the use of microfluidic platforms to diagnose, treat or prevent COVID-19. We start by summarizing recent microfluidic-based diagnostic solutions applicable to COVID-19. We then highlight the key roles microfluidics play in developing COVID-19 vaccines and testing how vaccine candidates perform, with a focus on RNA-delivery technologies and nano-carriers. Next, microfluidic-based efforts devoted to assessing the efficacy of potential COVID-19 drugs, either repurposed or new, and their targeted delivery to infected sites are summarized. We conclude by providing future perspectives and research directions that are critical to effectively prevent or respond to future pandemics.Article Citation - WoS: 15Citation - Scopus: 16Electromechanical Rt-Lamp Device for Portable Sars-Cov Detection(Elsevier, 2023) Tarım, Ergün Alperay; Öksüz, Cemre; Karakuzu, Betül; Appak, Özgür; Sayıner, Ayça Arzu; Tekin, Hüseyin CumhurRapid point-of-care tests for infectious diseases are essential, especially in pandemic conditions. We have developed a point-of-care electromechanical device to detect SARS-CoV-2 viral RNA using the reverse-transcription loop-mediated isothermal amplification (RT-LAMP) principle. The developed device can detect SARS-CoV-2 viral RNA down to 103 copies/mL and from a low amount of sample volumes (2 μL) in less than an hour of standalone operation without the need for professional labor and equipment. Integrated Peltier elements in the device keep the sample at a constant temperature, and an integrated camera allows automated monitoring of LAMP reaction in a stirring sample by using colorimetric analysis of unfocused sample images in the hue/saturation/value color space. This palm-fitting, portable and low-cost device does not require a fully focused sample image for analysis, and the operation could be stopped automatically through image analysis when the positive test results are obtained. Hence, viral infections can be detected with the portable device produced without the need for long, expensive, and labor-intensive tests and equipment, which can make the viral tests disseminated at the point-of-care.Article Citation - WoS: 10Citation - Scopus: 14An Electromechanical Lab-On Platform for Colorimetric Detection of Serum Creatinine(American Chemical Society, 2022) Karakuzu, Betül; Tarım, Ergün Alperay; Öksüz, Cemre; Tekin, Hüseyin CumhurChronic kidney disease (CKD) is a high-cost disease that affects approximately one in ten people globally, progresses rapidly, results in kidney failure or dialysis, and triggers other diseases. Although clinically used serum creatinine tests are used to evaluate kidney functions, these tests are not suitable for frequent and regular control at-home settings that obstruct the regular monitoring of kidney functions, improving CKD management with early intervention. This study introduced a new electromechanical lab-on-a-chip platform for point-of-care detection of serum creatinine levels using colorimetric enzyme-linked immunosorbent assay (ELISA). The platform was composed of a chip containing microreservoirs, a stirring bar coated with creatinine-specific antibodies, and a phone to detect color generated via ELISA protocols to evaluate creatinine levels. An electromechanical system was used to move the stirring bar to different microreservoirs and stir it inside them to capture and detect serum creatinine in the sample. The presented platform allowed automated analysis of creatinine in ~50 min down to ~1 and ~2 mg/dL in phosphate-buffered saline (PBS) and fetal bovine serum (FBS), respectively. Phone camera measurements in hue, saturation, value (HSV) space showed sensitive analysis compared to a benchtop spectrophotometer that could allow low-cost analysis at point-of-care.Article Citation - WoS: 37Citation - Scopus: 48Microfluidic-Based Virus Detection Methods for Respiratory Diseases(Springernature, 2021) Tarım, Ergün Alperay; Karakuzu, Betül; Öksüz, Cemre; Sarıgil, Öykü; Kızılkaya, Melike; Al-Ruweidi, Mahmoud Khatib A. A.; Yalçın, Hüseyin Çağatay; Özçivici, Engin; Tekin, Hüseyin CumhurWith the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.Conference Object Citation - WoS: 12Citation - Scopus: 17Wearable Respiratory Rate Sensor Technology for Diagnosis of Sleep Apnea(IEEE, 2020) Cinel, Göktürk; Tarım, Ergün Alperay; Tekin, Hüseyin CumhurSleep apnea is a disease that occurs during sleep, which affects the daily life of patients due to the obstruction of the upper respiratory tract and decreases oxygen level in blood and it may even lead to patient death in the later stage. Monitoring the patients regularly has absolute importance to prevent patient disorders caused by sleep apnea. Wearable sensor technologies and patient tracking systems provide diagnosis, treatment, and monitoring of patients, and procure better health services in medical fields. In addition to decreasing the workload of health institutions, remote patient monitoring systems can serve continuous monitoring and determine variable symptoms of the patients. In this paper, we propose a patient monitoring system, which will be used for diagnosis and monitoring of sleep apnea by tracking the respiratory rate of patients with wearable sensor technology. The respiratory rate is detected using either an accelerometer sensor to be placed on the patients' abdomen or a temperature sensor to be placed on their noses. The proposed system offers an increase in the versatility of patient monitoring systems and offers an alternative new technology in sleep apnea diagnosis.Article The Ordering of Smokers’ Toothpaste Choice Criteria With Fuzzy Model(Atatürk Üniversitesi, 2019) Tarım, Ergün Alperay; Kuruoğlu Kandemir, Emel; Mevsim, VildanAim: There are some measures that smokers can cease or prevent damage caused by smoking. They may also choose some product features that may be more helpful to them like toothpaste selection etc. The preferences of smokers vary because of the variety of toothpaste in the market and a high number of products. The aim of this study is to determine the importance of toothpaste selection criteria in order to determine the decision and toothpaste selection. Material and method: Fuzzy DEMATEL model is used effectively in decision making problems. This model, which can rank the decision criteria in order of importance even for a single individual, is a more effective and important model in ordering the decision criteria of a large number of individuals. In this study, fuzzy DEMATEL model was used to determine the importance of toothpaste selection criteria. In this study, 7 toothpaste selection criteria were determined by data obtained by taking user and expert opinions. After the determination of criteria, the information form was applied to the model to show the criterion importance preferences of smokers. Results: According to the preferences of smokers, the selection criteria of toothpaste were placed in the order with the fuzzy DEMATEL model. The most important criteria is toothpaste package appearance, while the least of the 7 criteria is determined as the criteria that Sensation of Person. Conclusion: As a result, the toothpaste properties that the smokers would prefer, ie the toothpaste selection criteria are listed in importance. In other words, it is given the ranking of preference criteria for smokers when choosing toothpaste.Conference Object Electromechanical Lab-On Platform for Creatinine Analysis Using Automated Elisa Protocols(Chemical and Biological Microsystems Society, 2020) Karakuzu, Betül; Tarım, Ergün Alperay; Öksüz, Cemre; Tekin, Hüseyin CumhurWe present an electromechanical lab-on-a-chip (LOC) platform for the automated serum creatinine detection applying enzyme-linked immunosorbent assay (ELISA) principle. In the platform, antibody covered bar selectively captures the creatinine in the sample and the electromechanical system allows automatic movement between the designed reservoirs containing assay solutions. At the end of the protocol, the absorbance value of the appeared color is measured to determine creatinine concentration in the sample. Since this system allows measuring automatically creatinine levels with minimum time and cost, it can be utilized for point-of-care monitoring of chronic kidney diseases (CKD) for the future. © 2020 CBMS-0001Conference Object The Ordering of Smokers' Criteria in Choosing Toothpaste With Fuzzy Dematel Model(European Publishing, 2018) Tarım, Ergün Alperay; Mevsim, Vildan; Kandemir, EmelSmokers give more harm to tooth and mouth flora than non-smokers. These conditions can affect the decision of smokers when buying toothpaste. Unlike non-smokers, expectations of toothpaste can vary. Regarding these, the aim of this study is to show which criteria are important to smokers in choosing toothpaste for dental health or related problems. These criteria are sorted according to their importance with the model to be applied.Article Citation - WoS: 5Citation - Scopus: 10Performance Evaluation of Webrtc-Based Online Consultation Platform(Türkiye Klinikleri Journal of Medical Sciences, 2019) Tarım, Ergün Alperay; Tekin, Hüseyin CumhurInformation technologies give patients the opportunity to communicate with medical professionals remotely. Telemedicine uses these technologies to provide advanced healthcare and medical services. We present a medical online consultation application based on Web Real-Time Communications (WebRTC) technology enabling chat, audio, and video calls. Communication architecture and protocols of the application are explained in detail. Additionally, the user interface of the application is shown via performed calls. The application is tested and evaluated on different network connections (3G, 4G, local, and DSL) and different browsers and mobile operating systems (Android, Chrome, Firefox, Internet Explorer, iOS, Opera, Safari). During calls, communication quality parameters such as round-trip time (RTT) and packet loss, obtained via the WebRTC application programming interface, are analyzed. 3G, 4G, and local connections show low packet losses (<1%). Packet losses are high (>1%) in Android, Chrome, iOS, Opera, and Safari for DSL connection, but RTT values are low (<100 ms) in all different conditions excluding iOS. In the presented application, RTT and packet loss remain lower than 100 ms and 1%, respectively, in various scenarios, indicating good communication quality. RTT and packet loss are related to total time and hang time parameters, which describe the necessary time to establish and to end a call. It is shown that communication quality of the application can simply be measured by analyzing the total time parameter. This enables predictable information for communication quality for WebRTC-based applications without continuously monitoring RTT and packet loss for the first time.