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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6

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Department: search.filters.department.Department of Electrical and Electronics EngineeringSubject: search.filters.subject.Biochemistry and molecular biology

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Now showing 1 - 5 of 5
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    PublicationOpen Access
    Coagulation measurement from whole blood using vibrating optical fiber in a disposable cartridge
    (Society of Photo-optical Instrumentation Engineers (SPIE), 2017) Çivitci, Fehmi; Barış, İbrahim; Yaralıoğlu, Göksenin; Department of Electrical and Electronics Engineering; Yaras, Yusuf Samet; Gündüz, Ali Bars; Sağlam, Gökhan; Ölçer, Selim; Ürey, Hakan; Other; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; N/A; N/A; N/A; N/A; 8579
    In clinics, blood coagulation time measurements are performed using mechanical measurements with blood plasma. Such measurements are challenging to do in a lab-on-a-chip (LoC) system using a small volume of whole blood. Existing LoC systems use indirect measurement principles employing optical or electrochemical methods. We developed an LoC system using mechanical measurements with a small volume of whole blood without requiring sample preparation. The measurement is performed in a microfluidic channel where two fibers are placed inline with a small gap in between. The first fiber operates near its mechanical resonance using remote magnetic actuation and immersed in the sample. The second fiber is a pick-up fiber acting as an optical sensor. The microfluidic channel is engineered innovatively such that the blood does not block the gap between the vibrating fiber and the pick-up fiber, resulting in high signal-to-noise ratio optical output. The control plasma test results matched well with the plasma manufacturer's datasheet. Activated-partial-thromboplastin-time tests were successfully performed also with human whole blood samples, and the method is proven to be effective. Simplicity of the cartridge design and cost of readily available materials enable a low-cost point-of-care device for blood coagulation measurements.
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    PublicationOpen Access
    An information theoretical analysis of human insulin-glucose system toward the internet of bio-nano things
    (Institute of Electrical and Electronics Engineers (IEEE), 2017) Department of Electrical and Electronics Engineering; Abbasi, Naveed Ahmed; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering
    Molecular communication is an important tool to understand biological communications with many promising applications in Internet of Bio-Nano Things (IoBNT). The insulin-glucose system is of key significance among the major intra-body nanonetworks, since it fulfills metabolic requirements of the body. The study of biological networks from information and communication theoretical (ICT) perspective is necessary for their introduction in the IoBNT framework. Therefore, the objective of this paper is to provide and analyze for the first time in the literature, a simple molecular communication model of the human insulin-glucose system from ICT perspective. The data rate, channel capacity, and the group propagation delay are analyzed for a two-cell network between a pancreatic beta cell and a muscle cell that are connected through a capillary. The results point out a correlation between an increase in insulin resistance and a decrease in the data rate and channel capacity, an increase in the insulin transmission rate, and an increase in the propagation delay. We also propose applications for the introduction of the system in the IoBNT framework. Multi-cell insulin glucose system models may be based on this simple model to help in the investigation, diagnosis, and treatment of insulin resistance by means of novel IoBNT applications.
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    PublicationOpen Access
    Bidirectional optical neuromodulation using capacitive charge-transfer
    (The Optical Society (OSA) Publishing, 2020) Department of Electrical and Electronics Engineering; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Melikov, Rustamzhon; Srivastava, Shashi Bhushan; Karatüm, Onuralp; Nizamoğlu, Sedat; Doğru-Yüksel, Itır Bakış; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; PhD Student; Researcher; PhD Student; Faculty Member; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; N/A; N/A; 130295; N/A; N/A; 40319
    Artificial control of neural activity allows for understanding complex neural networks and improving therapy of neurological disorders. Here, we demonstrate that utilization of photovoltaic biointerfaces combined with light waveform shaping can generate safe capacitive currents for bidirectional modulation of neurons. The differential photoresponse of the biointerface due to double layer capacitance facilitates the direction control of capacitive currents depending on the slope of light intensity. Moreover, the strength of capacitive currents is controlled by changing the rise and fall time slope of light intensity. This approach allows for high-level control of the hyperpolarization and depolarization of membrane potential at single-cell level. Our results pave the way toward advanced bioelectronic functionalities for wireless and safe control of neural activity.
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    PublicationOpen Access
    Maximum likelihood detection with Ligand receptors for diffusion-based molecular communications in internet of bio-nano things
    (Institute of Electrical and Electronics Engineers (IEEE), 2018) Kuşçu, Murat; Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering
    Molecular Communication (MC) is a bioinspired communication technique that uses molecules as a method of information transfer among nanoscale devices. MC receiver is an essential component having profound impact on the communication system performance. However, the interaction of the receiver with information bearing molecules has been usually oversimplified in modeling the reception process and developing signal detection techniques. In this paper, we focus on the signal detection problem of MC receivers employing receptor molecules to infer the transmitted messages encoded into the concentration of molecules, i.e., ligands. Exploiting the observable characteristics of ligand-receptor binding reaction, we first introduce a Maximum Likelihood (ML) detection method based on instantaneous receptor occupation ratio, as aligned with the current MC literature. Then, we propose a novel ML detection technique, which exploits the amount of time the receptors stay unbound in an observation time window. A comprehensive analysis is carried out to compare the performance of the detectors in terms of bit error probability. In evaluating the detection performance, emphasis is given to the receptor saturation problem resulting from the accumulation of messenger molecules at the receiver as a consequence of intersymbol interference. The results reveal that detection based on receptor unbound time is quite reliable even in saturation, whereas the reliability of detection based on receptor occupation ratio substantially decreases as the receiver gets saturated. Finally, we also discuss the potential methods of implementing the detectors.
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    PublicationOpen Access
    HotSprint: database of computational hot spots in protein interfaces
    (Oxford University Press (OUP), 2008) Tunçbağ, Nurcan; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Güney, Emre; Keskin, Özlem; Gürsoy, Attila; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 26605; 8745
    We present a new database of computational hot spots in protein interfaces: HotSprint. Hot spots are residues comprising only a small fraction of interfaces yet accounting for the majority of the binding energy. HotSprint contains data for 35 776 protein interfaces among 49 512 protein interfaces extracted from the multi-chain structures in Protein Data Bank (PDB) as of February 2006. The conserved residues in interfaces with certain buried accessible solvent area (ASA) and complex ASA thresholds are flagged as computational hot spots. The predicted hot spots are observed to correlate with the experimental hot spots with an accuracy of 76. Several machine-learning methods (SVM, Decision Trees and Decision Lists) are also applied to predict hot spots, results reveal that our empirical approach performs better than the others. A web interface for the HotSprint database allows users to browse and query the hot spots in protein interfaces; and it provides information for interface residues that are functionally and structurally important as well as the evolutionary history and solvent accessibility of residues in interfaces.