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Publication Metadata only A sparse representation strategy to eliminate pseudo-HFO events from intracranial EEG for seizure onset zone localization(Institute of Physics (IOP) Publishing, 2022) Besheli, Behrang Fazli; Sha, Zhiyi; Gavvala, Jay R.; Quach, Michael M.; Curry, Daniel J.; Sheth, Sameer A.; Francis, David J.; Henry, Thomas R.; Ince, Nuri F.; N/A; Karamürsel, Sacit; Gürses, Rabia Candan; Faculty Member; Faculty Member; School of Medicine; School of Medicine; 19597; 110149Objective. High-frequency oscillations (HFOs) are considered a biomarker of the epileptogenic zone in intracranial EEG recordings. However, automated HFO detectors confound true oscillations with spurious events caused by the presence of artifacts. Approach. We hypothesized that, unlike pseudo-HFOs with sharp transients or arbitrary shapes, real HFOs have a signal characteristic that can be represented using a small number of oscillatory bases. Based on this hypothesis using a sparse representation framework, this study introduces a new classification approach to distinguish true HFOs from the pseudo-events that mislead seizure onset zone (SOZ) localization. Moreover, we further classified the HFOs into ripples and fast ripples by introducing an adaptive reconstruction scheme using sparse representation. By visualizing the raw waveforms and time-frequency representation of events recorded from 16 patients, three experts labeled 6400 candidate events that passed an initial amplitude-threshold-based HFO detector. We formed a redundant analytical multiscale dictionary built from smooth oscillatory Gabor atoms and represented each event with orthogonal matching pursuit by using a small number of dictionary elements. We used the approximation error and residual signal at each iteration to extract features that can distinguish the HFOs from any type of artifact regardless of their corresponding source. We validated our model on sixteen subjects with thirty minutes of continuous interictal intracranial EEG recording from each. Main results. We showed that the accuracy of SOZ detection after applying our method was significantly improved. In particular, we achieved a 96.65% classification accuracy in labeled events and a 17.57% improvement in SOZ detection on continuous data. Our sparse representation framework can also distinguish between ripples and fast ripples. Significance. We show that by using a sparse representation approach we can remove the pseudo-HFOs from the pool of events and improve the reliability of detected HFOs in large data sets and minimize manual artifact elimination.Publication Metadata only An exploration of plastic deformation dependence of cell viability and adhesion in metallic implant materials(Elsevier, 2016) Gerstein, G.; Maier, H. J.; N/A; N/A; N/A; N/A; Department of Mechanical Engineering; Uzer, Benay; Toker, Sıdıka Mine; Cingöz, Ahmet; Önder, Tuğba Bağcı; Canadinç, Demircan; Researcher; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Mechanical Engineering; N/A; Graduate School of Sciences and Engineering; Graduate School of Health Sciences; School of Medicine; College of Engineering; N/A; 255504; N/A; 184359; 23433The relationship between cell viability and adhesion behavior, and micro-deformation mechanisms was investigated on austenitic 316L stainless steel samples, which were subjected to different amounts of plastic strains (5%, 15%, 25%, 35% and 60%) to promote a variety in the slip and twin activities in the microstructure. Confocal laser scanning microscopy (CLSM) and field emission scanning electron microscopy (FESEM) revealed that cells most favored the samples with the largest plastic deformation, such that they spread more and formed significant filopodial extensions. Specifically, brain tumor cells seeded on the 35% deformed samples exhibited the best adhesion performance, where a significant slip activity was prevalent, accompanied by considerable slip-twin interactions. Furthermore, maximum viability was exhibited by the cells seeded on the 60% deformed samples, which were particularly designed in a specific geometry that could endure greater strain values. Overall, the current findings open a new venue for the production of metallic implants with enhanced biocompatibility, such that the adhesion and viability of the cells surrounding an implant can be optimized by tailoring the surface relief of the material, which is dictated by the micro-deformation mechanism activities facilitated by plastic deformation imposed by machining.Publication Metadata only Analysis of hot region organization in hub proteins(Springer, 2010) N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Çukuroğlu, Engin; Gürsoy, Attila; Keskin, Özlem; PhD Student; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 8745; 26605Protein interaction maps constructed from binary interactions reveal that some proteins are highly connected to others (acting as hub proteins), whereas some others have a few interactions (at the edges of the map). This paper addresses hub proteins from a structural point: interfaces. It investigates how hot spots are organized in hub proteins (hot regions). We annotate interfaces as the ones between two date-hubs (DD), two party hubs (PP), and two non-hubs (NN). We investigate the physico-chemical properties of these three types of interfaces focusing on the accessible surface area distribution, hot region organization, and amino acid composition differences. Results reveal that there are significant differences between DD and PP interfaces. More of the hot spots are organized into the hot regions in DD interfaces compared to PP ones. A high fraction of the interfaces are covered by hot regions in DD interfaces. There are more distinct hot regions in DDs. Since the same (or overlapping) DD interfaces should be used repeatedly, different hot regions can be used to bind to different partners. Further, these hot region characteristics can be used to predict whether a given hub interface is involved in a DD or a PP interface type with 80% accuracy.Publication Metadata only Biomechanical restoration potential of pentagalloyl glucose after arterial extracellular matrix degeneration(Mdpi, 2019) Patnaik, Sourav S.; Pillalamarri, Narasimha Rao; Romero, Gabriela; Escobar, G. Patricia; Sprague, Eugene; Finol, Ender A.; Department of Mechanical Engineering; Pişkin, Şenol; Researcher; Department of Mechanical Engineering; College of Engineering; 148702The objective of this study was to quantify pentagalloyl glucose (PGG) mediated biomechanical restoration of degenerated extracellular matrix (ECM). Planar biaxial tensile testing was performed for native (N), enzyme-treated (collagenase and elastase) (E), and PGG (P) treated porcine abdominal aorta specimens (n = 6 per group). An Ogden material model was fitted to the stress-strain data and finite element computational analyses of simulated native aorta and aneurysmal abdominal aorta were performed. The maximum tensile stress of the N group was higher than that in both E and P groups for both circumferential (43.78 +/- 14.18 kPa vs. 10.03 +/- 2.68 kPa vs. 13.85 +/- 3.02 kPa; p = 0.0226) and longitudinal directions (33.89 +/- 8.98 kPa vs. 9.04 +/- 2.68 kPa vs. 14.69 +/- 5.88 kPa; p = 0.0441). Tensile moduli in the circumferential direction was found to be in descending order as N > P > E (195.6 +/- 58.72 kPa > 81.8 +/- 22.76 kPa > 46.51 +/- 15.04 kPa; p = 0.0314), whereas no significant differences were found in the longitudinal direction (p = 0.1607). PGG binds to the hydrophobic core of arterial tissues and the crosslinking of ECM fibers is one of the possible explanations for the recovery of biomechanical properties observed in this study. PGG is a beneficial polyphenol that can be potentially translated to clinical practice for preventing rupture of the aneurysmal arterial wall.Publication Metadata only Bisphosphonate-functionalized poly(β-amino ester) network polymers(Wiley, 2017) Güven, Melek Naz; Altuncu, Merve Seçkin; Eren, Tuğce Nur; Avcı, Duygu; N/A; Department of Chemistry; Acar, Havva Funda Yağcı; Duman, Fatma Demir; PhD Student; Faculty Member; Department of Chemistry; Graduate School of Science and Engineering; College of Sciences; N/A; 178902Three novel bisphosphonate-functionalized secondary diamines are synthesized and incorporated into poly(beta-amino ester)s (PBAEs) to investigate the effects of bisphosphonates on biodegradation and toxicity of PBAE polymer networks. These three novel amines, BPA1, BPA2, and BPA3, were prepared from the reactions of 1,4-butanediamine, 1,6-hexanediamine, or 4,9-dioxa-1,12-dodecanediamine with tetraethyl vinylidene bisphosphonate, respectively. The PBAE macromers were obtained from the aza-Michael addition reaction of these amines to 1,6-hexane diol diacrylate (HDDA) and poly(ethylene glycol) diacrylate (PEGDA, M-n=575) and photopolymerized to produce biodegradable gels. These gels with different chemistries exhibited similar degradation behavior with mass loss of 53-73% within 24 h, indicating that degradation is mostly governed by the bisphosphonate group. Based on the in vitro cytotoxicity evaluation against NIH 3T3 mouse embryonic fibroblast cells, the degradation products do not exhibit significant toxicity in most cases. It was also shown that PBAE macromers can be used as cross-linkers for the synthesis of 2-hydroxyethyl methacrylate hydrogels, conferring small and customizable degradation rates upon them. The materials reported have potential to be used as nontoxic degradable biomaterials. (C) 2017 Wiley Periodicals, Inc.Publication Metadata only Characterization of protein release from poly(ethylene glycol) hydrogels with crosslink density gradients(Wiley, 2014) N/A; N/A; Department of Chemical and Biological Engineering; Bal, Tuğba; Kepsütlü, Burcu; Kızılel, Seda; PhD Student; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; 353534; N/A; 28376Transplantation of cells within poly(ethylene glycol) (PEG) hydrogel scaffolds as effective immunoisolation barriers is becoming increasingly important strategy for tissue engineering and regenerative medicine. In these applications, crosslink density of these membranes has significant effect on the control of diffusion of many biomolecules such as nutrients, cellular wastes, and hormones. When these networks are designed with crosslink density gradients, alterations in network structure may have an effect on biomolecule diffusivity. The goal of this work was to synthesize PEG hydrogels via surface initiated photopolymerization for use in applications involving physiological protein delivery and cell encapsulation. For this purpose, PEG hydrogels of differing crosslink density gradients were formed via surface initiated photopolymerization, and the diffusion of model proteins with various molecular weights were observed through these PEG hydrogel scaffolds with defined properties. Diffusion coefficients were on the order of 10(-7)-10(-8) cm(2)/s and protein diffusion time scales varied from 5 min to 30 h. The results confirm that synthetic PEG hydrogels with crosslink density gradients are promising for controlled release of bioactive molecules and for covalent incorporation of ligands to support cell viability. (c) 2013 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 102A: 487-495, 2014.Publication Metadata only Computational pre-surgical planning of arterial patch reconstruction: parametric limits and in vitro validation(Springer, 2018) Salihoglu, Ece; Yerebakan, Can; Department of Mechanical Engineering; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; N/A; Lashkarinia, Seyedeh Samaneh; Pişkin, Şenol; Pekkan, Kerem; Bozkaya, Tijen Alkan; Researcher; Researcher; Faculty Member; Doctor; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; Koç University Hospital; N/A; 148702; 161845; 143793Surgical treatment of congenital heart disease (CHD) involves complex vascular reconstructions utilizing artificial and native surgical materials. A successful surgical reconstruction achieves an optimal hemodynamic profile through the graft in spite of the complex post-operative vessel growth pattern and the altered pressure loading. This paper proposes a new in silico patient-specific pre-surgical planning framework for patch reconstruction and investigates its computational feasibility. The proposed protocol is applied to the patch repair of main pulmonary artery (MPA) stenosis in the Tetralogy of Fallot CHD template. The effects of stenosis grade, the three-dimensional (3D) shape of the surgical incision and material properties of the artificial patch are investigated. The release of residual stresses due to the surgical incision and the extra opening of the incision gap for patch implantation are simulated through a quasi-static finite-element vascular model with shell elements. Implantation of different unloaded patch shapes is simulated. The patched PA configuration is pressurized to the physiological post-operative blood pressure levels of 25 and 45 mmHg and the consequent post-operative stress distributions and patched artery shapes are computed. Stress-strain data obtained in-house, through the biaxial tensile tests for the mechanical properties of common surgical patch materials, Dacron, Polytetrafluoroethylene, human pericardium and porcine xenopericardium, are employed to represent the mechanical behavior of the patch material. Finite-element model is experimentally validated through the actual patch surgery reconstructions performed on the 3D printed anatomical stenosis replicas. The post-operative recovery of the initially narrowed lumen area and post-optortuosity are quantified for all modeled cases. A computational fluid dynamics solver is used to evaluate post-operative pressure drop through the patch-reconstructed outflow tract. According to our findings, the shorter incisions made at the throat result in relatively low local peak stress values compared to other patch design alternatives. Longer cut and double patch cases are the most effective in repairing the initial stenosis level. After the patch insertion, the pressure drop in the artery due to blood flow decreases from 9.8 to 1.35 mm Hg in the conventional surgical configuration. These results are in line with the clinical experience where a pressure gradient at or above 50 mm Hg through the MPA can be an indication to intervene. The main strength of the proposed pre-surgical planning framework is its capability to predict the intraoperative and post-operative 3D vascular shape changes due to intramural pressure, cut length and configuration, for both artificial and native patch materials.Publication Open Access Correlation between the mechanical and histological properties of liver tissue(Elsevier, 2014) Department of Mechanical Engineering; Başdoğan, Çağatay; Yarpuzlu, Berkay; Ayyıldız, Mehmet; Tok, Olgu Enis; Aktaş, Ranan Gülhan; Faculty Member; Master Student; Faculty Member; Department of Mechanical Engineering; College of Engineering; School of Medicine; 125489; N/A; N/A; N/A; N/AIn order to gain further insight into the mechanisms of tissue damage during the progression of liver diseases as well as the liver preservation for transplantation, an improved understanding of the relation between the mechanical and histological properties of liver is necessary. We suggest that this relation can only be established truly if the changes in the states of those properties are investigated dynamically as a function of post mortem time. In this regard, we first perform mechanical characterization experiments on three bovine livers to investigate the changes in gross mechanical properties (stiffness, viscosity, and fracture toughness) for the preservation periods of 5, 11, 17, 29, 41 and 53 h after harvesting. Then, the histological examination is performed on the samples taken from the same livers to investigate the changes in apoptotic cell count, collagen accumulation, sinusoidal dilatation, and glycogen deposition as a function of the same preservation periods. Finally, the correlation between the mechanical and histological properties is investigated via the Spearman's Rank-Order Correlation method. The results of our study show that stiffness, viscosity, and fracture toughness of bovine liver increase as the preservation period is increased. These macroscopic changes are very strongly correlated with the increase in collagen accumulation and decrease in deposited glycogen level at the microscopic level. Also, we observe that the largest changes in mechanical and histological properties occur after the first 11-17 h of preservation. (C) 2013 Elsevier Ltd. All rights reserved.Publication Metadata only Effect of varying magnetic fields on targeted gene delivery of nucleic acid-based molecules(Springer, 2015) Oral, Özlem; Cikim, Taha; Zuvin, Merve; Gözüaçık, Devrim; Koşar, Ali; N/A; Department of Chemistry; Ünal, Özlem; Acar, Havva Funda Yağcı; PhD Student; Faculty Member; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; N/A; 178902Several physical methods have been developed to introduce nucleic acid expression vectors into mammalian cells. Magnetic transfection (magnetofection) is one such transfection method, and it involves binding of nucleic acids such as DNA, RNA or siRNA to magnetic nanoparticles followed by subsequent exposure to external magnetic fields. However, the challenge between high efficiency of nucleic acid uptake by cells and toxicity was not totally resolved. Delivery of nucleic acids and their transport to the target cells require carefully designed and controlled systems. In this study, we introduced a novel magnetic system design providing varying magnet turn speeds and magnetic field directions. The system was tested in the magnetofection of human breast (MCF-7), prostate (DU-145, PC-3) and bladder (RT-4) cancer cell lines using green fluorescent protein DNA as a reporter. Polyethylenimine coated superparamagnetic iron oxide nanoparticles (SPIONs) were used as nucleic acid carriers. Adsorption of PEI on SPION improved the cytocompatibility dramatically. Application of external magnetic field increased intracellular uptake of nanoparticles and transfection efficiency without any additional cytotoxicity. We introduce our novel magnetism-based method as a promising tool for enhanced nucleic acid delivery into mammalian cells.Publication Metadata only Er : YAG laser ablation of cerebellar and cerebral tissue(Springer-Verlag London Ltd, 2001) Gulsoy, M; Celikel, T; Canbeyli, R; Cilesiz, I; Department of Physics; Kurt, Adnan; Teaching Faculty; Department of Physics; College of Sciences; 194455With the availability of suitable fibres, the Er:YAG laser has become an indispensable tool for invasive neurosurgical applications as a source of precise ablation. The aim of this study was to investigate the ablative effects of the Er:YAG laser on brain tissue. The response of neuronal. tissue to 2.94 mum Er:YAG laser irradiation was investigated on excised rat brain specimens. Ablation craters were created in cerebral and cerebellar tissues using 0.3, 0.5 and 1.0 J single pulses of 150 mus duration. The corresponding average irradiances were 37.7 J/cm(2), 62.9 J/cm(2) and 125.8 J/cm(2), respectively. Craters were checked qualitatively, crater dimensions were measured and compared, and volume of ablated tissue was estimated. Laser-induced crater dimensions were found to be significantly different at different energy levels applied. Moreover, dimensions of craters on cerebral and cerebellar tissues were significantly different in terms of dimensions. We observed that with the Er:YAG laser ablation craters were created with practically no thermal damage to adjacent tissues. The differences observed in the response of cerebral and cerebellar cortical tissues were dependent on the anatomical and chemical differences.
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