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Publication Open Access 3D-printed multi-stimuli-responsive mobile micromachines(American Chemical Society (ACS), 2020) Lee, Yun-Woo; Ceylan, Hakan; Yasa, İmmihan Ceren; Department of Mechanical Engineering; Kılıç, Uğur; Sitti, Metin; Faculty Member; Department of Mechanical Engineering; School of Medicine; College of EngineeringMagnetically actuated and controlled mobile micromachines have the potential to be a key enabler for various wireless lab-on-a-chip manipulations and minimally invasive targeted therapies. However, their embodied, or physical, task execution capabilities that rely on magnetic programming and control alone can curtail their projected performance and functional diversity. Integration of stimuli-responsive materials with mobile magnetic micromachines can enhance their design toolbox, enabling independently controlled new functional capabilities to be defined. To this end, here, we show three-dimensional (3D) printed size-controllable hydrogel magnetic microscrews and microrollers that respond to changes in magnetic fields, temperature, pH, and divalent cations. We show two-way size-controllable microscrews that can reversibly swell and shrink with temperature, pH, and divalent cations for multiple cycles. We present the spatial adaptation of these microrollers for penetration through narrow channels and their potential for controlled occlusion of small capillaries (30 μm diameter). We further demonstrate one-way size-controllable microscrews that can swell with temperature up to 65% of their initial length. These hydrogel microscrews, once swollen, however, can only be degraded enzymatically for removal. Our results can inspire future applications of 3D- and 4D-printed multifunctional mobile microrobots for precisely targeted obstructive interventions (e.g., embolization) and lab- and organ-on-a-chip manipulations.
Publication Metadata only A new concept of motion preservation surgery of the cervical spine: PEEK rods for the posterior cervical region(Ios Press, 2020) Erbulut, Deniz Ufuk; N/A; Aydın, Ahmet Levent; Sasani, Mehdi; Öktenoğlu, Bekir Tunç; Özer, Ali Fahir; Doctor; Faculty Member; Faculty Member; Faculty Member; N/A; School of Medicine; School of Medicine; School of Medicine; Koç University Hospital; N/A; 219451; 220898; 1022Background: Laminectomy may cause kyphotic postoperative deformity in the cervical region leading to segmental instability over time. Laminoplasty may be an alternative procedure to laminectomy, as it protects the spine against post-laminectomy kyphosis; however, similar to laminectomy, laminoplasty may cause sagittal plane deformities by destructing or weakening the dorsal tension band. Objective: Using finite element analysis (FE), we attempted to determine whether a posterior motion preservation system (PEEK posterior rod system concept) could overcome the postoperative complications of laminectomy and laminoplasty and eliminate the side effects of rigid posterior stabilization in the cervical region. Methods: We compared PEEK rods in four different diameters with a titanium rod for posterior cervical fixation. The present study may lead to motion preservation systems of the cervical vertebra. RESULTS: When PEEK rod is compared with titanium rod, considerable increase in range of motion is observed. Conclusions: PEEK rod-lateral mass screw instrumentation systems may be useful in motion preservation surgery of the posterior cervical region.Publication Metadata only A review of bioresorbable implantable medical devices: materials, fabrication, and implementation(Wiley, 2020) N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Singh, Rahul; Bathaei, Mohammad Javad; İstif, Emin; Beker, Levent; PhD Student; PhD Student; Researcher; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 354990; 308798Implantable medical devices (IMDs) are designed to sense specific parameters or stimulate organs and have been actively used for treatment and diagnosis of various diseases. IMDs are used for long-term disease screening or treatments and cannot be considered for short-term applications since patients need to go through a surgery for retrieval of the IMD. Advances in bioresorbable materials has led to the development of transient IMDs that can be resorbed by bodily fluids and disappear after a certain period. These devices are designed to be implanted in the adjacent of the targeted tissue for predetermined times with the aim of measurement of pressure, strain, or temperature, while the bioelectronic devices stimulate certain tissues. They enable opportunities for monitoring and treatment of acute diseases. To realize such transient and miniaturized devices, researchers utilize a variety of materials, novel fabrication methods, and device design strategies. This review discusses potential bioresorbable materials for each component in an IMD followed by programmable degradation and safety standards. Then, common fabrication methods for bioresorbable materials are introduced, along with challenges. The final section provides representative examples of bioresorbable IMDs for various applications with an emphasis on materials, device functionality, and fabrication methods.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 Adaptive tracking algorithm for trajectory analysis of cells and layer-by-layer assessment of motility dynamics(Pergamon-Elsevier Science Ltd, 2022) Bayraktar, Halil; N/A; Department of Molecular Biology and Genetics; Qureshi, Mohammad Haroon; PhD Student; Faculty Member; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; Graduate School of Sciences and Engineering; College of Sciences; N/A; 105301Tracking biological objects such as cells or subcellular components imaged with time-lapse microscopy enables us to understand the molecular principles about the dynamics of cell behaviors. However, automatic object detection, segmentation and extracting trajectories remain as a rate-limiting step due to intrinsic challenges of video processing. This paper presents an adaptive tracking algorithm (Adtari) that automatically finds the op-timum search radius and cell linkages to determine trajectories in consecutive frames. A critical assumption in most tracking studies is that displacement remains unchanged throughout the movie and cells in a few frames are usually analyzed to determine its magnitude. Tracking errors and inaccurate association of cells may occur if the user does not correctly evaluate the value or prior knowledge is not present on cell movement. The key novelty of our method is that minimum intercellular distance and maximum displacement of cells between frames are dynamically computed and used to determine the threshold distance. Since the space between cells is highly variable in a given frame, our software recursively alters the magnitude to determine all plausible matches in the trajectory analysis. Our method therefore eliminates a major preprocessing step where a constant distance was used to determine the neighbor cells in tracking methods. Cells having multiple overlaps and splitting events were further evaluated by using the shape attributes including perimeter, area, ellipticity and distance. The features were applied to determine the closest matches by minimizing the difference in their magnitudes. Finally, reporting section of our software were used to generate instant maps by overlaying cell features and trajectories. Adtari was validated by using videos with variable signal-to-noise, contrast ratio and cell density. We compared the adaptive tracking with constant distance and other methods to evaluate performance and its efficiency. Our algorithm yields reduced mismatch ratio, increased ratio of whole cell track, higher frame tracking efficiency and allows layer-by-layer assessment of motility to characterize single-cells. Adaptive tracking provides a reliable, accurate, time efficient and user-friendly open source software that is well suited for analysis of 2D fluorescence microscopy video datasets.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 Analyzing the information distribution in the fMRI measurements by estimating the degree of locality(Institute of Electrical and Electronics Engineers (IEEE), 2013) Onal, Itir; Ozay, Mete; Firat, Orhan; Yarman Vural, Fatos T.; Department of Psychology; Öztekin, İlke; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; N/AIn this study, we propose a new method for analyzing and representing the distribution of discriminative information for data acquired via functional Magnetic Resonance Imaging (fMRI). For this purpose, we form a spatially local mesh with varying size, around each voxel, called the seed voxel. The relationship among each seed voxel and its neighbors is estimated using a linear regression model by minimizing the square error. Then, we estimate the optimal mesh size that represents the connections among each seed voxel and its surroundings by minimizing Akaike's Final Prediction Error (FPE) with respect to the mesh size. The degree of locality is represented by the optimum mesh size. Our results indicate that the local mesh size with the highest discriminative power varies across individual participants. The proposed method was tested on an fMRI study consisting of item recognition (IR) and judgment of recency (JOR) tasks. For each participant, the estimated arc weights of each local mesh with different mesh size are used to classify the type of memory judgment (i.e.IR or JOR). Classification accuracy for each participant was derived using k-Nearest Neighbor (k-NN) method. The results indicate that the proposed local mesh model with optimal mesh size can successfully represent discriminative information for neuroimaging data.Publication Metadata only Application of an asymmetric finite element model of the C2-T1 cervical spine for evaluating the role of soft tissues in stability(Elsevier Sci Ltd, 2014) N/A; N/A; N/A; Department of Mechanical Engineering; N/A; Erbulut, Deniz Ufuk; Zafarparandeh, Iman; Lazoğlu, İsmail; Özer, Ali Fahir; Researcher; PhD Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; School of Medicine; Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; 37661; N/A; 179391; 1022Different finite element models of the cervical spine have been suggested for evaluating the roles of ligaments, facet joints, and disks in the stability of cervical spine under sagittal moments. However, no comprehensive study on the response of the full cervical spine that has used a detailed finite element (FE) model (C2-T1) that considers the asymmetry about the mid-sagittal plane has been reported. The aims of this study were to consider asymmetry in a FE model of the full cervical spine and to investigate the influences of ligaments, facet joints, and disk nucleus on the stability of the asymmetric model during flexion and extension. The model was validated against various published in vitro studies and FE studies for the three main loading planes. Next, the C4-C5 level was modified to simulate different cases to investigate the role of the soft tissues in segmental stability. The FE model predicted that excluding the interspinous ligament (ISL) from the index level would cause excessive instability during flexion and that excluding the posterior longitudinal ligament (PLL) or the ligamentum flavum (LF) would not affect segmental rotation. During extension, motion increased when the facet joints were excluded. The model without disk nucleus was unstable compared to the intact model at lower loads and exhibited a similar rotation response at higher loads.Publication Metadata only Biomechanical comparison of transdiscal fixation and posterior fixation with and without transforaminal lumbar interbody fusion in the treatment of l5-s1 lumbosacral joint(Sage Publications Ltd, 2018) Ozalp, Hakan; Ozkaya, Mustafa; Demir, Teyfik; N/A; Yaman, Onur; Doctor; N/A; Koç University Hospital; 219524Transdiscal screw fixation is generally performed in the treatment of high-grade L5-S1 spondylolisthesis. The main thought of the study is that the biomechanical performances of the transdiscal pedicle screw fixation can be identical to standard posterior pedicle screw fixations with or without transforaminal lumbar interbody fusion cage insertion. Lumbosacral portions and pelvises of 45 healthy lambs' vertebrae were dissected. Animal cadavers were randomly and equally divided into three groups for instrumentation. Three fixation systems, L5-S1 posterior pedicle screw fixation, L5-S1 posterior pedicle screw fixation with transforaminal lumbar interbody fusion cage insertion, and L5-S1 transdiscal pedicle screw fixation, were generated. Axial compression, flexion, and torsion tests were conducted on test samples of each system. In axial compression, L5-S1 transdiscal fixation was less stiff than L5-S1 posterior pedicle screw fixation with transforaminal lumbar interbody fusion cage insertion. There were no significant differences between groups in flexion. Furthermore, L5-S1 posterior fixation was stiffest under torsional loads. When axial compression and flexion loads are taken into consideration, transdiscal fixation can be alternatively used instead of posterior pedicle screw fixation in the treatment of L5-S1 spondylolisthesis because it satisfies enough stability. However, in torsion, posterior fixation is shown as a better option due to its higher stiffness.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.