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Department: search.filters.department.Department of Molecular Biology and GeneticsSubject: search.filters.subject.Biomedical engineering

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Now showing 1 - 4 of 4
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    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; 105301
    Tracking 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.
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    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; 143793
    Surgical 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.
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    Increased energy loss due to twist and offset buckling of the total cavopulmonary connection
    (ASME, 2017) Arnaz, Ahmet; N/A; Department of Molecular Biology and Genetics; N/A; N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Oğuz, Gökçe Nur; Pişkin, Şenol; Ermek, Erhan; Donmazov, Samir; Altekin, Naz; Pekkan, Kerem; PhD Student; Researcher; Other; PhD Student; Undergraduate Student; Faculty Member; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 148702; N/A; N/A; N/A; 161845
    The hemodynamic energy loss through the surgically implanted conduits determines the postoperative cardiac output and exercise capacity following the palliative repair of single-ventricle congenital heart defects. In this study, the hemodynamics of severely deformed surgical pathways due to torsional deformation and anastomosis offset are investigated. We designed a mock-up total cavopulmonary connection (TCPC) circuit to replicate the mechanically failed inferior vena cava (IVC) anastomosis morphologies under physiological venous pressure (9, 12, 15 mmHg), in vitro, employing the commonly used conduit materials: Polytetrafluoroethylene (PTFE), Dacron, and porcine pericardium. The sensitivity of hemodynamic performance to torsional deformation for three different twist angles (0 deg, 30 deg, and 60 deg) and three different caval offsets (0 diameter (D), 0.5D, and 1D) are digitized in three dimensions and employed in computational fluid dynamic (CFD) simulations to determine the corresponding hydrodynamic efficiency levels. A total of 81 deformed conduit configurations are analyzed; the pressure drop values increased from 80 to 1070% with respect to the ideal uniform diameter IVC conduit flow. The investigated surgical materials resulted in significant variations in terms of flow separation and energy loss. For example, the porcine pericardium resulted in a pressure drop that was eight times greater than the Dacron conduit. Likewise, PTFE conduit resulted in a pressure drop that was three times greater than the Dacron conduit under the same venous pressure loading. If anastomosis twist and/or caval offset cannot be avoided intraoperatively due to the anatomy of the patient, alternative conduit materials with high structural stiffness and less influence on hemodynamics can be considered.
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    Noninvasive in vivo determination of residual strains and stresses
    (ASME, 2015) N/A; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Donmazov, Samir; Pişkin, Şenol; Pekkan, Kerem; PhD Student; Researcher; Faculty Member; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 148702; 161845
    Vascular growth and remodeling during embryonic development are associated with blood flow and pressure induced stress distribution, in which residual strains and stresses play a central role. Residual strains are typically measured by performing in vitro tests on the excised vascular tissue. In this paper, we investigated the possibility of estimating residual strains and stresses using physiological pressure-radius data obtained through in vivo noninvasive measurement techniques, such as optical coherence tomography or ultrasound modalities. This analytical approach first tested with in vitro results using experimental data sets for three different arteries such as rabbit carotid artery, rabbit thoracic artery, and human carotid artery based on Fung's pseudostrain energy function and Delfino's exponential strain energy function (SEF). We also examined residual strains and stresses in the human swine iliac artery using the in vivo experimental ultrasound data sets corresponding to the systolic-to-diastolic region only. This allowed computation of the in vivo residual stress information for loading and unloading states separately. Residual strain parameters as well as the material parameters were successfully computed with high accuracy, where the relative errors are introduced in the range of 0-7.5%. Corresponding residual stress distributions demonstrated global errors all in acceptable ranges. A slight discrepancy was observed in the computed reduced axial force. Results of computations performed based on in vivo experimental data obtained from loading and unloading states of the artery exhibited alterations in material properties and residual strain parameters as well. Emerging noninvasive measurement techniques combined with the present analytical approach can be used to estimate residual strains and stresses in vascular tissues as a precursor for growth estimates. This approach is also validated with a finite element model of a general two-layered artery, where the material remodeling states and residual strain generation are investigated.