Ph.D. Theses

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The mechanical and biological performance of the alternating sliding knots with different patterns in abdominal wound closure
(Thesis (Ph.D.) - Bogazici University. Institute of Biomedical Engineering, 1998., 1998.) Babetty, Zeina.; Altıntaş, Sabri.
New knot configurations, consisting of alternating strands with different patterns, have been studied from mechanical and biological perspectives in order to determine whether they would be suitable for abdominal surgery, as compared with conventional sliding knots. Mechanical properties of these new knots were compared with those of the classical sliding knots and single threads for silk and nylon sutures under dry conditions. From the mechanical perspective, the new knots showed better knot holding capacity and efficiency. In the in vivo implantation tests performed on the rat abdominal wall, the alternating sliding knots with different patterns were found to be more efficient and secure than the classical sliding knots. The knot configuration, postoperative period, suture material and size were important factors in determining the knot holding capacity. From the biological perspective, these new knots provoked tissue reaction similar to the classical sliding knots. Because nylon is less pliable than silk, its use resulted in higher effective knot volumes, causing more pronounced tissue reaction. To test the bacterial adherence to the knots, in vitro and in vivo tests were performed in rats. The degree of the elicited infection correlated well with the capability of bacteria to bind to the suture. It was observed that the knot configurations and the suture sizes did not have much effect on bacterial adherence. Due to the presence of interstices between throws, the knots had greater capacity to retain bacteria than the single threads for both silk and nylon, thus promoting infection. The elasticity and stress-relaxation properties of these knots were compared to those of single threads of silk and nylon. The elasticity of the knots, in general, was higher than that of the threads for both materials. The silk showed decreased elasticity at high extension levels, while nylon showed increased elasticity. In stress relaxation tests, the residual load fraction of the knots was found to be higher than that of the threads at all extension levels. A model was created to study the effect of several factors on the suture pullout force in the abdominal wall. Incisional direction, knot configuration, strain rate and tissue healing strength were important factors in determining the suture pullout force. In conclusion, we do recommend the use of the alternating sliding knots with different patterns in abdominal surgery instead of the currently used sliding knots.
Evaluation of altitude decompression procedures and development of new decompression strategies
(Thesis (Ph.D.) - Bogazici University. Institute of Biomedical Engineering, 1999., 1999.) Egi, Salih Murat.; Tan, Yusuf P.
Diving at altitude requires different tables than at sea level due to the reduction in surface level ambient pressure. In this work, the rationale for the algorithms extrapolating the sea level diving data are reviewed. When applied to different sets of maximum permissible tissue tensions (M value), the conservatism of an algorithm becomes a function of bottom time, depth and altitude. Aviation altitude exposure decompression sickness (DCS) data is also addressed. Animal experiments performed within the scope of this thesis proved that precordial bubbles can form during the ascent from sea level to 2000-m. supporting a far lower threshold for altitude DCS then the model outputs.Following three pioneering altitude diving expeditions to 2200, 3412 and 3980-m, a set of no-decompression stop (no-d) limits for 3500 m was calculated using linear extrapolation of US Navy M values decreased by 4 feet of sea water. This is a new method of altitude adaptation (NLHE, Nonlinear Hypobaric Extrapolation). These limits were tested at 3412-m. by 10 man/dive per profile without any case of DCS. 212 dives were achieved with a total bottom time of 4110 min. The mean DCS risk estimated according to precordial bubble scores (Spencer's Scale) ranges from 0.3% to 2.8% per profile. The last part of the thesis is devoted to the computation of decompression tables for 3500-m altitudes. This work suggests the use of a continuous variable for the compartment time constants, allowing the simulation of infinite number of compartments and reducing the discrepancy between different algorithms to a single M value expression.
A model of active and attentive vision
(Thesis (Ph.D.) - Bogazici University. Institute of Biomedical Engineering, 2002., 2002.) Soyer, Çağatay.; Bozma, H. Işıl.
Biological vision systems explore their environment by allocating their resources to interesting parts of a scene, using both physical and mental attention mechanisms. The result of this active and attentive vision behavior is a sequence of images obtained from different spatial locations at different times. However, temporal processes and integration mechanisms in the brain enable us to interpret this information and perceive a stable image of the environment. While models of such attention and perception mechanisms are invaluable to understand human vision, they are also increasingly used and improved by robotics and artificial intelligence researchers to achieve human-like performance. In a similar attempt, we propose a new and complete model of active vision behavior, based on confirmed biological evidence where available. The model consists of an attention system, temporal image sequence processing algorithms and an integrative visual memory. All components of the model are implemented on our mobile robot APES. Gaze control, sequence based scene recognition and visual integration tasks are assumed during experiments. Results of gaze control experiments clearly demonstrate a human-like selective attention behavior, which can be fully controlled by a number of parameters. In recognition and integration tasks, simple and complex scenes were successfully modeled and classified. Furthermore, our work on attentional image sequences raised a number of interesting questions, some of which have been answered in this thesis.
3-D gamma knife distribution by normoxic gel dosimetry near tissue inhomogeneties
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2005., 2005.) İşbakan, Fatih.; Ülgen, Yekta.
The primary goal in this study was to investigate the three dimensional dose distributions, near the areas of tissue inhomogeneities, in Gamma Knife Radiosurgery with the normoxic gel dosimetry. Following irradiation, when scanned in MR and post processing the MR images, dose imparted to any particular point in the gel phantom can be calculated via the true T2 relaxation time at that point. In the neighborhood of air-tissue inhomogeneity in the head, electronic disequilibrium can lead to errors in dose calculated with the treatment planning algorithms that presume the head as a homogeneous media. Two experiments were designed to investigate the inhomogeneity effects in the Gamma Knife radiosurgery: one experiment simulating the volume near the auditory canal cavity and, the other simulating the volume near the paranosal sinuses cavity. In the auditory canal cavity experiment, an identical balloon of a diameter of 16 cm with two corks placed on each side to represent the air cavities constitutes the inhomogeneous phantom. In the paranosal sinuses cavity experiment, a cylindrical cork is placed to represent the maximal sinuses. In both experiments, the homo geneous phantom is a spherical glass balloon filled with normoxic polymer gel. For dose calibrations, 100 ml vials filled with the same gel are irradiated at predefined doses, and the R2-dose calibration curve is extracted. Dose distributions are the results of a single shot, by using all 201 Cobalt sources, delivered to a known point in the phantoms. In the aspect of dosimetrical quality control, the Gamma Knife planning system predicted dose distribution is compared with the experimental results. In the homogeneous phantoms, the gel dosimetry calculated dose distribution is in good agreement with the GammaPlan predicted dose distribution. However, in the case of inhomogeneous phantoms, the dose distribution is spatially different and significant differences in dose levels are observed. The dose decrease near the air-tissue interface causes the overshooting of the dose by the GammaPlan. This underdosing effect can be essential for the lesions near tissue inhomogeneities. In the auditory canal cavity experiment, the diameter of the 50% isodose curves differ by 35% in the X axis and 1% in the Y axis for Z=105 mm axial plane; and by 39% in the X axis and 5% in the Z axis for Y=105 mm coronal plane in the inhomogeneous phantom as compared to the homogeneous phantom. In the paranosal sinuses cavity experiment, the diameter of the 50% isodose curves differ by 42% in the X axis and 47 %in the Y axis for Z=71mm axial plane; 42% in the X axis and 60%in the Y axis for Z=75 mm axial plane; 52% in the X axis and 70% in the Y axis for Z=79 mm axial plane respectively in the inhomogeneous phantom when compared to the homogeneous phantom. The dose decrease near the airtissue interface causes the Gamma Plan’s predicted dosage to be higher than that actually delivered. The resulting underdosing effect can be critical for the control of the lesions near tissue inhomogeneities.
Modeling of physiolsgical properties of stored human blood by complex impedance measurements
(Thesis (Ph.D.)-Bogazici University. Institute for Graduate of Biomedical Engineering, 2006., 2006.) Sezdi, Manâ.; Ülgen, Yekta.
In this study, the relationship between physiological properties of human blood,namely Na+, K+, Cl- concentrations, pH, 2,3-DPG and ATP, and its electrical parameters,the Cole-Cole parameters- the resistance of the extracellular fluid (Re), the resistance of the red cell interior fluid (Ri), phase angle (?), characteristic frequency (Fc) and thecapacitance of the cell membranes (Cm)- is investigated.Measurements are performed on 51 erythrocyte suspension (ES) samples, subject to42 days of storage at 4oC, on day 0, 10, 21, 35 and 42. On whole blood (WB) samples (31 samples) under 21 days of storage, same measurements are done on day 0, 10 and 21.Electrical measurements are performed in the frequency range from 100 kHz to 1 MHz atroom temperature. Multifrequency complex impedance data are fitted to Cole-Colediagrams using Least Mean Square algorithm to give Cole-Cole parameters for the equivalent electrical circuit model of blood samples.Variance analysis (ANOVA test) is used to evaluate differences in blood propertiesrelative to storage time. The relationship between the physiological and the electricalparameters of blood is investigated by regression analysis using SPSS. A multiple regression model is developed for ES and WB separately, where the physiologicalparameters are expressed in terms of the electrical parameters.In a case study, the models are tested for 20 donors, and it is seen that the model forWB is appropriate for predicting Na+, K+, Cl-, pH and ATP at all time, for ES the model is only appropriate for the first 35 storage days. The models can not estimate 2,3-DPG at all,at any time.This study clearly showed that complex impedance measurement technique can bea valuable tool in predicting the viability of stored blood.|Keywords: Na+-K+ ion current, Red blood cell, Blood storage lesions, Bioimpedance.
Biological effects of electromagnetic fields at mobile telecommunication frequencies
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2006., 2006.) Yürekli, Ali İhsan.; Özkan, Mehmed.
The increasing use of cellular phones and increasing number of base stations are becoming awidespread source of non-ionizing electromagnetic radiation. The immediate biological effectof electromagnetic (EM) radiation is the generation of heat in the body and it is generally evident under high levels of electromagnetic energy. However, some biological effects arelikely to occur even at low-level EM fields. In this study, a Gigahertz TransverseElectromagnetic (GTEM) test chamber was used as an exposure environment for plane waveconditions of far-field free space EM field propagation at the GSM Base Transceiver Station (BTS) frequency of 945 MHz and effects on oxidative stress in rats were investigated. Groupsof young adult male Wistar albino rats were kept inside the test chamber for 7 hours/day for aperiod of 8 days. When EM fields producing Specific Absorption Rate of 11.3 mW/kg(power density 3.67 Watt/square-meter), which is well below current exposure limits, were applied, MDA (malondialdehyde) level was found to increase and reduced glutathione (GSH)concentration was found to decrease significantly (p<0.0001). Additionally, there was a lesssignificant (p=0.0190) increase in SOD (superoxide dismutase) activity under EM exposure,when compared to the sham exposed group. Leukocyte counts before and after the experiment and vanil mandelic acid (VMA) levels during the experiment were also assessed. Weconclude that free radical mechanisms may have a probable role on the adverse effects of EM fields at mobile telecommunication frequencies.
Three dimensional modeling of the knee joint: prediction of ligament related gait abnormalities
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2007., 2007.) Akalan, N. Ekin.; Özkan, Mehmed.
The purpose of this study is to investigate the affect of anterior bundle of ACL (aACL), anterior portion of posterior cruciate ligament PCL (aPCL), anterior and deep portions of MCL (aMCL, dMCL) and the tibiofemoral articular contacts on to passive knee motion. A well accepted reference model for a normal tibio-femoral joint was reconstructed from the literature in which attachments of the bundles of the ligaments and the articular surfaces in medial and the lateral components were carefully defined. Another three dimensional dynamic tibiofemoral model which includes the isometric fascicles, aACL, aPCL, aMCL, dMCL, and the medial-lateral articular surfaces were represented as the constraints to predict the trajectory of the tibia on the femur during flexion. The tibiofemoral model was also integrated in to the dynamic patella-tibio-femoral model. The behavior of the knee model was also tested by simulating dynamic and static clinical tests such as knee extension exercise and drawing test. The patello- tibio-femoral model was integrated into full-body model to simulate people walk with normal and ACL deficient patterns. The predictions were closely agreed with the literatures and correspond well to measurements of the model which represents natural patello-tibio-femoral joint. The aACL, aPCL, aMCL, dMCL bundles and the medial-lateral articular surfaces might play a primary role to give the nature of distal femoral sphere like shape. The clinical significance of the work is that anything which changes the lengths and locations of the related ligaments may demolish natural constraints and force the articular structures in to unnatural shape which may make the knee to change contact behavior on the articular surface and may cause pain. The surgical treatments must be accurate enough to provide both ligament bundle geometries and articular geometry to achieve a problem free knee kinematics after the surgery.|Keywords: Knee, Kinematics, Geometry, Three-dimensional model, Ligament surgery.
Lesion detection in MR mammography: NMITR maps, dynamic and morphological descriptors
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2007., 2007.) Ertaş, Gökhan.; Gülçür, Halil Özcan.
In this thesis, algorithms, methods and techniques for dynamic contrast-enhanced magnetic resonance mammography (DCE-MRM) have been investigated to maximize sensitivity, specificity and reproducibility of breast cancer diagnoses. A novel lesion localization method that uses cellular neural networks (CNNs) was developed. The breast region was segmented from pre-contrast images using four specifically designed CNNs. A 3D normalized maximum intensity-time ratio (nMITR) map of the segmented breast was generated using a moving mask of 3×3 voxels on the dynamic images. This map was converted into a binary form and processed with a fuzzy CNN consisting of three layers of 11×11 cells to segment out lesions from the surrounding tissues and to filter-out deceptive enhancements. A set of decision rules based on volume and 3D eccentricity of the suspicious regions were applied to minimize false-positive detections. The system was tested on a dataset consisting of 7020 MR mammograms in 1170 slices from 39 patients with 37 malignant and 39 benign mass lesions and was found to perform well with falsepositive detections of 0.34/lesion, 0.10/slice and 0.67/case at a maximum detection sensitivity of 99%. Enhancement and morphological descriptors of breast lesions derived from 3D nMITR maps were also studied for malignancy detection. The mean, the maximum value, the standard deviation and the entropy were the enhancement features found to have high significance (P< 0.001) and diagnostic accuracy (0.86-0.97). nMITR-entropy had the best performance. Among the morphological descriptors studied, 3D convexity, complexity and extent were found to have higher diagnostic accuracies (ranging between 0.70-0.81) and better performance than their 2D versions. Contact surface area ratio was found to be the most significant and accurate descriptor (75% sensitivity, 88% specificity, 89% PPV and 74% NPV). The results demonstrate that nMITR maps inherently suppress enhancements due to normal parenchyma and blood vessels that surround lesions and have natural tolerance to small field homogeneities and thus are very effective for lesion localization and malignancy detection.
Statistical analysis of cognitive signals measured by fNIRS
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Çifçi, Rifat Koray.; Kahya, Yasemin.; Akın, Ata.
Further standardization in signal processing tools is needed in the area of functional near infrared spectroscopy (fNIRS) before it is recognized as a reliable neuroimaging modality. This thesis study attempts to present a comprehensive analysis of the feasibility of applying statistical inference methods to fNIRS signals. Using hierarchical linear models, both classical and Bayesian techniques are pursued and performances of different methods are presented on a comparative basis. The results obtained from a set of cognitive signals show that fNIRS can identify cognitive activity both at the subject and group levels. The analysis suggests that mixed or Bayesian hierarchical models are especially convenient for fNIRS signals. A related problem that is discussed in this thesis study is to relate the outcome of the statistical analysis with the underlying physiology. This problem is studied by putting constraints over the parameters to be estimated. Carrying the problem to a Bayesian framework, the constraints were turned into prior distributions and Gibbs sampling was used to infer from the posterior distributions. The results exhibit that in addition to preventing unlikely results to appear at the end of the analysis, using parameter constraints is also more efficient in revealing activations which are obscured by heavy noise. The last part of this thesis study departs from hypothesis-based statistical inference techniques and introduces the use of information-theoretic measures for fNIRS by particularly concentrating on neural complexity and functional clustering. It is demonstrated that this type of measures may capture organizational aspects of the brain which are hard to reveal with classical statistical inference techniques.|Keywords: Functional near infrared spectroscopy, Statistical inference, Bayesian statistics, General linear model, Constrained estimation, Complexity.
Multimodal investigation of fMRI and fNIRS derived breath hold BOLD signals with an expanded balloon model
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Emir, Uzay Emrah.; Akın, Ata.; Öztürk, Cengizhan.
Multimodal investigation of blood oxygenation level-dependent (BOLD) signal, using both functional near infrared spectroscopy (fNIRS) and functional magnetic resonance imaging (fMRI), may give further insight to the underlying physiological principles and the detailed transient dynamics of the vascular response. Utilizing a breath hold task (BHT), we measured deoxy-hemoglobin (HbR) and oxy-hemoglobin (HbO) changes via fNIRS and blood oxygen level dependent (BOLD) changes by fMRI. Measurements were taken in four volunteers asynchronously and carefully aligned for comparative analysis. In order to describe the main stimulus in BHT, partial pressure of carbon dioxide (PaCO2) parameter was integrated into the balloon model as the driving function of cerebral blood ow (CBF) which led to the development of an expanded balloon model (EBM). During BHT, the increase in HbR was observed later than the BOLD peak and coincided temporally with its post stimulus undershoot. Further investigation of these transients with PaCO2 integrated balloon model suggests that post stimulus undershoot measured by fMRI is dominated by slow return of cerebral blood volume (CBV). This was con rmed by fNIRS measurements. In addition, BOLD signal decreased with the increase of the initial level of PaCO2 derived from EBM, indicating an e ect of basal CBF level on the BOLD signal. In conclusion, a multimodal approach with an appropriate biophysical model gave a comprehensive description of the hemodynamic response during BHT.|Keywords: Functional near-infrared spectroscopy, Functional magnetic resonance imaging, BOLD signal, Partial pressure of CO2, Balloon model, Post stimulus undershoot.
Modeling and clustering analysis of pulmonary crackles
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Yeğiner, Mete.; Kahya, Yasemin.
The objective of this study is to perform two complementary analyses of pulmonary crackles, i.e. modeling and clustering, in order to interpret crackles in timefrequency domain and also determine the optimal number of crackle types and their characteristics using the modeling parameters. Since the crackles are superimposed on background vesicular sounds, a preprocessing method for the elimination of vesicular sounds from crackle waveform is also proposed for achieving accurate parameterization. The proposed modeling method, i.e. the wavelet network modeling, interprets the transient structure of crackles in the time-frequency space with a small number of components using the time-localization property of wavelets. In modeling analysis, complex Morlet wavelets are selected as transfer functions in the hidden nodes due to both their similarity with the crackle waveforms and their exibility in the modeling process. Clustering analysis of crackles probe the discrepancies found among the studies related with the crackle types and their corresponding characteristics. Since, in these studies, crackles are classi ed according to the auditory perception of the observers, there are inconsistencies found in the labeling of the same crackle. To overcome the inherent subjectivity, the crackles are classi ed in an unsupervised method using the EM clustering analysis. In this method, it is assumed that the crackle data can be interpreted with the multivariate Gaussian mixture model and, therefore, crackle clusters distribute normally in the feature spaces. The results strongly suggest the existence of a third crackle type, medium, in addition to the commonly used two types, i.e. ne and coarse. Moreover, the extracted characteristics of crackle types o er additional features for the computerized crackle-based analysis of pulmonary disorders.|Keywords: Lung Sounds, Pulmonary Crackles, Crackle Types, Wavelet Networks, Signal Modeling, EM Clustering, Vesicular Sound Elimination
The effect of dialysis environment and the clinical state of patients with chronic kidney failure on the high flux dialyzers
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Aksoy, Mehmet Emim.; Üçışık, A. Hikmet.; Usta, Metin.
In order to optimize the renal replacement therapies many researches have been going on for many years. The tendency for dialysis therapy is towards high flux hemodialysis in the last few years. For understanding the behavior of newly designed hollow fibers under high flux dialysis condition, new experiments should be designed. Experiments are designed to study the stability of the two different membranes, polysulfone and polyamide, from high flux dialyzers. Hemodialysis sessions were performed on a group of patients with dialysis ages less than two years and without any other accompanying disease. Microscopical studies performed on virgin and used dialysis membranes showed morphological changes during dialysis session. Mechanical tests revealed the differences in the mechanical properties of virgin and used membranes. The change in the degree of crystallinity of the polysulfone and polyamide membranes during dialysis was observed under X-Ray Diffraction (XRD). It was found that dialysis increases the crystallinity. This issue is very important for dialysis centers performing reuse procedures for dialysis centers, because any damage to dialysis membranes would cause very serious clinical complications. Differential scanning calorimetry (DSC) studies showed structural changes resulted by dialysis. Unlike the other analytical techniques used, the capacity of FTIR did not give enough information. The data obtained in the course of this study showed that high flux dialysis sessions cause irreversible structural changes, which may result in clinical complications during reuse of dialyzers.|Keywords: Hemodialysis, high flux, polysulfone, polyamide, stability.
Development of a new orthosis (neuro-orthosis) for the control of wrist movements in patients with carpal tunnel syndrome
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Uğurlu, Ümit.; Özkan, Mehmed.
Static wrist orthoses (SWOs) are used in carpal tunnel syndrome (CTS) with some drawbacks. As an alternate approach, an active closed-loop wrist control strategy was proposed to limit wrist movements. It was based on the electrical stimulation of antagonistic muscle(s) to prevent motion beyond preset limits. The purposes of the study were to determine whether the proposed “neuro-orthosis” (NeO) system resulted in less restriction in the function and strength of the hand compared to custom-made SWOs and its ability to limit the wrist movements. A case-control study was designed. 31 right-handed volunteers participated in the study. 12 of them were patients with CTS, and the others were healthy subjects. Function, dexterity, and strengths were measured under three different testing conditions: without orthosis, with a SWO, and with the NeO system. Standardized test instruments and test procedures were used for all measurements. Maximum angles at each direction were recorded while the NeO system was on and off. At the end of the SWO and the NeO test conditions the level of discomfort were questioned by means of 10 cm visual analog scale. SWOs caused significant decrements in most of the tests with respect to the noorthosis test condition. The NeO system also led to some limitations in the test scores. However it was found to be less constraining with respect to a SWO. Although the NeO was not able to strictly limit the movements into preset limit, the resulting movement range was still in the safe area. The NeO system resulted in more discomfort in general.|Keywords: Carpal tunnel syndrome, Orthosis, Electrical stimulation.
The nanostructural role of water in lamellar bone and its implications on osteonal bone mechanics: a micrographic and optomechanical study
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2008., 2008.) Utku, Feride Şermin.; Saybaşılı, Hale.; Yücesoy, Can A.
The microstructural organization of water in bone was investigated using the environmental scanning electron microscope to analyze the dimensional changes that occur during dehydration of equine osteonal bone. In longitudinal sections, 1.2% contraction perpendicular to the lamellae, 0% parallel to the lamellae; in transverse sections,1.4% contraction both parallel and perpendicular to the lamellae were observed. Scanning electron microscopy back scattered electron images showed that about half of an individual lamella is less mineralized, thus more hydrated, indicating that contractions perpendicular to lamellae are due to the presence of more water-filled rather than mineral-filled channels within the mineralized collagen fibril arrays. As these channels are also aligned with the crystal planes, the crystal arrays facilitate or hinder contraction in different directions. The mineralized collagen fibril arrays, laid down in the form of primary circumferential lamellar bone are replaced with secondary osteonal lamellar bone. The mechanical properties of these two types of lamellar bone are studied to understand how bone functions under load during the remodelling process. Twenty minipig cortical bone samples were tested using an optomechanical testing system. Deformation of tissue after each 2-micrometer compression increment was detected orthogonally in-plane (x,y) and out-of-plane (z). Linear regression of stress and strain of partially remodelled bones gave an E1and ν12 of 7.9 ± 2.1 GPa and 0.3. The circumferential lamellar bone had an average E1 of 9.4 ± 2.0 GPa compared to the average E1 of 6.8 ± 0.8 GPa for the osteonal bone.|Keywords: environmental scanning electron microscope, mineralized collagen fibril, bone water, electronic speckle pattern interferometry, mechanical properties of compact bone.
Clinical grade active guidewire and catheter for interventional cardiovascular MRI
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2009., 2009.) Kocatürk, Özgür.; Öztürk, Cengizhan.
The success and safety of interventional magnetic resonance imaging (MRI) procedures requires conspicuous intravascular instruments that can be distinguished from surrounding tissues. In this dissertation work, an "active" (receiver-coil) clinical grade vascular guidewire and guiding catheter were developed with enhanced visibility and favorable mechanical characteristics for MRI guided cardiovascular interventions. Both 0.035-inch guidewire and 7 Fr guiding catheter were designed combining two different antenna designs on independent channels. The devices incorporate a loop antenna to visualize the tip and determine orientation, and a dipole antenna to visualize the whole guidewire shaft. The MRI visibility performance and RF safety tests were performed at 1.5T in vitro and in vivo in swine. The two channel active guidewire design provided accurate tip position information with 0.97 0.42 mm and novel active shaft visibility technique was introduced to polymer based guiding catheter successfully without sacrificing device size or handling. Mechanical testing comparison with several commercially-available guidewires demonstrated that the new guidewire design provides the desired stiffer distal tip, moderate torquability, and pushability suitable for vascular applications. The RF power threshold and limitations were determined to provide reasonable amount of heating during MRI examination. This may enable a range of interventional procedures using real-time MRI.|Keywords: Interventional Magnetic Resonance Imaging, Active instrument, Equipment Design, Catheterization
Advanced computational tools for real-time MR imaging
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2009., 2009.) Saybaşılı, Haris.; Ademoğlu, Ahmet.; Öztürk, Cengizhan.
Real-time Magnetic Resonance Imaging (MRI) has the potential of successfully guiding interventional applications. Overall, the requirements of real-time MRI can be categorized as: (i) fast data acquisition, (ii) fast image reconstruction, and (iii) good image quality. Fast data acquisition is provided by optimized real-time sequences, by parallel MRI (pMRI) techniques, or by non-Cartesian acquisition schemes (e.g. spiral and radial trajectories). However, fast image reconstruction is non-trivial, especially when computations demanding pMRI methods or non-Cartesian trajectories are involved. Even though signal-to-noise ratio (SNR) can be relatively high during real-time imaging, spatial resolution is limited. Thus, improved visual feedback during real-time MRI guided interventions is a must. This thesis defined three specific aims to improve real-time imaging: (i) real-time image reconstruction for pMRI, (ii) real-time image reconstruction for non-Cartesian trajectories, and (iii) fast MRI post-processing for improved visual feedback during interventions. Thesis contributions include: (i) real-time hybrid domain TGRAPPA based pMRI reconstruction algorithm (currently the fastest TGRAPPA based algorithm), (ii) first real-time implementation of GRAPPA Operator Gridding algorithm for radial acquisitions, (iii) multi-phase 3D angiography roadmaps for MRI guided interventions, (iv) improved active device visualization during real-time MRI guided interventions, (v) integration of a real-time active device localizer algorithm.|Keywords: Real-time MRI, pMRI, Non-cartesian trajectories, Parallel processing, MRI guided interventions.
İnvestigation of the alterations in motor units in neurologic disorders by scanning electromyography
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2009., 2009.) Göker, İmran.; Ülgen, Yekta.
In this study, the alterations in the length of cross-sections of MU and the changes in maximum amplitude of MUAPs in each MU in patients with JME were investigated. An experimental setup of scanning EMG was built and 3-D cross sectional maps of the MUs were plotted in order to measure the length of cross-sections and to find the maximum amplitude of each MU. Three subject groups comprising nine patients with juvenile myoclonic epilepsy as JME group, ten healthy volunteers as normal control (NC) group and three patients with spinal muscular atrophy as SMA group were included. The age of the subjects ranged between 22 and 46. Five to eight measurements were performed from the biceps brachialis muscles of each subject. Data including 113 measurements in total acquired from with these measurements were stored in a computer and then were used to construct 3-D maps of MU territories. All three groups were compared in pairs by using 113 measurements with Student’s t-test. JME groups were found similar to SMA group in terms of both parameters. The difference between JME and NC groups was found as extremely significant. Since the increase in both parameters due to the reinnervation occurs in SMA group, significant difference is expected between SMA and NC group. These results were confirmed with Tukey’s HSD test by comparing three groups simultaneously. Three groups were also compared using the individual means of parameters with a non-parametric test such as Mann-Whitney test. A significant difference which is also confirmed again with Tukey’s HSD test was found between the JME and NC groups. In conclusion, since no neurogenic evidence was found in JME patients in conventional EMG previously higher length of cross-sections can be considered as structural.|Keywords: Scanning EMG, Juvenile Myoclonic Epilepsy, Motor Unit Territory, Electrophysiological Cross-section.
Accuracy improvements of NIRS and investigation of muscle oxidative metabolism
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2009., 2009.) Şayli, Ömer.; Akın, Ata.
In the rst part of the thesis, the e ect of fat layer on continuous wave near infrared spectroscopy (cw-NIRS) measurements were investigated in detail, both in terms of underestimation error (caused by homogeneous medium assumption) and crosstalk between chromophores because of homogeneous medium assumption and wavelength dependence of mean partial path length in the muscle layer. These errors have been investigated by Monte Carlo simulations with a skin-fat-muscle layered tissue model for a two wavelength system. The errors have been found to be higher for thicker fat thicknesses. A correction algorithm was proposed with the use of wavelength dependent partial path length in the muscle layer derived with Monte-Carlo simulations. Two detector cw-NIRS system was also analyzed and compared with 1-detector cw- NIRS system. The performance was promising but true assumption of initial optical coe cients of the layers poses a challenge for the performance. Muscle metabolism, fatigue and endurance was examined with usage of three simultaneous measurement modalities: cw-NIRS, SEMG and force-time for isometric hand grip exercise. The study revealed some physiological processes related to fatigue. A highly valued and statistically signi cant correlations were found between sEMG and cw-NIRS derived parameters especially at 50% maximal voluntary contraction along with biometrics for endurance prediction. These information could be important in sports applications, ergonomics, physical medicine and rehabilitation to monitor the recovery with objective parameters.|Keywords: Near infrared spectroscopy, Continuous wave near infrared spectroscopy, Monte Carlo simulations, Light propagation in tissue, Muscle oxidative metabolism, Tissue oxygenation, Endurance, Fatigue, Surface electromyography.
A neurovascular coupling model based on nitric oxide and carbon dioxide and its validation with two-photon microscopy imaging
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2010., 2010.) Yücel, Meryem Ayşe.; Akın, Ata.
Understanding neurovascular coupling is of paramount importance since while a normal coupling is vital for a healthy functioning brain, the impairment in coupling is the underlying factor of many neurodegenerative diseases. With this motivation, we aimed to test the still-debatable hypotheses and important aspects of neurovascular coupling: whether the coupling is controlled metabolically or neurogenically, how the coupling is propagated, what kinetics the cerebral metabolic rate of oxygen (CMRO2) follows during neuronal activity and the transient characteristics of the response during stimulus and after stimulus periods. We have modi ed recent models of neurovascular coupling adding the e ects of both nitric oxide (NO) kinetics, a well-known neurogenic vasodilator, and CO2 kinetics as a metabolic vasodilator to test the neurogenic and metabolic hypotheses. Using 2-photon microscopy imaging, we measured the vessel diameter changes in vivo in somatosensory cortex of Sprague Dawley rats during forepaw stimulation to investigate response transients and to test retrograde dilation hypothesis. Our results show that the dominant factor in the hemodynamic response is NO, however CO2 is important in modulating the shape of the response: causing poststimulus undershoot due to the washout e ect of cerebral blood ow (CBF) resulting in hypocapnia. The statistical analysis of our experimental results and their comparison with the modeling results give more insight into the transient characteristics of the response. Our results support retrograde dilation hypothesis and suggests a CMRO2 onset and return kinetics in seconds rather than in minutes during functional activity.|Keywords: Neurovascular coupling, Neurogenic hypothesis, Metabolic hypothesis, Nitric oxide, Carbon dioxide, 2-photon microscopy.
Skin tissue welding with near infrared lasers: investigation of the optimal parameters
(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2010., 2010.) Tabakoğlu, Haşim Özgür.; Gülsoy, Murat,
Laser tissue welding/soldering is an alternative to conventional closure techniques in surgery. In the present study, the closure capability and the contribution to recovery period of laser welding techniques were investigated through comparative experiments. E ects of three near infrared (NIR) wavelengths, 809 nm diode laser, 980 nm diode laser and 1070 nm ytterbium ber laser, were compared not only among themselves but also with classical manual suturing for skin closure competency. Lasers with di erent NIR wavelengths were delivered to skin incisions via optical bers and laser power was adjusted according to predosimetry studies. In dosimetry experiments all the three NIR lasers were tested for their e cacy in welding; besides, 809 nm diode laser was also tested for its e cacy in laser soldering. E ects of 980 nm laser welding at same energy but di erent irradiation levels were also compared. Throughout this period, healing was inspected at particular days (1, 4, 7, 14, 21) by histological and mechanical methods. Skin samples were stained with Hematoxylin and Eosin (H&E) in order to assess gross pathological changes along epidermis and dermis created either by photothermal laser tissue interactions or suturing and suture material itself. These changes were quanti ed as closure index (CI), thermally altered area (TAA), granulation area (GA) and epidermal thickness (ET) by using di erent microscopy techniques such as bright eld, polarized light and phase contrast. The laser welding techniques were found reliable in terms of immediate and mechanically strong closure compared to suturing.|Keywords: Skin welding/soldering, 809 nm diode laser, 980 nm diode laser, 1070-nm YFL, ICG, Tensile test, H&E staining, Closure index.

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