M.S. Theses
Permanent URI for this collection
Browse
Recent Submissions
Item Effects of prior stimulation on tactile evoked epidural field potentials in rat S1 cortex(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Akdeniz Karatay, Aslı.; Güçlü, Burak.Understanding how tactile sensation is processed in the somatosensory cortex is crucial for the development of neuroprostheses that can provide a realistic sense of touch. Exploring the electrophysiological basis of vibrotactile forward masking of fers valuable insights into how the brain integrates and responds to sequential sensory inputs. This understanding can help drive progress in the development of haptic inter faces and the enhancement of neuroprosthetic technologies designed to improve tactile perception. Epidural field potentials were recorded from the hind paw representation of the rat S1 cortex by using various experimental parameters. The effects of the prior stimulus on the test stimulus window measured as dB difference and latency difference were evaluated. The results indicated that all main factors had a significant impact on the dB difference. An increase in the amplitude of the prior stimulus was found to enhance suppression effects. The suppression decreased as the temporal gap in creased. By demonstrating the impact of the prior stimulus, the study underscores the fundamental influence of preceding sensory inputs in shaping subsequent sensory processing. NOTE Keywords : Primary Somatosensory Cortex, Epidural Field Potentials, Forward Mask ing, Neuroprosthetic.Item Mid-Air haptic sensations produced by ultrasound actuators in patients with carpal tunnel syndrome(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Akdağ, Mehmet Akif.; Güçlü, Burak.This thesis utilizes psychophysical experiments with mid-air haptic ultrasound actuators to assess carpal tunnel syndrome (CTS) patients’ tactile sensation. 19 female and one male patients (age: 33-61) with unilateral CTS took part in the experiments. We used a two-alternative forced choice task experiments to measure detection thresh olds around 250 Hz modulation frequency at the thenar eminence (TE) and at the index finger in affected and healthy hands. In addition, 15 female CTS patients par ticipated in a virtual reality-assisted hand exercise game with haptic feedback. The system usability scale (SUS) and exercise performance scores were evaluated. There was no significant difference in the threshold values from the TE between the CTS hand (M=0.85 au, SD=0.15) and the healthy hand (M=0.87 au, SD=0.16). The thresholds measured from the index fingers of CTS affected hands were all higher than the maxi mum stimulus level that could be produced by the ultrasonic actuators. For the healthy hands of 17 patients, the detection thresholds were (M=0.90 au, SD=0.09), and the remaining 3 had threshold values above the maximum output of the device. For the exercise game results, there was a significant correlation (ρ = 0.89, p < 0.001) between the SUS (M=80.17%, SD=18.33) and performance scores (M=83.31%, SD=14.80). Since the CTS was at an early stage and there may be a branching (palmar cutaneous branch) of the nerve before entering the carpal tunnel, thresholds were found similar in both hands at the TE. Unfortunately, the limitations of the haptic device did not allow a comparison between index fingers. Moreover, this device and novel technology may be used for the follow-up of the rehabilitation and the treatment of the CTS. As such, the usability of the system is above the criterion value, and in the future it can be improved not to be affected from the performance in the exercise games. NOTE Keywords: Touch, Psychophysics, Somatosensory System, Carpal Tunnel Syndrome, Pacinian Channel, Ultrasound Stimulus, Mid-Air Haptics.Item Generating non-normal distributions for interval schedules : effects on instrumental behavior(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Albayrak, Emirhan Buğra.; Schulz, Daniel.VI schedules are used in instrumental conditioning to obtain a relatively con stant response rate. In VI schedules, a reward is delivered following an operant re sponse, that is emitted after a variable time interval has passed. A peculiarity of VI schedules is that responding increases as time spent in an interval increases, producing output which is less uniform. To reduce this effect, positively skewed distributions have been implemented. However, non-normal distributions cannot be generated with cur rent number generators. Here, we have established a procedure in Microsoft Excel that generates non- normal distributions. We further ran instrumental conditioning proto cols utilizing the distributions we generated to see the effects on instrumental behavior. We hypothesized that our distributions will lead to a time independent behavior after discrimination training, in which animals learned to discriminate between existence of the stimulus and a no- stimulus context. First, we analyzed discrimination training by comparing lever press rates and lever press latencies across days of training and time within session. Then, to see how our distributions affected the time-dependency, we analyzed the relationship between time after stimulus onset and lever press rates during discrimination training performing correlation analyses. We found that the an imals pressed the lever less in the 21 st day of discrimination training in EXT state compared to the 1 st day. We also found that, although there was a significant moder ate correlation between time after stimulus and the lever press rate in the 1 st day of discrimination training, the correlation was not significant for the 21 st day. However, a curvilinear function explained over 70% of the variance in the data. Here we showed an easy-to-use method to generate non-normal distributions with Microsoft Excel. Our findings suggest that distributions generated by the given formula led to learning in rats in 21 days, but the lever press responses were not time independent contrary to our expectations. NOTE Keywords : Instrumental Conditioning, Variable Interval Schedules, Discrimination Training, Non-normal Distributions.Item Development of novel device technologies for safer MRI guided biopsy procedures(Thesis (Ph.D.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Uzun, Doğangün.; Kocatürk, Özgür.Interventional magnetic resonance imaging (iMRI) is a potent method that combines the benefits of minimally invasive procedures and the exquisite imaging capabilities of MRI. Therefore, performing biopsy operations under the guidance of realtime MR imaging can increase success and safety of operations by promising precise, accurate, and safe MR-guided biopsy operations. Designing visible and safe interventional equipment continues to be a major challenge in this field as MRI develops into a more accessible and suitable imaging modality for interventional procedures. In this thesis study novel device technologies that could improve the success of MR- guided biopsy procedures are introduced and tested. First, a novel optical fiber force sensor was designed and implemented into a needle to provide feedback on the axial force applied to the needle tip during MR-guided biopsy operations. Accurate force measurement, differentiation of different tissue types via stiffness detection capabilities, and the performance of the sensor under MRI were successfully tested through invitro experiments. Next, a novel method for increasing the visibility of MR-compatible interventional devices was introduced by using alternating current (AC) controlled conductive ink printed tracking markers. An elaborate analysis was performed to obtain the highest tracking marker conspicuity using the AC-controlled markers and three commonly used MRI pulse sequences. A Custom 20-gauge needle prototype and an MR-compatible current supply circuit were designed. MR-visibility and safety of the prototypes were tested through in-vitro experiments according to the international medical device test standards. Finally, the performance of the needle prototype and the current supply circuit was tested in a post-mortem animal experiment. NOTE Keywords : Interventional MRI, MR-guided biopsy, Fiber-optic force sensors, iMRI device tracking, AC-controlled markers.Item Interaction of magnetic nanoparticles with polymersomes for use as multimodal nanocarriers(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Uysal, Gizem.; İyisan, Banu.Magnetic nanoparticles (MNPs) are extensively used targets for drugs to help with early detection and the treatment of disease. However, drug targeting with MNPs in a specific site within the body is quite challenging to achieve. In these situations, pH-responsive polymersomes can provide an effective dual targeting opportunity by hosting both MNPs on their membrane and drugs in the core. Therefore, the overarching objective of this research is to develop pH-sensitive polymersome that interacts with Super Paramagnetic Iron Oxide Nanoparticles (SPIONs), intended for potential applications. SPIONs were chosen as magnetic nanoparticles since they have good biocompatibility. We hypothesize that, in an acidic environment, increased permeability of pH-sensitive polymersomes induces controlled release from the core; meanwhile guiding with MNPs makes these structures a multimodal tool. In our first aim, we will synthesize SPIONs with average sizes of 10-15 nm using the co-precipitation method. These SPIONs will be stabilized with β-Cyclodextrin. Following that, Poly (ethylene glycol) (PEG), 2-(diethylamino)ethyl methacrylate (DEAEMA) and Ferrocene units will form the multimodal polymeric nanocarrier system. After polymersome formation, SPIONs will be introduced to the system, aiming for interaction with the exterior of the polymersome membrane facilitated by the complexation of ferrocene and β- Cyclodextrin. Our second aim involves conducting a morphological analysis of these multimodal nanocarriers to ensure their integrity and assess the success of the interaction. The ultimate prospective of this study is to utilize these multimodal nanocarriers for image-guided applications, potentially extending their use to drug loading in future studies. NOTE Keywords : β-Cyclodextrin, Magnetic Nanoparticles, Nanobiotechnology,Polymersome, Iron Oxide.Item Investigation of protein corona formation on biodegradable nanocarriers(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Kelle, Damla.; İyisan, Banu.Biodegradable nanocarrier systems are significant tools for drug delivery sys tems since they enable prolonging the therapeutic effect of the chemotherapeutic drug by extending the release over a longer period of time. However, the most significant challenge of these systems is the protein corona (PC), the layer formed around the surface of nanocarriers by the adhesion of plasma proteins when nanocarriers are in jected into the body intravenously. Since the PC structure identifies the nanocarriers’ destiny in the body, it is required to be analyzed the proteins that form the PC struc ture comprehensively. In this study, proteins found in the hard protein corona (HPC) structure of two different biodegradable nanospheres (NSs), poly(lactide-co-glycolide) (PLGA) and polycaprolactone (PCL) NSs, were identified. For this purpose, distinct PLGA and PCL nanoparticles (NPs) were fabricated by miniemulsion/solvent evapo ration method, followed by the characterization by electron microscopy, dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Subsequently, PLGA and PCL NSs were treated with human plasma or FBS to form PC structure. Proteins in PC structures were analyzed by sodium dodecyl sulfate polyacrylamide gel elec trophoresis. Furthermore, each protein in the HPC structure were identified by liquid chromatography-mass spectrometry (LC- MS) and grouped according to their func tions. Moreover, doxorubicin hydrochloride, a significant chemotherapeutic drug, was encapsulated into PLGA NSs. Drug encapsulated NSs were characterized by DLS and ELS. Afterward, the PC structure around the surface of drug encapsulated NSs was formed by treating with human plasma or FBS. The impact of the PC on the drug release behavior of PLGA NSs was investigated at pH 7.4, a critical pH value to mimic the physiological environment. NOTE Keywords : Biodegradable Nanocarriers, Polymer Nanoparticles, Protein Corona.Item An unsupervised and refractoriness-supported algorithm design for real-time spike sorting(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Önder, Alparslan.; Ademoğlu, Ahmet.; Güçlü, Burak.Neural spike sorting algorithms have been used to group the action potentials in electrophysiological signals according to their characteristics to use them in neuroscience studies. In this study, we developed an unsupervised and online spike sorting algorithm that performs better than existing online and unsupervised sorting algorithms, calculates thresholds variably, and can be used for real-time studies when applied on FPGA boards. A template matching algorithm OSort, based on Euclidean distance, functioned as the base for this algorithm. We used the NEO method to detect the spikes and the Windowed Sinc Interpolation method to upsample the detected spikes four times. We developed a refractoriness control mechanism that works according to the peak points of the spikes to prevent assigning a spike to the wrong cluster. We designed a second block that considers the probability of a spike belonging to the second closest cluster to itself. It controls this issue to prevent assigning a spike to the wrong cluster if the spike waveforms of the different neurons are similar. We avoided using more complex mathematical operations like calculating standard deviation with the aim of future real-time studies on cheaper FPGA boards. When we compared the performance of our algorithm with the well-known algorithms in the literature, we saw that ours performed significantly better than the online ones and insignificantly worse than offline ones. The presented thesis shows that more accurate online and unsupervised spike sorting is possible without complex algorithms. It is expected that this kind of algorithms will support the increment in the number of neuroscience studies that use spike sorting. NOTE Keywords : Spike Sorting, MATLAB, Action Potentials, Detection, Clustering, Online, Unsupervised, Varying, Real-time.Item Synthesis and characterization of bovine serum albumin based nanocontainers for drug delivery appications(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2022) Topal, Elif Özlem.; İyisan, Banu.Polymeric nanocontainers which consist of both a core and a polymeric mem brane have an important role for drug delivery applications. They can carry active compounds like drugs, proteins in their core and their polymeric membrane prevent the living environment from the side effects of these carried compounds. There are various types of polymeric materials that can be natural or synthetic according to their source for the production of the polymeric nanocontainers. Also, the combina tions of different polymers are used to produce highly stable nanocontainers. The main goal of this thesis study is fabrication of totally biocompatible, biodegradable, durable, nanocontainers that consist of polymeric shell and lipid core. For these reasons, conju gates made of the Bovine Serum Albumin (BSA) which is a protein and Pectin which is a polysaccharide, were synthesized through the Maillard reaction based on reduc ing sugar and proteins without using external chemicals or enzyme. The effects of protein- polysaccharide weight ratio, pH adjustment were investigated to optimize the conjugate formulation. The produced conjugates were characterized via Protein As say, SDS-PAGE and FT-IR Analysis. The polymeric nanocontainers were produced through oil-in-water miniemulsion method by using the obtained BSA and Pectin con jugates. Addition of biocompatible stabilizers had a drastic influence on the resulting features on the nanocontainers which are extensively characterized by dynamic light scattering analysis, zeta potential measurements and STEM imaging. NOTE Keywords : Biopolymeric Nanocontainer, Maillard Reaction, BSA- Pectin Conjugates.Item Improving the quantification accuracy of Tc-99m mibi dual-phase parathyroid spect(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Aytaç, Bahadır.; Güveniş, Albert.Quantitative parathyroid SPECT imaging is a technique used to assess primary hyperparathyroidism that may have potential in the identification and differentiation of parathyroid lesions as well as the estimation of disease severity. Studying the effect of data acquisition parameters on the quantification error is important for maximizing the accuracy of this diagnostic technique. In this study, we examine the effects of different data acquisition parameters, namely the type of collimator, scatter correction status, and reconstruction iteration number on the quantification accuracy using computer simulation. The SIMIND Monte Carlo Simulation and CASToR iterative reconstruction program was used to simulate a commercially available SPECT camera (Siemens Symbia Intevo Gamma Camera) with a crystal size of 29.55cm and 128x128 matrix size. A digital cylindrical phantom filled with water was constructed. A 0.36 cm radius spherical adenoma filled with a uniform 1MBq/cc Tc99m-Sestamibi was placed within the phantom. Low-Energy High Resolution (LEHR) and Low Energy Ultra High Resolution (LEUHR) collimator models are tested. Along with the presence of Scatter correction and differing iteration numbers (x16, x32). An image FOV-based calibration method was used to gather quantitative information and check against the input radioactivity. The presence of scatter correction is observed to cause a 15-20 percent relative improvement in quantification accuracy. The optimal number of iterations produced a 10 percent relative improvement. Overall, accuracies as good as 7 percent in estimated activity concentration could be observed. Thus showcasing that the optimization of parameters can provide a significant improvement in quantification accuracy. Keywords: NOTE Keywords : SPECT, Monte Carlo Simulation, Quantification, Hyperparathyroidism.Item Polyethylenimine-capped gold nanoparticles in nucleic acid delivery(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Hınık, Aykut.; Öztürk, Cengizhan.; Aydın, Ömer.RNA interference is a gene editing tool applicable in cancer therapy. Nucleic acid delivery into the cells is challenging due to nucleic acid instability, insufficient cellu lar uptake, and endosomal entrapment. Polyethylenimine (PEI) is a positively charged polymer molecule widely used in nucleic acid delivery. PEI ensures increased endoso mal escape thanks to the proton sponge effect. However, PEI is known to be highly toxic because of molecular size and electrical charge. Gold nanoparticles (AuNPs) are attractive inorganic carriers with biocompatibility, easy synthesis, and adaptability of surface chemistry. In this study, it was aimed to synthesize polyethylenimine-capped gold nanoparticles (AuPEI-NPs) to investigate their cytotoxicity and nucleic acid de livery in breast cancer cells compared to free PEI. Resazurin assay demonstrated that AuPEI-NPs induced less cytotoxicity than free PEI until the 20 µg/ml concentration in breast cancer cells. Flow cytometry demonstrated that AuPEI-NPs yielded signif icantly higher cellular uptake of fluorescently tagged siRNA than PEI. In conclusion, this study demonstrated that AuPEI-NPs are promising nucleic acid carriers in gene therapy with a less cytotoxicity and better cellular uptake than free PEI in breast cancer cells.Item Deep learning-based virtual special staining of H&E stained tisue sections(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Kınalı, Fatma Nur.; Turan, Mehmet.Hematoxylin and eosin (H&E) staining, which is standardly applied to tissues in histopathological diagnosis, is an incredible tissue staining method that reveals the morphological features of tissues and cells and gives an idea about their biomolecular structures. However, a more accurate determination of tissue and cell structure and biomolecular components is essential for the diagnosis of diseases under the light micro scope. For this reason, histochemical, immunohistochemical, immunofluorescent and genetic techniques have been applied to tissues and cells and it has been aimed to reach the closest diagnosis to the truth. However, the number of these methods is quite high and depending on the method, they can be very complex and time- consuming in terms of procurement, cost, time requirement and application. Manual preparation of each is an expensive and labor-intensive process that requires complex and difficult methods of using many chemicals, and ready-to-use kits are often costly. Here, we propose a novel virtual staining tool that transforms H&E-stained tissue images into specially stained versions in just a few minutes. Virtual staining of some of the frequently used methods in daily pathology practice with a transformation that is derived through a learning process, using H&E slide as a basis, will make the use of these methods in the histopathological diagnosis process incredibly practical, inexpensive, simple and easy to apply in a short time. As well as, we propose a novel StainKid dataset of stomach and kidney tissue samples stained with a wide collection of histological stains. The StainKid dataset can make a significant contribution to the development of computer aided diagnosis in histopathology by paving the way for new artificial intelligence-based virtual staining techniques. NOTE Keywords : Histological Stain, Special Stain, Virtual Staining, Whole Slide Image, Generative Adversarial Network.Item Effect of IR780-loaded silica-coated gold nanorods for photodynamic therapy of cancer(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2023., 2023) Yünlü Doğruyol, Merve.; Gülsoy, Murat, 1967-Photodynamic therapy (PDT) is a new approach to cancer treatment that activates a photosensitizer (PS), a light-sensitive chemical, with a specific wavelength of light. PDT is a promising new method, however, the efficacy of PDT is still limited because of a low accumulation of PS in the target cell and limited penetration of light to the deeper tissue which prevents the killing of all cancer cells. As a result, cancer recurrence is inevitable. Gold nanostructures are good biocompatible carriers of PS. Increasing PS accumulation on the target site leads to the effective destruction of cancer cells, but different cancer cells require different approaches. One of the resistant colon cancer types is HCT116 and it needs a better approach to treatment. Gold nanorods (GNRs) have a high absorption spectrum at near-infrared (NIR) as compared with other types of Gold nanoparticles (GNPs). However, GNRs are limited for the loading amount of PS and they tend to aggregate within cells. To overcome these limitations, we will develop mesoporous silica-coated GNRs (GNRs@SiO2) for effective PS loading in this study. To test this hypothesis, we aim to test the PDT efficacy of IR780, as a PS, loaded GNRs@SiO2, (GNRs@ SiO2@IR780) and GNRs@SiO2@P EG (GNRs@SiO2@IR780@P EG). This investigation of PDT with GNRs@SiO2@IR780 and GNRs@SiO2@IR780@P EG will cause a dramatic decrease in colon cancer volume as compared with GNRs@SiO2 alone and GNRs@SiO2@P EG alone. NOTE Keywords : Photodynamic Therapy, Colon Cancer Cells, Gold Nanorods, Silica Coat ing, IR780.Item Predicting kidney tumor subtype from CT images using radiomics and clinical features(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Şirin, Duygu.; Güveniş, Albert.This study aims to evaluate the performance of machine learning methods in predicting the subtype (clear-cell vs. non-clear- cell) of kidney tumors using clinical patient and radiomics data from CT images. CT images of 192 malignant kidney tumor cases (142 clear-cell, 50 other) from TCIA’s KiTS-19 Challenge were used in the study. There were several different tumor subtypes in the other group, most of them being chromophobe or papillary RCC. Patient clinical data were combined with the radiomic features extracted from CT images. Features were extracted from 3D images and all of the slices were included in the feature extraction process. Initial dataset consisted of 1157 features of which 1130 were radiomics and 27 were clinical. Features were selected using Kruskal Wallis - ANOVA test followed by Lasso Regression. After feature selection, 8 radiomic features remained. None of the clinical features were considered important for our model as a result. Training set classes were balanced using SMOTE. Training data with the selected features were used to train the Coarse Gaussian SVM and Subspace Discriminant classifiers. Coarse Gaussian SVM was faster compared to Subspace Discriminant with a training time of 0.47 sec and 11000 obs/sec prediction speed. Training duration of Subspace Discriminant was 4.1 sec with 960 obs/sec prediction speed. For Coarse Gaussian SVM was found as 0.86 while for Subspace Discriminant AUC was 0.85. Both models produced promising results on classifying malignant tumors as ccRCC or non-ccRCC. NOTE Keywords : Kidney Tumor, Clear-Cell, Machine Learning, CT Imaging.Item Spatiotemporal graph convolutional neural networks for motor imagery EEG classification(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Alramly, Ahmed Mohamed Mohamed Mohamed.; Ademoğlu, Ahmet.Electroencephalography (EEG) has various applications in medicine, neuro-science, and neural engineering. It records the electrical activity of the brain tissues caused by the interaction among different neuronal communities. Numerous algorithms for the automatic classification of EEG signals have been developed. These algorithms work via extracting unique and non-redundant features from EEG signals. However, the majority of the proposed algorithms employ temporal components of EEG signals while disregarding the rich spatial network structure that underlies in the EEG. In this study, we propose a classification pipeline that uses the network structure of EEG data for a simultaneous representation of spatial and temporal features in the EEG signals. First, graph theory is utilized to model the EEG networks in two spatial domains; i) the sensor space and ii) the cortical source space. Second, a spatiotem- poral graph convolutional neural network (STGCNN) classification model is employed combining both temporal and spatial features of EEG data for its classification under motor imagery conditions. Additionally, the model is tested using the cortical source space data in each of the seven resting state brain networks individually to estimate their performance on classification accuracy. The results show that STGCNN model performs slightly better than the temporal convolutional neural network (CNN) models by 1.25%. NOTE Keywords : EEG, Spatiotemporal Graph Convolutional Neural Networks, Brain Networks.Item Assessment of effectiveness of muscle lengthening surgery in cerebral palsy using musculoskeletal modeling(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Biricik, Eda.; Yücesoy, Can A.Cerebral Palsy is a permanent movement disorder that manifests itself at early childhood, as poor coordination, and gait difficulty due to muscle spasticity and/or con tracture. Excessive knee flexion during gait e.g., crouch gait is a common impairment and often corrected by hamstring lengthening surgery. Such crouch gait is presumed to originate from shortness (i.e., contracture) and/or slowness in lengthening (i.e., spastic ity) of affected muscles and remedial surgery is considered to improve gait by increasing muscle length or its velocity. However, a third group of patients who neither has short nor slow hamstrings pre-operatively can still undergo surgery. The aim of the thesis is to investigate whether the gait of those patients improved after the surgery by testing the hypotheses: post-operatively, (i) the knee joint movement is improved (ii), the hip joint movement is deteriorated (iii), the gait deviation index (GDI) is increased (iv), muscle unit length do not change, and (v) pre-operative psoas muscle lengths were shorter. Findings showed that mean knee angle decreased significantly at the initial contact (0-3%), terminal stance (28-43%), and the terminal swing phases (95-100%) (p< 0.05). No significant effects were detected in the hip angle or the GDI. Additionally, no significant changes in the hamstring muscle lengths were found. Only half of the patients had shorter psoas muscle lengths pre-operatively. In conclusion, the excessive knee flexion of the patients was decreased without negatively affecting hip movement or gait overall. The improvement in the knee angle was achieved without any change in the muscle length of the hamstrings, suggesting that an isometric position shift of the target muscle occurs, which may be ascribed to post-surgical alterations in the epimuscular connections. NOTE Keywords : Hamstring lengthening surgery, Remedial surgery, Spasticity, Contrac ture, OpenSim, Musculoskeletal modeling, Psoas, Lengthening velocity, Muscle short ness, Cerebral Palsy.Item Proof-of-principle of ed-DBS (Experien-driven deep brain stimulation) in the hemiparkinson rat model(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Tamer, Betül.; Schulz, Daniel.Parkinson’s Disease (PD) is a neurodegenerative disease characterized by the progressive loss of dopamine (DA) neurons in the substantia nigra (SN). The loss of DA leads to debilitating motor symptoms, such as tremors, rigidity, and bradykinesia. Deep brain stimulation (DBS) is considered state- of-the-art in the treatment of motor symp toms in advanced PD. The standard practice is to stimulate the subthalamic nucleus (STN) or internal globus pallidus (GPi) continuously via surgically implanted elec trodes. However, continuous administration of DBS conflicts with the firing patterns of nigrostriatal DA neurons because these neurons generate rapid phasic DAergic sig nals in response to specific experiences, such as the presentation of a reward-predicting stimulus (S) or an unexpected reward (S*). This conflict may be one of the reasons for only moderate treatment efficacy of DBS. In our Boğazici University Scientific Research Projects (BAP) project, we hypothesize that treatment outcomes are enhanced if DBS is given acutely, in an experience dependent (ed) fashion that is tailored to specific ex periences of the subject, involving S -S* contingencies (Experience-driven (ed)-DBS to improve motor symptoms in the hemiparkinson rat model under grant number 15981). Towards a test of this hypothesis, we will a) integrate DBS with operant conditioning in which experiences can be completely controlled, and b) determine the value of ed DBS for the brain. In this thesis, we took initial steps towards achieving these aims. Specifically, we integrated the operant setup with DBS and tested the viability of our methods with two rats, one hemiparkinson rat and one control. In this thesis work, we report data which show support for the success of our behavioral training procedures, surgical approach, and integration of a conditioned inhibition procedure with ed-DBS. NOTE Keywords : Variable Interval Schedule, Discrimination Learning, Hemiparkinson Rat, 6-Hydroxydopamine, Apomorphine-Induced Rotation.Item Investigating the bacterial adhesion behaviour on bone surface mimicked chitosan membranes(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Uçak, Meltem.; Garipcan, Bora.; İyisan, Banu.An extremely serious post-op consequence of orthopedic replacement surgery is infection, which is currently challenging to treat with antibiotics. According to data, prosthesis infections correlate with biofilm formation that is highly resilient to host immune defenses and antibiotics. The main goal of this thesis is to examine the re lationship between topography and surface-cell and surface-bacteria interactions. The secondary objective is to determine whether it is possible to chemically alter potential implant surfaces and their topographical features to maximize cell-implant interactions while minimizing bacterial-implant interactions. Physicochemical characterization for Graphene Oxide (GO) coated bone surface mimicked Chitosan (BSM-CH-GOc) loaded Ampicillin sodium salt (Amp) or Tetracycline hydrochloride (Tetra) membranes were done via degradation test, Scanning Electron Microscopy (SEM) and drug release study. For cell study, mouse fibroblast (L929) was selected as a model mammalian cell line. Bacterial behavior on these membranes was investigated using the biofilm growth test. The rate of biofilm production was assessed and utilized as an indication in which Es cherichia Coli (ATCC 8739) and Staphylococcus aureus (ATCC 6538) were utilized as model organisms. It was found that while GO coated bone surface mimicked chitosan membranes had a noticeable effect on preventing bacterial biofilm formation, the pres ence of ampicillin sodium salt and tetracycline hydrochloride remarkably reduced the biofilm formation compared to the control groups. NOTE Keywords : Surface-cell interactions, Surface-bacteria interactions, Chitosan, Ampi cillin, Tetracycline.Item Effects of hamstring lengthening surgery on muscle-tendon velocities of patients with cerebral palsy(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2022., 2022) Turan, Fatma.; Yücesoy, Can A.Cerebral Palsy (CP) is a permanent movement disorder seen in early child hood, consisting of muscle spasticity and/or contracture, and difficulty in walking due to poor selective control. In CP patients, crouch gait with excessive knee flexion is usually corrected by hamstring lengthening surgery, which is believed to improve gait, by increasing the length or velocity of the spastic muscle. However, hamstring mus cles that may not be not short and slow before the surgery can also be operated on. The thesis aims to assess whether the gait of CP patients improved after the surgery by testing the following hypotheses: (i) knee joint movement does not improve post surgery, (ii) the hip joint movement was impaired pre -surgery, (iii) the gait deviation index (GDI) increases post- surgery, (iv) the muscle lenghtening velocity remains un changed in postsurgery, and (v) the pre-surgery psoas lenghtening velocity is slower than post-surgery. 8 limbs of 4 CP patients who had undergone hamstring lengthening surgery were included in the study. Pre-and post-surgery muscle lengthening veloc ity changes of patients were compared with reference to age-matched TD children (14 limbs of 7 participants) based on gait analysis data and using musculoskeletal modeling (OpenSim). Our results showed that post-surgery, mean knee angular velocity did not change significantly. No significant effect of surgery was shown in hip angular velocity or GDI. Moreover, no significant changes were shown in hamstring muscle lenghtening velocities. Only two of the preoperative patients had slow psoas muscle lenghtening ve locity. As a result, post-surgery improvement in knee movement was achieved without a significant change in hamstring muscle lenghtening velocity. NOTE Keywords : Muscle Shortness, Cerebral Palsy, Contracture, OpenSim, Hamstring Lengthening Surgery, Spasticity, Psoas, Lengthening Velocity.Item Evaluation of local oxygen consumption in human flexor digitorum suoerficialis muscle by near infrared spectroscopy(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2007., 2007.) Erdoğan, Sinem Burcu.; Akın, Ata.A strong relationship between mechanical and physiological conditions of skele- tal muscle determines the force generated by that muscle. The aim of this study was to evaluate the relationship between local oxygen consumption and local force produced during isometric contractions at varying biomechanical conditions. Another aim of the study was to investigate the e ect of relative position and absolute length changes on local energy consumption of exor digitorum super cialis (FDS) muscle during isomet- ric contractions performed at various muscle length and force levels. Nine healthy male subjects performed sustained isometric handgrip exercise by continuously pressing on a hand dynamometer. The handgrip exercise was performed while the wrist is (i) maximally exed, (ii) maximally extended and (iii) in neutral position. Local oxygen consumption (mVO2) and time course of recovery (trec) of FDS muscle were measured by functional near infrared spectroscopy (fNIRS). mVO2 and trec were linearly related with force level up to 40% of maximal voluntary contraction force (MVC) at all wrist positions (p<0.05). At each force level, mVO2 was observed to be lowest when the wrist was maximally extended (p=0.0004). Both parameters presented a decrease as the wrist was extended. The results imply that local energy consumption has a dependence on muscle relative position and length. It is suggested that myotendinious force transmission between a muscle and its surrounding structures might be a determinant of local of energy consumption.|Keywords: Near infrared spectroscopy, local oxygen consumption, isometric handgrip exercise.Item The effect of methylphenidate on brain hemodynamics of attention-deficit/hyperactivity disorder measured by functional near infrared spectroscopy(Thesis (M.S.)-Bogazici University. Institute of Biomedical Engineering, 2007., 2007.) Topaloğlu, Nermin.; Akın, Ata.Attention-deficit/hyperactivity disorder (ADHD) is a very common neurodevelopmental disorder. Approximately 30% 60% of individuals diagnosed with ADHD in youth have symptoms that persist into adulthood. This neurobehavioral disorder results in significant functional impairment. It decreases the life quality of the patients. Therefore, the need for recognition and treatment of patients with ADHD is necessary. Methylphenidate (MPH) is known to reduce hyperactivity in individuals with ADHD. Yet little is known about how it alters neural activity and how this relates to its clinical effects. Functional Near-Infrared Spectroscopy (fNIRS) is a portable, non-invasive brain imaging method measuring the changes in oxygenated hemoglobin [HbO2] and deoxyhemoglobin [HbH] levels particularly in prefrontal cortex. In this study, 15 adult, right handed cases with DSM-IV diagnosis of Attention deficit hyperactivity disorder (ADHD) were evaluated with fNIRS during a cognitive task which is Stroop test. The goal of this study is to examine MPH-induced hemodynamic changes during a cognitive activity, and to examine how these changes correlate with measures of behavioral response to the drug during Stroop task. It is found that MPH effectively decreased HbO levels. The reason of the decreased level of HbO after medication is vasoconstriction. MPH normalized the behavior during an executive function test. MPH has a great effect on the response time of the subjects to NS, CS, and IS. MPH always shortens the durations of the reaction times.|Keywords: Functional Near-Infrared Spectroscopy, Attention-Deficit/Hyperactivity Disorder (ADHD), Methylphenidate, Stroop task, adult.