Biyomedikal Anabilim Dalı

Gözü bağlı ve doğuştan görmeyen deneklerde dokunsal zihinde döndürme

Mental rotation is the process of imagining an object rotated into a different orientation in space. This well-known visual phenomenon may be used to understand the cognitive processing by applying it to the tactile modality. Linear correlation between response times and angular orientations of the explored objects shows the mental rotation effect.Twelve sighted, 12 congenitally blind subjects participated in this study. All subjects were right handed. Gender and age were balanced. The sighted were blindfolded through the experiments. Two tactile L-shaped objects were glued on cardboards as pairs rotated at ve orientations (0°, 45°, 90°, 135°, 180°). A passive touch method was developed, subjects' hands were steady on a platform and objects were placed andlifted with a lever. Subjects used their palms to passively touch the objects. The subjects were instructed to explore the objects tactually and decide if the pairs weresame or different, different meaning mirror as known to the experimenter. Response times and accuracies were recorded. Correlation analysis and ANOVA were performed using Matlab. Results showed that both the blindfolded and congenitally blind subjects used mental rotation process during tactile exploration of the stimuli.The results support the idea that an analog representation is used in the cortex which totally lacked visual input. The data presented in this study, combined with the literature further supports the hypothesis that spatial properties of the objects are encoded similarly for touch and vision.

Kemik yüzeyi taklit biyobozunur polimerik doku iskeleleri

Öz-hareketin paçini kanalında mutlak ve maskeli algılama eşiklerine etkisi

Bu tezde, ki³i periyodik olarak hareket ederken Paçini kanal n n mutlak ve maskeli e³ik de§erlerini ölçerek aktif dokunma duyusunu olu³turmaya çal ³t k. Önceki ara³t rmalardan yola ç karak mutlak e³ik de§erlerinin dü³mesini ve maskeleme etkinli §inin artmas n s nad k. Deneklerin sol orta parmak uçlar yar çap 0.685 cm olan bir aluminyum kontak ucuyla mekanik olarak uyar lm ³t r. Psiko ziksel e³ik de§erlerinin ölçümü üç ayr durumda tekrarlanm ³t r: statik durum, yava³ hareket (0.1-0.2 m/s), h zl hareket (0.5-0.6 ms/s). Hareketli durumdaki (yava³: -20.8 dB; h zl : -21.8 dB) e³ik seviyeleri pasif (-17.9 dB) duruma k yasla daha dü³ük ç km ³t r. E³li t testleri hareketli e³ik de§erlerinin pasif durumdan istatistiksel olarak farkl oldu§unu göstermi ³tir (pasif ve yava³: p=0.023, pasif ve h zl : p=0.024). Ayr ca maskeyle olu³an e³ik yükselmesi hareketle artm ³t r (pasif: 2.9 dB, yava³: 7.9 dB, h zl : 9.2 dB). Pasif durum ve hareketli durumlar aras ndaki maskeleme etkisi istatistiksel olarak anlaml ç km ³t r. Bu sonuçlara göre öz-hareketin Paçini kanal ndan kaynaklanan dokunma duyusunu iyile ³tirdi§i söylenebilir ancak h z n pek etkisi olmad § görülmü³tür. Maskeleme etkisi hareketle artm ³t r. Bu da duyudaki iyile³menin hem e³ik seviyesinde hem de e³ik üstünde olabildi§ini göstermektedir fakat öz-hareket s ras nda hem proprioseptif hem de motor sinyaller olu³tu§u için bu iyile³menin tam kayna§ ³u an bilinmemektedir. Anahtar Sözcükler: Psiko zik, bedensel duyu, titre³imsel uyar , Paçini, insan, aktif dokunma.

Predictability of cognitive performance based on functional neuroimaging via FNIRS

In neuropsychology many tasks have been used to determine the cognitive ability and/or flexibility of individuals to have any prior knowledge about the psychological condition or to state the level of neuropshcological disease of a person. This study presents the relations between behavioral performances and neuronal activation within and between two cognitive tasks; Tower of London (TOL) and color-word matching Stroop test which are utilize to obtain cognitive flexibility on decision making, attention and planning. Functional Near Infrared Spectroscopy method is used as functional neuroimaging tool. fNIRS results revealed that activations for both tasks mainly located in both left and right lateral side of prefrontal cortex. Behavioral outcomes such as reaction times of interference effect of stroop task and total planning time of TOL tasks were compared with neuroimaging findings. Right superior lateral prefrontal cortex (RSLPFC) activity during incongruent-neutral interferance showed positive correlation with difference of mean response times for correct answered incongruent and congruent trials. In addition we also observed negative corelation with activation of 7-move TOL task and reaction time in left and right lateral prefrontal cortex. At last, it has been presented that subjects have negative brain response(NBR) which is related with good performance (according to results of correlation analysis) during stroop task showed relatively positive brain response (PBR) during TOL task which indicates also good performance, whereas, lateral activation during TOL task is reduced for subjects have PBR in stroop task which can be stated as bad performance

Amino acid conjugated self assembly molecules modified Si wafers

In this thesis, Si wafer surface was modified with newly synthesized self-assembled monolayers to mimic a biocompatible micro-environment for the cells and to observe their behavior. Begin with; Si wafer is chosen as its availability is easy and well-established structures can be obtained in the surface modification without any interference. In the first step, Si wafers were cleaned and modification of surfaces was carried out with amino acid conjugated self-assembled molecules [Histidine-Self Assembled Molecule (His-SAM), and Leucine-Self Assembled Molecule (Leu-SAM)], (3-aminopropyl)triethoxysilane (APTES) and also poly-L-ornithine (PLO). The characterization of these samples were analyzed with contact angle measurements, X-Ray Photoelectron Spectroscopy (XPS), Atomic Force Microscopy (AFM), and ellipsometry. After characterization results were acquired, the cell culture studies were performed with L929 cells. In order to obtain information about cell proliferation, MTT assay (a colorimetric assay) was performed. According to these results, enhanced cell proliferation was achieved by the contribution of surface functional groups. Consequently, it has been observed that these controlled molecular structures on the surfaces of materials have a great potential for biomedical applications.

Functional connectivity network analysis of alzheimer and mild cognitive impairment patients

In our era, while the life span is expanding, neurodegenerative diseases, such as Alzheimer's disease (AD), pose a great threat upon the quality of life. In such a case, the best course of action would be to detect, modify or treat the pathologies before they become too severe. Since the main cause of AD is still unknown, further studies for possible biomarkers are needed. Therefore, in this study, the objective is to find a distinctive agent for AD and mild cognitive impairment (MCI) from an optimized auditory oddball task fMRI data via functional connectivity analysis. In order to achieve that, a group ICA approach using temporal concatenation of the subject data is adopted. Since, there are no studies investigating functional connectivity of AD and MCI during an oddball task, especially via group ICA, this study can enrich the literature. As the results are concerned, in group comparisons, no significant differences are found in spatial maps. On the other hand, there are promising findings in temporal course analysis of the components such as the multiple regression outcomes. Therefore, our next aim will be to perform a longutidinal study including both resting state and task related data for finding a better biomarker.

Investigation of the effects of FMOC amino acids modifications to osteoblast behaviour on RGO/Ti surface

In this thesis, adhesion, proliferation and morphology of osteoblast cells on functionalized RGO/Ti surface were investigated. Firstly, amino-functionalization with 3-aminopropyl phosphonic acid (APA) molecules on Ti surface was carried out. Graphene oxide flakes were immobilized on APA/Ti surfaces through interaction between the epoxy groups of GO and the amine groups of APA molecules. Reduced graphene oxide flakes on APA/Ti surface were performed by using hydrazine monohydrate treatment. In order to enhance further surface bioactivity, Fmoc amino acids having different the hydropathy indexes modified on RGO/Ti surface by the π-π bond. The chemistry and morphology of unmodified and modified Ti surfaces were characterized by using Water Contact Angle (WCA) measurements, X-ray Photoelectron Spectroscopy (XPS), Raman Spectroscopy, Atomic Force Microscopy (AFM) and Scanning Electron Microscopy (SEM). According to characterization results, Ti surfaces were coated with GO and RGO, as well as the surface hydrophilicity was controlled by functionalization with Fmoc amino acids successfully. Then, cell viability, proliferation and morphology were examined by using the MTT, Alamar Blue Assays and SEM, respectively. The in vitro studies indicated that the surface chemistry and nanometric roughnesses on designed materials remarkably enhanced cell behavior, especially with respect to initial adhesion and proliferation. Consequently, the development of novel interface at cell/implant has a great potential for increasing osseointegration in the field of bone tissue engineering.

Bone surface microenviroment mimicked biodegredable scaffolds for osteogenic stem cell differentiation

The change of the surface roughness, topography and stiffness as well as the chemical and/or biochemical components of the surfaces; might affect the cell-surface, cell-scaffold interface characteristics and may influence cellular behavior, which are important to investigate new bioprosthesis for tissue engineering applications. Thereby, in this thesis, mimicking bone surface microenvironment was aimed. Firstly, to produce a mould, bovine femur surface was mimicked by using Polydimethylsiloxane (PDMS). A biodegradable polymer, Poly (L-Lactic acid) was poured on the mould to obtain bone surface mimicked (BSM) scaffolds. Then, Bone Morphogenic Protein-2(BMP-2) was loaded on the scaffolds and its release profile was examined in-vitro conditions with Enzyme-Linked ImmunoSorbent Assay (ELISA). BSM scaffolds was modified either with hydroxyapatite (HA) or collagen type-I (Col-I) to construct these scaffolds, similar to the bone's natural micro- environment. Modified scaffolds were charac- terized with Water Contact Angle (WCA) measurements, Scanning Electron Micro- scope (SEM), X-Ray Photoelectron Spectroscopy (XPS), X-Ray Diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FTIR). Characterization studies were followed by cell culture studies. To analyze cell viability on the scaffolds, MTT was performed. To examine cell proliferation on the scaffolds, Alamar Blue was performed. The effect of the modifications on the controlled and directed osteogenic differentiation in in-vitro conditions was evaluated by using Alkaline Phosphatase Activity analysis, Alizarin Red and SEM EDAX tests.

Production and characterisation of poly(L-lactic acid)/graphene oxide nanofibers for nerve regeneration

The development of biodegradable polymeric nanofiber scaffolds for a potential effort to repair injured nerve cells attracts great interest in nerve tissue engineering field. Poly (L-lactic acid) (PLLA) has being widely used in development of nerve fiber studies due to its biocompatibility, easily shaped properties and degradation to low toxic lactic acid. However, its hydrophobicity and lack of binding sites for cel- lular activities restricts its use as implants. In this regard, this study involves the incorporation of Graphene Oxide (GO) into PLLA either electrospun GO with PLLA or coating GO onto the PLLA and PLLA/GO nanofibers to fabricate ideal scaffolds with appropriate physical, mechanical and chemical properties of nanofiber mimicking the properties of the peripheral nerve. Hence, PLLA and PLLA/GO nanofibers were prepared via processing PLLA and PLLA/GO solutions with electrospinning and so- lution parameters (the concentration of PLLA, GO ratio and composition of binary system) were optimized to obtain thin and bead free nanofibers. Then, the fabri- cated nanofibers were functionalized with 1,6-Hexamethylenediamine (HMDA) and then coated with GO sheets. The fabricated PLLA, PLLA/GO and GO coated PLLA and PLLA/GO nanofibers were characterized via Light Microscopy, Scanning Elec- tron Microscopy (SEM), Raman Spectroscopy, Ninhydrin assay, X-Ray Photoelectron Spectroscopy (XPS), tensile test and Water Contact Angle (WCA) measurement. The characterization results revealed that addition of GO either as filler or coating material enhanced physical, mechanical and chemical properties of nanofiber scaffold. In conclusion, the developed nanofiber scaffolds are promising for possible nerve regeneration application.

Laser biostimulation and monitorization of wound healing by means of bioimpedance measurements

Wound healing is critically important for the quality of life. Substantial number of patients suffering from non-healing chronic wounds and having serious difficulties in their daily life are reported in wound healing studies. However the exact mechanism of healing is not fully understood yet. Scientists have been investigating modalities for stimulating the wound healing process. Laser photobiomodulation has become widespread supporting the idea of therapeutic effects of laser irradiation in biological tissues recently. Conventional methods for following the healing generally lack of objectiveness and repeatability. Thus, a new non-invasive, repeatable and cost effective method was needed. The aim of this study was to investigate the laser photobiomodulation on wound healing and monitor the healing process in-vivo by means of multi-frequency electrical bioimpedance measurements. Photobiomodulated in-vitro cell proliferation examinations were followed by in-vivo experiments on cutaneous skin wounds. Changes in the electrical properties of the wounds were examined with multi-frequency electrical impedance measurements on predetermined days of healing. Morphological, histological and mechanical examinations were used to find out the relationship between electrical properties of tissues and cellular events occurring during the healing process. Our findings showed the biostimulating effects of laser irradiation both in-vitro and in-vivo. The electrical impedance measurement results supported the idea of laser biostimulation on healing of cutaneous skin wounds. It is also shown that electrical bioimpedance measurements may be considered as a supporting non-invasive method for monitoring the healing process of skin wounds.

Virtual reality-based advanced life support serious game

This thesis investigates the development and learning outcome of an immersive virtual reality (VR) serious game designed to improve the training of medical professionals in Advanced Life Support (ALS) procedures. More than a million healthcare professionals partake in ALS training each year. This high demand for highly skilled healthcare providers proficient in time-sensitive emergency interventions necessitates innovative approaches to training. The software developed for this thesis aims to facilitate this training process while paying proper attention to non-technical aspects of ALS that are generally overlooked by similar training serious games. This serious game is developed in Unity game engine using C# for Unity scripts and plug-ins. The scores of users are sent to a database using Experience Application Programming Interface (xAPI) calls and stored using a Learning Management System (LMS) and a Learning Record Store (LRS). There are two training modes and a final test mode that scores the user. An initial study was conducted on 29 participants to compare the efficiency of VR training and conventional training. One group trained in VR and the other trained in a classroom setting, before all participants took the same test. Another follow-up study was conducted on 12 participants to check the correlation of the scores form the VR test mode and a more conventional hands-on manikin simulation where all participants took both tests to see if their results were statistically similar. The findings show that VR training is non-inferior to conventional training for the most part and that VR test scores correlate with conventional test scores. These findings combined with the advantages of being a self-service training software indicate that this serious game can be utilized effectively as an additional training resource, and even shows potential to replace classroom training in the near future. Keywords: Advanced Life Support, Virtual Reality, Serious Game, Training Simulation.

Multi contrast mri based discriminants for neuro behcet syndrome subtypes

Daha sonra doldurulacaktir.Neuro–Behcet Syndrome (NBS) is extremely rare worldwide but has a higher prevalence in Türkiye, allowing meaningful cohort formation. The goal of this work is the characterization of white matter (WM) integrity by analyzing diffusion tensor imaging (DTI) metrics in NBS. Retrospective data from 14 patients and a control cohort of 38 healthy individuals were analyzed through WM segmentation in DTI data. The mean of DTI variables in WM of both groups were compared with Mann–Whitney U Test. λ2 and apparent diffusion coefficient (ADC) showed the highest statistical significant differences between the NBS and control cohorts. These indicate potentially that in addition to damage along the axons, the WM integrity is more significantly compromised in the axons transversally. Accordingly, WM DTI characterization in this study might be considered as the first step for investigating differentiating quantitative MR biomarkers for this family of neurological pathologies. Machine Learning (ML) results indicate that combining multiple diffusion metrics yields superior classification accuracy in distinguishing NBS patients from healthy controls compared to using individual variables alone. In particular ADC, even when paired with less discriminative variables, exhibited outstanding classification performance. The highest classification performance, achieving 100% accuracy, was obtained with λ3 and ADC. Notably, these results were achieved with a lower number of components, indicating that these DTI variables provide highly discriminative power with minimal feature complexity. This thesis establishes a foundation for future work aimed at enhancing classification accuracy through larger cohorts, inclusion of NBS subtypes, and personalized ML based on individual diffusion profiles. Keywords: Neuro–Behcet Syndrome, White Matter Integrity, Diffusion Tensor Imaging, Biomarker, Machine Learning, Classification.

Cough sound analysis and classification

The main objective of this study is to develop a classification system that analyzes cough sounds and distinguishes non-productive (dry) and productive (wet) cough types and cough sounds from non-cough sounds such as breath, voice, and snoring. The study extracted the features of cough sounds in time and frequency domains and considered their effects on classification performance. Autoregressive (AR) coefficients were used in the time domain, and Mel-Frequency Cepstral Coefficients (MFCC) and percentage frequency values representing energy distribution (25th, 50th, 75th, 90th) were used in the frequency domain. The Linear Discriminant Analysis (LDA) method was applied to reduce the feature space size and improve the classification performance. In the optimized low-dimensional feature space obtained with LDA, Support Vector Machines (SVM), Random Forest, k-Nearest Neighbors (k-NN), and Decision Tree algorithms from Machine Learning techniques were tested. The study used cough, breath, and speech sounds obtained from the COVID-19 audio database created by Cambridge University. In addition, snoring sounds were obtained from Google's Audio Set database. The performance of the classifiers was measured using the Leave-One-Out Cross-Validation (LOOCV) approach and evaluated with accuracy, sensitivity, specificity, and F1 scores. The results reveal the importance of MFCC, AR coefficients, and energy percentage frequencies in analyzing cough sounds. The results of this thesis study aim to contribute to non-invasive and mobile systems developed for diagnosing respiratory diseases by analyzing cough sounds.

Comparison of open source tumor growth simulation software and multiscale tumor modelling

Cancer is a complex disease that is comprised of many different cellular and tissue level organizations. Tumor growth simulation is vital in predicting the way tumors grow. Tumor modelling is used to shed light on cancer biology and is considered a promising method for developing more effective cancer therapies. In this study, the biological inputs and their respective outputs using the simulation approaches were systematically reviewed. A comparison table was produced that shows in detail the biological inputs for each simulation code. This is in contrast to the current agentbased model reviews that mostly focus on computer efficiency. Physicell was selected among the reviewed open-source software due to its integrated basic cell functions and microenvironment simulation capabilities. Tumor growth has been simulated in the Physicell v1.6.1 tumor simulation software. The A549 cell specific parameters have been used during the simulation and the effects of the initial oxygen concentration in the microenvironment were examined on outcome images. Growth rate of tumor cells increases with the increasing oxygen concentration in the microenvironment. Formation rate of necrotic core in the tumor structure reduces with the increasing oxygen concentration due to small number of hypoxic cells in the tumor structure. Based on our findings in the simulation, physicians can predict the hypoxic regions in tumor structure to plan a chemotherapy treatment dependent localized peripheral tissue considering the correlation between oxygen concentration and tumor growth rate.

Kalp ritmi bozukluklarının derin öğrenme ile otomatik tespiti

Bu tez çalışmasında, kalp ile ilgili anormallikler üzerine yapay zeka çalışması yapılmıştır. Kişilerin kaliteli bir yaşam sürdürebilmesi için kalp hastalıkları ve türlerinin erken teşhis edilmesi ve hastalığının derecesinin belirlenmesi tedavide kolaylık sağlaması için önemli bir rol oynamaktadır. Bu çalışmada kalp ritmi bozukluklarından atriyal fibrilasyon, ventriküler aritmi, ventriküler taşikardi, ventriküler fibrilasyon ritim bozuklukları ele alınmıştır. Ayrıca kalp hastalıkların tanı ve tedavisinde EKG vurularından çeşitli hastalıklar hakkında ön bilgi içermektedir. Modelleme aşamasında ResNet50, EfficientNetB0, MobileNetV3Large, Deit Base, Swin Tiny ve Beit Base gibi farklı modeller kullanılarak Miyokard Enfarktüsü (MI) ille ilgili komplikasyonların otomatik tanısına yönelik makine öğrenmesi ve derin öğrenme araştırmalarını desteklemektedir. Elde edilen sonuçlara göre Beit Base tüm değerlendirme ölçütlerinde en yüksek başarıya ulaşarak %98.39 doğruluk ve %1.61 hata oranı vermiştir. F1 skoru ile veri seti üzerinden en iyi sonucu veren modeldir. Ayrıca hassasiyet yönünden Swin Tiny doğruluk açısından Beit modeli aynı değerde olsa da doğruluk açısından düşük sonuçlar vermiştir. Diğer modellere bakıldığında ResNet50 MobileNetV3Large ve EficientNetB0 sırasıyla daha düşük performans göstermişlerdir. ResNet50 modeli %96.77 ile doğruluk ile öne çıkmıştır. MobileNetV3Large %95.16 ve EfficientNetB0 %94.09 düşük doğruluk değerlerini göstererek en düşük başarıyı ulaşmıştır. Sonuç olarak farklı dönüştürücü mimarilerinin EKG görüntülerinden MI ve ilgili komplikasyonları ayırt etmede üstün başarı sunmuştur. Bu modellerden Beit ve Swin Tiny yüksek doğruluk bir çözüm sunmaktadır. Bu tez çalışması derin öğrenme tabanlı teşhis sistemlerinin klinik karar destek sistemi olarak kullanılabileceğini ve hızlı uygulanabilir alternatifler sunabileceğini göstermektedir.

Investigation of protein corona formation on biodegradable nanocarriers

Biodegradable nanocarrier systems are significant tools for drug delivery systems 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 injected 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 structure 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 evaporation 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 electrophoresis. Furthermore, each protein in the HPC structure were identified by liquid chromatography-mass spectrometry (LC-MS) and grouped according to their functions. 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.

Investigation of the antibacterial and antibiofilm activity of Hypericum perforatum L. extract on bacteria isolated from used cosmetic tools

Cosmetic products provide an ideal environment for pathogenic microbes, while using shared cosmetic tools elevates the risk of microbial cross-contamination, leading to various infections. This research investigates the antibacterial and antibiofilm potential of Hypericum perforatum L. extract against bacteria isolated from cosmetic tools commonly used in Turkey. In this study, 40 cosmetic tools in total (foundation sponges, blush brushes, eyeshadow brushes, and lipstick brushes) obtained from various beauty salons located in Istanbul were analyzed. For bacterial identification, samples were inoculated onto selective media, including MacConkey, Eosin Methylene Blue, Mannitol Salt, and blood agar. Antibiotic tolerance microbial profiles were established by applying the Kirby-Bauer disk diffusion technique against CTX (30 µg), GM (10 µg), SP (10 µg), CIP (5 µg), Augmentin (20/10 µg), TE (30 µg), AK (30 µg), CFZ (15 µg), and KF (30 µg). Additionally, the multiple antibiotic resistance index (MARI) was calculated to assess antibiotic insensitivity. Bacterial biofilm activity was determined using the crystal violet staining method. Bacterial growth was detected in 31 out of a total of 40 cosmetic tools (77.5%). The isolated bacteria were identified as 32.25% Gram-positive cocci, 22.59% Gram-negative bacilli, and 45.16% Gram-positive bacilli. 25.80% of the bacteria grew on oxacillin-supplemented MSA medium, confirming them as methicillin-resistant Staphylococcus aureus (MRSA). Additionally, 70.97% of bacteria showed alpha hemolysis activity on blood agar. The maximum resistance against antibiotics was detected against CTX (30) at 41.93%, whereas bacteria were found to be susceptible to CIP (5), TE (30), AK (30), and CN (10). Pharmaceutical-grade H. perforatum L. extract exhibited 51.61% antibacterial and 60.23% antibiofilm activity, while the extract obtained from the local market showed 35.48% antibacterial and 87.55% antibiofilm activity. This investigation highlights the effects against bacterial growth and biofilm formation properties of H. perforatum L. extract, suggesting its potential use as an alternative for preventing infections associated with cosmetic tools.]

Tıkayıcı uyku apnesinin konuşma sinyallerinin doğrusal olmayan analizleri ile tespit edilmesi

Tıkayıcı Uyku Apnesi (TUA) en sık görülen uyku bozukluklarından biridir. TUA Altın Standart Tanı Yöntemi Polisomnografidir. TUA tanısı, bir gece uykusu boyunca çok sayıda fizyolojik parametrenin kaydı ve bu kayıtların skorlanması sonucunda konulabilmektedir. Uygulanması sırasında karşılaşılan zorluklar ve maliyetinin yüksek olması nedeniyle, son yıllarda TUA tespitinde Polisomnografinin yerine basitleştirilmiş yaklaşımların geliştirilmesine yönelik çalışmalar önem kazanmıştır. Hastaların evlerinde kendi başlarına kaydedebilecekleri fizyolojik parametrelerin ve TUA belirteçlerinden biri olan horlama seslerinin değerlendirilmesini içeren çalışmalar, apne tespitinde belli oranda başarı göstermişlerdir. Ancak bu yöntemlerde gece boyunca kayıt yapılması dezavantajı ortadan kaldırılamamıştır. Son yıllarda, solunum ve ses yolunun ortak olmasını dikkate alan çalışmalarda, hastalar uyanıkken kaydedilen birkaç dakikalık ünlü harfleri içeren konuşma seslerinin klasik ses analizleriyle değerlendirilmesi yaklaşımıyla TUA tespitine odaklanılmıştır. Bu çalışmada, literatürdeki çalışmalardan farklı olarak, TUA hastalarında uyku sırasında sarkarak solunum yolunu tıkayan kaslar (art damak, yumuşak damak, küçük dil veya dil kökü) tarafından üretilen ünsüz sesler kullanılarak yüksek doğrulukla TUA tespiti yapmak amaçlanmıştır. Çalışmada, 20 TUA hastası ve 20 sağlıklı denekten alınan; {/ca/, /ci/, /cı/, /cu/, /ga/, /gi/, /gı/, /gu/, /ha/, /hi/, /hı/, /hu/, /ka/, /ki/, /kı/, /ku/, /na/, /ni/, /nı/, /nu/, /sa/, /si/, /sı/, /su/} ünsüz ve {/a/, /i/, /ı/, /u/} ünlü seslerin doğrusal olmayan doğasını ortaya koyan özellikleri hesaplanmış ve bunların TUA tespit başarımları, K En Yakın Komşu (K-EYK) ve Destek Vektör Makineleri (DVM) sınıflayıcılarıyla değerlendirilmiştir. Öncelikle doğrusal olmayan özelliklerle sadece ünlü, sadece ünsüz ve tüm sesler için sınıflama yapılmıştır. Ardından, doğrusal olmayan özelliklere klasik ses analizlerinde kullanılan bazı özellikler eklenerek, yapılan sınıflama işlemleri tekrarlanmıştır. Doğrusal olmayan özelliklerle elde edilen TUA tespit doğrulukları; ünlü, ünsüz ve tüm sesler için sırasıyla, K-EYK ile %97,5, %97,5 ve %100; DVM sınıflayıcısıyla %95, %97,5 ve %96,25 olmuştur. Hem doğrusal olmayan hem de klasik ses analizine ait özelliklerin birlikte kullanıldığı sınıflamalarda ise K-EYK sınıflama doğruluğu sadece ünlü seslerde artarak %100'e ulaşmış, diğer gruplarda neredeyse değişiklik olmamıştır. Bu uygulamadaki DVM doğrulukları ise ünlüler ve tüm sesler için bir miktar artarken (%98,75), ünsüz seslerde (%97,5) değişmemiştir. Bu sonuçlar, ünsüz sesler için doğrusal olmayan özelliklerin ayırt edici olduğunu göstermektedir. Elde edilen sonuçlar, doğrusal olmayan özelliklerin hem ünsüz hem de ünlü sesler için, klasik ses analizleri ile literatürde elde edilenlerden çok daha yüksek TUA tespit başarımı sağladığını göstermektedir. Sonuç olarak bu tez çalışmasında, TUA hastası kişilerden alınacak birkaç dakikalık ses kaydı ve doğrusal olmayan analizlerle daha önce klasik ses analizlerini kullanarak TUA tespiti yapan çalışmaların ulaştığı başarım değerlerinin oldukça üzerinde değerlere ulaşılmıştır. Çalışmada önerilen sistemin, başarılı TUA ön tanısı yapılabileceği öngörülmektedir.

Manyetit (Fe3O4) manyetik nanomalzemelerin boyut değişiminin çalışma koşullarına bağlı incelenmesi

Manyetik nanomalzemelerin (MNP) biyomedikal uygulamaları 30 yıldan fazla bir süredir araştırılmaktadır. MNP'ler tıpta; ilaç hedefleme sistemleri, hipertermi, biyosensör, manyetik hücre ayırma ve manyetik rezonans görüntülemede (MRG) kontrast ajanları gibi birçok alanda kullanılmaktadır. Özellikle vücut içi MNP kullanımında manyetik malzemelerin küçük boyutlu olması istenmektedir. Bu malzemelere kaplama yapıldığında ya da ilaç bağlandığında boyutu artmaktadır. MNP ne kadar küçük boyutta üretilirse kaplama sonrası vücut içi kullanım olasılığı o kadar artmaktadır. Bu çalışma MNP'lerin boyut değişiminin çalışma koşullarına bağlı değişimini incelemek amacıyla yapılmıştır. Birlikte çökelme yöntemi ile elde edilecek manyetik nanomalzemelerin pH, sıcaklık, karıştırma hızı ve kullanılan bazın türü gibi koşullar değiştirilerek boyut değişimi izlenmiştir. Ayrıca bu boyut değişimleri manyetik nanomalzemelerin termal özelliklerini, mekanik özelliklerini, optik özelliklerini elektrik özelliklerini ve manyetik özelliklerini değiştirecektir. Yeni özellikler yeni uygulama alanları doğuracaktır. Bu değişimler sayesinde hangi koşullarda en iyi özelliklere sahip olan ve en küçük boyutta manyetik nanomalzemenin oluştuğu tespit edilmiştir. Farklı çalışma koşulları kullanılarak elde edilen örneklerin karakterizasyon testlerinde; XRD ile sentezlenen MNP'lerin manyetit (Fe3O4) olup olmadığı kontrol edilmiştir. FESEM, demir oksit çekirdeğinin morfolojisini gözlemlemeye ve gerçek çapını tahmin etmeye izin verir. SEM analizinde MNP' lerin küresel yapıda olup olmadıkları ve MNP çekirdeklerin çapları dolayısıyla boyutları ölçülmüştür. MNP' lerin ön boyut incelenmesi dispersiyon durumundaki nanoparçacıkların hidrodinamik çapını ölçen dinamik ışık saçılımı (DLS) ile karakterize edilmiştir. VSM analizinde oda sıcaklığında elde edilen manyetizasyonun, manyetik alanla değişimine bakılarak MNP' lerin manyetik davranışları belirlenmiştir. Tanecikler arasındaki itme ve çekme değerine etkisi olan yüzey yükü zeta (ζ) potansiyel analizi ile karakterize edilmiştir.

Farklı katyonlarla çapraz bağlanmış aljinat boncuklarının şişme özelliklerinin karşılaştırılması

Polymers are widely employed in many different applications, they are difficult to recycle and generally are not biodegradable. Scientific interest in creating biodegradable and biocompatible polymers has increased, especially for use in biology and medicine, because they come from natural sources, also they are non-toxic and environmentally benign, so we can make hydrogel from them. Superabsorbent polymers can be made by improving the characteristics of hydrogels, which are three-dimensional cross-linked structures with exceptional water retention. It plays important role in nutrients, medical, tissue engineering and protection of the environment, naturally occurring polysaccharide that is derived from brown algae and bacteria. It is essential in biological uses like wound healing, medication delivery and tissue regeneration because it has special qualities like gelling, moisture retention and film-forming capacity. Aqueous alginate solutions are preferred due to the biocompatibility and flexibility in crosslinking. Also, their mechanical strength, permeability and functional properties through the incorporation of organic and inorganic materials or the application of diverse crosslinking strategies. They combined with synthetic polymers demonstrate enhanced mechanical strength and healing properties, facilitating increased tissue regeneration and regulated drug release. Even with specific disadvantages like lower carrying ability, novel developments in alginate compounds are expanding their uses, especially in the fields of renewable material development and wound healing. Alginate beads have been cross-linked using different cations, including calcium, which has strong antibacterial properties. Beads may affect the wound healing purposes and are increased by presence of certain particles, which have the ability to regulate or making small changes, typically, so as to improve it or take it less excessive to the immune system response and antibacterial properties. Flexible framework for creating biologically compatible substances have built-in antibacterial characteristics appropriate for a range of biomedical applications were provided using cation cross-linked alginate materials. In this study, 2% alginate solution was used for crosslinking with different cations to produce beads, these beads were applied by swelling test in different solution. And by comparing their antibacterial properties, the current study aims to figure out if the cation selection influences the antibacterial property of the beads and how they inhibit bacterial growth.

Aljinat-argil kompozitlerinde knisel bir kaplama yöntemiyle hazırlanan riboflavinin kontrollü salımı

Riboflavin is important for energy production and metabolic mechanisms and is considered an essential element. Alginate and montmorillonite are natural materials used as bio-based carriers due to their inherent properties. biocompatibility, and the ability to release active ingredients from the formulation in a controlled release. This study aimed to develop a controlled-release system for riboflavin using an encapsulation method using sodium alginate, which has high gelling properties, and montmorillonite (MMT), in the presence of carboxymethylcellulose (CMC), bound to calcium ions. The goal was to improve stability and bioavailability through a sustainable and biocompatible system. The release kinetic and encapsulation efficiency of beads were examined in simulated gastrointestinal media. The results. show that hydrogel matrix encapsulation of riboflavin ensures a sustained release rate and good pH protection, following zero-order kinetics. The formula in this study has a significant potential for applications in the pharmaceutical and food industries, as well as high-efficiency packaging solutions.

Schizochytrium sp.'den ekstrakte edilen lipitlerin antimikrobiyal ve anti-biyofilm aktiviteleri. S31 mikroalgi

Biotechnology has been developing tools and procedures for the benefit of living things for many years. In most of these studies, the production of essential metabolic compounds is prioritized for human health. One of the crucial substances for human health that has gained popularity recently is omega-3 fatty acids. Alternative sources of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been searched since fish oils, the main commercial sources of omega-3 fatty acids, have heavy metal content, especially mercury, limited availability, and an unpleasant odor. Schizochytrium sp. S31 is a microalga with a high concentration of polyunsaturated fatty acids, particularly DHA. Because of its high DHA content and low heavy metal levels, heterotrophic cultivation of Schizochytrium sp. S31 provides an excellent opportunity to provide alternative omega-3 sources. It also contains a variety of bioactive substances that can be utilized as medicinal raw materials, food additives, animal feed, biodiesel and antimicrobial agents. In this study, optimum conditions were applied to cultivate Schizochytrium sp. S31 heterotrophically and the nutritional composition of the dry biomass were analysed. According to the results, 45% protein, 5% total fat and 37% carbohydrate were obtained. Downstream processes, including cell lysis and lipid extraction, were adjusted in order to increase overall lipid content of Schizochytrium sp. S31. Five distinct solvent mixtures—hexane, hexane/ethanol (2:1), ethanol, methanol, and hexane/methanol (2:1)—as well as two different cell lysis techniques —mortar and pestle and ultrasonication—were examined and compared. Based on the results of cell lysis and lipid extraction, ultrasonication of hexane /methanol (2:1) enhanced the total lipid yields to 34% with a transparent appearance. According to the GCMS analysis results, 10.4% DHA and 16.11% EPA fatty acids were obtained. Total Omega-3 Fatty Acids and Total Omega-3 + Omega-6 Fatty Acids ratio were calculated as 27.42% and 32.15% respectively. The antibacterial effects of Schizochytrium sp. S31 oil samples were also investigated on Gram-negative pathogens, Pseudomonas aeruginosa, Escherichia coli 35218 and Klebsiella pneumonia, which cause many different human infections, as well as the Gram-positive pathogen Streptococcus mutans. At the same time, their effects on biofilm formation in Pseudomonas aeruginosa, Escherichia coli 35218 bacteria were investigated. The Schizochytrium sp. S31 oil sample was found to have anti-pathogenic activity on pathogenic bacteria of Pseudomonas aeruginosa, Escherichia coli 35218, Klebsiella pneumonia and Streptococcus mutans. The surface adhesion ability and biofilm formation capability of P. aeruginosa and Escherichia coli 35218 strain, which are widely employed as model bacteria in biofilm research, were dramatically inhibited in the presence of a Schizochytrium sp. S31 oil sample.

Detection of chemometric markers in liver tissue using infrared spectroscopy

Among the leading contributors of fetal alcohol spectrum disorder (FASD) is perinatal alcohol usage, which is characterized by neurodevelopmental dysfunction and growth retardation. Studies have mostly examined how alcohol affects the tissues of the brain. The effects of alcohol usage during pregnancy on the fetal liver are yet unknown at the molecular level. The aim of the study is to determine spectroscopic biomarkers referring to the results of prenatal exposure to alcohol in the liver of newborn mice. There were three main groups of samples: Negative control group, gavage control group (positive control), and group with gavage + alcohol. which is treated between postnatal days (PD) 3 and 20 with 3.0 g/kg body weight of ethanol in a liter of artificially enhanced milk (.02 ml/g). In accordance with that, there were three different groups of samples, for these groups, these three different groups of samples were measured using FTIR spectra, and in statistical analysis, these spectral data were evaluated. In the classification of spectral data, three main regions were significant: Fingerprint region (800 to 1800 cm-1), lipid region (3000 to 2800 cm-1) and water region and O-H stretch region (3000 to 3600 cm-1). For normalization, a standard normal variate (SNV) normalization technique was evaluated after the baseline correction. For statistical analysis, principal component analysis (PCA) was evaluated using R statistical language with FactoMineR package. According to the results of this study, it can be proposed that FTIR is an effective tool for development of chemometric markers in liver tissue, especially for the observation of the consequences of consuming alcohol on female rats. Possible chemometric biomarkers detected in this study are related to the lipids and found as follows: 2960 cm-1, 2873 cm-1, 1454 cm-1 and 1398 cm-1. Further studies can reveal the levels of alcohol consumption and detection of other markers.

The development of fiber optic biosensor for the detection of protein aggregates

α-synuclein oligomers play a crucial role in the early diagnosis of Parkinson's disease (PD). In this study, a mercaptoundecanoic acid (MUA)-capped gold nanorod (GNR)-coated and chitosan (CH)-immobilized fiber optic probe has shown considerable sensitivity of its detection. The proposed U-shaped fiber optic biosensor based on localized surface plasmon resonance (LSPR) was applied to detect α-syn oligomer (OA) biomarker. By analyzing OA concentrations, the biosensor achieved a limit of detection of (LOD) 11 pM within the concentration range of 10-100 pM and the sensitivity value was found as 502.69 ∆λ/RIU. Upon analysis of the CV% (coefficient of variation) and accuracy/recovery values, it is revealed that the sensor successfully fulfilled the criteria for success, displaying accuracy/recovery values within the range of 80%-120% and CV% values below 20%. This sensor presents significant advantages, including high sensitivity, specificity, and ability to detect very low concentrations of OA. In conclusion, the suggested U-shaped fiber optic biosensor has the potential to be valuable in the early detection of PD from a clinical perspective.

Design and optimization of a nanoparticle based magnetic hyperthermia device

Compared to their healthy counterparts, cancer cells are affected more adversely by higher temperatures which can be achieved with magnetic nanoparticle magnetic hyperthermia (MNP–MH) by elevating the temperature to 41 − 45 o C range. In MNP–MH the energy is transferred between an applied alternating magnetic field (AMF) and MNPs' magnetization. Accordingly, devices producing AMFs are designed around dedicated coils driven by RF amplifiers. Herein, new analytical coil performance criteria were conceived and used in assessing the performance of different coil geometries that were numerically simulated. Subsequently, three best performing geometries were physically implemented and experiments were realized using a novel placeholder grid for physical performance measurements and validating newly defined criteria. An economically viable RF amplifier was designed and built.