Browsing by Subject "Tissue"
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Item Open Access Altçizge modellemesi kullanarak kolon bez tespiti(IEEE, 2011-04) Özgül, Etkin Barış; Sökmensüer, C.; Gündüz-Demir, ÇiğdemKolon adenokarsinomu, kolon bez yapılarında değişimlere yol açar. Patologlar bezlerdeki bu değişimleri değerlendirerek kolon adenokarsinom tanı ve derecelendirmesi yaparlar. Ancak değişimlerin değerlendirme süreci kaydadeğer öznellik taşıyabilir. Bezlerin matematiksel özniteliklerle karakterize edilmesiyle bu öznelliği azaltabilmek olasıdır. Bunun içinse ilk aşama, bezlerin yerlerinin otomatik olarak tespit edilmesidir. Literatürdeki bez tespit etme yöntemleri çoğunlukla piksel tabanlıdır. Ancak doku görüntüleri, doğaları gereği ve biyopsi hazırlama ve görüntü alma işlemlerindeki değişkenlik nedeni ile piksel bazında değişkenlik gösterebilir. Öte yandan, bu değişkenliğe rağmen, bezleri oluşturan doku bileşenlerinin uzaysal dağılımı benzer özellik gösterir. Bu dağılımı gözönüne alarak tasarlanan yöntemler, bölütleme başarısını artırma potansiyeline sahiptir. Bu çalışmada önerdiğimiz yöntem, ilk olarak, doku bileşenlerinin dağılımını, bu bileşenler üzerinde oluşturduğu bir çizge ile modeller. Daha sonra, oluşturduğu bu çizgeyi altçizgelere ayırır ve bu altçizgelerin öznitelikleri yardımıyla bezleri tespit eder. Kolon doku görüntüleri üzerinde yaptığımız çalışmalar, önerilen bu yöntemin bezlerin yüksek doğrulukta tespit edilmesinde umut verici sonuçlar verdiğini göstermiştir. The colon adenocarcinoma causes changes in glandular structures of colon tissues. Pathologists assess these changes to diagnose and grade the colon adenocarcinoma. However, this assessment may consist of a considerable amount of subjectivity. It is possible to reduce this subjectivity by characterizing the glands with mathematical features. For that, the first step is to detect gland locations. In literature, most of the gland detection methods are pixel-based. However, tissue images may show pixel-level variances due to their nature and differences in biopsy preparation and image acquisition procedures. On the other hand, in spite of these variances, the distribution of tissue components forming glands show similar properties. The methods that consider this distribution has the potential of improving the performance. The method proposed in this study first models the distribution of the components by constructing a graph on them. Then, it breaks the constructed graph down into subgraphs and detects the glands using the features of these subgraphs. The experiments conducted on colon tissue images show that the proposed method leads to promising results for detecting the glands. © 2011 IEEE.Item Open Access Amphiphilic peptide coated superparamagnetic iron oxide nanoparticles for in vivo MR tumor imaging(Royal Society of Chemistry, 2016) Ozdemir, A.; Ekiz, M. S.; Dilli, A.; Güler, Mustafa O.; Tekinay, A. B.Magnetic resonance imaging (MRI) is a noninvasive imaging technique that provides high spatial resolution and depth with pronounced soft-tissue contrast for in vivo imaging. A broad variety of strategies have been employed to enhance the diagnostic value of MRI and detect tissue abnormalities at an earlier stage. Superparamagnetic iron oxide nanoparticles (SPIONs) are considered to be suitable candidates for effective imaging due to their small size, versatile functionality and better biocompatibility. Here, we demonstrate that coating SPIONs with proline-rich amphiphilic peptide molecules through noncovalent interactions leads to a water-dispersed hybrid system suitable as an MRI contrast agent. Cellular viability and uptake of amphiphilic peptide coated SPIONs (SPION/K-PA) were evaluated with human vascular endothelial cells (HUVEC) and estrogen receptor (ER) positive human breast adenocarcinoma (MCF-7) cells. The efficiency of SPION/K-PA as MRI contrast agents was analyzed in Sprague-Dawley rats with mammary gland tumors. MR imaging showed that SPION/K-PA effectively accumulated in tumor tissues, enhancing their imaging potential. Although nanoparticles were observed in reticuloendothelial system organs (RES) and especially in the liver and kidney immediately after administration, the MR signal intensity in these organs diminished after 1 h and nanoparticles were subsequently cleared from these organs within two weeks. Histological observations also validated the accumulation of nanoparticles in tumor tissue at 4 h and their bioelimination from the organs of both healthy and tumor-bearing rats after two weeks.Item Open Access Bioactive nanomaterials for neural engineering(Springer, Cham, 2016) Sever, Melike; Uyan, İdil; Tekinay, Ayse B.; Güler, Mustafa O.; Zhang, L. G.; Kaplan, D. L.Nervous system is a highly complex interconnected network and higher organisms including humans have limited neural regeneration capacity. Neurodegenerative diseases result in significant cognitive, sensory, or motor impairments. Following an injury in the neural network, there is a balance between promotion and inhibition of regeneration and this balance is shifted to different directions in central nervous system (CNS) and peripheral nervous system (PNS). More regeneration capacity is observed in the PNS compared to the CNS. Although, several mechanisms play roles in the inhibitory and growth-promoting natures of the CNS and PNS, extracellular matrix (ECM) elements are key players in this process. ECM is a three-dimensional environment where the cells migrate, proliferate, and differentiate (Rutka et al. 1988; Pan et al. 1997). After a comprehensive investigation of the interactions between the ECM proteins and cell receptors, the ECM environment was found to regulate significant cellular processes such as survival, proliferation, differentiation, and migration (Yurchenco and Cheng 1994; Aszodi et al. 2006). Its components have major roles not only in neurogenesis during development of the nervous system but also in normal neural functioning during adulthood (Hubert et al. 2009).Item Open Access Burst-mode thulium all-fiber laser delivering femtosecond pulses at a 1 GHz intra-burst repetition rate(Optical Society of America, 2017) Elahı, P.; Kalaycıoğlu, H.; Akçaalan, Ö.; Şenel, Ç.; Ilday, F. Ö.We report on the development of, to the best of our knowledge, the first ultrafast burst-mode laser system operating at a central wavelength of approximately 2 μm, where water absorption and, consequently, the absorption of most biological tissue is very high. The laser comprises a harmonically mode-locked 1-GHz oscillator, which, in turn, seeds a fiber amplifier chain. The amplifier produces 500 ns long bursts containing 500 pulses with 1 GHz intra-burst and 50 kHz inter-burst repetition rates, respectively, at an average power of 1 W, corresponding to 40 nJ pulse and 20 μJ burst energies, respectively. The entire system is built in an all-fiber architecture and implements dispersion management such that output pulses are delivered directly from a single-mode fiber with a duration of 340 fs without requiring any external compression. This gigahertz-repetition-rate system is intended for ablation-cooled laser material removal in the 2 μm wavelength region, which is interesting for laser surgery due to the exceptionally high tissue absorption at this wavelength.Item Open Access Cell-graph mining for breast tissue modeling and classification(IEEE, 2007-08) Bilgin, C.; Demir, Çiğdem; Nagi, C.; Yener, B.We consider the problem of automated cancer diagnosis in the context of breast tissues. We present graph theoretical techniques that identify and compute quantitative metrics for tissue characterization and classification. We segment digital images of histopatological tissue samples using k-means algorithm. For each segmented image we generate different cell-graphs using positional coordinates of cells and surrounding matrix components. These cell-graphs have 500-2000 cells(nodes) with 1000-10000 links depending on the tissue and the type of cell-graph being used. We calculate a set of global metrics from cell-graphs and use them as the feature set for learning. We compare our technique, hierarchical cell graphs, with other techniques based on intensity values of images, Delaunay triangulation of the cells, the previous technique we proposed for brain tissue images and with the hybrid approach that we introduce in this paper. Among the compared techniques, hierarchical-graph approach gives 81.8% accuracy whereas we obtain 61.0%, 54.1% and 75.9% accuracy with intensity-based features, Delaunay triangulation and our previous technique, respectively. © 2007 IEEE.Item Open Access Design of a novel MRI compatible manipulator for image guided prostate interventions(IEEE, 2005-02) Krieger, A.; Susil, R. C.; Ménard, C.; Coleman, J. A.; Fichtinger, G.; Atalar, Ergin; Whitcomb, L. L.This paper reports a novel remotely actuated manipulator for access to prostate tissue under magnetic resonance imaging guidance (APT-MRI) device, designed for use in a standard high-field MRI scanner. The device provides three-dimensional MRI guided needle placement with millimeter accuracy under physician control. Procedures enabled by this device include MRI guided needle biopsy, fiducial marker placements, and therapy delivery. Its compact size allows for use in both standard cylindrical and open configuration MRI scanners. Preliminary in vivo canine experiments and first clinical trials are reported.Item Open Access Differences in the accumulation and distribution profile of heavy metals and metalloid between male and female crayfish (Astacus leptodactylus)(2013) Tunca, E.; Ucuncu, E.; Ozkan, A.D.; Ulger, Z.E.; Cansizoǧlu, A.E.; Tekinay, T.Concentrations of selected heavy metals and a metalloid were measured by ICP-MS in crayfish (Astacus leptodactylus) collected from Lake Hirfanli, Turkey. Aluminum (Al), chromium (52Cr, 53Cr), copper ( 63Cu, 65Cu), manganese (Mn), nickel (Ni) and arsenic (As) were measured in the exoskeleton, gills, hepatopancreas and abdominal muscle tissues of 60 crayfish of both genders. With the exception of Al, differences were determined between male and female cohorts for the accumulation trends of the above-mentioned elements in the four tissues. It was also noted that the accumulation rates of Ni and As were significantly lower in gill tissue of females compared to males and no significant difference was observed for Cu isotopes in female crayfish. Cluster Analysis (CA) recovered similar results for both genders, with links between accumulations of Ni and As being notable. Accumulation models were described separately for male and female crayfish using regression analysis, and are presented for models where R2 > 0.85. © 2013 Springer Science+Business Media New York.Item Open Access Fiber laser-microscope system for femtosecond photodisruption of biological samples(Optical Society of America, 2012-02-22) Yavaş, Seydi; Erdoğan, Mutlu; Gürel, Kutan; İlday, F. Ömer; Eldeniz, Y. B.; Tazebay, Uygar H.We report on the development of a ultrafast fiber lasermicroscope system for femtosecond photodisruption of biological targets. A mode-locked Yb-fiber laser oscillator generates few-nJ pulses at 32.7 MHz repetition rate, amplified up to ~125 nJ at 1030 nm. Following dechirping in a grating compressor, ~240 fs-long pulses are delivered to the sample through a diffraction-limited microscope, which allows real-time imaging and control. The laser can generate arbitrary pulse patterns, formed by two acousto-optic modulators (AOM) controlled by a custom-developed fieldprogrammable gate array (FPGA) controller. This capability opens the route to fine optimization of the ablation processes and management of thermal effects. Sample position, exposure time and imaging are all computerized. The capability of the system to perform femtosecond photodisruption is demonstrated through experiments on tissue and individual cells.Item Open Access Frequency optimization in high intensity focused ultrasound(IEEE, 2014-09) Yetik, H.; Arıyurek, Cemre; Bozkurt, A.; Ergun, A. S.In high intensity focused ultrasound (HIFU) the choice of transducer frequency depends on the target depth and tissue type. At high frequencies attenuation does not permit enough acoustical power to be transmitted to the target whereas at low frequencies the transmitted power is not absorbed efficiently. Hence, there exists an optimum frequency at which the power deposited at the target is maximum. In this study, we verified this relation experimentally using MR compatible focused transducers, ex-vivo tissue samples and magnetic resonance (MR) thermometry. © 2014 IEEE.Item Open Access Glycosaminoglycan-Mimetic Signals Direct the Osteo/Chondrogenic Differentiation of Mesenchymal Stem Cells in a Three-Dimensional Peptide Nanofiber Extracellular Matrix Mimetic Environment(American Chemical Society, 2016-02) Arslan, E.; Güler, Mustafa O.; Tekinay, A. B.Recent efforts in bioactive scaffold development focus strongly on the elucidation of complex cellular responses through the use of synthetic systems. Designing synthetic extracellular matrix (ECM) materials must be based on understanding of cellular behaviors upon interaction with natural and artificial scaffolds. Hence, due to their ability to mimic both the biochemical and mechanical properties of the native tissue environment, supramolecular assemblies of bioactive peptide nanostructures are especially promising for development of bioactive ECM-mimetic scaffolds. In this study, we used glycosaminoglycan (GAG) mimetic peptide nanofiber gel as a three-dimensional (3D) platform to investigate how cell lineage commitment is altered by external factors. We observed that amount of fetal bovine serum (FBS) presented in the cell media had synergistic effects on the ability of GAG-mimetic nanofiber gel to mediate the differentiation of mesenchymal stem cells into osteogenic and chondrogenic lineages. In particular, lower FBS concentration in the culture medium was observed to enhance osteogenic differentiation while higher amount FBS promotes chondrogenic differentiation in tandem with the effects of the GAG-mimetic 3D peptide nanofiber network, even in the absence of externally administered growth factors. We therefore demonstrate that mesenchymal stem cell differentiation can be specifically controlled by the combined influence of growth medium components and a 3D peptide nanofiber environment.Item Open Access Graph walks for classification of histopathological images(IEEE, 2013) Olgun, Gülden; Sokmensuer, C.; Gündüz-Demir, ÇiğdemThis paper reports a new structural approach for automated classification of histopathological tissue images. It has two main contributions: First, unlike previous structural approaches that use a single graph for representing a tissue image, it proposes to obtain a set of subgraphs through graph walking and use these subgraphs in representing the image. Second, it proposes to characterize subgraphs by directly using distribution of their edges, instead of employing conventional global graph features, and use these characterizations in classification. Our experiments on colon tissue images reveal that the proposed structural approach is effective to obtain high accuracies in tissue image classification. © 2013 IEEE.Item Open Access Heparin mimetic peptide nanofiber gel promotes regeneration of full thickness burn injury(Elsevier Ltd, 2017) Yergoz, F.; Hastar, N.; Cimenci, C. E.; Ozkan, A. D.; Güler, Mustafa O.; Tekinay, A. B.; Tekinay, T.; Güler, Mustafa O.Burn injuries are one of the most common types of trauma worldwide, and their unique physiology requires the development of specialized therapeutic materials for their treatment. Here, we report the use of synthetic, functional and biodegradable peptide nanofiber gels for the improved healing of burn wounds to alleviate the progressive loss of tissue function at the post-burn wound site. These bioactive nanofiber gels form scaffolds that recapitulate the structure and function of the native extracellular matrix through signaling peptide epitopes, which can trigger angiogenesis through their affinity to basic growth factors. In this study, the angiogenesis-promoting properties of the bioactive scaffolds were utilized for the treatment of a thermal burn model. Following the excision of necrotic tissue, bioactive gels and control solutions were applied topically onto the wound area. The wound healing process was evaluated at 7, 14 and 21 days following injury through histological observations, immunostaining and marker RNA/protein analysis. Bioactive peptide nanofiber-treated burn wounds formed well-organized and collagen-rich granulation tissue layers, produced a greater density of newly formed blood vessels, and exhibited increased re-epithelialization and skin appendage development with minimal crust formation, while non-bioactive peptide nanofibers and the commercial wound dressing 3M™ Tegaderm™ did not exhibit significant efficiency over sucrose controls. Overall, the heparin-mimetic peptide nanofiber gels increased the rate of repair of burn injuries and can be used as an effective means of facilitating wound healing.Item Open Access High-speed, thermal damage-free ablation of brain tissue with femtosecond pulse bursts(IEEE, 2016) Kerse, Can; Yavaş, Seydi; Kalaycıoğlu, Hamit; Asik M.D.; Akçaalan, Önder; İlday, F. ÖmerWe report a novel ultrafast burst mode fiber laser system and results on ablation of rat brain tissue at rates approaching an order of magnitude improvement over previous reports, with no discernible thermal damage. © 2015 IEEE.Item Open Access Influence of phase function on modeled optical response of nanoparticle-labeled epithelial tissues(2011) Cihan, C.; Arifler, D.Metal nanoparticles can be functionalized with biomolecules to selectively localize in precancerous tissues and can act as optical contrast enhancers for reflectance-based diagnosis of epithelial precancer. We carry out Monte Carlo (MC) simulations to analyze photon propagation through nanoparticle-labeled tissues and to reveal the importance of using a proper form of phase function for modeling purposes. We first employ modified phase functions generated with a weighting scheme that accounts for the relative scattering strengths of unlabeled tissue and nanoparticles. To present a comparative analysis, we repeat ourMCsimulations with simplified functions that only approximate the angular scattering properties of labeled tissues. The results obtained for common optical sensor geometries and biologically relevant labeling schemes indicate that the exact form of the phase function used as model input plays an important role in determining the reflectance response and approximating functions often prove inadequate in predicting the extent of contrast enhancement due to labeling. Detected reflectance intensities computed with different phase functions can differ up to ̃60% and such a significant deviation may even alter the perceived contrast profile. These results need to be taken into account when developing photon propagation models to assess the diagnostic potential of nanoparticle-enhanced optical measurements. © 2011 Society of Photo-Optical Instrumentation Engineers (SPIE).Item Open Access Kanser tanısı için kolon bezlerinin matematiksel analizi(IEEE, 2009-04) Çığır, Celal; Sökmensüer, C.; Gündüz-Demir, ÇiğdemNeoplastic diseases including cancer cause organizational changes in tissues. Histopathological examination, which is routinely used for the diagnosis and grading of these diseases, relies on pathologists to identify such tissue changes under a microscope. However, as this examination mainly relies on the visual interpretation of pathologists, it may lead to a considerable amount of subjectivity. To reduce the subjectivity level, it is proposed to use computational methods that provide objective measures. These methods quantify the tissue changes associated with disease by defining features on tissue images. In this paper, colon glands are mathematically analyzed making use of different feature extraction approaches. In this analysis, morphological, intensity-based, and textural features are investigated and glands are classified using these features. Working on the images of 108 colon tissues of 36 patients, our experiments demonstrate that this classification leads to promising results for differentiating normal glands from the cancerous ones. ©2009 IEEE.Item Open Access Kelime histogram modeli ile histopatolojik görüntü sınıflandırılması(IEEE, 2011-04) Özdemir, Erdem; Sökmensüer, C.; Gündüz-Demir, ÇiğdemColon cancer, which is one of the most common cancer type, could be cured with its early diagnosis. In the current practice of medicine, there are many screening techniques such as colonoscopy, sigmoidoscopy, and stool test, however the most effective and most widely used method for cancer diagnosis is to take tissue sections with biopsy and examine them under a microscope. As this examination is based on visual interpretation, it may lead to subjective decisions and diagnostic differences among pathologists. The need of reducing inter-variability in cancer diagnosis has led to studies for extraction of features from biopsy images and development of algorithms that give objective results. In this paper, we propose a method for the automated classification of a colon tissue image with the features extracted from a histogram that models the existence of image regions determined in an unsupervised way. Experiments on colon tissue images show that the proposed method leads to more successful results compared to its counterparts. Moreover, the proposed method, which uses color intensities for feature extraction, has the potential of giving better results with the use of additional features. © 2011 IEEE.Item Open Access Materials for articular cartilage regeneration(Bentham Science Publishers B.V., 2012) Tombuloglu, Ayşegül; Tekinay, Ayşe B.; Güler, Mustafa O.Many health problems remaining to be untreatable throughout the human history can be overcome by utilizing new biomedical materials. Healing cartilage defects is one of the problems causing significant health issue due to low regeneration capacity of the cartilage tissue. Scaffolds as three-dimensional functional networks provide promising tools for complete regeneration of the cartilage tissue. Diversity of materials and fabrication methods give rise to many forms of scaffolds including injectable and mechanically stable ones. Various approaches can be considered depending on the condition of cartilage defect. A scaffold should maintain tissue function within a short time, and should be easily applied in order to minimally harm the body. This review will cover several patents and other publications on materials for cartilage regeneration with an outlook on essential characteristics of materials and scaffolds.Item Open Access Model-based spectral analysis of photon propagation through nanoparticle-labeled epithelial tissues(SPIE, 2011) Cihan, Can; Arifler, D.Metal nanoparticles can function as optical contrast enhancers for reflectance-based diagnosis of epithelial precancer. We carry out Monte Carlo simulations to model photon propagation through normal tissues, unlabeled precancerous tissues, and precancerous tissues labeled with gold nanospheres and we compute the spectral reflectance response of these different tissue states. The results indicate that nanoparticle-induced changes in the spectral reflectance profile of tissues depend not only on the properties of these particles but also on the source-detector geometry used. When the source and detector fibers are oriented side by side and perpendicular to the tissue surface, the reflectance intensity of precancerous tissue is lower compared to that of normal tissue over the entire wavelength range simulated and addition of nanospheres enhances this negative contrast. When the fibers are tilted toward each other, the reflectance intensity of precancerous tissue is higher compared to that of normal tissue and labeling with nanospheres causes a significant enhancement of this positive contrast. The results also suggest that model-based spectral analysis of photon propagation through nanoparticle-labeled tissues provides a useful framework to quantify the extent of achievable contrast enhancement due to external labeling and to assess the diagnostic potential of nanoparticle-enhanced optical measurements. © 2011 SPIE-OSA.Item Open Access One-Step Fabrication of Biocompatible Multifaceted Nanocomposite Gels and Nanolayers(American Chemical Society, 2017) Topuz, F.; Bartneck, M.; Pan, Y.; Tacke, F.Nanocomposite gels are a fascinating class of polymeric materials with an integrative assembly of organic molecules and organic/inorganic nanoparticles, offering a unique hybrid network with synergistic properties. The mechanical properties of such networks are similar to those of natural tissues, which make them ideal biomaterial candidates for tissue engineering applications. Existing nanocomposite gel systems, however, lack many desirable gel properties, and their suitability for surface coatings is often limited. To address this issue, this article aims at generating multifunctional nanocomposite gels that are injectable with an appropriate time window, functional with bicyclononynes (BCN), biocompatible and slowly degradable, and possess high mechanical strength. Further, the in situ network-forming property of the proposed system allows the fabrication of ultrathin nanocomposite coatings in the submicrometer range with tunable wettability and roughness. Multifunctional nanocomposite gels were fabricated under cytocompatible conditions (pH 7.4 and T = 37 °C) using laponite clays, isocyanate (NCO)-terminated sP(EO-stat-PO) macromers, and clickable BCN. Several characterization techniques were employed to elucidate the structure-property relationships of the gels. Even though the NCO-sP(EO-stat-PO) macromers could form a hydrogel network in situ on contact with water, the incorporation of laponite led to significant improvement of the mechanical properties. BCN motifs with carbamate links were used for a metal-free click ligation with azide-functional molecules, and the subsequent gradual release of the tethered molecules through the hydrolysis of carbamate bonds was shown. The biocompatibility of the hydrogels was examined through murine macrophages, showing that the material composition strongly affects cell behavior.Item Open Access Peptide functionalized superparamagnetic iron oxide nanoparticles as MRI contrast agents(The Royal Society of Chemistry, 2011) Sulek, S.; Mammadov, B.; Mahcicek, D. I.; Sozeri, H.; Atalar, Ergin; Tekinay, A. B.; Güler, Mustafa O.Magnetic resonance imaging (MRI) attracts great attention in cellular and molecular imaging due to its non-invasive and multidimensional tomographic capabilities. Development of new contrast agents is necessary to enhance the MRI signal in tissues of interest. Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents for signal enhancement as they have revealed extraordinary magnetic properties at the nanometre size and their toxicity level is very low compared to other commercial contrast agents. In this study, we developed a new method to functionalize the surface of SPIONs. Peptide amphiphile molecules are used to coat SPIONs non-covalently to provide water solubility and to enhance biocompatibility. Superparamagnetic properties of the peptide-SPION complexes and their ability as contrast agents are demonstrated. In vitro cell culture experiments reveal that the peptide-SPION complexes are biocompatible and are localized around the cells due to their peptide coating.