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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Targeting cancer cells via tumor-homing peptide CREKA functional PEG nanoparticles(Elsevier, 2016) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Okur, Aysu Ceren; Erkoç, Pelin; Kızılel, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 28376Targeting cell microenvironment via nano-particle based therapies holds great promise for treatment of various diseases. One of the main challenges in targeted delivery of nanoparticles for cancer therapy includes reduced localization of delivery vehicles at tumor site. The therapeutic efficacy of drugs can be improved by recruiting delivery vehicles towards specific region of tumorigenesis in the body. Here, we demonstrate an effective approach in creating PEG particles via water-in-water emulsion technique where tumor-homing peptide CREKA was used for functionalization. Simultaneous conjugation of laminin peptide IKVAV into hydrogel network and influence of altered combinations of ligands on intracellular uptake of anticancer drugs by HeLa cells were investigated. CREKA conjugated hydrogel nanoparticles were more effective to improve apoptotic effects of the model drug Doxorubicin (DOX) compared to that of particles conjugated with other peptides. Fluorescence intensity analysis on confocal micrographs suggested significantly higher cellular uptake of CREKA conjugated PEG particles than internalization of nanoparticles in other groups. We observed that fibrin binding ability of PEG particles could be increased up to 94% through CREKA conjugation. Our results suggest the possibility of cancer cell targeting via CREKA-functional PEG nanoparticles.Publication Metadata only Performance measures for video object segmentation and tracking(IEEE-Inst Electrical Electronics Engineers Inc, 2004) Erdem, Çiğdem Eroğlu; Sankur, Bülent; Department of Electrical and Electronics Engineering; Tekalp, Ahmet Murat; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 26207We propose measures to evaluate quantitatively the performance of video object segmentation and tracking methods without ground-truth (GT) segmentation maps. The proposed measures are based on spatial differences of color and motion along the boundary of the estimated video object plane and temporal differences between the color histogram of the current object plane and its predecessors. They can be used to localize (spatially and/or temporally) regions where segmentation results are good or bad; and/or they can be combined to yield a single numerical measure to indicate the goodness of the boundary segmentation and tracking results over a sequence. The validity of the proposed performance measures without GT have been demonstrated by canonical correlation analysis with another set of measures with GT on a set of sequences (where GT information is available). Experimental results are presented to evaluate the segmentation maps obtained from various sequences using different segmentation approaches.Publication Metadata only Prognostic significance of metastatic lymph node ratio in patients with pN3 gastric cancer who underwent curative gastrectomy(Karger, 2019) Bilici, Ahmet; Şeker, Mesut; Öven, Basak B.; Ölmez, Ömer Fatih; Yıldız, Özcan; Ölmüşçelik, Oktay; Hamdard, Jamshid; Açıkgöz, Özgür; Çakır, Aslı; Öncel, Mustafa; Selçukbiricik, Fatih; Kapran, Yersu; Balık, Emre; Faculty Member; Faculty Member; Faculty Member; School of Medicine; School of Medicine; School of Medicine; 202015; 168101; 18758Background: Lymph node involvement is an important prognostic factor in patients with gastric cancer. The aim of this study was to determine the prognostic significance of metastatic lymph node ratio (MLNR) and compare it to the number of lymph node metastasis in pN3 gastric cancer. Methods: We retrospectively analyzed 207 patients with pN3 gastric cancer who had undergone radical gastrectomy. Prognostic factors and MLNR were evaluated by univariate and multivariate analysis. Results: An MLNR of 0.75 was found to be the best cut-off value to determine the prognosis of patients with pN3 gastric cancer (p = 0.001). The MLNR was significantly higher in patients with large-sized and undifferentiated tumors, vascular, lymphatic and perineural invasion, and total gastrectomy. In multivariate analysis, MLNR (p = 0.041), tumor differentiation (p = 0.046), and vascular invasion (p = 0.012) were found to be independent prognos-tic factors for disease-free survival, while both MLNR (p < 0.001) and pN stage (p = 0.002) were independent prognostic indicators, as was tumor size, for overall survival. There was significant difference with respect to the recurrence patterns between MLNR groups. Lymph node and peritoneal recurrences were significantly higher in patients with MLNR > 0.75 compared to the MLNR < 0.75 group (p < 0.05). However, recurrence patterns were similar between pN3a and pN3b. Conclusion: Our results showed that MLNR was a useful indicator to determine the prognosis and recurrence patterns of patients with radically resected gastric cancer. Moreover, MLNR is a beneficial and reliable technique for evaluating lymph node metastasis.Publication Metadata only The effect of marital violence on infertility distress among a sample of Turkish women(Royan Inst, 2014) Şahiner, Gönül; Bakır, Bilal; Akyüz, Aygül; Seven, Memnun; Faculty Member; Faculty Member; School of Nursing; School of Nursing; 42416; 32470Background: The aim of this study was to determine the relationship between marital violence and distress level among women with a diagnosis of infertility. Materials and Methods: This cross-sectional study consisted of 139 married women diagnosed as primary infertile who applied to an in vitro fertilization (IVF) center in Turkey, between September and December 2009. A descriptive information questionnaire developed by the researcher was used for data collection. In addition, an infertility distress scale (IDS) for determining the severity effect of infertility and the scale for marital violence against women (SDVW) for determining level of marital violence against the women were used. Results: The total IDS score of the study sample was 37.76 +/- 10.53. There was no significant relationship between the age and education level of the women and the total IDS score. The total IDS score was higher in women who did not work and those being treated for infertility for more than three years. The total SDVW score of the study sample was 67.0 +/- 8.26. The total SDVW score was higher in women who had been trying to have a child for more than six years and had received infertility treatment for longer than three years. The employment status of the women and physical, emotional, and sexual violence scores had a statistically significant relationship with the IDS scores. The emotional violence score was found to have the highest significance among the variables affecting total IDS score. Conclusion: Marital violence is a factor increasing the distress of infertile women. Healthcare staff serving infertile couples should consider the possibility of domestic violence against women as a factor affecting the psychological infertility distress level.Publication Metadata only 2.3-μm Tm3+: YLF laser passively Q-switched with a Cr2+: ZnSe saturable absorber(Optical Soc Amer, 2017) N/A; N/A; Canbaz, Ferda; Yorulmaz, İsmail; Sennaroğlu, Alphan; PhD Student; PhD Student; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 23851We report, what is to our knowledge, the first passively Q-switched operation of a 2.3-mu m Tm3+ : YLF laser by using a Cr2+ : ZnSe saturable absorber. In the experiments, a tunable Ti3+ : sapphire laser was used to end pump the Tm3+ : YLF gain medium inside an x cavity. A Cr2+ : ZnSe saturable absorber was also included in the cavity to initiate passive Q switching. At all pump power levels above lasing threshold, passively Q-switched operation of the Tm3+ : YLF laser could be obtained at 2309 nm with pulse durations and repetition frequencies in the ranges of 1.21.4 mu s and 0.3-2.1 kHz, respectively. Analysis of power dependent repetition rate data further gave an estimated value of 3.1% for the round-trip saturable loss of the Cr2+ : ZnSe saturable absorber.Publication Metadata only Cutaneous foreign body granulomas associated with lipolytic cocktail: who is the enemy, mesotherapy or drugs injected?(Taylor & Francis Inc, 2017) Kutlubay, Zekayi; İnce, Ümit; Engin, Burhan; N/A; Gökalp, Hilal; Doctor; N/A; Koç University Hospital; N/AMesotherapy is widely used for its lipolytic effect as an alternative procedure to surgical methods. Although many benefits of lipolytic mesotherapy have been observed, numerous side effects have also been reported. Here, we report a case of cutaneous foreign body granulomas that occurred after lipolytic rnesotherapy.Publication Metadata only Unguales plattenepithelkarzinom bei einem patienten mit mal de meleda(Wiley, 2016) Baykal, Can; Sarı, Şule Öztürk; Uyguner, Zehra Oya; Ekinci, Algun Polat; Demir, Özgür; Babuna, Goncagül; Büyükbabani, Nesimi; N/A; Kayserili, Hülya; Faculty Member; School of Medicine; 7945N/APublication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.Publication Metadata only A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for pi-stacking interactions: dimers of benzene and planar C-6(Springer, 2015) Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for pi-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C-6 moieties. Moller-Plesset (MP2, SCS-MP2) and coupled cluster [CCSD(T)] calculations show that such generated basis sets provide an accurate description of p-stacking systems with favorable computation times compared to the standard augmented basis sets. The addition of these off-center functions eliminates the linear dependence of the augmented basis sets, which is one of the most encountered numerical problems during calculation of the oligomers of polyaromatic hydrocarbons (PAH). In this work, we present a comparative study of the general characteristics of the potential energy surfaces for the parallel stacked and T-shape conformations of benzene and planar C6 clusters, using a combination of cc-PVXZ and our optimized functions. We discuss properties, such as the depth and curvature of the potential functions, short and long distance behavior, and the frictional forces between two model monomers.Publication Metadata only Clinical evaluation of dental enamel defects and oral findings in coeliac children(Istanbul Univ Press, Istanbul Univ Rectorate, 2018) Bicak, Damla Aksit; Urganci, Nafiye; Akyuz, Serap; Usta, Merve; Alev, Burcin; Yarat, Aysen; N/A; Kızılkan, Nuray Uslu; Faculty Member; School of Medicine; 221274Purpose To examine dental hard and soft tissue changes of coeliac children in order to increase the awareness of the pediatric dentists in prediagnosis of especially undiagnosed coeliac disease. Materials and methods Sixty children, 28 (46.7%) boys and 32 (53.3%) girls whose ages were between 6 to 16 years were included in the present study. Thirty children who had undergone endoscopy and diagnosed with the coeliac disease in the Sisli Hamidiye Etfal Hospital, Istanbul, Turkey, formed the study group. Also, thirty children clinically suspected of having the coeliac disease with the same gastrointestinal complaints had undergone endoscopy and proven not coeliac were chosen as the control group. Oral examination involved assessment of dentition and specific and unspecific dental enamel defects. Also, soft tissue lesions, clinical delay of the dental eruption, salivary flow rate, pH, and buffering capacity were examined. Results Twenty coeliac patients had enamel defects, however none in the control subjects. In the coeliac group, all enamel defects were diagnosed in permanent teeth and as specific in all children. Grade I dental enamel defects found mainly in the incisors. The clinical delayed eruption was observed in 10 (33.3%) of 30 coeliac children and none of the children in the control group. While the level of DMFT/S numbers and stimulated salivary flow rate were found significantly lower in the coeliac group, pH was found significantly higher. Conclusion Oral cavity may be involved in coeliac disease and pediatric dentists can play an important role in the early diagnosis of the coeliac disease.