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Publication Metadata only “Smart poisoning” of Co/SiO2 catalysts by sulfidation for chirality-selective synthesis of (9,8) single-walled carbon nanotubes(2016) Yuan, Yang; Karahan, H. Enis; Wei, Li; Zhai, Shengli; Lau, Raymond; Chen, Yuan; N/A; Yıldırım, Cansu; Birer, Özgür; Master Student; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/AThe chirality-selective synthesis of relatively large (diameter > 1 nm) single-walled carbon nanotubes (SWCNTs) is of great interest for a variety of practical applications, but only a few catalysts are available so far. Previous studies suggested that S (compounds) can enhance the chirality-selectivity of Co catalysts in SWCNT synthesis, however, the mechanism behind is not fully understood, and no tailorable methodology has yet been developed. Here, we demonstrate a facile approach to achieve the chirality-selective synthesis of SWCNTs by the sulfidation-based poisoning of silica-supported Co catalysts using a mixture of H2S and H2. The UV-vis-NIR, photoluminescence, and Raman spectroscopy results together show that the resulting SWCNTs have a narrow diameter distribution of around 1.2 nm, and (9,8) nanotubes have an abundance of ∼38% among the semiconducting species. More importantly, the carbon yield achieved by the sulfided catalyst (2.5 wt%) is similar to that of the nonsulfided one (2.7 wt%). The characterization of the catalysts by X-ray diffraction, X-ray photoelectron spectroscopy, X-ray fluorescence, and H2 temperature-programmed reduction shows that the sulfidation leads to the formation of Co9S8 nanoparticles. However, Co9S8 nanoparticles are reduced back to regenerate metallic Co nanoparticles during the synthesis of SWCNTs, which maintain a high carbon yield. In this process, Co9S8 nanoparticles seemingly intermediate the production of Co nanoparticles with narrow size distribution. Due to the fact that the poisoning step improves the quality of the end-product rather than hampering the growth process, we have coined the process developed as “smart poisoning”. This study not only reveals the mechanism behind the beneficial role of S in the selective synthesis of relatively large SWCNTs but also presents a promising method to create chirality-selective catalysts with high activity for scalable synthesis.Publication Metadata only 1,3-bis(gamma-aminopropyl)tetramethyldisiloxane modified epoxy resins: curing and characterization(Elsevier, 1998) Department of Chemistry; Department of Chemistry; Yılgör, Emel; Yılgör, İskender; Researcher; Faculty Member; Department of Chemistry; College of Sciences; College of Sciences; 40527; 24181Incorporation of siloxane oligomers with reactive organofunctional terminal groups, such as amine, epoxy and carboxy, into the structure of epoxy networks, provides improvements in the fracture toughness, water absorption and surface properties of the resultant systems. 1,3-bis(gamma-aminopropyl) tetramethyldisiloxane (DSX) was used as a model curing agent and modifier in bis(4-aminocyclohexyl)methane (PACM-20) cured diglycidyl ether of bisphenol-A (DGEBA) based epoxy resins. Curing reactions followed by differential scanning calorimetry indicated faster reaction rates between DSX and DGEBA as compared with PACM-20 and DGEBA. Mechanical characterization of the modified products showed improvements in tensile and impact strengths as expected. Glass transition temperatures of these materials showed a decrease with an increase in DSX content.Publication Metadata only 18F-FDG PET/CT mean suv and metabolic tumor volume for mean survival time in non-small cell lung cancer(Lippincott Williams and Wilkins, 2015) Kurtipek, Ercan; Çaycı, Mustafa; Düzgün, Nuri; Esme, Hıdır; Terzi, Yüksel; Bakdık, Süleyman; Ünlü, Yaşar; Burnik, Cengiz; Bekçi, Taha Tahir; N/A; Aygün, Murat Serhat; Teaching Faculty; School of Medicine; Koç University Hospital; 291692Objective: The study was designed to determine the relationship between survival time of standardized uptake value (SUVmax and SUVmean) and metabolic tumor volume (MTV) in patients with non-small cell lung cancer (NSCLC), and examine the impact of demographic, clinical, and radiological data of these patients on survival. Materials and Methods: We performed a retrospective analysis of the records of 79 patients with NSCLC who presented to our hospital between May 2010 and March 2013, received a final diagnosis, and underwent 18F-FDG PET/CT for staging. Clinical, radiological, and 18F-FDG PET/CT parameters with an impact on prognosis such as the SUVmax of the primary tumor as calculated by the volumetric region of interest in the 18F-FDG PET/CT scans during initial diagnosis, mean SUV of the tumor, and MTV obtained with a threshold of SUVmax greater than 2.5 were recorded and statistically analyzed. A statistical analysis was carried out based on the clinical, radiological, and PET/CT findings of the patients who were divided into 2 groups: survivors and nonsurvivors. Results: Seventy patients (88.6%) were men, and 9 (11.4%) were women. The mean age was 63.65 ± 11.51 years in the nonsurvivor group (n = 40) versus 62.74 ± 10.60 years in the survivor group (n = 39) (Table 1). The mean survival time from diagnosis was 7.9 ± 6.52 months in the nonsurvivor group versus 14.09 ± 7.41 months in the survivor group. The mean survival time was 12.9 ± 7.9 months for those aged 60 or younger, whereas it was 9.9 ± 7.2 years for those aged 60 or older. According to the Cox regression analysis, higher MTV [relative risk (RR), 1.006; P = 0.03] and mean SUVmax (mSUV) (RR, 1.302; P = 0.03) had a significant impact on shortening of the mean survival time. However, no statistical significance was reached for SUVmax measurements (RR, 0.970; P = 0.39). Furthermore, there was a significant relationship between increased tumor size (andlt;2 cm, 2-4 cm, and ≥4 cm) and shortened mean survival time (P = 0.03). Conclusion: The present study showed that MTV and mSUV of FDG PET/CT scans of the tumor, but not SUVmax, had a significant impact on survival time of patients with NSCLC. Based on this result, we believe that we might have more accurate information about the survival time of our patients if we also evaluate mSUV and MTV in combination with mSUV, which is frequently used for diagnosis and monitoring of patients with NSCLC during our daily practice. © 2015 Wolters Kluwer Health, Inc. All rights reserved.Publication Metadata only 3D model retrieval using probability density-based shape descriptors(IEEE Computer Society, 2009) Akgul, Ceyhun Burak; Sankur, Buelent; Schmitt, Francis; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We address content-based retrieval of complete 3D object models by a probabilistic generative description of local shape properties. The proposed shape description framework characterizes a 3D object with sampled multivariate probability density functions of its local surface features. This density-based descriptor can be efficiently computed via kernel density estimation (KDE) coupled with fast Gauss transform. The nonparametric KDE technique allows reliable characterization of a diverse set of shapes and yields descriptors which remain relatively insensitive to small shape perturbations and mesh resolution. Density-based characterization also induces a permutation property which can be used to guarantee invariance at the shape matching stage. As proven by extensive retrieval experiments on several 3D databases, our framework provides state-of-the-art discrimination over a broad and heterogeneous set of shape categories.Publication Metadata only 3D reconstruction of real objects with high resolution shape and texture(Elsevier, 2004) Schmitt, F; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We present a robust and accurate system for 3D reconstruction of real objects with high resolution shape and texture. Our reconstruction method is passive, the only information needed being 2D images obtained with a calibrated camera from different view angles as the object rotates on a turntable. The triangle surface model is obtained by a scheme combining octree construction and marching cubes algorithm, which is adapted to the shape from silhouette problem. We develop a texture mapping strategy based on surface particles to adequately address photography related problems such as inhomogeneous lighting, highlights and occlusion. Reconstruction results are included to demonstrate the attained quality.Publication Open Access 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Metadata only 3D ultrasound assessment of effect of controlled ovarian stimulation on endometrioma volume(Oxford University Press (OUP), 2016) Seyhan, A.; Balaban, B.; Urman, Cumhur Bülent; Ata, Mustafa Barış; Faculty Member; Faculty Member; School of Medicine; School of Medicine; 12147; 232576N/APublication Metadata only 5-hydroxytryptamine does not reduce sympathetic nerve activity or neuroeffector function in the splanchnic circulation(Elsevier, 2015) Darios, Emma S.; Barman, Susan M.; Morrison, Shaun F.; Davis, Robert P.; Seitz, Bridget M.; Burnett, Robert; Watts, Stephanie W.; N/A; Orer, Hakan S.; Faculty Member; School of Medicine; 53477Infusion of 5-hydroxytryptamine (5-HT) in conscious rats results in a sustained (up to 30 days) fall in blood pressure. This is accompanied by an increase in splanchnic blood flow. Because the splanchnic circulation is regulated by the sympathetic nervous system, we hypothesized that 5-HT would: 1) directly reduce sympathetic nerve activity in the splanchnic region; and/or 2) inhibit sympathetic neuroeffector function in splanchnic blood vessels. Moreover, removal of the sympathetic innervation of the splanchnic circulation (celiac ganglionectomy) would reduce 5-HT-induced hypotension. In anaesthetized Sprague-Dawley rats, mean blood pressure was reduced from 101 ± 4 to 63 ± 3 mm Hg during slow infusion of 5-HT (25 μg/kg/min, i.v.). Pre- and postganglionic splanchnic sympathetic nerve activity were unaffected during 5-HT infusion. In superior mesenteric arterial rings prepared for electrical field stimulation, neither 5-HT (3, 10, 30 nM), the 5-HT1B receptor agonist CP 93129 nor 5-HT1/7 receptor agonist 5-carboxamidotryptamine inhibited neurogenic contraction compared to vehicle. 5-HT did not inhibit neurogenic contraction in superior mesenteric venous rings. Finally, celiac ganglionectomy did not modify the magnitude of fall or time course of 5-HT-induced hypotension when compared to animals receiving sham ganglionectomy. We conclude it is unlikely 5-HT interacts with the sympathetic nervous system at the level of the splanchnic preganglionic or postganglionic nerve, as well as at the neuroeffector junction, to reduce blood pressure. These important studies allow us to rule out a direct interaction of 5-HT with the splanchnic sympathetic nervous system as a cause of the 5-HT-induced fall in blood pressure. © 2015 Elsevier B.V. All rights reserved.Publication Metadata only A 35--μm pitch IR thermo-mechanical MEMS sensor with AC-coupled optical readout(IEEE-Inst Electrical Electronics Engineers Inc, 2015) Ferhanoğlu, Onur; Torun, Hamdi; N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Adiyan, Ulaş; Çivitçi, Fehmi; Ürey, Hakan; PhD Student; Researcher; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; 194282; 8579A thermo-mechanical MEMS detector with 35-mu m pixel pitch is designed, fabricated, and characterized. This fabricated design has one of the smallest pixel sizes among the IR thermo-mechanical MEMS sensors in the literature. The working principle of the MEMS detector is based on the bimaterial effect that creates a deflection when exposed to IR radiation in the 812-mu m waveband. The nanometer level out of plane mechanical motion is observed in response to IR heating of the pixel, which is detected by a diffraction grating-based optical readout. Performance of MEMS sensor arrays with optical readout have been limited by a large DC bias that accompanies a small AC signal. We developed a novel optical setup to reduce the DC term and the related noise using an AC-coupled detection scheme. Detailed noise characterization of the pixel and the readout system is reported in this paper. The noise equivalent temperature difference of our detector is measured as 216 mK using f/0.86 lens with the AC-coupled optical readout. Finally, we obtained a thermal image using a single MEMS pixel combined with a scanning configuration. Despite the reduced pixel size, the measured noise levels are comparable to the state-of-the-art thermo-mechanical IR sensors.Publication Metadata only A 5-year analysis of demographics, cycle characteristics and reproductive outcomes of 907 egg freezing cycles in patients with diminished ovarian reserve and age-related fertility decline(Elsevier Science Inc, 2019) Çil, Aylin P.; Abalı, Remzi; Boza, Ayşen; Karakış, Lale S.; Ceyhan, Mehmet; Aksakal, Ece; Bahçeci, Mustafa; Urman, Bülent; Keleş, İpek; Öktem, Özgür; Ata, Mustafa Barış; Doctor; Doctor; Faculty Member; School of Medicine; Koç University Hospital; N/A; 102627; 182910