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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Preface of the special issue on global multiobjective optimization(Springer, 2021) Miettinen, Kaisa; Department of Business Administration; Sayın, Serpil; Faculty Member; Department of Business Administration; College of Administrative Sciences and Economics; 6755N/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 Spectroscopic characterization of Tm3+:TeO2-K2O-Nb2O5 glasses for 2- μm lasing applications(Elsevier Science Bv, 2012) Kurt, Adnan; Speghini, Adolfo; Bettinelli, Marco; Department of Physics; Department of Physics; Department of Physics; Görgülü, Adil Tolga; Çankaya, Hüseyin; Sennaroğlu, Alphan; Master Student; Researcher; Faculty Member; Department of Physics; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; 23851We have performed detailed experiments to investigate the spectroscopic properties of a new type of tellurite based host doped with thulium: Tm2O3:(0.70)TeO2-(0.15)K2O-(0.15)Nb2O5 having Tm2O3 concentrations of 0.125, 0.25, 0.5, and 1.0 mol%. By performing a Judd-Ofelt analysis of the absorption bands, we obtained average radiative lifetimes of 2.57 +/- 0.20 and 0.35 +/- 0.01 ms for the H-3(4) and F-3(4) levels, respectively. Furthermore, we also observed that an increase in the Tm2O3 concentration from 0.125 to 1.0 mol% results in a decrease of the measured fluorescence lifetime from 814 to 439 mu s and from 258 to 47 mu s for the H-3(4) and F-3(4) levels, respectively, due to efficient non-radiative decay. The highest quantum efficiency of 32% was obtained for the sample doped with 0.125 mol% Tm2O3 for the H-3(4) level. Results show that cross relaxation becomes important as the ion concentration is increased, leading to the quenching of the 1460-nm band and enhancement of the 1860-nm emission. The highest emission cross section of 6.85 x 10(-21) Cm-2 measured for the 1860-nm band reveals the potential of this host for the development of 2-mu m lasers in bulk glass as well as fiber media. (C) 2011 Published by Elsevier B.V.Publication Metadata only TNF-alpha inhibition prevents cognitive decline and maintains hippocampal BDNF levels in the unpredictable chronic mild stress rat model of depression(Elsevier, 2015) Şahin, Tuğce Demirtaş; Karson, Ayşe; Yazır, Yusufhan; Bayramgürler, Dilek; Utkan, Tijen; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269Previous findings have shown that patients with depression express higher levels of proinflammatory cytokines such as TNF-alpha and IL-6. We have recently found that Infliximab (a TNF-alpha inhibitor) decreased anhedonia and despair-like behavior in the rat unpredictable chronic mild stress (UCMS) model of depression suggesting that inflammation might play an important role in depression. An increasing number of studies suggest that inflammation is also associated with cognitive impairments. The current study aimed to investigate the effect of UCMS on the cognitive performance of rats and their hippocampal BDNF levels and the effect of chronic Infliximab (5 mg/kg/weekly, i.p.) treatment on these measures. Rats were subjected to different types of stressors daily for a period of 56 days to induce depression-like state. The UCMS resulted in impairments in spatial and emotional memory acquisition and retention with no effect on the level of locomotor activity. These behavioral effects of UCMS were accompanied by reduction in the level of BDNF in the CA1 and CA3 regions of the hippocampus. Chronic Infliximab treatment prevented the UCMS-induced cognitive impairments as well as the reduction in the levels of hippocampal brain-derived neurotrophic factor (BDNF). These results suggest that Infliximab improves the spatial and emotional memory impairments induced by chronic stress in rats likely through its effects on hippocampal function by modulating inflammation.Publication Metadata only On the rate of convergence of a classifier based on a transformer encoder(IEEE-Inst Electrical Electronics Engineers Inc, 2022) Gurevych, Iryna; Kohler, Michael; Department of Computer Engineering; Şahin, Gözde Gül; Faculty Member; Department of Computer Engineering; College of Engineering; 366984Pattern recognition based on a high-dimensional predictor is considered. A classifier is defined which is based on a Transformer encoder. The rate of convergence of the misclassification probability of the classifier towards the optimal misclassification probability is analyzed. It is shown that this classifier is able to circumvent the curse of dimensionality provided the a posteriori probability satisfies a suitable hierarchical composition model. Furthermore, the difference between the Transformer classifiers theoretically analyzed in this paper and the ones used in practice today is illustrated by means of classification problems in natural language processing.Publication Metadata only How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues(Cell Press, 2005) Haliloğlu, Türkan; Ma, Buyong; Nussinov, Ruth; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high-frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.Publication Metadata only Structural changes in a Schiff base molecular assembly initiated by scanning tunneling microscopy tip(Institute of Physics (IOP) Publishing, 2016) Tomak, A.; Bacaksiz, C.; Mendirek, G.; Sahin, H.; Hur, D.; Gorgun, K.; Senger, R. T.; Peeters, F. M.; Zareie, H. M.; N/A; Birer, Özgür; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/AWe report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.Publication Metadata only Intersectional stigmas are associated with lower viral suppression rates and antiretroviral therapy adherence among women living with HIV(Lippincott Williams and Wilkins (LWW), 2022) Pala, Andrea Norcini; Kempf, Mirjam-Colette; Konkle-Parker, Deborah; Wilson, Tracey E.; Tien, Phyllis C.; Wingood, Gina; Neilands, Torsten B.; Johnson, Mallory O.; Weiser, Sheri D.; Logie, Carmen H.; Turan, Janet M.; Department of Psychology; Turan, Bülent; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 219712Objectives: To explore the associations between intersectional poverty, HIV, sex, and racial stigma, adherence to antiretroviral therapy (ART), and viral suppression among women with HIV (WHIV). Design: We examined intersectional stigmas, self-report ART adherence, and viral suppression using cross-sectional data. Methods: Participants were WHIV (N = 459) in the Women's Adherence and Visit Engagement, a Women's Interagency HIV Study substudy. We used Multidimensional Latent Class Item Response Theory and Bayesian models to analyze intersectional stigmas and viral load adjusting for sociodemographic and clinical covariates. Results: We identified five intersectional stigma-based latent classes. The likelihood of viral suppression was approximately 90% lower among WHIV who experienced higher levels of poverty, sex, and racial stigma or higher levels of all intersectional stigmas compared with WHIV who reported lower experiences of intersectional stigmas. ART adherence accounted for but did not fully mediate some of the associations between latent intersectional stigma classes and viral load. Conclusion: The negative impact of intersectional stigmas on viral suppression is likely mediated, but not fully explained, by reduced ART adherence. We discuss the research and clinical implications of our findings.Publication Metadata only Pseudoduality and complex geometry in sigma models(World Scientific Publ Co Pte Ltd, 2013) Department of Mathematics; Sarısaman, Mustafa; Researcher; Department of Mathematics; College of Sciences; 217652We study the pseudoduality transformations in two-dimensional N = (2, 2) sigma models on Kahler manifolds. We show that structures on the target space can be transformed into the pseudodual manifolds by means of (anti) holomorphic preserving mapping. This map requires that torsions related to individual spaces and riemann connection on pseudodual manifold must vanish. We also consider holomorphic isometries which puts additional constraints on the pseudoduality.Publication Metadata only Cell scientist to watch - Elif Nur Fırat-Karalar(Company Biologists Ltd, 2019) Breuer, Manuel; N/A; Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; N/A; Faculty Member; Department of Molecular Biology and Genetics; N/A; College of Sciences; N/A; 206349N/A