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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only 1200 nm pumped Tm3+:Lu2O3 ceramic lasers(Optical Soc Amer, 2018) Özharar, Sarper; N/A; Department of Physics; Toker, Işınsu Baylam; Sennaroğlu, Alphan; PhD Student; Faculty Member; Department of Physics; N/A; College of Sciences; N/A; 23851We report on an experimental demonstration of a 1200-nm pumped Tm3+:Lu2O3 ceramic laser. By using a gain-switched, tunable Cr4+:forsterite laser, the excitation spectrum was measured, with optimum pumping bands centered near 1198 nm, 1204 nm, and 1211 nm. The highest slope efficiency of 21.5% was obtained at the pump wavelength of 1204 nm. Comparative energy efficiency measurements performed near 1200-nm and 800-nm pumping further showed that nearly 40% improvement was obtained in slope efficiency measured with respect to the incident pump energy for 1200-nm pumping. A transition was further observed from single-wavelength operation at 2066 nm to dual-wavelength operation near 2066 nm and 1967 nm for absorbed pump energies above 50 mu J. In this regime, two consecutive output pulses were observed in the time domain. The shortest temporal duration of the first pulse was 1.1 mu s at the incident pulse energy of 105 mu J. The duration and build-up time of the second pulse remained around 5.9 mu s and 18.5 mu s. We believe that the improved energy efficiency demonstrated for the 1.5% Tm3+:Lu2O3 ceramic with 1200-nm pumping can be used as an alternative scheme for the excitation of Tm3+:Lu2O3 ceramic lasers.Publication Metadata only A biallelic ANTXR1 variant expands the anthrax toxin receptor associated phenotype to tooth agenesis(Wiley, 2018) Dinckan, Nuriye; Du, Renqian; Akdemir, Zeynep C.; Bayram, Yavuz; Jhangiani, Shalini N.; Doddapaneni, Harsha; Hu, Jianhong; Muzny, Donna M.; Guven, Yeliz; Aktoren, Oya; Boerwinkle, Eric; Gibbs, Richard A.; Posey, Jennifer E.; Lupski, James R.; Uyguner, Zehra O.; Letra, Ariadne; N/A; Kayserili, Hülya; Faculty Member; School of Medicine; 7945Tooth development is regulated by multiple genetic pathways, which ultimately drive the complex interactions between the oral epithelium and mesenchyme. Disruptions at any time point during this process may lead to failure of tooth development, also known as tooth agenesis (TA). TA is a common craniofacial abnormality in humans and represents the failure to develop one or more permanent teeth. Many genes and potentially subtle variants in these genes contribute to the TA phenotype. We report the clinical and genetic impact of a rare homozygous ANTXR1 variant (c.1312C>T), identified by whole exome sequencing (WES), in a consanguineous Turkish family with TA. Mutations in ANTXR1 have been associated with GAPO (growth retardation, alopecia, pseudoanodontia, and optic atrophy) syndrome and infantile hemangioma, however no clinical characteristics associated with these conditions were observed in our study family. We detected the expression of Antxr1 in oral and dental tissues of developing mouse embryos, further supporting a role for this gene in tooth development. Our findings implicate ANTXR1 as a candidate gene for isolated TA, suggest the involvement of specific hypomorphic alleles, and expand the previously known ANTXR1-associated phenotypes.Publication Metadata only A case of drop foot due to piriformis syndrome(Springer Heidelberg, 2015) Yıldırım, Pelin; Güler, Tuba; Özer, Tülay; Gündüz, Osman Hakan; N/A; Mısırlıoğlu, Tuğçe Özekli; Doctor; N/A; Koç University Hospital; 175999N/APublication Metadata only A case of secondary hemophagocytic lymphohistiocytosis (HLH) following incomplete kawasaki's disease (KD). Importance of distinguishing recurrent kd from HLH(2014) Kebudi, R.; Dindar, A.; Gürakan, F.; Devecioğlu, O.; Sözmen, Banu Oflaz; Faculty Member; School of Medicine; 198711N/APublication Metadata only A coarse grained simulation study on the morphology of aba triblock copolymers(Elsevier, 2019) Onarana, Gülşah; Yurtsever, Mine; Department of Chemistry; Yılgör, İskender; Faculty Member; Department of Chemistry; College of Sciences; 24181The Dissipative Particle Dynamics (DPD) simulation technique was used to elucidate the composition-dependent equilibrium morphological behavior of three different symmetric ABA triblock copolymers, which were; poly(epsilon-caprolactone)-poly(dimethylsiloxane)-poly(epsilon-caprolactone) (PCL-PDMS-PCL), poly(epsilon-caprolactone)-poly(ethylene oxide)-poly(epsilon-caprolactone) (PCL-PEO-PCL) and poly(L-lactide)-poly(dimethylsiloxane)-poly(L-lactide) (PLLA-PDMS-PLLA). These polymers were chosen due to their biomedical and biotechnological importance. Polymeric A and B blocks were modeled as connected chain of beads with varying incompatibility. The impact of the block incompatibilities on the microphase separation as well as on the equilibrium phase behaviors were investigated at the mesoscopic scale. A detailed visual analysis of the DPD images and constructed phase diagram showed that quite different equilibrium morphologies were attainable by controlling the molecular weights of the blocks and the strength of the intermolecular interaction between them. More compatible A and B blocks underwent lamellar to cylindrical and cylindrical to spherical phase transitions at lower B block concentrations. Our results clearly showed that, Flory-Huggins interaction parameter (chi) and degree of polymerization (N) were the only control parameters, which determined the shape and size of the phase domains, as well as the extent of equilibrium nanophase separation. Our DPD simulated morphologies were compared with experimental images obtained by Atomic Force Microscopy (AFM).Publication Metadata only A combined clinical and computational approach to understand the SOD1(A4T)-mediated pathogenesis of rapidly progressive familial amyotrophic lateral sclerosis(Springer Heidelberg, 2022) Diker, Sevda; Gelener, Pınar; Teralı, Kerem; Ergören, Mahmut Çerkez; Ersin, Tan; N/A; N/A; Tunca, Ceren; Başak, Ayşe Nazlı; Researcher; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; School of Medicine; N/A; 1512Here, we aim to provide a comprehensive clinical and biomolecular description of familial amyotrophic lateral sclerosis (fALS) in a 25-year-old female patient with respect to the SOD1(A4T) genotype. The clinical diagnosis of the disease was based on family history, neurological examination, electroneurophysiological studies, and revised El Escorial criteria. The heterozygous presence of the A4T mutation in the proband was confirmed by PCR coupled with Sanger sequencing of exon 1 of the SOD1 gene. The mutation was introduced in silico into the three-dimensional structure of the native protein. After energy minimization and quality assessment, non-covalent interactions around threonine-4 and changes in protein stability were calculated computationally. The patient differed widely in age at onset, initial neurological symptoms and findings, and survival time from her kindred, in which several members are affected. SOD1(A4T)-linked fALS in this case had bulbar involvement at onset, a combination of lower and upper motor neuron signs and showed rapid progression. Unlike alanine-4, threonine-4 failed to engage in hydrophobic interactions with the vicinal non-polar amino acids. The overall fold of the modeled SOD1(A4T) mutant remained intact, but unfolding free energy estimations disclosed a decrease in the protein's stability. We report a phenotypically distinct patient with fALS due to the SOD1(A4T) mutation and further expand the largest pedigree ever published for SOD1(A4T)-linked fALS. Genotype-phenotype correlation in fALS is complex, and it demands detailed clinical investigation and advanced scientific research. Awareness of the broadened phenotypic spectrum might potentially enhance the diagnosis and genetic counseling of fALS.Publication Metadata only A communication theoretical modeling of axonal propagation in hippocampal pyramidal neurons(IEEE-Inst Electrical Electronics Engineers Inc, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Understandingthe fundamentals of communication among neurons, known as neuro-spike communication, leads to reach bio-inspired nanoscale communication paradigms. In this paper, we focus on a part of neuro-spike communication, known as axonal transmission, and propose a realistic model for it. The shape of the spike during axonal transmission varies according to previously applied stimulations to the neuron, and these variations affect the amount of information communicated between neurons. Hence, to reach an accurate model for neuro-spike communication, the memory of axon and its effect on the axonal transmission should be considered, which are not studied in the existing literature. In this paper, we extract the important factors on the memory of axon and define memory states based on these factors. We also describe the transition among these states and the properties of axonal transmission in each of them. Finally, we demonstrate that the proposed model can follow changes in the axonal functionality properly by simulating the proposed model and reporting the root mean square error between simulation results and experimental data.Publication Metadata only A comparison of parenting dimensions between deaf and hearing children(Sage Publications Inc, 2016) Ekim, Ayfer; N/A; Ocakçı, Ayşe Ferda; Faculty Member; School of Nursing; 1729Effective parenting is vital for intellectual, physical, social, and emotional development of a child. This study examined the differences between the parenting dimensions of deaf children and healthy ones. The sample of the study consisted of 292 children and their parents (146 of them deaf children and 146 of them healthy ones). Dimensions of parenting (warmth, rejection, structure, chaos, autonomy, and coercion) were measured using the Parent as Social Context Questionnaire. The mean scores of the positive parenting dimensions of warmth and autonomy of deaf children were significantly lower; however, the mean scores of the negative dimensions of chaos and coercion of deaf children were significantly higher than those of healthy ones. Deaf children can become successful adults with the help of their parents. Our results regarding parenting dimensions will be a guide for future nursing interventions planned to develop the relationships between deaf children and their parents.Publication Metadata only A correlation-based and spectrum-aware admission control mechanism for multimedia streaming in cognitive radio sensor networks(Wiley, 2017) Hosseini, Elahe S.; Esmaeelzadeh, Vahid; Berangi, Reza; Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 6647Bandwidth management and traffic control are critical issues to guarantee the quality of service in cognitive radio networks. This paper exploits a network load refinement approach to achieve the efficient resource utilization and provide the required quality of service. A connection admission control approach is introduced in cognitive radio multimedia sensor networks to provide the data transmission reliability and decrease jitter and packet end-to-end delay. In this approach, the admission of multimedia flows is controlled based on multimedia sensors' correlation information and traffic characteristics. We propose a problem, connection admission control optimization problem, to optimize the connection admission control operation. Furthermore, using a proposed weighting scheme according to the correlation of flows issued by multimedia sensors enables us to convert the connection admission control optimization problem to a binary integer-programming problem. This problem is a kind of a Knapsack problem that is solved by a branch and bound method. Simulation results verify the proposed admission control method's effectiveness and demonstrate the benefits of admission control and traffic management in cognitive radio multimedia sensor networks.Publication Metadata only A cross sectional study evaluating the relationship of acne to androgenetic alopecia subtype and severity(Springer, 2024) Kazan, Didem; Gencebay, Gullu; Caf, Nazli; Esen, Beril Kara; Oba, Muazzez Cigdem; Özkoca, Defne; Koç University HospitalThe circulating androgens have a role in the pathogenesis of both acne vulgaris and androgenetic alopecia; an association between these two have been found previously. The aim of this study is to investigate the relationship of the severity of acne vulgaris lesions to the subtype of AGA; and to validate the relationship between severities of acne vulgaris and AGA. This study was conducted cross-sectionally at five different dermatology clinics. Male and female androgenetic alopecia patients with comorbid acne vulgaris have been included. The age, gender, severity of acne lesions, subtype of androgenetic alopecia and the severity of androgenetic alopecia were noted. The severity of acne lesions were graded according to the Global Acne Severity Scale and androgenetic alopecia was graded according to the Hamilton and Ludwig Scales. SPSS v 21 was used for the statistical analysis. A total of 101 patients have been included (12 male and 89 female). The mean age of the patients with severe acne was statistically significantly lower (p = 0.020). The difference in terms of gender was statistically insignificant (p = 0.388). The severity of acne vulgaris was found to be independent of the severity and of the subtype of AGA; p = 0.623 and 0.870 respectively. Neither a relationship between the severity of androgenetic alopecia and severity of acne; nor a relationship between acne severity and androgenetic alopecia subtype were found in this study. Thus we report that, acne severity is independent of the subtype and stage of the co-existing androgenetic alopecia.Publication Metadata only A deformation-based approach to tuning of magnetic micromechanical resonators(2018) Yalçınkaya, Arda D.; Department of Mechanical Engineering; N/A; Department of Mechanical Engineering; Biçer, Mahmut; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 115108Resonance frequency tuning in magnetic micromechanical resonators remains a primary field of study for frequency reference applications. The use of magnetic micromechanical resonators for innovative timing, oscillator and sensing applications necessitates a platform for the precise control of the resonance frequency. The present work addresses a deformation based technique for tuning the resonance frequency of nickel micromechanical resonators. Frequency response is measured through magnetic actuation and optical readout. The tuning approach is based on a combination of flexural deformation and uniaxial strain. The bending deformation is achieved by using a DC current through the microbeam. This magnetomotive mechanism reduces the resonance frequency by about 13% for a maximum DC current of 80 mA. A substrate bending method is used for applying uniaxial strain to increase the resonance frequency by about 8%. A bidirectional frequency modulation is thus demonstrated by utilizing both deformation techniques. The interpretation of results is carried out by finite element analysis and electromechanical analogy in an equivalent circuit. Using deformation techniques, this study provides a rigorous approach to control the resonance frequency of magnetic micromechanical resonators.Publication Metadata only A developmental study of glutamatergic neuron populations in the ventrobasal and the lateral geniculate nucleus of the thalamus: Comparing Genetic Absence Rats from Strasbourg (GAERS) and normal control wistar rats(Elsevier, 2017) Kirazhi, Ozlem; Yildizel, Sercan; Onat, Filiz; Kaptanoglu, Erkan; Çavdar, Safiye; Faculty Member; School of Medicine; 1995An imbalance of GABAergic inhibition and glutamatergic excitation is suspected to be the cause of absence epileptic seizures. Absence seizures are known to be generated in thalamocortical circuitry. In the present study we used light microscopy immunohistochemistry to quantify the density of glutamate+ve neurons at two developmental stages (P10 and P60) in two thalamic nuclei, the ventrobasal (VB) and lateral geniculate nucleus (LGN) in Wistar rats and compared the results with similar data obtained from genetic absence epilepsy rats from Strasbourg (GAERS). Rats were perfused transcardially with glutaraldehyde and paraformaldehyde fixative, then samples from VB and LGN were removed from each animal and sectioned. The glutamatergic neurons were labelled using light-microscopic glutamate immunohistochemistry. The disector method was used to quantify the glutamate+ve neurons in VB and LGN of GAERS and Wistar rats. The data were statistically analyzed. The distribution of the glutamate+ve neurons in the VB thalamic nucleus showed a significant reduction in the neuronal profiles per unit thalamic area from P10 to P60 in both Wistar and GAERS. The decrease was greater in the GAERS compared to the Wistar animals. However, in the LGN no reduction was observed either in the Wistar or in the GAERS. Comparing the density of glutamate+ve neurons in the VB thalamic nucleus of P10 of Wistar animals with of P10 GAERS showed statistically significant greater densities of these neurons in GAERS than in the Wistar rats. However no significant difference was present at P60 between the Wistar and GAERS animals. The disproportional decrease in GAERS may be related to the onset of absence seizures or may be related to neurogenesis of absence epilepsy. (C) 2016 ISDN. Published by Elsevier Ltd. All rights reserved.Publication Metadata only A differential integrability condition for two-dimensional Hamiltonian systems(Czech Technical Univ Prague, 2014) N/A; Department of Mathematics; Mostafazadeh, Ali; Faculty Member; Department of Mathematics; College of Sciences; 4231We review, restate, and prove a result due to Kaushal and Korsch [Phys. Lett. A 276, 47 (2000)] on the complete integrability of two-dimensional Hamiltonian systems whose Hamiltonian satisfies a set of four linear second order partial differential equations. In particular, we show that a two- dimensional Hamiltonian system is completely integrable, if the Hamiltonian has the form H = T + V where V and T are respectively harmonic functions of the generalized coordinates and the associated momenta.Publication Metadata only A dynamic model of an overhung rotor with ball bearings(Sage, 2011) Şanlıtürk, K. Y.; N/A; Çakmak, Onur; PhD Student; Graduate School of Sciences and Engineering; N/AA ball bearing comprising rolling elements, inner and outer rings, and a cage structure can be described as a multi-body system (MBS). In order to predict the dynamic behaviour and resonance characteristics of a rotor-ball bearing system, it can be modelled and analysed as a MBS with flexible and rigid parts. In this study, a ball bearing is modelled with MBS approach using MSC ADAMS commercial software. The Hertzian theory is used for modelling the contact dynamics between the balls and the rings. The ball bearing model is then assembled with the rotor model which comprised a shaft and a disc positioned at the free end of the shaft. The ball bearing model is used with both flexible and rigid shaft assumptions in order to highlight the differences between the two cases. For the flexible shaft case, the MBS model also included a finite element model of the shaft. As expected, it is necessary to include the flexibility of the shaft in the model in order to to predict the changes in the modal characteristics of the system as a function of the rotor speed. Furthermore, including the gyroscopic effects leads to observe the forward and backward travelling modes with different natural frequencies. The effects of the bearing diametral clearance and localized defects on the inner and outer rings are modelled and analysed using the model developed. Also, the effects of the rotor unbalance on the vibration level of the whole system are examined. A test rig - consisting of two ball bearings, a shaft, and a disc - is also designed and developed so as to validate the theoretical model using experimental data. Order tracking and modal analyses are carried out and Campbell diagrams are obtained. Finally, the theoretical and the experimental results are compared and a refined MBS model is obtained for further analyses.Publication Metadata only A Fourier transform spectrometer using resonant vertical comb actuators(Institute of Physics (IOP) Publishing, 2006) Wolter, Alexander; N/A; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579The design, fabrication and characterization of a novel out-of-plane vertical comb-drive actuator based lamellar grating interferometer (LGI) is reported. The interferometer utilizes resonant mode vertical comb actuators, where comb fingers are simultaneously used for actuation and as a movable diffraction grating, making the device very compact. The Fourier transform of the zeroth order intensity pattern as a function of the optical path difference gives the spectrum of light. The main advantages offered by the proposed device are a long travel range (i.e. good spectral resolution), a large clear aperture (i.e. high light efficiency), and a very simple, robust and compact spectrometer structure. Peak-to-peak 106 mu m out-of-plane deflection is observed in ambient pressure and at 28 V, corresponding to a theoretical spectral resolution of about 0.4 nm in the visible band and 3.6 nm at 1.5 mu m. A simple CMOS compatible process based on bulk micromachining of a silicon-on-insulator wafer is used for the device fabrication.Publication Metadata only A fredholm alternative-like result on power bounded operators(Scientific Technical Research Council Turkey-Tubitak, 2011) Yavuz, Onur; Department of Mathematics; Ülger, Ali; Faculty Member; Department of Mathematics; College of Sciences; N/ALet X be a complex Banach space and T:X\rightarrow X be a power bounded operator, i.e., \sup_{n \geq 0}\ T^n\Publication Metadata only A general test for SSD portfolio efficiency(Springer, 2015) Kopa, Milos; N/A; Post, Gerrit Tjeerd; Other; Graduate School of Business; N/AWe develop and implement a Linear Programming test to analyze whether a given investment portfolio is efficient in terms of second-order stochastic dominance relative to all possible portfolios formed from a set of base assets. In case of efficiency, the primal model identifies a sub-gradient vector of a utility function that rationalizes the evaluated portfolio. In case of inefficiency, the dual model identifies a second, efficient portfolio that dominates the evaluated portfolio. The test gives a general necessary and sufficient condition, and can deal with general linear portfolio restrictions, inefficiency degree measures, and scenarios with unequal probabilities. We also develop a compact version of the test that substantially reduces computational burden at the cost of losing information about the dual dominating portfolio in case of inefficiency. An application to US investment benchmark data qualifies a broad stock market index as significantly inefficient, and suggests that no risk-averse investor would hold the market index in the face of attractive premiums offered by some more concentrated investment portfolios.Publication Metadata only A genetic cause for intractable seizures: atypical Gaucher disease with a novel pathological variant(WILEY, 2024) Üçem, Selen; Avcı, Şahin; Gürses, Rabia Candan; School of Medicine; Koç University HospitalPublication Metadata only A glimpse into the future of TAVR(Wiley-Blackwell, 2016) Marmagkiolis, Konstantinos; N/A; Çilingiroğlu, Mehmet; Other; School of Medicine; Koç University Hospital; N/AImportant differences still exist in the management of patients who receive TAVR in Europe and in the USA. Provisional participation of cardiovascular surgeons and imaging cardiologists, use of TEE, general anesthesia with endotracheal intubation, and length of stay are some of the major differences which may define the future of TAVR in the USA. TAVR procedure will most likely be performed without CT surgery presence and with limited echocardiographic imaging guidance in USA in the near future as it is already being done in Europe.Publication Metadata only A historical sociology of disability: human validity and invalidity from antiquity to early modernity(Sage Publications India Pvt Ltd, 2022) N/A; Bozkurt, Ozancan; Master Student; Graduate School of Social Sciences and Humanities; N/AN/A