Mühendislik ve Doğa Bilimleri Fakültesi

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Citation - WoS: 22
Citation - Scopus: 25
Absolute Configuration and Biological Profile of Pyrazoline Enantiomers as Mao Inhibitory Activity
(Wiley, 2019) Goksen, Umut Salgin; Sarıgül, Sevgi; Bultinck, Patrick; Herrebout, Wouter; Doğan, İlknur; Yelekçi, Kemal; Uçar, Gülberk; Kelekçi, Nesrin Gökhan
A new racemic pyrazoline derivative was synthesized and resolved to its enantiomers using analytic and semipreparative high-pressure liquid chromatography. The absolute configuration of both fractions was established using vibrational circular dichroism. The in vitro monoamine oxidase (MAO) inhibitory profiles were evaluated for the racemate and both enantiomers separately for the two isoforms of the enzyme. The racemic compound and both enantiomers were found to inhibit hMAO-A selectively and competitively. In particular the R enantiomer was detected as an exceptionally potent and a selective MAO-A inhibitor (K-i = 0.85 x 10(-3) +/- 0.05 x 10(-3) mu M and SI: 2.35 x 10(-5)) whereas S was determined as poorer compound than R in terms of K-i and SI (0.184 +/- 0.007 and 0.001). The selectivity of the enantiomers was explained by molecular modeling docking studies based on the PDB enzymatic models of MAO isoforms.
Citation - WoS: 8
Citation - Scopus: 9
Antifungal Screening and in Silico Mechanistic Studies of an In-House Azole Library
(2019) Sarı, Suat; Kart, Didem; Sabuncuoğlu, Suna; Doğan, İnci Selin; Özdemir, Zeynep; Bozbey, İrem; Gencel, Melis; Eşsiz, Şebnem; Reynisson, Jóhannes; Karakurt, Arzu; Saraç, Selma; Dalkara, Sevim
Systemic Candida infections pose a serious public health problem with high morbidity and mortality. C. albicans is the major pathogen identified in candidiasis; however, non-albicans Candida spp. with antifungal resistance are now more prevalent. Azoles are first-choice antifungal drugs for candidiasis; however, they are ineffective for certain infections caused by the resistant strains. Azoles block ergosterol synthesis by inhibiting fungal CYP51, which leads to disruption of fungal membrane permeability. In this study, we screened for antifungal activity of an in-house azole library of 65 compounds to identify hit matter followed by a molecular modeling study for their CYP51 inhibition mechanism. Antifungal susceptibility tests against standard Candida spp. including C. albicans revealed derivatives 12 and 13 as highly active. Furthermore, they showed potent antibiofilm activity as well as neglectable cytotoxicity in a mouse fibroblast assay. According to molecular docking studies, 12 and 13 have the necessary binding characteristics for effective inhibition of CYP51. Finally, molecular dynamics simulations of the C. albicans CYP51 (CACYP51) homology model's catalytic site complexed with 13 were stable demonstrating excellent binding.
Citation - WoS: 11
Citation - Scopus: 11
Application of Epidemic Models To Phase Transitions
(Taylor & Francis Ltd, 2012) Bilge, Ayşe Hümeyra; Pekcan, Önder; Gürol, M. V.
The Susceptible-Infected-Recovered (SIR) and Susceptible-Exposed-Infected-Recovered (SEIR) models describe the spread of epidemics in a society. In the typical case, the ratio of the susceptible individuals fall from a value S-0 close to 1 to a final value S-f, while the ratio of recovered individuals rise from 0 to R-f = 1 - S-f. The sharp passage from the level zero to the level R-f allows also the modeling of phase transitions by the number of "recovered" individuals R(t) of the SIR or SEIR model. In this article, we model the sol-gel transition for polyacrylamide-sodium alginate (SA) composite with different concentrations of SA as SIR and SEIR dynamical systems by solving the corresponding differential equations numerically and we show that the phase transitions of "classical" and "percolation" types are represented, respectively, by the SEIR and SIR models.
Citation - WoS: 2
Citation - Scopus: 3
Aryl Butenoic Acid Derivatives as a New Class of Histone Deacetylase Inhibitors: Synthesis in Vitro Evaluation and Molecular Docking Studies
(Scientific Technical Research Council Turkey-Tubitak, 2014) Esiyok, Peruze Ayhan; Seven, özlem; Eymur, Guluzar; Tatar, Gamze Bora; Erden, Didem Dayangaç; Yelekçi, Kemal; Yurter, Hayat; Demir, Ayhan S.
New aryl butenoic acid derivatives have been synthesized by combining hydroxy- or methoxy-substituted phenyl rings as the capping group with a double bond in the short linker as well as metal binding groups enoic ester and salts bearing either methyl or morpholine. These compounds have been shown to possess promising histone deacetylase inhibition activities via in vitro fluorometric assay and molecular docking studies.
Citation - WoS: 1
Citation - Scopus: 2
A Bayesian Approach To Developing a Strategic Early Warning System for the French Milk Market
(Halmstad University, 2017) Bisson, Christophe; Gürpınar, Furkan
A new approach is provided in our paper for creating a strategic early warning system allowing the estimation of the future state of the milk market as scenarios. This is in line with the recent call from the EU commission for tools that help to better address such a highly volatile market. We applied different multivariate time series regression and Bayesian networks on a pre-determined map of relations between macro-economic indicators. The evaluation of our findings with root mean square error (RMSE) performance score enhances the robustness of the prediction model constructed. Our model could be used by competitive intelligence teams to obtain sharper scenarios, leading companies and public organisations to better anticipate market changes and make more robust decisions.
Citation - WoS: 5
Citation - Scopus: 7
Biclustering Expression Data Based on Expanding Localized Substructures
(Springer-Verlag Berlin, 2009) Erten, Cesim; Sözdinler, Melih
Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. We provide a method LEB (Localize-and-Extract Biclusters) which reduces the search space into local neighborhoods within the matrix by first localizing correlated structures. The localization procedure takes its roots from effective use of graph-theoretical methods applied to problems exhibiting a similar structure to that of biclustering. Once interesting structures are localized the search space reduces to small neighborhoods and the biclusters are extracted from these localities. We evaluate the effectiveness of our method with extensive experiments both using artificial and real datasets.
Citation - WoS: 2
Citation - Scopus: 2
Broadband Matching Via Reflection Function Optimization
(Wiley, 2017) Şengül, Metin Y.
In this paper a practical approach is presented for designing broadband matching networks via reflection function optimization. In the proposed algorithm the input or output reflection function of the matching network is expressed in terms of three real polynomials describing the matching network load and generator reflection coefficients. Next one of the polynomials is optimized to get minimum reflection function values in the passband. Then matching network topology and element values are obtained via the formed input reflection coefficient expression. Two examples are presented to explain the usage of the new approach. Copyright (c) 2016 John Wiley & Sons Ltd.
Citation - WoS: 2
Citation - Scopus: 3
Broadband Matching Via Unequal Length Cascaded Transmission Lines
(World Scientific Publ Co Pte Ltd, 2017) Şengül, Metin Y.
In this paper a new approach based on the real frequency technique (RFT) has been proposed to solve broadband matching problems using cascaded unequal length transmission lines. At the end of the design process optimum characteristic impedance and delay values of transmission lines are obtained. Two examples are given to illustrate the utilization of the proposed approach.
Broadband Microwave Amplifier Design With Lumped Elements
(Walter De Gruyter Gmbh, 2016) Şengül, Metin Y.
This study introduces a broadband microwave amplifier design that utilizes the measured scattering parameters of active devices without assuming an initial topology for the matching networks or an analytic form of the system transfer function. The algorithm can be extended to design multistage broadband microwave amplifiers. An example is given to illustrate the application of the proposed method. It was found that the proposed method provides very good initials for CAD tools to further improve amplifier performance by working on the element values.
Citation - WoS: 18
Citation - Scopus: 19
Carboxylic Acid Derivatives Display Potential Selectivity for Human Histone Deacetylase 6: Structure-Based Virtual Screening Molecular Docking and Dynamics Simulation Studies
(Elsevier Science, 2018) Uba, Abdullahi Ibrahim; Yelekçi, Kemal
Human histone deacetylase 6 (HDAC6) has been shown to play a major role in oncogenic cell transformation via deacetylation of alpha-tubulin making it a viable target of anticancer drug design and development. The crystal structure of HDAC6 catalytic domain 2 has been recently made available providing avenues for structure-based drug design campaign. Here in our continuous effort to identify potentially selective HDAC6 inhibitors structure-based virtual screening of similar to 72 461 compounds was carried out using Autodock Vina. The top 100 compounds with calculated Delta G < -10 kcal/mol were manually inspected for binding mode orientation. Furthermore the top 20 compounds with reasonable binding modes were evaluated for selectivity by further docking against HDAC6 and HDAC7 using Autodock4. Four compounds with a carboxylic fragment displayed potential selectivity for HDAC6 over HDAC7 and were found to have good druglike and ADMET properties. Their docking complexes were then submitted to 10 ns-molecular dynamics (MD) simulation using nanoscale MD (NAMD) software to examine the stability of ligand binding modes. These predicted inhibitors remained bound to HDAC6 in the presence of water and ions and the root-mean-square deviation (RMSD) radius of gyration (Rg) and nonbond distance (protein-ligand) profiles suggested that they might be stable over time of the simulation. This study may provide scaffolds for further lead optimization towards the design of HDAC6 inhibitors with improved selectivity. (C) 2018 Elsevier Ltd. All rights reserved.
Citation - WoS: 17
Citation - Scopus: 16
Cation Effect on Slow Release From Alginate Beads: a Fluorescence Study
(Springer/Plenum Publishers, 2014) Kaygusuz, Hakan; Erim, F. Bedia; Pekcan, Önder; Evingür, Gülşen Akin
In this study spherical alginate beads containing pyranine (P-y) as a fluorescence probe were prepared by ionotropic gelation of a sodium alginate solution. The steady state fluorescence technique was used to study pyranine release from the alginate beads crosslinked with calcium barium and aluminum ions respectively. The slow release of P-y was observed with the time drive mode of the spectrophotometer at 512 nm. Fluorescence emission intensity (I-p) from P-y was monitored during the release process and the encapsulation efficiency (EE) of pyranine from the alginate beads was calculated. The Fickian Diffusion model was used to measure the release coefficients D-sl. It was seen that the slow release coefficients of pyranine from the alginate beads crosslinked with Ca2+ Ba2+ and Al3+ ions increased in the following order: D-sl (Al3+)> D-sl (Ca2+)> D-sl (Ba2+). In contrast the initial amount of pyranine and EE into the beads showed the reverse behavior.
Citation - WoS: 1
Citation - Scopus: 4
Channel Estimation in Underwater Cooperative Ofdm System With Amplify-And Relaying
(IEEE, 2012) Şenol, Habib; Panayırcı, Erdal; Erdoğan, Mustafa; Uysal, Murat
This paper is concerned with a challenging problem of channel estimation for amplify-and-forward cooperative relay based orthogonal frequency division multiplexing (OFDM) systems in the presence of sparse underwater acoustic channels and of the correlative non-Gaussian noise. We exploit the sparse structure of the channel impulse response to improve the performance of the channel estimation algorithm due to the reduced number of taps to be estimated. The resulting novel algorithm initially estimates the overall sparse channel taps from the source to the destination as well as their locations using the matching pursuit (MP) approach. The correlated non-Gaussian effective noise is modeled as a Gaussian mixture. Based on the Gaussian mixture model an efficient and low complexity algorithm is developed based on the combinations of the MP and the space-alternating generalized expectation-maximization (SAGE) technique to improve the estimates of the channel taps and their location as well as the noise distribution parameters in an iterative way. The proposed SAGE algorithm is designed in such a way that by choosing the admissible hidden data properly on which the SAGE algorithm relies a subset of parameters is updated for analytical tractability and the remaining parameters for faster convergence Computer simulations show that underwater acoustic (UWA) channel is estimated very effectively and the proposed algorithm has excellent symbol error rate and channel estimation performance.
Citation - WoS: 13
Characterization of Mps Capped Cds Quantum Dots and Formation Self-Assembled Quantum Dots Thin Films on a Glass Substrate
(Natl Inst R&D Materials Physics, 2011) Koç, Kenan; Tepehan, Fatma Zehra; Tepehan, Galip Gültekin
Colloidal powdered and thin film forms of MPS capped CdS quantum dots have been produced by combination of colloidal chemistry and sol-gel method. Nanoparticles were self-assembled directly on a glass substrate using spin coating method without introducing any matrix. Colloidal powdered and thin film forms were characterised by absorbance photolimunescence XRD FT-IR HRTEM and AFM measurements. The HRTEM images give a grain size of 2.5-3.0 nm and this is in agreement with the values found in the absorbance and XRD measurement. Average size of the quantum dots increase with increasing of heat treatment temperature due to Oswald ripening.
Chebyshev Nets Formed by Ricci Curves in a 3-Dimensional Weyl Space
(Elsevier Science Bv, 2005) Yıldırım, Gülçin Çivi; Özdeğer, Abdülkadir
In this paper Ricci curves in a 3-dimensional Weyl space W-3(g T) are defined and it is shown that any 3-dimensional Chebyshev net formed by the three families of Ricci curves in a W-3(g T) having a definite metric and Ricci tensors is either a geodesic net or it consists of a geodesic subnet the members of which have vanishing second curvatures. In the case of in indefinite Ricci tensor only one of the members of the geodesic subnet under consideration has a vanishing second curvature. (c) 2004 Elsevier B.V. All rights reserved.
Chelate Extraction of Transition Metal Ions by Ethylene Diamine Diacetic Acid With N-Substituted Octadecyl Groups
(Taylor & Francis Inc, 2002) Bıçak, Niyazi; Şungur, Şana Kutun; Tan, Nükhet; Gazi, Mustafa
An organic-soluble chelating agent NN'-di-n-octadecyl ethylenediamine-NN'-diacetic acid (DOED) has been synthesized in two steps by (i) condensation of dibromoethane with 1-amino octadecane (octadecylamine) and (ii) subsequent reaction with sodium chloro acetate in alcohol-water mixture. The chelating agent in 2-ethylhexanol-cyclohexanol (1:1) solutions shows extremely high chelating ability for Ni(II) Co(II) Cu(II) Fe(111) Cr(III) and Cd(II) ions in neutral aqueous solutions. Extractions take place by the formation of (1:1) ligand-to-metal complexes and extraction coefficients are in the range 0.74-0.99. The ligand can be regenerated almost quantitatively by washing its complexes with 1M HCl and 0.2 M NaOH solutions successively. In each extraction step the organic solution exhibits a clear-cut phase separation and does not need salting out. The chelating agent can be regenerated and recycled more than 24 times without losing its extracting ability due to nonhydrolyzability of linkages in its structure. Experiments indicate that in high metal concentrations (more than 1 M) the solvent mixture itself is able to extract appreciable amounts of metal ions (33-53%). The solubility in organic solvents induced by long aliphatic chains seems to be general and the method presented offers possibility of large scale chelate extraction of metal ions of relatively low concentrations.
Collective Enhancement of Nuclear State Densities by the Shell Model Monte Carlo Approach
(IOP Publishing Ltd, 2015) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
The shell model Monte Carlo (SMMC) approach allows for the microscopic calculation of statistical and collective properties of heavy nuclei using the framework of the configuration-interaction shell model in very large model spaces. We present recent applications of the SMMC method to the calculation of state densities and their collective enhancement factors in rare-earth nuclei.
Citation - Scopus: 11
Competitive Intelligence and Information Technology Adoption of Smes in Turkey: Diagnosing Current Performance and Identifying Barriers
(Halmstad University, 2013) Wright, Sheila; Bisson, Christophe; Duffy, Alistair P.
The need for SMEs to behave in a more concise and coherent competitive fashion is well recognised. This study reports on an empirical study of SMEs in Turkey. Their responses were applied to a behavioural and information technology adoption framework which enabled the identification of areas where changes would be required for these firms to begin operating at a higher level of competence. The findings revealed significant scope for improvements on all strands of the diagnostic framework: attitude gathering location technology support IT systems support and finally use of intelligence-based output by decision-makers. Through free form responses it was also possible to identify barrier to higher level adoption and performance inhibiters which were subsequently categorised and assessed for significance.
Citation - WoS: 10
Citation - Scopus: 12
Contraction Blockers for Graphs With Forbidden Induced Paths
(Springer-Verlag Berlin, 2015) Diner, Öznur Yaşar; Paulusma, Daniel; Picouleau, Christophe; Ries, Bernard
We consider the following problem: can a certain graph parameter of some given graph be reduced by at least d for some integer d via at most k edge contractions for some given integer k? We examine three graph parameters: the chromatic number clique number and independence number. For each of these graph parameters we show that when d is part of the input this problem is polynomial-time solvable on P-4-free graphs and NP-complete as well as W[1]-hard with parameter d for split graphs. As split graphs form a subclass of P-5-free graphs both results together give a complete complexity classification for P-l-free graphs. The W[1]-hardness result implies that it is unlikely that the problem is fixed-parameter tractable for split graphs with parameter d. But we do show on the positive side that the problem is polynomial-time solvable for each parameter on split graphs if d is fixed i.e. not part of the input. We also initiate a study into other subclasses of perfect graphs namely cobipartite graphs and interval graphs.
Citation - WoS: 8
Citation - Scopus: 10
Controlling the Growth of Particle Size and Size Distribution of Silica Nanoparticles by the Thin Film Structure
(Springer, 2012) Uysal, Bengü Özuğur; Tepehan, Fatma Zehra
Nanostructured silicondioxide thin films were prepared by sol-gel spin coating technique. The SiO2 films were made using a conventional mixture of tetraethoxysilane (TEOS) deionized water and ethanol with various NH3/TEOS ratios. The nanostructured silica films were made using a mixture of the SiO2 sol and regular SiO2 sol to control the enlargement of the particles inside the films. The structural morphological and optical characterizations of the as-deposited and annealed films were carried out using X-ray diffraction (XRD) atomic force microscopy scanning electron microscopy NKD spectrophotometer and ultraviolet-visible (UV-vis) spectroscopy. The transmittance data of the infrared spectra of the films were recorded using an FT-IR Spectrometer. The XRD studies showed that as-deposited films were amorphous and the formation of the alfa-cristobalite phase of the silica film was investigated at annealing temperature close to 1100 A degrees C. Optical properties of the transmittance spectra in the s and p-polarization modes were collected. Refractive indices and extinction coefficients were determined with respect to the NH3/TEOS ratios in the compositions of the films. Optical cut-off wavelength values were investigated from the extrapolation of the absorbance spectra which was estimated from the UV-vis spectroscopy measurements. A red shift in the absorption threshold indicated that the size of silica nanoparticles was increased by an increase in the NH3/TEOS volume ratio from 1:64 to 1:8.
Citation - WoS: 2
Citation - Scopus: 3
Corrected Panel-Reactive Antibody Positivity Rates for Hypersensitized Patients in Turkish Population With Calculated Panel-Reactive Antibody Software
(Elsevier Science Inc, 2017) Karadeniz, Sedat Tanju; Akgül, Sebahat Usta; Öğret, Yeliz; Çiftçi, Hayriye Şentürk; Bayraktar, Adem; Bakkaloğlu, Hüseyin; Çalışkan, Yaşar Kerem; Yelekçi, Kemal; Türkmen, Aydin; Aydın, Ali Emin; Oğuz, Fatma Savran; Çarin, Mahmut Nezih; Aydın, Filiz
however the rate was 86.2% using the cPRA. Discussion. cPRA shows the rate of the rejected donors according to all unacceptable antigens. The need for a list of unacceptable antigens in place of the PRA positivity rate is a real change in the sensitization-dependent calculation as cPRA positivity rate. Conclusion. In principal implementation of cPRA will encourage many centers and laboratories to adopt a standard measurement of sensitization in Turkey. It will increase the chances of better donor match particularly for hypersensitized patients by the creation of an unacceptable mismatch program using cPRA software.

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