WoS İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/4465

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Citation - WoS: 12
Citation - Scopus: 15
Accurate Refinement of Docked Protein Complexes Using Evolutionary Information and Deep Learning
(Imperıal College Press, 2016) Akbal-Delibas, Bahar; Farhoodi, Roshanak; Pomplun, Marc; Haspel, Nurit
One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work we introduced AccuRefiner a machine learning based tool for refining protein-protein complexes. Given a docked complex the refinement tool produces a small set of refined versions of the input complex with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The method employs a unique ranking tool that accurately predicts the RMSD of docked complexes with respect to the native structure. In this work we use a deep learning network with a similar set of features and five layers. We show that a properly trained deep learning network can accurately predict the RMSD of a docked complex with 1.40 angstrom error margin on average by approximating the complex relationship between a wide set of scoring function terms and the RMSD of a docked structure. The network was trained on 35000 unbound docking complexes generated by RosettaDock. We tested our method on 25 different putative docked complexes produced also by RosettaDock for five proteins that were not included in the training data. The results demonstrate that the high accuracy of the ranking tool enables AccuRefiner to consistently choose the refinement candidates with lower RMSD values compared to the coarsely docked input structures.
Advanced Signal Processing Algorithms for Wireless Communications
(Springer-Verlag Berlin, 2006) Panayırcı, Erdal; Çırpan, Hakan Ali
Traditional wireless technologies are not well suited to meet the extremely demanding requirements of providing the very high data rates with the ubiquity mobility and portability characteristic of cellular systems. Some fundamental barriers related to the nature of the radio channel as well as the limited bandwidth availability at the frequencies of interest stand in the way. Unique sets of efficient advanced signal processing algorithms and techniques is the one of the primary enablers that will allow lifting these limits primarily due to the impressive advent of low cost and low power digital signal processors. As an application of advanced signal processing techniques we will consider the solution of blind phase noise estimation and data detection problem via a computationally efficient sequential Monte Carlo (SMC) methodology in this paper.
Citation - WoS: 9
Citation - Scopus: 12
Affective Modulation of Working Memory Maintenance: the Role of Positive and Negative Emotions
(UNIV ECONOMICS) Gökçe, Ahu; Zinchenko, Artyom; Annac, Efsun; Conci, Markus; Geyer, Thomas
The present study investigated the impact of task-irrelevant emotional images on the retention of information in spatial working memory (WM). Two experiments employed a delayed matching-to-sample task where participants had to maintain the locations of four briefly presented squares. After a short retention interval, a probe item appeared and participants were required to indicate whether the probe position matched one of the previously occupied square positions. During the retention interval, task-irrelevant negative, positive, or neutral emotional pictures were presented. The results revealed a dissociation between negative and positive affect on the participants' ability to hold spatial locations in WM. While negative affective pictures reduced WM capacity, positive pictures increased WM capacity relative to the neutral images. Moreover, the specific valence and arousal of a given emotional picture was also related to WM performance: While higher valence enhanced WM capacity, higher levels of arousal in turn reduced WM capacity. Together, our findings suggest that emotions up- or down-regulate attention to items in WM and thus modulate the short-term storage of visual information in memory.
Analysis and Optimization of Matching Networks-I Getting Started With Ads
(Springer-Verlag Berlin, 2008) Şengül, Metin Y.
[Abstract Not Available]
Analysis and Optimization of Matching Networks-Ii Getting Started With Microwave Office
(Springer-Verlag Berlin, 2008) Şengül, Metin Y.
[Abstract Not Available]
Citation - WoS: 1
Citation - Scopus: 2
Analysis of Local and Centralized Control of Pv Inverters for Voltage Support in Distribution Feeders
(IEEE, 2021) Ceylan, Oguzhan; Paudyal, Sumit; Pisica, Ioana
Higher photovoltaic penetration on distribution system brings operational challenges including overvoltage issues. With smart inverters, efficient voltage control can be achieved through adjusting active/reactive powers of inverters. However, reactive power may not be as effective as active power in regulating voltage due to high R/X ratio of distribution networks. Thus, active power curtailment (APC) techniques in coordination with reactive power control are required in distribution networks. In this study, we aim to evaluate the performances of a sensitivity based method and an optimal power flow (OPF) based centralized method of reactive power control (in coordination with APC) from inverters in managing voltage profile on distribution networks. We performed simulations on a 730-node MV/LV system upto 100% PV penetration. Based on the case studies using different penetration levels of PVs, we observed that: a) sensitivity based method is not always able to solve overvoltage issues and energy curtailments are high, and b) OPF-based method can ensure that voltage remains within the operational bound with significantly less energy curtailment.
Citation - WoS: 4
Citation - Scopus: 4
Analysis of the Effects of Intermodal Terminals for the Solutions of Urban Logistics Problems in Istanbul City
(Springer International Publishing Ag, 2016) Görçün, Ömer Faruk
We analyzed the urban logistics problems in Istanbul City and we tried to show the solutions of these problems thanks to intermodal freight terminals. Istanbul is a center of trade tourism and industry
Citation - WoS: 7
Citation - Scopus: 7
Anytime. Everywhere. Mobile Learning in Higher Education: Creating a Gis Course
(Springer-Verlag Berlin, 2012) Erkollar, Alptekin; Oberer, Birgit
The course concepts introduced in this contribution were implemented in 2011 in a university in Turkey and show an approach for integrating mobile learning modules in higher education. The results of the course show the advantages as well as potential for improvement of the system and the use of it in higher education.
Applications of Eigenvalue Counting and Inclusion Theorems in Model Order Reduction
(Springer-Verlag Berlin, 2010) Yetkin, E. Fatih; Dağ, Hasan
We suggest a simple and an efficient iterative method based on both the Gerschgorin eigenvalue inclusion theorem and the deflation methods to compute a Reduced Order Model (ROM) to lower greatly the order of a given state space system. This method is especially efficient in symmetric state-space systems but it works for the other cases with some modifications.
The Association of Gvhd With Hla Dr Alleles, Ifn-Gamma, Tgf-Beta, and Mbl2 Gene Polymorphism
(Wiley, 2019) Oğuz, Rusdu; Çiftçi, Hayriye Şentürk; Gökçe, Muge; Öğret, Yeliz; Karadeniz, Sedat Tanju; Pehlivan, Sacide; Aydın, Filiz
[Abstract Not Available]
Citation - WoS: 2
Better Late Than Never? the Role of Policy in the Turkish Cinematic Revival
(Intellect Ltd, 2010) Behlil, Melis
[Abstract Not Available]
Citation - WoS: 5
Citation - Scopus: 5
Block Elimination Distance
(Springer Japan Kk, 2022) Diner, Oznur Yasar; Giannopoulou, Archontia C.; Stamoulis, Giannos; Thilikos, Dimitrios M.
We introduce the parameter of block elimination distance as a measure of how close a graph is to some particular graph class. Formally, given a graph class g, the class B(G) contains all graphs whose blocks belong to G and the class A(G) contains all graphs where the removal of a vertex creates a graph in G. Given a hereditary graph class G, we recursively define G((k)) so that G((0)) = B(G) and, if k >= 1 G((k)) B(A(G((k-1))) ) N We show that, for every nontrivial hereditary class g, the problem of deciding whether G is an element of G((k)) is NP-complete. We focus on the case where G is minor-closed and we study the minor obstruction set of G((k)) i.e., the minor-minimal graphs not in G((k)). We prove that the size of the obstructions of G((k)) is upper bounded by some explicit function ofk and the maximum size of a minor obstruction of G. This implies that the problem of deciding whether G is an element of G((k)) is constructively fixed parameter tractable, when parameterized by k. Finally, we give two graph operations that generate members of G((k)) from members of G((k -1)) and we prove that this set of operations is complete for the class O of outerplanar graphs.Please check and confirm if the authors Given and Family names have been correctly identified for author znur YaYar Diner. All authors names have been identified conectly. Please confirm if the corresponding author is correctly identified. Amend if necessary.This is correct
Block Elimination Distance
(Springer international Publishing Ag, 2021) Diner, Oznur Yasar; Giannopoulou, Archontia C.; Stamoulis, Giannos; Thilikos, Dimitrios M.
We introduce the parameter of block elimination distance as a measure of how close a graph is to some particular graph class. Formally, given a graph class G, the class B(G) contains all graphs whose blocks belong to G and the class A(G) contains all graphs where the removal of a vertex creates a graph in G. Given a hereditary graph class G, we recursively define G((k)) so that G((0)) = B(G) and, if k >= 1, G((k)) = B(A(G((k-1)))). The block elimination distance of a graph G to a graph class G is the minimum k such that G is an element of G((k)) and can be seen as an analog of the elimination distance parameter, defined in [J. Bulian & A. Dawar. Algorithmica, 75(2):363-382, 2016], with the difference that connectivity is now replaced by biconnectivity. We show that, for every non-trivial hereditary class G, the problem of deciding whether G. G(k) is NPcomplete. We focus on the case where G is minor-closed and we study the minor obstruction set of G((k)) i.e., the minor-minimal graphs not in G((k)). We prove that the size of the obstructions of G((k)) is upper bounded by some explicit function of k and the maximum size of a minor obstruction of G. This implies that the problem of deciding whether G is an element of G((k)) is constructively fixed parameter tractable, when parameterized by k. Our results are based on a structural characterization of the obstructions of B(G), relatively to the obstructions of G. Finally, we give two graph operations that generate members of G((k)) from members of G((k-1)) and we prove that this set of operations is complete for the class O of outerplanar graphs. This yields the identification of all members O boolean AND G((k)), for every k is an element of N and every non-trivial minor-closed graph class G.
Citation - WoS: 4
Citation - Scopus: 5
Broadband Equalizer Design With Commensurate Transmission Lines Via Reflectance Modeling
(IEICE-INST ELECTRONICS INFORMATION COMMUNICATIONS ENG, 2008) Şengül, Metin Y.; Yarman, Sıddık Binboğa
In this paper an alternative approach is presented to design equalizers (or matching networks) with commensurate (or equal length) transmission lines. The new method automatically yields the matching network topology with characteristic impedances of the commensurate lines. In the implementation process of the new technique first the driving point impedance data of the matching network is generated by tracing a pre-selected transducer power gain shape without optimization. Then it is modelled its it realizable bounded-real input reflection coefficient in Richard domain which ill turn yields the desired equalizer topology with line characteristic impedances. This process results in an excellent initial design for the commercially available computer aided design (CAD) packages to generate final circuit layout for fabrication. An example is given to illustrate the utilization of the new method. It is expected that the proposed design technique is employed as it front-end to commercially available computer aided design (CAD) packages which generate the actual equalizer circuit layout with physical dimensions for mass production.
Citation - WoS: 3
Citation - Scopus: 3
Challenges of Teaching in a Different Culture: An Auto-Ethnographic Study
(Cognizant Communication Corp, 2021) Kozak, Metin
Teaching in a different culture and environment is always a challenging issue. This may last from a few months to a few years, depending on the consequences of personal characteristics and environmental situations. Based on a personal experience, this article investigates the possible cultural differences between the lecturer and students in a teaching environment and understanding how the student perceptions may gradually change and the student -lecturer interaction may evolve until the semester ends. In a methodological way, the conclusions were drawn out of a mixed-method approach that is composed of a personal observation of the lecturer (etic), and expressions, both verbal and written, and memories of other persons (students) within the same class (emit). In lights of Hofstede's cultural dimensions, the study addresses a list of practical implications as the lessons learned-presumably the best way to cope with the challenges of teaching in a different culture.
Change of the Built Environment in Jerusalem During the Late Ottoman Period (1840–1917)
(Routledge, 2025) Alioğlu, E.F.
The establishment of Jerusalem, the holy city of three monotheistic religions on a global scale, dates to 4000 BCE. The city has been settled by various civilizations and has had walls protecting its borders since ancient times. Throughout history, Jerusalem has been influenced by Assyrian, Babylonian, Persian, Hellenic, Roman, Byzantine, Islamic States, and Ottoman periods. The Ottoman Empire first took control of the city in 1517 and then again in 1840, when they regained dominance in Syria and Palestine. In 1841, Jerusalem was separated from the Damascus Province and directly linked to Istanbul. This marked a period of modernization for the Ottoman Empire, following the Tanzimat Edict of 1839. This led to significant changes in legal, administrative, social, economic, political, and zoning fields, transforming the appearance of Ottoman cities. This article will discuss how existing structures were managed in Jerusalem during the final period of Ottoman rule, the regulations for constructing new buildings, the preservation of ancient monuments, and the enforcement of new laws. © 2025 Elsevier B.V., All rights reserved.
Citation - WoS: 7
Channel Modeling for Visible Light Communications
(Springer-Verlag Berlin, 2016) Miramirkhani, Farshad; Uysal, Murat; Panayırcı, Erdal
In this chapter, we present a novel and realistic channel modeling approach for visible light communications that overcomes the limitations of previous works. In our work, we consider wavelength dependency, effect of realistic light sources as well as different types of reflections such as specular and mixed cases of diffuse and specular. We use nonsequential ray tracing algorithms to calculate the detected power and path lengths from source to detector for each ray. These are then processed to yield the channel impulse responses for various indoor environments. We further present a channel characterization study where channel parameters such as channel DC gain, root mean square delay spread, coherence bandwidth, mean excess delay are calculated for different environments.
Citation - WoS: 1
Chaotic - Deterministic or Random Nature of Earthquakes: a Phase Space Analysis
(Symmetrion, 2023) Pekcan, Onder; Arsan, Taner
Using the phase space approach, time series analysis of high EV1 and low EV2 intense two different earthquakes that occurred at the nearly same precise spot, at different times, and were measured with the same sensor of a broadband station were studied. Time series data of strong, large (EV1) and weak, small (EV2) two earthquake events were analyzed by dividing them into three different regions. Fractal dimensions of the EV1 and EV2 were produced using the box-counting algorithm for east-west (BHE), north-south (BHN), and vertical (BHZ) components. The small, weak earthquake, EV2, created a larger fractal dimension in phase space by implying its random nature in all regions. However, EV1 is a strong, large earthquake that presents deterministic oscillatory behavior at a long-time region. Oscillatory behavior can be named surface wave. EV2 exhibits weak, high-frequency ground oscillations similar to fibrillation before and after the earthquake in the long-term areas.
Citation - WoS: 1
Citation - Scopus: 1
Collectivity in Heavy Nuclei in the Shell Model Monte Carlo Approach
(EDP Sciences, 2014) Özen, Cem; Alhassid, Yoram; Nakada, Hitoshi
The microscopic description of collectivity in heavy nuclei in the framework of the configuration-interaction shell model has been a major challenge. The size of the model space required for the description of heavy nuclei prohibits the use of conventional diagonalization methods. We have overcome this difficulty by using the shell model Monte Carlo (SMMC) method which can treat model spaces that are many orders of magnitude larger than those that can be treated by conventional methods. We identify a thermal observable that can distinguish between vibrational and rotational collectivity and use it to describe the crossover from vibrational to rotational collectivity in families of even-even rare-earth isotopes. We calculate the state densities in these nuclei and find them to be in close agreement with experimental data. We also calculate the collective enhancement factors of the corresponding level densities and find that their decay with excitation energy is correlated with the pairing and shape phase transitions.
Commercial Agency Contract and Comparison With Similar Contracts (exclusive Distribution, Franchising, Brokerage, and Commission Contracts)
(Springer International Publishing Ag, 2020) Kazmaci, Ozge Uzun
The contract between the merchant and the commercial agent is a commercial agency contract. This contract creates a continuing obligation for each party. Commercial agency contract is not defined in any Act but commercial agent is defined in Turkish Commercial Code. However, the provisions regarding commercial agency in Turkish Commercial Code are not sufficient. Therefore, it is important to compare commercial agency contract with similar agreements in order to determine the legal nature of the contract and provisions to be applied to the contract in case of a legal conflict. Agency contracts have some differences and similarities with similar contracts such as exclusive distribution, franchising, brokerage, and commission contracts. Agency contract, unlike brokerage and commission, is a permanent contract. Recognition of monopoly in an agency contract is not a necessary element. However, it is necessary to recognize the monopoly on exclusive distribution contract.

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