Scopus İndeksli Yayınlar Koleksiyonu

Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/1248

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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.
Citation - WoS: 12
Citation - Scopus: 15
Acute Aortic Valve Regurgitation Secondary To Blunt Chest Trauma
(Texas Heart Inst., 2001) Ünal, Mehmet; Demirsoy, Ergun; Göğüş, Abdullah; Arbatlı, Harun; Hamzaoğlu, Azmi; Sönmez, Bingür
Blunt injury to the cardiac valves leads to progressive acute ventricular failure which often requires urgent surgical management In this case report we describe an acute aortic valve rupture caused by air-bag inflation during an automobile accident. Laceration of an aortic valve cusp was treated successfully with urgent aortic valve replacement. A concomitant orthopedic injury was treated electively 15 days after cardiac surgery. Acute aortic valve rupture is a very rare complication of blunt chest trauma. We discuss how to diagnose and manage this potentially catastrophic event.
Citation - Scopus: 12
Acute Gastrointestinal Complications After Open Heart Surgery
(Asia Publishing Exchange Pte Ltd, 2000) Akpınar, Belhhan; Sağbaş, Ertan; Güden, Mustafa; Kemertas, Kubilay; Sönmez, Bingür; Bayındır, Osman; Demiroğlu, Cemşid
Retrospective analysis revealed that 24 of 4401 adult patients (0.5%) developed severe gastrointestinal complications after open heart surgery during a 3-year period from January 1995. There were 4 women (17%) and 20 men (83%). Mean age was 61.7 ± 2.02 years. Gastrointestinal bleeding (33.3%) mesenteric ischemia (20.8%) pancreatitis (20.8%) hepatic dysfunction (16.7%) and cholecystitis (16.7%) were the most common complications. Mortality was 41.7% (10 patients). During the same period mortality in the patients who did not develop gastrointestinal complications was 1.89% (p < 0.0001). Emergency basis reoperation combined operations peripheral vascular disease diabetes mellitus chronic lung disease and impaired left ventricle function were found to be risk factors for the development of postoperative gastrointestinal complications.
Citation - Scopus: 12
Affective Modulation of Working Memory Maintenance: the Role of Positive and Negative Emotions
(University of Economics and Human Sciences in Warsaw, 2021) Gokce,A.; Zinchenko,A.; Annac,E.; Conci,M.; Geyer,T.
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. © 2021 University of Finance and Management in Warsaw. All rights reserved.
Citation - WoS: 4
Citation - Scopus: 6
Agent-Based Optimization To Estimate Nash Equilibrium in Power Markets
(Taylor & Francis Inc, 2013) Yücekaya, Ahmet; Valenzuela, Jorge
In most deregulated power markets firms bid daily into a day-ahead power market. The auction mechanism supply and demand determine the equilibrium at each hour. In this environment firms aim to maximize their revenues by carefully determining their bids. This requires the development of effective computational methods that help them estimate their competitors' behaviors under incomplete information. In this article an agent-based method that uses particle swarm optimization is described to simulate the behavior of market participants. Particle swarm optimization is used in the bidding process and an agent-based model is applied to find a Nash equilibrium. Different stopping conditions are used to determine the equilibrium. Experimental results are presented for two power systems.
Aging and Robotization: the Duality Between Generations and Robot Adoption
(Digital initiatives Univ Waterloo Lib, 2023) Aydin, Asli
This paper examines the bilateral relationship between the robot adoption and the age characteristics of the employment. The study analyzes the reciprocal effects of robotization on different generations and presents the analysis of the effects of age groups on the robotization of countries. Based on an instrumentalization of the System GMM estimation method of a dynamic panel dataset of 28 selected countries over 2004 and 2016, the results show that the number of young workers is affected negatively from robotization, whereas there is a positive impact of robot adoption on old workers. Evidence further suggests that robotization is triggered by the density of young workers in the workforce of the country.
Citation - WoS: 1
Citation - Scopus: 1
Archival Lives of Popular Culture: Our Introduction
(WILEY, 2021-01) Altınay, Rustem Ertuğ; Jokic, Olivera
[Abstract Not Available]
Attractiveness Differentially Affects Direct Versus Indirect Face Evaluations in Two Cultures
(Sage Publications Inc, 2023) Cassidy, Brittany S.; Saribay, S. Adil; Yuksel, Huseyin; Kleisner, Karel
Although decades of research have identified facial features relating to people's evaluations of faces, specific features have largely been examined in isolation from each other. Recent work shows that considering the relative importance of these features in face evaluations is important to test theoretical assumptions of impression formation. Here, we examined how two facial features of evolutionary interest, facial attractiveness and facial-width-to-height ratio (FWHR), relate to evaluations of faces across two cultures. Because face evaluations are typically directly measured via self-reports, we also examined whether these features exert differential effects on both direct and indirect face evaluations. Evaluations of standardized photos naturally varying in facial attractiveness and FWHR were collected using the Affect Misattribution Procedure in the United States and Turkey. When their relative contributions were considered in the same model, facial attractiveness, but not FWHR, related to face evaluations across cultures. This positive attractiveness effect was stronger for direct versus indirect evaluations across cultures. These findings highlight the importance of considering the relative contributions of facial features to evaluations across cultures and suggest a culturally invariant role of attractiveness when intentionally evaluating faces.
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: 14
Citation - Scopus: 16
Bayesian Compressive Sensing for Primary User Detection
(Inst Engineering Technology-IET, 2016) Başaran, Mehmet; Erküçük, Serhat; Cirpan, Hakan Ali
In compressive sensing (CS)-based spectrum sensing literature most studies consider accurate reconstruction of the primary user signal rather than detection of the signal. Furthermore possible absence of the signal is not taken into account while evaluating the spectrum sensing performance. In this study Bayesian CS is studied in detail for primary user detection. In addition to assessing the signal reconstruction performance and comparing it with the conventional basis pursuit approach and the corresponding lower bounds signal detection performance is also considered both analytically and through simulation studies. In the absence of a primary user signal the trade-off between probabilities of detection and false alarm is studied as it is equally important to determine the performance of a CS approach when there is no active primary user. To reduce the computation time and yet achieve a similar detection performance finally the effect of number of iterations is studied for various systems parameters including signal-to-noise-ratio compression ratio mean value of accumulated energy and threshold values. The presented framework in this study is important in the overall implementation of CS-based approaches for primary user detection in practical realisations such as LTE downlink OFDMA as it considers both signal reconstruction and detection.
Citation - WoS: 3
Citation - Scopus: 3
Beliefs of Living Donors About Recipients' End-Stage Liver Failure and Surgery for Organ Donation
(Elsevier Science Inc, 2017) Krespi-Boothby, Margörit Rita; Tankurt, A.; Acarli, Koray; Kanmaz, Turan; Yankol, Yucel; Kalayoğlu, Murat
Background. The concept of beliefs could provide a basis for how donors may perceive recipients' end-stage liver failure (ESLF) and surgery for organ donation. However there is no such quantitative study. Therefore the objective of this study was to explore beliefs of living donors about recipients' ESLF and surgery for organ donation. Methods. The sample comprised 16 living donors who donated a part of their liver to a patient who had ESLF. The data were analyzed by following established procedures for inductive qualitative analysis. Results. Analysis showed that donors' beliefs can be viewed in a number of groups. Beliefs about recipients' ESLF included diverse explanations for ESLF (blaming oneself and physicians) and physical symptoms (developmental slowing down). Beliefs about being a donor included reasons for being a donor (performing a good deed being healed) barriers to being a donor (other people being ignorant and selfish) ways to manage these barriers (following one's gut feeling) and factors facilitating being a donor (the feeling that one does not have many people to leave behind). Beliefs about surgery for organ donation included physical effects (pain feeling stiff). Beliefs about organ donation included views that general organ donation should be encouraged and that people's awareness should be raised. Conclusions. Existing psychological perspectives could help to interpret some beliefs. Nevertheless other beliefs not previously reported could be considered as targets for individual consultations/psycho-educational programs for fostering emotional well-being.
Citation - WoS: 8
Citation - Scopus: 9
Between Anchors and Aspirations: a New Family of Bargaining Solutions
(Springer, 2019) Karagözoğlu, Emin; Keskin, Kerim; Özcan-Tok, Elif
We study the salience and power of reference points in determining the effective anchors and aspirations in bargaining problems. Along this line we enrich the analysis of the standard bargaining model with two new parameters: the first parameter can be interpreted as the effectiveness (or salience) of the reference point in determining the anchor whereas the second parameter can be interpreted as its effectiveness in shaping agents' aspirations. Utilizing these parameters we provide a unifying framework for the study of bargaining problems with a reference point. The two-parameter family of bargaining solutions we obtain encompasses some well-known solutions as special cases. We offer multiple characterizations for each individual member of this family as well as two characterizations for the whole solution family in bilateral bargaining problems.
Citation - Scopus: 4
Bilateral Macrostomia as an Isolated Deformity and Its Repair With a Modified Technique
(Springer Verlag, 2002) Peker, Fatih; Açıkel, Cengiz; Karacaoğlu, Ercan; Durak, Nazım
A 3-year-old boy with bilateral congenital macrostomia as an isolated clinical entity is presented. Although this is a rare deformity, it causes functional and cosmetic problems which are difficult to correct. The skin, muscle, and mucosal components of the deformity were separately repaired using a modification of Kaplan's technique.
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: 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 - Scopus: 2
C-Reactive Protein as a Pre-Procedural Predictor of Early and Late Outcomes of Percutaneous Coronary Interventions
(Springer New York, 2003) Aytekin, Saide; Çatakoğlu, Alp Burak; Aytekin, Vedat; Demiroğlu, Cemşid; Kocazeybek, Bekir Sami
To examine the predictive value of pre-procedural CRP level in patients undergoing percutaneous coronary intervention (PCI) regardless of having unstable or stable angina pectoris or myocardial infarction. Blood sampling for CRP measurement in patients undergoing PCI: 116 consecutive patients who underwent single vessel PCI were evaluated. Exclusion criteria were multilesion PCI, total occlusion, left ventricular ejection fraction < 30%, left bundle branch block and intercurrent inflammatory conditions known to be associated with an acute phase response. Major adverse coronary events (MACE) were defined as the occurrence of death, fatal or nonfatal myocardial infarction, and need for coronary artery revascularization with either bypass grafting or repeat angioplasty. End-points were assessed at hospital discharge, 30 days, 3 and 6 months following the index procedure. 62 (53%) patients had CRP levels < 0.5 mg/dl, and 54 (47%) had > 0.5 mg/dl. There were no significant difference in the occurrence of MACE in early in-hospital and 30 days follow up periods, between the two groups (0 vs. 5.5%) (p = ns) whereas the incidence of MACE after 3 months of the procedure was significantly different between the two groups (1.6 vs. 11%) (p < 0.05) and also after 6 months (9.5 vs 24.5%) (p < 0.05). The negative predictive value of CRP measurement is 98.4%. High levels of pre-procedural CRP show association with the higher incidence of MACE after 3 months of the follow-up period and negative CRP tests seems to have high predictive value to compare the patients who will be free of MACE after successful PCI. SciVal Topic Prominence
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.
Citation - WoS: 2
Citation - Scopus: 2
Challenges of the Filter Paper Suction Measurements in Geosynthetic Clay Liners: Effects of Method, Time, Capillarity, and Hysteresis
(Amer Soc Testing Materials, 2022) Acikel, A. S.; Bouazza, A.; Singh, R. M.; Gates, W. P.; Rowe, R. K.
Time and method dependencies, lack of sufficient capillary connections, and wetting-drying hysteresis may cause inaccurate results from filter paper tests (FPTs) when used for suction measurements of geosynthetic clay liners (GCLs). These limitations of the filter paper method for suction measurements of GCLs were investigated using initially dry contact, initially wet contact, and noncontact FPTs. Wetting-drying hysteresis was observed in the initially dry contact and noncontact FPTs and was significantly higher in the latter. The initially wet contact and initially dry contact FPTs were reliable in measuring matric and total suction, respectively. These two methods can provide suction measurements from both the cover and the carrier geotextile sides of the GCLs (i.e., from the hydratable surfaces of the GCL after installation on site), thus allowing suction measurements without impacting the integrity of the geotextile-bentonite-geotextile structure. Suction measurements on a granular bentonite-based GCL showed higher time dependency compared with powdered bentonite-based GCLs. For the specific GCLs and conditions tested, the woven and nonwoven scrim-reinforced geotextile structure causes pronounced capillary break effects on the hydratable surface of GCL. In contrast, the woven geotextile structure has a minimal impact. When the FPT procedures are applied to GCLs, the interpretation of the results requires careful consideration of the method and time dependencies, wetting-drying hysteresis, capillary breaks, and how the measurements of total or matric suction are performed.
CHAOTIC – DETERMINISTIC OR RANDOM NATURE OF EARTHQUAKES: A PHASE SPACE ANALYSIS
(Symmetrion, 2023) Pekcan,O.; Arsan,T.
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. © 2023, Symmetrion. All rights reserved.

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