WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article GenShare: A Blockchain-Based Genomic Data Sharing Platform(Association for Computing Machinery, 2026-01-27) Dedeturk, B.A.; Soran, A.; Bakir-Güngör, B.Every day, hundreds of gigabytes of data are produced due to the exponential growth of next-generation sequencing and omics technologies. By combining omics data with other data types, such as electronic health record data, panomics research is actively attempting to uncover novel and potentially useful biomarkers. For the effective analysis of high-throughput-derived omics data, it is imperative to establish robust and reliable platforms that prioritize ethical considerations while effectively managing privacy, ownership concerns, and the responsible sharing of data. The GenShare model was proposed to provide an efficient platform that fits these needs. GenShare is a hybrid platform that utilizes blockchain technology. Paillier’s homomorphic encryption scheme in tandem with Intel Software Guard Extension (SGX) serves to enable the sharing of genomic data, execution of count queries, and statistical analysis of genomic data while preserving privacy and avoiding compromise of sensitive information. The objective of this paradigm is to confront security and privacy concerns through the integration of homomorphic encryption and SGX, addressing additional challenges associated with Hyperledger Fabric and Ethereum. In pursuit of this objective, the implementation of the system involved establishing the Hyperledger Fabric network, with various workloads employed to assess the network’s efficiency. Consequently, it was hypothesized that the new GenShare model would enhance the data collection and dissemination cycle and serve as a proficient platform catering to the needs of its users. © 2026 Copyright held by the owner/author(s).Article Citation - WoS: 1Citation - Scopus: 1Photoluminescent Carbon Dots for Sensitive and Selective Cu2+ Ion Detection(Institute of Physics, 2026-01-07) Sahin-Tiras, K.; Karabel Ocal, S.; Mutlugün, E.; Sahin Tiras, KevserGreen-emitting carbon dots (CDs) were synthesized via a solvent-free, vacuum-assisted method using citric acid and urea. The CDs exhibited strong photoluminescence and served as selective, sensitive probes for Cu2+ detection in water, with a detection limit of 26 nM. Among the tested metal ions, Cu2+ induced the most significant PL quenching. Time-resolved photoluminescence measurements of the CDs in the presence of Cu2+ ions revealed a minimal change in lifetime, despite a significant decrease in PL intensity, along with unchanged UV-vis absorption, indicating a mixed quenching mechanism. The sensor’s applicability was confirmed in raisin extract and tea infusion, showing notable PL suppression. With their simplicity, selectivity, and sensitivity, these CDs offer promising potential as nanosensors for detecting Cu2+ in environmental and real-world analytical settings. © 2026 The Author(s). Published by IOP Publishing Ltd.Article CRISPR/Cas9-mediated Metabolic Engineering of Endophytic Pseudomonas Loganensis Sp. Nov. for the Production of Nutritionally Valuable Carotenoids(American Chemical Society, 2026-01-02) Arslansoy, N.; Karaman, M.Z.; Fidan, O.Carotenoids with significant nutritional and antioxidant properties have been widely utilized in the food, feed, pharmaceutical, and cosmetic industries. They improve the nutritional value of foodstuffs and have been used as natural food colorants. However, their current supply chain is mainly dependent on extraction from plants and chemical synthesis, both of which have bottlenecks, including environmental concerns, toxicity, and allergenicity. To address global demand for sustainable and environmentally friendly production of nutrients, we engineered the endophytic Pseudomonas loganensis sp. nov. as a niche microbial chassis for nutritionally valuable carotenoid production. Using CRISPR-Cas9, we knocked out key carotenogenic genes to construct strains capable of producing zeaxanthin, lycopene, and β-carotene. Additionally, an overexpression plasmid was introduced to produce astaxanthin. HPLC analysis confirmed the successful production of four target carotenoids. The culture conditions and media compositions were optimized using response surface methodology, resulting in a ∼5-fold increase in the titers of zeaxanthin (13.4 mg/L), lycopene (9.67 mg/L), and β-carotene (23.53 mg/L), and a ∼12-fold increase in astaxanthin titer (1 mg/L) compared to LB medium without optimization. Our results indicate the potential of endophytic bacteria as a microbial chassis for carotenoid bioproduction, underscoring the potential of synthetic biology to contribute to global efforts toward nutritional security and sustainable food systems. © 2026 The Authors. Published by American Chemical SocietyErratum Correction to “Multifaceted Effects of the Dielectric Component within Plasmon-Assisted Light-Emitting Structures”(American Chemical Society, 2025-12-17) Kulakovich, O.; Muravitskaya, A.; Ramanenka, A.; Efimova, T.; Krukov, V.; Mutlugün, E.; Gaponenko, S.In the original version of the article, the affiliation of Hilmi Volkan Demir needs following correction. The first affiliation of the author “Department of Electrical-Electronics Engineering, Abdullah Gul University, Kayseri 38080, Turkey” should be replaced by the affiliation “UNAM – Institute of Materials Science and Nanotechnology and The National Nanotechnology Research Center and Department of Electrical and Electronics Engineering, Department of Physics, Bilkent University, Ankara 06800, Turkey”. Therefore, the correct affiliations for H.V.D. are “UNAM – Institute of Materials Science and Nanotechnology and The National Nanotechnology Research Center and Department of Electrical and Electronics Engineering, Department of Physics, Bilkent University, Ankara 06800, Turkey; LUMINOUS! Center of Excellence for Semiconductor Lighting and Displays, School of Electrical and Electronic Engineering, School of Physical and Mathematical Sciences, School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore”. © 2025 American Chemical SocietyArticle Colloidal Photodetectors Based on Engineered Multishelled InP Based Quantum Dots(Institute of Physics, 2026-01-08) Akrema; Erol, E.; Savaş, M.; Yazici, A.; Erdem, T.; Mutlugün, E.; Faruk Yazıcı, AhmetIn this work, we present a straightforward and cost-effective approach to synthesize multi-shell InP/ZnSe/ZnSeS/ZnS quantum dots (QDs) that show promising potential for use in photodetectors. By carefully layering ZnSe, ZnSeS, and ZnS shells around an InP core, we were able to enhance the stability and optical performance of the QDs, achieving a narrow emission peak of 45 nm and a high photoluminescence quantum yield of 55%. These QDs were then integrated into simple photodetector devices, which possessed impressive sensitivity and detection capabilities. Specifically, our devices achieved a peak responsivity of 0.54 A W−1 and a detectivity of 2.22 × 1011 Jones at 400 nm with a 5 V bias. This study highlights the potential of InP-based QDs as a safer and more sustainable alternative to traditional QDs that contain toxic heavy metals, offering a viable path forward for developing high-performance optoelectronic devices. Our findings suggest that these InP/ZnSe/ZnSeS/ZnS QDs could be a key material for the next generation of high-performance optoelectronic devices, especially in applications that require highly sensitive and stable photodetectors. © 2026 The Author(s). Published by IOP Publishing Ltd.Book Part Citation - WoS: 5Citation - Scopus: 5Wireless MEMS for Smart Grids(Woodhead Publ Ltd, 2017) Tuna, G.; Gungor, V. C.; Dursun, B.Article Citation - WoS: 7Citation - Scopus: 8Using Students' Performance to Improve Ontologies for Intelligent E-Learning System(Edam, 2015) Icoz, Kutay; Sanalan, Vehbi A.; Cakar, Mehmet Akif; Ozdemir, Esra Benli; Kaya, SukruOntologies have often been recommended for E-learning systems, but few efforts have successfully incorporated student data to represent knowledge conceptualizations. Defining key concepts and their relations between each other establishes the backbone of our E-learning system. The system guides an individual student through his/her course by evaluating their progress and suggesting instructional material to review based upon their answers. Three main tasks are performed within this framework: building ontologies for the course, measuring a student's understanding level for the concepts, and making personal suggestions to create an individualized learning environment. This paper presents: the integration of ontologies, assisted with student data, together with an intelligent Recommendation Module for the development of an E-learning system; the comparison and correction adaption of ontology from students' mind maps; and the assessment of students' actual weaknesses in comparison to what Recommendation Module suggests. The sample of 127 students, five classrooms, was conveniently selected among seventh grade students of a demographically average school in a major city in Turkey. The students' achievement was assessed and the scores for different questions were investigated for associations with concepts made in the students' minds. The results provided significant correlations among scores, and a fit model for the concepts represented by questions. The student suggested model slightly differed from the ontology map from the experts. Based on the data-supported model, the Recommendation Module more accurately determined the students' learning deficiencies and suggested concepts to be reviewed.Conference Object Citation - WoS: 7Citation - Scopus: 12Use of Topological Data Analysis in Motor Intention Based Brain-Computer Interfaces(European Signal Processing Conference, EUSIPCO, 2018-09) Altindis, Fatih; Yilmaz, Bulent; İçöz, Kutay; Borisenok, S.This study aims to investigate the use of topological data analysis in electroencephalography (EEG) based on brain-computer interface (BCI) applications. Our study focused on extracting topological features of EEG signals obtained from the motor cortex area of the brain. EEG signals from 8 subjects were used for forming data point clouds with a real-time simulation scenario and then each cloud was processed with JPlex toolbox in order to find out corresponding Betti numbers. These numbers represent the topological structure of the point data cloud related to the persistent homologies, which differ for different motor activity tasks. The estimated Betti numbers has been used as features in k-NN classifier to discriminate left or right hand motor intentions. © 2019 Elsevier B.V., All rights reserved.Book Part Citation - WoS: 1Citation - Scopus: 4Understanding Communication via Diffusion: Simulation Design and Intricacies(Springer International Publishing AG, 2017) Acar, Bilal; Akkaya, Ali; Genc, Gaye; Yilmaz, H. Birkan; Kuran, M. Sukru; Tugcu, Tuna; Şükrü Kuran, M.Understanding Communication via Diffusion (CvD) is key to molecular communications research since it dominates the movement at the nano-scale. The researcher needs to properly understand the random diffusion of the molecules for the analysis of a molecular communication system. This chapter aims explaining the dynamics of diffusion from a communication engineer's perspective as well as providing useful hints for an effective simulation design by discussing some key intricacies. The chapter starts with a brief survey of simulators for molecular communications, followed by the basics of the simulation of Brownian motion and CvD. Several intricacies are addressed to help the researcher in simulation design, such as the number of replications required in terms of movement and bit sequence. We utilize this information further by discussing the design of more complex CvD systems such as tunnel-based approach that utilizes destroyer molecules and distributed simulator design based on HLA. Introduction of more complex CvD systems provides significant improvements in data rate and communications in general, bridging the gap between human-scale and nano-scale systems and enabling nanonetworking as a viable technology.Conference Object Turkish English Teachers' Professional Teacher Self as One of the Possible Selves(Elsevier Science Bv, 2016-10) Demirezen, Mehmet; Ozonder, OzgulThis study reports the results of a study exploring Turkish English teachers' professional self in relation to teacher education. The study also examines the relationship between the participants' educational background, teaching experience and their professional self The study was carried out in Ankara, Turkey. The participants of the study were English language instructors of Hacettepe University, School of Foreign Languages. A total of 43 English instructors (females: 36 and males: 7) voluntarily participated in the study, responding to a questionnaire composed of 40 items regarding teacher professional self. The results of the Professional Self Questionnaire revealed that the rate of Turkish English teachers' professional self was very high (81%, M=4.09). Also, there was a significant difference in participants' professional self depending on their educational background. The results indicated that the participants' professional self did not differ significantly in relation to their teaching experience. (C) 2016 Published by Elsevier Ltd.