Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Correction Chlorinated Phosphorene for Energy Application (vol 231, 112625, 2024)(Elsevier, 2024) Hassani, Nasim; Yagmurcukardes, Mehmet; Peeters, Francois M.; Neek-Amal, Mehdi[No Abstract Available]Article Citation - WoS: 1Citation - Scopus: 2First Measurement of the Forward Rapidity Gap Distribution in Ppb Collisions at √snn=8.16 Tev(Amer Physical Soc, 2023) Karapınar, Güler; CMS Collaboration; Ambrogi, F.; Bergauer, T.; Dragicevic, M.; Ero, J.; Zhokin, A.For the first time at LHC energies, the forward rapidity gap spectra from proton-lead collisions for both proton and lead dissociation processes are presented. The analysis is performed over 10.4 units of pseudorapidity at a center-of-mass energy per nucleon pair of ffisffi than in previous measurements of diffractive production in proton-nucleus collisions. For lead dissociation processes, which correspond to the pomeron-lead event topology, the EPOS-LHC generator predictions are a factor of 2 below the data, but the model gives a reasonable description of the rapidity gap spectrum shape. For the pomeron-proton topology, the EPOS-LHC, QGSJET II, and HIJING predictions are all at least a factor of 5 lower than the data. The latter effect might be explained by a significant contribution of ultraperipheral photoproduction events mimicking the signature of diffractive processes. These data may be of significant help in understanding the high energy limit of quantum chromodynamics and for modeling cosmic ray air showers.Article Citation - WoS: 3Citation - Scopus: 3Liquid Metal-Tunable Miniaturized Bimodal Cavity for Enhanced Measurement Accuracy in the Ism Bands(Ieee-inst Electrical Electronics Engineers inc, 2024) Karatay, Anil; Yaman, FatihEnhancing measurement accuracy or reducing the effect of the neighboring modes in resonant cavities may necessitate the separation of mode frequencies. However, in ISM-band measurement configurations utilizing a rectangular or cylindrical cavity, the placement of the first two modes at 2.45 and 5.8 GHz is unattainable, necessitating the presence of additional modes in between that would potentially degrade measurement accuracy. This article begins with an analytical approach, employing Lagrange multipliers for the first time to reveal the level of separation achievable in the frequency domain between the initial two modes within these types of conventional cavities. The analytical results were also verified with a numerical grid search. Subsequently, innovative strategies have been introduced to surpass this intrinsic constraint that reduces the measurement accuracy in various applications. A novel miniaturized cavity configuration has been proposed to operate bimodally at 2.45 and 5.8 GHz and manufactured with a 3-D printer. It has been ensured that there are no physical modes present in between, and measurements of the structure have been conducted. Another notable innovation of the article is the capability of tuning the proposed cavity structure by means of liquid metal displacement. Thus, a more flexible tuning method compared to mechanical tuning techniques can be achieved, enabling precise adjustment of the desired measurement frequency. Good agreement between the simulation and measurement results has been reported.Article Citation - WoS: 3Citation - Scopus: 3Light-Induced Synthesis of Single-Crystalline Gold Microplates in an Open System(Amer Chemical Soc, 2023) Akkuş, Betül; Mert Balcı, FadimeBottom-up synthesis of large single-crystalline gold microplates is of key importance to catalysis, nanophotonics, bioengineering, and plasmonics. However, easy, low-cost, room-temperature, and high-yield synthesis of large gold microplates with several micrometers in lateral size and a few tens of nanometers in thickness by using photochemical synthesis in an open system is still challenging. We herein report on an easy and cost-effective photochemical synthesis of single-crystalline gold microplates with lateral sizes up to around 40 mu m and tens of nanometers in thickness in a few hours of reaction time in an open system containing a lyotropic liquid crystal, which is formed by self-assembly of 10-lauryl ether in a strong acid, sulfuric acid, along with water. We have found that by changing the reaction parameters, such as the reaction time, the concentration of gold ions in the liquid crystal, etc., the thickness and size of the microplates can be easily controlled. Most importantly, the liquid crystalline phase is completely preserved after completion of the photochemical reaction. The microplates can be easily isolated and transferred to different media such as alcohol and water for further studies, or they can be immediately used on a substrate after completion of the reaction. The results obtained in this study will allow us to understand the growth mechanism of gold microplates in open systems, and they will find applications in a variety of critical areas, such as plasmonics, nanophotonics, and catalysis.Article Citation - WoS: 7Citation - Scopus: 9Politics of Waiting for Transformation in Protracted Urban Renewal Projects in Turkey(Sage Publications Ltd, 2023) Ay, Deniz; Penpecioglu, MehmetThis paper explores the politics of 'waiting' as a mode of governance in large-scale urban redevelopment projects. In designated renewal areas, residents/landowners are often subject to several episodes of waiting: waiting for the public authority for information on redevelopment visions; waiting for the plans and projects to become public; waiting for the court ruling if they appeal the plans; waiting for demolition upon plan approvals; and, finally, waiting for the constructions to be completed. Given the complexity of actors and institutions involved in the waiting, it becomes a conflictual political process. This prolonged waiting leads to an ongoing temporariness and precarious spaces of urban renewal. The course of waiting affects the reorganization of the city space now and in the future. We analyze two protracted urban renewal projects from Turkey, Fikirtepe in Istanbul and Karabaglar in Izmir, to explore how residents' decade-long waiting for urban change are shaped and how these diverse waiting experiences lead to different outcomes for the progression of the state-imposed urban renewal agendas. While Karabaglar residents have unified around active bottom-up resistance from the beginning to challenge the project-based plans the central government imposed, Fikirtepe residents pursued individual-level negotiations with developers to maximize private returns following the zoning incentives the public authority gave. Despite the socio-spatial similarities between these designated urban renewal project sites, variances in residents' collective waiting strategies have led to different urban politics around project-based urban change.Conference Object Serum Creatinine Detection in a Microfluidic Chip Using a Smartphone Camera(Chemical and Biological Microsystems Society, 2022) Karakuzu, B.; Tarim, E.A.; Tekin, H.C.We present a microfluidic chip platform to detect serum creatinine levels using the enzyme-linked immunosorbent assay (ELISA) principle. In the platform, surface modified microfluidic channel sensitively captured target molecules from the serum sample, and then ELISA protocol was applied inside the channels. Afterward, the blue color formed as a result of the enzymatic reaction was measured via a smartphone camera. The proposed strategy allows the detection of creatinine rapidly in a minute amount of the serum samples without the need for expensive equipment. Thus, chronic kidney disease (CKD) could be monitored easily at point-of-care settings via the proposed creatinine detection strategy. © 2022 MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.Conference Object Magnetic Levitation-Based Viscosity Measurement in a Microcappilary Channel(Chemical and Biological Microsystems Society, 2022) Doyran, O.; Tekin, H.C.Viscosity, has been known as the key rheological parameter, to characterize biological, chemical and physical material properties. In this work, we have developed a magnetic levitation-based viscosity measurement method in a microcapillary channel. For this purpose, polymer microspheres are utilized as microsensors to correlate solution viscosity to microspheres' velocity while microspheres are balanced at a stable levitation position. This inexpensive and practical system enables rapid viscosity measurement from low amount of sample. © 2022 MicroTAS 2022 - 26th International Conference on Miniaturized Systems for Chemistry and Life Sciences. All rights reserved.Conference Object Quote Detection: a New Task and Dataset for Nlp(Association for Computational Linguistics, 2023) Tekir, S.; Güzel, A.; Tenekeci, S.; Haman, B.U.Quotes are universally appealing. Humans recognize good quotes and save them for later reference. However, it may pose a challenge for machines. In this work, we build a new corpus of quotes and propose a new task, quote detection, as a type of span detection. We retrieve the quote set from Goodreads and collect the spans through a custom search on the Gutenberg Book Corpus. We run two types of baselines for quote detection: Conditional random field (CRF) and summarization with pointer-generator networks and Bidirectional and Auto-Regressive Transformers (BART). The results show that the neural sequence-to-sequence models perform substantially better than CRF. From the viewpoint of neural extractive summarization, quote detection seems easier than news summarization. Moreover, model fine-tuning on our corpus and the Cornell Movie-Quotes Corpus introduces incremental performance boosts. Finally, we provide a qualitative analysis to gain insight into the performance. © 2023 Association for Computational Linguistics.Article Citation - Scopus: 6Functional Characterization of a Novel Cyp119 Variant To Explore Its Biocatalytic Potential(John Wiley and Sons Inc, 2022) Sakalli, T.; Surmeli, N.B.Biocatalysts are increasingly applied in the pharmaceutical and chemical industry. Cytochrome P450 enzymes (P450s) are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. P450s catalyze reactions using nicotinamide adenine dinucleotide phosphate (NAD(P)H) cofactor and electron transfer proteins. Alternatively, P450s can utilize hydrogen peroxide (H2O2) as an oxidant, but this pathway is inefficient. P450s that show higher efficiency with peroxides are sought after in industrial applications. P450s from thermophilic organisms have more potential applications as they are stable toward high temperature, high and low pH, and organic solvents. CYP119 is an acidothermophilic P450 from Sulfolobus acidocaldarius. In our previous study, a novel T213R/T214I (double mutant [DM]) variant of CYP119 was obtained by screening a mutant library for higher peroxidation activity utilizing H2O2. Here, we characterized the substrate scope; stability toward peroxides; and temperature and organic solvent tolerance of DM CYP119 to identify its potential as an industrial biocatalyst. DM CYP119 displayed higher stability than wild-type (WT) CYP119 toward organic peroxides. It shows higher peroxidation activity for non-natural substrates and higher affinity for progesterone and other bioactive potential substrates compared to WT CYP119. DM CYP119 emerges as a new biocatalyst with a wide range of potential applications in the pharmaceutical and chemical industry. © 2021 International Union of Biochemistry and Molecular Biology, Inc.Article Citation - Scopus: 4Quasi-Supervised Strategies for Compound-Protein Interaction Prediction(John Wiley and Sons Inc, 2022) Çakı, O.; Karaçalı, B.In-silico compound-protein interaction prediction addresses prioritization of drug candidates for experimental biochemical validation because the wet-lab experiments are time-consuming, laborious and costly. Most machine learning methods proposed to that end approach this problem with supervised learning strategies in which known interactions are labeled as positive and the rest are labeled as negative. However, treating all unknown interactions as negative instances may lead to inaccuracies in real practice since some of the unknown interactions are bound to be positive interactions waiting to be identified as such. In this study, we propose to address this problem using the Quasi-Supervised Learning (QSL) algorithm. In this framework, potential interactions are predicted by estimating the overlap between a true positive dataset of compound-protein pairs with known interactions and an unknown dataset of all the remaining compound-protein pairs. The potential interactions are then identified as those in the unknown dataset that overlap with the interacting pairs in the true positive dataset in terms of the associated similarity structure. We also address the class-imbalance problem by modifying the conventional cost function of the QSL algorithm. Experimental results on GPCR and Nuclear Receptor datasets show that the proposed method can identify actual interactions from all possible combinations. © 2021 Wiley-VCH GmbH.