Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
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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: 6Citation - Scopus: 5Gelatin-Containing Porous Polycaprolactone Polyhipes as Substrates for 3d Breast Cancer Cell Culture and Vascular Infiltration(Frontiers Media Sa, 2024) Jackson, Caitlin E.; Doyle, Iona; Khan, Hamood; Williams, Samuel F.; Dikici, Betul Aldemir; Ledesma, Edgar Barajas; Claeyssens, FrederikTumour survival and growth are reliant on angiogenesis, the formation of new blood vessels, to facilitate nutrient and waste exchange and, importantly, provide a route for metastasis from a primary to a secondary site. Whilst current models can ensure the transport and exchange of nutrients and waste via diffusion over distances greater than 200 mu m, many lack sufficient vasculature capable of recapitulating the tumour microenvironment and, thus, metastasis. In this study, we utilise gelatin-containing polymerised high internal phase emulsion (polyHIPE) templated polycaprolactone-methacrylate (PCL-M) scaffolds to fabricate a composite material to support the 3D culture of MDA-MB-231 breast cancer cells and vascular ingrowth. Firstly, we investigated the effect of gelatin within the scaffolds on the mechanical and chemical properties using compression testing and FTIR spectroscopy, respectively. Initial in vitro assessment of cell metabolic activity and vascular endothelial growth factor expression demonstrated that gelatin-containing PCL-M polyHIPEs are capable of supporting 3D breast cancer cell growth. We then utilised the chick chorioallantoic membrane (CAM) assay to assess the angiogenic potential of cell-seeded gelatin-containing PCL-M polyHIPEs, and vascular ingrowth within cell-seeded, surfactant and gelatin-containing scaffolds was investigated via histological staining. Overall, our study proposes a promising composite material to fabricate a substrate to support the 3D culture of cancer cells and vascular ingrowth.Article Citation - WoS: 1Citation - Scopus: 1An Iris Segmentation Scheme Based on Bendlets(Springer London Ltd, 2023) Aghazadeh, Nasser; Abbasi, Mandana; Noras, ParisaDue to the effect of agents such as ambiance, transition channel, and other agents, images are polluted by noise during collection, transition, and compaction, leading to decrease image quality. Noise can decrease the accuracy of the next stages of image processing systems. Therefore, one of the vital stages in the novel processing systems is denoising. This article offers a novel image denoising approach using bendlets. Other multi-scale transformations (such as wavelets, curvelets, and shearlets) cannot recognize properties such as location, direction, and curvature of discontinuities well in piecewise stable images. To solve this problem, bendlets are suggested in this article. Bendlets differ from other multi-scale transformations in that an additional bending parameter is utilized for recognizing the curvature of discontinuities. Bendlets need a fewer number of coefficients to identify curvatures than other multi-scale transformations. Furthermore, they help to make the edges more obvious. The suggested approach is utilized on the UBIRIS.V2 database. It earns better accuracy and stability than other multi-scale transformations.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.Article Citation - WoS: 1Citation - Scopus: 1Light-Dark and Activity Rhythm Therapy (l-Dart) To Improve Sleep in People With Schizophrenia Spectrum Disorders: a Single-Group Mixed Methods Study of Feasibility, Acceptability and Adherence(MDPI, 2023) Faulkner, Sophie; Didikoğlu, Altuğ; Byrne, Rory; Drake, Richard; Bee, PennyPeople with a diagnosis of schizophrenia often have poor sleep, even when their psychotic symptoms are relatively well managed. This includes insomnia, sleep apnoea, hypersomnia, and irregular or non-24 h sleep-wake timing. Improving sleep would better support recovery, yet few evidence-based sleep treatments are offered to this group. This paper presents a mixed methods feasibility and acceptability study of Light-Dark and Activity Rhythm Therapy (L-DART). L-DART is delivered by an occupational therapist over 12 weeks. It is highly personalisable to sleep phenotypes and circumstances. Ten participants with schizophrenia spectrum diagnoses and sleep problems received L-DART; their sleep problems and therapy goals were diverse. We measured recruitment, attrition, session attendance, and adverse effects, and qualitatively explored acceptability, engagement, component delivery, adherence, activity patterns, dynamic light exposure, self-reported sleep, wellbeing, and functioning. Recruitment was ahead of target, there was no attrition, and all participants received the minimum 'dose' of sessions. Acceptability assessed via qualitative reports and satisfaction ratings was good. Adherence to individual intervention components varied, despite high participant motivation. All made some potentially helpful behaviour changes. Positive sleep and functioning outcomes were reported qualitatively as well as in outcome measures. The findings above support testing the intervention in a larger randomised trial ISRCTN11998005.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.Article Citation - Scopus: 10Use of Magic Sandwich Echo and Fast Field Cycling Nmr Relaxometry on Honey Adulteration With Corn Syrup(John Wiley and Sons Ltd, 2022) Berk, B.; Cavdaroglu, C.; Grunin, L.; Ardelean, I.; Kruk, D.; Mazi, B.G.; Oztop, M.H.BACKGROUND: Adulteration is defined as the intentional addition of a material that is not a part of the nature. In this study, a non-conventional time domain nuclear magnetic resonance (TD-NMR) pulse sequence: magic sandwich echo (MSE) was used to detect the adulteration of honey by glucose syrup (GS) and high fructose corn syrup (HFCS) accompanied with T1 and T2 relaxation times. Also, fast field cycling NMR (FFC-NMR) relaxometry and multivariate analysis were performed to investigate the adulteration. RESULTS: Higher maltose in GS and changing glucose to water ratio of HFCS gave high correlation with the crystal content values. In HFCS adulteration, two separate populations of protons having different T2 values were detected and T1 times were also used to determine GS adulteration. Addition of GS increased T1 while addition of HFCS increased T2, significantly. CONCLUSION: The results showed that it is possible to differentiate the unadulterated and adulterated honey samples by using TD-NMR relaxation times and crystal content values obtained by the MSE sequence. By FFC-NMR relaxometry, not only GS addition but also the amount of GS was examined. The multivariate analysis technique of principal component analysis was able to distinguish the types of adulterants. © 2021 Society of Chemical Industry. © 2021 Society of Chemical Industry.Article Citation - Scopus: 13Her2-Targeted, Degradable Core Cross-Linked Micelles for Specific and Dual Ph-Sensitive Dox Release(John Wiley and Sons Inc, 2022) Bayram, N.N.; Ulu, G.T.; Topuzoğulları, M.; Baran, Y.; Dinçer, İşoğlu, S.Here, a targeted, dual-pH responsive, and stable micelle nanocarrier is designed, which specifically selects an HER2 receptor on breast cancer cells. Intracellularly degradable and stabilized micelles are prepared by core cross-linking via reversible addition−fragmentation chain-transfer (RAFT) polymerization with an acid-sensitive cross-linker followed by the conjugation of maleimide–doxorubicin to the pyridyl disulfide-modified micelles. Multifunctional nanocarriers are obtained by coupling HER2-specific peptide. Formation of micelles, addition of peptide and doxorubicin (DOX) are confirmed structurally by spectroscopical techniques. Size and morphological characterization are performed by Zetasizer and transmission electron microscope (TEM). For the physicochemical verification of the synergistic acid-triggered degradation induced by acetal and hydrazone bond degradation, Infrared spectroscopy and particle size measurements are used. Drug release studies show that DOX release is accelerated at acidic pH. DOX-conjugated HER2-specific peptide-carrying nanocarriers significantly enhance cytotoxicity toward SKBR-3 cells. More importantly, no selectivity toward MCF-10A cells is observed compared to HER2(+) SKBR-3 cells. Formulations cause apoptosis depending on Bax and Caspase-3 and cell cycle arrest in G2 phase. This study shows a novel system for HER2-targeted therapy of breast cancer with a multifunctional nanocarrier, which has higher stability, dual pH-sensitivity, selectivity, and it can be an efficient way of targeted anticancer drug delivery. © 2021 Wiley-VCH GmbH