Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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  • Article
    A Novel Technique Using Integral Transforms and Residual Functions for Nonlinear Partial Fractional Differential Equations Involving Caputo Derivatives
    (Public Library of Science, 2024) Khan, Z.A.; Riaz, M.B.; Liaqat, M.I.; Akgül, A.
    Fractional nonlinear partial differential equations are used in many scientific fields to model various processes, although most of these equations lack closed-form solutions. For this reason, methods for approximating solutions that occasionally yield closed-form solutions are crucial for solving these equations. This study introduces a novel technique that combines the residual function and a modified fractional power series with the Elzaki transform to solve various nonlinear problems within the Caputo derivative framework. The accuracy and effectiveness of our approach are validated through analyses of absolute, relative, and residual errors. We utilize the limit principle at zero to identify the coefficients of the series solution terms, while other methods, including variational iteration, homotopy perturbation, and Adomian, depend on integration. In contrast, the residual power series method uses differentiation, and both approaches encounter difficulties in fractional contexts. Furthermore, the effectiveness of our approach in addressing nonlinear problems without relying on Adomian and He polynomials enhances its superiority over various approximate series solution techniques. © 2024 Khan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration
    (Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, Funda
    In recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.
  • Article
    Citation - WoS: 1
    Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems
    (Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide Alsoy
    In this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.
  • Correction
    Diaph1-Deficiency Is Associated With Major T, Nk and Ilc Defects in Humans (vol 44, 175, 2024)
    (Springer/plenum Publishers, 2025) Azizoglu, Zehra Busra; Babayeva, Royala; Haskologlu, Zehra Sule; Acar, Mustafa Burak; Ayaz-Guner, Serife; Okus, Fatma Zehra; Eken, Ahmet
    [No Abstract Available]
  • Article
    Citation - WoS: 4
    Citation - Scopus: 4
    Organolabeler: a Quick and Accurate Annotation Tool for Organoid Images
    (Amer Chemical Soc, 2024) Kahveci, Burak; Polatli, Elifsu; Bastanlar, Yalin; Guven, Sinan
    Organoids are self-assembled 3D cellular structures that resemble organs structurally and functionally, providing in vitro platforms for molecular and therapeutic studies. Generation of organoids from human cells often requires long and costly procedures with arguably low efficiency. Prediction and selection of cellular aggregates that result in healthy and functional organoids can be achieved by using artificial intelligence-based tools. Transforming images of 3D cellular constructs into digitally processable data sets for training deep learning models requires labeling of morphological boundaries, which often is performed manually. Here, we report an application named OrganoLabeler, which can create large image-based data sets in a consistent, reliable, fast, and user-friendly manner. OrganoLabeler can create segmented versions of images with combinations of contrast adjusting, K-means clustering, CLAHE, binary, and Otsu thresholding methods. We created embryoid body and brain organoid data sets, of which segmented images were manually created by human researchers and compared with OrganoLabeler. Validation is performed by training U-Net models, which are deep learning models specialized in image segmentation. U-Net models, which are trained with images segmented by OrganoLabeler, achieved similar or better segmentation accuracies than the ones trained with manually labeled reference images. OrganoLabeler can replace manual labeling, providing faster and more accurate results for organoid research free of charge.
  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    An Experimental and Comparative Study on Passive and Active Pcm Cooling of a Battery With/Out Copper Mesh and Investigation of Pcm Mixtures
    (Elsevier, 2024) Samancioglu, Umut Ege; Gocmen, Sinan; Madani, Seyed Saeed; Ziebert, Carlos; Nuno, Fernando; Huang, Jack; Cetkin, Erdal
    The carbon emission contribution to global warming accelerated both research on and transition to electric vehicles (EVs). Drivers demand high power, fast acceleration and less charging times. All these demands require high C rate charging/discharging demands from batteries. The rate of heat generation is exponentially proportional to C rates which decreases battery lifetime and may lead to thermal runaway. However, a battery thermal management system decreases thermal runaway risk and decelerates battery degradation via controlling battery temperature. In this paper, we first document the thermal conductivity enhancement via copper foam into phase change material (PCM) domain to uncover their possible use in EV thermal management applications. Maximum 15.93 times increment is achieved with a specific copper foam. Then, physical properties and behaviors of distinct PCM mixtures are documented. Homogeneity of mixtures is associated with the chemistry of PCMs and the mixture melting point is proportional to the volume weighted average of melting temperatures. The results document that the PCM with relatively lower melting point is beneficial when end of discharge temperatures considered, except for high discharge rate of 2C. Temperature uniformity across the battery increases with relatively higher melting point PCM. Experiments also document that the amount of PCM volume lost via insertion of copper foam yields higher end of discharge temperatures. Overall, both PCM and copper foam enhances temperature homogeneity and their benefit becomes more sensible during drive cycles relative to continuous charge/discharge use cases.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Invasion/Chemotaxis- and Extravasation-Chip Models for Breast Cancer Bone Metastasis
    (Public Library Science, 2024) Firatligil-Yildirir, Burcu; Bati-Ayaz, Gizem; Nonappa, Devrim; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden
    Bone is one of the most frequently targeted organs in metastatic cancers including the breast. Breast cancer bone metastasis often results in devastating outcomes as limited treatment options are currently available. Therefore, innovative methods are needed to provide earlier detection and thus better treatment and prognosis. Here, we present a new approach to model bone-like microenvironments to detect invasion and extravasation of breast cancer cells using invasion/chemotaxis (IC-) and extravasation (EX-) chips, respectively. Our results show that the behaviors of MDA-MB-231 breast cancer cells on IC- and EX-chip models correlate with their in vivo metastatic potential. Our culture model constitutes cell lines representing osteoblasts, bone marrow stromal cells, and monocytes embedded in three-dimensional (3D) collagen I-based extracellular matrices of varying composition and stiffness. We show that collagen I offers a better bone-like environment for bone cells and matrix composition and stiffness regulate the invasion of breast cancer cells. Using in situ contactless rheological measurements under cell culture conditions, we show that the presence of cells increased the stiffness values of the matrices up to 1200 Pa when monitored for five days. This suggests that the cellular composition has a significant effect on regulating matrix mechanical properties, which in turn contribute to the invasiveness. The platforms we present here enable the investigation of the underlying molecular mechanisms in breast cancer bone metastasis and provide the groundwork of developing preclinical tools for the prediction of bone metastasis risk.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 2
    Investigation of the Biocompatibility of Various Pulp Capping Materials on Zebrafish Model
    (Public Library Science, 2024) Karahan, Meltem; Eliacik, Bahar Basak Kiziltan; Cagiral, Umut; Iscan, Evin; Ozhan, Gunes
    Testing the biocompatibility of commercially available dental materials is a major challenge in dental material science. In the present study, the biocompatibility of four commercially available dental materials Mineral Trioxide Aggregate, Biodentine, Harvard BioCal-CAP and Oxford ActiveCal PC was investigated. The biocompatibility analysis was performed on zebrafish embryos and larvae using standard toxicity tests such as survivability and hatching rates. Comparative toxicity analysis of toxicity was performed by measuring apoptosis using acridine orange dye and whole mount immunofluorescence methods on zebrafish larvae exposed to the dental materials at different dilutions. Toxicity analysis showed a significant decrease in survival and hatching rates with increasing concentration of exposed materials. The results of the apoptosis assay with acridine orange showed greater biocompatibility of Biodentine, Oxford ActiveCal PC, Harvard BioCal-CAP and Biodentine compared to MTA, which was concentration dependent. Consequently, this study has shown that showed resin-modified calcium silicates are more biocompatible than traditional calcium silicates.
  • Article
    Citation - Scopus: 5
    Exploring the Structural Insights of Thermostable Geobacillus Esterases by Computational Characterization
    (American Chemical Society, 2024) Sürmeli,Y.; Durmuş,N.; Şanlı-Mohamed,G.
    This study conducted an in silico analysis of two biochemically characterized thermostable esterases, Est2 and Est3, from Geobacillus strains. To achieve this, the amino acid sequences of Est2 and Est3 were examined to assess their biophysicochemical properties, evolutionary connections, and sequence similarities. Three-dimensional models were constructed and validated through diverse bioinformatics tools. Molecular dynamics (MD) simulation was employed on a pNP-C2 ligand to explore interactions between enzymes and ligand. Biophysicochemical property analysis indicated that aliphatic indices and theoretical Tm values of enzymes were between 82-83 and 55-65 °C, respectively. Molecular phylogeny placed Est2 and Est3 within Family XIII, alongside other Geobacillus esterases. DeepMSA2 revealed that Est2, Est3, and homologous sequences shared 12 conserved residues in their core domain (L39, D50, G53, G55, S57, G92, S94, G96, P108, P184, D193, and H223). BANΔIT analysis indicated that Est2 and Est3 had a significantly more rigid cap domain compared to Est30. Salt bridge analysis revealed that E150-R136, E124-K165, E137-R141, and E154-K157 salt bridges made Est2 and Est3 more stable compared to Est30. MD simulation indicated that Est3 exhibited greater fluctuations in the N-terminal region including conserved F25, cap domain, and C-terminal region, notably including H223, suggesting that these regions might influence esterase catalysis. The common residues in the ligand-binding sites of Est2-Est3 were determined as F25 and L167. The analysis of root mean square fluctuation (RMSF) revealed that region 1, encompassing F25 within the β2-α1 loop of Est3, exhibited higher fluctuations compared to those of Est2. Overall, this study might provide valuable insights for future investigations aimed at improving esterase thermostability and catalytic efficiency, critical industrial traits, through targeted amino acid modifications within the N-terminal region, cap domain, and C-terminal region using rational protein engineering techniques. © 2024 The Authors. Published by American Chemical Society.
  • Conference Object
    Citation - Scopus: 4
    Circular Economy in the Built Environment: a Systematic Literature Review on the Role of Digital Technologies Across Regional Contexts
    (Institute of Physics, 2024) Aral,D.; Kayaçetin,N.C.; Durmuş Arsan,Z.
    The built environment has a significant role in ecosystems and resource depletion. Therefore, its transition from linear into the circular economy (CE) is critical yet still progressing. While research on CE in the built environment (BE) is growing, an in-depth understanding of facilitators as digital technologies (DT) is required to accelerate its implementation. Investigating these digitalization efforts, considering the regional variations of developed and developing economies, needs to be deepened. This study aims to demonstrate state-of-the-art CE research, providing insight into how digital technology preferences evolved through regional context as a facilitator in the built environment. For this purpose, 80 articles were assessed by (i) descriptive and (ii) thematic analysis through a systematic literature review (SLR). The descriptive analysis highlights the trends in the literature on CE-enabling DT in the built environment. The thematic analysis indicates the prominent DT to facilitate the transition with a link to the regional context and related variations. The results identify integrated DT in CE studies and their relevance to the economic levels of several countries, and they show research gaps to guide future research. This study contributes to an emerging field of research at the nexus of the built environment, the circular economy, and digital technology by mapping regional research tendencies. © 2024 Institute of Physics Publishing. All rights reserved.