WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Citation - WoS: 13Citation - Scopus: 13Why Do Muse Stem Cells Present an Enduring Stress Capacity? Hints From a Comparative Proteome Analysis(MDPI, 2021-02-19) Acar, Mustafa B.; Aprile, Domenico; Ayaz-Guner, Serife; Guner, Huseyin; Tez, Coskun; Di Bernardo, Giovanni; Galderisi, UmbertoMuse cells are adult stem cells that are present in the stroma of several organs and possess an enduring capacity to cope with endogenous and exogenous genotoxic stress. In cell therapy, the peculiar biological properties of Muse cells render them a possible natural alternative to mesenchymal stromal cells (MSCs) or to in vitro-generated pluripotent stem cells (iPSCs). Indeed, some studies have proved that Muse cells can survive in adverse microenvironments, such as those present in damaged/injured tissues. We performed an evaluation of Muse cells' proteome under basic conditions and followed oxidative stress treatment in order to identify ontologies, pathways, and networks that can be related to their enduring stress capacity. We executed the same analysis on iPSCs and MSCs, as a comparison. The Muse cells are enriched in several ontologies and pathways, such as endosomal vacuolar trafficking related to stress response, ubiquitin and proteasome degradation, and reactive oxygen scavenging. In Muse cells, the protein-protein interacting network has two key nodes with a high connectivity degree and betweenness: NFKB and CRKL. The protein NFKB is an almost-ubiquitous transcription factor related to many biological processes and can also have a role in protecting cells from apoptosis during exposure to a variety of stressors. CRKL is an adaptor protein and constitutes an integral part of the stress-activated protein kinase (SAPK) pathway. The identified pathways and networks are all involved in the quality control of cell components and may explain the stress resistance of Muse cells.Article Citation - WoS: 1Citation - Scopus: 2WSA-Supplements and Proper Classes(MDPI, 2022-08-17) Demirci, Yilmaz Mehmet; Turkmen, ErgulIn this paper, we introduce the concept of wsa-supplements and investigate the objects of the class of short exact sequences determined by wsa-supplement submodules, where a submodule U of a module M is called a wsa-supplement in M if there is a submodule V of M with U + V = M and U boolean AND V is weakly semiartinian. We prove that a module M is weakly semiartinian if and only if every submodule of M is a wsa-supplement in M. We introduce CC-rings as a generalization of C-rings and show that a ring is a right CC-ring if and only if every singular right module has a crumbling submodule. The class of all short exact sequences determined by wsa-supplement submodules is shown to be a proper class which is both injectively and co-injectively generated. We investigate the homological objects of this proper class along with its relation to CC-rings.Article Citation - WoS: 10Citation - Scopus: 11Time-Dependent Reduction of Calcium Oscillations in Adipose-Derived Stem Cells Differentiating Towards Adipogenic and Osteogenic Lineage(MDPI, 2021-09-23) Torre, Enrico C.; Bicer, Mesude; Cottrell, Graeme S.; Widera, Darius; Tamagnini, FrancescoAdipose-derived mesenchymal stromal cells (ASCs) are multipotent stem cells which can differentiate into various cell types, including osteocytes and adipocytes. Due to their ease of harvesting, multipotency, and low tumorigenicity, they are a prime candidate for the development of novel interventional approaches in regenerative medicine. ASCs exhibit slow, spontaneous Ca2+ oscillations and the manipulation of Ca2+ signalling via electrical stimulation was proposed as a potential route for promoting their differentiation in vivo. However, the effects of differentiation-inducing treatments on spontaneous Ca2+ oscillations in ASCs are not yet fully characterised. In this study, we used 2-photon live Ca2+ imaging to assess the fraction of cells showing spontaneous oscillations and the frequency of the oscillation (measured as interpeak interval-IPI) in ASCs undergoing osteogenic or adipogenic differentiation, using undifferentiated ASCs as controls. The measurements were carried out at 7, 14, and 21 days in vitro (DIV) to assess the effect of time in culture on Ca2+ dynamics. We observed that both time and differentiation treatment are important factors associated with a reduced fraction of cells showing Ca2+ oscillations, paralleled by increased IPI times, in comparison with untreated ASCs. Both adipogenic and osteogenic differentiation resulted in a reduction in Ca2+ dynamics, such as the fraction of cells showing intracellular Ca2+ oscillations and their frequency. Adipogenic differentiation was associated with a more pronounced reduction of Ca2+ dynamics compared to cells differentiating towards the osteogenic fate. Changes in Ca2+ associated oscillations with a specific treatment had already occurred at 7 DIV. Finally, we observed a reduction in Ca2+ dynamics over time in untreated ASCs. These data suggest that adipogenic and osteogenic differentiation cell fates are associated with specific changes in spontaneous Ca2+ dynamics over time. While this observation is interesting and provides useful information to understand the functional correlates of stem cell differentiation, further studies are required to clarify the molecular and mechanistic correlates of these changes. This will allow us to better understand the causal relationship between Ca2+ dynamics and differentiation, potentially leading to the development of novel, more effective interventions for both bone regeneration and control of adipose growth.Article Citation - WoS: 4Citation - Scopus: 4The Use of Dynamic Cognitive Behavioural Therapy (DCBT) in Social Anxiety Disorder (SAD): A Theoretical Integration Initiative(MDPI, 2022-11-30) Kaya, M. SiyabendPsychotherapy theorists can often become fervent advocates of the schools they follow and place the doctrines of the theories they adopt above all else. This situation can sometimes turn into a war of theories between researchers as well. However, therapists should not aim to shape therapy sessions according to their methods but to use them in line with clients' needs. Although it is emphasised that the integration of both psychoanalytic and cognitive behavioural therapy techniques, which is going to be named dynamic cognitive behavioural therapy (DCBT) in this case report, will provide more effective and permanent treatment, a discernible gap exists regarding the integration of these theories and their use in psychotherapy. Taking into account this gap, it is considered important to use this approach with a client who has a social anxiety disorder (SAD). Therefore, this study aims to describe the almost forgotten DCBT approach step by step through a case report and reveal the effectiveness of this approach. As a result, DCBT seems to be effective in the treatment of SAD.Article Citation - WoS: 4Citation - Scopus: 4The Inter-Relationships of Territorial Quality of Life With Residential Expansion and Densification: A Case Study of Regions in EU Member Countries(MDPI, 2024-03-19) Ustaoglu, Eda; Williams, BrendanHigh-density urban development is promoted by both global and local policies in response to socio-economic and environmental challenges since it increases mobility of different land uses, decreases the need for traveling, encourages the use of more energy-efficient buildings and modes of transportation, and permits the sharing of scarce urban amenities. It is therefore argued that increased density and mixed-use development are expected to deliver positive outcomes in terms of contributing to three pillars (social, economic, and environmental domains) of sustainability in the subject themes. Territorial quality of life (TQL)-initially proposed by the ESPON Programme-is a composite indicator of the socio-economic and environmental well-being and life satisfaction of individuals living in an area. Understanding the role of urban density in TQL can provide an important input for urban planning debates addressing whether compact development can be promoted by referring to potential efficiencies in high-density, mixed land use and sustainable transport provisions. Alternatively, low-density suburban development is preferable due to its benefits of high per capita land use consumption (larger houses) for individual households given lower land prices. There is little empirical evidence on how TQL is shaped by high-density versus low-density urban forms. This paper investigates this topic through providing an approach to spatially map and examine the relationship between TQL, residential expansion, and densification processes in the so-called NUTS2 (nomenclature of terrestrial units for statistics) regions of European Union (EU) member countries. The relative importance of each TQL indicator was determined through the entropy weight method, where these indicators were aggregated through using the subject weights to obtain the overall TQL indicator. The spatial dynamics of TQL were examined and its relationship with residential expansion and densification processes was analysed to uncover whether the former or the latter process is positively associated with the TQL indicator within our study area. From our regression models, the residential expansion index is negatively related to the TQL indicator, implying that high levels of residential expansion can result in a reduction in overall quality of life in the regions if they are not supported by associated infrastructure and facility investments.Article Citation - WoS: 3Citation - Scopus: 6Simple Staining of Cells on a Chip(MDPI, 2022-11-13) Kosker, Fatma Betul; Aydin, Omer; Icoz, KutaySimple staining of cells is a widely used method in basic medical diagnostics, education, and research laboratories. The stains are low-cost, but the extensive consumption results in excessive toxic waste generation. Thus, to decrease the amount of toxic waste resulting from the cell staining procedure is a need. In this study, we developed a magnetically driven and compartmentalized passive microfluidic chip to perform simple staining of human eukaryotic cells, K562 cells, and lymphocyte cells derived from patients. We demonstrated simple staining on cells with trypan blue, methylene blue, crystal violet, and safranin for high, medium, and low cell densities. The stained cells were imaged using a bright field optical microscope and a cell phone to count cells on the focal plane. The staining improved the color signal of the cell by 25-135-pixel intensity changes for the microscopic images. The validity of the protocol was determined using Jurkat and MDA-MB-231 cell lines as negative controls. In order to demonstrate the practicality of the system, lymphocyte cells derived from human blood samples were stained with trypan blue. The color intensity changes in the first and last compartments were analyzed to evaluate the performance of the chip. The developed method is ultra-low cost, significantly reduces the waste generated, and can be integrated with mobile imaging devices in terms of portability. By combining microfabrication technology with cell staining, this study reported a novel contribution to the field of microfluidic biosensors. In the future, we expect to demonstrate the detection of pathogens using this method.Article Citation - WoS: 33Citation - Scopus: 36Shape Fidelity Evaluation of Alginate-Based Hydrogels Through Extrusion-Based Bioprinting(MDPI, 2022-11-07) Temirel, Mikail; Dabbagh, Sajjad Rahmani; Tasoglu, SavasExtrusion-based 3D bioprinting is a promising technique for fabricating multi-layered, complex biostructures, as it enables multi-material dispersion of bioinks with a straightforward procedure (particularly for users with limited additive manufacturing skills). Nonetheless, this method faces challenges in retaining the shape fidelity of the 3D-bioprinted structure, i.e., the collapse of filament (bioink) due to gravity and/or spreading of the bioink owing to the low viscosity, ultimately complicating the fabrication of multi-layered designs that can maintain the desired pore structure. While low viscosity is required to ensure a continuous flow of material (without clogging), a bioink should be viscous enough to retain its shape post-printing, highlighting the importance of bioink properties optimization. Here, two quantitative analyses are performed to evaluate shape fidelity. First, the filament collapse deformation is evaluated by printing different concentrations of alginate and its crosslinker (calcium chloride) by a co-axial nozzle over a platform to observe the overhanging deformation over time at two different ambient temperatures. In addition, a mathematical model is developed to estimate Young's modulus and filament collapse over time. Second, the printability of alginate is improved by optimizing gelatin concentrations and analyzing the pore size area. In addition, the biocompatibility of proposed bioinks is evaluated with a cell viability test. The proposed bioink (3% w/v gelatin in 4% alginate) yielded a 98% normalized pore number (high shape fidelity) while maintaining >90% cell viability five days after being bioprinted. Integration of quantitative analysis/simulations and 3D printing facilitate the determination of the optimum composition and concentration of different elements of a bioink to prevent filament collapse or bioink spreading (post-printing), ultimately resulting in high shape fidelity (i.e., retaining the shape) and printing quality.Article Citation - WoS: 20Citation - Scopus: 26Quality, Nutritional Properties, and Glycemic Index of Colored Whole Wheat Breads(MDPI, 2023-09-08) Koksel, Hamit; Cetiner, Buket; Shamanin, Vladimir P.; Tekin-Cakmak, Z. Hazal; Pototskaya, Inna V.; Kahraman, Kevser; Morgounov, Alexey I.The main aim of this study was to investigate the quality and nutritional properties (dietary fiber, phenolic, antioxidant contents, and glycemic index) of breads made from whole wheat flours of colored wheats. White (cultivar Agronomicheskaya 5), red (Element 22), purple (EF 22 and Purple 8), and blue (Blue 10) colored wheats were used in the study. The whole wheat flours of Blue 10 and Purple 8 had higher farinograph stability, lower softening degree, and higher quality numbers indicating that they had better rheological properties. Bread produced from whole wheat flour of blue-colored grain had significantly higher loaf volume and better symmetry, crust color, crumb cell structure, and softness values among others (p < 0.05). The whole wheat bread produced using Element 22 had the highest crust and crumb L* color values, while Purple 8 and EF 22 had the lowest crust and crumb L* color values, suggesting that purple-colored grains have a tendency to make whole wheat bread with darker crust and crumb color. Bread produced from cultivar Blue 10 had the lowest firmness values while Element 22 had the highest firmness values. The highest total phenolic content and antioxidant capacity values were obtained from the whole wheat bread sample from purple-colored wheat (Purple 8). The whole wheat flour of Element 22 had the highest total dietary fiber content among all samples (p < 0.05). The differences between whole wheat bread samples in terms of total dietary fiber and glycemic index were not statistically significant. The results of the present study indicated that colored wheats can be used to produce whole wheat breads with higher nutritional properties and acceptable quality characteristics.Article Citation - WoS: 3Citation - Scopus: 3HER2-Specific Peptide (LTWWYSPY) and Antibody (Herceptin) Targeted Core Cross-Linked Micelles for Breast Cancer: A Comparative Study(MDPI, 2023-02-22) Bayram, Nazende Nur; Ulu, Gizem Tugce; Abdulhadi, Nusaibah Abdulsalam; Guerdap, Seda; Isoglu, Ismail Alper; Baran, Yusuf; Isoglu, Sevil Dincer; Gürdap, SedaThis study aims to prepare a novel breast cancer-targeted micelle-based nanocarrier, which is stable in circulation, allowing intracellular drug release, and to investigate its cytotoxicity, apoptosis, and cytostatic effects, in vitro. The shell part of the micelle is composed of zwitterionic sulfobetaine ((N-3-sulfopropyl-N,N-dimethylamonium)ethyl methacrylate), while the core part is formed by another block, consisting of AEMA (2-aminoethyl methacrylamide), DEGMA (di(ethylene glycol) methyl ether methacrylate), and a vinyl-functionalized, acid-sensitive cross-linker. Following this, a targeting agent (peptide (LTVSPWY) and antibody (Herceptin((R)))), in varying amounts, were coupled to the micelles, and they were characterized by H-1 NMR, FTIR (Fourier-transform infrared spectroscopy), Zetasizer, BCA protein assay, and fluorescence spectrophotometer. The cytotoxic, cytostatic, apoptotic, and genotoxic effects of doxorubicin-loaded micelles were investigated on SKBR-3 (human epidermal growth factor receptor 2 (HER2)-positive) and MCF10-A (HER2-negative). According to the results, peptide-carrying micelles showed a higher targeting efficiency and better cytostatic, apoptotic, and genotoxic activities than antibody-carrying and non-targeted micelles. Also, micelles masked the toxicity of naked DOX on healthy cells. In conclusion, this nanocarrier system has great potential to be used in different drug-targeting strategies, by changing targeting agents and drugs.Article Citation - WoS: 3Citation - Scopus: 5Experimental Investigation on the Bonding Strength of Knotted CFRP Bars in Bulk Plastics(MDPI, 2023-04-25) Ciftci, CihanImproving the interfacial bonding strength of CFRP materials is crucial for enabling the development of novel composite beam structures with higher specific bending strength demanded by the composite industry. In this research study, for reinforced bulk plastic composites, the aim is to enhance the interfacial bonding strength of CFRP bar elements in bulk plastics by on the formation of knots. In this context, firstly, the knotted CFRP bars with varying cross-sectional areas were manufactured under laboratory conditions for the experimental investigation on the effect of knots on bonding strength. Commercially available smooth-surfaced CFRP bars were also purchased to be used as the reference. Then, all these CFRP bars were subjected to pull-out tests by using in bulk plastics. According to the test results, it was observed that the interfacial bonding strength of CFRP bars in bulk plastic materials could be increased up to 233% because of the knots.