PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Editorial Advances in Natural Building and Construction Materials(MDPI, 2025-12-16) Strzalkowski, Pawel; Sousa, Luis; Koken, Ekin; Strzałkowski, PawełArticle 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: 11Citation - Scopus: 12Towards Analysis and Optimization for Contact Zone Temperature Changes and Specific Wear Rate of Metal Matrix Composite Materials Produced From Recycled Waste(MDPI, 2021-09-08) Gunes, Aydin; Salur, Emin; Aslan, Abdullah; Kuntoglu, Mustafa; Giasin, Khaled; Pimenov, Danil Yurievich; Sahin, Omer SinanTribological properties are important to evaluate the in-service conditions of machine elements, especially those which work as tandem parts. Considering their wide range of application areas, metal matrix composites (MMCs) serve as one of the most significant materials equipped with desired mechanical properties such as strength, density, and lightness according to the place of use. Therefore, it is crucial to determine the wear performance of these materials to obtain a longer life and to overcome the possible structural problems which emerge during the production process. In this paper, extensive discussion and evaluation of the tribological performance of newly produced spheroidal graphite cast iron-reinforced (GGG-40) tin bronze (CuSn10) MMCs, including optimization, statistical, graphical, and microstructural analysis for contact zone temperature and specific wear rate, are presented. For this purpose, two levels of production temperature (400 and 450 degrees C), three levels of pressure (480, 640, and 820 MPa), and seven different samples reinforced by several ingredients (from 0 to 40 wt% GGG-40, pure CuSn10, and GGG-40) were investigated. According to the obtained statistical results, the reinforcement ratio is remarkably more effective on contact zone temperature and specific wear rate than temperature and pressure. A pure CuSn10 sample is the most suitable option for contact zone temperature, while pure GGG-40 seems the most suitable material for specific wear rates according to the optimization results. These results reveal the importance of reinforcement for better mechanical properties and tribological performance in measuring the capability of MMCs.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 Role of Long Non-Coding RNA X-Inactive Transcript (XIST) in Neuroinflammation and Myelination: Insights From Cerebral Organoids and Implications for Multiple Sclerosis(MDPI, 2025-04-29) Pepe, Nihan Aktas; Acar, Busra; Zararsiz, Gozde Erturk; Guner, Serife Ayaz; Sen, Alaattin; Erturk Zararsiz, Gozde; Ayaz Guner, Serife; Aktas Pepe, NihanBackground/Objectives: X-inactive-specific transcript (XIST) is a factor that plays a role in neuroinflammation. This study investigated the role of XIST in neuronal development, neuroinflammation, myelination, and therapeutic responses within cerebral organoids in the context of Multiple Sclerosis (MS) pathogenesis. Methods: Human cerebral organoids with oligodendrocytes were produced from XIST-silenced H9 cells, and the mature organoids were subsequently treated with either FTY720 or DMF. Gene expression related to inflammation and myelination was subsequently analyzed via qRT-PCR. Immunofluorescence staining was used to assess the expression of proteins related to inflammation, myelination, and neuronal differentiation. Alpha-synuclein protein levels were also checked via ELISA. Finally, transcriptome analysis was conducted on the organoid samples. Results: XIST-silenced organoids presented a 2-fold increase in the expression of neuronal stem cells, excitatory neurons, microglia, and mature oligodendrocyte markers. In addition, XIST silencing increased IL-10 mRNA expression by 2-fold and MBP and PLP1 expression by 2.3- and 0.6-fold, respectively. Although XIST silencing tripled IBA1 protein expression, it did not affect organoid MBP expression. FTY720, but not DMF, distinguished MBP and IBA1 expression in XIST-silenced organoids. Furthermore, XIST silencing reduced the concentration of alpha-synuclein from 300 to 100 pg/mL, confirming its anti-inflammatory role. Transcriptomic and gene enrichment analyses revealed that the differentially expressed genes are involved in neural development and immune processes, suggesting the role of XIST in neuroinflammation. The silencing of XIST modified the expression of genes associated with inflammation, myelination, and neuronal growth in cerebral organoids, indicating a potential involvement in the pathogenesis of MS. Conclusions: XIST may contribute to the MS pathogenesis as well as neuroinflammatory diseases such as and Alzheimer's and Parkinson's diseases and may be a promising therapeutic target.Article Citation - WoS: 18Citation - Scopus: 21Optimization Study on Surface Roughness and Tribological Behavior of Recycled Cast Iron Reinforced Bronze MMCs Produced by Hot Pressing(MDPI, 2021-06-17) Gunes, Aydin; Sahin, Omer Sinan; Duzcukoglu, Hayrettin; Salur, Emin; Aslan, Abdullah; Kuntoglu, Mustafa; Pimenov, Danil YurievichSurface roughness reflects the quality of many operational parameters, namely service life, wear characteristics, working performance and tribological behavior of the produced part. Therefore, tribological performance is critical for the components used as tandem parts, especially for the MMCs (Metal Matrix Composites) which are a unique class of materials having extensive application areas such as aerospace, aeronautics, marine engineering and the defense industry. Current work covers the optimization study of production parameters for surface roughness and tribological indicators of newly produced cast iron reinforced bronze MMCs. In this context, two levels of temperature (400 and 450 degrees C), three levels of pressure (480, 640 and 820 MPa) and seven levels of reinforcement ratios (60/40, 70/30, 80/20, 90/10, 100/0 of GGG40/CuSn10, pure bronze-as received and pure cast iron-as received) are considered. According to the findings obtained by Taguchi's signal-to-noise ratios, the reinforcement ratio has a dominant effect on surface roughness parameters (Ra and Rz), the coefficient of friction and the weight loss in different levels. In addition, 100/0 reinforced GGG40/CuSn10 gives minimum surface roughness, pure cast iron provides the best weight loss and pure bronze offers the desired coefficient of friction. The results showed the importance of material ingredients on mechanical properties by comparing a wide range of samples from starting the production phase, which provides a perspective for manufacturers to meet the market supply as per human requirements.Article Citation - WoS: 2Citation - Scopus: 4Influence of Basalt Aggregate Crushing Technology on Its Geometrical Properties-Preliminary Studies(MDPI, 2023-01-08) Duchnowska, Magdalena; Strzalkowski, Pawel; Bakalarz, Alicja; Kazmierczak, Urszula; Koken, Ekin; Karwowski, Piotr; Stepien, Tomasz; Strzałkowski, PawełThe use of mineral aggregates is related to the increasing demand in construction, railway and road infrastructures. However, mineral aggregates can appear to be of variable quality, directly affecting their suitability for respective earthwork applications. Since the production of mineral aggregates should ensure the standardized, high-quality requirements of the final product, rock-crushing mechanisms should be investigated in a detailed manner. In this context, the aim of the present study is to evaluate and analyze the geometric parameters of basalt aggregates as a result of several rock comminution processes. Basalt aggregates from two deposits in Poland were used in the study. The samples are differentiated regarding both lithological variances, mineral composition as well as the host rock's tuff content. The rock comminution processes were conducted using two types of crushers, namely the laboratory-scale jaw and cone crushers. The feed for crushing was designed based on the original geometric grain composition and the separated feed in the form of flaky and non-flaky particles. The crushability test results demonstrated that the interparticle compression in the jaw crusher resulted in finer products compared to the one in the cone crusher. It was also observed that the flakiness and shape indexes decreased after crushing, both in the feed with the original geometric composition of the grains and those with flaky and non-flaky particles. Nevertheless, a higher flakiness index was obtained after the crushing of non-flaky particles and a lower one after the crushing of flaky particles. The flakiness index for grains below 16 mm after the crushing process was less than 10%, which indicates a more favorable result compared to the original feed. In addition, it was shown that flaky and non-cubical particles were accumulated in the finest (below 8 mm) and coarsest (above 20 mm) fractions in jaw and cone crushing processes, receiving flakiness and shape indexes ranging up to 80-100%. Finally, it was also observed that the lithological variances of the feed material have a significant impact on the particle size distribution of the product. More profoundly, basalt aggregates with a higher tuff content and weathering degree have a higher degree of crushing. The present study, in this context, provides accurate and satisfying information on understanding the crushing mechanisms of two important crushing equipment as well as their rock-crusher interactions.Article Citation - WoS: 11Citation - Scopus: 11Guidelines for Natural Stone Products in Connection With European Standards(MDPI, 2023-10-26) Strzalkowski, Pawel; Koken, Ekin; Sousa, Luis; Strzałkowski, PawełThe selection of ornamental stones for specific applications requires technical guidance since it should be based on the durability, service life, and aesthetic value of the stones. In most cases, these fundamentals provide quantitative data on the usability and performance of ornamental stones. The present study attempts to put forward a quantitative classification system for natural stone products concerning critical rock properties. For this purpose, fundamental physical and mechanical rock properties are listed based on European standards. Then, minimum limit values are proposed for different applications of natural stone products based on retrospective analyses of numerous ornamental stone applications. The suggested limit values based on several physical and mechanical rock properties can guide relevant engineers to initially consider possible rock types for use as natural stones in a wide range of applications. In this context, it is believed that the present study contributes to the natural stone industry by discussing the minimum limit values for the consideration of a wide range of rock types possibly usable in the dimension stone industry.Article Citation - WoS: 16Citation - Scopus: 26Gaussian of Differences: A Simple and Efficient General Image Fusion Method(MDPI, 2023-08-15) Kurban, RifatThe separate analysis of images obtained from a single source using different camera settings or spectral bands, whether from one or more than one sensor, is quite difficult. To solve this problem, a single image containing all of the distinctive pieces of information in each source image is generally created by combining the images, a process called image fusion. In this paper, a simple and efficient, pixel-based image fusion method is proposed that relies on weighting the edge information associated with each pixel of all of the source images proportional to the distance from their neighbors by employing a Gaussian filter. The proposed method, Gaussian of differences (GD), was evaluated using multi-modal medical images, multi-sensor visible and infrared images, multi-focus images, and multi-exposure images, and was compared to existing state-of-the-art fusion methods by utilizing objective fusion quality metrics. The parameters of the GD method are further enhanced by employing the pattern search (PS) algorithm, resulting in an adaptive optimization strategy. Extensive experiments illustrated that the proposed GD fusion method ranked better on average than others in terms of objective quality metrics and CPU time consumption.Article Citation - WoS: 4Citation - Scopus: 4Evaluation of Selected Plant Phenolics Via Beta-Secretase Inhibition, Molecular Docking, and Gene Expression Related to Alzheimer's Disease(MDPI, 2024-10-28) Akyurek, Tugba Ucar; Orhan, Ilkay Erdogan; Deniz, F. Sezer Senol; Eren, Gokcen; Acar, Busra; Sen, Alaattin; Şenol Deniz, F. Sezer; Uçar Akyürek, TugbaBackground: The goal of the current study was to investigate the inhibitory activity of six phenolic compounds, i.e., rosmarinic acid, gallic acid, oleuropein, epigallocatechin gallate (EGCG), 3-hydroxytyrosol, and quercetin, against beta-site amyloid precursor protein cleaving enzyme-1 (BACE1), also known as beta-secretase or memapsin 2, which is implicated in the pathogenesis of Alzheimer's disease (AD). Methods and Results: The inhibitory potential against BACE1, molecular docking simulations, as well as neurotoxicity and the effect on the AD-related gene expression of the selected phenolics were tested. BACE1 inhibitory activity was carried out using the ELISA microplate assay via fluorescence resonance energy transfer (FRET) technology. Molecular docking experiments were performed in the human BACE1 active site (PDB code: 2WJO). Neurotoxicity of the compounds was carried out in SH-SY5Y, a human neuroblastoma cell line, by the Alamar Blue method. A gene expression analysis of the compounds on fourteen genes linked to AD was conducted using the real-time polymerase chain reaction (RT-PCR) method. Rosmarinic acid, EGCG, oleuropein, and quercetin (also used as the reference) were able to inhibit BACE1 with their respective IC50 values 4.06 +/- 0.68, 1.62 +/- 0.12, 9.87 +/- 1.01, and 3.16 +/- 0.30 mM. The inhibitory compounds were observed to occupy the non-catalytic site of the BACE1. However, hydrogen bonds were found to be present between rosmarinic acid and EGCG and aspartic amino acid D228 in the catalytic site. Oleuropein and quercetin effectively suppressed the expression of PSEN, APOE, and CLU, which are recognized to be linked to the pathogenesis of AD. Conclusions: The outcomes of the work bring quercetin, EGCG, and rosmarinic acid to the forefront as promising BACE1 inhibitors.