PubMed İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/397
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Article Citation - WoS: 1Two-Local Modifications of Sachdev-Ye Model With Quantum Chaos(American Physical Society, 2026-01-27) Hanada, M.; Van Leuven, S.; Oktay, O.; Tezuka, M.The Sachdev-Ye-Kitaev (SYK) model may provide us with a good starting point for the experimental study of quantum chaos and holography in the laboratory. Still, the four-local interaction of fermions makes quantum simulation challenging, and it would be good to search for simpler models that keep the essence. In this paper, we argue that the four-local interaction may not be important by introducing a few models that have two-local interactions. The first model is a generalization of the spin-SYK model, which is obtained by replacing the spin variables with SU(d) generators. Simulations of this class of models might be straightforward on qudit-based quantum devices. We study the case of d=3,4,5,6 numerically and observe quantum chaos already for two-local interactions in a wide energy range. We also introduce modifications of spin-SYK and SYK models that have similar structures as the SU(d) model (e.g., H=∑p,qJpqχpχp+1χqχq+1 instead of the original SYK Hamiltonian H=∑p,q,r,sJpqrsχpχqχrχs), which shows strongly chaotic features although the interaction is essentially two-local. These models may be a good starting point for the quantum simulation of the original SYK model. ©2026 American Physical Society.Article Citation - WoS: 1Citation - Scopus: 1Effect of Yttrium/Lanthanum-Doped Ultrasonically Assisted Nano-Hydroxyapatite on Remineralization and Bracket Bond Strength in Artificial Enamel Lesions(BMC, 2025-09-29) Ozturk, Taner; Mammadov, Elshan; Bulduk Karakaya, Humeyra; Yagci, Filiz; Dayan, Serkan; Yagci, AhmetBackground This in vitro study aimed to evaluate the remineralization efficacy of ultrasonically assisted yttrium fluoride-doped (Ult-YF3-nHAP) and lanthanum fluoride-doped (Ult-LaF3-nHAP) nano-hydroxyapatite (nHAP) on artificially induced enamel lesions (aWSLs), and to compare their performance with acidulated phosphate fluoride (APF) gel, fluoride varnish, casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), and resin infiltrant (ICON). Methods This in vitro study followed a four-phase design: enamel lesion creation, application of remineralization agents, a 14-day treatment protocol, and post-treatment analyses using QLF, Micro-CT, SEM-EDX, and SBS testing. This study included 168 extracted human premolars, divided into eight experimental groups (n = 21 per group): (1) Demineralized control (no remineralization treatment), (2) Acidulated phosphate fluoride (APF) gel, (3) Fluoride varnish, (4) Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP), (5) Ultrasonically assisted nHAP (Control nHAP), (6) Ult-YF3-nHAP, (7) Ult-LaF3-nHAP, and (8) Resin infiltrant (ICON). The aWSLs were created under laboratory conditions. Brackets were bonded to the teeth with composite material, and aWSLs were created under laboratory conditions. After lesion formation and at the end of the experimental process, micro-computed tomography (Micro-CT) and laser-assisted quantitative light fluorescence (QLF) analysis were performed to assess lesion progression and remineralization. Additionally, scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX) and shear bond strength (SBS) tests were conducted at the end of the study. Statistical analysis was performed using one-way ANOVA, Kruskal-Wallis, and Mann-Whitney U tests, with a significance level of p < 0.05. Results The bracket bond strength test data showed no significant differences between the groups (p = 0.156). Significant differences were found among groups for QLF fluorescence recovery (Delta F, p < 0.001), with the Ult-YF3-nHAP group showing the greatest increase (median: +0.5, IQR: -1.4 to + 0.7), while the control group showed the greatest decrease (median: -12.1, IQR: -12.4 to -10.2). Micro-CT analysis also revealed significant differences between groups (p = 0.008). The APF Gel group showed values comparable to those of all other experimental groups. The highest remineralization values were recorded in the Ult-YF3-nHAP group (6.87 +/- 3.03 mm(3)), whereas the lowest values were found in the Varnish group. The demineralized control group had significantly higher values than the Varnish group, but lower than the Ult-LaF3-nHAP group. SEM-EDX analysis revealed that fluoride weight was significantly lower in the Tooth Mousse and Varnish groups compared to the other experimental groups (p < 0.001). Ca/P ratio was significantly lower in the demineralized control, Varnish, and Ult-YF3-nHAP groups than in other experimental groups (p = 0.002). Conclusion Ult-YF3-nHAP showed higher efficacy in remineralization of aWSLs compared to fluoride-based treatments, CPP-ACP, and resin infiltrant. The highest remineralization was detected in the Ult-YF3-nHAP group by micro-CT and QLF analysis, while fluoride varnish gave the lowest result.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: 6Citation - Scopus: 7The Determination of Distinctive Single Nucleotide Polymorphism Sets for the Diagnosis of Behcet's Disease(IEEE Computer Soc, 2022-05-01) Isik, Yunus Emre; Gormez, Yasin; Aydin, Zafer; Bakir-Gungor, BurcuBehcet's Disease (BD) is a multi-system inflammatory disorder in which the etiology remains unclear. The most probable hypothesis is that genetic tendency and environmental factors play roles in the development of BD. In order to find the essential reasons, genetic changes on thousands of genes should be analyzed. Besides, there is a need for extra analysis to find out which genetic factor affects the disease. Machine learning approaches have high potential for extracting the knowledge from genomics and selecting the representative Single Nucleotide Polymorphisms (SNPs) as the most effective features for the clinical diagnosis process. In this study, we have attempted to identify representative SNPs using feature selection methods, incorporating biological information and aimed to develop a machine-learning model for diagnosing Behcet's disease. By combining biological information and machine learning classifiers, up to 99.64 percent accuracy of disease prediction is achieved using only 13,611 out of 311,459 SNPs. In addition, we revealed the SNPs that are most distinctive by performing repeated feature selection in cross-validation experiments.Article Citation - Scopus: 23Synthesis and Comprehensive in Vivo Activity Profiling of Olean-12-en-28-ol, 3β-Pentacosanoate in Experimental Autoimmune Encephalomyelitis: A Natural Remyelinating and Anti-Inflammatory Agent(American Chemical Society, 2023-01-04) Şenol, Halil; Ozgun-Acar, Özden; Daǧ, Aydan; Eken, Ahmet; Guner, Hüseyin; Aykut, Zaliha Gamze; Sen, AlaattinMultiple sclerosis (MS) treatment has received much attention, yet there is still no certain cure. We herein investigate the therapeutic effect of olean-12-en-28-ol, 3β-pentacosanoate (OPCA) on a preclinical model of MS. First, OPCA was synthesized semisynthetically and characterized. Then, the mice with MOG<inf>35-55</inf>-induced experimental autoimmune/allergic encephalomyelitis (EAE) were given OPCA along with a reference drug (FTY720). Biochemical, cellular, and molecular analyses were performed in serum and brain tissues to measure anti-inflammatory and neuroprotective responses. OPCA treatment protected EAE-induced changes in mouse brains maintaining blood-brain barrier integrity and preventing inflammation. Moreover, the protein and mRNA levels of MS-related genes such as HLD-DR1, CCL5, TNF-α, IL6, and TGFB1 were significantly reduced in OPCA-treated mouse brains. Notably, the expression of genes, including PLP, MBP, and MAG, involved in the development and structure of myelin was significantly elevated in OPCA-treated EAE. Furthermore, therapeutic OPCA effects included a substantial reduction in pro-inflammatory cytokines in the serum of treated EAE animals. Lastly, following OPCA treatment, the promoter regions for most inflammatory regulators were hypermethylated. These data support that OPCA is a valuable and appealing candidate for human MS treatment since OPCA not only normalizes the pro- and anti-inflammatory immunological bias but also stimulates remyelination in EAE. © 2023 Elsevier B.V., All rights reserved.Article Citation - WoS: 6Citation - Scopus: 6Sleep-Aware Wavelength and Bandwidth Assignment Scheme for TWDM PON(Springer, 2021-06) Butt, Rizwan Aslam; Faheem, Muhammad; Ashraf, M. Waqar; Arfeen, Asad; Memon, Kamran Ali; Khawaja, AttaullahThe energy efficiency and delay performance of PON are two inversely related phenomena. Higher sleep time of the Optical Network Units (ONUs) results in higher upstream (US) delays due to increased traffic queues during the ONU Asleep state. Although an efficient dynamic bandwidth and wavelength assignment (DWBA) scheme can decrease US delays by minimizing the bandwidth waste and improving the fairness of bandwidth distribution among the ONUs. However, the conventional DWBA schemes are not designed to work with cyclic sleep mode (CSM) and they keep on assigning bandwidth to ONUs even if the ONU is in Asleep state leading to wastage of bandwidth and degraded CSM performance. Therefore, in this work a sleep aware DWBA scheme for TWDM PON is presented to coordinate with CSM mode. It only assign bandwidth to Active ONUs during the guaranteed phase, surplus phase and excess phase allocation phases which minimizes the bandwidth waste and the bandwidth lost at the ONU end. The wavelength switching process is also improved by only considering the Active state ONUs to balance the traffic load on all the wavelengths. The simulation results support our claim as the SA-DWBA scheme on average achieves DWBA schemes due to up to 50% to 65% higher energy savings compared to other due to longer ONU Asleep times. However, the increased upstream delays of all the traffic classes in SA-DWBA scheme remain within the set delay limit of 50 ms.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: 28Citation - Scopus: 31Proteomic and Biological Analysis of the Effects of Metformin Senomorphics on the Mesenchymal Stromal Cells(Frontiers Media S.A., 2021-10-05) Acar, Mustafa Burak; Ayaz-Guner, Serife; Gunaydin, Zeynep; Karakukcu, Musa; Peluso, Gianfranco; Di Bernardo, Giovanni; Galderisi, UmbertoSenotherapeutics are new drugs that can modulate senescence phenomena within tissues and reduce the onset of age-related pathologies. Senotherapeutics are divided into senolytics and senomorphics. The senolytics selectively kill senescent cells, while the senomorphics delay or block the onset of senescence. Metformin has been used to treat diabetes for several decades. Recently, it has been proposed that metformin may have anti-aging properties as it prevents DNA damage and inflammation. We evaluated the senomorphic effect of 6 weeks of therapeutic metformin treatment on the biology of human adipose mesenchymal stromal cells (MSCs). The study was combined with a proteome analysis of changes occurring in MSCs' intracellular and secretome protein composition in order to identify molecular pathways associated with the observed biological phenomena. The metformin reduced the replicative senescence and cell death phenomena associated with prolonged in vitro cultivation. The continuous metformin supplementation delayed and/or reduced the impairment of MSC functions as evidenced by the presence of three specific pathways in metformin-treated samples: 1) the alpha-adrenergic signaling, which contributes to regulation of MSCs physiological secretory activity, 2) the signaling pathway associated with MSCs detoxification activity, and 3) the aspartate degradation pathway for optimal energy production. The senomorphic function of metformin seemed related to its reactive oxygen species (ROS) scavenging activity. In metformin-treated samples, the CEBPA, TP53 and USF1 transcription factors appeared to be involved in the regulation of several factors (SOD1, SOD2, CAT, GLRX, GSTP1) blocking ROS.Article Citation - WoS: 15Citation - Scopus: 15PriPath: Identifying Dysregulated Pathways From Differential Gene Expression via Grouping, Scoring, and Modeling With an Embedded Feature Selection Approach(BMC, 2023-02-23) Yousef, Malik; Ozdemir, Fatma; Jaber, Amhar; Allmer, Jens; Bakir-Gungor, BurcuBackgroundCell homeostasis relies on the concerted actions of genes, and dysregulated genes can lead to diseases. In living organisms, genes or their products do not act alone but within networks. Subsets of these networks can be viewed as modules that provide specific functionality to an organism. The Kyoto encyclopedia of genes and genomes (KEGG) systematically analyzes gene functions, proteins, and molecules and combines them into pathways. Measurements of gene expression (e.g., RNA-seq data) can be mapped to KEGG pathways to determine which modules are affected or dysregulated in the disease. However, genes acting in multiple pathways and other inherent issues complicate such analyses. Many current approaches may only employ gene expression data and need to pay more attention to some of the existing knowledge stored in KEGG pathways for detecting dysregulated pathways. New methods that consider more precompiled information are required for a more holistic association between gene expression and diseases.ResultsPriPath is a novel approach that transfers the generic process of grouping and scoring, followed by modeling to analyze gene expression with KEGG pathways. In PriPath, KEGG pathways are utilized as the grouping function as part of a machine learning algorithm for selecting the most significant KEGG pathways. A machine learning model is trained to differentiate between diseases and controls using those groups. We have tested PriPath on 13 gene expression datasets of various cancers and other diseases. Our proposed approach successfully assigned biologically and clinically relevant KEGG terms to the samples based on the differentially expressed genes. We have comparatively evaluated the performance of PriPath against other tools, which are similar in their merit. For each dataset, we manually confirmed the top results of PriPath in the literature and found that most predictions can be supported by previous experimental research.ConclusionsPriPath can thus aid in determining dysregulated pathways, which applies to medical diagnostics. In the future, we aim to advance this approach so that it can perform patient stratification based on gene expression and identify druggable targets. Thereby, we cover two aspects of precision medicine.Article Citation - WoS: 5Citation - Scopus: 5Novel Antimicrobial Peptide Design Using Motif Match Score Representation(IEEE Computer Soc, 2024-11) Soylemez, Ummu Gulsum; Yousef, Malik; Kesmen, Zulal; Bakir-Gungor, BurcuAntimicrobial peptides (AMPs) have drawn the interest of the researchers since they offer an alternative to the traditional antibiotics in the fight against antibiotic resistance and they exhibit additional pharmaceutically significant properties. Recently, computational approaches attemp to reveal how antibacterial activity is determined from a machine learning perspective and they aim to search and find the biological cues or characteristics that control antimicrobial activity via incorporating motif match scores. This study is dedicated to the development of a machine learning framework aimed at devising novel antimicrobial peptide (AMP) sequences potentially effective against Gram-positive/Gram-negative bacteria. In order to design newly generated sequences classified as either AMP or non-AMP, various classification models were trained. These novel sequences underwent validation utilizing the "DBAASP: strain-specific antibacterial prediction based on machine learning approaches and data on AMP sequences" tool. The findings presented herein represent a significant stride in this computational research, streamlining the process of AMP creation or modification within wet lab environments.