Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
Browse
18 results
Search Results
Article Functional Characterization of Loss of RNF43 Reveals Neuronal Defects in a Caenorhabditis Elegans Model(MDPI, 2026) Kazan, Hasan Huseyin; Turkyilmaz, Zafer; Ekim, Burcu; Kaya, Cem; Ergun, Mehmet Ali; Sonmez, Kaan; Güzel, SinemRing finger protein 43 (RNF43) encodes a transmembrane E3 ubiquitin ligase that negatively regulates canonical Wnt signaling and is classically associated with serrated polyposis syndrome and colorectal cancer. In this study, regarding a homozygous truncating RNF43 variant (NM_001305545.1:c.1906C>T; p.Gln636Ter) in a patient segregating with a severe neurodevelopmental phenotype characterized by developmental delay, neonatal hypotonia, recurrent seizures, progressive microcephaly, and bilateral optic atrophy, the loss of polarity defective 1 (plr-1), an ortholog of RNF43, was modeled in Caenorhabditis elegans and the phenotype was primarily characterized. The results demonstrated that loss of the plr-1 disrupted gamma aminobutyric acid (GABA)ergic axon organization, reduced locomotor speed calculated from 60 s recordings, and altered developmental growth. These findings expand the phenotypic spectrum of RNF43 and support a dosage-dependent developmental role.Article Strategic Modeling of Hybrid Smart Micro Energy Communities: A Decision-Oriented Approach(MDPI, 2026-02-10) Perez-Sanchez, Modesto; Coronado-Hernandez, Oscar E.; McNabola, Aonghus; Erdfarb, Alex; Ramos, Helena M.; Demircan, Isil; Koca, KemalHybrid renewable energy systems are increasingly important for enabling sustainable and resilient energy supply in rural smart communities, yet existing tools often lack the ability to integrate environmental variability, multi-technology interactions, and economic-environmental assessment in a unified framework. This study presents Hybrid Smart Micro Energy Community (HySMEC), a novel modeling approach that combines high-resolution meteorological data, technology-specific generation models, detailed demand characterization, and financial analysis to evaluate hybrid configurations of hydropower, solar PV, wind, battery storage, and grid interaction. Hourly simulations capture seasonal dynamics and system behavior under realistic technical efficiencies, investment costs, and emission factors, enabling a transparent assessment of energy flows, self-consumption, and grid dependence. The results show that hybrid systems can achieve competitive economic performance, low Levelized Costs of Energy, and significant CO2 emission reductions across diverse rural community profiles, even when space or demand constraints are present. The analysis confirms the technical feasibility and environmental benefits of integrating multiple renewable sources with storage, highlighting the importance of self-consumption ratios in improving system profitability. Overall, HySMEC provides a robust and scalable tool to support data-driven design and optimization of distributed energy systems, offering valuable insights for researchers, planners, and decision-makers involved in sustainable rural energy development.Article Citation - WoS: 1Citation - Scopus: 1Raster Orientation Effects on the Adhesion of iCVD-Deposited PSA Thin Films on FDM-Printed PLA(MDPI, 2026-01-30) Yilmaz, Kurtulus; Gursoy, Mehmet; Gunes, Aydin; Karaman, MustafaThe adhesion performance of pressure-sensitive adhesive (PSA) thin films on additively manufactured polymers is strongly governed by surface anisotropy induced during printing. In this study, PSA thin films based on 2-ethylhexyl acrylate (EHA) and acrylic acid (AA) were deposited by initiated chemical vapor deposition (iCVD) onto fused deposition modeling (FDM) printed PLA substrates with different raster orientations (0 degrees, 30 degrees, 60 degrees, and 90 degrees). The deposited films exhibited high optical transparency on glass, and thicknesses consistent with the targeted deposition. Adhesion performance was evaluated using tensile and three-point bending tests, revealing a strong dependence on raster orientation. The 0 degrees raster orientation yielded the highest shear adhesion strengths, reaching 12.03 N/cm2 under tensile loading and 4.59 N/cm2 under bending, along with the largest failure displacements. In contrast, specimens printed at 90 degrees exhibited an approximately 47% reduction in tensile shear adhesion strength and limited deformation prior to failure. SEM analysis showed that raster alignment parallel to the loading direction promoted extensive adhesive deformation and PSA fibrillation, whereas higher raster angles resulted in predominantly interfacial debonding. These results demonstrate that raster orientation is a critical design parameter for tuning PSA adhesion on FDM-printed PLA substrates without modifying adhesive chemistry.Article Frequency-Based Deep Occlusion Awareness Instance Segmentation(MDPI, 2026-02-26) Guzel, Yasin; Aydin, Zafer; Talu, Muhammed FatihOne major challenge faced by deep learning-based methods that detect target objects in the form of bounding boxes is object occlusion. High degrees of occlusion significantly diminish the accuracy of instance segmentation. Nonetheless, complex-valued Fourier descriptors can robustly represent object boundaries using minimal information. In this study, the impact of integrating Fourier descriptors-renowned for their strong representational capacity-with deep network models (UNet) that exhibit high generalization performance on instance segmentation accuracy was investigated. Within the scope of the research, nine network models were designed based on different strategies for utilizing frequency components. These variants fall into four strategy families: (i) UNet-style spectrum regression on fixed low-frequency windows (FUNet), (ii) magnitude-guided frequency selection/ROI construction (FUNet-Thr, FUNet-BBox), (iii) sequence models over tokenized FFT coefficients (BiLSTM Patch/Sorted), and (iv) encoder-only spectrum predictors with different depth/capacity (EncoderFFT1/2). To fairly evaluate the models' performance in segmenting objects subjected to disruptive factors (e.g., occlusion, blurring, noise), a specialized synthetic dataset was prepared. The task is formulated as single-target (single-instance), single-class segmentation. This dataset, automatically generated according to initial parameter values, contains images of objects moving at various speeds within a single frame. Among these models, the one termed FUNet, which relies on partial matching of central frequency components, achieved the highest segmentation accuracy despite the disruptive effects. Under the challenging Dataset 8 setting, the proposed FUNet achieved the highest overlap-based performance (Dice = 0.9329, IoU = 0.8842) among Attention U-Net, U-Net, and FourierNet, with statistically significant gains confirmed by paired per-image tests.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: 5Citation - Scopus: 5The 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: 6Citation - Scopus: 7The 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.