PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 2Citation - Scopus: 2Image Processing and Artificial Neural Network Based Determination of Surface Mean Texture Depth on Lab-Controlled Chip Seal Pavement Samples(Nature Portfolio, 2024) Gokalp, Islam; Uz, Volkan Emre; Barstugan, Mucahid; Balci, Mehmet CanBecause surface texture is nearly the sole indicator of pavement functional properties and highly correlated with critical operational characteristics of roadways like traffic noise and safety, the change in pavement surface texture because of traffic loadings and environment has to be evaluated routinely. There are numerous direct or indirect evaluation techniques in the market. However, most of these methods have some limitations like requiring lane closure or being expensive. In this study, a 2D image processing method was established to estimate the surface mean texture depth (MTD) of chip sealed pavements. We produced chip sealed pavement samples in the laboratory with different aggregate type, shape, and size ranging between 2 and 19 mm to cover wide range of live conditions. Two well-known conventional test methods, Sand Patch (SP) and Hydrotimer (HT), were used to determine MTDs of chip seal samples. Subsequently numerous photos were taken on surface of the samples with a camera for 2-D image processing that was done based on surface void ratio (SVR) approach. With the image processing, SVR of all samples were determined. At the point of whether there is a relationship or not, correlation analysis was made between the MTDs obtained with SP and HT and the data obtained by SVR approach with the artificial neural network method. The results show that the proposed SVR approach construed on 2D image processing method can be a reliable alternative to evaluate the surface texture of pavements.Article Citation - WoS: 9Citation - Scopus: 6Fluorescence Lifetime Multiplexing With Fluorogen Activating Protein Fast Variants(Nature Portfolio, 2024) Bogdanova, Yulia A.; Solovyev, Ilya D.; Baleeva, Nadezhda S.; Myasnyanko, Ivan N.; Gorshkova, Anastasia A.; Gorbachev, Dmitriy A.; Baranov, Mikhail S.In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling. A genetically encoded labeling system uses smallest-in-class fluorogen-activating protein tags for time-resolved fluorescence multiplexed cellular imaging, offering monoexponential decay and potential for sophisticated fluorescence lifetime analysis.Article Citation - WoS: 6Citation - Scopus: 6Tumour-Intrinsic Endomembrane Trafficking by Arf6 Shapes an Immunosuppressive Microenvironment That Drives Melanomagenesis and Response To Checkpoint Blockade Therapy(Nature Portfolio, 2024) Wee, Yinshen; Wang, Junhua; Wilson, Emily C.; Rich, Coulson P.; Rogers, Aaron; Tong, Zongzhong; Grossmann, Allie H.Tumour-host immune interactions lead to complex changes in the tumour microenvironment (TME), impacting progression, metastasis and response to therapy. While it is clear that cancer cells can have the capacity to alter immune landscapes, our understanding of this process is incomplete. Herein we show that endocytic trafficking at the plasma membrane, mediated by the small GTPase ARF6, enables melanoma cells to impose an immunosuppressive TME that accelerates tumour development. This ARF6-dependent TME is vulnerable to immune checkpoint blockade therapy (ICB) but in murine melanoma, loss of Arf6 causes resistance to ICB. Likewise, downregulation of ARF6 in patient tumours correlates with inferior overall survival after ICB. Mechanistically, these phenotypes are at least partially explained by ARF6-dependent recycling, which controls plasma membrane density of the interferon-gamma receptor. Collectively, our findings reveal the importance of endomembrane trafficking in outfitting tumour cells with the ability to shape their immune microenvironment and respond to immunotherapy. The small GTPase ARF6 is known to regulate endocytosis and recycling of plasma membrane proteins. Here the authors show that tumourintrinsic ARF6 promotes an immunosuppressive microenvironment that accelerates melanoma progression but that is vulnerable to immune checkpoint blockade, mechanistically linked to ARF6-dependent recycling of interferon-gamma receptors in tumour cells.Article Citation - WoS: 9Citation - Scopus: 11Mesenchymal Stem Cells From Adipose Tissue Prone To Lose Their Stemness Associated Markers in Obesity Related Stress Conditions(Nature Portfolio, 2024) Al-Sammarraie, Sura Hilal Ahmed; Ayaz-Guner, Serife; Acar, Mustafa Burak; Simsek, Ahmet; Siniksaran, Betuel Seyhan; Bozalan, Habibe Damla; Ozcan, ServetObesity is a health problem characterized by large expansion of adipose tissue. During this expansion, genotoxic stressors can be accumulated and negatively affect the mesenchymal stem cells (MSCs) of adipose tissue. Due to the oxidative stress generated by these genotoxic stressors, senescence phenotype might be observed in adipose tissue MSCs. Senescent MSCs lose their proliferations and differentiation properties and secrete senescence-associated molecules to their niche thus triggering senescence for the rest of the tissue. Accumulation of senescent cells in adipose tissue results in decreased tissue regeneration and functional impairment not only in the close vicinity but also in the other tissues. Here we hypothesized that declined tissue regeneration might be associated with loss of stemness markers in MSCs population. We analyzed the expression of several stemness-associated genes of in vitro cultured MSCs originated from adipose tissue of high-fat diet and normal diet mice models. Since the heterogenous MSCs population covers a small percentage of the pluripotent stem cells, which have roles in proliferation and tissue regeneration, we measured the percentage of these cells via TRA-1-60 pluripotent state antigen. Additionally, by conducting a shotgun proteomic approach using LC-MS/MS, whole cell proteome of the adipose tissue MSCs of high-fat diet and normal diet mice were analyzed and identified proteins were evaluated via gene ontology and PPI network analysis. MSCs of obese mice showed senescent phenotype and altered cell cycle distribution due to a hostile environment with oxidative stress in adipose tissue where they reside. Additionally, the number of pluripotent markers expressing cells declined in the MSC population of the high-fat diet mice. Gene expression analysis evidenced the loss of stemness with a decrease in the expression of stemness-associated genes. Of the proteomic comparison of the normal and the high-fat diet group, MSCs revealed that stemness-associated molecules were decreased while inflammation and senescence-associated phenotypes emerged in obese mice MSCs. Our results showed us that the MSCs of adipose tissue may lose their stemness properties due to obesity-associated stress conditions.Article Citation - WoS: 7Citation - Scopus: 7Colorimetric Detection of Serum Creatinine on a Miniaturized Platform Using Hue-Saturation Space Analysis(Nature Portfolio, 2024) Tarim, E. Alperay; Tekin, H. CumhurChronic kidney disease (CKD) is a widespread condition with considerable health and economic impacts globally. However, existing methodologies for serum creatinine assessment often involve prolonged wait times and sophisticated equipment, such as spectrometers, hindering real-time diagnosis and care. Innovative solutions like point-of-care (POC) devices are emerging to address these challenges. In this context, there is a recognized need for remote, regular, automated, and low-cost analysis of serum creatinine levels, given its role as a critical parameter for CKD diagnosis and management. This study introduces a miniaturized system with integrated heater elements designed for precise serum creatinine measurement. The system operates based on the Jaffe method and accurate serum creatinine measurement within a microreservoir chip. Smartphone-based image processing using the hue-saturation-value (HSV) color space was applied to captured images of microreservoirs. The creatinine analyses were conducted in serum with a limit of detection of similar to 0.4 mg/dL and limit of quantification of similar to 1.3 mg/dL. Smartphone-based image processing employing the HSV color space outperformed spectrometric analysis for creatinine measurement conducted in serum. This pioneering technology and smartphone-based processing offer the potential for decentralized renal function testing, which could significantly contribute to improved patient care. The miniaturized system offers a low-cost alternative ($87 per device), potentially reducing healthcare expenditures (similar to $0.5 per test) associated with CKD diagnosis and management. This innovation could greatly improve access to diagnosis and monitoring of CKD, especially in regions where access to sophisticated laboratory equipment is limited.Article Citation - WoS: 75Citation - Scopus: 73Proton Transport Through Nanoscale Corrugations in Two-Dimensional Crystals(Nature Portfolio, 2023) Wahab, O. J.; Daviddi, E.; Xin, B.; Sun, P. Z.; Griffin, E.; Colburn, A. W.; Unwin, P. R.Defect-free graphene is impermeable to all atoms(1-5) and ions(6,7) under ambient conditions. Experiments that can resolve gas flows of a few atoms per hour through micrometre-sized membranes found that monocrystalline graphene is completely impermeable to helium, the smallest atom(2,5). Such membranes were also shown to be impermeable to all ions, including the smallest one, lithium(6,7). By contrast, graphene was reported to be highly permeable to protons, nuclei of hydrogen atoms(8,9). There is no consensus, however, either on the mechanism behind the unexpectedly high proton permeability(10-14) or even on whether it requires defects in graphene's crystal lattice(6,8,15-17). Here, using high-resolution scanning electrochemical cell microscopy, we show that, although proton permeation through mechanically exfoliated monolayers of graphene and hexagonal boron nitride cannot be attributed to any structural defects, nanoscale non-flatness of two-dimensional membranes greatly facilitates proton transport. The spatial distribution of proton currents visualized by scanning electrochemical cell microscopy reveals marked inhomogeneities that are strongly correlated with nanoscale wrinkles and other features where strain is accumulated. Our results highlight nanoscale morphology as an important parameter enabling proton transport through two-dimensional crystals, mostly considered and modelled as flat, and indicate that strain and curvature can be used as additional degrees of freedom to control the proton permeability of two-dimensional materials. A study using high-resolution scanning electrochemical cell microscopy attributes proton permeation through defect-free graphene and hexagonal boron nitride to transport across areas of the structure that are under strain.