Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Article Citation - WoS: 1Citation - Scopus: 1Lithium Treatment Rescues Dysfunctional Autophagy in the Cell Models of Tay-Sachs Disease(Academic Press Inc., 2024) Basirli,H.; Can,M.; Sengul,T.; Seyrantepe,V.Tay-Sachs disease is a rare lysosomal storage disorder (LSD) caused by a mutation in the HexA gene coding β-hexosaminidase A enzyme. The disruption of the HexA gene causes the accumulation of GM2 ganglioside resulting in progressive neurodegeneration in humans. Surprisingly, Hexa−/− mice did not show neurological phenotypes. Our group recently generated a murine model of Tay-Sachs disease exhibiting excessive GM2 accumulation and severe neuropathological abnormalities mimicking Tay-Sachs patients. Previously, we reported impaired autophagic flux in the brain of Hexa/-Neu3−/− mice. However, regulation of autophagic flux using inducers has not been clarified in Tay-Sachs disease cells. Here, we evaluated the effects of lithium treatment on dysfunctional autophagic flux using LC3 and p62 in the fibroblast and neuroglia of Hexa−/-Neu3−/− mice and Tay-Sachs patients. We discovered the clearance of accumulating autophagosomes, aggregate-prone metabolites, and GM2 ganglioside under lithium-induced conditions. Our data suggest that targeting autophagic flux with an autophagy inducer might be a rational therapeutic strategy for the treatment of Tay-Sachs disease. © 2024 Elsevier Inc.Article Citation - WoS: 6Citation - Scopus: 6Biomolecular Fingerprints of the Effect of Zoledronic Acid on Prostate Cancer Stem Cells: Comparison of 2d and 3d Cell Culture Models(Academic Press Inc., 2024) Güler,G.; Acikgoz,E.; Mukhtarova,G.; Oktem,G.Revealing the potential of candidate drugs against different cancer types without disrupting normal cells depends on the drug mode of action. In the current study, the drug response of prostate cancer stem cells (PCSCs) to zoledronic acid (ZOL) grown in two-dimensional (2D) and three-dimensional (3D) culture systems was compared using Fourier transform-infrared (FT-IR) spectroscopy which is a vibrational spectroscopic technique, supporting by biochemical assays and imaging techniques. Based on our data, in 2D cell culture conditions, the ZOL treatment of PCSCs isolated according to both C133 and CD44 cell surface properties induced early/late apoptosis and suppressed migration ability. The CD133 gene expression and protein levels were altered, depending on culture systems. CD133 expression was significantly reduced in 2D cells upon ZOL treatment. FT-IR data revealed that the integrity, fluidity, and ordering/disordering states of the cell membrane and nucleic acid content were altered in both 2D and 3D cells after ZOL treatment. Regular protein structures decrease in 2D cells while glycogen and protein contents increase in 3D cells, indicating a more pronounced cytotoxic effect of ZOL for 2D cells. Untreated 3D PCSCs exhibited an even different spectral profile associated with IR signals of lipids, proteins, nucleic acids, and glycogen in comparison to untreated 2D cells. Our study revealed significant differences in the drug response and cellular constituents between 2D and 3D cells. Exploring molecular targets and/or drug-action mechanisms is significant in cancer treatment approaches; thus, FT-IR spectroscopy can be successfully applied as a novel drug-screening method in clinical research. © 2024 Elsevier Inc.Article Citation - WoS: 7Citation - Scopus: 9Analysis of a Novel Sensor Interrogation Technique Based on Fiber Cavity Ring-Down (crd) Loop and Otdr(Academic Press Inc., 2018) Yüksel, Kıvılcım; Yılmaz, AnılWe present the analysis of a remote sensor based on fiber Cavity Ring-Down (CRD) loop interrogated by an Optical Time Domain Reflectometer (OTDR) taking into account both practical limitations and the related signal processing. A commercial OTDR is used for both pulse generation and sensor output detection. This allows obtaining a compact and simple design for intensity-based sensor applications. This novel sensor interrogation approach is experimentally demonstrated by placing a variable attenuator inside the fiber loop that mimics a sensor head.Article Citation - WoS: 12Citation - Scopus: 11Poor Modules With No Proper Poor Direct Summands(Academic Press Inc., 2018) Alizade, Rafail; Büyükaşık, Engin; López-Permouth, Sergio; Yang, LiuAs a mean to provide intrinsic characterizations of poor modules, the notion of a pauper module is introduced. A module is a pauper if it is poor and has no proper poor direct summand. We show that not all rings have pauper modules and explore conditions for their existence. In addition, we ponder the role of paupers in the characterization of poor modules over those rings that do have them by considering two possible types of ubiquity: one according to which every poor module contains a pauper direct summand and a second one according to which every poor module contains a pauper as a pure submodule. The second condition holds for the ring of integers and is just as significant as the first one for Noetherian rings since, in that context, modules having poor pure submodules must themselves be poor. It is shown that the existence of paupers is equivalent to the Noetherian condition for rings with no middle class. As indecomposable poor modules are pauper, we study rings with no indecomposable right middle class (i.e. the ring whose indecomposable right modules are pauper or injective). We show that semiartinian V-rings satisfy this property and also that a commutative Noetherian ring R has no indecomposable middle class if and only if R is the direct product of finitely many fields and at most one ring of composition length 2. Structure theorems are also provided for rings without indecomposable middle class when the rings are Artinian serial or right Artinian. Rings for which not having an indecomposable middle class suffices not to have a middle class include commutative Noetherian and Artinian serial rings. The structure of poor modules is completely determined over commutative hereditary Noetherian rings. Pauper Abelian groups with torsion-free rank one are fully characterized.Article Citation - WoS: 10Citation - Scopus: 12Statistical Approach To Tunneling Time in Attosecond Experiments(Academic Press Inc., 2017) Demir, Durmuş Ali; Güner, TuğrulTunneling, transport of particles through classically forbidden regions, is a pure quantum phenomenon. It governs numerous phenomena ranging from single-molecule electronics to donor–acceptor transition reactions. The main problem is the absence of a universal method to compute tunneling time. This problem has been attacked in various ways in the literature. Here, in the present work, we show that a statistical approach to the problem, motivated by the imaginary nature of time in the forbidden regions, lead to a novel tunneling time formula which is real and subluminal (in contrast to various known time definitions implying superluminal tunneling). In addition to this, we show explicitly that the entropic time formula is in good agreement with the tunneling time measurements in laser-driven He ionization. Moreover, it sets an accurate range for long-range electron transfer reactions. The entropic time formula is general enough to extend to the photon and phonon tunneling phenomena.Article Citation - WoS: 5Citation - Scopus: 7A Practical Approach for Optical Characterization of a Film Coated on the Optical Fiber(Academic Press Inc., 2017) Ekici, Çağın; Dinleyici, Mehmet SalihPhase Diffraction (PD) Phase Diffraction. which is a result of the interaction of light waves with a transparent object, is exploited to characterize precisely optical properties of dielectric films coated on the optical fiber without harming any feature of the sample. Typical fiber sensor applications require films coated on the side surface of the optical fiber and optical properties of that curved films are crucial for design purposes. In this study, three Polyvinyl Alcohol (PVA) films are prepared, their thicknesses are estimated based on the phase diffraction method by fitting experimental results with a mathematical model within 2.3% error. The outcomes of this practical method show good agreement with findings of the destructive Scanning Electron Microscopy (SEM) measurements. The method has the potential to allow real time monitoring abrupt changes of surrounding medium's properties and to examine coating quality (i.e. thickness uniformity) of the film.Article Citation - WoS: 27Citation - Scopus: 29Differentiation of Wines With the Use of Combined Data of Uv-Visible Spectra and Color Characteristics(Academic Press Inc., 2016) Şen, İlknur; Tokatlı, FigenUV-visible spectra and color parameters of monovarietal wines with orthogonal partial least square-discriminant analysis (OPLS-DA) were shown to be practical and rapid methods for classification purposes. Red and white wines from the 2006-2009 vintages were characterized in terms of color, anthocyanin content and UV-visible spectra. Syrah and Cabernet Sauvignon wines had high color density and intensity. Kalecik Karasi wines had the highest CIELab parameters and the lowest color density. Boğazkere and Öküzgözü wines showed similarities with respect to their high red color parameters and were distinct from other wines. Merlot, Syrah and Öküzgözü wines had the highest total anthocyanin content (61.9-55. mg/L as median values). White wines made from Chardonnay, Muscat and Emir grapes were found to have different color characteristics. The vintage-based discrimination of red wines was mostly apparent in total anthocyanin contents. Different UV wavelength regions were found to be effective in classification with respect to variety and vintage. Correct classification rates in the validation set were 100% and 75%, for varietal and vintage classifications, respectively. This study demonstrated the potential of combination of UV-visible spectra and color characteristics to be used in the authentication of wines.Article Citation - WoS: 1Citation - Scopus: 1Hereditary Rings With Countably Generated Cotorsion Envelope(Academic Press Inc., 2014) Guil Asensio, Pedro A.; Pusat, DilekLet R be a left hereditary ring. We show that if the left cotorsion envelope C(RR) of R is countably generated, then R is a semilocal ring. In particular, we deduce that C(RR) is finitely generated if and only if R is a semiperfect cotorsion ring. Our proof is based on set theoretical counting arguments. We also discuss some possible extensions of this result.Article Citation - WoS: 19Citation - Scopus: 19Rings and Modules Characterized by Opposites of Injectivity(Academic Press Inc., 2014) Alizade, Rafail; Büyükaşık, Engin; Er, NoyanIn a recent paper, Aydoǧdu and López-Permouth have defined a module M to be N-subinjective if every homomorphism N→M extends to some E(N)→M, where E(N) is the injective hull of N. Clearly, every module is subinjective relative to any injective module. Their work raises the following question: What is the structure of a ring over which every module is injective or subinjective relative only to the smallest possible family of modules, namely injectives? We show, using a dual opposite injectivity condition, that such a ring R is isomorphic to the direct product of a semisimple Artinian ring and an indecomposable ring which is (i) a hereditary Artinian serial ring with J2 = 0; or (ii) a QF-ring isomorphic to a matrix ring over a local ring. Each case is viable and, conversely, (i) is sufficient for the said property, and a partial converse is proved for a ring satisfying (ii). Using the above mentioned classification, it is also shown that such rings coincide with the fully saturated rings of Trlifaj except, possibly, when von Neumann regularity is assumed. Furthermore, rings and abelian groups which satisfy these opposite injectivity conditions are characterized.Article Citation - WoS: 12Citation - Scopus: 13The Discrimination of Raw and Uht Milk Samples Contaminated With Penicillin G and Ampicillin Using Image Processing Neural Network and Biocrystallization Methods(Academic Press Inc., 2013) Ünlütürk, Sevcan; Pelvan, Merve; Ünlütürk, Mehmet S.This paper utilized a neural network for texture image analysis to differentiate between milk, either raw or ultra high temperature (UHT) with antibiotic residues (e.g., penicillin G and ampicillin) and milk without antibiotic residues. The biocrystallization method was applied to obtain biocrystallogram images for milk samples spiked with penicillin G and ampicillin at different concentration levels. The biocrystallogram images were used as an input for a designed neural network called the image processing neural network (ImgProcNN). The visual differences in these images that were based on textural properties, including the distribution of crystals on the circular grass underlay, the thin or thick structure of the crystal needles, and the angles between the branches and the side needles, were used to discriminate the antibiotic-free milk samples from samples with antibiotic residues. The visual description and definition of these images have major disadvantages. In this study, the ImgProcNN was developed to overcome the shortcomings of these visual descriptions and definitions. Overall, the neural network achieved an average recognition performance between 86% and 100%. This high level of recognition suggests that the neural network used in this paper has potential as a method for discriminating raw and UHT milk samples contaminated with different antibiotics.