Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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Book Part Citation - Scopus: 3Advances and Future Perspective of Graphene Field Effect Transistors (gfets) for Medical Diagnostics and Point-Of Tools(World Scientific Publishing, 2022) İnanç, Dilce; Mutlu, Mustafa Umut; Karabacak, Soner; Yıldız, Ümit HakanRecently, major focus has been centered to enhance the capability of graphenebased devices and to facilitate utilization of graphene for biological applications by lowering its toxicity. In this chapter, from synthesis to applications, many of the conspicuous characteristics of graphene have been elaborately reviewed. We primarily focused on graphene-based field effect transistor (FET) for medical diagnostics and point-of-care applications. The device configurations and their application potential as well as sensing capability of various graphene FETs (GFETs) have been discussed. Here, we have also presented several aspects and advantages of GFETs in medical applications while discussing their pros and cons in commercialization. We address the advances and challenges for GFET-based sensing platforms for the medical applications and elaborate the combination strategy of GFETs with the existing commercial systems. © 2023 by World Scientific Publishing Co. Pte. Ltd.Article Citation - Scopus: 3Development of Chrono-Spectral Gold Nanoparticle Growth Based Plasmonic Biosensor Platform(Elsevier, 2024) Sözmen, Alper Baran; Elveren, Beste; Erdoğan, Duygu; Mezgil, Bahadır; Baştanlar, Yalın; Yıldız, Ümit Hakan; Arslan Yıldız, AhuPlasmonic sensor platforms are designed for rapid, label-free, and real-time detection and they excel as the next generation biosensors. However, current methods such as Surface Plasmon Resonance require expertise and well-equipped laboratory facilities. Simpler methods such as Localized Surface Plasmon Resonance (LSPR) overcome those limitations, though they lack sensitivity. Hence, sensitivity enhancement plays a crucial role in the future of plasmonic sensor platforms. Herein, a refractive index (RI) sensitivity enhancement methodology is reported utilizing growth of gold nanoparticles (GNPs) on solid support and it is backed up with artificial neural network (ANN) analysis. Sensor platform fabrication was initiated with GNP immobilization onto solid support; immobilized GNPs were then used as seeds for chrono-spectral growth, which was carried out using NH2OH at varied incubation times. The response to RI change of the platform was investigated with varied concentrations of sucrose and ethanol. The detection of bacteria E.coli BL21 was carried out for validation as a model microorganism and results showed that detection was possible at 102 CFU/ml. The data acquired by spectrophotometric measurements were analyzed by ANN and bacteria classification with percentage error rates near 0% was achieved. The proposed LSPR-based, label-free sensor application proved that the developed methodology promises utile sensitivity enhancement potential for similar sensor platforms. © 2024 The Author(s)Article Citation - WoS: 1Citation - Scopus: 1The Soft Nanodots as Fluorescent Probes for Cell Imaging: Analysis of Cell and Spheroid Penetration Behavior of Single Chain Polymer Dots(Wiley, 2024) Yücel, Müge; Onbaş, Rabia; Arslan Yıldız, Ahu; Yıldız, Ümit HakanThis study describes the formation, size control, and penetration behavior of polymer nanodots (Pdots) consisting of single or few chain polythiophene-based conjugated polyelectrolytes (CPEs) via nanophase separation between good solvent and poor solvent of CPE. Though the chain singularity may be associated with dilution nanophase separation suggests that molecules of a good solvent create a thermodynamically driven solvation layer surrounding the CPEs and thereby separating the single chains even in their poor solvents. This statement is therefore corroborated with emission intensity/lifetime, particle size, and scattering intensity of polyelectrolyte in good and poor solvents. Regarding the augmented features, Pdots are implemented into cell imaging studies to understand the nuclear penetration and to differentiate the invasive characteristics of breast cancer cells. The python based red, green, blue (RGB) color analysis depicts that Pdots have more nuclear penetration ability in triple negative breast cancer cells due to the different nuclear morphology in shape and composition and Pdots have penetrated cell membrane as well as extracellular matrix in spheroid models. The current Pdot protocol and its utilization in cancer cell imaging are holding great promise for gene/drug delivery to target cancer cells by explicitly achieving the very first priority of nuclear intake. The penetration capability of cationic soft nanodots in to tumor models of breast cancer is demonstrated. The image analysis based on fluorescence intensity variation reveals the characteristics of translocation of nanodots in dense mediums such as tumor models.imageArticle Citation - WoS: 7Citation - Scopus: 6Thickness Gradient in Polymer Coating by Reactive Layer-By Assembly on Solid Substrate(Amer Chemical Soc, 2023) Özenler, Sezer; Alkan, Ali Ata; Gunay, Ufuk Saim; Dağlar, Özgün; Durmaz, Hakan; Yıldız, Ümit HakanThe study describes a simple yet robust methodology for forming gradients in polymer coatings with nanometer-thickness precision. The thickness gradients of 0-20 nm in the coating are obtained by a reactive layer-by-layer assembly of polyester and polyethylenimine on gold substrates. Three parameters are important in forming thickness gradients: (i) the incubation time, (ii) the incubation concentration of the polymer solutions, and (iii) the tilt angle of the gold substrate during the dipping process. After examining these parameters, the characterization of the anisotropic surface obtained under the best conditions is presented in the manuscript. The thickness profile and nanomechanical characterization of the polymer gradients are characterized by atomic force microscopy. The roughness analysis has demonstrated that the coating exhibited decreasing roughness with increasing thickness. On the other hand, Young's moduli of the thin and thick coatings are 0.50 and 1.4 MPa, respectively, which assured an increase in mechanical stability with increasing coating thickness. Angle-dependent infrared spectroscopy reveals that the C-O-C ester groups of the polyesters exhibit a perpendicular orientation to the surface, while the C=C groups are parallel to the surface. The surface properties of the polymer gradients are explored by fluorescence microscopy, proving that the dye's fluorescence intensity increases as the coating thickness increases. The significant benefit of the suggested methodology is that it promises thickness control of gradients in the coating as a consequence of the fast reaction kinetics between layers and the reaction time.Conference Object Citation - WoS: 3Citation - Scopus: 3Halloysite Nanotube Loaded Polyamide Nanocomposites: Structural, Morphological, Mechanical, Thermal and Processing Behaviors(American Institute of Physics, 2023) Akar, Alinda Öykü; Yıldız, Ümit Hakan; Tayfun, ÜmitIn this study, the polyamide 6 (PA) matrix was reinforced with the purified, fine ground and amino-silane treated halloysite nanotubes (HNT) at different concentrations. The preparation of composites was carried out using a lab-scale twin-screw micro-compounder with loading ratios at 0.5, 1, 3, and 20% by weight, and the test samples were prepared by the injection-molding process. According to mechanical test results, additions of HNT to the PA matrix caused slight improvements in tensile strength and Youngs' modulus parameters. The optimum concentrations for all of the additives used were estimated by comparison of mechanical test data. The addition of aminosilane-modified HNT resulted in a higher impact performance at high loading levels up to 3% concentrations. Further addition of HNT caused a reduction in the mechanical parameters of composites. Thermal studies revealed that the glass transition temperature of PA shifted to higher values after HNT mineral inclusions. Thermo-mechanical results showed that storage moduli of PA exhibited improvement with an increase in HNT content. The distributions of HNT clay into the PA phase were visualized with SEM images. Based on these observations, a high level of dispersion homogeneity was achieved for lower filling ratios. According to melt-flow and force measurements, composites filled with 20% of HNT displayed a remarkable increase in exerted force during melt-blending. © 2023 Author(s).Article Citation - WoS: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Qun, David Lee Chao; Ammanath, Gopal; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit HakanPolarity induced vapochromic and vapoluminescent properties of cationic poly-3-alkoxythiophene derivatives (PT) casted on polyvinylidene fluoride (PVDF) membranes are reported. PT with six different pendant groups are designed to differentially interact with volatile organic compounds (VOC) of varying polarities, thereby enabling their classification. PT exhibit a rapid vapochromic response with a concurrent modulation of vapoluminescence due to the non-covalent cation-? interactions between the pendant groups and the PT backbone. Adsorption of VOC on pendant groups alters the conformation of PT backbone, thus resulting in an increase in intensity and blue shifting of fluorescence emission within the visible spectrum. The vapoluminescent responses are found to be more sensitive with a limit of detection (LOD) of ?7 ppm and a wider dynamic range as compared to the vapochromic responses with a LOD of ?60 ppm for the detection of a model VOC: chloroform. Notably, all the PT illustrate an instantaneous recovery of colour and luminescence upon desorption of VOC. PT interaction with VOC of varying polarities was ascertained using density functional theory (DFT) and principal component analysis (PCA) methodologies. In summary, the polarity induced vapochromic and vapoluminescent properties of PT could yield a selective and sensitive vapochromic and fluorometric dual-mode VOC detection platform. © 2023Article Citation - WoS: 1Citation - Scopus: 1A Multi-Layered Graphene Based Gas Sensor Platform for Discrimination of Volatile Organic Compounds Via Differential Intercalation(Royal Society of Chemistry, 2023) Özkendir İnanç, Dilce; Ng, Zhi Kai; Başkurt, Mehmet; Keleş, Berfin; Vardar, Gökay; Şahin, Hasan; Tsang, Siu Hon; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Teo, EhtSelective and sensitive detection of volatile organic compounds (VOCs) is of critical importance for environmental monitoring, disease diagnosis and industrial applications. Among VOCs, assay development for primary alcohols has captured significant research attention since their toxicity causes adverse effects on gastrointestinal and central nerve systems, resulting in irreversible blindness, and coma, and can be even fatal at high exposure levels. However, selective detection of primary alcohols is extremely challenging owing to the similarity in their molecular structure and characteristic groups. Herein, we have attempted to investigate the differential methanol (MeOH)-ethanol (EtOH) discriminative properties of single-layer, bi-layer, and multi-layer graphene morphologies. Chemiresistors fabricated using the three morphologies of graphene illustrate discriminative MeOH-EtOH responses, which is attributed to the phenomenon of differential intercalation of MeOH within layered graphene morphologies as compared to that of EtOH. This hypothesis is verified by density functional theory calculations, which revealed that the adsorption of EtOH molecules on the graphene surface is more energetically favorable as compared to that of MeOH molecules, thereby inhibiting their intercalation within the layered graphene morphologies. It is further evaluated that the degree of MeOH intercalation increases with increasing layers of graphene for obtaining differential MeOH-EtOH responses. Experimental results suggest possibilities to develop selective and sensitive MeOH assays fabricated using various graphene morphologies in a combinatorial sensor array format.Article Citation - WoS: 4Citation - Scopus: 4Colorimetric Assaying of Exosomal Metabolic Biomarkers(MDPI, 2023) Yan, Evelias; Goyal, Garima; Yıldız, Ümit Hakan; Boehm, Bernhard O.; Palaniappan, AlagappanExosomes released into the extracellular matrix have been reported to contain metabolic biomarkers of various diseases. These intraluminal vesicles are typically found in blood, urine, saliva, breast milk, cerebrospinal fluid, semen, amniotic fluid, and ascites. Analysis of exosomal content with specific profiles of DNA, microRNA, proteins, and lipids can mirror their cellular origin and physiological state. Therefore, exosomal cargos may reflect the physiological processes at cellular level and can potentially be used as biomarkers. Herein, we report an optical detection method for assaying exosomal biomarkers that supersedes the state-of-the-art time consuming and laborious assays such as ELISA and NTA. The proposed assay monitors the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy) propyltriethylammonium bromide) upon interacting with aptamers/peptide nucleic acids in the presence or absence of target biomarkers. As a proof of concept, this study demonstrates facile assaying of microRNA, DNA, and advanced glycation end products in exosomes isolated from human plasma with detection levels of ~1.2, 0.04, and 0.35 fM/exosome, respectively. Thus, the obtained results illustrate that the proposed methodology is applicable for rapid and facile detection of generic exosomal biomarkers for facilitating diseases diagnosis.Conference Object Citation - WoS: 1Citation - Scopus: 1Biomimetic Peptide-Conjugated Membranes for Developing an Artificial Cornea(IEEE, 2022) Sunal, Gülşah; Pulat, Günnur; Akgün, İsmail Hakkı; Güven, Sinan; Yıldız, Ümit Hakan; Karaman, Ozan; Horzum, NesrinThe corneal endothelium is composed of a single layer of specialized endothelial cells, protecting, and nourishing the inner surface of the cornea. Corneal endothelial cells do not proliferate after birth and their number decrease with age. Trauma, inflammation, or surgical intervention can cause cell loss. When damage is extensive and the density of corneal endothelial cells decreases to a critical level, it results in corneal edema and vision loss. Besides them, when corneal endothelium has irreversible damage, the only treatment way is corneal transplantation. But there are some drawbacks such as finding donors, immune reactions, and the number of patients waiting on the transplantation lists for years. Tissue engineering approaches can provide promising alternatives for the regeneration of corneal endothelium tissue. Peptides can be used to modify and functionalize the scaffolds, allowing for the production of bioactive and biomimetic surfaces. Peptide-modified scaffold surfaces might direct and enhance the behaviors of cells. In this study, the aim was to functionalize the polycaprolactone (PCL) membranes with tissue-specific peptides and to characterize the peptide-conjugated membranes by Fourier-Transform Infrared Spectroscopy (FTIR), Scanning Electron Microscopy (SEM), and X-ray Photoelectron Spectroscopy (XPS) analysis. The synthesized peptides were successfully conjugated on the PCL biomembranes.Article Citation - WoS: 35Citation - Scopus: 44Current Trends and Challenges in Point-Of Urinalysis of Biomarkers in Trace Amounts(Elsevier, 2022) Yeasmin, Sanjida; Ammanath, Gopal; Önder, Ahmet; Yan, Evelias; Yıldız, Ümit Hakan; Palaniappan, Alagappan; Liedberg, BoUrinalysis enables non-invasive point-of-care (POC) testing of numerous biomarkers at their physiological and elevated levels, obviating the need for sophisticated equipment or trained personnel. POC urinalysis is used to identify biomarkers that are rich in urine (greater than 1 μM), such as lactate, uric acid, glucose, ions, and adenosine. Urine also contains biomarkers such as small molecules, nucleic acids, neurotransmitters, and drugs in trace amounts (less than 1 μM). These biomarkers are of significant importance for health care monitoring, diagnosis of various disorders (cancer, metabolic diseases, etc.) and illicit drug control (cocaine, steroids, etc.). While POC detection of urinary biomarkers at higher concentration (μM to mM) levels is feasible, direct assaying of biomarkers in nM to fM levels is challenging, as assay responses are typically masked by interferences from the urine sample matrix. This report is a consolidated review of emerging trends and challenges in the POC urinalysis for detecting biomarkers that are less abundant in urine. The sensing mechanisms, analytical device fabrication, discrete and integrated sample pre-treatment procedures for POC assaying of urinary markers in trace amounts are elaborated. Subsequently, the utilization of smart data analytics for facilitating personalized urinalysis is presented. A comprehensive outlook on associated challenges in POC urinalysis of biomarkers in trace amounts is further provided, which would facilitate the advancement of POC urinalysis for a wide range of healthcare applications.