PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - Scopus: 20Estrus Detection and Dairy Cow Identification With Cascade Deep Learning for Augmented Reality-Ready Livestock Farming(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Arıkan, İ.; Ayav, T.; Seçkin, A.Ç.; Soygazi, F.Accurate prediction of the estrus period is crucial for optimizing insemination efficiency and reducing costs in animal husbandry, a vital sector for global food production. Precise estrus period determination is essential to avoid economic losses, such as milk production reductions, delayed calf births, and disqualification from government support. The proposed method integrates estrus period detection with cow identification using augmented reality (AR). It initiates deep learning-based mounting detection, followed by identifying the mounting region of interest (ROI) using YOLOv5. The ROI is then cropped with padding, and cow ID detection is executed using YOLOv5 on the cropped ROI. The system subsequently records the identified cow IDs. The proposed system accurately detects mounting behavior with 99% accuracy, identifies the ROI where mounting occurs with 98% accuracy, and detects the mounting couple with 94% accuracy. The high success of all operations with the proposed system demonstrates its potential contribution to AR and artificial intelligence applications in livestock farming. © 2023 by the authors.Article Citation - Scopus: 13Her2-Targeted, Degradable Core Cross-Linked Micelles for Specific and Dual Ph-Sensitive Dox Release(John Wiley and Sons Inc, 2022) Bayram, N.N.; Ulu, G.T.; Topuzoğulları, M.; Baran, Y.; Dinçer, İşoğlu, S.Here, a targeted, dual-pH responsive, and stable micelle nanocarrier is designed, which specifically selects an HER2 receptor on breast cancer cells. Intracellularly degradable and stabilized micelles are prepared by core cross-linking via reversible addition−fragmentation chain-transfer (RAFT) polymerization with an acid-sensitive cross-linker followed by the conjugation of maleimide–doxorubicin to the pyridyl disulfide-modified micelles. Multifunctional nanocarriers are obtained by coupling HER2-specific peptide. Formation of micelles, addition of peptide and doxorubicin (DOX) are confirmed structurally by spectroscopical techniques. Size and morphological characterization are performed by Zetasizer and transmission electron microscope (TEM). For the physicochemical verification of the synergistic acid-triggered degradation induced by acetal and hydrazone bond degradation, Infrared spectroscopy and particle size measurements are used. Drug release studies show that DOX release is accelerated at acidic pH. DOX-conjugated HER2-specific peptide-carrying nanocarriers significantly enhance cytotoxicity toward SKBR-3 cells. More importantly, no selectivity toward MCF-10A cells is observed compared to HER2(+) SKBR-3 cells. Formulations cause apoptosis depending on Bax and Caspase-3 and cell cycle arrest in G2 phase. This study shows a novel system for HER2-targeted therapy of breast cancer with a multifunctional nanocarrier, which has higher stability, dual pH-sensitivity, selectivity, and it can be an efficient way of targeted anticancer drug delivery. © 2021 Wiley-VCH GmbHArticle Citation - Scopus: 4Comparative Proteomic Analysis of Leishmania Parasites Isolated From Visceral and Cutaneous Leishmaniasis Patients(Cambridge University Press, 2022) Dinç, M.; Yalçln, T.; Çavuş, I.; Özbilgin, A.Leishmaniasis is an infectious disease in which different clinical manifestations are classified into three primary forms: visceral, cutaneous and mucocutaneous. These disease forms are associated with parasite species of the protozoan genus Leishmania. For instance, Leishmania infantum and Leishmania tropica are typically linked with visceral (VL) and cutaneous (CL) leishmaniasis, respectively; however, these two species can also cause other form to a lesser extent. What is more alarming is this characteristic, which threatens current medical diagnosis and treatment, is started to be acquired by other species. Our purpose was to address this issue; therefore, gel-based and gel-free proteomic analyses were carried out on the species L. infantum to determine the proteins differentiating between the parasites caused VL and CL. In addition, L. tropica parasites representing the typical cases for CL were included. According to our results, electrophoresis gels of parasites caused to VL were distinguishable regarding the repetitive down-regulation on some specific locations. In addition, a distinct spot of an antioxidant enzyme, superoxide dismutase, was shown up only on the gels of CL samples regardless of the species. In the gel-free approach, 37 proteins that were verified with a second database search using a different search engine, were recognized from the comparison between VL and CL samples. Among them, 31 proteins for the CL group and six proteins for the VL group were determined differentially abundant. Two proteins from the gel-based analysis, pyruvate kinase and succinyl-coA:3-ketoacid-coenzyme A transferase analysis were encountered in the protein list of the CL group. Copyright © The Author(s), 2021. Published by Cambridge University Press.Article Citation - Scopus: 7High-Pressure Structural Studies and Pressure-Induced Sensitisation of 3,4,5-Trinitro(Royal Society of Chemistry, 2023) Atceken, N.; Hemingway, J.; Bull, C.L.; Liu, X.; Michalchuk, A.A.L.; Konar, S.; Morrison, C.A.Herein we report the first high-pressure study of the energetic material 3,4,5-trinitro-1H-pyrazole (3,4,5-TNP) using neutron powder diffraction and single-crystal X-ray diffraction. A new high-pressure phase, termed Form II, was first identified through a substantial change in the neutron powder diffraction patterns recorded over the range 4.6-5.3 GPa, and was characterised further by compression of a single crystal to 5.3 GPa in a diamond-anvil cell using X-ray diffraction. 3,4,5-TNP was found to be sensitive to initiation under pressure, as demonstrated by its unexpected and violent decomposition at elevated pressures in successive powder diffraction experiments. Initiation coincided with the sluggish phase transition from Form I to Form II. Using a vibrational up-pumping model, its increased sensitivity under pressure can be explained by pressure-induced mode hardening. These findings have potential implications for the safe handling of 3,4,5-TNP, on the basis that shock- or pressure-loading may lead to significantly increased sensitivity to initiation. © 2023 The Royal Society of Chemistry.Review Citation - WoS: 13Citation - Scopus: 13Oxygen Delivery Biomaterials in Wound Healing Applications(WILEY-V C H VERLAG GMBH, 2023) Bayraktar, Sema; Üstün, Cansu; Kehr, Nermin SedaOxygen (O2) delivery biomaterials have attracted great interest in the treatment of chronic wounds due to their potential applications in local and continuous O2 generation and delivery, improving cell viability until vascularization occurs, promoting structural growth of new blood vessels, simulating collagen synthesis, killing bacteria and reducing hypoxia-induced tissue damage. Therefore, different types of O2 delivery biomaterials including thin polymer films, fibers, hydrogels, or nanocomposite hydrogels have been developed to provide controlled, sufficient and long-lasting O2 to prevent hypoxia and maintain cell viability until the engineered tissue is vascularized by the host system. These biomaterials are made by various approaches, such as encapsulating O2 releasing molecules into hydrogels, polymer microspheres and 3D printed hydrogel scaffolds and adsorbing O2 carrying reagents into polymer films of fibers. In this article, different O2 generating sources such as solid inorganic peroxides, liquid peroxides, and photosynthetic microalgae, and O2 carrying perfluorocarbons and hemoglobin are presented and the applications of O2 delivery biomaterials in promoting wound healing are discussed. Furthermore, challenges encountered and future perspectives are highlighted. Oxygen delivery (O2) biomaterials have attracted great interest in the treatment of chronic wounds due to their ability to continuously deliver oxygen and support cell viability. Therefore, various O2 generating sources such as solid inorganic peroxides, liquid peroxides and photosynthetic microalgae, and O2-carrying perfluorocarbons and hemoglobin are incorporated into different biomaterial networks for wound healing applications.imageArticle Citation - WoS: 2Citation - Scopus: 2Investigating Influences of Intravenous Fluids on Huvec and U937 Monocyte Cell Lines Using the Magnetic Levitation Method(ROYAL SOC CHEMISTRY, 2023) Keçili, Seren; Kaymaz, Sumeyra Vural; Özoğul, Beyzanur; Tekin, H. Cumhur; Elitaş, MeltemIntravenous fluids are being widely used in patients of all ages for preventing or treating dehydration in the intensive care units, surgeries in the operation rooms, or administering chemotherapeutic drugs at hospitals. Dextrose, Ringer, and NaCl solutions are widely received as intravenous fluids by hospitalized patients. Despite their widespread administration for over 100 years, studies on their influences on different cell types have been very limited. Increasing evidence suggests that treatment outcomes might be altered by the choice of the administered intravenous fluids. In this study, we investigated the influences of intravenous fluids on human endothelial (HUVEC) and monocyte (U937) cell lines using the magnetic levitation technique. Our magnetic levitation platform provides label-free manipulation of single cells without altering their phenotypic or genetic properties. It allows for monitoring and quantifying behavior of single cells by measuring their levitation heights, deformation indices, and areas. Our results indicate that HUVEC and U937 cell lines respond differently to different intravenous fluids. Dextrose solution decreased the viability of both cell lines while increasing the heterogeneity of areas, deformation, and levitation heights of HUVEC cells. We strongly believe that improved outcomes can be achieved when the influences of intravenous fluids on different cell types are revealed using robust, label-free, and efficient methods. Label-free analysis of cells exposed to intravenous fluids can be achieved through magnetic levitation technology coupled with cell-morphology characterization.Article Citation - WoS: 10Citation - Scopus: 11Liquefaction of Oak Wood Using Various Solvents for Bio-Oil Production(AMER CHEMICAL SOC, 2023) Öcal, Bulutcem; Yüksel, AslıRapidly increasing global energy demand resulting from the growing population and worldwide development has increased the consumption of limited fossil fuel. The usage causes severe environmental deterioration by CO2 emission, which has sparked interest in finding green, renewable, and sustainable alternative sources of energy. Bio-oil, derived from several biomasses via liquefaction, is a promising candidate to replace fossil fuels. Turkey's land (27%) is covered with forested areas (consisting of mostly oak trees). Therefore, it has great potential for cheap lignocellulosic feedstock forest residues from industrial applications and harvesting. In the present study, the thermal liquefaction of oak wood particles (OWP) was performed using various solvents in addition to water, namely, ethanol, 1-butanol, and 1,4-dioxane. The experiments were carried out in a batch reactor for 1 and 2 h residence times at different temperatures (210, 240, and 270 degrees C). Bio-oil samples obtained at 270 degrees C and a 1 h residence time determined as optimum conditions were analyzed with TGA, CHNS elemental analysis, FTIR, and GC-MS. 1,4-Dioxane showed the best performance in yielding the maximum bio-oil with 51.8% at those conditions. The higher heating values of the bio-oils ranged from 22.1 to 35 MJ/kg. Phenolic groups were the predominant components of bio-oil produced from OWP, while the intensity of alcohols, ketones, and acids varied based on used solvents. Based on energy recovery calculations, the enhancement of pristine OWP's energy efficiency depended on bio-oil yield, and quality was confirmed for all solvent types (1,4-dioxane > 1-butanol > water > ethanol).Article Citation - Scopus: 3A Reaction-Based Scenario for Fluorescence Probing of Au(iii) Ions in Human Cells and Plants(Royal Soc Chemistry, 2023) Eren, Merve Cevik; Eren, Ahmet; Dartar, Suay; Kaya, Beraat Umur; Ucuncu, Muhammed; Varlikli, Canan; Emrullahoglu, MustafaA BODIPY-based fluorophore decorated with a gold specific reactive handle (e.g., 2-alkynylallyl alcohol) displayed a ratiometric fluorescence change in response to Au3+ ions with extraordinary selectivity over other competing metal species, including Hg2+, Cu2+, Zn2+ and Pd2+. By way of a gold-catalyzed intramolecular cyclisation-isomerisation reaction sequence, a BODIPY construct with an extended p-conjugation transformed into a new structure with a relatively short p-system. This unique chemical transformation was accompanied by, and resulted in, a dramatic shift in the emission and absorption wavelength, which could be monitored as distinct changes in the color of the solution's emission. Apart from its outstanding analytical performance in solution, including a quick response time (<10 s), unique specificity, a high-fold ratio-metric change (62-fold), and a remarkably low detection limit (358 nM), the probe also proved useful in monitoring Au3+ ions in human cells and plants (e.g., Nicotiana benthamiana).Article 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.Article Citation - WoS: 3Citation - Scopus: 3Synthesis, Cytotoxicity, and Antibacterial Studies of 2,4,5,6-Substituted Hexahydro-1h(Wiley, 2023) Yetişkin, Egehan; Gündoğdu, Özlem; Mete, Derya; Celebioglu, Neslihan; Kara, Yunus; Şanlı-Mohamed, GulsahIn this study, synthesis of novel isoindole-1,3-dione analogues bearig halo, hydroxy, and acetoxy groups at the position 4,5,6 of the bicyclic imide ring was performed to examine their potential anticancer effects against some cell lines. A multistep chemical pathway was used to synthesize the derivatives. The cytotoxic effect of trisubstituted isoindole derivatives were evaluated by determining cellular viability using the MTT assay against A549, PC-3, HeLa, Caco-2, and MCF-7 cell lines. The C-2 selective ring-opening products were obtained from the ring-opening reaction of 5-alkyl/aryl-2-hydroxyhexahydro-4H-oxireno[2,3-e]isoindole-4,6(5H)-diones with nucleophiles such as chloride (Cl-) and bromide (Br-) ions. In addition, the ring-opening products halodiols were converted to their related acetates. The anticancer activity of synthesized isoindole-1,3-dione derivatives was investigated against HeLa, A549, MCF-7, PC3, and Caco-2 cells in vitro and resulted in varies cytotoxic effect depend on the group attached to the isoindole molecule. Furthermore, the evaluation of the antimicrobial action of trisubstituted isoindole derivatives against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria was assessed and found out selective inhibition of the both bacterial growth via different trisubstituted isoindole derivatives. The results of this work encourage further research on the potential utilization of trisubstituted isoindole derivatives as cytotoxic and antimicrobial agents.