WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Citation - WoS: 5Citation - Scopus: 7Targeting the Panoptosome Using Necrostatin-1 Reduces Panoptosis and Protects the Kidney Against Ischemia-Reperfusion Injury in a Rat Model of Controlled Experimental Nonheart-Beating Donor(Elsevier Science inc, 2024) Dokur, Mehmet; Uysal, Erdal; Kucukdurmaz, Faruk; Altinay, Serdar; Polat, Sait; Batcioglu, Kadir; Yeni, Sema Nur DokurPurpose. Reducing renal ischemia is crucial for the function and survival of grafts from non- heartbeat donors, as it leads to inflammatory responses and tubulointerstitial damage. The primary concern with organs from nonheartbeat donors is the long warm ischemia period and reperfusion injury following renal transplantation. This study had two main goals; one goal is to determine how Necrostatin-1 targeting the PANoptosome affects PANoptosis in the nonheartbeating donor rat model. The other goal is to fi nd out if Necrostatin-1 can protect the kidney from ischemic injury for renal transplantation surgery. Methods. Twenty-four rats were grouped randomly as control and Necrostatin-1 in this experimental animal study, and we administered 1.65 mg/kg of Necrostatin-1 intraperitoneally to the experimental group for 30 minutes before cardiac arrest. We removed the rats' left kidneys and measured various oxidative stress marker measures such as malondialdehyde, superoxide dismutase, catalase, GPx, and 8-hydroxy-2-deoxyguanosine levels. We then subjected the tissues to immunohistochemical analysis, electron microscopy, and histopathological analysis. Findings. The Necrostatin-1 group had a lower total tubular injury score (P < .001) and less Caspase-3, gasdermin D, and mixed lineage kinase domain-like protein expression. Additionally, the apoptotic index of the study group was lower (P < .001). Furthermore, the study group had higher levels of superoxide dismutase and GPx (P < .05), whereas malondialdehyde levels were reduced (P = .009). Electron microscopy also revealed a significant improvement in tissue structure in the Necrostatin-1 group. Conclusion. Necrostatin-1 protects against ischemic acute kidney injury in nonheart-beating donor rats by inhibiting PANoptosis via the blockade of RIPK1. As a result of this, Necrostatin1 may offer novel opportunities for protecting donor kidneys from renal ischemia-reperfusion injury during transplantation in patients with end-stage kidney disease requiring a renal transplantation.Article Citation - WoS: 1Citation - Scopus: 1Completeness of Energy Eigenfunctions for the Reflectionless Potential in Quantum Mechanics(Aip Publishing, 2024) Erman, Fatih; Turgut, O. TeomanThere are a few exactly solvable potentials in quantum mechanics for which the completeness relation of the energy eigenstates can be explicitly verified. In this article, we give an elementary proof that the set of bound (discrete) states together with the scattering (continuum) states of the reflectionless potential form a complete set. We also review a direct and elegant derivation of the energy eigenstates with proper normalization by introducing an analog of the creation and annihilation operators of the harmonic oscillator problem. We further show that, in the case of a single bound state, the corresponding wave function can be found from the knowledge of continuum eigenstates of the system. Finally, completeness is shown by using the even/odd parity eigenstates of the Hamiltonian, which provides another explicit demonstration of a fundamental property of quantum mechanical Hamiltonians.Conference Object Citation - WoS: 1The Effects of Novel Telomerase Activators on Human Adipose-Derived Mesenchymal Stem Cell (had-Msc) Proliferation and Osteogenic Differentiation(Georg Thieme verlag Kg, 2022) Kuru, G.; Kucuksolak, M.; Pulat, G.; Karaman, O.; Bedir, E.[No Abstract Available]Conference Object Kinematic Design of a Novel Finger Exoskeleton Mechanism for Rehabilitation Exercises(Springer international Publishing Ag, 2024) Kiper, Gokhan; Inanc, EmirhanThe paper presents the kinematic design of a novel low-cost two degree-of-freedom finger exoskeleton mechanism to be used for rehabilitation exercises for post-stroke or injured patients. The first degree-of freedom is for the flexion/extension of metacarpophalangeal joint and is achieved via a planar 4-bar loop. The second degree-of-freedom is for the simultaneous flexion/extension of distal/proximal interphalangeal joints and is achieved via an over-constrained double-spherical 6-bar linkage, where 3 of the links are the phalanges of the finger and 2 of the joints are finger joints themselves. So, the number of extra links are less compared to other designs in the literature. The motion of an index finger is recorded via image processing. The four-bar mechanism part is designed for optimum transmission angle characteristics. The formulation and application of the kinematic synthesis of the 6-bar linkage is presented. The design is verified via a prototype.Article Citation - WoS: 1Citation - Scopus: 1Thickness-Dependent Characteristics and Oxidation of 2d-Cadmium(Royal Soc Chemistry, 2024) Gulucu, Arda; Sahin, HasanIn this study, the structural, electronic, and vibrational properties of the thinnest crystal structure that can be obtained by thinning bulk Cd down to a monolayer are investigated by performing first-principles calculations. Total energy optimization and dynamic stability calculations reveal that the single layer crystal structure has a hexagonal unitcell with a two-atomic basis where alternating layers are formed by trigonal arrangements of Cd atoms. Softening occurs with decreasing zone center optical phonon frequencies as a result of structural relaxation when going from a bulk to a single layer (SL) structure. It is also shown that the thinnest structure obtained from bulk Cd crystals maintains its metallic features despite the dimensional crossover. In addition, it is predicted through calculations that the SL Cd crystal strongly interacts with oxygen and that the oxidized regions even undergo chemical transformation to form a CdO crystal. In the double-layer CdO crystal resulting from the oxidation of individual Cd layers, the layers are connected to each other with partially covalent bonds, and this structure is a semiconductor with a band gap of 2.10 eV. On the one hand, the robust metallic structure of the thinnest possible Cd crystal provides flexibility for its use in nanoscale applications, on the other hand, the fact that its electronic properties can be changed by oxidation is important for optoelectronic device applications. In this study, the structural, electronic, and vibrational properties of the thinnest crystal structure that can be obtained by thinning bulk Cd down to a monolayer are investigated by performing first-principles calculations.Article Citation - WoS: 6Citation - Scopus: 6Evaluation of the Extracts of Purple Basil (<i>ocimum Basilicum</I> L.) as Natural Ph-Indicator Dyes Anticipated To Be Utilised in Intelligent Food Packaging-An Optimisation Study(Wiley, 2024) Erez, Elif; Bayramoğlu, Beste; Bayramoglu, BestePurple basil (Ocimum basilicum L.) extract has significant potential as a natural colorimetric pH-indicator material owing to its abundance in anthocyanins. This contribution is the first to optimise the ultrasound-assisted extraction of purple basil by response surface methodology in terms of maximum total monomeric anthocyanin (TMA) content and pH-dependent increase in green intensity (IGI) using a three-level, three-factor Box-Behnken design. The latter was considered as a measure of the pH-indicator ability of the extracts. The independent variables were ethanol concentration, solvent/solid ratio, and extraction time for two types of solvents [aqueous ethanol with 0.1% (v/v) acetic acid (Ac) or hydrochloric acid]. Optimum conditions were determined for single and combined responses. The extracts were further characterised according to total phenolic content (TPC), percentage polymeric colour (PPC), 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS) antioxidant, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities. All models explained more than 93% of the variability. The combined response model for the Ac-acidified system gave more favourable optimal conditions [55.25% (v/v) ethanol, 30 mL/g solvent/solid ratio and 39.24 min] regarding lower ethanol consumption and shorter times. Validation experiments verified the model successfully predicted the responses. The corresponding TMA, IGI, PPC, TPC, ABTS, and DPPH values were determined as 4.83 +/- 0.18 mg cyanidin-3-glucoside equivalent, 2.29 +/- 0.05, 68.07 +/- 3.17, 28.79 +/- 1.54 mg gallic acid equivalent, 55.85 +/- 1.71 mg Trolox equivalent, and 16.80 +/- 1.08 mg ascorbic acid equivalent per gram dry weight, respectively.Article Citation - WoS: 1Citation - Scopus: 1Effect of Urbanization on Groundwater Resources Hydrodynamics and Bearing Capacity: a Case Study From the Bayraklı Region, Izmir, ̇ Türkiye(Geological Society of London, 2024) Öztürk,B.; İşbuğa,V.; Bilgiç,E.; Baba,A.The bearing capacity of soil is a critical factor in the design of foundations for civil engineering structures. The bearing capacity depends on soil properties, as well as the location of the water table. A rise in the groundwater level can be dramatic, especially in highly urbanized regions, and can affect the bearing capacity of foundations. In this study, groundwaterlevel fluctuations in a highly urbanized region in Izmir, the third largest city in Türkiye, was monitored over a 1 year period, and ̇ its effect on reducing the bearing capacity, which is not considered in foundation design and construction, was investigated. For this purpose, four observation wells equipped with groundwater data loggers were used to determine the variations in groundwater level over 1 year. Using the Terzaghi approach to calculate the bearing capacity, normalized bearing capacity plots for various foundation width/depth (B/Df) ratios were generated for all four observation wells. Remarkable bearing capacity changes of 10.94, 8.21, 7.62 and 9.29% were observed in four different observation wells (OW-1, OW-3, OW-6 and OW-9, respectively). The study showed that changes in groundwater level in the region caused by urbanization poses a potential risk to the sustainability of previously constructed foundations. © 2024 The Author(s).Article Citation - WoS: 239Citation - Scopus: 291Performance of the Cms Level-1 Trigger in Proton-Proton Collisions at √s = 13 Tev(Institute of Physics, 2020) Sirunyan, A.M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Dragicevic, M.; Erö, J.; Bunichev, V.At the start of Run 2 in 2015, the LHC delivered proton-proton collisions at a center-of-mass energy of 13 TeV. During Run 2 (years 2015-2018) the LHC eventually reached a luminosity of 2.1 × 1034 cm-2s-1, almost three times that reached during Run 1 (2009-2013) and a factor of two larger than the LHC design value, leading to events with up to a mean of about 50 simultaneous inelastic proton-proton collisions per bunch crossing (pileup). The CMS Level-1 trigger was upgraded prior to 2016 to improve the selection of physics events in the challenging conditions posed by the second run of the LHC. This paper describes the performance of the CMS Level-1 trigger upgrade during the data taking period of 2016-2018. The upgraded trigger implements pattern recognition and boosted decision tree regression techniques for muon reconstruction, includes pileup subtraction for jets and energy sums, and incorporates pileup-dependent isolation requirements for electrons and tau leptons. In addition, the new trigger calculates high-level quantities such as the invariant mass of pairs of reconstructed particles. The upgrade reduces the trigger rate from background processes and improves the trigger efficiency for a wide variety of physics signals. © 2020 CERN for the benefit of the CMS collaboration.