Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection

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  • Book Part
    Computational Approaches for Antibody-Based Drug Design
    (Institute of Physics Publishing, 2024) Gunes, S.; Arkca, I.; Atik, S.B.; Ulucan-Karnak, F.; Sezgin, H.T.; Uyar, A.
    This chapter includes various aspects of antibodies with a major emphasis on computational tools in antibody design. In this scope, current antibody databases, computational tools, and approaches for modelling antibodies and nanobodies, the structure, and interface prediction are analyzed. On the other hand, various antibody design techniques such as grafting, the significance of antibody-drug conjugates, and how computational methods contribute to the development of therapeutic antibodies are discussed with relevant strategies in the literature. Lastly, the production cost and the rising market value of antibodies are emphasized. © IOP Publishing Ltd 2023. All rights reserved.
  • Book Part
    Application of Geothermal Energy in Hydrogen Production
    (Taylor and Francis, 2024) Ayzit, T.; Özmumcu, A.; Baba, A.
    Compared to other renewable resources, geothermal energy is a low-cost, technically proven, reliable, clean, and safe energy source that has been used in various fields and applications for many decades. These energy sources can be used directly or by conversion to other forms of energy. The use of geothermal energy for various purposes such as electricity, heating, cooling, greenhouses, dry food, thermal tourism, fisheries, and mineral extraction is widespread in many countries. Today’s installed geothermal capacity is dominated by the United States with about 3.7 GW, followed by Indonesia (2.1 GW), the Philippines (1.9 GW), Turkey (1.7 GW), and New Zealand. Global geothermal power generation capacity at the end of 2020 was 15.6 GW. The top ten geothermal producers account for nearly 90% of the global market, and many countries, especially Europe, plan to invest in geothermal soon. Looking at the direct use of geothermal energy for thermal applications, only four countries (China, Turkey, Iceland, and Japan) account for three-quarters of the energy consumed. Hydrogen can provide a number of benefits for future energy systems. Hydrogen can serve as storage for intermittent renewables or provide grid services. It can replace natural gas in industrial heating processes that are otherwise difficult to decarbonise. Therefore, geothermal resources can be used to produce clean hydrogen. Within this section, the importance and use of geothermal energy have been highlighted. At the same time, detailed information is given about the importance of hydrogen, its production, and its use in connection with geothermal energy. © 2025 selection and editorial matter, Mohammad Reza Rahimpour, Mohammad Amin Makarem, and Parvin Kiani.
  • Book Part
    Citation - Scopus: 2
    Comparative Mapping
    (CRC Press, 2024) Frary, A.; Doganlar, S.; Ratnaparkhe, M.B.
    In the mid 1980s, restriction fragment length polymorphism (RFLP) analysis was first applied to plants for the purposes of creating genetic linkage maps. Using the maps developed for major crop species, the genes controlling qualitative and quantitative traits could be detected and then selected for (via closely linked molecular markers) in breeding programs. Advances in DNA marker technology not only allowed the rapid generation of high-resolution plant genetic maps, but also facilitated detailed comparisons among species. When complementary molecular markers are mapped across related species, it is then possible to align the chromosomes of those species to create comparative linkage maps. In this way, genomic similarities between species are revealed so that genetic information about one species may be extended to others and evolutionary inferences drawn. © 2008, CRC Press. All rights reserved.
  • Article
    Citation - WoS: 5
    Citation - Scopus: 7
    Targeting 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 Dokur
    Purpose. 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: 2
    Citation - Scopus: 2
    Fabrication of Bioactive Helix Aspersa Extract-Loaded Chitosan-Based Bilayer Wound Dressings for Skin Tissue Regeneration
    (Amer Chemical Soc, 2024) Perpelek, Merve; Tıhmınlıoğlu, Funda; Tamburaci, Sedef; Karakasli, Ahmet; Tihminlioglu, Funda
    In recent years, there has been a notable shift toward exploring plant and animal extracts for the fabrication of tissue engineering structures that seamlessly integrate with the human body, providing both biological compatibility and physical reinforcement. In this particular investigation, we synthesized bilayer wound dressings by incorporating snail (Helix aspersa) secretions, comprising mucus and slime, into chitosan matrices via lyophilization and electrospinning methodologies. A nanofiber layer was integrated on top of the porous structure to mimic the epidermal layer for keratinocyte activity as well as acting as an antibacterial barrier against possible infection, whereas a porous structure was designed to mimic the dermal microenvironment for fibroblast activity. Comprehensive assessments encompassing physical characterization, antimicrobial efficacy, in vitro bioactivity, and wound healing potential were conducted on these bilayer dressings. Our findings revealed that the mucus and slime extract loading significantly altered the morphology in terms of nanofiber diameter and average pore size. Snail extracts loaded on a nanofiber layer of bilayer dressings showed slight antimicrobial activity against Staphylococcus epidermidis and Escherichia coli. An in vitro release study of slime extract loaded in the nanofiber layer indicated that both groups 1 and 2 showed a burst release up to 6 h, and a sustained release was observed up to 96 h for group 1, whereas slime extract release from group 2 continued up to 72 h. In vitro bioactivity assays unveiled the favorable impact of mucus and slime extracts on NIH/3T3 fibroblast and HS2 keratinocyte cell attachment, proliferation, and glycosaminoglycan synthesis. Furthermore, our investigations utilizing the in vitro scratch assay showcased the proliferative and migratory effects of mucus and slime extracts on skin cells. Collectively, our results underscore the promising prospects of bioactive snail secretion-loaded chitosan constructs for facilitating skin regeneration and advancing wound healing therapies.
  • Article
    Citation - WoS: 1
    Comparison of Cell-Penetrating and Fusogenic Tat-Ha2 Peptide Performance in Peptideplex, Multicomponent, and Conjugate Sirna Delivery Systems
    (Amer Chemical Soc, 2024) Uz, Metin; Bulmus, Volga; Altinkaya, Sacide Alsoy
    In this study, the performance of the cell-penetrating and fusogenic peptide, TAT-HA2, which consists of a cell-permeable HIV trans-activator of transcription (TAT) protein transduction domain and a pH-responsive influenza A virus hemagglutinin protein (HA2) domain, was comparatively evaluated for the first time in peptideplex, multicomponent, and conjugate siRNA delivery systems. TAT-HA2 in all three systems protected siRNA from degradation, except in the conjugate system with a low Peptide/siRNA ratio. The synergistic effect of different peptide domains enhanced the transfection efficiency of multicomponent and conjugate systems compared to that of peptideplexes, which was attributed to the surface configuration of TAT-HA2 peptides depending on the nature of attachment. Particularly, the multicomponent system showed better cellular uptake and endosomal escape than the peptideplexes, resulting in enhanced siRNA delivery in the cytoplasm. In addition, the presence of cleavable disulfide bonds in multicomponent and conjugate systems promoted the effective siRNA delivery in the cytoplasm, resulting in improved gene silencing activity. The multicomponent system reduced the level of luciferase expression in SKOV3 cells to 45% (+/- 4). In contrast, the conjugate system and the commercially available siRNA transfection agent, Lipofectamine RNAiMax, caused luciferase suppression down to 55% (+/- 2) at a siRNA dose of 100 nM. For the same dose, the peptideplex system could only reduce the luciferase expression to 65% (+/- 5). None of the developed systems showed significant toxicity at any dose. Overall, the TAT-HA2 peptide is promising as a siRNA delivery vector; however, its performance depends on the nature of attachment and, as a result, its surface configuration on the developed delivery system.
  • Correction
    Diaph1-Deficiency Is Associated With Major T, Nk and Ilc Defects in Humans (vol 44, 175, 2024)
    (Springer/plenum Publishers, 2025) Azizoglu, Zehra Busra; Babayeva, Royala; Haskologlu, Zehra Sule; Acar, Mustafa Burak; Ayaz-Guner, Serife; Okus, Fatma Zehra; Eken, Ahmet
    [No Abstract Available]
  • Article
    An Interior Inverse Generalized Impedance Problem for the Modified Helmholtz Equation in Two Dimensions
    (Wiley-v C H verlag Gmbh, 2025) Yaman, Olha Ivanyshyn; Ozdemir, Gazi
    We consider the inverse interior problem of recovering the surface impedances of the cavity from sources and measurements placed on a curve inside of it. The uniqueness issue is investigated, and a hybrid method is proposed for the numerical solution. The approach takes advantages of both direct and iterative schemes, such as it does not require an initial guess and has an accuracy of a Newton-type method. Presented numerical experiments demonstrate the feasibility and effectiveness of the approach.
  • Article
    Citation - WoS: 2
    Citation - Scopus: 1
    Gliflozins, Sucrose and Flavonoids Are Allosteric Activators of Lecithin-Cholesterol Acyltransferase
    (Nature Portfolio, 2024) Niemela, Akseli; Giorgi, Laura; Nouri, Sirine; Yurttas, Betul; Rauniyar, Khushbu; Jeltsch, Michael; Koivuniemi, Artturi
    Lecithin-cholesterol acyltransferase (LCAT) serves as a pivotal enzyme in preserving cholesterol homeostasis via reverse cholesterol transport, a process closely associated with the onset of atherosclerosis. Impaired LCAT function can lead to severe LCAT deficiency disorders for which no pharmacological treatment exists. LCAT-based therapies, such as small molecule positive allosteric modulators (PAMs), against LCAT deficiencies and atherosclerosis hold promise, although their efficacy against atherosclerosis remains challenging. Herein we utilized a quantitative in silico metric to predict the activity of novel PAMs and tested their potencies with in vitro enzymatic assays. As predicted, sodium-glucose cotransporter 2 (SGLT2) inhibitors (gliflozins), sucrose and flavonoids activate LCAT. This has intriguing implications for the mechanism of action of gliflozins, which are commonly used in the treatment of type 2 diabetes, and for the endogenous activation of LCAT. Our results underscore the potential of molecular dynamics simulations in rational drug design.
  • Article
    Citation - WoS: 5
    Citation - Scopus: 5
    An Experimental and Comparative Study on Passive and Active Pcm Cooling of a Battery With/Out Copper Mesh and Investigation of Pcm Mixtures
    (Elsevier, 2024) Samancioglu, Umut Ege; Gocmen, Sinan; Madani, Seyed Saeed; Ziebert, Carlos; Nuno, Fernando; Huang, Jack; Cetkin, Erdal
    The carbon emission contribution to global warming accelerated both research on and transition to electric vehicles (EVs). Drivers demand high power, fast acceleration and less charging times. All these demands require high C rate charging/discharging demands from batteries. The rate of heat generation is exponentially proportional to C rates which decreases battery lifetime and may lead to thermal runaway. However, a battery thermal management system decreases thermal runaway risk and decelerates battery degradation via controlling battery temperature. In this paper, we first document the thermal conductivity enhancement via copper foam into phase change material (PCM) domain to uncover their possible use in EV thermal management applications. Maximum 15.93 times increment is achieved with a specific copper foam. Then, physical properties and behaviors of distinct PCM mixtures are documented. Homogeneity of mixtures is associated with the chemistry of PCMs and the mixture melting point is proportional to the volume weighted average of melting temperatures. The results document that the PCM with relatively lower melting point is beneficial when end of discharge temperatures considered, except for high discharge rate of 2C. Temperature uniformity across the battery increases with relatively higher melting point PCM. Experiments also document that the amount of PCM volume lost via insertion of copper foam yields higher end of discharge temperatures. Overall, both PCM and copper foam enhances temperature homogeneity and their benefit becomes more sensible during drive cycles relative to continuous charge/discharge use cases.