WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Gamma Secretase Inhibitors, DAPT and MK0752, Exhibit Synergistic Anticancer Effects with Cisplatin and Docetaxel in 2D and 3D Models of Breast Cancer(TÜBİTAK Scientific & Technological Research Council of Turkey, 2025) Telli, Kubra; Gubat, Johannes; D'Arcy, Padraig; Ozuysal, Ozden YalcinBackground/aim: Breast cancer remains a major malignancy among women, and severe side effects and the development of acquired drug resistance frequently hinder current therapeutic strategies. The Notch signaling pathway, a key regulator of cell fate, is commonly dysregulated in breast cancer and associated with poor prognosis. Gamma-secretase inhibitors (GSIs) block Notch receptor activation and have shown potential anticancer efficacy. This study aimed to investigate the synergistic activity of two commonly used GSIs, DAPT and MK0752, combined with docetaxel or cisplatin in both 2D and 3D breast cancer models. Materials and methods: Triple-negative, highly metastatic MDA-MB-231 and ER+/PR+ MCF-7 breast cancer cell lines were treated with DAPT or MK0752 alone or in combination with docetaxel or cisplatin. Drug efficacy and potential synergism were evaluated in 2D monolayer cultures and 3D spheroid models. Sequential treatment strategies were also assessed, where docetaxel or cisplatin was administered prior to GSI exposure. Results: Both MDA-MB-231 and MCF-7 cell lines exhibited notable sensitivity to DAPT and MK0752 combinations with docetaxel or cisplatin in 2D and 3D cultures. Synergistic enhancement of cytotoxicity was observed, particularly in sequential treatment regimens. Pretreatment with docetaxel or cisplatin followed by GSI exposure demonstrated superior growth inhibition compared with either monotherapy or simultaneous combination treatments. Conclusion: This study highlights the therapeutic potential of combining GSIs with standard chemotherapeutics to overcome drug resistance in breast cancer. The observed synergy and sequencing effects provide a strong basis for further mechanistic and translational investigations to optimize GSI-based combinational therapy strategies.Article Brewing Property in Onedimensional City? Exploring Starbucks' Locational Strategies-Impacts in the Case of Izmir, Türkiye(University Cueca, 2026) Coskun, Yagmur Asci; Penpencioglu, MehmetThe article examines Starbucks'locational strategies and their impact on urban spaces, drawing on Rossi's concept of the "one-dimensional city." As global brands increasingly shape urban environments, three key effects emerge: rising property prices near stores, the concentration of locations in malls, transit hubs, and walkable areas, and alignment with urban landscapes standardized by major transportation infrastructure decisions. Similar to many cities in the Global South, Starbucks in & Idot;zmir functions both as a product and a driver of property-driven, rent-seeking urban development.Empirical evidence reveals that its locational strategies enhance accessibility, increase property values, and reshape the built environment. Through spatial analysis, the article examines Starbucks locations within a walkability and accessibility framework, highlighting their concentration in high-value districts with strong public transit connections.This research underscores how global brands reinforce socio-economic divides, transform urban spaces, and promote consumption-driven urbanization through their integration into global capitalism and real estate dynamics.Article Mock Alexander Polynomials(Australian National University, 2025) Gügümcü, Neslihan; Kauffman, L.H.In this paper, we construct Mock Alexander polynomials for starred links and linkoids in surfaces. These polynomials are defined as state summations on link or linkoid diagrams that satisfy f = n, where f denotes the number of regions and n denotes the number of crossings of diagrams. These new invariants are chirality and reversibility sensitive. © The authors.Article Participatory Action for and Through Ecological Integrity: Toroidality as a Circular Design Model(Institute for Research and Community Services, Institut Teknologi Bandung, 2025) Yurt, C.; Deniz, D.The ecological crisis corrupts natural cycles, damages networks of organisms, and disrupts the ecosystem equilibrium. In response to the ecological crisis, the concept of circularity proposes reformative actions. However, these actions are insufficient to reverse the crisis and achieve ecological integrity because they are non-holistic and based on human concerns and priorities. A more inclusive and integrative mindset is necessary for better-functioning circular processes. In this regard, this research presents a theoretical framework for an alternative circular design model – Toroidality – which is driven by collective knowledge and participatory action. Toroidality functions through the integrative capacity of collective knowledge and collaboration among human and non-human stakeholders in the ecosystem. Based on the intertwined cycles of collective knowledge and collective value-creation, Toroidality becomes a self-feeding circular design model. Through its four-phased circular design processes, Toroidality claims to generate solutions that have regenerative capacities. This article clarifies the conceptual background, theoretical framework and complementary notions to present the fundamentals of Toroidality. After this initial explanatory article, the dynamics of the phases and interactions among the stakeholders are aimed to be explored and reported in the following research, through a real-life case study. © 2025 Published by ITB Institute for Research and Community Services.Article Citation - WoS: 2Citation - Scopus: 3Evaluation of Hydro-Geochemical Processes Controlling Groundwater Quality in Balkh Center (Mazar-e-Sharif) Northern Afghanistan(Elsevier, 2025) Farahmand, Asadullah; Zaryab, Abdulhalim; Ameri, Nasrullah; Ali, Shakir; Eqrar, Mohammad NaimBackground: Groundwater in Afghanistan stands as the predominant water source employed for potable consumption, household utilization, irrigation, and industrial applications. Major cities of Afghanistan are largely dependent on groundwater resources. However, the groundwater quality of major cities in Afghanistan, including Mazar-e-Sharif city was not investigated in detail. Objective: This study aims to conduct a comprehensive analysis of the hydrochemical characteristics of the Mazare-Sharif groundwater, identify the factors influencing groundwater quality, and evaluate the groundwater contamination sources. Methods: A total of 18 groundwater samples were collected during the dry season (June 2020) and analyzed for various physico-chemical parameters. Methods such as multivariate statistical analyses, geochemical modeling, water quality index (WQI), and spatial distribution of groundwater quality were employed to evaluate the hydro-geochemistry of the study area. Results: The results reveal that 1) The prevailing groundwater within the study area is predominantly characterized by Na-(Ca)-HCO3 and Ca-(Mg)-SO4 water types. 2) Physicochemical variables such as NO3-, F-, TDS, and SO42-exceeded the World Health Organization (WHO) safe limits in many wells. 3) Hydro-geochemical processes such as silicate weathering, cation exchange, and gypsum dissolution controls the groundwater chemistry. 4) Cl/ Br ratios reveal, that high salinity may originate from evaporitic lacustrine and evaporite deposits and found to be localized in nature. 5) The Water Quality Index (WQI) classification suggests that approximately 60 % of the groundwater samples fall into poor to very poor water quality categories, highlighting substantial public health concerns. Major contaminants like nitrate and fluoride were found to be higher than the safe limit in nearly half of the samples. Conclusion: The findings of this study hold value for decision-makers in formulating a proficient strategy for the management of groundwater resources in Mazar-e-Sharif City in achieving the UN sustainable goal (SDG) of providing sustainable water for all. Furthermore, new advanced techniques like environmental isotopes should be analyzed to evaluate groundwater hydro-chemical evolution in the future to enhance our understanding.Article Understanding the Synthesis Mechanism of Arginine Functionalized Silver/Silver Chloride Nanoparticles Using Sugar Ligands(Elsevier, 2025) Bolat, Suheda; Degirmenci, Suna; Gumus, Abdurrahman; Sancak, Zafer; Yazgan, DrisIn this study, we performed a mechanistic study to understand how the sugar ligand chemistry affected the morphology, size and surface chemistry of Ag/AgCl_NPs synthesized in the presence of L-Arginine hydrochloride and L-Arginine/KCl mixture. The sugar ligands Lactose p-methoxyaniline (LMA) and Galactose 5-aminosalicylic acid (G5AS) resulted in formation of sheet-like Ag/AgCl_NPs while Lactose sulfanilic acid (LSA) and Lactose psulfonyldianiline (LPSA) caused the formation of anisotropic and film-like Ag/AgCl_NPs. The UV-Vis based mechanistic studies showed that the presence of Arginine posed a strong effect on how G5AS and LMA ligands interact with silver ions while the effect was more complicated for the LSA and LPSA ligands due to the fact that they form complexation with Ag+ ions. The mechanism was further investigated using infrared (IR) studies that showed the increases in Argine and chloride ion concentrations resulted in differentiation of the surface chemistry of the Ag/AgCl_NPs, and appearance of Arginine related IR bands became clearer in the case of cointroduction of Arginine and the sugar ligands. The characterized nanoparticles were then used as antibacterial agent for multidrug resistant Escherichia coli species for which less than 10 mu M minimum inhibitory concentrations were obtained. The promising antibacterial activity, which could be assigned to the presence of Arginine, was independent from the sugar ligand chemistry and nanoparticles' morphology and size. Particularly, large Ag/AgCl_NP film forming capacity can call further research to be exploited as coating materials for antibacterial application.Article Citation - WoS: 7Citation - Scopus: 6Polymeric Biomaterials for Periodontal Tissue Engineering and Periodontitis(Royal Soc Chemistry, 2024) Yuruk, Gizem; Demir, Yagmur Damla; Vural, Sevra; Kehr, Nermin SedaThe periodontium is one of the most complex tissues in the body because its structure is formed by a hierarchical combination of soft and hard tissues. Due to its complex architecture, the treatment and regeneration of damaged periodontal tissue caused by diseases is still a challenge in biomedicine. The most common disease of the periodontium is periodontitis, which occurs when the periodontium becomes infected and inflamed as a bacterial biofilm forms in the mouth. Recently, various biocompatible biomaterials made of natural and synthetic polymers have been developed for periodontal tissue regeneration or treatment due to their superior properties such as controlled drug and bioactive molecule delivery, mimicking the 3D network of tissue, biocompatibility, antibacterial and mechanical properties. In particular, biomaterials designed for drug delivery, such as hydrogels, scaffolds, films, membranes, micro/nanoparticles and fibers, and additively manufactured biomaterials have undergone in vitro and in vivo testing to confirm their potential clinical utility in periodontal regeneration and periodontitis treatment. This review explores recent advances in the use of biomaterials for the prevention and/or treatment of periodontal regeneration and periodontitis. Specifically, it emphasizes advancements in drug/biomolecule delivery and the use of additively manufactured biomaterials for addressing periodontal issues.Article Gypsophila Eriocalyx Roots Inhibit Proliferation, Migration, and Tgf-Β Signaling in Melanoma Cells(Walter de Gruyter GmbH, 2025) Azbazdar, Yagmur; Ozhan, Gunes; Helvacioglu, SelinObjectives: Melanoma is a highly malignant and serious form of skin cancer. In addition to the standard treatments, complementary approaches, including phytotherapy, are also used to alleviate symptoms and improve patient well- being. This study aims to investigate the anticancer effects of Gypsophila eriocalyx (GE), an endemic species from Türkiye, on melanoma cells. We set out to determine the efficacy of GE in inhibiting melanoma cell proliferation, migration, and growth, and to explore its underlying mechanisms. Methods: We examined the impact of GE on the prolifera- tion of two melanoma cell lines, Malme-3M and SK-MEL-28, and assessed its developmental toxicity in zebrafish em- bryos. Next, we evaluated GE’s influence on colony forma- tion and wound healing in melanoma cells, as well as its ability to induce apoptosis and affect the TGF-β/Smad signaling pathway, by measuring pathway reporter activity and target gene expression. Results: GE inhibited cell proliferation in melanoma cell lines at concentrations 104 to 488 times lower than those required for normal non-malignant L929 fibroblast cells. In zebrafish embryos, GE demonstrated developmental toxicity only at concentrations above 50 μg/mL. GE treatment significantly impaired the colony formation and wound healing abilities of melanoma cells, indicating reduced pro- liferation and migration. Moreover, GE induced apoptosis in melanoma cells and inhibited the TGF-β/Smad signaling pathway, as evidenced by decreased pathway reporter activity and target gene expression. Conclusions: This study highlights the potential of GE as a novel therapeutic agent in melanoma treatment by demon- strating its ability to inhibit tumor growth and progressionReview Citation - WoS: 1Citation - Scopus: 2Organ-On Platforms for Drug Development, Cellular Toxicity Assessment, and Disease Modeling(Tubitak Scientific & Technological Research Council Turkey, 2024) Khurram, Muhammad Maaz; Cinel, Gokturk; Yesil Celiktas, Ozlem; Bedir, ErdalOrgans-on-chips (OoCs) or microphysiological platforms are biomimetic systems engineered to emulate organ structures on microfluidic devices for biomedical research. These microdevices can mimic biological environments that enable cell-cell interactions on a small scale by mimicking 3D in vivo microenvironments outside the body. Thus far, numerous single and multiple OoCs that mimic organs have been developed, and they have emerged as forerunners for drug efficacy and cytotoxicity testing. This review explores OoC platforms to highlight their versatility in studies of drug safety, efficacy, and toxicity. We also reflect on the potential of OoCs to effectively portray disease models for possible novel therapeutics, which is difficult to achieve with traditional 2D in vitro models, providing an essential basis for biologically relevant research.Article Citation - WoS: 1Citation - Scopus: 1Investigation of Flow and Heat Transfer Performance of Gyroid Structure as Porous Media(Turkish Soc Thermal Sciences Technology, 2024) Genc, Alper Mete; Karadeniz, Ziya HaktanThere are active and passive methods used to improve heat transfer. One of the passive methods is utilising porous media with high heat transfer surface area. Porous media are divided into two groups: regular and irregular structures. One of the regular structures is triply periodic minimal surfaces (TPMS), which have been studied quite frequently recently. In this study, heat transfer and flow analysis of a Gyroid geometry, one of the most used TPMS in the literature, is investigated numerically considering the conjugate heat transfer conditions. A single porosity is considered (epsilon = 0.6), and aluminium, ceramic and PLA are selected for the heat exchanger material to examine the temperature change in the heat exchanger. To understand the different flow characteristics, Reynolds numbers are assumed to be 19.12, 95.61 and 172.09. The fluid inlet temperature is assumed to be constant at 298.15 K, and the initial temperature of the heat exchanger is assumed to be constant at 278.15 K to be consistent with the regenerative heat recovery temperature difference in ventilation standards. Nusselt numbers under different operating conditions are compared, and it is the ceramic material with low thermal diffusivity is at the highest level despite its low thermal conductivity. At the highest Reynolds number, it provided approximately 6% better heat transfer than the aluminium heat exchanger.