WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7150
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Article Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We(Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, MalihehInvestigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.Article Citation - WoS: 8Protective and Therapeutic Effects of Milrinone on Acoustic Trauma in Rat Cochlea(Springer, 2019) Ceylan, Seyit Mehmet; Uysal, Erdal; Altinay, Serdar; Sezgin, Efe; Bilal, Nagihan; Petekkaya, Emine; Gulbagci, Mustafa EmreObjectiveThe aim of this study was to investigate the potential protective and therapeutic effects of milrinone, a specific phosphodiesterase (PDE) III inhibitor, on acoustic trauma-induced cochlear injury and apoptosis.MethodsA total number of 30 healthy Wistar albino rats were evenly divided into five groups as follows: group 1 was assigned as control group; group 2 and 3 were assigned as low-dosage groups (0.25mg/kg) in which milrinone was administered 1h before acoustic trauma (AT) and 2h after AT, respectively; group 4 and 5 were assigned as high-dosage groups (0.50mg/kg) in which the drug was administered 1h before AT and 2h after AT, respectively. Except control group, all treatment groups received a single dosage of milrinone for 5days. Distortion product otoacoustic emissions (DPOAE) measurements were recorded before AT as well as at second and fifth post-traumatic days. At the end of fifth day, all rats were sacrificed and the cochlea of the rats was removed for histopathological evaluation. In addition, the groups were compared in terms of apoptotic index via caspase-3 staining.ResultsIn terms of signal-to-noise ratio (SNR), there was no statistically significant difference among the groups following AT (p>0.05). After 5days of milrinone treatment, the best SNR values were found in group 5, though all groups did not statistically differ (p>0.05). In histopathological evaluation, vacuolization, inflammation, and edema scores in all treatment groups were statistically lower than those of the control group (p<0.05). In group 2 and 4 where the drug was administered before AT, the inflammation and apoptosis index was lower than those of group 3 and 5 where the drug was administered after AT (p<0.0001).ConclusionWe reveal that milrinone has a protective effect on cochlear damage in the experimental acoustic model of rats. This protective effect was more apparent following the pre-traumatic milrinone administration, and is associated with its effect on decreasing inflammation and apoptosis. Based on DPOAE measurements following AT, especially in the group 5 (high-dosage group), milrinone may also have a therapeutic effect.Article Reflection on Designing: Metacognitive Interventions to Enhance Metacognitive Awareness, Motivation, and Performance in Design Learning(Springer, 2025) Yazici, Gizem; Dogan, FehmiDesign education involves ill-defined problem-solving that demands both creativity and self-regulation. While metacognitive awareness significantly enhances learning outcomes and motivation, there is limited empirical evidence on how to systematically foster this skill in design studios. This study aims to investigate whether metacognitive interventions increase architecture students' metacognitive awareness levels, academic goal orientations, and design course success. In a quasi-experimental design, 84 third-year architecture students were divided into experimental (n = 58) and control (n = 26) groups. Pre-post-test data were collected using the MAI and AGOQ scales. Three structured interventions were implemented in the experimental group over six weeks. In the students who received the interventions, significant increases were observed in metacognitive awareness, mastery-performance goal orientation, and design course grades. In students with high awareness, mastery orientation, metacognitive awareness, and design course grades increased significantly, while in students with low awareness, metacognitive awareness and performance orientation increased. Pretest MAI and AGOQ scores accounted for 72.8% of the variance in grades, with MAI showing the strongest positive influence. Learning and proving orientations were moderately and positively correlated to grades, while avoidance orientation showed a moderate negative correlation. Metacognitive interventions enhance learning outcomes in design education by supporting metacognition and motivation.Article Citation - WoS: 2Citation - Scopus: 1Isolation, Purification, Structural Characterization, and Encapsulation of Sulforaphane From Cabbage Seeds Using the Ionic Gelation Method(Springer, 2025) Oner, Beste; Aydin, Ozgun Koprualan; Okkali, Gaye Sumer; Sarikahya, Nazli Boke; Nadeem, Hilal Sahin; KaymakErtekin, FigenSulforaphane (SFN), a phytochemical with anticancer and antibacterial properties, is a secondary metabolite found in cabbage (both in the plants and seeds), a member of the Brassica (crusifer) family. However, pure sulforaphane is volatile, sensitive to pH, temperature, light, and oxygen, and is also only oil-soluble, limiting its stability and bioaccessibility. Therefore, encapsulation is required to enhance stability and control its release. In this study, sulforaphane-rich extracts were first obtained from cabbage seeds using a hybrid ultrasonic-microwave extraction method yielding 24.35%, with a sulforaphane content of 8202.68 mu g/g DM, followed by purification of sulforaphane through chromatography. Structural elucidation was performed using H-1-NMR, C-13-NMR, and QTOF LC/MS. The pure SFN (> 90% purity) was encapsulated using the ionic gelation method to improve its bioaccessibility and stability. Various coating material combinations, sodium alginate/chitosan and sodium alginate/pectin were evaluated for the encapsulation process. Fourier-transform infrared spectroscopy (FTIR) was used to investigate the relationship between the coating materials, and the most efficient combination was selected. Optimization of process variables using central composite rotatable design (CCRD) identified the optimal conditions: 1.41% sulforaphane-oil mixture, 0.18% chitosan, and 6.88 min waiting time. Under these conditions, microcapsules were produced with high encapsulation efficiency (76.02%) and low solubility (4.78%). & Idot;n vitro bioaccessibility studies further confirmed minimal sulforaphane release during the oral and gastric phases, with a low release in the intestinal phase. These results demonstrate the effectiveness of the encapsulation system in protecting sulforaphane under harsh gastrointestinal conditions.Article Task-Specific Dynamical Entropy Variations in EEG as a Biomarker for Parkinson's Disease Progression(Springer, 2025) Onay, Fatih; Karacali, BilgeUncovering the neuronal mechanisms un-derlying optimal behavioral performance is essential to understand how the brain dynamically adapts to changing conditions. In Parkinson's disease (PD), these neuronal mechanisms are disrupted and lead to impairments in motor coordination and higher-order cognitive functions. This study investigates neuronal dynamics during a lower-limb pedaling task by analyzing the dynamical entropy of EEG signals in healthy controls (HC), PD patients, and PD patients with freezing of gait (PDFOG). We examined both average entropy changes and entropy variability across trials to characterize task-specific neural adaptations across disease progression. Results showed that PD and PDFOG patients exhibited decreased levels of permutation entropy in frontal and parietal regions, which may be associated with loss of cognitive adapta-tion due to altered information processing. Additionally, Vasicek's entropy variability in both PD groups was significantly diminished in occipital and left frontal regions, suggesting reduced cognitive capacity to dy-namically allocate neuronal resources during task engagement. We extended this analysis to the classification of groups using LDA and SVM classifiers, where entropy-derived features achieved a classification accuracy of up to 96.15% when distinguishing HC from PDFOG patients. This dynamical entropic framework provides a novel approach for capturing neural complexity changes during task performance, revealing subtle cognitive-motor impairments in PD. Understanding the maintenance of cognitive information processing and flexibility in response to motor and cognitive task demands could be a useful tool to track PD diagnosis and progression in addition to resting-state analyses.Article Comparative Proteomic Analysis of Dental-Origin Stem Cells: Insights Into Regenerative Potential(Springer, 2025) Tez, Banu Cicek; Durukan, Sebahat Melike; Yildir, Selin Kubra; Cokkececi, Murat; Boyvat, Dudu; Altinsoy, Nilay; Ozcan, ServetTeeth are a significant source of stem cells and have clinical importance for regenerative medicine. A human tooth harbors different kinds of stem cells in the dental pulp (DPSC) or the periodontal ligament (PDLSC). Also exfoliated teeth in childhood contain a special type of stem cells in their pulp called Stem cells from Human Exfoliated Deciduous teeth (SHED). All these stem cells have features and capacities that vary depending on their niche. Here we investigated the proteomic properties of three types of stem cells that originated from human teeth. We isolated and cultured the DPSCs, PDLSCs, and SHED cells. After validating MSC populations via immunophenotyping, we performed a mass spectrometry-based proteomic approach to identify and relatively quantify whole cell and secreted proteins. Identified proteins were evaluated by using Gene Ontology and Reactome pathway analysis tools. Our data reveal that SHED cells represented inflammation, hypoxia, and nutrient deficiency-associated ontologies in both their secretome and whole-cell proteomes. The whole-cell proteome of PDLSCs consisted of differentiation and proliferation-associated molecules while their secretory molecules were mainly associated with inflammation, ECM organization, and immune response. Among dental-originated stem cells, DPSCs appeared to be the healthiest and clinically relevant in terms of proteomic properties with their proliferation, growth factor signaling, and stemness-associated molecules in their secretome and whole-cell proteome. Obtained results demonstrated that every type of stem cell from dental origin has unique proteomic features that are altered by their location and physiological conditions. The findings may help researchers improve the dental stem-cell-based regenerative medicine approaches.Correction Citation - WoS: 11Measurement of Jet Multiplicity Distributions in T(t)over-Bar Production in pp Collisions at √s = 7 TeV (Vol 74, 3014, 2014)(Springer, 2015) Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Woods, N.Article Citation - WoS: 15Search for Supersymmetry in pp Collisions at √s=7 TeV in Events With a Single Lepton, Jets, and Missing Transverse Momentum(Springer, 2013) Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Aguilo, E.; Swanson, J.Results are reported from a search for new physics processes in events containing a single isolated high-transverse-momentum lepton (electron or muon), energetic jets, and large missing transverse momentum. The analysis is based on a 4.98 fb(-1) sample of proton-proton collisions at a center-of-mass energy of 7 TeV, obtained with the CMS detector at the LHC. Three separate background estimation methods, each relying primarily on control samples in the data, are applied to a range of signal regions, providing complementary approaches for estimating the background yields. The observed yields are consistent with the predicted standard model backgrounds. The results are interpreted in terms of limits on the parameter space for the constrained minimal supersymmetric extension of the standard model, as well as on cross sections for simplified models, which provide a generic description of the production and decay of new particles in specific, topology based final states.Article Citation - WoS: 1Staging Nişantaşı: Cultural Conflicts and Ideological Representations of Urban Space in Turkish Tv Culture(Springer, 2025) Catalbas, Zeynep Ceylan Gezer; Akpınar, İpek; Akpinar, IpekThis paper examines how urban spaces become sites of ideological contestation through their representation in popular media, focusing specifically on Ni & scedil;anta & scedil;& imath;, a historically significant neighborhood in Istanbul that embodies the class tensions within T & uuml;rkiye's modernization narrative. Drawing on cultural geography as a theoretical framework, the study analyzes how this distinctive urban space functions as both physical setting and symbolic element in post-2000 Turkish television dramas. Since the expansion of private broadcasting, these TV series have emerged as powerful agents in shaping public consciousness about space, class, and identity. Through semiotic analysis of selected programs, this research reveals how Ni & scedil;anta & scedil;& imath;'s portrayal constructs and reinforces social class distinctions in contemporary Turkish society. The findings demonstrate that urban geography serves as a reflective surface for cultural and social conflict, with television representations amplifying Ni & scedil;anta & scedil;& imath;'s multi-layered spatial identity formed through historical processes, societal dynamics, and personal narratives. By connecting these representations to broader patterns of class differentiation in T & uuml;rkiye, this study contributes to our understanding of how media portrayals of urban spaces simultaneously reflect and reinforce class distinction through collective social imaginaries.Article Citation - WoS: 1Citation - Scopus: 1Fabrication of Electrospun Polycaprolactone Nanofibrous Mats Loaded With Purple Basil Extract (Ocimum Basilicum L.) as Colorimetric Ph Indicator Films(Springer, 2025) Erez, Elif; Eroglu, Ahmet Emin; Bayramoglu, BesteIntelligent packaging with colorimetric pH indicators revolutionizes traditional food packaging by enabling real-time food quality monitoring. This study used electrospinning to develop pH indicator films from polycaprolactone (PCL) incorporating purple basil extract (PBE). Nanofibrous films containing 0.2% PBE (PCLN_0.2PBE), 0.4% PBE (PCLN_0.4PBE), and 0.6% PBE (PCLN_0.6PBE) were fabricated using different electrospinning conditions. The PCLNs fabricated with a voltage of 20 kV and a flow rate of 1.6 mL/h exhibited the most uniform and bead-free morphology according to scanning electron microscopy. The chemical, thermal, mechanical, and wetting characterization of the films was performed by Fourier transform infrared spectroscopy, differential scanning calorimetry, thermal gravimetric analysis, texture analysis, and contact angle analysis, respectively. Both PCLN_0.4PBE and PCLN_0.6PBE films displayed fast (4-5 s) and clear color transitions (Delta E > 3.5) to successive pH buffers within the range critical for food deterioration, while they exhibited excellent color changes (Delta E > 5) for pH variations of at least two units. The PCLN_0.6 PBE film displayed a Delta E of similar to 5 in only 5 min of exposure to ammonia vapor, whereas PCLN_0.4PBE showed a similar color change for over 15 min. The interaction between the films and acidic and alkaline semi-solid foods was simulated using gelatin gels at pH 2.5 and 11, respectively. Both films displayed significant color transitions (Delta E > similar to 9) within 15 min of contact with the gels, with the response from PCLN_0.6 PBE being more pronounced. The color stability in both films was maintained for up to 14 days at 4 degrees C, offering potential early warnings against food spoilage. PBE release was evaluated against different food simulants. The highest release occurred in 50% ethanol; the films demonstrated resistance to 3% acetic acid. The findings indicate that electrospun PCL films integrated with PBE have a promising potential to serve as colorimetric pH indicators for monitoring the freshness of food products.