PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 2Citation - Scopus: 2Tuning the Solid Phase Fluorescence Emission From Long Wavelength Visible To Near-Infrared in Oxazol-5 Derivatives: Structure–property Relationship, Theoretical and Experimental Studies(Springer, 2023) Nazlı, İbrahim Hanif; Yakalı, Gül; Topkaya, Derya; İzmirli, Merve; Uzun, Sema Demirci; Alp, SerapMost of the fluorescent molecules among organic π-conjugated materials show blue or green emission in the solid phase but few of them emit red-shifted visible and near-infrared light in the material science. To create molecules emitting for this feature, two π-conjugated oxazol-5-one derivatives containing donor (OCH3) and acceptor groups (NO2) were synthesized. Their optical and charge-transport properties were investigated through experimental and theoretical methods including the single crystal X-ray crystallography, Hirshfeld Surface Analysis, photophysical studies and Density Functional Theory (DFT), respectively. In addition, FT-IR, 1H-NMR, 13C-NMR spectroscopy, cyclic voltammetry (CV) measurements were performed. According to our results, both molecules may provide the significant pathway of development of long wavelength visible and red emissive features in solid phase with the aggregation induced enhanced emission (AIEE) properties particularly in the fields of OLEDs, optical communication, defence and bioimaging.Article Citation - WoS: 11Citation - Scopus: 12Investigation of the Best Possible Methods for Wind Turbine Blade Waste Management by Using Gis and Fahp: Turkey Case(Springer, 2022) Öztürk, Samet; Karipoğlu, FatihThe aim of this study is to present the status and projections of wind turbine blade retirement in Turkey; to investigate the number of retiring WT blades in the regional, manufacturer, and material aspects; and to discuss the management methods for retired WT blades. To determine the best possible wind turbine blade waste management methods for Turkey, a combined application of Geographical Information Systems (GIS) and the Fuzzy Analytical Hierarchy Process (FAHP) is used in this study. It is found that around nine thousand WT blades will become waste between 2020 and 2039 in Turkey, corresponding to around 80,500 tons of waste. On average, 52,325 tons of glass/carbon and 28,175 tons of polymers will be accumulated between 2020 and 2039 from wind turbine blades. More than half of the WT blade waste will come from two WT manufacturers, namely, Enercon and Nordex. Aegean and Marmara regions will provide 74% of the blade waste, where 33% of them will be 2 MW and 2.5 MW sizes of WT blades. Furthermore, a case study is applied to Izmir city to demonstrate the results of FAHP for finding the best available method to dispose of WT blades. The results show that using blade waste as filling material is the best alternative, while waste-to-energy is the last favorable option for blade waste management. Finally, sensitivity analyses are applied to demonstrate the robustness of the results for the inclusion of new alternatives and the bias of experts’ judgments.Article Citation - WoS: 14Citation - Scopus: 18The use of video clickstream data to predict university students’ test performance: A comprehensive educational data mining approach(Springer, 2022) Yürüm, Ozan Raşit; Taşkaya Temizel, Tuğba; Yıldırım, SonerVideo clickstream behaviors such as pause, forward, and backward offer great potential for educational data mining and learning analytics since students exhibit a significant amount of these behaviors in online courses. The purpose of this study is to investigate the predictive relationship between video clickstream behaviors and students’ test performance with two consecutive experiments. The first experiment was performed as an exploratory study with 22 university students using a single test performance measure and basic statistical techniques. The second experiment was performed as a conclusive study with 16 students using repeated measures and comprehensive data mining techniques. The findings show that a positive correlation exists between the total number of clicks and students’ test performance. Those students who performed a high number of clicks, slow backward speed or doing backwards or pauses achieved better test performance than those who performed a lower number of clicks, or who used fast-backward or fast-forward. In addition, students’ test performance could be predicted using video clickstream data with a good level of accuracy (Root Mean Squared Error Percentage (%RMSE) ranged between 15 and 20). Furthermore, the mean of backward speed, number of pauses, and number/percentage of backwards were found to be the most important indicators in predicting students’ test performance. These findings may help educators or researchers identify students who are at risk of failure. Finally, the study provides design suggestions based on the findings for the preparation of video-based lectures.Article Citation - WoS: 6Citation - Scopus: 8Intervention for Hepatic and Pulmonary Metastases in Breast Cancer Patients: Prospective, Multi-Institutional Registry Study-Imet, Protocol Mf 14-02(Springer, 2022) Soran, Atilla; Özbaş, Serdar; Özçınar, Beyza; Işık, Arda; Doğan, Lütfi; Şenol, Kazım; Dağ, Ahmet; Karanlık, Hasan; Aytaç, Özgür; Karadeniz Çakmak, Güldeniz; Dalcı, Kubilay; Doğan, Mutlu; Sezer, Atakan Y.; Gökgöz, Şehsuvar; Özyar, Enis; Sezgin, EfeBackground: One fourth of early-stage breast cancer cases become metastatic during the follow-up period. Limited metastasis is a metastatic disease condition in which the number of metastatic sites and the extent of the disease both are limited, and the disease is amenable to metastatic intervention. This prospective study aimed to evaluate intervention for limited metastases in the lung, liver, or both. Methods: The study enrolled luminal A/B and/or human epidermal growth factor receptor 2 (HER2)-neu+ patients with operable lung and/or liver metastases in the follow-up assessment after completion of primary breast cancer treatment and patients with a diagnosis of metastasis after 2014. Demographic, clinical, tumor-specific, and metastasis detection-free interval (MDFI) data were collected. Bone metastasis in addition to lung and liver metastases also was included in the analysis. The patients were divided into two groups according to the method of treatment for metastases: systemic therapy alone (ST) group or intervention (IT) group.Article Citation - WoS: 5Citation - Scopus: 5The Designing of a Gel Formulation With Chitosan Polymer Using Liposomes as Nanocarriers of Amphotericin B for a Non-Invasive Treatment Model of Cutaneous Leishmaniasis(Springer, 2022) Gürbüz, Nergiz; Çetin Uyanıkgil, Emel Öykü; Özbel, Yusuf; Töz, SerayPurpose Leishmaniasis is a disease caused by different Leishmania spp., which are transmitted to humans by a bite of infected female sand flies. Cutaneous leishmaniasis (CL, oriental sore), visceral leishmaniasis (VL), and mucocutaneous leishmaniasis (MCL) are three main clinical forms, however, only CL and VL are seen in Turkey. Cutaneous leishmaniasis is characterized by skin lesion(s) and is one of the most important vector-borne diseases in Turkey with over 2000 cases reported annually in 40 out of 81 provinces. The treatment is usually made invasively and painfully by intralesional injection of pentavalent antimony compounds. Non-invasive and innovative treatment methods are needed as aimed in this study. Methods In the present study, one of the classical antileishmanial drugs, amphotericin B (AmB), encapsulated in liposomes was evaluated using non-invasive design based on chitosan, which is a nontoxic, biocompatible and biodegradable polymer. To avoid the invasive effect of conventional intralesional needle application, the drug was encapsulated in liposomes and incorporated into a chitosan gel for applying topically on the skin lesion. The efficacy of encapsulation of amphotericin B into liposomes and the drug release from liposomes were studied. The chitosan gel was evaluated for viscosity, flowability, appearance and pH. The efficacy of the drug embedded into chitosan gel, liposomal AmB alone and chitosan gel alone in four different concentrations was also tested using Leishmania spp. promastigotes in vitro. Results The findings have shown that AmB was encapsulated into the liposomes with high efficiency (86.6%) and long-term physical and chemical stability. Therefore, designed liposomal formulation was suitable for sustained release. The appearance of the drug-embedded chitosan gel was transparent and appropriate. Chitosan gels showed non- Newtonian behavior and plastic flow. The liposomal AmB also showed higher efficacy with no parasites in all concentrations while drug embedded into chitosan gel and chitosan gel alone were effective in two higher concentrations. The lower efficacy of the drug-embedded chitosan gel in 24 h in in-vitro study was probably due to slow release of the drug. Conclusion The gel design created in this study will provide ease of use for the lesions of CL patients that do not have a specific number, size, and shape. Follow-up studies by the ex-vivo macrophage infection model with Leishmania intracellular amastigote forms and Leishmania-infected animal models are needed to understand the present design's efficacy better.Article Citation - WoS: 7Citation - Scopus: 7Connexin 32 Overexpression Increases Proliferation, Reduces Gap Junctional Intercellular Communication, Motility and Epithelial-To Transition in Hs578t Breast Cancer Cells(Springer, 2022) Uğur, Deniz; Güngül, Taha Buğra; Yücel, Simge; Özçivici, Engin; Yalçın Özuysal, Özden; Meşe Özçivici, GülistanConnexins (Cx) are primary components of gap junctions that selectively allow molecules to be exchanged between adjacent cells, regulating multiple cellular functions. Along with their channel forming functions, connexins play a variety of roles in different stages of tumorigenesis and their roles in tumor initiation and progression is isoform- and tissue-specific. While Cx26 and Cx43 were downregulated during breast tumorigenesis, Cx32 was accumulated in the cytoplasm of the cells in lymph node metastasis of breast cancers and Cx32 was further upregulated in metastasis. Cx32's effect on cell proliferation, gap junctional communication, hemichannel activity, cellular motility and epithelial-to-mesenchymal transition (EMT) were investigated by overexpressing Cx32 in Hs578T and MCF7 breast cancer cells. Additionally, the expression and localization of Cx26 and Cx43 upon Cx32 overexpression were examined by Western blot and immunostaining experiments, respectively. We observed that MCF7 cells had endogenous Cx32 while Hs578T cells did not and when Cx32 was overexpressed in these cells, it caused a significant increase in the percentages of Hs578T cells at the S phase in addition to increasing their proliferation. Further, while Cx32 overexpression did not induce hemichannel activity in either cell, it decreased gap junctional communication between Hs578T cells. Additionally, Cx32 was mainly observed in the cytoplasm in both cells, where it did not form gap junction plaques but Cx32 overexpression reduced Cx43 levels without affecting Cx26. Moreover, migration and invasion potentials of Hs578T and migration in MCF7 were reduced upon Cx32 overexpression. Finally, the protein level of mesenchymal marker N-cadherin decreased while epithelial marker ZO-1 and E-cadherin increased in Hs578T cells. We observed that Cx32 overexpression altered cell proliferation, communication, migration and EMT in Hs578T, suggesting a tumor suppressor role in these cells while it had minor effects on MCF7 cells.Article Citation - WoS: 8Citation - Scopus: 8Association Analysis of Germination Level Cold Stress Tolerance and Candidate Gene Identification in Upland Cotton (gossypium Hirsutum L.)(Springer, 2022) Akköse Baytar, Asena; Peynircioğlu, Ceng; Sezener, Volkan; Frary, Anne; Doğanlar, SamiCotton originated from ancestors in the Gossypium genus that grew in semi-desert habitats. As a result, it is adversely affected by low temperatures especially during germination and the first weeks of growth. Despite this, there are relatively few molecular studies on cold stress in cotton. This limitation may present a future breeding handicap, as recent years have witnessed increased low temperature damage to cotton production. Cold tolerance is a sustainable approach to obtain good production in case of extreme cold. In the present study, 110 Upland cotton (Gossypium hirsutum) genotypes were evaluated for cold tolerance at the germination stage. We identified vigorous genotypes with cold-related parameters that outperformed the panel’s average performance (x¯ = 76.9% CG, 83.9% CSI, 167.5 CWVI). Molecular genetic diversity analysis with 101 simple sequence repeat (SSR) markers yielding 416 loci was used to select tolerant genotypes that could be important materials for breeding this trait. A total of 16 marker-cold tolerance trait associations (p < 0.005) were identified with 10 of them having major effects (PVE > 10%). Based on the positions of these markers, candidate genes for cold tolerance in the G. hirsutum genome were identified. Three of these markers (BNL0569, CIR081 and CIR202) are important candidates for use in marker-assisted breeding for cold tolerance because they mapped to genes previously associated with cold tolerance in other plant species such as Arabidopsis thaliana, rice and tomato.Article Citation - WoS: 6Citation - Scopus: 5Excessive Replacement Changes Drive Evolution of Global Sheep Prion Protein (prnp) Sequences(Springer, 2022) Sezgin, Efe; Teferedegn, Eden Yitna; Ün, Cemal; Yaman, YalçınSheep prion protein (PRNP) is the major host genetic factor responsible for susceptibility to scrapie. We aimed to understand the evolutionary history of sheep PRNP, and primarily focused on breeds from Turkey and Ethiopia, representing genome-wise ancient sheep populations. Population molecular genetic analyses are extended to European, South Asian, and East Asian populations, and for the first time to scrapie associated haplotypes. 1178 PRNP coding region nucleotide sequences were analyzed. High levels of nucleotide diversity driven by extensive low-frequency replacement changes are observed in all populations. Interspecific analyses were conducted using mouflon and domestic goat as outgroup species. Despite an abundance of silent and replacement changes, lack of silent or replacement fixations was observed. All scrapie-associated haplotype analyses from all populations also showed extensive low-frequency replacement changes. Neutrality tests did not indicate positive (directional), balancing or strong negative selection or population contraction for any of the haplotypes in any population. A simple negative selection history driven by prion disease susceptibility is not supported by the population and haplotype based analyses. Molecular function, biological process enrichment, and protein-protein interaction analyses suggested functioning of PRNP protein in multiple pathways, and possible other functional constraint selections. In conclusion, a complex selection history favoring excessive replacement changes together with weak purifying selection possibly driven by frequency-dependent selection is driving PRNP sequence evolution. Our results is not unique only to the Turkish and Ethiopian samples, but can be generalized to global sheep populations.