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Öğe Time-dependent lateral diffusion in WO3 thin films(Elsevier, 2023) Karakurt, İsmail; Başar, Günay; Leiderer, Paul; Parlatan, Şeyma; Arapoğlu, NihanWe have studied the anomalous lateral diffusion process in thin tungsten trioxide films by optical means. The diffusion process seems to start at imperfections within the film a few seconds after the H ion intercalation begins, and progresses parallel to the surface of the film. We measured the mean square displacement of the diffusion front and used its time-dependence to calculate the instantaneous diffusion coefficient. The anomalous exponents are found to be 2.24 and 2.92 for 400 nm and 270 nm thick films, respectively. We explain the observed large diffusion coefficients and depth dependence of the expansion of the film by interfacial job-sharing diffusion of electrons and protons. Raman measurements were also carried out on virgin films, and on films after the lateral diffusion. Although the observed spectrum after the lateral diffusion is, in general, consistent with the literature for H intercalated films, we observe an additional strong band at 855 cm?1. This lateral diffusion process is observed to be irreversible; therefore, it has to be avoided in electrochromic switching devices based on WO.Öğe Determination of protein amount in nanosized synthetic liposomes by Surface Enhanced Raman Spectroscopy (SERS)(Çanakkale Onsekiz Mart University, 9) Parlatan, ŞeymaAccurate characterization of synthetic liposomes is essential since they give information about the vesic ular structures in bodily fluids such as extracellular vesicles. The characterization tasks are generally the determina tion of the sizes of the liposomes and the profiling of the liposomes' content. Optical tweezers and Surface Enhanced Raman Spectroscopy (SERS) were used to profile the nanosized liposomes. The size distribution of the trapped lip osomes (140 nm on average) was found by using Einstein's Brownian motion equation, consistent with the size dis tribution obtained from dynamic light scattering measurements. Besides, Gramicidin-encapsulated liposomes were measured using SERS, and statistically significant differentiation was found in Raman intensities between liposome populations with altering concentrations of proteins. This study uniquely measured size distributions of nano-sized liposomes with conventional optical tweezers (without plasmonics) and determined the chemical differences between empty and protein encapsulated liposomes with high accuracy using Raman spectroscopy.Öğe Malign mezotelyomada kemoterapi uygulamaları(DergiPark, 2022) Işık, Ulaş; Şimşek, Melih; Gürbüz, OrkunAmaç: Malign mezotelyoma, mezotel hücrelerinden kaynaklanan agresif bir malignitedir. Prognozu kötüdür ve medyan genel sağkalım 12 aydır. Malign plevral mezotelyomanın altta yatan en önemli nedeni daha önceki asbest maruziyetidir. Bu çalışmada malign mezotelyoma tanısı olan hastaların demografik özellikleri ve tedavi sonuçlarının değerlendirilmesi amaçlandı. Gereç ve Yöntem: Çalışmada tıbbi onkoloji bölümüne Ocak 2009 ile Mayıs 2020 tarihleri arasında başvuran malign mezotelyoma tanılı hastaların verileri retrospektif olarak değerlendirildi. Toplam 26 hastanın verilerine ulaşıldı. Veriler hasta dosyalarından ve dijital veri işleme sisteminden elde edildi. Verilerin değerlendirilmesinde istatistiksel analiz programı kullanıldı. Yüzde ve ortalamalar ile dağılımları hesaplandı. Bulgular: Hastaların medyan yaşı 65 (33-80) ve ortalama yaşı 61,8±12,9 idi. Hastaların sekizi erkek ve 18’i kadındı. Hastaların hiçbirinde mesleki asbest maruziyeti öyküsü yoktu. En sık etkilenen bölge plevraydı. Bir bifazik, bir sarkomatoid ve 24 epiteloid malign mezotelyoma vardı. Evre 1 hastalığı olan dört, evre 2 hastalığı olan bir, evre 3 hastalığı olan yedi ve evre 4 hastalığı olan 14 hasta mevcuttu. İlk sıra tedavide en çok pemetrekset-sisplatin kombinasyonu tercih edilirken, ikinci sırada en çok kullanılan tedavi tek ajan gemsitabin idi. Sonuç: Bu çalışmada, topraktaki asbest nedeniyle Türkiye’nin endemik bir bölgesinden gelen malign mezotelyoma hastalarının verileri değerlendirildi. Bu veriler ışığında, literatür ile uyumlu sağkalım sonuçları ve literatüre uygun tedavilerin yapıldığı sonucuna varıldı. Gelecekteki çalışmalarla farklı coğrafi bölgelerden elde edilecek veriler, hastalığın ortaya çıkışını önlemeye ve daha etkili tedavi stratejileri ile daha iyi klinik sonuçlara ulaşılmasına yardımcı olacaktır.Öğe Atrial fibrillation designation with micro-Raman spectroscopy and scanning acoustic microscope(Nature Research, 2022) Parlatan, Uğur; Parlatan, Şeyma; Şen, Kübra; Keçoğlu, İbrahim; Ulukan, Mustafa Özer; Karakaya, Atalay; Erkanlı, Korhan; Türkoğlu, Halil; Uğurlucan, Murat; Ünlü, Mehmet Burçin; Tanören, BukemAtrial fibrillation (AF) is diagnosed with the electrocardiogram, which is the gold standard in clinics. However, sufficient arrhythmia monitoring takes a long time, and many of the tests are made in only a few seconds, which can lead arrhythmia to be missed. Here, we propose a combined method to detect the effects of AF on atrial tissue. We characterize tissues obtained from patients with or without AF by scanning acoustic microscopy (SAM) and by Raman spectroscopy (RS) to construct a mechano-chemical profile. We classify the Raman spectral measurements of the tissue samples with an unsupervised clustering method, k-means and compare their chemical properties. Besides, we utilize scanning acoustic microscopy to compare and determine differences in acoustic impedance maps of the groups. We compared the clinical outcomes with our findings using a neural network classification for Raman measurements and ANOVA for SAM measurements. Consequently, we show that the stiffness profiles of the tissues, corresponding to the patients with chronic AF, without AF or who experienced postoperative AF, are in agreement with the lipid-collagen profiles obtained by the Raman spectral characterization. © 2022, The Author(s).Öğe Raman tweezers as an alternative diagnostic tool for paroxysmal nocturnal hemoglobinuria(2021) Soysal, Kaan Batu; Parlatan, Şeyma; Mastanzade, Metban; Özbalak, Murat; Yenerel, Mustafa Nuri; Ünlü, Mehmet Burçin; Başar, Günay; Parlatan, UğurParoxysmal nocturnal hemoglobinuria (PNH) is a rare disease characterized by hemolysis of red blood cells (RBC) and venous thrombosis. The gold standard method for the diagnosis of this disease is flow cytometry. Here, we propose a combined optical tweezers and Raman spectral (Raman tweezers) approach to analyze blood samples from volunteers with or without PNH conditions. Raman spectroscopy is a well-known method for investigating a material's chemical structure and is also used in molecular analysis of biological compounds. In this study, we trap individual RBCs found in whole blood samples drawn from PNH patients and the control group. Evaluation of the Raman spectra of these cells by band component analysis and machine learning shows a significant difference between the two groups. The specificity and the sensitivity of the training performed by support vector machine (SVM) analysis were found to be 81.8% and 78.3%, respectively. This study shows that an immediate and high accuracy test result is possible for PNH disease by employing Raman tweezers and machine learning.Öğe Endogenous retrovirus HERV-K6 and HERV-K11 polymorphisms’ analyses in head and neck squamous cell carcinoma patients(Elsevier B.V., 2021) Karlık, Elif; Gürbüz, Orkun; Yıldız, Yemliha; Gözükırmızı, NerminMany tumors, such as melanoma, breast cancer, germ cell tumors, renal cancer or ovarian cancer, express HERV proteins, mainly HERV-K (HML6) and HERV-K (HML2). However, there is no report showing any relation between squamous cell carcinoma of head and neck (HNSCC) and HERVs in literature. Here we report the polymorphic changes of HERV-K6 and HERV-K11 in tumor tissue samples of HNSCC patients comparing with healthy individuals. For this purpose, genomic DNAs from tumor tissue samples of 2 healthy individuals and of 8 HNSCC patients were isolated and IRAP-PCR was performed. IRAP-PCR analyses demonstrated that there were 18–73% polymorphism rates for HERV-K6 and 38–100% polymorphism rates for HERV-K11 among all the samples. There were also polymorphic changes between two control materials. Therefore, HERV-K6 polymorphisms may arise on an individual-specific basis. In the previous studies, some associations have been reported between the expression of HERVs and some cancer types or other major diseases. However, few reports have analyzed HERV-K movements among HNSCC patients. This report is the first study investigating HERV-K6 and HERV-K11 retrotransposon polymorphic changes in HNSCC patients.
