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Öğe Analysis of follicular fluid and serum markers of oxidative stress in women with unexplained infertility by Raman and machine learning methods(Wiley, 2023) Depciuch, Joanna; Paja, Wieslaw; Pancerz, Krzysztof; Uzun, Ozgur; Bulut, Huri; Tarhan, Nevzat; Guleken, ZozanOocytes are surrounded by a fluid called follicular fluid, which provides an essential microenvironment for developing oocytes in human fertility. Various molecules exist in antral follicles, including proteins, steroid hormones, polysaccharides, metabolites, reactive oxygen species, and antioxidants. Oxidative stress is involved in the etiology of defective oocyte development or poor oocyte and embryo quality. Raman spectroscopy, a noninvasive method, can be used for biological diagnostics and direct chemical identification of follicular fluid. Therefore, we measured the oxidative index of follicular fluids and then attempted Raman spectroscopy on the follicular fluids combined with machine learning techniques to identify, detect, and quantify follicular fluid of unexplained infertility-diagnosed women as a safe and effective tool to use as adjacent for clinical studies. This was a retrospective study set in an academic hospital where the patients were selected from an unexplained infertility-diagnosed population in the in vitro fertilization (IVF) center. Raman spectra of 128 follicular fluid samples (n = 63 control; and 65 unexplained infertility) were obtained. To profile Raman-based results of follicular fluid, oxidative load measurements, multivariate analysis, correlation tests, and six machine learning methods were used. Raman bands associated with oxidative load and amide III and lipids differed significantly. Classification using stacks of Raman signals was applied by random forest, C5.0 decision tree algorithm, k-nearest neighbors, deep neural networks, support vector machine, and XGBoost trees algorithms achieved an overall accuracy of 92.04% to 99.17% in assigned correctly. Group has an oxidative load in their follicle fluids consistent with clinical results and biochemical measurements and performing testing based on Raman spectra validated by kNN clustering and SVM object vector separation machine learning methods. The study suggests that Raman spectroscopy can detect changes in follicle fluid in unexplained infertility.Öğe Assessment of oxidative stress effects in serum determined by FT-IR spectroscopy in cholangiocarcinoma patients(AMG Transcend Association, 2023) Bulut, Huri; Tarhan, Nevzat; Büyük, Melek; Serin, Kürşat Rahmi; Ulukaya, Engin; Depciuch, Joanna; Parlinska-Wojtan, Magdalena; Güleken, ZozanCholangiocarcinoma (CCA) is a heterogeneous malignant tumor containing intrahepatic and extrahepatic bile ducts and gallbladder carcinoma. Mostly diagnosed at an advanced stage with a <5% cure chance. Early-stage diagnosis may increase the number of patients who reach curative treatment. Fourier Transform InfraRed (FT-IR) spectroscopy was used to detect chemical changes in serum collected from CCA patients vs. healthy individuals. The study aims to correlate the FTIR spectra with biochemical indices such as TAS, TOS, OSI, and total protein levels. Decreased TAS and increased TOS, OSI, and total protein levels in CCA patients vs. healthy individuals were found. FTIR spectra showed higher absorbance of the peaks corresponding to C–O and bending vibration of C–O–H groups in CCA patients, while more CH2 functional groups than lipids could be seen in the FTIR spectra of controls serum. PLS analysis showed IR ranges of 1500 cm-1 to 1700 cm-1, and 2700 cm-1 to 3000 cm-1 were able to distinguish between CCA from controls, respectively. PCA confirmed this, while HCA did not differentiate between CCA and those without the disease. Lipids and some functional groups changes caused by oxidative stress can be applied to predict CCA by using FTIR spectroscopy. © 2022 by the authors.Öğe Diagnosis of endometriosis using endometrioma volume and vibrational spectroscopy with multivariate methods as a noninvasive method(Elsevier Science, 2022) Güleken, Zozan; Bulut, Huri; Depciuch, Joanna; Tarhan, NevzatEndometriomas are typically an advanced form of endometriosis that leads to the formation of scar tissue, adhesions, and an inflammatory reaction. There is no certain serum marker for the diagnosis of endometriosis. This study aims to research the correlation between the amount of peaks corresponding to proteins and lipids with the volume of endometrioma and determine the chemical structure of blood serum collected from women suffering from endometriosis patients with endometrioma and healthy subjects using Fourier Transform Infrared (FTIR) spectroscopy. FTIR spectroscopy is used as a non-invasive diagnostic technique for the discrimination of endometriosis women with endometrioma and control blood sera. The FTIR spectra of 100 serum samples acquired from 50 patients and 50 healthy individuals were used for this study. For this purpose, multivariate analyses such as Principal Component Analysis (PCA), Partial Last Square analysis (PLS) with Variables Importance in Projection (VIP), and probability models, were performed. Our results showed that FTIR range 1500 cm-1 and 1700 cm-1 and around 2700 cm-1 - 3000 cm-1, regions may be used for the diagnosis of endometriosis. Also, we find that proteins and lipids fraction increase with the volume of endometrioma. Moreover, PLS and VIP analysis suggested that lipids could be helpful in the diagnosis of endometriosis women with endometrioma.Öğe Differential of cholangiocarcinoma disease using Raman spectroscopy combined with multivariate analysis(2022) Depciuch, Joanna; Parlinska-Wojtan, Magdalena; Serin, Kürşat Rahmi; Bulut, Huri; Ulukaya, Engin; Tarhan, Nevzat; Güleken, ZozanCholangiocarcinoma (CCA) is a type of cancer, which 5-year survival is lower than 20 %, and which is detected mostly in advanced stage of the disease. Unfortunately, there are no diagnostic tools, which could show changes in the body indicating the development of the disease. Therefore, in this study, we investigate Raman spectroscopy as a promising analytical tool in medical diagnostics and as a method, which would allow to distinguish between healthy patients and patients suffering from cholangiocarcinoma. The obtained Raman spectra showed, that lower intensities of peaks corresponding to amino acids and proteins, as well as higher intensities of peaks originating from lipids vibrations were observed in healthy individuals in comparison with cancer patients. Moreover, Partial Last Square (PLS), Principal Component Analysis (PCA) and Hierarchical Component Analysis (HCA) of Raman spectra indicate that the ranges between 800 cm-1 and 1800 cm-1, 3477 cm-1 -3322 cm-1 and 1394 cm-1 -1297 cm-1 allow to distinguish cancer patients from healthy ones. The obtained results showed, that Raman spectroscopy is a good candidate, to become in future one of the diagnostic tools of Cholangiocarcinoma.Öğe Spectrochemical and biochemical assay comparison study of the healing effect of the aloe vera and hypericum perforatum loaded nanofiber dressings on diabetic wound(Elsevier, 2021) Güleken, Zozan; Depciuch, Joanna; Ege, Hasan; İlbay, Gül; Kalkandelen, Cevriye; Özbeyli, Dilek; Bulut, Huri; Tarhan, Nevzat; Erdem Kuruca, SerapDiabetic wounds have a slow healing process and easy to be infected. In addition to current drug treatments, supportive approaches are needed for diabetic wound treatment. In this study, we aimed to load Aloe Vera (AV) and Hypericum perforatum oil (HPO) with PCL/Ge (Poly (?-caprolactone)/Gelatine) polymeric biodegradable by electrospinning method into nanofiber dressings on an experimental diabetic wound model to compare the diabetic wound healing effect. Changes in the amount and chemical structure of phospholipids, proteins, and lipids were investigated in the blood and serum samples of the animals using Fourier transform infrared (FTIR) analysis. To evaluate biological events associated with the wound repair process in inflammatory phase we used oxidant and antioxidant status to determine the healing status of wounds such as Total antioxidant status (TAS), Total oxidant level (TOS) and tumor necrosis factor alpha (TNF-?) levels. TOS level increased in DM groups and decreased in the AV and HPO group. Oxidative stress index decreased and TNF-? level increased in the HPO group. FTIR spectra showed changes in the phospholipids, proteins, and carbon chain of lipids in the whole blood as well as serum of DM rats. FTIR spectra combined with Principal component analysis (PCA) showed, that treated DM rats by AV and HPO caused return chemical structure of blood and serum to this observed in control group. Higher similarity with control group for HPO rats was observed. HPO is better than AV in the alternative for healing on diabetic wound. Thus, we have demonstrated that IR spectroscopy and multivariate data analysis and biochemical assays are consistent and correlative with each other.
