Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/11727/4809
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Item Searching For The Urine Osmolality Surrogate: An Automated Machine Learning Approach(2022) Topcu, Deniz Ilhan; Bayraktar, Nilufer; https://orcid.org/0000-0002-1219-6368; https://orcid.org/0000-0002-7886-3688; 000819864400001; E-3717-2019; Y-8758-2018Objectives Automated machine learning (AutoML) tools can help clinical laboratory professionals to develop machine learning models. The objective of this study was to develop a novel formula for the estimation of urine osmolality using an AutoML tool and to determine the efficiency of AutoML tools in a clinical laboratory setting. Methods Three hundred routine urinalysis samples were used for reference osmolality and urine clinical chemistry analysis. The H2O AutoML engine completed the machine learning development steps with minimum human intervention. Four feature groups were created, which include different urinalysis measurements according to the Boruta feature selection algorithm. Method comparison statistics including Spearman correlation, Passing-Bablok regression analysis were performed, and Bland Altman plots were created to compare model predictions with the reference method. The minimum allowable bias (24.17%) from biological variation data was used as the limit of agreement. Results The AutoML engine developed a total of 183 ML models. Conductivity and specific gravity had the highest variable importance. Models that include conductivity, specific gravity, and other urinalysis parameters had the highest R-2 (0.70-0.83), and 70-84% of results were within the limit of agreement. Conclusions Combining urinary conductivity with other urinalysis parameters using validated machine learning models can yield a promising surrogate. Additionally, AutoML tools facilitate the machine learning development cycle and should be considered for developing ML models in clinical laboratories.Item Serum endocan levels in fresh IVF/ICSI cycles in women with endometriosis: a comparative prospective study(2022) Ceran, Mehmet Ufuk; Yilmaz, Nafiye; Colak, Eser; Bayraktar, Nilufer; Tohma, Yusuf Aytac; Zeyneloglu, Hulusi BulentBackground: The current study tested the level of endocan, which is thought to have an effective role in both endothelial dysfunction and inflammation, in infertile women with endometriosis treated with in vitro fertilizationlintracytoplasmic sperm injection (IVF/ICSI). It is based on the hypothesis of chronic inflammation in the pathophysiology of endometriosis. Methods: This prospective case control study included a total of 64 women who were in the IVF/ICSI program. The women were divided into two groups: endometriosis (n = 32) and non-endometriosis (n = 32). Their baseline characteristics, stimulation parameters, and IVF/ICSI outcomes (clinical pregnancy and live birth rates) were recorded. Blood samples collected at the beginning of the IVE cycle for endocan levels were analyzed with a sandwich enzyme immunoassay and the results were documented. Results: The endocan levels in the endometriosis group were significantly higher than those in the non-endometriosis group, i.e., 5010 pg/mL and 2738 pg/mL, respectively (p < 0.05). A significant weakly positive correlation was found between endocan levels and the presence of endometriosis (p < 0.05, r: 0.284). The cut-off value for endometriosis was determined as 4693 pg/mL with a sensitivity of 53.13% and a specificity of 78.12%. Clinical pregnancy was insignificantly higher in the non-endometriosis group (p = 0.079). However, live birth rates were significantly higher in the non-endometriosis group (p < 0.05). No correlation was found between clinical pregnancy and live birth rate and endocan levels (p > 0.05). Conclusion: High endocan levels were detected in women who underwent IVF/ICSI treatment for endometriosis and infertility and there was a positive correlation between them. However, there was no relationship between endocan levels and IVF/ICSI outcomes.Item Severe chronic periodontitis is not common in Acromegaly: Potential protective role of gingival BMP-2(2021) Bascil, Sibel; Turhan Iyidir, Ozlem; Bayraktar, Nilufer; Ertorer, Melek Eda; Bascil Tutuncu, Neslihan; 0000-0002-0225-2477; 0000-0001-5305-6807; 0000-0002-7886-3688; 0000-0001-7357-8709; 0000-0002-1816-3903; 33421969; K-7904-2019; Y-8758-2018; ABI-3705-2020; ABG-5027-2020Background/aim : Advanced chronic periodontitis is observed rarely in acromegaly. Periodontal tissue including the alveolar bone is seemed to be spared from the systemic metabolic derangements of bone in this patient population. Chronic elevation of growth hormone, IGF-1, and bone morphogenetic proteins may play a role in periodontal tissue regeneration in acromegalics. In this study, we aimed to evaluate the potential roles of local gingival bone morphogenetic proteins (BMP) in periodontal tissue pathology in acromegaly. Materials and methods: Thirty-five patients with acromegaly and 22 healthy subjects were recruited. All the participants were examined by the same periodontologist for the diagnosis of periodontal diseases. BMP-2 and-4 were studied in gingival crevicular fluid. Results: Gingival BMP-2 and BMP-4 levels were similar in acromegaly and control groups in general, with and without chronic periodontitis. For all the participants, gingival BMP-2 levels were statistically lower in those participants with chronic periodontitis then those without periodontitis (29.4 +/- 11.2 vs. 41.2 +/- 23.2, respectively, p = 0.027). Causal relation between the gingival BMP levels and periodontal tissue health status was tested with one way ANOVA which revealed a significant difference between gingival BMP-2 levels in those with different degrees of periodontal tissue pathology (p = 0.025). When analyzed separately, gingival BMP-2 levels revealed a causal relation with the degree of periodontal pathology with borderline significance only in patients with acromegaly (p = 0.057). Conclusion: Acromegaly is a disease with an unexpectedly low frequency of advanced periodontitis, irrespective of the long disease duration and pathognomonic oral manifestations. BMP-2 might have a protective role against chronic advanced periodontitis in these patients.Item Detection of COVID-19 by Machine Learning Using Routine Laboratory Tests(2021) Cubukcu, Hikmet Can; Topcu, Deniz Ilhan; Bayraktar, Nilufer; Gulsen, Murat; Sari, Nuran; Arslan, Ayse Hande; 0000-0002-1219-6368; 0000-0002-7886-3688; 34791032; E-3717-2019; Y-8758-2018Objectives The present study aimed to develop a clinical decision support tool to assist coronavirus disease 2019 (COVID-19) diagnoses with machine learning (ML) models using routine laboratory test results. Methods We developed ML models using laboratory data (n = 1,391) composed of six clinical chemistry (CC) results, 14 CBC parameter results, and results of a severe acute respiratory syndrome coronavirus 2 real-time reverse transcription-polymerase chain reaction as a gold standard method. Four ML algorithms, including random forest (RF), gradient boosting (XGBoost), support vector machine (SVM), and logistic regression, were used to build eight ML models using CBC and a combination of CC and CBC parameters. Performance evaluation was conducted on the test data set and external validation data set from Brazil. Results The accuracy values of all models ranged from 74% to 91%. The RF model trained from CC and CBC analytes showed the best performance on the present study's data set (accuracy, 85.3%; sensitivity, 79.6%; specificity, 91.2%). The RF model trained from only CBC parameters detected COVID-19 cases with 82.8% accuracy. The best performance on the external validation data set belonged to the SVM model trained from CC and CBC parameters (accuracy, 91.18%; sensitivity, 100%; specificity, 84.21%). Conclusions ML models presented in this study can be used as clinical decision support tools to contribute to physicians' clinical judgment for COVID-19 diagnoses.Item Endothelial dysfunction and insulin resistance in young women with polycystic ovarian syndrome(2014) Yavuz Taslipinar, Mine; Kilic, Nedret; Bayraktar, Nilufer; Guler, Ismail; Gulcan Kurt, Yasemin; Goktas, Tayfun; Taner, Mehmet Zeki; Himmetoglu, Mehmet Ozdemir; Yaman, Halil; Taslipinar, Abdullah; 25539546Background/aim: To evaluate whether there is a correlation between insulin resistance and nitric oxide-related endothelial dysfunction in patients with polycystic ovarian syndrome (PCOS). Materials and methods: The study was conducted with 25 young women with PCOS and 25 young healthy women, between 18 and 35 years of age. Plasma asymmetric dimethylarginine (ADMA) levels, serum nitric oxide (NO) levels, and homeostatic model assessment of insulin resistance (HOMA-IR) rates were measured in both the patient and control groups. Results: Plasma ADMA levels were significantly higher in PCOS patients than in the controls (P = 0.001). Serum NO levels were significantly lower in patients than in the controls (P = 0.008). The HOMA-IR rates, accepted as an insulin resistance parameter, were significantly higher in patients than in the controls (P = 0.001). Conclusion: Results of the present study indicate that, independent of age, body mass index, and blood lipid profile, there is significant insulin resistance in PCOS patients. However, no correlation was found between HOMA-IR as an insulin resistance determinant and altered ADMA and NO levels. This finding may indicate that there are additional mechanisms of cardiovascular risks in PCOS patients other than insulin resistance.Item Serum Neuron-specific Enolase Levels in Preterm and Term Newborns and in Infants 1-3 Months of Age(2015) Abbasoglu, Aslihan; Sarialioglu, Faik; Yazici, Nalan; Bayraktar, Nilufer; Haberal, Aysegul; Erbay, Ayse; 25315754Background: Elevated serum levels of neuron-specific enolase (NSE) was initially assumed to be specific to neuronal tumors (particularly neuroblastoma), but is now known to accompany nontumoral conditions and tumors other than neuroblastomas. There is a need to establish normal ranges for NSE, especially in early infancy. The aims of this study were to determine reference values for NSE in newborns and young infants and to assess whether NSE levels in early infancy (i.e., preterm infants and term infants) differ from the adult reference range for this enzyme. Methods: We enrolled 140 healthy babies, which included 40 preterm newborns (3-15 days old and born at 28-42 weeks gestation), 40 term newborns (< 1 month old and born at term), and 60 young infants 1-3 months old (n = 20 per subgroup of 1-, 2-, and 3-month-old infants). The determination of NSE levels was performed by the electrochemiluminescence immunoassay (ECLIA) method using the Elecysys 2010 device (Roche Diagnostics, Mannheim, Germany). The mean serum NSE levels for the preterm newborns was 21.83 +/- 15.06 ng/mL [95% confidence interval (95%Cl), 16.95-26.71 ng/mL]; term newborns, 18.06 +/- 12.83 ng/mL (95%Cl, 13.94-22.19 ng/mL); and young infants, 9.09 +/- 4.38 ng/mL (95%Cl, 7.96 -10.23 ng/mL). The mean serum NSE level for infants 1-3 months old was within the ECLIA kit's normal range (4.7-18 ng/mL for adults), whereas the corresponding means for the preterm and term newborns were higher (p < 0.001, for both). Conclusion: Our findings suggest that adult reference values should not be applied to the pre-term and term age groups. Copyright (C) 2014, Taiwan Pediatric Association. Published by Elsevier Taiwan LLC. All rights reserved.Item Comparison of Carvedilol and Metoprolol for Preventing Contrast-Induced Nephropathy after Coronary Angiography(2015) Yilmaz, Mustafa; Aydinalp, Alp; Okyay, Kaan; Tekin, Abdullah; Bal, Ugur Abbas; Bayraktar, Nilufer; Yildirir, Aylin; Muderrisoglu, Haldun; 26195972Aims: Contrast-induced nephropathy (CIN) is one of the most common causes of hospital-acquired acute renal failure. Oxidative stress and vasoconstriction might play key roles in its pathogenesis. In a few experimental models, antioxidant properties of carvedilol have been documented. The aim of this study was to analyze and compare the effects of carvedilol and metoprolol on the development of CIN in patients undergoing coronary angiography. Methods: One hundred patients currently taking metoprolol and 100 patients currently taking carvedilol were enrolled into the study. Venous blood samples were obtained before and 48 h after contrast administration. Cystatin C and malondialdehyde values were examined and compared. CIN was defined as a creatinine increase of at least 25% or 0.5 mg/dl from the baseline value. Results: Seven patients in the carvedilol group (7%) and 22 patients in the metoprolol group (22%) developed CIN (p = 0.003). In the metoprolol group, the median cystatin C concentration increased significantly from 978 to 1,086 ng/ml (p = 0.001) 48 h after radiocontrast administration. In the carvedilol group, the median cystatin C concentration did not change significantly (1,143 vs. 1,068 ng/ml; p = 0.94). In the metoprolol group, the mean malondialdehyde concentration increased significantly from 7.09 +/- 1.48 to 8.38 +/- 2.6 nmol/l (p < 0.001). In the carvedilol group, the mean serum malondialdehyde concentration did not change significantly (7.44 +/- 1.21 vs. 7.56 +/- 1.11 nmol/l; p = 0.59). Conclusion: When compared to metoprolol, carvedilol might decrease oxidative stress and subsequent development of CIN. (C) 2015 S. Karger AG, BaselItem Alternative tumor markers in the diagnosis of ovarian cancer(2016) Karakaya, Burcu Kisa; Baser, Eralp; Bildaci, Berk; Comert, Esra Cabuk; Bayraktar, Nilufer; Dursun, Polat; Kuscu, Esra; Ayhan, Ali; 0000-0002-0992-6980; 0000-0002-7886-3688; 27629130; AAI-8792-2021; Y-8758-2018; AAJ-5802-2021Objective: The aim of the study was to assess the usefulness of various tumor markers (CA125, HE4, bcl2) measured in serum, urine and saliva in the differential diagnosis of adnexal masses. Material and methods: Our study was conducted at the Baskent University Medical School, Department of Obstetrics and Gynecology, Ankara, Turkey, between November 2010 and March 2011. Fifty patients with a suspicion of malignant adnexal mass and 30 controls were included in the study. Serum and urine CA-125, HE4, and bcl2 levels were evaluated for their role in the diagnosis of epithelial ovarian cancer (EOC). Results: Serum CA-125 and HE4 levels, and urine HE4 levels were significantly higher in malignant cases as compared to controls (p < 0.05). Mean levels of bcl2 in saliva and urine were similar in malignant cases and controls (p > 0.05). Conclusions: We demonstrated that serum CA125, serum HE4 and urine HE4 levels were elevated in patients with ovarian cancer. These findings should be assessed in future studies with larger sample sizes in order to reach more definite conclusions.Item Cystatin-C and TGF-beta levels in patients with diabetic nephropathy(2016) Takir, Mumtaz; Unal, Asli Dogruk; Kostek, Osman; Bayraktar, Nilufer; Demirag, Nilgun Guvener; 0000-0002-7886-3688; 27745866; Y-8758-2018Objective: To evaluate renal impairment in type 2 diabetic patients with normoalbuminuria or microalbuminuria by detection of serum cystatin C and serum and urinary TGF-beta levels. Methods: Cross-sectional study conducted at the Department of Endocrinology in Baskent University School of Medicine. Patients with type 2 diabetes mellitus without known overt diabetic nephropathy were included in the study. Recruited patients were stratified into four groups, matched in terms of age, gender, microalbuminuria level and estimated GFR calculated with MDRD. Results: 78 patients were enrolled. They were categorized into four groups depending on their urinary albumin excretion and estimated glomerular filtration rate. Macrovascular complication was found to be higher in patients with microalbuminuria than in other patients (p < 0.01), but there were no differences in terms of other diabetic complications. Serum cystatin C level was significantly higher in normoalbuminuric group one patients, while serum and urinary TGF-beta 1 levels were higher in microalbuminuric group two patients. The serum level of cystatin C was found to negatively correlate with eGFR in group two patients (r = -0.892, p < 0.001). Finally, there was a negative correlation between eGFR and cystatin C in all the patient groups (r = -0.726, p=0.001). Conclusions: Although urinary albumin excretion is recommended for the detection of type two diabetic nephropathy, there is a group of patients with decreased eGFR but without increased urinary albumin excretion, in which serum cystatin C level was indicated to be used as an early biomarker of diabetic nephropathy. (C) 2016 Published by Elsevier Espana, S.L.U. on behalf of Sociedad Espanola de Nefrologia.