Yazar "Suner A." seçeneğine göre listele
Listeleniyor 1 - 12 / 12
Sayfa Başına Sonuç
Sıralama seçenekleri
Öğe Clustering methods for single-cell RNA-sequencing expression data: Performance evaluation with varying sample sizes and cell compositions(De Gruyter, 2019) Suner A.A number of specialized clustering methods have been developed so far for the accurate analysis of single-cell RNA-sequencing (scRNA-seq) expression data, and several reports have been published documenting the performance measures of these clustering methods under different conditions. However, to date, there are no available studies regarding the systematic evaluation of the performance measures of the clustering methods taking into consideration the sample size and cell composition of a given scRNA-seq dataset. Herein, a comprehensive performance evaluation study of 11 selected scRNA-seq clustering methods was performed using synthetic datasets with known sample sizes and number of subpopulations, as well as varying levels of transcriptome complexity. The results indicate that the overall performance of the clustering methods under study are highly dependent on the sample size and complexity of the scRNA-seq dataset. In most of the cases, better clustering performances were obtained as the number of cells in a given expression dataset was increased. The findings of this study also highlight the importance of sample size for the successful detection of rare cell subpopulations with an appropriate clustering tool. © 2019 Walter de Gruyter GmbH, Berlin/Boston.Öğe Comparison of five survival models: Breast cancer registry data from Ege University cancer research center [Beş sagkalim modelinin karşi{dotless}laşti{dotless}ri{dotless}lmasi{dotless}: Ege üniversitesi kanser araştirma merkezinden elde edilen meme kanseri kayitlarina ait veriler](Turkiye Klinikleri, 2010) Aktürk Hayat E.; Suner A.; Uyar B.; Dursun O.; Orman M.N.; KItapçioglu G.Objective: In this study, we aimed to compare the results of the survival analysis of the patients with breast cancer using Weibull, Gamma, Gompertz, Log-Logistic and Log-Normal parametric models. Material and Methods: The data obtained from 5457 patients with breast cancer from Ege University Cancer Research Centre between 1992 and 2007 was used in this study. The patients were divided into two groups with respect to their ages, they were divided into two groups as 49 and below and 50 and above. The Log rank test was applied to compare the survival curves of the two age groups obtained by Kaplan Meier method. A survival analysis was conducted by using Weibull, Gamma, Gompertz, Loglogistic and Lognormal distribution of parametric models. Results: Survival curves of two groups were compared by using a log-rank test and no statistical significant difference was found between the two groups. In the analysis of the survival periods using parametric models, the age variable is taken as the covariate. To determine the best model among parametric models, Akaike Information Criteria (AIC) was exploited. The results of the study revealed that the survival model found by the Gompertz distribution was the most appropriate one. Conclusion: By using AIC, the models obtained via Weibull, Loglogistic, Lognormal, Gamma and Gompertz were compared and the most suitable model for the obtained data distribution was determined. Although the AIC values for the five distributions in question were very close to each other, the Gompertz distribution, which had the lowest AIC value, was determined as the most suitable model. © 2010 by Türkiye Klinikleri.Öğe Different selection dynamics of S and RdRp between SARS-CoV-2 genomes with and without the dominant mutations(Elsevier B.V., 2021) Koçhan N.; Eskier D.; Suner A.; Karakülah G.; Oktay Y.SARS-CoV-2 is a betacoronavirus responsible for the COVID-19 pandemic that has affected millions of people worldwide. Pharmaceutical research against COVID-19 and the most frequently used tests for SARS-CoV-2 both depend on the genomic and peptide sequences of the virus for their robustness. Therefore, understanding the mutation rates and content of the virus is critical. Two key proteins for SARS-CoV-2 infection and replication are the S protein, responsible for viral entry into the cells, and RdRp, the RNA polymerase responsible for replicating the viral genome. Due to their roles in the viral cycle, these proteins are crucial for the fitness and infectiousness of the virus. Our previous findings had shown that the two most frequently observed mutations in the SARS-CoV-2 genome, 14408C>T in the RdRp coding region, and 23403A>G in the S gene, are correlated with higher mutation density over time. In this study, we further detail the selection dynamics and the mutation rates of SARS-CoV-2 genes, comparing them between isolates carrying both mutations, and isolates carrying neither. We find that the S gene and the RdRp coding region show the highest variance between the genotypes, and their selection dynamics contrast each other over time. The S gene displays higher tolerance for positive selection in mutant isolates early during the appearance of the double mutant genotype, and undergoes increasing negative selection over time, whereas the RdRp region in the mutant isolates shows strong negative selection throughout the pandemic. © 2021 Elsevier B.V.Öğe Differential expression of full-length and NH2terminally truncated FAM134B isoforms in normal physiology and cancer(American Physiological Society, 2020) Keles U.; Iscan E.; Yilmaz H.E.; Karakülah G.; Suner A.; Bal E.; Kahyaoglu S.Keles U, Iscan E, Yilmaz HE, Karakulah G, Suner A, Bal E, Tasdemir N, Cavga AD, Ekin U, Mutlu Z, Kahyaoglu S, Serdar MA, Atabey N, Ozturk M. Differential expression of full-length and NH2terminally truncated FAM134B isoforms in normal physiology and cancer. Am J Physiol Gastrointest Liver Physiol 319: G733-G747, 2020. First published October 14, 2020; doi:10.1152/ ajpgi.00094.2020.-Selective autophagy of the endoplasmic reticulum (ER), namely ER-phagy, is mediated by ER-localized receptors, which are recognized and sequestered by GABARAP/LC3B-decorated phagophores and transferred to lysosomes for degradation. Being one such receptor, FAM134B plays critical roles in cellular processes such as protein quality control and neuronal survival. FAM134B has also been associated with different cancers, although its exact role remains elusive. We report here that the FAM134B gene encodes not one but at least two different protein isoforms: the full-length and the NH2terminally truncated forms. Their relative expression shows extreme variation, both within normal tissues and among cancer types. Expression of full-length FAM134B is restricted to the brain, testis, spleen, and prostate. In contrast, NH2 terminally truncated FAM134B is dominant in the heart, skeletal muscle, kidney, pancreas, and liver. We compared wild-type and knockout mice to study the role of the Fam134b gene in starvation. NH2terminally truncated FAM134B-2 was induced in the liver, skeletal muscle, and heart but not in the pancreas and stomach following starvation. Upon starvation, Fam134b-/-mice differed from wild-type mice by less weight loss and less hyperaminoacidemic and hypocalcemic response but increased levels of serum albumin, total serum proteins, and a-amylase. Interestingly, either NH2terminally truncated FAM134B or both isoforms were downregulated in liver, lung, and colon cancers. In contrast, upregulation was observed in stomach and chromophobe kidney cancers. NEW & NOTEWORTHY We reported tissues expressing FAM134B-2 such as the kidney, muscle, heart, and pancreas, some of which exhibit stimulated expression upon nutrient starvation. We also demonstrated the effect of Fam134b deletion during ad libitum and starvation conditions. Resistance to weight loss and hypocalcemia, accompanied by an increase in serum albumin and a-amylase levels, indicate critical roles of Fam134b in physiology. Furthermore, the differential expression of FAM134B isoforms was shown to be significantly dysregulated in human cancers. © 2020 American Physiological Society. All rights reserved.Öğe Effects of environmental factors and storage conditions on the performance of Olysetw Plus against sand flies in WHO cone bioassays(Oxford University Press, 2016) Karakuş M.; Kasap O.E.; Günay F.; Oğuz G.; Demir S.; Suner A.; Alten B.; Özbel Y.Background: Leishmaniasis, visceral and cutaneous, is seen in Turkey and has both public and veterinary importance. So far, four Leishmania species and their vectors have been detected in Turkey. Vector control is essential in endemic areas and several personal protection methods are available including long-lasting insecticidal nets (LLINs). In this study, we aimed to measure the effects of usage and storage conditions on LLINs in a villagescale study. Methods: Olyset® Plus bed nets were set up in different climatic conditions (rain, exposed to sunlight and humidity) and collected after 6 months. The effectiveness of bed nets were tested by WHO's cone test method using wild-caught sand flies. Results: Bed nets, which were placed directly exposed to sunlight (A1, A2) showed lower (17.2%) knock down effect compared to bed nets placed indoors (A3, B1). Twenty-four hour mortality was 100% for the five study groups (A2, A3, B1, C1, C2) whereas group A1 was found to have a lower mortality rate (44.4%). Conclusion: Bed nets need to avoid direct exposure to sunlight. When used and stored in appropriate conditions (cool, well-ventilated place away from sunlight) they can be used as an effective vector control tool in endemic areas. © The Author 2016.Öğe Evaluation of pyrethroid susceptibility in culex pipiens of Northern Izmir Province, Turkey(Tehran University of Medical Sciences, 2018) Guntay O.; Yikilmaz M.S.; Ozaydin H.; Izzetoglu S.; Suner A.Background: Mosquitoes, being a nuisance species, are considered as one of the most important species in public health control programs due to their role as a vector in mosquito-borne diseases observed in humans and animals. We evaluated the susceptibility status of Culex pipiens collected from northern Izmir, Turkey in 2011-16. Methods: Mosquito larvae, collected from three different locations in northern İzmir, were reared in the laboratory. Adult susceptibility bioassays were performed using the WHO insecticide-impregnated papers including deltamethrin 0.05%, permethrin 0.75%, ?-cypermethrin 0.05% and cyfluthrin 0.15%. In addition, adult bioassays were performed after the pre-exposure to piperonyl butoxide (PBO) to determine the contribution of P450 detoxification enzymes to the phenotypic resistance. Results: In all of the three populations, high levels of resistance were observed (mortalities<63%) to all of the four pyrethroids. Different pyrethroids but with the same mode of action can exhibit significantly different phenotypic resistance in a single population. PBO bioassays also showed that P450 detoxification enzymes can have diverse effects on different pyrethroids. Conclusion: Using just one chemical in a class of insecticide can be misleading for resistance studies. © 2018 Tehran University of Medical Sciences. All rights reserved.Öğe Mobile learning in a flipped classroom: Findings from a “5-lecture-5” blended learning design for large classes(De Gruyter Open Ltd, 2022) Yilmaz Y.; Suner A.; Yilmaz O.Objective: We aimed to develop and evaluate a mobile learning (m-learning) design for large group application learning based on flipped classroom approach within an integrated curriculum of medical faculty. Materials and methods: Totally 359 students enrolled in a two-credit course during the 2017-2018 academic year. An instructional design called 5-Lecture-5 (5L5) was implemented via mobile application. This design is a blend of m-learning and flipped classroom approaches, with pre-, during-, and post-lecture elements. Data were analysed using Chi-square, Mann-Whitney U, and Kruskal-Wallis tests. Open-ended questions and course observations were analysed thematically and reported together. Results: Of the participating students, 26.96% who saw the first announcement examined pre-lecture materials and 55.43% attended face-to-face lecture. Achievement test scores of those who attended lecture were significantly higher (p = 0.027). Correct response rates for each question were 99.30, 72.10, 58.70, and 94.40%, respectively. Consequently, students demonstrated positive attitude towards m-learning (M = 170.15 ± 28.48). The most preferred positive aspects were “active learning,” “interactive,” “entertaining,” “useful,” and “repeatable.” Conclusions: M-learning activities within a flipped classroom with instant feedback were found to increase participation and interaction levels of students in classroom setting, resulting in their increased enjoyment and engagement. © 2021 Yusuf Yilmaz et al.Öğe Plasma levels of antioxidant vitamins in patients with acromegaly: A case-control study(Maghira and Maas Publications, 2019) Kutbay N.O.; Yurekli B.S.; Simsir I.Y.; Suner A.; Seckiner S.; Kucukerdonmez O.; Saygili F.OBJECTIVE: The aim of this study was to compare antioxidant Vitamin C and Vitamin E levels in the non-acromegaly control group and in patients with acromegaly with and without remission. MATERIAL AND METHODS: In this study, 100 cases, acromegaly patients of 57% (n=57, 29F, 28M, mean ages of 49.5±12.1) and control subjects of 43% (n=43, 29F, 14M, mean ages of 49.6±9.2). Acromegaly patients were classified into two groups; active acromegaly (AA; n=33) and controlled acromegaly (CA; n=24). RESULTS: Vitamin C levels were significantly lower in the acromegaly group [7.6 (4.7) mg/L, as median (IQR)] when compared to the control group [12.2 (5.5) mg/L, as median (IQR)] (p <0.001). Vitamin E levels didn't show a significant difference between the acromegaly and the control groups (14.2±3.6 vs. 14.8±3.7, as mean±SD, respectively, p = 0.439). Correlation analysis showed that Vitamin C levels were not significantly associated with clinical, anthropometric and laboratory parameters in the acromegaly group. Vitamin E levels were significantly associated with the total cholesterol, triglyceride, LDL-C, HDL-C, APO Al, APO B both in the acromegaly and the control groups. CONCLUSION: This study is the first one to investigate the relationship between the levels of Vitamin C & E and anthropometric & metabolic parameters in acromegaly patients and control group. In our study, Vitamin C level was significantly lower in the acromegaly group compared to the level in the control group. There was no significant difference in Vitamin E levels between the acromegaly and control group. © 2019 Maghira and Maas Publications. All rights reserved.Öğe Preoperative and postoperative (1st and 3rd month) metabolic data of patients who underwent bariatric surgery [Bariatrik cerrahi yapılan hastalarımızın preoperatif ve postoperatif metabolik verileri (1. ve 3. ay)](Turkiye Klinikleri, 2015) Kutbay N.Ö.; Yürekli B.S.; Özışık H.; Altun İ.; Suner A.; Şimşir I.Y.; Fırat Ö.; Erdoğan M.; Çetinkalp Ş.; Özgen G.; Saygılı F.Purpose: The growing prevalence of obesity has become a major concern. The efficacy of medical treatment, diet and behavior therapy in morbidly obese patients is limited. Obesity surgery is a treatment option for selected morbidly obese patients.Material and Method: Data of 47 patients (n=39 women, 8 men) who underwent bariatric surgery were investigated. Results: Out of 47 patients, 20 underwent Roux-en-Y gastric bypass (RYGB) (43%) and 27 had sleeve gastrectomy (SG) (57%). The mean age of the patients was 37±9.5 (19-59) years. 17% of patients were men and 83% were women. In the analysis of data on weight that could be found for 31 out of 47 patients, we detected preoperative and postoperative (1st and 3rd month) mean weight values as 125.4±15.9 kg, 112.7±13.2 kg (p<0.001) and 100.9±17.5 kg (p<0.001), respectively. In addition, the analysis of the data on mean fasting plasma glucose (FPG) levels which could be found for 23 out of 47 patients, showed us that preoperative and postoperative (1st and 3rd month) FPG levels were 100.9±17.5 mg/dL, 91.6±10.9 mg/dL(p=0.03) and 87.3±2.0 mg/dL, respectively. Only 1 patient had diabetes before the surgery. In the RYGB group, the mean change in weight was 12.4±5.5 kg in the 1st month and 22.2±8.6 kg in the 3rd month (compared to the weights in the preoperative period). Moreover, in the SG group,the mean change in weight was 13.7±4.5 kg in the 1st month and 23.4±5.8 kg in the 3rd month. No statistically significant difference was found between the weight changes in the 1st and the 3rd month as for surgery types. Discussion: After bariatric surgery, significant loss in weight and reduction in FPG occurred in short-term. © 2015, Galenos Yayincilik. All rights reserved.Öğe Prolactin effect on blood glucose and insülin in breastfeeding women(Elsevier Ltd, 2019) Ozisik H.; Suner A.; Cetinkalp S.Introduction: Prolactin plays a significant role in lactation and prolactin levels are increasing physiologically in pregnancy and breastfeeding period. There might be different mechanisms during breastfeeding between prolactin and insülin levels. In order to highlighten this mechanisms we compared the plasma levels of glucose, insülin, prolactin, C-peptid in basal situations and after taking 75 gr carbonhydrate, 20 gr protein, 23 gr fat in breastfeeding and in non lactating women. Material and methods: Participiants and measurements: The study population included 12 breastfeeding women and 11 healthy non lactating women as a control group. We collected information on age, history of gestational diabetes mellitus, family history of diabetes mellitus, natality, the symptoms of hypoglycemia. Weight, height and waist circumference were measured and body mass index (BMI) was calculated as weight (kg)/height (m 2 ). Results: Prolactin was inversely correlated with HbA1c and 2. hour C peptide (p=0.005, r=-0.564; p=0.008, r=-0.539). Prolactin was not significantly correlated with HOMA-IR, HOMA-IS, AUC-I or AUC-G. Prolactin levels were higher in breastfeeding women (median:34.98 µg/L) than in non lactating women (median:12.21 µg/L, p<0.001). There was a significant association between age and fasting glucose (p=0.018, r=-0.665), 2. hour glucose (p=0.049, r=0.578) in breastfeeding women. Discussion: In our study, we displayed prolactin was inversely correlated with HbA1c and 2. hour C peptide. Some studies in the past demonstrated that higher prolactin levels had importantly lower prevelance of type 2 diabetes. Our findings supported this situation. © 2019 Diabetes IndiaÖğe StatXFinder: a web-based self-directed tool that provides appropriate statistical test selection for biomedical researchers in their scientific studies(SpringerOpen, 2015) Suner A.; Karakülah G.; Koşaner Ö.; Dicle O.The improper use of statistical methods is common in analyzing and interpreting research data in biological and medical sciences. The objective of this study was to develop a decision support tool encompassing the commonly used statistical tests in biomedical research by combining and updating the present decision trees for appropriate statistical test selection. First, the decision trees in textbooks, published articles, and online resources were scrutinized, and a more comprehensive unified one was devised via the integration of 10 distinct decision trees. The questions also in the decision steps were revised by simplifying and enriching of the questions with examples. Then, our decision tree was implemented into the web environment and the tool titled StatXFinder was developed. Finally, usability and satisfaction questionnaires were applied to the users of the tool, and StatXFinder was reorganized in line with the feedback obtained from these questionnaires. StatXFinder provides users with decision support in the selection of 85 distinct parametric and non-parametric statistical tests by directing 44 different yes–no questions. The accuracy rate of the statistical test recommendations obtained by 36 participants, with the cases applied, were 83.3 % for “difficult” tests, and 88.9 % for “easy” tests. The mean system usability score of the tool was found 87.43 ± 10.01 (minimum: 70—maximum: 100). A statistically significant difference could not be seen between total system usability score and participants’ attributes (p value >0.05). The User Satisfaction Questionnaire showed that 97.2 % of the participants appreciated the tool, and almost all of the participants (35 of 36) thought of recommending the tool to the others. In conclusion, StatXFinder, can be utilized as an instructional and guiding tool for biomedical researchers with limited statistics knowledge. StatXFinder is freely available at http://webb.deu.edu.tr/tb/statxfinder. © 2015, Suner et al.Öğe TAp73? is Upregulated in the Most Common Human Cancers(NLM (Medline), 2022) Iscan E.; Karakülah G.; Ekin U.; Ozturk M.; Uzuner H.; Suner A.The transcription factor p73 is a member of the p53 tumor suppressor gene family and one of the key regulators of apoptosis. TP73 gene encodes two protein isoforms classes with diverse functions, TAp73 and DNp73, and TAp73 expression in tumor tissues is altered. Unlike the TP53 gene, TP73 is not mutated in cancers. Here, we sought to explore the expression of p73 isoforms across eight major cancer types using the publicly available data deposited at the GDC data portal and the TSVdb database. Our results showed that TAp73? is overexpressed in breast invasive carcinoma, stomach adenocarcinoma, lung squamous cell carcinoma, colon adenocarcinoma, and esophageal carcinoma tumors, whereas the expression of DNp73 isoforms is downregulated in breast invasive carcinoma (DNp73?,?,?), Prostate Adenocarcinoma (DNp73?), Lung Adenocarcinoma (DNp73?), Lung Squamous Cell Carcinoma (DNp73?) tumors. In summary, this study revealed that TAp73? has higher expression than the DNp73 isoforms in several cancer types.
