Simulation of steady-state response of tip-sample interaction for a torsional cantilever in tapping mode atomic force microscopy for material characterization in nanoscale

Ankara : The Department of Electrical and Electronics Engineering and the Institute of Engineering and Sciences of Bilkent University, 2010.Thesis (Master's) -- Bilkent University, 2010.Includes bibliographical references leaves 40-43.Dynamic atomic force microscopy (AFM) techniques involving multifrequency excitation or detection schemes offer improved compositional sensitivity and quantitative material property imaging. A correct interpretation of cantilever vibrations in multifrequency excitation and detection schemes demands an improved understanding of the effects of enhanced high frequency vibrations on the steady-state dynamics of the cantilever and in particular, on the tip-sample interaction force. In this thesis, a simulation background is developed with proper modelling of tip-sample ensemble for accurate simulation of tip-sample interaction when multifrequency excitation and detection schemes are utilized. The simulation results are analyzed and used for material characterization. The tip-sample ensemble is modelled as a multiple degree of freedom system that includes torsional mode and higher order flexural modes of the cantilever. The nonlinear behavior of sample surface is also included in the model. This mechanical model is transformed into an electrical circuit and an electrical circuit simulator is used to find steady-state of the circuit. Thereby, a simulation of steady-state dynamics of multifrequency imaging schemes is achieved.Using the developed simulation tool, the effect of torsional vibrations and higher order flexural vibrations on steady-state of tip-sample interaction is investigated. The tip trajectory and tip-sample interaction force are calculated for torsional harmonic cantilevers. The potential of torsional harmonic cantilevers in reconstruction of tip-sample interaction force for the quantitative estimation of material properties is verified. Change in amplitude of torsional harmonics with respect to elastic modulus (sensitivity) is investigated. It is shown that sensitivity of a particular torsional harmonic changes with sample stiffness and higher harmonics are more sensitive to change in stiffness. Additionally, a noise analysis of torsional harmonic cantilevers is made and included in the simulations. The tip-sample interaction force is recovered from the simulated torsional vibration signal and the effective elastic modulus of the sample is estimated. It is observed that accuracy of the estimation is affected by number of torsional harmonics used in the recovery of interaction force.Selvi, Şeref BurakM.S

Presentation of data mining applications in web based geovisual analytical environment: Example of COVID-19 vaccine tweets

Mekânsal görsel analitik, mekânsal bilgilerin etkileşimli görsel ara yüzlerle ele alındığı analitik akılyürütme bilimidir. Mekânsal görsel analitik sistemleri sayesinde, Twitter gibi sosyal medyaplatformlarındaki büyük veri setlerinden bir konu hakkında elde edilen veriler son kullanıcıya etkileşimliharitalama sistemleriyle sunulabilir. 11 Mart 2020’de Dünya Sağlık Örgütü’nün COVID-19 salgınınıduyurmasının ardından Twitter veri trafiğinde de ciddi bir artış görülmüştür. Bu çalışmada, COVID-19salgını döneminin önemli tartışmalarından biri olan COVID-19 aşıları hakkındaki tweet trafiğininzamansal ve mekânsal gelişimi veri madenciliği teknikleriyle incelenmiş ve görsel analitik ortamdasunulmuştur. Bu çalışma ile twitter gibi sosyal medya platformlarının sahip olduğu büyük veri olarakkabul edilen veri setlerinin veri madenciliği yöntemleriyle analiz edilerek afet ve kriz yönetimi açısındanönemli çıkarımlar yapılabileceği ortaya konmuştur.Spatial visual analytics is the science of analytical reasoning in which spatial information is handled with interactive visual interfaces. Thanks to spatial visual analytics systems, data obtained from large data sets on social media platforms such as Twitter can be presented to the end user with interactive mapping systems. After the World Health Organization announced the COVID-19 outbreak on March 11, 2020, there has been a significant increase in Twitter data traffic. In this study, the temporal and spatial development of tweet traffic about COVID-19 vaccines, which is one of the important discussions of the COVID-19 epidemic period, was examined with data mining techniques and presented in a visual analytical environment. With this study, it has been revealed that important inferences can be made in terms of disaster and crisis management by analyzing the data sets, which are accepted as big data, of social media platforms such as twitter with data mining methods

POTENTIAL PROTECTIVE ROLE OF SDF-1 AND CXCR4 GENE VARIANTS IN THE DEVELOPMENT OF DEMENTIA

Background: The aim of this study was to evaluate the role of polymorphisms of stromal cell-derived factor-1 (SDF-1) and chemokine receptor-4 (CXCR4) genes in dementia susceptibility in a Turkish population. Subjects and methods: The study group included 61 dementia patients, while the control group comprised 82 healthy individuals. Gene polymorphisms of SDF-1 3’A G801A (rs1801157) and CXCR4 C138T (rs2228014) were genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. Results: A significantly reduced risk for developing dementia was found for the group bearing an A allele for SDF-1 3’A polymorphism (p=0.009; x2=6.812; OR=0.626; 95%CI= 0.429-0.913). The frequency of the CXCR4 TT and TC genotype was significantly lower in patients with dementia compared to controls (p=0.028; x2=5.583; OR=0.215; 95%CI=0.05-0.914); (p=0.027; x2=4.919; OR=0.484; 95% CI= 0.246-0.955). Additionally, combined genotype analysis showed that the frequency of SDF1 GACXCR4 CC was significantly lower in patients with dementia in comparison with those of controls (p=0.049; OR=0.560; 95% CI= 0.307±1.020). Conclusions: Our study provides new evidence that SDF1 A and CXCR4 T alleles may be associated with a decreased dementia risk. The present study is important because to our knowledge, it is the first one to be conducted in a Turkish population to date, but we believe that more patients and controls are needed to obtain statistically significant results

The assessment of bacterial nanocellulose functionalized with metal nanoparticles

[Excerpt] Introduction Biocompatibility is one of the mandatory requirements of indwelling medical devices to avoid foreign body reactions and consequential surgical removal.This research was funded by FEDER funds through the Operational Competitiveness Program–COMPETE, under the project POCI-01-0247-FEDER-068924 and by National Funds through Fundação para a Ciência e Tecnologia (FCT), under the project UID/CTM/00264/2020. Cátia Alves, Liliana Melro, Behnaz Mehravani, and Ana Isabel Ribeiro acknowledge FCT, MCTES, FSE, and UE PhD grants 2022.10454.BD, 2020.04919.BD, 2022.13094.BD, and SFRH/BD/137668/2018

Using cluster analysis methods for multivariate mapping of traffic accidents

Many factors affect the occurrence of traffic accidents. The classification and mapping of the different attributes of the resulting accident are important for the prevention of accidents. Multivariate mapping is the visual exploration of multiple attributes using a map or data reduction technique. More than one attribute can be visually explored and symbolized using numerous statistical classification systems or data reduction techniques. In this sense, clustering analysis methods can be used for multivariate mapping. This study aims to compare the multivariate maps produced by the K-means method, K-medoids method, and Agglomerative and Divisive Hierarchical Clustering (AGNES) method, which among clustering analysis methods, with real data. The results from the study will suggest which clustering methods should be preferred in terms of multivariate mapping. The results show that the K-medoids method is more appropriate in terms of clustering success. Moreover, the aim is to reveal spatial similarities in traffic accidents according to the results of traffic accidents that occur in different years. For this aim, multivariate maps created from traffic accident data of two different years in Turkey are used. The methods are compared, and the use of the maps produced with these methods for risk management and planning is discussed. Analysis of the maps reveals significant similarities for both years

USING CLUSTER ANALYSIS METHODS FOR MULTIVARIATE MAPPING

Çok değişkenli haritalama mekânsal objelere ait birden çok özelliğin harita kullanılarak görsel sunumudur. Çeşitli veri hazırlama ve istatistiksel sınıflandırma teknikleri kullanılarak mekânsal objelere ait birden çok özellik görsel olarak incelenebilir ve kartografik işaretlerle gösterilebilir. Bu kapsamda kümeleme analizi yöntemleri de çok değişkenli haritalama için kullanılabilir. Bu çalışmada kümeleme analiz yöntemlerinden kortalama yöntemi, k-temsilci yöntemi ve Birleştirici Hiyerarşik Kümeleme yöntemi ele alınmıştır. Bu yöntemlerle Türkiye'deki üç ayrı yıla ait trafik kaza verileri kullanılarak oluşturulan sınıflar ve üretilen çok değişkenli haritalar kullanılarak bu yöntemlerin karşılaştırılması yapılmış, bu yöntemlerle üretilen haritaların risk yönetimi ve planlamada kullanılabilirliği üzerinde durulmuştur.Multivariate mapping is the visual exploration of spatial objects with multiple attributes using a map. More than one attribute can be visually explored and symbolized using numerous statistical classification systems or data reduction techniques. In this sense, clustering analysis methods can be used for multivariate mapping. In this study, among clustering analysis methods, k-means method, k-medoids method and Agglomerative Hierarchical Clustering method were selected. For this purpose, multivariate maps created from traffic accident data of two different years in Turkey were used. The methods were compared using the maps produced with these methods and effectiveness of these maps in risk management and planning were discussed

Reduction of the argyrophilic nucleolar organizing region associated protein synthesis with age in buccal epithelial cells of healthy individuals

WOS: 000351531100012PubMed: 25082567Background Nucleolus organizer regions (NORs) consist of the rRNA coding gene family (rDNA) in the cell nucleus. The argyrophilic proteins are selectively stained with silver nitrate and bind these regions. It was reported that NOR (rDNA) activity decreases in human lymphocytes, fibroblasts and bone marrow with age. However, to our knowledge there have not been any studies related to the NORs in oral epithelial cells of healthy individuals. Aim Our aim is to detect any correlation between age and Total AgNOR area/Total nucleus area (TAA/TNA) values in buccal epithelial cells of healthy individuals. Methods Oral epithelial cells from 50 healthy individuals (age range of 2-80 years old) were spread onto a clean glass slide, air dried and fixed. Then the AgNOR staining protocol was performed on these cells. TAA/TNA ratio and AgNOR dots were calculated using software. From each person 50 oral epithelial cells were evaluated. Results Statistically significant correlations were found between mean TAA/TNA values and age (Rsq = 0.534, p < 0.001 for linear and Rsq = 0.728, p < 0.0001 for polynominal regression), and between AgNOR number and age (Rsq = 0.621, p < 0.001 for linear and Rsq = 0.693, p < 0.0001 for polynominal regression). Conclusion There is a significant correlation between age and AgNOR amount (ribosome biosynthesis rate) in buccal epithelial cells of healthy individuals. AgNORs in buccal epithelial cells may be used for detection of age.Erciyes University Research FundErciyes University [TSY-08-559]; Medical Research Council of Erciyes University (ERUBAP)Erciyes University [TSY-08-559]Erciyes University Research Fund has supported this research; contract Grant Number: TSY-08-559. This study is the essential part of the MS thesis of Burak Selvi. The Medical Research Council of Erciyes University (ERUBAP, Project No. TSY-08-559) supported this work

Biologically Transformed Propolis Exhibits Cytotoxic Effect on A375 Malignant Melanoma Cells In Vitro

Propolis has been used for its health benefits, due to high phenolic content. Recently it has been shown that the extraction methods which yielded phenolic molecules, affected the anti-oxidant and anticancer effect of propolis. In our previous study we showed that biotransformation of propolis via Lactobacillus plantarum might increase antioxidative effect. In this study, we investigated the cytotoxic effect of this propolis sample on A375 melanoma cells. The propolis samples were extracted in water. The phenolic molecules were determined with LC MS/MS. Cytotoxicity was evaluated by means of the WST. Water-extracted propolis samples were incubated with L. plantarum (1.5%) in 37 °C for 24 h. A375 cells were treated by propolis with doses of from 25 to 1000 µg/mL, for periods of 24 h, 48 h and 72 h. Cytotoxicity MTT tests were performed. The significantly high phenolic compounds mainly; Quercetine (514 ng/mL), rutin (623 ng/mL), ellagic acid (331 ng/mL), epicatechin (125 ng/mL) were found in propolis samples IC50 values were 412.5 µg/mL (24 h) and 314 µg/mL (48 h) and 353 µg/mL (72 h). In conclusion, our data showed that the cytotoxic effect of biologically transformed propolis which have high content of rutin, quercetin, ellagic acid, epicatechin. Biotransformation might be a useful strategy to increase bioavailability of phenolic molecules in propolis

Hydroxycinnamic Acids in Wild Blueberry and Effects of Hydroxycinnamic Acids on Apoptosis Induction in Cancer Cell Culture

: In this study, the fruits and leaves of wild blueberries grown naturally in our country will be evaluated by using different infusion and boiling methods. Blueberry teas; leaves, raw fruit, dried and shredded raw fruit, fruit beans and seedless raw fruit of different infusions were used after boiling them for 1 min, 3 min, 5 min, 7 min, 10 min. Phenolic levels were determined by LC MS/MS technique. The antioxidant and activities of all products in the vitro HCT-116 colon cancer cell line were analyzed by spectrophotometric methods. MDA and TEAC were evaluated for antioxidant activity. Cytotoxicity and viability tests were performed by adding WST-8 (Water Soluble Tetrazolium Salt-8) solution. For apoptosis, TRAIL and Apaf-1 ELISA Kit were used for the activation of caspases of intrinsic and extrinsic pathways