Search results for: Ilhan Keskin

Authors: Ilhan Keskin, Hasan Bulent Kantarci

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In this study, one of the tools of Islamic financing known as “Sukuk” a non-interest bearing investment which has started to be implemented in Turkey and the world as a whole is discussed. In order to increase the vitality and efficiency of the economy, by taking lessons from the recent economic crisis new developments in the banking and investment sector are being expanded. The purpose of all investors is to obtain more revenue through the use of capital. The inability of traditional investment tools to meet the expectations of investors and the interest based financial system where one investor benefits at the expense of another there has been the need for a different, reliable and non-interest bearing financial market that is consistent with the Islamic rule. As a result an alternative and more reliable interest free financing tool “Sukuk” rental certificates covering people who are sensitive to Islamic rules, appeal to all segments, hidden remaining capital that contributes to the economy, reduce disparities in income distribution, common risk sharing system of profit and loss sharing has emerged. Today, for the structural countries by examining the state of the world market economy the applicability, enactment and future issues associated with this attractive kind of Islamic finance namely the “Sukuk” market has been explained.

Keywords: Islamic finance, islamic markets, non-interest bearing, rental certificates

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Authors: Yavuz Bağcı, Levent Keskin

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The study was carried out in 2011-2014 period to determine plant-based hand tools uses of plants in Kadınhanı (Konya) and surrounding villages. A total of 153 individuals, who lived or were living during this study in 4 towns, 37 villages and 9 neighborhood were interviewed. It was found that of a total about 20 plants belonging to 10 families in the study area, about 60 hand-made goods were used by peoples for various purposes.

Keywords: ethnobotanic, handmade, Kadınhanı, Konya, plant-human relationship

Procedia PDF Downloads 389

Authors: Ahmet Y. Arabul, Ibrahim Senol, Fatma Keskin Arabul, Mustafa G. Aydeniz, Yasemin Oner, Gokhan Kalkan

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In the standards of IEC 60076-2 and IEC 60076-7, three different hot-spot temperature estimation methods are suggested. In this study, the algorithms which used in hot-spot temperature calculations are analyzed by comparing the algorithms with the results of an experimental set-up made by a Transformer Monitoring System (TMS) in use. In tested system, TMS uses only top oil temperature and load ratio for hot-spot temperature calculation. And also, it uses some constants from standards which are on agreed statements tables. During the tests, it came out that hot-spot temperature calculation method is just making a simple calculation and not uses significant all other variables that could affect the hot-spot temperature.

Keywords: Hot-spot temperature, monitoring system, power transformer, smart grid

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Authors: Yildiray Keskin, Omer Acan, Murat Akkus

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In this paper, the solution of fractional diffusion equations is presented by means of the reduced differential transform method. Fractional partial differential equations have special importance in engineering and sciences. Application of reduced differential transform method to this problem shows the rapid convergence of the sequence constructed by this method to the exact solution. The numerical results show that the approach is easy to implement and accurate when applied to fractional diffusion equations. The method introduces a promising tool for solving many fractional partial differential equations.

Keywords: fractional diffusion equations, Caputo fractional derivative, reduced differential transform method, partial

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Authors: Abdulhamit Donder, Erhan Ilhan Konukseven

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Grinding operation is performed in order to obtain desired surfaces precisely in machining process. The needed relative motion between the cutting tool and the workpiece is generally created either by the movement of the cutting tool or by the movement of the workpiece or by the movement of both of them as in our case. For all these cases, the coherence level between the movements and the interaction forces is a key influential parameter for efficient grinding. Therefore, in this work, spectral coherence analysis has been performed to investigate the coherence level between grinding interaction forces and the movement of the workpiece on our robotic-grinding experimental setup in METU Mechatronics Laboratory.

Keywords: coherence analysis, correlation, FFT, grinding, hanning window, machining, Piezo actuator, reverse arrangements test, spectral analysis

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Authors: O. Acan, Y. Keskin

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In this study, we will carry out a comparative study between the reduced differential transform method, the adomian decomposition method, the variational iteration method and the homotopy analysis method. These methods are used in many fields of engineering. This is been achieved by handling a kind of 2-Dimensional and forth-order partial differential equations called the Kuramoto–Sivashinsky equations. Three numerical examples have also been carried out to validate and demonstrate efficiency of the four methods. Furthermost, it is shown that the reduced differential transform method has advantage over other methods. This method is very effective and simple and could be applied for nonlinear problems which used in engineering.

Keywords: reduced differential transform method, adomian decomposition method, variational iteration method, homotopy analysis method

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Authors: Fatma Keskin Arabul, Ibrahim Senol, Ahmet Yigit Arabul, Ali Rifat Boynuegri

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On account of the concern of the fossil fuel is depleting and its negative effects on the environment, interest in alternative energy sources is increasing day by day. However, considering the importance of transportation in human life, instead of oil and its derivatives fueled vehicles with internal combustion engines, electric vehicles which are sensitive to the environment and working with electrical energy has begun to develop. In this study, simulation was carried out for providing energy management and recovering regenerative braking in fuel cell-battery hybrid electric vehicle. The main power supply of the vehicle is fuel cell on the other hand not only instantaneous power is supplied by the battery but also the energy generated due to regenerative breaking is stored in the battery. Obtained results of the simulation is analyzed and discussed.

Keywords: electric vehicles, fuel cell, battery, regenerative braking, energy management

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Authors: Guray Arslan, Riza Secer Orkun Keskin

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Numerical investigations were conducted to study the influence of flexural reinforcement ratio on the diagonal cracking strength and ultimate shear strength of reinforced concrete (RC) beams without stirrups. Three-dimensional nonlinear finite element analyses (FEAs) of the beams with flexural reinforcement ratios ranging from 0.58% to 2.20% subjected to a mid-span concentrated load were carried out. It is observed that the load-deflection and load-strain curves obtained from the numerical analyses agree with those obtained from the experiments. It is concluded that flexural reinforcement ratio has a significant effect on the shear strength and deflection capacity of RC beams without stirrups. The predictions of the diagonal cracking strength and ultimate shear strength of beams obtained by using the equations defined by a number of codes and researchers are compared with each other and with the experimental values.

Keywords: finite element, flexural reinforcement, reinforced concrete beam, shear strength

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Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Ilhan Dogan

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An in silico analysis of Brachypodium distachyon, Triticum aestivum, Festuca arundinacea, Lolium perenne, Hordeum vulgare subsp. vulgare of the Pooideaea was performed based on complete chloroplast genomes including rbcL coding and trnH-psbA intergenic spacer regions alone to compare phylogenetic resolving power. Neighbor-joining, Minimum Evolution, and Unweighted Pair Group Method with arithmetic mean methods were used to reconstruct phylogenies with the highest bootstrap supported the obtained data from whole chloroplast genome sequence. The highest and lowest values from nucleotide diversity (π) analysis were found to be 0.315813 and 0.043495 in rbcL coding region in chloroplast genome and complete chloroplast genome, respectively. The highest transition/transversion bias (R) value was recorded as 1.384 in complete chloroplast genomes. F. arudinacea-L. perenne clade was uncovered in all phylogenies. Sequences of rbcL and trnH-psbA regions were not able to resolve the Pooideae phylogenies due to lack of genetic variation.

Keywords: chloroplast DNA, Pooideae, phylogenetic analysis, rbcL, trnH-psbA

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Authors: Yasin Kutuk, Bengi Yanik Ilhan

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Previous studies investigate the wage differentiations among regions in Turkey between couples who work in the same industry and those who work in different industries by using the models that is appropriate for cross sectional data. However, since there is no available panel data for this investigation in Turkey, pseudo panels using repeated cross-section data sets of the Household Labor Force Surveys 2004-2014 are employed in order to open a new way to examine wage differentiation patterns. For this purpose, household heads are separated into groups with respect to their household composition. These groups’ membership is assumed to be fixed over time such as age groups, education, gender, and NUTS1 (12 regions) Level. The average behavior of them can be tracked overtime same as in the panel data. Estimates using the pseudo panel data would be consistent with the estimates using genuine panel data on individuals if samples are representative of the population which has fixed composition, characteristics. With controlling the socioeconomic factors, wage differentiation of household income is affected by social, cultural and economic changes after global economic crisis emerged in US. It is also revealed whether wage differentiation is changing among the birth cohorts.

Keywords: wage income, same industry, pseudo panel, panel data econometrics

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Authors: GüLcan Keskin

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In a globalizing world, it is more difficult for developing counties to gain a competitive advantage compared to developed countries. Entrepreneurship is an important factor for economic growth in developing countries. Entrepreneurship is not only in the success of an entrepreneur’s own businesses, but also plays an important role in regional and national development. Entrepreneurship is the factor that triggers change for the country to accelerate the creation, dissemination, and implementation of new thoughts, leading to the emergence of industries that supports economic growth and development as it increases productivity by creating a competitive advantage. Therefore, it is an important factor for countries to develop economically and socially in a global world. As the know-how of the local products belongs to the region, it is a value that should not be lost. Having know-how provides a competitive advantage to the region. On the other hand, traditional products can be tailored to today’s trade understanding to appeal to more audiences. The primary aim of the study is to examine the interaction mechanism between traditional products and innovation in the context of related literature. The second aim of the study is to show the effect the traditional products to competitive advantage.

Keywords: e-commerce, economic growth, entrepreneurship, traditional products

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Authors: Ali Bayram, Burak Uz, Ilhan Dolasik, Remzi Yiğiter

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The GABARAP (GABAA-receptor-associated protein) family consists of GABARAP, GABARAPL1 (GABARAP-like 1) and GABARAPL2 (GABARAP-like 2). GABARAPL1, like GABARAP, was described to interact with both GABAA receptor and tubulin, and to be involved in intracellular GABAA receptor trafficking and promoting tubulin polymerization. In addition, GABARAPL1 is thought to be involved in various physiological (autophagosome closure, regulation of circadian rhythms) and/or pathological mechanisms (cancer, neurodegeneration). Alzheimer’s disease (AD) is a progressive neuro degenerative disorder characterized with impaired cognitive functions. Disruption of the GABAergic neuro transmission as well as cholinergic and glutamatergic interactions, may also be involved in the pathogenesis of AD. GABARAPL1 presents a regulated tissue expression and is the most expressed gene among the GABARAP family members in the central nervous system. We, herein, conducted a study to investigate the GABARAPL1 mRNA expression levels in patients with AD. 50 patients with AD and 49 control patients were enrolled to the present study. Messenger RNA expression levels of GABARAPL1 were detected by real-time polymerase chain reaction. GABARAPL1 mRNA expression in AD / control patients was 0,495 (95% confidence interval: 0,404-0,607), p= 0,00000002646. Reduced activity of GABARAPL1 gene might play a role, at least partly, in the pathophysiology of AD.

Keywords: Alzheimer’s disease, GABARAPL1, mRNA expression, RT-PCR

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Authors: F. Berna Benli, Özgür Keskin

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Lately, many mathematicians have been studied the statistical convergence of a sequence of fuzzy numbers. We know that Lambda-statistically convergence is a kind of convergence between ordinary convergence and statistical convergence. In this paper, we will introduce the new kind of convergence such as λ-levelwise statistical convergence. Then, we will define the concept of the λ-levelwise statistical cluster and limit points of a sequence of fuzzy numbers. Also, we will discuss the relations between the sets of λ-levelwise statistical cluster points and λ-levelwise statistical limit points of sequences of fuzzy numbers. This work has been extended in this paper, where some relations have been considered such that when lambda-statistical limit inferior and lambda-statistical limit superior for lambda-statistically convergent sequences of fuzzy numbers are equal. Furthermore, lambda-statistical boundedness condition for different sequences of fuzzy numbers has been studied.

Keywords: fuzzy number, λ-levelwise statistical cluster points, λ-levelwise statistical convergence, λ-levelwise statistical limit points, λ-statistical cluster points, λ-statistical convergence, λ-statistical limit points

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Authors: Serap Keskin Tunç, Cennet Neslihan Eroğlu, Sevinç Şahin, Selda Seçkin

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It has been suggested that various viruses may play a role in the pathogenesis of cancerous oral lesions in the literature. The aim of this study was to investigate the presence of both possible precancerous viral markers (HPV, HHV8, HSV1, HSV2, and EBV), and p53 and Ki-67 in the dental follicles of asymptomatic impacted teeth. A hundred healthy volunteers, older than 18 years old, included in the study. Dental follicles of extracted impacted teeth were excised and fixated in 10% formaldehyde. Histopathological and immunohistochemical examinations using HPV (containing HPV 8 and HPV 11), p16 (containing HPV 16), HHV8, HSV1, HSV2, EBV, p53 and Ki-67 antibodies were carried out. Also, the immunohistochemical results were correlated with the clinicopathological feature by Chi-square test statistically No dysplasia or neoplasm was observed. 62% of the cases were positive for p16, 32% were positive for EBV, 26% were positive for HSV1, immunohistochemically. All cases were immunonegative for HPV, HSV2, and HHV8. There was statistically significant correlation between overexpression of p53 with both EBV and p16 positivity (p<0.05). Direct correlation between higher expression of Ki-67 between EBV immunopositivity was detected (p<0.05). Thus, these viruses may be suggested to show trophism to the dental follicles acting as a reservoir. In conclusion, all dental follicles of extracted impacted teeth should be examined histopathologically in order to detect and prevent possible viral oncogenesis.

Keywords: dental follicles, Ki67, p53, precancerous markers viral markers

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Authors: Turan Çalban, Nursel Keskin, Sabri Çolak, Soner Kuşlu

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Gypsum (CaSO4.2H2O) is a mineral that is found in large quantities in the Turkey and in the World. The dissolution of this mineral in the diammonium hydrogen phosphate solutions has not been studied so far. Investigation of the dissolution and dissolution kinetics gypsum in diammonium hydrogen phosphate solutions will be useful for evaluating of solid wastes containing gypsum. In this study, parameters such as diammonium hydrogen phosphate concentration, temperature and stirring speed affecting on the dissolution rate of the gypsum in diammonium hydrogen phosphate solutions were investigated. In experimental studies have researched effectiveness of the selected parameters. The dissolution of gypsum were examined in two parts at low and high temperatures. The experimental results were successfully correlated by linear regression using Statistica program. Dissolution curves were evaluated shrinking core models for solid-fluid systems. The activation energy was found to be 34.58 kJ/mol and 44.45 kJ/mol for the low and the high temperatures. The dissolution of gypsum was controlled by chemical reaction both low temperatures and high temperatures. Reaction rate expressions of dissolution of gypsum at the low temperatures and the high temperatures controlled by chemical reaction are as follows, respectively. = k1.e-5159.5/T.t = k2.e-5346.8/T.t Where k1 and k2 are constants depending on the diammonium hydrogen phosphate solution concentration, the solid/liquid ratio, the stirring speed and the particle size.

Keywords: diammonium hydrogen phosphate, dissolution kinetics, gypsum, kinetics.

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Authors: Zeynep Karakoc, Hasan Ilhan Mutaf

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Plaque removal efficacy of different dental brushes and mouth wash during fixed orthodontic appliance therapy was evaluated in this single-blind, crossover and prospective study. Thirty orthodontic patients aged 18 and over undergoing fixed appliance therapy at the end of leveling stage were divided into three groups. Subjects brushed their teeth with a toothbrush under standardized conditions for a period of 30 days prior to inter-dental care products. The same procedure was repeated each time with a different, randomly assigned inter-dental care products in a crossover design. (Inter-dental brush, powered inter-dental brush and mouth wash). At start and end of each removal period, plaque indexes of participants were scored. Each brush achieved statistically significant plaque removal; however, there were no statistical differences among groups for all surfaces of teeth when the plaque score was evaluated. The mouth wash group presented significant improvement in reduction of visible plaque on mesial and distal surfaces of posterior teeth. (-60.9 %, P< .001) Plaque removal for right and left side of mouth showed no significant differences within groups, only mouth wash was more efficient in right side than left side. It is concluded that effectiveness of plaque removal may not be related to the kind of inter-dental products directly. However, toothbrush when used with inter-dental care products is significantly better at removing plaque deposits from fixed appliance patients.

Keywords: orthodontics, dental care, brush, plaque

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Authors: Mehmet Akif Bütüner, İlhan Koşalay

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Hydroelectric power plants (HEPPs) are renewable energy power plants with the highest installed power in the world. While the control systems operating in these power plants ensure that the system operates at the desired operating point, it is also responsible for stopping the relevant unit safely in case of any malfunction. While these control systems are expected not to miss signals that require stopping, on the other hand, it is desired not to cause unnecessary stops. In traditional control systems including modern systems with SCADA infrastructure, alarm conditions to create warnings or trip conditions to put relevant unit out of service automatically are usually generated with predefined limits regardless of different operating conditions. This approach results in alarm/trip conditions to be less likely to detect minimal changes which may result in serious malfunction scenarios in near future. With the methods proposed in this research, routine behavior of the oil circulation of hydraulic governor of a HEPP will be modeled with machine learning methods using historical data obtained from SCADA system. Using the created model and recently gathered data from control system, oil pressure of hydraulic accumulators will be estimated. Comparison of this estimation with the measurements made and recorded instantly by the SCADA system will help to foresee failure before becoming worse and determine remaining useful life. By using model outputs, maintenance works will be made more planned, so that undesired stops are prevented, and in case of any malfunction, the system will be stopped or several alarms are triggered before the problem grows.

Keywords: hydroelectric, governor, anomaly detection, machine learning, regression

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Authors: Ozlem Bahadir Acikara, Mert Ilhan, Ekin Kurtul, Karel Smejkal, Esra Kupeli Akkol

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Present study is aimed to investigate in vitro inhibitory effects of the extracts prepared from the aerial parts of Podospermum canum (Asteraceae) on hyaluronidase, collagenase, and elastase enzymes using a bioassay-guided fractionation. Inhibitory effects of the extract, sub-extracts, fractions obtained by column chromatography, and isolated compounds on collagenase, elastase, and hyaluronidase were performed by using in vitro enzyme inhibitory assays based on spectrophotometric evaluation. The ethyl acetate and remaining water extracts prepared from the plant displayed significant inhibitory activities on collagenase and elastase, while petroleum ether and chloroform extracts did not show any inhibitory activity. Eleven known compounds: arbutin, 6'-O-caffeoylarbutin, cichoriin, 3,5-dicaffeoylquinic acid methyl ester, apigenin-7-O-β-glucoside, luteolin-7-O-β-glucoside, apigenin-7-O-β-rutinoside, isoorientin, orientin, vitexin, procatechuic acid, and compound 4-hydroxy-benzoic acid 4-(6-O-α-rhamnopyranosyl-β-glucopyranosyl) benzyl ester have been obtained from ethyl acetate sub-extract of the plant through bioassay-guided fractionation and isolation. Results of the present study have revealed that among the isolated compounds, apigenin-7-O-β-glucoside, luteolin-7-O-β-glucoside, apigenin-7-O-β-rutinoside and isoorientin showed potent enzyme inhibitory activities. However, methanolic extract of P. canum displayed a greater inhibitory activity than fractions and isolated compounds both on collagenase and elastase.

Keywords: Asteraceae, collagenase, elastase, hyaluronidase, Podospermum canum

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Authors: Alisan Kayabolen, Dilek Keskin, Ferit Avcu, Andac Aykan, Fatih Zor, Aysen Tezcaner

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Adipose tissue engineering is a promising field for regeneration of soft tissue defects. However, only very thin implants can be used in vivo since vascularization is still a problem for thick implants. Another problem is finding a biocompatible scaffold with good mechanical properties. In this study, the aim is to develop a thick vascularized adipose tissue that will integrate with the host, and perform its in vitro and in vivo characterizations. For this purpose, a hydrogel of decellularized adipose tissue (DAT) and fibroin was produced, and both endothelial cells and adipocytes that were differentiated from adipose derived stem cells were encapsulated in this hydrogel. Mixing DAT with fibroin allowed rapid gel formation by vortexing. It also provided to adjust mechanical strength by changing fibroin to DAT ratio. Based on compression tests, gels of DAT/fibroin ratio with similar mechanical properties to adipose tissue was selected for cell culture experiments. In vitro characterizations showed that DAT is not cytotoxic; on the contrary, it has many natural ECM components which provide biocompatibility and bioactivity. Subcutaneous implantation of hydrogels resulted with no immunogenic reaction or infection. Moreover, localized empty hydrogels gelled successfully around host vessel with required shape. Implantations of cell encapsulated hydrogels and histological analyses are under study. It is expected that endothelial cells inside the hydrogel will form a capillary network and they will bind to the host vessel passing through hydrogel.

Keywords: adipose tissue engineering, decellularization, encapsulation, hydrogel, vascularization

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Authors: Esra Danaci, Tugba Kavalali Erdogan, Sevil Masat, Selin Keskin Kiziltepe, Tugba Cinarli, Zeliha Koc

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This study was conducted in a descriptive and cross-sectional manner to determine that factors that influence the self-efficacy and self-sufficiency levels among oncology patients. The research was conducted between January 24, 2017 and September 24, 2017 in the oncology and hematology departments of a university hospital in Turkey with 179 voluntary inpatients. The data were collected through the Self-Sufficiency/Self-Efficacy Scale and a 29-question survey, which was prepared in order to determine the sociodemographic and clinical properties of the patients. The Self-Sufficiency/Self-Efficacy Scale is a Likert-type scale with 23 articles. The scale scores range between 23 and 115. A high final score indicates a good self-sufficiency/self-efficacy perception for the individual. The data were analyzed using percentage analysis, one-way ANOVA, Mann Whitney U-test, Kruskal Wallis test and Tukey test. The demographic data of the subjects were as follows: 57.5% were male and 42.5% were female, 82.7% were married, 46.4% were primary school graduate, 36.3% were housewives, 19% were employed, 93.3% had social security, 52.5% had matching expenses and incomes, 49.2% lived in the center of the city. The mean age was 57.1±14.6. It was determined that 22.3% of the patients had lung cancer, 19.6% had leukemia, and 43.6% had a good overall condition. The mean self-sufficiency/self-efficacy score was 83,00 (41-115). It was determined that the patients' self-sufficiency/self-efficacy scores were influenced by some of their socio-demographic and clinical properties. This study has found that the patients had high self-sufficiency/self-efficacy scores. It is recommended that the nursing care plans should be developed to improve their self-sufficiency/self-efficacy levels in the light of the patients' sociodemographic and clinical properties.

Keywords: oncology, patient, self-efficacy, self-sufficiency

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Authors: Tugba Sevinc Gamsiz, Emine Koroglu, Ozcan Keskin

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Aim: Nonalcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease in the general population. The higher mortality and morbidity among NAFLD patients and lack of symptoms makes early detection and management important. In our study, we aimed to evaluate the relationship between noninvasive imaging and biochemical markers in diabetic and nondiabetic patients diagnosed with NAFLD. Materials and Methods: The study was conducted from (September 2017) to (December 2017) on adults admitted to Internal Medicine and Gastroenterology outpatient clinics with hepatic steatosis reported on ultrasound or transient elastography within the last six months that exclude patients with other liver diseases or alcohol abuse. The data were collected and analyzed retrospectively. Number cruncher statistical system (NCSS) 2007 program was used for statistical analysis. Results: 116 patients were included in this study. Diabetic patients compared to nondiabetics had significantly higher Controlled Attenuation Parameter (CAP), Liver Stiffness Measurement (LSM) and fibrosis values. Also, hypertension, hepatomegaly, high BMI, hypertriglyceridemia, hyperglycemia, high A1c, and hyperuricemia were found to be risk factors for NAFLD progression to fibrosis. Advanced fibrosis (F3, F4) was present in 18,6 % of all our patients; 35,8 % of diabetic and 5,7 % of nondiabetic patients diagnosed with hepatic steatosis. Conclusion: Transient elastography is now used in daily clinical practice as an accurate noninvasive tool during follow-up of patients with fatty liver. Early diagnosis of the stage of liver fibrosis improves the monitoring and management of patients, especially in those with metabolic syndrome criteria.

Keywords: diabetes, elastography, fatty liver, fibrosis, metabolic syndrome

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Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

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Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

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Authors: Gökçe Erdemir, İlhan Yaylım, Serap Erdem-Kuruca, Musa Mutlu Can

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It has been determined that the main reason for the death of cancer disease is caused by metastases rather than the primary tumor. The cells that leave the primary tumor and enter the circulation and cause metastasis in the secondary organs are called "circulating tumor cells" (CTCs). The presence and number of circulating tumor cells has been associated with poor prognosis in many major types of cancer, including breast, prostate, and colorectal cancer. It is thought that knowledge of circulating tumor cells, which are seen as the main cause of cancer-related deaths due to metastasis, plays a key role in the diagnosis and treatment of cancer. The fact that tissue biopsies used in cancer diagnosis and follow-up are an invasive method and are insufficient in understanding the risk of metastasis and the progression of the disease have led to new searches. Liquid biopsy tests performed with a small amount of blood sample taken from the patient for the detection of CTCs are easy and reliable, as well as allowing more than one sample to be taken over time to follow the prognosis. However, since these cells are found in very small amounts in the blood, it is very difficult to capture them and specially designed analytical techniques and devices are required. Methods based on the biological and physical properties of the cells are used to capture these cells in the blood. Early diagnosis is very important in following the prognosis of tumors of epithelial origin such as breast, lung, colon and prostate. Molecules such as EpCAM, vimentin, and cytokeratins are expressed on the surface of cells that pass into the circulation from very few primary tumors and reach secondary organs from the circulation, and are used in the diagnosis of cancer in the early stage. For example, increased EpCAM expression in breast and prostate cancer has been associated with prognosis. These molecules can be determined in some blood or body fluids to be taken from patients. However, more sensitive methods are required to be able to determine when they are at a low level according to the course of the disease. The aim is to detect these molecules found in very few cancer cells with the help of sensitive, fast-sensing biosensors, first in breast cancer cells reproduced in vitro and then in blood samples taken from breast cancer patients. In this way, cancer cells can be diagnosed early and easily and effectively treated.

Keywords: electrochemical biosensors, breast cancer, circulating tumor cells, EpCAM, Vimentin, Cytokeratins

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Authors: Hilal Keskin, Gülzade Uysal

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This study was conducted to determine the effect of bedside music mobile use on physiological parameters and pain level during intestinal stomaterapy in infants. The study was carried out with 66 babies (music mobile group: 33, Control group: 33) who were followed in the pediatric surgery and urology unit of Kanuni Sultan Süleyman Training and Research Hospital between December 2018- October 2019. Data were collected using the “Data Collection Form” and “FLACC Pain Scale.” They were evaluated using the appropriate statistical methods in the SPSS 22.0 program. The difference between the descriptive features of music mobile and control group was not significant (p> 0.05) groups are distributed homogeneously. When the in-group results were examined; There was no significant change in the mean values of Hearth Peak Beat (HPB), SpO2 and blood pressure of the infants in the music mobile group during stomaterapy (p>0.05). Body temperature and Face, Leg, Activity, Cry, Consolability (FLACC) Pain Scale scores were found to increase immediately after stomaterapy (p<0.05). It was found that the mean scores of KTA, body temperature and FLACC pain of the babies in the control group increased significantly after the stomaterapy and SpO2 value decreased (p <0,05). After 15 minutes from stomatherapy, KTA, blood pressure, body temperature and FLACC pain scores averaged; although SpO2 value increased, it was determined that it could not reach pre-stomaterapy value. Results between groups; KTA, SpO2, systolic/diastolic blood pressure, body temperature, and FLACC pain score mean values between groups were homogeneous before stomaterapy (p> 0.05). In the control group, a significant increase was found in the mean scores of KTA, body temperature and FLACC pain after stomaterapy compared to the bedside music mobile group, and a significant decrease in SpO2 values (p <0.05). In the control group, the mean body temperature and FLACC pain scores of the infants 15 minutes after stomaterapy were significantly increased and the SpO2 values were significantly lower than the bedside music group (p <0.05). According to the results of the research; The use of bedside music mobile during intestinal stomaterapy was found to be effective in decreasing the physiological parameters and pain level. It can be recommended for use in infants during painful interventions.

Keywords: intestinal stomatherapy, infant, musical mobile, pain, physiological parameters

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Authors: Engin Eroğlu, Oktay Yıldız, Necmi Aksoy, Akif Keten, Mehmet Kıvanç Ak, Şeref Keskin, Elif Atmaca, Sertaç Kaya

Abstract:

Nowadays, green spaces in urban areas are under threat and decreasing their percentages in the urban areas because of increasing population, urbanization, migration, and some cultural changes in quality. An important element of the natural landscape water and water-related natural ecosystems are exposed to corruption due to these pressures. A landscape has owned many different types of elements or units, a more dominant structure than other landscapes as good or bad perceptible extent different direction and variable reveals a unique structure and character of the landscape. Whereas landscapes deal with two main groups as urban and rural according to their location on the world, especially intersection areas of urban and rural named semi-urban or semi-rural present variety landscape features. The main components of the landscape are defined as patch-matrix-corridor. The corridors include quite various vegetation types such as riparian, wetland and the others. In urban areas, natural water corridors are an important elements of the diversity of the riparian vegetation cover. In particular, water corridors attract attention with a natural diversity and lack of fragmentation, degradation and artificial results. Thanks to these features, without a doubt, water corridors are the important component of all cities in the world. These corridors not only divide the city into two separate sides, but also assured the ecological connectivity between the two sides of the city. The main objective of this study is to determine the vegetation and habitat features of urban stream corridor according to environmental interactions. Within this context, this study will be realized that 'Asar Suyu' is an important component of the city of Düzce. Moreover, the riparian zone touched contiguous area borders of the city and overlaid the urban development limits of the city, determining of characteristics of the corridor will be carried out as floristic and habitat analysis. Consequently, vegetation structure and habitat features which play an important role between riparian zone vegetation covers and environmental interaction will be determined. This study includes first results of The Scientific and Technological Research Council of Turkey (TUBITAK-116O596; 'Determining of Landscape Character of Urban Water Corridors as Visual and Ecological; A Case Study of Asar Suyu in Duzce').

Keywords: corridor, Duzce, landscape ecology, riparian vegetation

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Authors: Mustafa İlhan Akbaş, Özlem Garibay, Ivan Garibay

Abstract:

The economic entities in innovation ecosystems form various industry clusters, in which they compete and cooperate to survive and grow. Within a successful and stable industry cluster, the entities acquire different roles that complement each other in the system. The universities and research centers have been accepted to have a critical role in these systems for the creation and development of innovations. However, the real effect of research institutions on regional economic growth is difficult to assess. In this paper, we present our approach for the identification of the impact of research activities on the regional entrepreneurship for a specific high-tech industry: optics and photonics. The optics and photonics has been defined as an enabling industry, which combines the high-tech photonics technology with the developing optics industry. The recent literature suggests that the growth of optics and photonics firms depends on three important factors: the embedded regional specializations in the labor market, the research and development infrastructure, and a dynamic small firm network capable of absorbing new technologies, products and processes. Therefore, the role of each factor and the dynamics among them must be understood to identify the requirements of the entrepreneurship activities in optics and photonics industry. There are three main contributions of our approach. The recent studies show that the innovation in optics and photonics industry is mostly located around metropolitan areas. There are also studies mentioning the importance of research center locations and universities in the regional development of optics and photonics industry. These studies are mostly limited with the number of patents received within a short period of time or some limited survey results. Therefore the first contribution of our approach is conducting a comprehensive analysis for the state and recent history of the photonics and optics research in the US. For this purpose, both the research centers specialized in optics and photonics and the related research groups in various departments of institutions (e.g. Electrical Engineering, Materials Science) are identified and a geographical study of their locations is presented. The second contribution of the paper is the analysis of regional entrepreneurship activities in optics and photonics in recent years. We use the membership data of the International Society for Optics and Photonics (SPIE) and the regional photonics clusters to identify the optics and photonics companies in the US. Then the profiles and activities of these companies are gathered by extracting and integrating the related data from the National Establishment Time Series (NETS) database, ES-202 database and the data sets from the regional photonics clusters. The number of start-ups, their employee numbers and sales are some examples of the extracted data for the industry. Our third contribution is the utilization of collected data to investigate the impact of research institutions on the regional optics and photonics industry growth and entrepreneurship. In this analysis, the regional and periodical conditions of the overall market are taken into consideration while discovering and quantifying the statistical correlations.

Keywords: entrepreneurship, industrial clusters, optics, photonics, emerging industries, research centers

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Authors: Deybith Venegas-Rojas, Sercan Keskin, Svenja Riekeberg, Sana Azim, Stephanie Manz, R. J. Dwayne Miller, Hoc Khiem Trieu

Abstract:

Liquid Transmission Electron Microscopy (TEM) is a growing area with a broad range of applications from physics and chemistry to material engineering and biology, in which it is possible to image in-situ unseen phenomena. For this, a nanofluidic device is used to insert the nanoflow with the sample inside the microscope in order to keep the liquid encapsulated because of the high vacuum. In the last years, Si3N4 windows have been widely used because of its mechanical stability and low imaging contrast. Nevertheless, the pressure difference between the inside fluid and the outside vacuum in the TEM generates bulging in the windows. This increases the imaged fluid volume, which decreases the signal to noise ratio (SNR), limiting the achievable spatial resolution. With the proposed device, the membrane is fortified with a microstructure capable of stand higher pressure differences, and almost removing completely the bulging. A theoretical study is presented with Finite Element Method (FEM) simulations which provide a deep understanding of the membrane mechanical conditions and proves the effectiveness of this novel concept. Bulging and von Mises Stress were studied for different membrane dimensions, geometries, materials, and thicknesses. The microfabrication of the device was made with a thin wafer coated with thin layers of SiO2 and Si3N4. After the lithography process, these layers were etched (reactive ion etching and buffered oxide etch (BOE) respectively). After that, the microstructure was etched (deep reactive ion etching). Then the back side SiO2 was etched (BOE) and the array of free-standing micro-windows was obtained. Additionally, a Pyrex wafer was patterned with windows, and inlets/outlets, and bonded (anodic bonding) to the Si side to facilitate the thin wafer handling. Later, a thin spacer is sputtered and patterned with microchannels and trenches to guide the nanoflow with the samples. This approach reduces considerably the common bulging problem of the window, improving the SNR, contrast and spatial resolution, increasing substantially the mechanical stability of the windows, allowing a larger viewing area. These developments lead to a wider range of applications of liquid TEM, expanding the spectrum of possible experiments in the field.

Keywords: liquid cell, liquid transmission electron microscopy, nanofluidics, nanofluidic cell, thin films

Procedia PDF Downloads 230