Search results for: Gulseren Mutlu

Authors: Busra Mutlu Ipek, Merve Mutlu, Ahmet Mutlu

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Novel coronavirus COVID-19, which has recently influenced the world, poses a great threat to humanity. In order to overcome this challenging situation, scientists are working on developing effective vaccine against coronavirus. Many experts and researchers have also produced articles and done studies on this highly important subject. In this direction, this special topic was chosen for article to make a contribution to this area. The purpose of this article is to perform RNA sequence analysis of selected virus forms in the Coronaviridae family and predict/classify SARS-CoV-2 (COVID-19) from other selected complete genomes in coronaviridae family using proposed Artificial Neural Network(ANN) algorithm.

Keywords: Coronaviridae family, COVID-19, RNA sequencing, ANN, neural network

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Authors: Gulseren Mutlu, Gurupdesh Pandher

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This paper studies the strategic interplay between innovation, incentives, expropriation threat and disputes arising from expropriation from an intra-organization perspective. We present a simple principal-agent model with hidden actions and hidden information in which two employees can choose how much (innovative) effort to exert, whether to expropriate the innovation of the other employee and whether to dispute if innovation is expropriated. The organization maximizes its expected payoff by choosing the optimal reward scheme for both employees as well as whether to encourage or discourage disputes. We analyze two mechanisms under which innovative ideas are not expropriated. First, we show that under a non-contestable mechanism (in which the organization discourages disputes among employees), the organization has to offer a “rent” to the potential expropriator. However, under a contestable mechanism (in which the organization encourages disputes), there is no need for such rent. If the cost of resolving the dispute is negligible, the organization’s expected payoff is higher under a contestable mechanism. Second, we develop a comparable team mechanism in which innovation takes place as a result of the joint efforts of employees and innovation payments are made based on the team outcome. We show that if the innovation value is low and employees have similar productivity, then the organization is better off under a contestable mechanism. On the other hand, if the innovation value is high, the organization is better off under a team mechanism. Our results have important practical implications for the design of innovation reward system for employees, hiring policy and governance for different companies.

Keywords: innovation, incentives, expropriation threat, dispute resolution

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Authors: Gülseren Kırbaş Doğan, Emin Karakurt, Mushap Kuru, Hilmi Nuhoğlu

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Developmental anomalies can be caused by defects in bone tissue, cartilage tissue, or primitive mesenchymal tissue. Genetic-, environmental-, teratogenic-, faulty breeding selection–, or feeding-related anomalies can be observed either locally or systemically. This study aimed to evaluate in detail the various anomalies in six calves according to pathological and anatomical investigations. Six calves were delivered to the Department of Pathology at the Kafkas University Faculty of Veterinary Medicine between 2017 and 2019. These calves comprised one with anencephaly, one with the diencephalic syndrome, one with Schistosoma reflexum, two with anasarca, and one with nasal and calvarium openings. After necropsy, samples were taken from the organs, foreseen, and routine pathological examinations were performed. Following these procedures, the calves were brought to the anatomy laboratory and anatomically examined. As a result, various anomalies in 6 calves were evaluated according to pathological and anatomical investigations. These findings are believed to contribute to the literature.

Keywords: anatomy, anomaly, calf, pathology

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Authors: Metehan Mutlu, Meltem Elitas

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This study aims to provide an automated method for placing the balloon uterine stents after hysteroscopy adhesiolysis. Currently, there are no automatized tools to place the balloon uterine stent; therefore, surgeons into the endometrial cavity manually fit it. However, it is very hard to pass the balloon stent through the cervical canal, which is roughly 10mm after the surgery. Our method aims to provide an effective and practical way of placing the stent, by automating the procedure through our designed device. Furthermore, our device does the required tasks fast compared to traditional methods, reduces the narcosis time, and decreases the bacterial contamination risks.

Keywords: balloon uterine stent, endometrial cavity, hysteroscopy, motorized-tool

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Authors: Erdal Akyol, Mutlu Alkan

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Multi criteria decision analysis (MDCA) covers both data and experience. It is very common to solve the problems with many parameters and uncertainties. GIS supported solutions improve and speed up the decision process. Weighted grading as a MDCA method is employed for solving the geotechnical problems. In this study, geotechnical parameters namely soil type; SPT (N) blow number, shear wave velocity (Vs) and depth of underground water level (DUWL) have been engaged in MDCA and GIS. In terms of geotechnical aspects, the settlement suitability of the municipal area was analyzed by the method. MDCA results were compatible with the geotechnical observations and experience. The method can be employed in geotechnical oriented microzoning studies if the criteria are well evaluated.

Keywords: GIS, spatial analysis, multi criteria decision analysis, geotechnics

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Authors: Hülya Kuru Mutlu, Mustafa Kulakcı, Uğur Serincan

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The sun is one of the latest developments in renewable energy sources, which has a variety of application. Solar energy is the most preferred renewable energy sources because it can be used directly, it protects the environment and it is economic. In this work, we investigated that important parameter of GaAs-based solar cells with respect to the growth temperature. The samples were grown on (100) oriented p-GaAs substrates by solid source Veeco GEN20MC MBE system equipped with Ga, In, Al, Si, Be effusion cells and an Arsenic cracker cell. The structures of the grown samples are presented. After initial oxide desorption, Sample 1 and Sample 2 were grown at about 585°C and 535°C, respectively. From the grown structures, devices were fabricated by using the standard photolithography procedure. Current-voltage measurements were performed at room temperature (RT). It is observed that Sample 1 which was grown at 585°C has higher efficiency and fill factor compared to Sample 2. Hence, it is concluded that the growth temperature of 585°C is more suitable to grow GaAs-based solar cells considering our samples used in this study.

Keywords: molecular beam epitaxy, solar cell, current-voltage measurement, Sun

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Authors: Esra Cansever Mutlu, Muge Sennaroglu Bostan, Fatemeh Bahadori, Ebru Toksoy Oner, Mehmet S. Eroglu

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Paclitaxel is used in treatment of different cancer types mainly breast, ovarian, lung and Kaposi’s sarcoma. It is poorly soluble in water; therefore, currently used formulations tremendously show side-effects and high toxicity. Encapsulation of the drug in a nano drug carrier which causes both reducing side effects and increasing drug activity is a desired new approach for the nano-medicine to target the site of cancer. In this study, synthesis of a novel nano paclitaxel formulation made of a new amphiphilic monomer was followed by the investigation of its pharmacological properties. UV radical polymerization was carried out by using the monomer Lecithin-2-Acrylamido-2-methylpropane (L-AMPS) and the drug-spacer, to obtain sterically high stabilized, biocompatible and biodegradable phospholipid nanoparticles, in which the drug paclitaxel (Pxl) was encapsulated (NanoPxl). Particles showed high drug loading capacity (68%) and also hydrodynamic size less than 200 nm with slight negative surface charge. The drug release profile was obtained and in vitro cytotoxicity test was performed on MCF-7 cell line. Consequently, these data indicated that paclitaxel loaded Lecithin-AMPS/PCL-MAC nanoparticles can be considered as a new, safe and effective nanocarrier for the treatment of breast cancer.

Keywords: paclitaxel, nanoparticle, drug delivery, L-AMPS

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Authors: Gulseren Kirbas, Mushap Kuru, Buket Bakir, Ebru Karadag Sari

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Capra (mountain goat) is a genus comprising nine species. The domestic goat (C. aegagrus hircus) is a subspecies of the wild goat that is domesticated. This study aimed to determine the anatomical structure of the salpinx and ovary of the Anatolian wild goat (C. aegagrus aegagrus). Animals that were taken to the Kafkas University Wildlife Rescue and Rehabilitation Center, Kars, Turkey, because of various reasons, such as traffic accidents and firearm injuries, were used in this study. The salpinges and ovaries of four wild goats of similar ages, which could not be rescued by the Center despite all interventions, were dissected. Measurements were taken from the right-left salpinx and ovary using digital calipers. The weights of each ovary and salpinx were measured using a precision scale (min: 0.0001 g − max: 220 g, code: XB220A; Precisa, Swiss). The histological structure of the tissues was examined after weighing the organs. The tissue samples were fixed in 10% formaldehyde for 24 h. Then a routine procedure was applied, and the tissues were embedded in paraffin. Mallory’s modified triple staining was used to demonstrate the general structure of the salpinx. The salpinx was found to consist of three different regions (infundibulum, ampulla, and isthmus). These regions consisted of tunica mucosa, tunica muscularis, and tunica serosa. The prismatic epithelial cells were observed in the lamina epithelialis of tunica mucosa in every region, but the prismatic fimbrae cells occurred most in the infundibulum. The ampulla was distinguished by its many mucosal folds. It was the longest region of the salpinx and was joined to the isthmus via the ampullary–isthmus junction. Isthmus was the caudal end of the salpinx joined to the uterus and had the thickest tunica muscularis compared with the other regions. The mean length of the ovary was 13.22 ± 1.27 mm, width was 8.46 ± 0.88 mm, the thickness was 5.67 ± 0.79 mm, and weight was 0.59 ± 0.17 g. The average length of the salpinx was 58.11 ± 14.02 mm, width was 0.80 ± 0.22 mm, the thickness was 0.41 ± 0.01 mm, and weight was 0.30 ± 0.08 g. In conclusion, the Anatolian wild goat, which is included in wildlife diversity in Turkey, has been disappearing due to illegal and uncontrolled hunting as well as traffic accidents in recent years. These findings are believed to contribute to the literature.

Keywords: Anatolian wild goat, anatomy, ovary, salpinx

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Authors: Serdal Sabanci, Mutlu Çevik, Derya Tezcan, Cansu Çelebi, Filiz Içier

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Ultrasound is defined as sound waves having frequencies higher than 20 kHz, which is greater than the limits of the human hearing range. In recent years, ultrasonic treatment is an emerging technology being used increasingly in the food industry. It is applied as an alternative technique for different purposes such as microbial and enzyme inactivation, extraction, drying, filtration, crystallization, degas, cutting etc. Red beetroot (Beta vulgaris L.) is a root vegetable which is rich in mineral components, folic acid, dietary fiber, anthocyanin pigments. In this study, the application of low frequency high intensity ultrasound to the red beetroot slices and red beetroot juice for different treatment times (0, 5, 10, 15, 20 min) was investigated. Ultrasonicated red beetroot slices were also squeezed immediately. Changes on colour, betanin, pH and titratable acidity properties of red beetroot juices (the ultrasonicated juice (UJ) and the juice from ultrasonicated slices (JUS)) were determined. Although there was no significant difference statistically in the changes of color value of JUS samples due to ultrasound application (p>0.05), the color properties of UJ samples ultrasonicated for low durations were statistically different from raw material (p<0.05). The difference between color values of UJ and raw material disappeared (p>0.05) as the ultrasonication duration increased. The application of ultrasound to red beet root slices adversely affected and decreased the betanin content of JUS samples. On the other hand, the betanin content of UJ samples increased as the ultrasonication duration increased. Ultrasound treatment did not affect pH and titratable acidity of red beetroot juices statistically (p>0.05). The results suggest that ultrasound technology is the simple and economical technique which may successfully be employed for the processing of red beetroot juice with improved color and betanin quality. However, further investigation is still needed to confirm this.

Keywords: red beetroot, ultrasound, color, betanin

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Authors: Sebnem Canikli Engin, Mutlu Sevinc, Hasan Guzelbektes

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In this study, we aim to define the effects of erythromycin and bethanechol which are prokinetic agents, on the value of abomasal discharge in healthy, diarrhea and premature calves. In the work, 5 healty calves, 12 diarrheaic calves and 12 premature calves, amounting to a total of 29 calves. In healty calves work; the same 5 calves were used for controlled, erythromycin and bethanechol studies (there was a 48-hour waiting period between each work). In diarrheic calves work; 12 diarrheic calves were used during the study (4 of them for control group, 4 of them bethanechol group and last 4 calves erythromycin group). In premature calves works; 12 premature calves were used during the study (4 of them for control group, 4 of them bethanechol group and last 4 calves erythromycin group). 10 mg/kg IM dose of erythromycin were applied to each erythromycin group, 0,07 mg/kg IM dose of bethanechol were applied on bethanechol group. No drugs were applied to the control group and substitution milk was given to all calves. 50 mg/kg acetominophen and 25 gram/L glucose have been added into the substitution milk to evaluate the speed of gastrointestinal motility with the test results of absorptions of acetominophen and glucose. The blood samples have been taken before substitution milk application and 30, 60, 90, 120, 180, 240 and 300 minutes after substitution milk application. Respiratory rates and number of heartbeats were also recorded during the test time. No changes were observed in the number of heartbeats, respiratory rates and general conditions for all groups after drug application. It is observed that, the feces of some calves became slightly watery and viscous and premature calves generaly defecated after 180 minutes. When Cmax, Tmax and AUC values of acetaminophen and glucose are compared with control group’s after applying erythromycin on the calves in the premature group, we obtain higher Cmax (P<0,05), shorter Tmax and greather AUC (P>0,05) values. In conclusion, according to clinical and laboratory findings, it may be stated that the application of 10 mg/kg doze of erythromycin IM has provided faster abomazal emptying in premature calves.

Keywords: abomazal emptying, bethanechol, calf, erythromycin

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Authors: Maryam Parsian, Pelin Mutlu, Ufuk Gunduz

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Two-dimensional cell culture affords simplicity and low cost, but it has serious limitations; lacking cell-cell and cell-matrix interactions that are present in tissues. Cancer cells grown in 3D culture systems have distinct phenotypes of adhesion, growth, migration, invasion as well as profiles of gene and protein expression. These interactions cause the 3D-cultured cells to acquire morphological and cellular characteristics relevant to in vivo tumors. Palbociclib is a chemotherapeutic agent for the treatment of ER-positive and HER-negative metastatic breast cancer. Poly-amidoamine (PAMAM) dendrimer is a well-defined, special three-dimensional structure and has a multivalent surface and internal cavities that can play an essential role in drug delivery systems. In this study, palbociclib is loaded onto the magnetic PAMAM dendrimer. Hanging droplet method was used in order to form 3D spheroids. The possible toxic effects of both free drug and drug loaded nanoparticles were evaluated in 2D and 3D MCF-7, MD-MB-231 and SKBR-3 breast cancer cell culture models by performing MTT cell viability and Alamar Blue assays. MTT analysis was performed with six different doses from 1000 µg/ml to 25 µg/ml. Drug unloaded PAMAM dendrimer did not demonstrate significant toxicity on all breast cancer cell lines. The results showed that 3D spheroids are clearly less sensitive than 2D cell cultures to free palbociclib. Also, palbociclib loaded PAMAM dendrimers showed more toxic effect than free palbociclib in all cell lines at 2D and 3D cultures. The results suggest that the traditional cell culture method (2D) is insufficient for mimicking the actual tumor tissue. The response of the cancer cells to anticancer drugs is different in the 2D and 3D culture conditions. This study showed that breast cancer cells are more resistant to free palbociclib in 3D cultures than in 2D cultures. However, nanoparticle loaded drugs can be more cytotoxic when compared to free drug.

Keywords: 2D and 3D cell culture, breast cancer, palbociclibe, PAMAM magnetic nanoparticles

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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: Ece Cigdem Mutlu, Burak Alakent

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Maintaining the quality of manufactured products at a desired level depends on the stability of process dispersion and location parameters and detection of perturbations in these parameters as promptly as possible. Shewhart control chart is the most widely used technique in statistical process monitoring to monitor the quality of products and control process mean and variability. In the application of Xbar control charts, sample standard deviation and sample mean are known to be the most efficient conventional estimators in determining process dispersion and location parameters, respectively, based on the assumption of independent and normally distributed datasets. On the other hand, there is no guarantee that the real-world data would be normally distributed. In the cases of estimated process parameters from Phase I data clouded with outliers, efficiency of traditional estimators is significantly reduced, and performance of Xbar charts are undesirably low, e.g. occasional outliers in the rational subgroups in Phase I data set may considerably affect the sample mean and standard deviation, resulting a serious delay in detection of inferior products in Phase II. For more efficient application of control charts, it is required to use robust estimators against contaminations, which may exist in Phase I. In the current study, we present a simple approach to construct robust Xbar control charts using average distance to the median, Qn-estimator of scale, M-estimator of scale with logistic psi-function in the estimation of process dispersion parameter, and Harrell-Davis qth quantile estimator, Hodge-Lehmann estimator and M-estimator of location with Huber psi-function and logistic psi-function in the estimation of process location parameter. Phase I efficiency of proposed estimators and Phase II performance of Xbar charts constructed from these estimators are compared with the conventional mean and standard deviation statistics both under normality and against diffuse-localized and symmetric-asymmetric contaminations using 50,000 Monte Carlo simulations on MATLAB. Consequently, it is found that robust estimators yield parameter estimates with higher efficiency against all types of contaminations, and Xbar charts constructed using robust estimators have higher power in detecting disturbances, compared to conventional methods. Additionally, utilizing individuals charts to screen outlier subgroups and employing different combination of dispersion and location estimators on subgroups and individual observations are found to improve the performance of Xbar charts.

Keywords: average run length, M-estimators, quality control, robust estimators

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Authors: Elif Gencturk, Ekin Yurdakul, Ahmet Y. Celik, Senol Mutlu, Kutlu O. Ulgen

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Yeast cells are generally used as a model system of eukaryotes due to their complex genetic structure, rapid growth ability in optimum conditions, easy replication and well-defined genetic system properties. Thus, yeast cells increased the knowledge of the principal pathways in humans. During fermentation, carbohydrates (hexoses and pentoses) degrade into some toxic by-products such as 5-hydroxymethylfurfural (5-HMF or HMF) and furfural. HMF influences the ethanol yield, and ethanol productivity; it interferes with microbial growth and is considered as a potent inhibitor of bioethanol production. In this study, yeast single cell behavior under HMF application was monitored by using a continuous flow single phase microfluidic platform. Microfluidic device in operation is fabricated by hot embossing and thermo-compression techniques from cyclo-olefin polymer (COP). COP is biocompatible, transparent and rigid material and it is suitable for observing fluorescence of cells considering its low auto-fluorescence characteristic. The response of yeast cells was recorded through Red Fluorescent Protein (RFP) tagged Nop56 gene product, which is an essential evolutionary-conserved nucleolar protein, and also a member of the box C/D snoRNP complexes. With the application of HMF, yeast cell proliferation continued but HMF slowed down the cell growth, and after HMF treatment the cell proliferation stopped. By the addition of fresh nutrient medium, the yeast cells recovered after 6 hours of HMF exposure. Thus, HMF application suppresses normal functioning of cell cycle but it does not cause cells to die. The monitoring of Nop56 expression phases of the individual cells shed light on the protein and ribosome synthesis cycles along with their link to growth. Further computational study revealed that the mechanisms underlying the inhibitory or inductive effects of HMF on growth are enriched in functional categories of protein degradation, protein processing, DNA repair and multidrug resistance. The present microfluidic device can successfully be used for studying the effects of inhibitory agents on growth by single cell tracking, thus capturing cell to cell variations. By metabolic engineering techniques, engineered strains can be developed, and the metabolic network of the microorganism can thus be manipulated such that chemical overproduction of target metabolite is achieved along with the maximum growth/biomass yield.  

Keywords: COP, HMF, ribosome biogenesis, thermoplastic microbioreactor, yeast

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Authors: Busra Gundede, Ozal Mutlu, Nagihan Gulsoy

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Background: Over the years, material research has led to the development of numerous metals and alloys for using in biomedical applications. One of the major tasks of biomaterial research is the functionalization of the material surface to improve the biocompatibility according to a specific application. 316L and 316L alloys are excellent for various bio-applications. This research was investigated the effect of titanium (Ti), niobium (Nb), and zirconium (Zr) additives on injection molded austenitic grade 316L stainless steels in vitro biocompatibility. For this purpose, cytotoxic tests were performed to evaluate the potential biocompatibility of the specimens. Materials and Methods: 3T3 fibroblast were cultivated in DMEM supplemented with 10% fetal bovine serum and %1 penicillin-streptomycin at 37°C with 5% CO2 and 95%humidity. Trypsin/EDTA solution was used to remove cells from the culture flask. Cells were reseeded at a density of 1×105cell in 25T flasks. The medium change took place every 3 days. The trypan blue assay was used to determine cell viability. Cell viability is calculated as the number of viable cells divided by the total number of cells within the grids on the cell counter machine counted the number of blue staining cells and the number of total cells. Cell viability should be at least 95% for healthy log-phase cultures. MTT assay was assessed for 96-hours. Cells were cultivated in 6-well flask within 5 ml DMEM and incubated as same conditions. 0,5mg/ml MTT was added for 4-hours and then acid-isoprohanol was added for solubilize to formazan crystals. Cell morphology after 96h was investigated by SEM. The medium was removed, samples were washed with 0.15 M PBS buffer and fixed for 12h at 4- 8°C with %2,5 gluteraldehyte. Samples were treated with 1% osmium tetroxide. Samples were then dehydrated and dried, mounted on appropriate stubs with colloidal silver and sputter-coated with gold. Images were collected using a scanning electron microscope. ROS assay is a cell viability test for in vitro studies. Cells were grown for 96h, ROS solution added on cells in 6 well plate flask and incubated for 1h. Fluorescence signal indicates ROS generation by cells. Results: Trypan Blue exclusion assay results were 96%, 92%, 95%, 90%, 91% for negative control group, 316L, 316L-Ti, 316L-Nb and 316L-Zr, respectively. Results were found nearly similar to each other when compared with control group. Cell viability from MTT analysis was found to be 100%, 108%, 103%, 107%, and 105% for the control group, 316L, 316L-Ti, 316L-Nb and 316L-Zr, respectively. Fluorescence microscopy analysis indicated that all test groups were same as the control group in ROS assay. SEM images demonstrated that the attachment of 3T3 cells on biomaterials. Conclusion: We, therefore, concluded that Ti, Nb and Zr additives improved physical properties of 316L stainless. In our in vitro experiments showed that these new additives did not modify the cytocompatibility of stainless steel and these additives on 316L might be useful for biomedical applications.

Keywords: 316L stainles steel, biocompatibility, cell culture, Ti, Nb, Zr

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