Search results for: Pakize Neslihan Taslı

Authors: Pakize Neslihan Taslı, Alev Cumbul, Gul Merve Yalcın, Fikrettin Sahin

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A key experimental trial in the regeneration of large oral and craniofacial defects is the neogenesis of osseous and ligamentous interfacial structures. Currently, oral regenerative medicine strategies are unpredictable for repair of tooth supporting tissues destroyed as a consequence of trauma, chronic infection or surgical resection. A different approach combining the gel-casting method with Hydroxy Apatite HA-based scaffold and different cell lineages as a hybrid system leads to successively mimic the early stage of tooth development, in vitro. HA is widely accepted as a bioactive material for guided bone and tooth regeneration. In this study, it was reported that, HA porous scaffold preparation, characterization and evaluation of structural and chemical properties. HA is the main factor that exists in tooth and it is in harmony with structural, biological, and mechanical characteristics. Here, this study shows mimicking immature tooth at the late bell stage design and construction of HA scaffolds for cell transplantation of human Adipose Stem Cells (hASCs), human Bone Marrow Stem Cells (hBMSCs) and Gingival Epitelial cells for the formation of human tooth dentin-pulp-enamel complexes in vitro. Scaffold characterization was demonstrated by SEM, FTIR and pore size and density measurements. The biological contraction of dental tissues against each other was demonstrated by mRNA gene expressions, histopatologic observations and protein release profile by ELISA tecnique. The tooth shaped constructs with a pore size ranging from 150 to 300 µm arranged by gathering right amounts of materials provide interconnected macro-porous structure. The newly formed tissue like structures that grow and integrate within the HA designed constructs forming tooth cementum like tissue, pulp and bone structures. These findings are important as they emphasize the potential biological effect of the hybrid scaffold system. In conclusion, this in vitro study clearly demonstrates that designed 3D scaffolds shaped as a immature tooth at the late bell stage were essential to form enamel-dentin-pulp interfaces with an appropriate cell and biodegradable material combination. The biomimetic architecture achieved here is providing a promising platform for dental tissue engineering.

Keywords: tooth regeneration, tissue engineering, adipose stem cells, hydroxyapatite tooth engineering, porous scaffold

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Authors: Enver Kucukkulahli, Pakize Erdogmus, Kemal Polat

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The 2D image segmentation is a significant process in finding a suitable region in medical images such as MRI, PET, CT etc. In this study, we have focused on 2D MRI images for image segmentation process. We have designed a GUI (graphical user interface) written in MATLABTM for 2D MRI images. In this program, there are two different interfaces including data pre-processing and image clustering or segmentation. In the data pre-processing section, there are median filter, average filter, unsharp mask filter, Wiener filter, and custom filter (a filter that is designed by user in MATLAB). As for the image clustering, there are seven different image segmentations for 2D MR images. These image segmentation algorithms are as follows: PSO (particle swarm optimization), GA (genetic algorithm), Lloyds algorithm, k-means, the combination of Lloyds and k-means, mean shift clustering, and finally BBO (Biogeography Based Optimization). To find the suitable cluster number in 2D MRI, we have designed the histogram based cluster estimation method and then applied to these numbers to image segmentation algorithms to cluster an image automatically. Also, we have selected the best hybrid method for each 2D MR images thanks to this GUI software.

Keywords: image segmentation, clustering, GUI, 2D MRI

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Authors: Neslihan Karatas, Sibel Ecemis Kilic

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This paper aims to examine macro-scale plans and projects/investments which have been prepared for İzmir since The Republican Period. Macro projects that were proposed by central government, local government, industry and urban actors such as the chamber of commerce will be discussed and these projects and its reflections to the city's macro scale planning decisions will be evaluated based on existing development. Effects of macro plans, the related private and public investments, the developments of unplanned/specific projects to the current city form will be discussed. The factors and plans which determine urban form and the problems caused by unanticipated/uncontrolled developments will be evaluated. The proposals will be developed about more efficient planning process.

Keywords: Izmir, macro projects, macro investments, planning

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Authors: Pakize Ozlem Kurt Polat, Gizem Metin, Koksal Yagdi

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In order to evaluate the effect of the different sources of salt on germination and early growth of five wheat cultivars (Katea, Bezostaja, Koksal-2000, Golia, Pehlivan) an experiment was conducted at the seed laboratory of the Uludag University, Agricultural Faculty, Department of Field Crops in Bursa/Turkey. Seeds were applied in five different resources media (KCl % 2, KCl %4, KNO₃ %0,5, KH₂PO₄ %0,5, PEG %10) and distilled water as the control). The seed was fully immersed in priming media at a temperature of 24ᵒC for durations of 12 and 24hours. Six different agronomic characters (seed germination, stem length, stem weight, radicle length, fresh weight, dry weight) were measured in 7th days and 14th days. Maximum seed germination percentage of seven days are Pehlivan was observed when the seeds were applied by KH₂PO₄ and Katea by distilled water as a control. The most stem length and stem weight were obtained for seeds were applied by KH₂PO₄ %0,5 with Katea and Bezostja immersed in priming media at 12h intervals beginning 7d after planting. Seeds were applied KH₂PO₄ %0,5 media produced maximum radicle length by Koksal and dry weight by Katea. The freshest weight obtains in Katea by KNO₃ %0,5 immersed in priming media at 24h. The most germination percent, dry weight, stem length of fourteen days was observed in Katea which subjected to KH₂PO₄ %0,5 solution. The most radicle length was observed Katea and Koksal in media of KH₂PO₄ %0,5. The most stem length was obtained for seeds were applied by KH₂PO₄ %0,5 and KNO₃ with Katea and Bezostaja. When the applied chemicals and all days examined KH₂PO₄ %0,5 treatment in fourteen days and immersed for the duration of 24 hours had better effects than other medias, seven days treatments and 12hours immersed. As a result of this research, the best response of media for the wheat germination can be said that the KH₂PO₄ %0,5 immersed in priming media at 24h intervals beginning 14 days after planting.

Keywords: germination, priming, seedling growth, wheat

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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: Neslihan Genckal, Reha Gursoy, Vedat Z. Dogan

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In this study, dynamic responses of composite plates on elastic foundations subjected to impact and moving loads are investigated. The first order shear deformation (FSDT) theory is used for moderately thick plates. Pasternak-type (two-parameter) elastic foundation is assumed. Elastic foundation effects are integrated into the governing equations. It is assumed that plate is first hit by a mass as an impact type loading then the mass continues to move on the composite plate as a distributed moving loading, which resembles the aircraft landing on airport pavements. Impact and moving loadings are modeled by a mass-spring-damper system with a wheel. The wheel is assumed to be continuously in contact with the plate after impact. The governing partial differential equations of motion for displacements are converted into the ordinary differential equations in the time domain by using Galerkin’s method. Then, these sets of equations are solved by using the Runge-Kutta method. Several parameters such as vertical and horizontal velocities of the aircraft, volume fractions of the steel rebar in the reinforced concrete layer, and the different touchdown locations of the aircraft tire on the runway are considered in the numerical simulation. The results are compared with those of the ABAQUS, which is a commercial finite element code.

Keywords: elastic foundation, impact, moving load, thick plate

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Authors: Cahit Demetgul, Sahin Bayraktar, Neslihan Beyazit

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Metalloenzymes are enzyme proteins containing metal ions, which are directly bound to the protein or to enzyme-bound nonprotein components. One of the major metalloenzymes that play a key role in oxidation reactions is catechol oxidase, which shows catecholase activity i.e. oxidation of a broad range of catechols to quinones through the four-electron reduction of molecular oxygen to water. Studies on the model compounds mimicking the catecholase activity are very useful and promising for the development of new, more efficient bioinspired catalysts, for in vitro oxidation reactions. In this study, a new tetradentate asymmetrical Schiff-base and its Cu(II) complex were synthesized by condensation of 4-nitro-1,2-phenylenediamine with 6-formyl-7-hydroxy-5-methoxy-2-methylbenzopyran-4-one and by using an appropriate Cu(II) salt, respectively. The prepared compounds were characterized by elemental analysis, FT-IR, NMR, UV-Vis and magnetic susceptibility. The catecholase-mimicking activity of the new Schiff Base Cu(II) complex was performed for the oxidation of 3,5-di-tert-butylcatechol (3,5-DTBC) in methanol at 25 °C, where the electronic spectra were recorded at different time intervals. The yield of the quinone (3,5-DTBQ) was determined from the measured absorbance at 400 nm of the resulting solution. The compatibility of catalytic reaction with Michaelis-Menten kinetics was also investigated. In conclusion, we have found that our new Schiff Base Cu(II) complex presents a significant capacity to catalyze the oxidation reaction of the catechol to o-quinone.

Keywords: catecholase activity, Michaelis-Menten kinetics, Schiff base, transition metals

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Authors: Neslihan Beyazit, Sahin Bayraktar, Cahit Demetgul

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Transition metal ions have an important role in biochemistry and biomimetic systems and may provide the basis of models for active sites of biological targets. The presence of copper(II), iron(II) and zinc(II) is crucial in many biological processes. Tetradentate N2O2 donor Schiff base ligands are well known to form stable transition metal complexes and these complexes have also applications in clinical and analytical fields. In this study, we present salient structural features and the details of cathecholase activity of Fe(II) complex of a new Schiff Base ligand. A new asymmetrical N2O2 donor Schiff base ligand and its Fe(II) complex were synthesized by condensation of 4-nitro-1,2 phenylenediamine with 6-formyl-7-hydroxy-5-methoxy-2-methylbenzopyran-4-one and by using an appropriate Fe(II) salt, respectively. Schiff base ligand and its metal complex were characterized by using FT-IR, 1H NMR, 13C NMR, UV-Vis, elemental analysis and magnetic susceptibility. In order to determine the kinetics parameters of catechol oxidase-like activity of Schiff base Fe(II) complex, the oxidation of the 3,5-di-tert-butylcatechol (3,5-DTBC) was measured at 25°C by monitoring the increase of the absorption band at 390-400 nm of the product 3,5-di-tert-butylcatequinone (3,5-DTBQ). The compatibility of catalytic reaction with Michaelis-Menten kinetics also investigated by the method of initial rates by monitoring the growth of the 390–400 nm band of 3,5-DTBQ as a function of time. Kinetic studies showed that Fe(II) complex of the new N2O2 donor Schiff base ligand was capable of acting as a model compound for simulating the catecholase properties of type-3 copper proteins.

Keywords: catecholase activity, Michaelis-Menten kinetics, Schiff base, transition metals

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Authors: Sibel Ecemis Kilic, Neslihan Karatas

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The concept of urban renewal came up with interventions to the urban areas which have social and economic problems aimed at gaining the city. In Turkey after 2000, urban renewal has become a frequent topic on the agenda; regulations have been developed in this regard. Urban renewal project would be a focal point for the formation of the city in the near future. The future of the city is directly related to how to achieve these applications. Urban renewal policies will be decisive in the positive or negative development of the potential of the existing renewal process. Urban renewal is seen as a refreshing new planned action for reshaping unplanned and uncontrolled growth of big cities/metropolitan areas. In this context, Izmir is one of the largest metropolitan areas which came on the agenda of urban renewal application in the recent period. Izmir, which is the third largest city of Turkey, is an important trade and port city. The city, located west of Turkey, is a gate opening to Europe. In particular, continued its development rapidly after the Republican Period, it has become an important big city today. Assessment of the current situation shows that the majority of existing residential areas was formed with squatters and unplanned settlements in Izmir city center. Therefore, an important part of these areas have significant problems in terms of the quality of life, safety, and environmental quality. Legal residential areas which have had developed before 2000 is seen inadequate security in terms of an earthquake. In this study, the central policies in Turkey and local policies in İzmir about urban renewal will be considered. In addition, urban renewal projects that are being implemented or applied in Izmir were discussed and suggestions will be developed in accordance with this policy.

Keywords: urban transformation, Izmir, urban planning, urban renewal

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Authors: Mustafa Midilli, Mustafa Salman, Omer Hakan Muglali, Tülay Ögretmen, Sena Cenesiz, Neslihan Ormanci

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This study examined the effects of zinc (Zn) from different sources and microbial phytase on the broiler performance, biochemical parameters and digestibility of nutrients when they were added to broiler diets containing low available phosphorus. A total of 875, 1-day-old male broilers of the Ross 308 strain were randomly separated into two control groups (positive and negative) and five treatment groups each containing 125 birds; each group was divided into 5 replicates of 25 birds. The positive control (PC) group was fed a diet containing adequate concentration (0.45%) of available phosphorus due to mineral premix (except zinc) and feeds. The negative control (NC) group was fed a basal diet including low concentration (0.30%) of available phosphorus due to mineral premix (except zinc) and feeds. The basal diet was supplemented with 0.30% phosphorus and 500 FTU phytase (PH); 0.30% phosphorus and organic zinc (OZ; 75mg/kg of Zn from Zn-proteinate); 0.30% phosphorus and inorganic zinc (IZ; 75 mg/kg of Zn from ZnSO4); 0.30% phosphorus, organic zinc and 500 FTU phytase (OZ + PH); and 0.30% phosphorus, inorganic zinc and 500 FTU phytase (IZ + PH) in the treatment groups 1, 2, 3, 4 and 5, respectively. The lowest value for mean body weight was in the negative control group on a diet containing low available phosphorus. The use of supplementation with organic and inorganic zinc alone or in combination with microbial phytase significantly (P<0.05) increased the digestibility of Zn in the male broilers. Supplementation of those diets with OZ + PH or IZ + PH was very effective for increasing the body weight, body weight gain and the feed conversion ratio. In conclusion, the effects on broilers of diets with low phosphorus levels may be overcome by the addition of inorganic or organic zinc compounds in combination with microbial phytase.

Keywords: broiler, performance, phytase, phosphorus, zinc

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Authors: Neslihan Cetin

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In this study, we will aim to analyze how the period of the state of emergency in Turkey lead to gaps in law and the formation of areas in which there was a complete lack of supervision. The state of emergency that was proclaimed following the coup attempt of July 15, 2016, continued until July 18, 2018, that is to say, 2 years, without taking into account whether the initial circumstances persisted. As part of this work, we claim that the state of emergency provided the executive power with important tools for governing, which it took constant use. We can highlight how the concern for security at the center of the basic considerations of the people in a city was exploited as a foundation by the military power in Turkey to interfere in the political, legal, and social spheres. The constitutions of 1924, 1961, and 1982 entrusted the army with the role of protector of the integrity of the state. This became an instrument at the hands of the military to legitimize their interventions in the name of public security. Its interventions in the political field are indeed politically motivated. The constitution, the legislative, and regulatory systems are modified and monopolized by the military power that dominates the legislative, regulatory, and judicial power, leading to a state of exception. With the political convulsions over a decade, the government was able to usurp the instrument called the state of exception. In particular, the decree-laws of the state of emergency, which the executive makes frequent and generally abusive use, became instruments in the hands of the government to take measures that it wishes to escape from the rules and the pre-established control mechanisms. Thus the struggle against the political opposition becomes more unbalanced and destructive. To this must also be added the ineffectiveness of ex-post controls and domestic remedies. This research allows us to stress how a legal concept, such as ‘the state of emergency’ can be politically exploited to make it a legal weapon that continues to produce victims.

Keywords: constitutional law, state of emergency, rule of law, instrumentalization of law

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Authors: Neslihan Ozman Say, Jim Gilmour, Pratik Desai, William Zimmerman

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Landfill leachate treatment has been attracting researchers recently for various environmental and economical reasons. Leachate discharge to receiving waterbodies without treatment causes serious detrimental effects including partial oxygen depletion due to high biological oxygen demand (BOD) and chemical oxygen demand (COD) concentrations besides toxicity of heavy metals it contains and high ammonia concentrations. In this study, it is aimed to show microalgal ammonia removal performances of a wild microalgae consortia as an alternative treatment method and determine the dominant leachate tolerant species for this consortia. For the microalgae species identification experiments a microalgal consortium which has been isolated from a local pond in Sheffield inoculated in %5 diluted raw landfill leachate and acclimated to the leachate by batch feeding for a month. In order to determine the most tolerant microalgal consortium, four different untreated landfill leachate samples have been used as diluted in four different ratios as 5%, 10%, 20%, and 40%. Microalgae cell samples have been collected from all experiment sets and have been examined by using 18S rDNA sequencing and specialised gel electrophoresis which are adapted molecular biodiversity methods. The best leachate tolerant algal consortium is being used in order to determine ammonia removal performances of the culture in a microbubble assisted photobioreactor (PBR). A porous microbubble diffuser which is supported by a fluidic oscillator is being used for dosing CO₂ and air mixture in the PBR. It is known that high mass transfer performance of microbubble technology provides a better removal efficiency and a better mixing in the photobioreactor. Ammonia concentrations and microalgal growth are being monitored for PBR currently. It is aimed to present all the results of the study in final paper submission.

Keywords: ammonia removal from leachate, landfill leachate treatment, microalgae species identification, microbubble assisted photobioreactors

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Authors: Neslihan Sahin Celik, Ali Eraslan

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Mathematical model and modeling are one of the topics that have been intensively discussed in recent years. In line with the results of the PISA studies, researchers in many countries have begun to question how much students in school-education system are prepared to solve the real-world problems they encounter in their future professional lives. As a result, many mathematics educators have begun to emphasize the importance of new skills and understanding such as constructing, Hypothesizing, Describing, manipulating, predicting, working together for complex and multifaceted problems for success in beyond the school. When students increasingly face this kind of situations in their daily life, it is important to make sure that students have enough experience to work together and interpret mathematical situations that enable them to think in different ways and share their ideas with their peers. Thus, model eliciting activities are one of main tools that help students to gain experiences and the new skills required. This research study was carried on the town center of a big city located in the Black Sea region in Turkey. The participants were eighth-grade students in a middle school. After a six-week preliminary study, three students in an eighth-grade classroom were selected using criterion sampling technique and placed in a focus group. The focus group of three students was videotaped as they worked on a model eliciting activity, the Summer Job Problem. The conversation of the group was transcribed, examined with students’ written work and then qualitatively analyzed through the lens of Blum’s (1996) modeling processing cycle. The study results showed that eighth grade students can successfully work with the model eliciting, develop a model based on the two parameters and review the whole process. On the other hand, they had difficulties to relate parameters to each other and take all parameters into account to establish the model.

Keywords: middle school, modeling, mathematical modeling, summer job problem

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Authors: Pakize Ozlem Kurt Polat

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GMO (genetically modified organism) is the result of a laboratory process where genes from the DNA of one species are extracted and artificially forced into the genes of an unrelated plant or animal. This technology includes; nucleic acid hybridization, recombinant DNA, RNA, PCR, cell culture and gene cloning techniques. The studies are divided into three groups of properties transferred to the transgenic plant. Up to 59% herbicide resistance characteristic of the transfer, 28% resistance to insects and the virus seems to be related to quality characteristics of 13%. Transgenic crops are not included in the commercial production of each product; mostly commercial plant is soybean, maize, canola, and cotton. Day by day increasing GMO interest can be listed as follows; Use in the health area (Organ transplantation, gene therapy, vaccines and drug), Use in the industrial area (vitamins, monoclonal antibodies, vaccines, anti-cancer compounds, anti -oxidants, plastics, fibers, polyethers, human blood proteins, and are used to produce carotenoids, emulsifiers, sweeteners, enzymes , food preservatives structure is used as a flavor enhancer or color changer),Use in agriculture (Herbicide resistance, Resistance to insects, Viruses, bacteria, fungi resistance to disease, Extend shelf life, Improving quality, Drought , salinity, resistance to extreme conditions such as frost, Improve the nutritional value and quality), we explain all this methods step by step in this research. GMO has advantages and disadvantages, which we explain all of them clearly in full text, because of this topic, worldwide researchers have divided into two. Some researchers thought that the GMO has lots of disadvantages and not to be in use, some of the researchers has opposite thought. If we look the countries law about GMO, we should know Biosafety law for each country and union. For this Biosecurity reasons, the problems caused by the transgenic plants, including Turkey, to minimize 130 countries on 24 May 2000, ‘the United Nations Biosafety Protocol’ signed nudes. This protocol has been prepared in addition to Cartagena Biosafety Protocol entered into force on September 11, 2003. This protocol GMOs in general use by addressing the risks to human health, biodiversity and sustainable transboundary movement of all GMOs that may affect the prevention, transit covers were dealt and used. Under this protocol we have to know the, ‘US Regulations GMO’, ‘European Union Regulations GMO’, ‘Turkey Regulations GMO’. These three different protocols have different applications and rules. World population increasing day by day and agricultural fields getting smaller for this reason feeding human and animal we should improve agricultural product yield and quality. Scientists trying to solve this problem and one solution way is molecular biotechnology which is including the methods of GMO too. Before decide to support or against the GMO, should know the GMO protocols and it effects.

Keywords: biotechnology, GMO (genetically modified organism), molecular marker

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Authors: Neslihan Şahin Çelik, Ali Eraslan

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In recent years, mathematics educators have frequently stressed the necessity of instructing students about models and modeling approaches that encompass cognitive and metacognitive thought processes, starting from the first years of school and continuing on through the years of higher education. The purpose of this study is to examine the thought processes of 4th-grade primary school students in their modeling activities and to explore the difficulties encountered in these processes, if any. The study, of qualitative design, was conducted in the 2015-2016 academic year at a public state-school located in a central city in the Black Sea Region of Turkey. A preliminary study was first implemented with designated 4th grade students, after which the criterion sampling method was used to select three students that would be recruited into the focus group. The focus group that was thus formed was asked to work on the model eliciting activity of the Paper Airplane Problem and the entire process was recorded on video. The Paper Airplane Problem required the students to determine the winner with respect to: (a) the plane that stays in the air for the longest time; (b) the plane that travels the greatest distance in a straight-line path; and (c) the overall winner for the contest. A written transcript was made of the video recording, after which the recording and the students' worksheets were analyzed using the Blum and Ferri modeling cycle. The results of the study revealed that the students tested the hypotheses related to daily life that they had set up, generated ideas of their own, verified their models by making connections with real life, and tried to make their models generalizable. On the other hand, the students had some difficulties in terms of their interpretation of the table of data and their ways of operating on the data during the modeling processes.

Keywords: primary school students, model eliciting activity, mathematical modeling, modeling process, paper airplane problem

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Authors: Neslihan Sahin Celik, Ali Eraslan

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As a result of PISA (Program for International Student Assessments) survey that tests how well students can apply the knowledge and skills they have learned at school to real-life challenges, the new and redesigned mathematics education programs in many countries emphasize the necessity for the students to face complex and multifaceted problem situations and gain experience in this sense allowing them to develop new skills and mathematical thinking to prepare them for their future life after school. At this point, mathematical models and modeling approaches can be utilized in the analysis of complex problems which represent real-life situations in which students can actively participate. In particular, model eliciting activities that bring about situations which allow the students to create solutions to problems and which involve mathematical modeling must be used right from primary school years, allowing them to face such complex, real-life situations from early childhood period. A qualitative study was conducted in a university foundation primary school in the city center of a big province in 2013-2014 academic years. The participants were 4th grade students in a primary school. After a four-week preliminary study applied to a fourth-grade classroom, three students included in the focus group were selected using criterion sampling technique. A focus group of three students was videotaped as they worked on the Crime Problem. The conversation of the group was transcribed, examined with students’ written work and then analyzed through the lens of Blum and Ferri’s modeling processing cycle. The results showed that primary fourth-grade students can successfully work with model eliciting problem while they encounter some difficulties in the modeling processes. In particular, they developed new ideas based on different assumptions, identified the patterns among variables and established a variety of models. On the other hand, they had trouble focusing on problems and occasionally had breaks in the process.

Keywords: primary school, modeling, mathematical modeling, crime problem

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Authors: Neslihan Ozsoy Taskiran, Miray Dayioglu, Belgin Gunbey, Banu Yucel, Cigdem Takma, Unal Karik, Tugce Olgun, Levent Aydin

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A greater wax moth (Galleria mellonella L.), which is one of the most important pests after Varroa, plays a role in the transportation of many pathogens into the hive as well as damage to the honeycombs, and beekeepers suffer economically. Due to the risk that some of the methods against this pest may cause residue in bee products, and it can be harmful to the health of people who consume these products. Therefore, the most appropriate, most economical, and effective method should be applied in the moth control. For this purpose, in the first phase of the project (2017-2018), planned to be 2-stage in the Aegean Agricultural Research Institute in 2017-2020, the honeycombs, certified with good agricultural practice, were kept in a favorable condition for moths. Later, applications (Sulfur - B401 - Walnut (Leaf & Smoker) - lavender essential oil (1cc & 2cc & 3cc & 4cc) - laurel essential oil (1cc & 2cc & 3cc & 4cc) - control) were applied to the honeycombs with moths. In 2017, the B401 group had the highest wax moth damage area, and the group with the lowest wax moth damage area was determined as lavender 1cc; In 2018, the highest wax moth damage area was found in the walnut smoker group, while the lowest wax moth damage area was found in sulfur, walnut leaves, laurel 1cc - 2cc - 4cc, lavender 1cc - 2cc - 3cc - 4cc and control groups. In addition, sulfur residue amount (mean 128,18 mg/kg) in honeycomb was measured in the sulfur-treated group. Phase 1 of the project was completed, and the most important sub-groups among walnut (leaf) - lavender (1cc) and laurel (4cc) groups were identified. Accordingly, it is planned to carry out these treatments ((sulfur - B401 - walnut (leaf) - lavender (1cc) and laurel (4cc)) on honeycombs with do not contain moths, and later, it is planned to examine the effects of the treatment on the offspring area and honey yield by giving these honeycombs to the hives, in the 2nd stage of the project (2019-2020).

Keywords: honey bee, lavender essential oil, laurel essential oil, walnut, wax moth

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Authors: Neslihan Taskale Karatug, Mustafa Akcelik

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Some literature data show that misL protein play a role on host immune response formed against Salmonella Typhimurium. The aim of the present study is to learn the role of the protein in S. Typhimurium pathogenicity. To describe certain functions of the protein, primarily recombinant misL protein was produced and purified. PCR was performed using a primer set targeted to passenger domain of the misL gene on S. Typhimurium LT2 genome. Amplicon and pet28a vector were enzymatically cleaved with EcoRI and NheI. The digested DNA materials were purified with High Pure PCR Product Purification Kit. The ligation reaction was achieved with the pure products. After preparation of competent Escherichia coli Dh5α, ligation mix was transformed into the cell by electroporation. To confirm the existence of insert gene, recombinant plasmid DNA of Dh5α was isolated with high pure plasmid DNA kit. Proved the correctness of recombinant plasmid was electroporated to BL21. The cell was induced by IPTG. After induction, the presence of recombinant protein was checked by SDS-PAGE. The recombinant misL protein was purified using HisPur Ni-NTA spin colon. The pure protein was shown by SDS-PAGE and western blot immünoassay. The concentration of the protein was measured BCA Protein Assay kit. In the wake of ligation with digested products (2 kb misL and 5.4 kb pet28a) visualised on gel size of the band was about 7.4 kb and was named as pNT01. The pNT01 recombinant plasmid was transformed into Dh5α and colonies were chosen in selective medium. Plasmid DNA isolation from them was carried out. PCR was achieved on the pNT01 to check misL and 2 kb band was observed on the agarose gel. After electroporation of the plasmid and induction of the cell, 68 kDa misL protein was seen. Subsequent to the purification of the protein, only a band was observed on SDS-PAGE. Association of the pure protein with anti-his antibody was verified by the western blot assay. The concentration of the pure misL protein was determined as 345 μg/mL. Production of polyclonal antibody will be achieved by using the obtained pure recombinant misL protein as next step. The role of the protein will come out on the immune system together some assays.

Keywords: cloning, Escherichia coli, recombinant protein purification, Salmonella Typhimurium

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Authors: Neslihan Demirci, Serdar Durdağı

Abstract:

Mycobacterium tuberculosis is still a worldwide disease-causing agent that, according to WHO, led to the death of 1.5 million people from tuberculosis (TB) in 2020. The bacteria reside in macrophages located specifically in the lung. There is a known quadruple drug therapy regimen for TB consisting of isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB). Over the past 60 years, there have been great contributions to treatment options, such as recently approved delamanid (OPC67683) and bedaquiline (TMC207/R207910), targeting mycolic acid and ATP synthesis, respectively. Also, there are natural compounds that can block the tryptophanyl-tRNA synthetase (TrpRS) enzyme, chuangxinmycin, and indolmycin. Yet, already the drug resistance is reported for those agents. In this study, the newly released TrpRS enzyme structure is investigated for potential inhibitor drugs from already synthesized molecules to help the treatment of resistant cases and to propose an alternative drug for the quadruple drug therapy of tuberculosis. Maestro, Schrodinger is used for docking and molecular dynamic simulations. In-house library containing ~8000 compounds among FDA-approved indole-containing compounds, a total of 57 obtained from the ChemBL were used for both ATP and tryptophan binding pocket docking. Best of indole-containing 57 compounds were subjected to hit expansion and compared later with virtual screening workflow (VSW) results. After docking, VSW was done. Glide-XP docking algorithm was chosen. When compared, VSW alone performed better than the hit expansion module. Best scored compounds were kept for ten ns molecular dynamic simulations by Desmond. Further, 100 ns molecular dynamic simulation was performed for elected molecules according to Z-score. The top three MMGBSA-scored compounds were subjected to steered molecular dynamic (SMD) simulations by Gromacs. While SMD simulations are still being conducted, ponesimod (for multiple sclerosis), vilanterol (β₂ adrenoreceptor agonist), and silodosin (for benign prostatic hyperplasia) were found to have a significant affinity for tuberculosis TrpRS, which is the propulsive force for the urge to expand the research with in vitro studies. Interestingly, top-scored ponesimod has been reported to have a side effect that makes the patient prone to upper respiratory tract infections.

Keywords: drug repurposing, molecular dynamics, tryptophanyl-tRNA synthetase, tuberculosis

Procedia PDF Downloads 99

Authors: Emre Kishalı, Neslihan TürkmenoğLu Bayraktar

Abstract:

Historical buildings may face various impacts throughout their life cycle. There have been environmental, structural, public works actions on old monuments influencing sustainability and maintenance issues. As a result, ancient monuments can have been undergone various changes in the context of restoration and repair. Currently, these buildings face integrated conditions including city planning macro solutions, old intervention methods, modifications in building envelope and artefacts in terms of conservation. Moreover, documentation of phases is an essential for assessing the historical building, yet it can result in highly complicated and interwoven issues. Herein, two monuments constructed in the 16th century are selected as case studies in Kocaeli, Turkey which are located in different micro climatic conditions and/or exposed to different interventions and which are important for the city as cultural property. Pertev Paşa Mosque (also known as Yenicuma Mosque) -constructed by Architect Sinan-; Gebze Çoban Mustafa Paşa Mosque -constructed in 1523 and known as the work of Architect Sinan but various names asserted as the architect of building according to resources. Active water infiltration and damages, recent material interventions, hidden niches, and foundation techniques of the mosque are investigated via Infrared Thermography under the project of 114K284, “Non-Destructive Test Applications, in the Context of Planned Conservation, through Historical Mosques of Kocaeli: Coban Mustafa Pasa Mosque, Fevziye Mosque and Pertev Pasa Mosque” funded by TUBITAK. It is aimed to reveal active deteriorations on building elements generated by unwanted effects of structural and climatic conditions, historical interventions, and modifications by monitoring the variation of surface temperature and humidity by IRT visualization method which is an important non- destructive process for investigation of monuments in the conservation field in the context of planned conservation. It is also concluded that in-situ monitoring process via IRT through different climatic conditions give substantial information on the behaviour of the envelope to the physical environmental conditions by observation of thermal performance, degradations. However, it is obvious that monitoring of historical buildings cannot be pursued by implementing a single non-destructive technique to have complete data of the structure.

Keywords: IRT, non-destructive test, planned conservation, mosque

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