PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/20.500.14365/2

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Citation - WoS: 19
Citation - Scopus: 20
G4catchall: a G-Quadruplex Prediction Approach Considering Atypical Features
(Academic Press Ltd- Elsevier Science Ltd, 2019) Doluca, Osman
Motivation: In vivo discovery of G-quadruplex-forming sequences would provide the most relevant G-quadruplexes along a genomic DNA or an RNA molecule, however it is difficult to perform due to the small size of G-quadruplexes, the existence of different topologies, and the additional influence of environmental factors and ligands present during experimentation. In vitro discovery on the other hand is not only unable to simulate in vivo conditions but also, is not practical for large sequences due to limited resources. The immediate solution continues to be the computational prediction although, not always in agreement with experimental findings. This is often due to features that are not conventionally accepted for G-quadruplexes such as disrupted G-tracts or extremely long loops. Results: Here, we propose a novel tool for the discovery of putative G-quadruplexes with better accuracy through consideration of the features of previously missed G-quadruplex-forming sequences. Comparing against a set of experimentally confirmed sequences, a sensitivity as high as 99% and Youden's J-statistics of as high as 0.91 is achieved; an improvement over other computational approaches. More importantly, we showed that the allowance of a single atypical G-tract which includes a mismatched or a bulging non-guanine nucleotide, and a single loop of extreme size benefits the overall prediction. (C) 2018 Elsevier Ltd. All rights reserved.
Citation - WoS: 43
Citation - Scopus: 51
Municipal Solid Waste Management Via Mathematical Modeling: a Case Study in Istanbul, Turkey
(Academic Press Ltd- Elsevier Science Ltd, 2019) Ayvaz-Cavdaroglu, Nur; Coban, Asli; Firtina-Ertis, Irem
The prominence of managing municipal solid waste (MSW) in an efficient and effective manner is increasing from day to day. In this paper, the solid waste management (SWM) system of Istanbul is analyzed by applying the techniques from mathematical programming methodology. In this manner, the solutions of the two optimization problems which aim to minimize the total cost and the environmental effects of SWM, respectively, are presented in this study. Additionally, a sensitivity analysis is performed and a multi-objective problem that combines two problems is presented. In this regard, the application of five MSW management technologies which are currently in use in Istanbul on six waste components is analyzed; and the optimal solution regarding the best mixture of these technologies is developed on a given waste composition. Besides, this optimal solution is compared with the current practice in Istanbul; and recommendations are presented about possible future investments for the policymakers. The results of the study emphasize the importance of material recovery and incineration facilities to improve profitability and to minimize environmental side effects. In particular, material recovery facility (MRF) should be expanded to be able to treat all of metal, paper and plastic from a cost management perspective. Incineration (INC) facility should also be expanded in order to treat plastics or organic waste from a Greenhouse Gas (GHG) minimization perspective. In addition to this, landfill appears to be the most prominent treatment technique according to the current problem parameters. However, regarding the waste composition, the amount of organic waste must be decreased by more than 37% for other waste streams to be treated in different facilities other than landfill. Anaerobic digestion and composting facilities need to be more cost-effective for becoming economically feasible. The methodology represented in this study can be extended and generalized to other cities around the world once the correct problem parameters are specified.
Citation - WoS: 48
Citation - Scopus: 56
An Optimization Model for Carbon Capture & Storage/Utilization Vs. Carbon Trading: a Case Study of Fossil-Fired Power Plants in Turkey
(Academic Press Ltd- Elsevier Science Ltd, 2018) Agrali, Semra; Uctug, Fehmi Gorkem; Turkmen, Burcin Atilgan
We consider fossil-fired power plants that operate in an environment where a cap and trade system is in operation. These plants need to choose between carbon capture and storage (CCS), carbon capture and utilization (CCU), or carbon trading in order to obey emissions limits enforced by the government. We develop a mixed-integer programming model that decides on the capacities of carbon capture units, if it is optimal to install them, the transportation network that needs to be built for transporting the carbon captured, and the locations of storage sites, if they are decided to be built. Main restrictions on the system are the minimum and maximum capacities of the different parts of the pipeline network, the amount of carbon that can be sold to companies for utilization, and the capacities on the storage sites. Under these restrictions, the model aims to minimize the net present value of the sum of the costs associated with installation and operation of the carbon capture unit and the transportation of carbon, the storage cost in case of CCS, the cost (or revenue) that results from the emissions trading system, and finally the negative revenue of selling the carbon to other entities for utilization. We implement the model on General Algebraic Modeling System (GAMS) by using data associated with two coal-fired power plants located in different regions of Turkey. We choose enhanced oil recovery (EOR) as the process in which carbon would be utilized. The results show that CCU is preferable to CCS as long as there is sufficient demand in the EOR market. The distance between the location of emission and location of utilization/storage, and the capacity limits on the pipes are an important factor in deciding between carbon capture and carbon trading. At carbon prices over $15/ton, carbon capture becomes preferable to carbon trading. These results show that as far as Turkey is concerned, CCU should be prioritized as a means of reducing nationwide carbon emissions in an environmentally and economically rewarding manner. The model developed in this study is generic, and it can be applied to any industry at any location, as long as the required inputs are available. (C) 2018 Elsevier Ltd. All rights reserved.
The Role of Waste Pickers in Individual Waste Separation Behavior
(Academic Press Ltd- Elsevier Science Ltd, 2025) Sorkun, Metehan Feridun; Ozen, Sukru; Can, Seda
This study examines the role of waste pickers in individual waste separation behavior. Given the environmental and economic importance of waste separation, this behavior has been extensively studied, but the influence of waste pickers-who perform waste separation as a livelihood, potentially substituting for the voluntary efforts expected from individuals-has been overlooked. Using stratified random sampling in I(center dot)zmir, Turkey, we collected data from 670 individuals to test our hypotheses via the factor score regression method. The results validated our hypothesis that individuals with positive attitudes toward waste pickers intend to help them by separating and providing recyclable materials. However, we could not validate our hypotheses that positive individual attitudes toward waste pickers decrease individuals' sense of responsibility for separating waste, which consequently weakens the impacts of commonly studied factors (e.g., personal attitude, subjective norm, and perceived behavioral control effectiveness) on individual waste separation behavior. Our post-analysis revealed that a positive attitude toward waste pickers leads to greater individual responsibility through the intention to help, which then weakens the effects of personal attitude and perceived behavioral control on waste separation intention and behavior. By considering the role of waste pickers, our study advances the understanding of individual waste separation behavior in contexts where informal recycling activities are prevalent. Our findings have important implications for policymakers seeking to optimize waste management systems by leveraging the contributions of waste pickers.

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