Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/395
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Article TEffectBayes: A Nextflow Pipeline for Exploring the Potential Effect of Transposable Elements in Gene Regulatory Network with Multi-Omic Bayesian Network Model(Springer Heidelberg, 2026-03-10) Karakülah, Gökhan; Güner, Hüseyin; Kutlu, Necati KaanTransposable elements (TEs) are critical contributors to gene regulatory networks, yet their repetitive and abundant nature complicates efforts to elucidate their precise regulatory roles. While existing computational tools facilitate systematic identification of associations between TEs and gene expression, these methods typically cannot account for confounding variables or capture causal and directional interactions. To address these limitations, we developed TEffectBayes, a Nextflow-based pipeline leveraging a multi-omic Bayesian network (BN) framework designed to systematically infer directional, probabilistic regulatory dependencies involving TEs. TEffectBayes integrates diverse omics datasets, including RNA-seq-derived gene and locus-specific TE expression, along with ChIP-seq-based histone modification data processed via custom R and Python scripts. Integrated multi-omic datasets are subsequently employed to build gene-centric Bayesian models, enabling robust inference of context-dependent, probabilistic relationships between TEs, chromatin modifications, and gene expression. TEffectBayes thus provides a reproducible and scalable computational framework for unraveling the complex regulatory landscape shaped by TEs. In summary, TEffectBayes supports systematic prioritization of TE-chromatin-gene regulatory candidates for downstream benchmarking and experimental validation, enabling hypothesis-driven follow-up studies in diverse biological contexts. The pipeline, along with comprehensive user tutorials and example datasets, is publicly accessible at https://github.com/nkaan-kutlu/TEffectBayes.Article G-C3N4@Fe3O4 Nanomaterial Synthesis for Magnetic Solid-Phase Extraction and Photocatalytic Removal of Basic Blue 3(Springer Heidelberg, 2025-12-16) Kizil, Nebiye; Kayaci, Nilgun; Erbilgin, Duygu Erkmen; Yola, Mehmet Lutfi; Yilmaz, Erkan; Soylak, MustafaThe present research synthesized a g-C3N4@Fe3O4 hybrid material for efficient magnetic solid-phase extraction (MSPE) and photocatalytic degradation of Basic Blue 3 (BB3) dye from wastewater. Characterization of the synthesized g-C3N4@Fe3O4 was conducted through Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), scanning electron microscopy (SEM), and energy-dispersive X-ray spectroscopy (EDX). The optimization of the method was carried out by examining parameters such as pH, g-C3N4@Fe3O4 amount, sample volume, and adsorption/desorption duration. In addition, analytical performance criteria such as limit of detection (LOD), limit of quantification (LOQ), and relative standard deviation (RSD) of the MSPE method were calculated as 1.29 mu g L-1, 4.28 mu g L-1, and 1.9%, respectively. The method was applied to real samples, including wastewater and textiles, and validated through addition/recovery studies for the magnetic solid-phase extraction procedure. The recoveries were gained between 91 and 100%. The reusability synthesized g-C3N4@Fe3O4 was also evaluated. The recoveries for Basic Blue 3 dye decreased to 81% after the fourth experiment. Furthermore, the photocatalytic performance of the g-C3N4@Fe3O4 hybrid material was evaluated due to its good surface area and strong interaction with Basic Blue 3 dye. The photocatalytic activity of g-C3N4@Fe3O4 hybrid material was calculated as 96.8% for 100 mg in 300 min.Article Crashworthiness Evaluation of 3D-Printed Hybrid-Design Multi-Cell Energy Absorbers Under Lateral Compression for Unmanned Aerial Vehicles(Springer Heidelberg, 2025-11-25) Atahan, M. Gokhan; Zeybek, Halil; Ozturk, SezginEnergy absorbers can be strategically integrated into critical areas of unmanned aerial vehicles to protect their structural integrity and electronic components in the event of an accident. In this study, hybrid-design multi-cell energy absorber configurations were proposed, and their crashworthiness performance and collapse mechanisms were comparatively analyzed. Hybrid energy absorbers were designed considering circular, square, hexagonal, and re-entrant unit cell geometries. The energy absorber configurations were produced via additive manufacturing. Compared to the single-cell circular energy absorber, the hybrid-design multi-cell approach resulted in a higher peak crushing force value, while offering considerable enhancements in other crashworthiness parameters. Configuration 3 is recommended for use in energy absorber applications in unmanned aerial vehicles due to its superior crashworthiness performance. Moreover, in hybrid-design multi-cell energy absorbers, the selection of layer geometries significantly influences deformation capability. Compared to the single-cell circular configuration (Configuration 1), Configuration 3 demonstrated superior crashworthiness performance by increasing the MCF, EA, and SEA values by 7.47, 4.47, and 1.41 times, respectively.Article Integrated Quantitative Modelling for the Dimension Stone Quality Evaluation: Implications for Sustainable Resource Management(Springer Heidelberg, 2025-09-30) Koken, Ekin; Strzalkowski, Pawel; Strzałkowski, PawełThe growing demand for dimensional stones in construction and monument conservation requires fast, repeatable and scientifically valid quality assessment procedures. The present study, in this context, established a solid foundation for quantifying the quality of dimension stones by adopting two quantitative methods: the Suitability Index (SI) and Dimension Stone Field Performance Coefficient (DSFPC). Both methods were coded in the MATLAB environment and implemented for 20 different rock types used in various dimension stone applications in Turkey. Evaluations based on the above-mentioned methods demonstrate that the DSFPC provides a more conservative assessment than the SI method. Additionally, engineering interpretations derived from the SI and DSFPC approaches are compared with recently published classification systems developed for the dimension stone industry. Focusing on this comparison, it is concluded that the adopted methods offer a more holistic evaluation framework compared to the approaches based solely on a single input parameter, such as effective porosity (ne), uniaxial compressive strength (UCS), or B & ouml;hme abrasion value (BAV) of rocks. Furthermore, it is concluded that the adopted methods complement each other by yielding supportive outcomes. The coded methods can be adapted to other lithological series and integrated with spatial information systems to support decision-making in mining and construction sectors. From this point of view, the present study may be considered a case study supporting holistic approaches to sustainable resource management in the dimension stone industry.Article Citation - WoS: 3Citation - Scopus: 2Theoretical and Experimental Analysis of Wave Impact Pressures on Curved Seawalls(Springer Heidelberg, 2013-01-10) Mamak, Mustafa; Guzel, HasanExperimental model tests were performed in a wave flume with regular waves to measure the magnitude and distribution of impact pressures caused by breaking waves on a curved seawall model having different radii of curvatures. The base structure of the wall has a foreshore slope of 1/10. Theoretical studies based on pressure impulse theory were carried out to obtain the numerical results of breaking wave impact pressures on curved seawalls. The boundary element method was used for the numerical solution of the governing equation. The novel aspect of this study was to investigate the applicability of pressure impulse theory to curved seawalls. The results showed that the pressure impulse model can be used to model the wave impact pressures and their distribution on curved seawall models with good accuracy. A slight decrease has been observed in pressures for increasing radii of curvatures, especially for the case which the water depth at wall was 14 cm. The location of the maximum impact pressure was found to occur above the still water level for all cases tested in this study.Article Citation - WoS: 174Citation - Scopus: 193The Significance of Renewable Energy Use for Economic Output and Environmental Protection: Evidence From the Next 11 Developing Economies(Springer Heidelberg, 2017-04-08) Paramati, Sudharshan Reddy; Sinha, Avik; Dogan, EyupIncreasing economic activities in developing economies raise demand for energy mainly sourced from conventional sources. The consumption of more conventional energy will have a significant negative impact on the environment. Therefore, attention of policy makers has recently shifted towards the promotion of renewable energy generation and uses across economic activities to ensure low carbon economy. Given the recent scenario, in this paper, we aim to examine the role of renewable energy consumption on the economic output and CO2 emissions of the next fastest developing economies of the world. The study employs several robust panel econometric models by using annual data from 1990 to 2012. Empirical findings confirm the significant long-run association among the variables. Similarly, results show that renewable energy consumption positively contributes to economic output and has an adverse effect on CO2 emissions. Given our findings, we suggest policy makers of those economies to initiate further effective policies to promote more renewable energy generation and uses across economic activities to ensure sustainable economic development.Article Citation - WoS: 347Citation - Scopus: 388The Influence of Renewable and Non-Renewable Energy Consumption and Real Income on CO2 Emissions in the USA: Evidence From Structural Break Tests(Springer Heidelberg, 2017-03-14) Dogan, Eyup; Ozturk, IlhanThe objective of this study is to explore the influence of the real income (GDP), renewable energy consumption and non-renewable energy consumption on carbon dioxide (CO2) emissions for the United States of America (USA) in the environmental Kuznets curve (EKC) model for the period 1980-2014. The Zivot-Andrews unit root test with a structural break and the Clemente-Montanes-Reyes unit root test with a structural break report that the analyzed variables become stationary at first-differences. The Gregory-Hansen cointegration test with a structural break and the bounds testing for cointegration in the presence of a structural break show CO2 emissions, the real income, the quadratic real income, renewable and non-renewable energy consumption are cointegrated. The long-run estimates obtained from the ARDL model indicate that increases in renewable energy consumption mitigate environmental degradation whereas increases in non-renewable energy consumption contribute to CO2 emissions. In addition, the EKC hypothesis is not valid for the USA. Since we use time-series econometric approaches that account for structural break in the data, findings of this study are robust, reliable and accurate. The US government is advised to put more weights on renewable sources in energy mix, to support and encourage the use and adoption of renewable energy and clean technologies, and to increase the public awareness of renewable energy for lower levels of emissions.Article Citation - WoS: 6Citation - Scopus: 6The Influence of Cement Kiln Dust on Strength and Durability Properties of Cement-Based Systems(Springer Heidelberg, 2022-06-06) Hakkomaz, Hadiye; Yorulmaz, Hediye; Durak, Ugur; Ilkentapar, Serhan; Karahan, Okan; Atis, Cengiz DuranThere are very few studies in the literature on the usage of CKD in cementitious systems. This article presents the laboratory study results on the influence of cement kiln dust (CKD) on the properties of mortar made with cement kiln dust and Portland cement. The article aims to prevent CKD's (known as a hazardous waste product) damage to nature by utilizing CKD in cementitious systems and contributing to sustainability by reducing cement amount in the cementitious system. For this purpose, 5%, 10%, 15%, and 20% of CKD were replaced with cement and binary cementitious systems were formed. For all mortar mixes, the water/binder ratio was kept constant at 0.5, and the sand/binder ratio was 3. Workability, dry unit weight, water absorption ratio and porosity, flexural strength, compressive strength, abrasion, carbonation, and high-temperature resistance tests were performed on the mortar specimens. Based on the results of laboratory work, it was observed that the replacement of CKD with cement reduces the workability of fresh mortar. Compressive and flexural strengths of CKD-added mixtures were found to be equivalent or insignificantly lower than that of the control sample. The addition of CKD had a negligible effect on water absorption and porosity of samples. Besides, the residual compressive strength determined after the elevated temperature test for the sample made with CKD were found to be equivalent or higher compared to the control sample. Present laboratory studies showed that utilization of CKD in cementitious mortar system is feasible in terms of testing conducted.Article Citation - WoS: 131Citation - Scopus: 135The Influence of Biomass Energy Consumption on CO2 Emissions: A Wavelet Coherence Approach(Springer Heidelberg, 2016-06-23) Bilgili, Faik; Ozturk, Ilhan; Kocak, Emrah; Bulut, Umit; Pamuk, Yalcin; Mugaloglu, Erhan; Baglitas, Hayriye H.In terms of today, one may argue, throughout observations from energy literature papers, that (i) one of the main contributors of the global warming is carbon dioxide emissions, (ii) the fossil fuel energy usage greatly contributes to the carbon dioxide emissions, and (iii) the simulations from energy models attract the attention of policy makers to renewable energy as alternative energy source to mitigate the carbon dioxide emissions. Although there appears to be intensive renewable energy works in the related literature regarding renewables' efficiency/impact on environmental quality, a researcher might still need to follow further studies to review the significance of renewables in the environment since (i) the existing seminal papers employ time series models and/or panel data models or some other statistical observation to detect the role of renewables in the environment and (ii) existing papers consider mostly aggregated renewable energy source rather than examining the major component(s) of aggregated renewables. This paper attempted to examine clearly the impact of biomass on carbon dioxide emissions in detail through time series and frequency analyses. Hence, the paper follows wavelet coherence analyses. The data covers the US monthly observations ranging from 1984:1 to 2015 for the variables of total energy carbon dioxide emissions, biomass energy consumption, coal consumption, petroleum consumption, and natural gas consumption. The paper thus, throughout wavelet coherence and wavelet partial coherence analyses, observes frequency properties as well as time series properties of relevant variables to reveal the possible significant influence of biomass usage on the emissions in the USA in both the short-term and the long-term cycles. The paper also reveals, finally, that the biomass consumption mitigates CO2 emissions in the long run cycles after the year 2005 in the USA.Article Citation - WoS: 103Citation - Scopus: 127The Impacts of Organizational Green Culture and Corporate Social Responsibility on Employees' Responsible Behaviour Towards the Society(Springer Heidelberg, 2022-04-12) Abbas, Jawad; Dogan, EyupCorporate social responsibility (CSR) initiatives and organizational green culture (OGC) play a significant role in developing organizations and society. However, the extent to which these activities encourage organizational employees to act socially responsible outside their workplace is yet to be explored. This study uses the Operant conditioning theory to examine the effect of OGC and CSR activities on employees' responsible behaviour towards the society (ERBS) outside their organizations. To collect data, we focused on employees of public and private manufacturing and services firms and analysed it using the structural equation modelling (SEM) technique). It is found that OGC and CSR activities significantly reshape employees' behaviour, and they tend to behave in a socially responsible manner in society. Moreover, the relationship between OGC and ERBS' is partially mediated by CSR. It is also found that female workers tend to behave more socially responsibly than male workers. This study suggests that firms should adopt a green culture and CSR practices since it promotes socially responsible behaviour (a better citizen) among their employee, which is essential for a sustainable society.