Sürdürülebilir Yeşil Kampüs Koleksiyonu / Sustainable Green Campus Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7755
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Article Citation - WoS: 2Citation - Scopus: 3Integrating Spatiotemporal Dynamics of Natural Capital Security and Urban Ecosystem Carbon Metabolism(Springer Verlag, 2018) Demirkesen, Ali Can; Evrendilek, FatihThe purpose of the study is to address and quantify the increase in urban expansion and carbon (C) metabolism burden on ecosystem service value (ESV), net ecosystem productivity (NEP), and C storage of urban footprint. Urban footprint is required to meet the demands arising from economic consumption and production as well as waste accumulation and assimilation. Spatiotemporal changes in main land covers (LCs) were detected using remotely sensed data (Landsat 5 and 8, and digital elevation model) between 1987 and 2016. Changes in ESV and C influx, efflux and pools associated with LC dynamics were approximated using global proxies for a western Mediterranean region in Turkey of 54,162 km2. Urban expansion over the 29-year period decreased ESV by 22% ($7.28 ± 0.4 billion), NEP by 4.3% (2.3 ± 9 Gg C), and total ecosystem C pool by 10.9% (1008.3 ± 1006 Gg C) and led to a 62.8% appropriation of the total NEP (50.1 ± 51 Gg C) of the urban footprint in 2016. The main cause of the environmental degradation across the study region was the loss of the seminatural areas. Our findings emphasize that the deterioration rate of ecosystems should be slowed down by natural capital-friendly decisions and should not exceed rehabilitation rate of damaged ecosystems in the face of rapidly increasing burdens of the cities on their footprint.Article Citation - WoS: 75Citation - Scopus: 74Scaffold-Free Three-Dimensional Cell Culturing Using Magnetic Levitation(Royal Society of Chemistry, 2018) Türker, Esra; Demirçak, Nida; Arslan Yıldız, AhuThree-dimensional (3D) cell culture has emerged as a pioneering methodology and is increasingly utilized for tissue engineering, 3D bioprinting, cancer model studies and drug development studies. The 3D cell culture methodology provides artificial and functional cellular constructs serving as a modular playground prior to animal model studies, which saves substantial efforts, time and experimental costs. The major drawback of current 3D cell culture methods is their dependency on biocompatible scaffolds, which often require tedious syntheses and fabrication steps. Herein, we report an easy-to-use methodology for the formation of scaffold-free 3D cell culture and cellular assembly via magnetic levitation in the presence of paramagnetic agents. To paramagnetize the cell culture environment, three different Gadolinium(iii) chelates were utilized, which led to levitation and assembly of cells at a certain levitation height. The assembly and close interaction of cells at the levitation height where the magnetic force was equilibrated with gravitational force triggered the formation of complex 3D cellular structures. It was shown that Gd(iii) chelates provided an optimal levitation that induced intercellular interactions in scaffold-free format without compromising cell viability. NIH 3T3 mouse fibroblasts and HCC827 non-small-cell lung cancer cells were evaluated via the magnetic levitation system, and the formation of 3D cell culture models was validated for both cell lines. Hereby, the developed magnetic levitation system holds promises for complex cellular assemblies and 3D cell culture studies.Article Citation - WoS: 46Citation - Scopus: 57Recent Advances in Magnetic Levitation: a Biological Approach From Diagnostics To Tissue Engineering(American Chemical Society, 2018) Türker, Esra; Arslan Yıldız, AhuThe magnetic levitation technique has been utilized to orientate and manipulate objects both in two dimensions (2D) and three dimensions (3D) to form complex structures by combining various types of materials. Magnetic manipulation holds great promise for several applications such as self-assembly of soft substances and biological building blocks, manipulated tissue engineering, as well as cell or biological molecule sorting for diagnostic purposes. Recent studies are proving the potential of magnetic levitation as an emerging tool in biotechnology. This review outlines the advances of newly developing magnetic levitation technology on biological applications in aqueous environment from the biotechnology perspective.Article Citation - WoS: 45Citation - Scopus: 45The First Countrywide Monitoring of Selected Pops: Polychlorinated Biphenyls (pcbs), Polybrominated Diphenyl Ethers (pbdes) and Selected Organochlorine Pesticides (ocps) in the Atmosphere of Turkey(Elsevier Ltd., 2018) Kurt Karakuş, Perihan Binnur; Ugranlı Çiçek, Tuğba; Sofuoğlu, Sait Cemil; Çelik, Halil; Güngörmüş, Elif; Gedik, Kadir; Sofuoğlu, Aysun; Ökten, Hatice Eser; Birgül, Aşkın; Alegria, Henry; Jones, Kevin C.Atmospheric levels of 43 PCBs, 22 OCPs, and 14 PBDEs were determined in 16 cities at urban and rural sites by passive sampling to generate the first large-scale nationwide dataset of POP residues in Turkey's atmosphere. Sampling campaign was performed from May 2014 to April 2015 with three-month sampling periods at locations on east-west and north-south transects through the country to investigate seasonal and spatial variations, including long range atmospheric transport (LRAT). Factor analysis was conducted to infer on the potential sources. Overall average Σ43PCBs concentration was 108 ± 132 pg/m3. PCB-118 (26.3 ± 44.6 pg/m3) was the top congener, and penta-CBs had the highest contribution with 54.3%. ΣDDTs had the highest annual mean concentration with 134 ± 296 pg/m3 among the OCP groups among which the highest concentration compound was p'p-DDE (97.6 ± 236 pg/m3). Overall average concentration of Σ14PBDEs was 191 ± 329 pg/m3 with the highest contribution from BDE-190 (42%). Comparison of OCPs and PCBs concentrations detected at temperatures which were above and below annual average temperature indicated higher concentrations in the warmer periods, hence significance of secondary emissions for several OCPs and Σ43PCBs, as well as inference as LRAT from secondary emissions. The first nationwide POPs database constructed in this study, point to current use, local secondary emissions, and LRAT for different individual compounds, and indicate the need for regular monitoring. The first country-wide passive sampling of selected POPs showed no unequivocal trends reflecting transitional location of Turkey.Article Citation - WoS: 21Citation - Scopus: 27Exploring the Impact of External Shading System on Cognitive Task Performance, Alertness and Visual Comfort in a Daylit Workplace Environment(SAGE Publications Inc., 2019) Leccese, F.; Salvodori, G.; Öner, Merve; Kazanasmaz, Zehra TuğçeThe authors examined the effect of external shading system on cognitive performance, alertness and visual comfort of visual display terminal (VDT) users under two realistic office lighting settings in this study. Daylight was the source of illumination being considered as the most significant and preferred one. A total of 26 participants performed visual and cognitive demanding tasks as well as providing subjective alertness, performance and visual evaluations in a full-scale mock-up VDT workstation. Two trials (with and without shading system) were executed during one experimental session. Results revealed that the use of a shading system improves the performance of a user on colour-naming task requiring sustained attention, while no differential effects were observed on tasks involving other cognitive skills such as search velocity and vigilance. Within-subject performance differences were more pronounced during morning hours. Higher performance was reported in some cognitive tests when the subjective sensation of visual discomfort was lower.Article Citation - WoS: 37Citation - Scopus: 362d Vibrational Properties of Epitaxial Silicene on Ag(111)(IOP Publishing Ltd., 2017) Solonenko, Dmytro; Gordan, Ovidiu D.; Le Lay, Guy; Şahin, Hasan; Cahangirov, Seymur; Zahn, Dietrich R. T.; Vogt, PatrickThe two-dimensional silicon allotrope, silicene, could spur the development of new and original concepts in Si-based nanotechnology. Up to now silicene can only be epitaxially synthesized on a supporting substrate such as Ag(111). Even though the structural and electronic properties of these epitaxial silicene layers have been intensively studied, very little is known about its vibrational characteristics. Here, we present a detailed study of epitaxial silicene on Ag(111) using in situ Raman spectroscopy, which is one of the most extensively employed experimental techniques to characterize 2D materials, such as graphene, transition metal dichalcogenides, and black phosphorous. The vibrational fingerprint of epitaxial silicene, in contrast to all previous interpretations, is characterized by three distinct phonon modes with A and E symmetries. Both, energies and symmetries of theses modes are confirmed by ab initio theory calculations. The temperature dependent spectral evolution of these modes demonstrates unique thermal properties of epitaxial silicene and a significant electron-phonon coupling. These results unambiguously support the purely two-dimensional character of epitaxial silicene up to about 300°C, whereupon a 2D-to-3D phase transition takes place. The detailed fingerprint of epitaxial silicene will allow us to identify it in different environments or to study its modifications.Article Citation - WoS: 89Citation - Scopus: 105Spatial and Temporal Variations in Atmospheric Vocs, No2, So2, and O3 Concentrations at a Heavily Industrialized Region in Western Turkey, and Assessment of the Carcinogenic Risk Levels of Benzene(Elsevier Ltd., 2015) Yılmaz Civan, Mihriban; Elbir, Tolga; Seyfioğlu, Remzi; Kuntasal, Öznur Oğuz; Bayram, Abdurrahman; Doğan, Güray; Yurdakul, Sema; Andiç, Özgün; Müezzinoğlu, Aysen; Sofuoğlu, Sait Cemil; Pekey, Hakan; Pekey, Beyhan; Bozlaker, Ayşe; Odabaşı, Mustafa; Tuncel, GürdalAmbient concentrations of volatile organic compounds (VOCs), nitrogen dioxide (NO2), sulphur dioxide (SO2) and ground-level ozone (O3) were measured at 55 locations around a densely populated industrial zone, hosting a petrochemical complex (Petkim), a petroleum refinery (Tupras), ship-dismantling facilities, several iron and steel plants, and a gas-fired power plant. Five passive sampling campaigns were performed covering summer and winter seasons of 2005 and 2007. Elevated concentrations of VOCs, NO2 and SO2 around the refinery, petrochemical complex and roads indicated that industrial activities and vehicular emissions are the main sources of these pollutants in the region. Ozone concentrations were low at the industrial zone and settlement areas, but high in rural stations downwind from these sources due to NO distillation. The United States Environmental Protection Agency's positive matrix factorization receptor model (EPA PMF) was employed to apportion ambient concentrations of VOCs into six factors, which were associated with emissions sources. Traffic was found to be highest contributor to measured ∑VOCs concentrations, followed by the Petkim and Tupras.Median cancer risk due to benzene inhalation calculated using a Monte Carlo simulation was approximately 4 per-one-million population, which exceeded the U.S. EPA benchmark of 1 per one million. Petkim, Tupras and traffic emissions were the major sources of cancer risk due to benzene inhalation in the Aliaga airshed. Relative contributions of these two source groups changes significantly from one location to another, demonstrating the limitation of determining source contributions and calculating health risk using data from one or two permanent stations in an industrial area.Article Citation - WoS: 6Citation - Scopus: 7Utilization of Electrospun Polystyrene Membranes as a Preliminary Step for Rapid Diagnosis(John Wiley and Sons Inc., 2016) Işık, Tuğba; Horzum, Nesrin; Yıldız, Ümit Hakan; Liedberg, Bo; Demir, Mustafa MuammerRecent advances in clinical practice drive deoxyribonucleic acid (DNA) as an important class of biomarker. Monitoring the change in their concentration suggests the initiation and/or progression of various disorders. However, low quantity of DNA biomarkers in body fluids requires a delicate isolation methodology that provides efficient separation and easy handling. This study describes a newer-generation separation technology relying on electrospun fibers of sub-micrometer diameter of a commodity polymer for DNA biomarkers in simulative serum. Fibrous polystyrene membranes are prepared by electrospinning and they are subjected to post-modification with Au. The composite membranes may provide a convenient environment for the removal of bovine serum albumin (BSA) from BSA and DNA mixtures. The eluent can be used as an efficient tool for detection of DNA biomarkers associated with diagnosis of numerous life-threatening diseases.Article Citation - WoS: 19Citation - Scopus: 29One Step Forward, Two Steps Back; Xeno-Micrornas Reported in Breast Milk Are Artifacts(Public Library of Science, 2016) Bağcı, Caner; Allmer, JensBackground: MicroRNAs (miRNAs) are short RNA sequences that guide post-transcriptional regulation of gene expression via complementarity to their target mRNAs. Discovered only recently, miRNAs have drawn a lot of attention. Multiple protein complexes interact to first cleave a hairpin from nascent RNA, export it into the cytosol, trim its loop, and incorporate it into the RISC complex which is important for binding its target mRNA. This process works within one cell, but circulating miRNAs have been described suggesting a role in cell-cell communication. Motivation: Viruses and intracellular parasites like Toxoplasma gondii use miRNAs to manipulate host gene expression from within the cellular environment. However, recent research has claimed that a rice miRNA may regulate human gene expression. Despite ongoing debates about these findings and general reluctance to accept them, a recent report claimed that foodborne plant miRNAs pass through the digestive tract, travel through blood to be incorporated by alveolar cells excreting milk. The miRNAs are then said to have some immunerelated function in the newborn. Principal Findings: We acquired the data that supports their claim and performed further analyses. In addition to the reported miRNAs, we were able to detect almost complete mRNAs and found that the foreign RNA expression profiles among samples are exceedingly similar. Inspecting the source of the data helped understand how RNAs could contaminate the samples. Conclusion: Viewing these findings in context with the difficulties foreign RNAs face on their route into breast milk and the fact that many identified foodborne miRNAs are not from actual food sources, we can conclude beyond reasonable doubt that the original claims and evidence presented may be due to artifacts. We report that the study claiming their existence is more likely to have detected RNA contamination than miRNAs.Article Citation - WoS: 11Citation - Scopus: 10Assessment of Construction Techniques and Material Usage in Izmir Rural Houses(Taylor and Francis Ltd., 2015) Tunçoku, Selim Sarp; İnceköse, Ülkü; Akış, Tonguç; Yalçın, Mehmet AliThe domestic architecture in the rural villages of ̄zmir comprises a unique built environment with their masonry wall textures, semi-open sofas, round tiled-hipped roofs, and chimneys, and represents an important part of the cultural and architectural heritage. This assessment is mainly based on field observations that focus on the architectural and structural layout of intact, damaged, and destroyed houses. During field observation and the analysis of data certain plan typologies and relationships between the geological formations of the region and choice of materials and construction techniques were observed. While load-bearing masonry and timber skeleton systems are common, extensive use of timber laces, stone, and fired or adobe brick masonry with mud mortar and timber frames infilled with masonry materials were frequently seen. Generally, round timber elements such as wall plates, laces, lintels, posts, and frames of flooring systems are used. Architectural degenerations in authentic houses, defective details and partially due to the earthquake-prone nature of the region seismicity have been evaluated. An overall approach for the preservation and sustainability of this heritage is suggested.
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