OpenAIRE Collection / OpenAIRE Koleksiyonu
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Conference Object Kurumsal Arşiv Kavramı ve Openaıreplus Projesi(2012) Gürdal, Gültekin; Türkfidanı, Ata; Keten, Burcu; Holt, İlkayBilimsel bilgiye erişimin maliyetindeki artış, maddi sınırlamaları gündeme getirmiş, araştırma çıktılarının ilgili bilim insanlarına ulaşmasında sorunlar yaşanmaya başlanmıştır. Bu durum, bilimsel araştırmaları destekleyen/fon sağlayan ve araştırma yürüten kurum/kuruluşları harekete geçirmiştir. Günümüzde, kamu kaynaklarıyla desteklenen araştırmalardan üretilen bilimsel yayınların ücretsiz olarak herkesin erişimine açılması, açık erişim olarak yayımlanması, yoğun bir biçimde tartışılmaktadır. Avrupa Birliği (AB) de 7. Çerçeve Programı kapsamında, kamu kaynakları ile yaratılan projelerden elde edilen çıktıların kamu yararına geri sunulmasını hedeflenmektedir. Türkiye’de de araştırma kurumları bazında aktif ortaklıklar kurulmaya başlanmıştır. Bu bağlamda, bildiride AB Projeleri’nin çıktılarına ait makale, rapor ve veri setlerinin kamu ile açık erişim yoluyla paylaşılacağı bir platform olarak kurulan ve desteklenen, Türkiye’deki yürütücülüğü İzmir Yüksek Teknoloji Enstitüsü Kütüphanesi tarafından sürdürülen OpenAIREplus Projesi’nin yansımaları konusunda bilgi sunulmaya çalışılacaktır.Presentation Açık Bilim: Neler Oluyor? Openaıre, Türkiye, İyte(Izmir Institute of Technology, 2019) Gürdal, Gültekin11 Nisan 2019 tarihinde İYTE evsahipliğinde gerçekleştirilen "Açık Bilim Yolunda: Bilimi Özgür Bırak Semineri" sırasında gerçekleştirilen sunumdur.Article Silika Yüzeylerin Islanma Hareketlerinin Moleküler Dinamik ile Modellenmesi(Gazi Üniversitesi, 2018) Barışık, MuratYeni üretim tekniklerine paralel olarak nano-boyutlu teknolojiler çok geniş bir uygulama alanında kullanılmaya başlanmakta ve yeni uygulamalar geliştirmek için keşfedilmesi ve anlaşılması gereken konular süratle artmaktadır. Bu doğrultuda, yeni uygulamalarda sıkça yer bulan silikon ve silikon-dioksitin mikro/nano boyutlardaki malzeme özelliklerinin anlaşılmasına büyük ihtiyaç oluşmaktadır. Özellikle bu yüzeylerin ıslanma hareketlerinin anlaşılabilmesi ve hatta kullanılacak uygulamaya göre ayarlanabilmesi sayısız uygulama için önem arz etmektedir. Bu nedenlerle, nano-teknolojide sıkça kullanılan silikon-dioksit malzemesinin ve su moleküllerinin nano-ölçeklerde moleküler olarak modellenmesi bu çalışmada gerçekleştirildi. Modelleme molekuler dinamik hesaplamaları ile yapıldı. Silikon-dioksit yüzey üzerinde nano su damlacıkları oluşturup, denge halinde oluşan ıslatma açısı ölçümleri yapıldı. Literatürde işlem yükünü azaltmak için sıklıkla uygulanan, katı yüzey termal titreşimlerinin ıslatmaya olan etkisinin ihmal edilmesi ve modellenmemesinin ıslatma açısına olan etkisi incelendi. Katı moleküllerin termal titreşimlerinin ıslatma modellenen ıslatma fiziğine baskın bir etkisi olduğu görüldü. Geçtiğimiz yıllarda doğa taklidi olarak bilinen çalışma çevreleri tarafından hayata geçirilmeye çalışılan Lotus yaprağı etkisi temelli yüzey ıslatma kontrolu moleküler seviyede uygulandı. Yüzey üzerinde oluşturulan nano boyutlardaki yüzey yapılarının ıslanma açısını değiştirebildiği gösterildi. Temiz (0 0 1) silika yüzeyinde nano ölçek çizgi gerilimi etkisi altında ölçülen ıslanma açısının deneysel silika ıslanma açısı aralığında olduğu bulundu.Article Citation - WoS: 9Citation - Scopus: 10Novel Hybrid Process for the Conversion of Microcrystalline Cellulose To Value-Added Chemicals: Part 2: Effect of Constant Voltage on Product Selectivity(Springer Verlag, 2017) Akın, Okan; Yüksel, AslıIn this study, electrochemical degradation of microcrystalline cellulose (MCC) under hot-compressed water was investigated via application of constant voltage on reaction medium. Constant voltage ranges from 2.5 to 8.0 V was applied between anode (Titanium) and cathode (reactor wall). As an electrolyte and proton source 5–25 mM of H2SO4 was used. Reactions were carried out in a specially designed batch reactor (450 mL) made of T316 for 240 min at temperature of 200 °C.MCC decomposition products such as glucose, fructose, furfural, 5-HMF and levulinic acid were detected and quantified by High Performance Liquid Chromatography (HPLC). In the absence of electrolyte, applied voltage (2.5 and 4.0 V) decreased the total organic carbon (TOC) yield, in contrast at 8.0 V, TOC yield increased to 13%. Application of 8.0 V in hydrothermal conditions alter MCC decomposition pathway selectively to furfural (15%). Addition of electrolyte (5 mM, H2SO4) and application of 2.5 V potential increased TOC (54%) and changed the decomposition pathway in favor of 5-HMF (30%) and levulinic acid (21%). The structural changes in solid residues of electrochemically reacted MCC was analyzed by Fourier Transform Infrared Spectroscopy (FTIR) and found that MCC particles functionalized by carboxylic acid and sulfonated groups by the application of constant voltage to reaction medium. In the presence of electrolyte, under certain voltage (2.5 V), functionalization of solid particles became more obvious in FTIR spectrum results. Therefore, change in the selectivity values of degradation products were conducted with the functionalization of MCC particles due to applied voltage under sub-critical conditions.Article Alteration of Protein Localization and Intracellular Calcium Content Due To Connexin26 D50a and A88v Mutations(Türk Biyokimya Derneği, 2017) Aypek, Hande; Meşe, GülistanIntroduction: Connexins (Cx) play essential roles in cellular homeostasis by forming gap junctions and non-junctional hemichannels. In vitro characterization of Cx26 mutations causing keratitis-ichthyosis-deafness (KID) syndrome, were shown to form leaky hemichannels. The molecular/ cellular mechanisms affected by aberrant hemichannels have recently been elucidated. Here, we further wanted to characterize Cx26 KID syndrome mutations, D50A and A88V, which were shown to form aberrant hemichannels and remained unaddressed in the literature. Methods: Neurobiotin uptake assay in HeLa and N2A cells transfected with Cx26-WT, D50A or A88V verified the presence of aberrant hemichannels and immunofluorescent staining with fluorescent microscopy determined cellular localization of Cx26. Finally, intracellular calcium content was examined by using calcium indicator, Fluo-3AM, and flow cytometer. Results: Cx26-D50A and A88V mutations prevented the formation of gap junction plaques at cell-cell appositions and mutant proteins were observed to localize to the Golgi apparatus. Further, comparison of intracellular calcium content showed an increase in calcium amount in cells containing Cx26-D50A and A88V relative to Cx26-WT. Conclusion: Retention of Cx26 in the Golgi apparatus and alteration in the intracellular calcium content due to KID syndrome mutations may influence various cellular processes that might contribute to development of epidermal phenotypes.Article Citation - WoS: 19Citation - Scopus: 23Valorization of Hazelnut Shell Waste in Hot Compressed Water(Elsevier Ltd., 2017) Gözaydın, Gökalp; Yüksel, AslıHydrothermal conversion of waste hazelnut shell in hot compressed water, green and environmentally friendly medium, was investigated under different operating conditions to clarify the effects of reaction temperature, reaction time, acid concentration and acid kind (H2SO4 and H3PO4) on the production of value-added chemicals with high temperature/high pressure autoclave. In literature, to our best knowledge, there is no study about the production of levulinic acid, as a high value chemical, from waste hazelnut shell in hot-compressed water without using any mineral and heterogeneous catalyst. Hydrothermal reactions were conducted at 150–280 °C for reaction times of 15 to 120 min with various H2SO4 and H3PO4 concentrations varying from 0 to 125 mM. The detailed liquid product species were identified with High Performance Liquid Chromatography (HPLC) and gaseous products were analyzed by Gas Chromatography with a Thermal Conductivity Detector (GC-TCD). The main identified liquid compounds were levulinic acid, acetic acid and furfural while carbon dioxide and carbon monoxide were the major gaseous products. Increasing the reaction temperature (280 °C) and reaction time (120 min) resulted in a significant increment on the conversion (65.40%) as well as levulinic acid yield (13.05%). The production of levulinic acid was enhanced with H2SO4 addition; whereas treatments with H3PO4 improved the furfural production.Article Citation - WoS: 4Citation - Scopus: 5Analytical Solution of Micro-/Nanoscale Convective Liquid Flows in Tubes and Slits(Springer, 2017) Kalyoncu, Gülce; Barışık, MuratAnalytical solutions examining heat transport in micro-/nanoscale liquid flows were developed. Using the energy equation coupled with fully developed velocity, we solved developing temperature profiles with axial conduction and viscous dissipation terms. A comprehensive literature review provided the published range of velocity slip and temperature jump conditions. While molecular simulations and experiments present constant slip and jump values for a specific liquid/surface couple independent of confinement size, non-dimensional forms of these boundary conditions were found appropriate to calculate non-equilibrium as a function of flow height. Although slip and jump conditions are specific for each liquid/surface couple and hard to obtain, we proposed modeling of the slip and jump as a function of the surface wetting, in order to create a general, easy to measure methodology. We further developed possible correlations to calculate jump using the slip value of the corresponding surface and tested in the results. Fully developed Nu showed strong dependence on slip and jump. Heat transfer stopped when slip and jump coefficients became higher than a certain value. Strong variation of Nu in the thermal development length was observed for low slip and jump cases, while an almost constant Nu in the flow direction was found for high slip and jump coefficients. Variation of temperature profiles was found to dominate the heat transfer through the constant temperature surface while surface and liquid temperatures became equal at heat transfer lengths comparable with confinement sizes for no-dissipation cases. In case of non-negligible heat dissipation, viscous heating dominated the Nu value by enhancing the heating while decreasing the heat removal in cooling cases. Implementation of proposed procedure on a micro-channel convection problem from a micro-fluidics application showed the dominant effect of the model defining the slip and jump relationship. Direct use of kinetic gas theory resulted in an increase of Nu by an increase in non-equilibrium, while models developed from published liquid slip and jump values produced an opposite behavior.Master Thesis Interactions of Cancer Cells and Macrophages on the Egf-Egfr Axis: Chemotaxis, Haptotaxis or Direct Contact?(Izmir Institute of Technology, 2017) Önal, Sevgi; Pesen Okvur, Devrim; Bulmuş Zareie, Esma VolgaBreast cancer cells (BCC) and macrophages are known to interact via epidermal growth factor (EGF) produced by macrophages and colony stimulating factor-1 (CSF-1) produced by BCC. Despite contradictory findings, this interaction is perceived as a paracrine loop. Yet, the underlying mechanism of interaction remains unclear. Here, we investigated interactions of BCC with macrophages in 2D and 3D. BCC did not show chemotaxis to macrophages in custom designed 3D cell-on-a-chip devices, which was in agreement with ELISA results showing that macrophage-derived-EGF was not secreted into macrophage-conditioned-medium. Live cell imaging of BCC in the presence and absence of iressa showed that macrophages but not macrophage-derivedmatrix modulated adhesion and motility of BCC in 2D. 3D co-culture experiments in matrigel and collagen showed that BCC changed their multicellular organization in the presence of macrophages. In custom designed 3D co-culture cell-on-a-chip devices, macrophages reduced and promoted migration of BCC in matrigel and collagen, respectively. Furthermore, adherent but not suspended BCC endocytosed EGFR when in contact with macrophages. Collectively, our data revealed that macrophages showed chemotaxis towards BCC-derived-CSF-1 whereas BCC required direct contact to interact with macrophage-derived-EGF. We propose that the interaction between cancer cells and macrophages is a paracrine-juxtacrine loop of CSF-1 and EGF, respectively.Article Citation - WoS: 12Citation - Scopus: 13The Extended Graetz Problem for Micro-Slit Geometries; Analytical Coupling of Rarefaction, Axial Conduction and Viscous Dissipation(Elsevier Ltd., 2016) Kalyoncu, Gülce; Barışık, MuratIn order to support the recent MEMS and Lab-on-a-chip technologies, we studied heat transport in micro-scale slit channel gas flows. Since the micro convection transport phenomena diverges from conventional macro-scale transport due to rarefaction, axial conduction and viscous heating, an accurate understanding requires a complete coupling of these effects. For such cases, we studied heat transfer in hydrodynamically developed, thermally developing gas flows in micro-slits at various flow conditions. The analytical solution of the energy equation considered both the heat conduction in the axial direction and heat dissipation of viscous forces. Furthermore, updated boundary conditions of velocity slip and temperature jump were applied based on Knudsen number of flow in order to account for the non-equilibrium gas dynamics. Local Nusselt number (Nu) values were calculated as a function of Peclet (Pe), Knudsen (Kn) and Brinkman (Br) numbers which were selected carefully according to possible micro-flow cases. Strong variation of Nu in thermal development length was found to dominate heat transfer behavior of micro-slits with short heating lengths for early slip flow regime. For this instance, influence of axial conduction and viscous dissipation was equally important. On the other hand, high Kn slip flow suppressed the axial conduction while viscous heating in a small surface-gas temperature difference case mostly determined the fully developed Nu and average heat transfer behavior as a function of Kn value.Article Citation - WoS: 11Citation - Scopus: 12Novel Hybrid Process for the Conversion of Microcrystalline Cellulose To Value-Added Chemicals: Part 1: Process Optimization(Springer Verlag, 2016) Akın, Okan; Yüksel, AslıIn this paper, a novel hybrid process for the treatment of microcrystalline cellulose (MCC) under hot-compressed water was investigated by applying constant direct current on the reaction medium. Constant current range from 1A to 2A was applied through a cylindrical anode made of titanium to the reactor wall. Reactions were conducted using a specially designed batch reactor (450 mL) made of SUS 316 stainless steel for 30–120 min of reaction time at temperature range of 170–230 °C. As a proton donor H2SO4 was used at concentrations of 1–50 mM. Main hydrolysis products of MCC degradation in HCW were detected as glucose, fructose, levulinic acid, 5-HMF, and furfural. For the quantification of these products, High Performance Liquid Chromatography (HPLC) and Gas Chromatography with Mass Spectroscopy (GC–MS) were used. A ½ fractional factorial design with 2-level of four factors; reaction time, temperature, H2SO4 concentration and applied current with 3 center points were built and responses were statistically analyzed. Response surface methodology was used for process optimization and it was found that introduction of 1A current at 200 °C to the reaction medium increased Total Organic Carbon (TOC) and cellulose conversions to 62 and 81 %, respectively. Moreover, application of current diminished the necessary reaction temperature and time to obtain high TOC and cellulose conversion values and hence decreased the energy required for cellulose hydrolysis to value added chemicals. Applied current had diverse effect on levulinic acid concentration (29.9 %) in the liquid product (230 °C, 120 min., 2 A, 50 mM H2SO4). © 2016, Springer Science+Business Media Dordrecht.