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Publication Metadata only ‘Anti-commutable’ local pre-Leibniz algebroids and admissible connections(Elsevier, 2023) Department of Physics; N/A; Dereli, Tekin; Doğan, Keremcan; Faculty Member; PhD Student; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; 201358; N/AThe concept of algebroid is convenient as a basis for constructions of geometrical frameworks. For example, metric-affine and generalized geometries can be written on Lie and Courant algebroids, respectively. Furthermore, string theories might make use of many other algebroids such as metric algebroids, higher Courant algebroids, or conformal Courant algebroids. Working on the possibly most general algebroid structure, which generalizes many of the algebroids used in the literature, is fruitful as it creates a chance to study all of them at once. Local pre-Leibniz algebroids are such general ones in which metric-connection geometries are possible to construct. On the other hand, the existence of the 'locality operator', which is present for the left-Leibniz rule for the bracket, necessitates the modification of torsion and curvature operators in order to achieve tensorial quantities. In this paper, this modification of torsion and curvature is explained from the point of view that the modification is applied to the bracket instead. This leads one to consider 'anti-commutable' local pre-Leibniz algebroids which satisfy an anti-commutativity-like property defined with respect to a choice of an equivalence class of connections. These 'admissible' connections are claimed to be the necessary ones while working on a geometry of algebroids. This claim is due to the fact that one can prove many desirable properties and relations if one uses only admissible connections. For instance, for admissible connections, we prove the first and second Bianchi identities, Cartan structure equations, Cartan magic formula, the construction of Levi-Civita connections, the decomposition of connection in terms of torsion and non-metricity. These all are possible because the modified bracket becomes anti-symmetric for an admissible connection so that one can apply the machinery of almost-or pre-Lie algebroids. We investigate various algebroid structures from the literature and show that they admit admissible connections which are metric-compatible in some generalized sense. Moreover, we prove that local pre-Leibniz algebroids that are not anti-commutable cannot be equipped with a torsion-free, and in particular Levi-Civita, connection.Publication Metadata only (Im)moral borders in practice(Taylor & Francis, 2021) El Qadim, Nora; Isleyen, Beste; de Vries, Leonie Ansems; Hansen, Signe Sofie; Lisle, Debbie; Simonneau, Damien; N/A; Karadağ, Sibel; Researcher; Migration Research Program at Koç University (MIReKoç) / Göç Araştırmaları Uygulama ve Araştırma Merkezi (MIReKoç); N/A; N/AThis Forum aims to push existing debates in critical border and migration studies over the featuring of morals, ethics and rights in everyday practices relating to the governance of the mobility of non-citizen populations. Its contributors steer away from the actual evaluation or advocacy of the good/just/ethical, focusing instead on the sociological examination of morals and ethics in practice, i.e. how actors understand morally and ethically the border and migration policies they implement or resist. A proliferating interest in the discursive and non-discursive materialisation of moral and ethical elements in asylum and migration policies has examined the intertwinement of care and control logics underlying the management of refugee camps, borders and borderzones, and hotspots alongside the deployment of search-and-rescue operations. Nevertheless, recent research has shown the need to unpack narratives and actions displaying values and symbols that are not necessarily encompassed within this intertwinement of compassion and repression. We argue that there is a need to pay more attention to the diversity, plurality and the operation of morality, ethics and rights in settings and geographies, and of including a diversity of actors both across and beyond EUrope.Publication Metadata only 21 fs Cr:LiSAF laser mode locked with a single-walled carbon nanotube saturable absorber(Optical Soc Amer, 2019) Bae, Ji Eun; Rotermund, Fabian; Demirbaş, Ümit; N/A; N/A; N/A; Department of Physics; Tanısalı, Gökhan; Toker, Işınsu Baylam; Taşçı, Mısra; Sennaroğlu, Alphan; PhD Student; PhD Student; Undergraduate Student; Faculty Member; Department of Physics; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; School of Medicine; College of Sciences; N/A; N/A; N/A; 23851We report the shortest femtosecond pulses directly generated from a solid-state laser that is mode locked by using a single-walled carbon nanotube saturable absorber (SWCNT-SA). In the experiments, we used a 660 nm diode-pumped, low-threshold extended-cavity Cr:LiSAF laser operating around 850 nm with a repetition rate of 47.9 MHz. The SWCNT-SA mode-locked Cr:LiSAF laser produced 21 fs pulses with a time-bandwidth product of 0.56 by using only 210 mW of pump power. Pump-probe spectroscopy measurements showed that the SWCNT-SA exhibited saturable absorption with slow and fast decay times of 2.7 ps and 0.4 ps. The single-pass modulation depth and saturation fluence of the SWCNT-SA were further determined as 0.3% and 45 mu J/cm(2) at the pump wavelength of 850 nm.Publication Metadata only 268th ENMC workshop - Genetic diagnosis, clinical classification, outcome measures, and biomarkers in Facioscapulohumeral Muscular Dystrophy (FSHD): Relevance for clinical trials(Elsevier B.V., 2023) Montagnese F, de Valle K, Lemmers RJLF, Mul K, Dumonceaux J, Voermans N; 268th ENMC workshop participants.; Oflazer, Piraye; ; School of Medicine;Highlights This ENMC workshop has seen the participation of many important stakeholders working together to improve trial readiness in FSHD: patients and patients’ organizations (FSHD-Europe, FSHD-Society and FSHD Global), neuromuscular clinicians, geneticists, basic researchers, representatives of the TREAT-NMD network, the FSHD-CTRN and EMA. COMs represent useful tools for the standardized collection of clinical features but need to be selected to match the clinical setting of use. For patient care, they need to be informative, with practical and time efficient utility so as not to detract from clinical care. For clinical trial purposes, the need to be reliable, valid, meaningful and sensitive to change to better depict therapeutic responses. An optimized clinical evaluation and genetic test form is one of the goals of WG1 and 2. A diagnostic flowchart for FSHD1 and FSHD2 has been proposed. Another important unmet need for clinical trial readiness in FSHD is the identification of good therapeutic biomarkers, which ideally should be quantitative, non-invasive, applicable across the entire range of disease severity, sensitive to change, reliable and clinically meaningful. The WG 3 will produce standard operating procedures (SOPs) for DUX4 detection. Similarly, large differences in the reporting of studies performed on animal models, thus hindering interpretation, repeatability and comparison of the results need to be addressed. Guidelines regarding minimum information for publication of work including animal models for FSHD will therefore be published.Publication Metadata only 2d -> 3d polycatenated and 3d -> 3d interpenetrated metal-organic frameworks constructed from thiophene-2,5-dicarboxylate and rigid bis(imidazole) ligands(Elsevier, 2014) Erer, Hakan; Yesilel, Okan Zafer; Arici, Mursel; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Hydrothermal reactions of rigid 1,4-bis(imidazol-1-yl)benzene (dib) and 1,4-bis(imidazol-1-yl)-2, 5-dimethylbenzene (dimb) with deprotonated thiophene-2,5-dicarboxylic acid (H(2)tdc) in the presence of Zn(II) and Cd(II) salts in H2O produced three new metal-organic frameworks, namely, [Zn(mu-tdc)(H2O) (mu-dib)](n) (1), [Cd(mu-tdc)(H2O)(mu-dib)(n) (2), and {[Cd-2(mu(3)-tdc)(2)(mu-dimb)(2)] center dot (H2O)}(n) (3). These MOFs were characterized by FT-IR spectroscopy, elemental, thermal (TG, DTA, DTG and DSC), and single-crystal X-ray diffraction analyses. Isomorphous complexes 1 and 2 reveal polycatenated 2D+2D -> 3D framework based on an undulated (4,4)-sql layer. Complex 3 exhibits a new 4-fold interpenetrating 3D framework with the point symbol of 6(6). Molecular simulations were used to assess the potentials of the complexes for H-2 storage application. Moreover, these coordination polymers exhibit blue fluorescent emission bands in the solid state at room temperature.Publication Metadata only 3D printed kombucha biomaterial as a tissue scaffold and L929 cell cytotoxicity assay(Wiley, 2024) Yanbakan, Edaguel; Tuncel, Tugba; Kocak Sezgin, Ayse; Bozoglan, Emirhan; Berikten, Derya; Kar, Fatih; Department of Molecular Biology and Genetics; Bağlan, İlkyaz; Department of Molecular Biology and Genetics; College of SciencesTissue engineering includes the construction of tissue-organ scaffold. The advantage of three-dimensional scaffolds over two-dimensional scaffolds is that they provide homeostasis for a longer time. The microbial community in Symbiotic culture of bacteria and yeast (SCOBY) can be a source for kombucha (kombu tea) production. In this study, it was aimed to investigate the usage of SCOBY, which produces bacterial cellulose, as a biomaterial and 3D scaffold material. 3D printable biomaterial was obtained by partial hydrolysis of oolong tea and black tea kombucha biofilms. In order to investigate the usage of 3D kombucha biomaterial as a tissue scaffold, "L929 cell line 3D cell culture" was created and cell viability was tested in the biomaterial. At the end of the 21st day, black tea showed 51% and oolong tea 73% viability. The cytotoxicity of the materials prepared by lyophilizing oolong and black tea kombucha beverages in fibroblast cell culture was determined. Black tea IC50 value: 7.53 mg, oolong tea IC50 value is found as 6.05 mg. Fibroblast viability in 3D biomaterial + lyophilized oolong and black tea kombucha beverages, which were created using the amounts determined to these values, were investigated by cell culture Fibroblasts in lyophilized and 3D biomaterial showed viability of 58% in black tea and 78% in oolong tea at the end of the 7th day. In SEM analysis, it was concluded that fibroblast cells created adhesion to the biomaterial. 3D biomaterial from kombucha mushroom culture can be used as tissue scaffold and biomaterial.Publication Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.Publication Metadata only 3D surface topography analysis in 5-axis ball-end milling(Elsevier, 2017) N/A; Department of Mechanical Engineering; Khavidaki, Sayed Ehsan Layegh; Lazoğlu, İsmail; PHD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 179391This article presents a new analytical model to predict the topography and roughness of the machined surface in 5-axis ball-end milling operation for the first time. The model is able to predict the surface topography and profile roughness parameters such as 3D average roughness (Sa) and 3D root mean square roughness (Sq) by considering the process parameters such as the feedrate, number of flutes, step over and depth of cut as well as the effects of eccentricity and tool runout in 5-axis ball-end milling. This model allows to simulate the effects of the lead and tilt angles on the machined surface quality in the virtual environment prior to the costly 5-axis machining operations. The effectiveness of the introduced surface topography prediction model is validated experimentally by conducting 5-axis ball-end milling tests in various cutting conditions. (C) 2017 Published by Elsevier Ltd on behalf of CIRP.Publication Metadata only A Bayesian generalized linear model for Crimean–Congo hemorrhagic fever incidents(Springer, 2018) Ryu, Duchwan; Bilgili, Devrim; Liang, Faming; Ebrahimi, Nader; Ergönül, Önder; Faculty Member; School of Medicine; 110398Global spread of the Crimean-Congo hemorrhagic fever (CCHF) is a fatal viral infection disease found in parts of Africa, Asia, Eastern Europe and Middle East, with a fatality rate of up to 30%. A timely prediction of the prevalence of CCHF incidents is highly desirable, while CCHF incidents often exhibit nonlinearity in both temporal and spatial features. However, the modeling of discrete incidents is not trivial. Moreover, the CCHF incidents are monthly observed in a long period and take a nonlinear pattern over a region at each time point. Hence, the estimation and the data assimilation for incidents require extensive computations. In this paper, using the data augmentation with latent variables, we propose to utilize a dynamically weighted particle filter to take advantage of its population controlling feature in data assimilation. We apply our approach in an analysis of monthly CCHF incidents data collected in Turkey between 2004 and 2012. The results indicate that CCHF incidents are higher at Northern Central Turkey during summer and that some beforehand interventions to stop the propagation are recommendable. Supplementary materials accompanying this paper appear on-line.Publication Metadata only A bi-criteria optimization model to analyze the impacts of electric vehicles on costs and emissions(Elsevier, 2017) N/A; N/A; Department of Industrial Engineering; Kabatepe, Bora; Türkay, Metin; Master Student; Faculty Member; Department of Industrial Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 24956Electric vehicles (EV) are emerging as a mobility solution to reduce emissions in the transportation sector. The studies environmental impact analysis of EVs in the literature are based on the average energy mix or pre-defined generation scenarios and construct policy recommendations with a cost minimization objective. However, the environmental performance of EVs depends on the source of the marginal electricity provided to the grid and single objective models do not provide a thorough analysis on the economic and environmental impacts of EVs. In this paper, these gaps are addressed by a four step methodology that analyzes the effects of EVs under different charging and market penetration scenarios. The methodology includes a bi-criteria optimization model representing the electricity market operations. The results from a real-life case analysis show that EVs decrease costs and emissions significantly compared to conventional vehicles.