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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 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 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 Open Access 3D printed microneedles for point of care biosensing applications(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Department of Mechanical Engineering; Sarabi, Misagh Rezapour; Nakhjavani, Sattar Akbar; Taşoğlu, Savaş; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Koç Üniversitesi İş Bankası Yapay Zeka Uygulama ve Araştırma Merkezi (KUIS AI)/ Koç University İş Bank Artificial Intelligence Center (KUIS AI); Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 291971Microneedles (MNs) are an emerging technology for user-friendly and minimally invasive injection, offering less pain and lower tissue damage in comparison to conventional needles. With their ability to extract body fluids, MNs are among the convenient candidates for developing biosensing setups, where target molecules/biomarkers are detected by the biosensor using the sample collected with the MNs. Herein, we discuss the 3D printing of microneedle arrays (MNAs) toward enabling point-of-care (POC) biosensing applications.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 A comparative study on the effect of monodisperse Au and Ag nanoparticles on the performance of organic photovoltaic devices(Elsevier, 2021) Kacus, Hatice; Sevim, Melike; Biber, Mehmet; Baltakesmez, Ali; Aydogan, Sakir; Department of Chemistry; Metin, Önder; Faculty Member; Department of Chemistry; College of Sciences; 46962The monodisperse Au (similar to 5 nm) and Ag (similar to 3 nm) nanoparticles used in this study were obtained using surfactant-assistant solvothermal methods and characterized by XRD TEM and SEM. Then, these nanoparticles were embedded into the P3HT:PCBM photoactive layer at different ratios and the effects of the nanoparticles on the performance of the organic solar cells have been studied by varying the loading percent of the NPs in the range of 0.5-2 wt%. The best solar cell composition was determined to be 1 wt% for Au NPs and 0.5 wt% for Ag NPs. Optical absorption spectrum of P3HT:PCBM, P3HT:PCBM:AuNPs and P3HT:PCBM:AgNPs active layers were obtained using UV-visible spectroscopy. The J-V plots of ITO/PEDOT:PSS/P3HT:PCBM/LiF/Al solar cells having 1.10(-6) m(2) OSC area and with different Au NPs and Ag NPs loading ratios in the P3HT:PCBM were obtained under air mass (AM) 1.5G illumination. Open circuit voltage, short-circuit current density, fill factor, and power conversion efficiency of the OSC were calculated. The highest PCE values were obtained as 3.35% for Au NPs and as 3.50% for Ag NPs doped devices. This increase in PCEs was explained by a plasmonic effect that stems from the metallic NPs.Publication Metadata only A computational-graph partitioning method for training memory-constrained DNNs(Elsevier, 2021) Wahib, Mohamed; Dikbayir, Doga; Belviranli, Mehmet Esat; N/A; Department of Computer Engineering; Qararyah, Fareed Mohammad; Erten, Didem Unat; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 219274Many state-of-the-art Deep Neural Networks (DNNs) have substantial memory requirements. Limited device memory becomes a bottleneck when training those models. We propose ParDNN, an automatic, generic, and non-intrusive partitioning strategy for DNNs that are represented as computational graphs. ParDNN decides a placement of DNN's underlying computational graph operations across multiple devices so that the devices' memory constraints are met and the training time is minimized. ParDNN is completely independent of the deep learning aspects of a DNN. It requires no modification neither at the model nor at the systems level implementation of its operation kernels. ParDNN partitions DNNs having billions of parameters and hundreds of thousands of operations in seconds to few minutes. Our experiments with TensorFlow on 16 GPUs demonstrate efficient training of 5 very large models while achieving superlinear scaling for both the batch size and training throughput. ParDNN either outperforms or qualitatively improves upon the related work.Publication Metadata only A construal level account of the impact of religion and god on prosociality(Sage, 2020) N/A; N/A; Department of Business Administration; Canlı, Zeynep Gürhan; Karataş, Mustafa; PhD Student; Faculty Member; Department of Business Administration; Graduate School of Business; College of Administrative Sciences and Economics; N/A; 16135This research shows that the two most prevalent religious constructs-God and religion-differentially impact cognition. Activating thoughts about God (vs. religion) induces a relatively more abstract (vs. concrete) mindset (Studies 1a-1c). Consequently, time donation intentions (Study 2) and actual monetary donations (Study 3) after a God (vs. religion) prime increase when people are presented an abstractly (vs. concretely) framed donation appeal. Similarly, people donate more money to distant (vs. close) donation targets, which are construed relatively abstractly (vs. concretely), when a religious speech activates predominantly God-specific (vs. religion-specific) thoughts (Study 4). These effects are mediated by "feeling right" under construal level fit (Study 3). Overall, this research significantly advances extant knowledge on religious cognition and past research on the link between religion and prosociality.Publication Metadata only A data-driven optimization framework for routing mobile medical facilities(2020) Yücel, Eda; Bozkaya, Burçin; Gökalp, Cemre; Department of Industrial Engineering; Salman, Fatma Sibel; Faculty Member; Department of Industrial Engineering; College of Engineering; 178838We study the delivery of mobile medical services and in particular, the optimization of the joint stop location selection and routing of the mobile vehicles over a repetitive schedule consisting of multiple days. Considering the problem from the perspective of a mobile service provider company, we aim to provide the most revenue to the company by bringing the services closer to potential customers. Each customer location is associated with a score, which can be fully or partially covered based on the proximity of the mobile facility during the planning horizon. The problem is a variant of the team orienteering problem with prizes coming from covered scores. In addition to maximizing total covered score, a secondary criterion involves minimizing total travel distance/cost. We propose a data-driven optimization approach for this problem in which data analyses feed a mathematical programming model. We utilize a year-long transaction data originating from the customer banking activities of a major bank in Turkey. We analyze this dataset to first determine the potential service and customer locations in Istanbul by an unsupervised learning approach. We assign a score to each representative potential customer location based on the distances that the residents have taken for their past medical expenses. We set the coverage parameters by a spatial analysis. We formulate a mixed integer linear programming model and solve it to near-optimality using Cplex. We quantify the trade-off between capacity and service level. We also compare the results of several models differing in their coverage parameters to demonstrate the flexibility of our model and show the impact of accounting for full and partial coverage.