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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3

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    Humoral response to SARS-COV-2 MRNA vaccination in previous non-responder kidney transplant recipients after short-term withdrawal of mycophenolic acid
    (Frontiers, 2022) Benning, Louise; Morath, Christian; Kühn, Tessa; Bartenschlager, Marie; Kim, Heeyoung; Beimler, Joerg; Buylaert, Mirabel; Nusshag, Christian; Kälble, Florian; Reineke, Marvin; Töllner, Maximilian; Schaier, Matthias; Klein, Katrin; Blank, Antje; Schnitzler, Paul; Zeier, Martin; Bartenschlager, Ralf; Thuong Hien Tran; Speer, Claudius; Süsal, Caner; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; Koç University Hospital; 351800
    Seroconversion rates after COVID-19 vaccination are significantly lower in kidney transplant recipients compared to healthy cohorts. Adaptive immunization strategies are needed to protect these patients from COVID-19. In this prospective observational cohort study, we enrolled 76 kidney transplant recipients with no seroresponse after at least three COVID-19 vaccinations to receive an additional mRNA-1273 vaccination (full dose, 100 mu g). Mycophenolic acid was withdrawn in 43 selected patients 5-7 days prior to vaccination and remained paused for 4 additional weeks after vaccination. SARS-CoV-2-specific antibodies and neutralization of the delta and omicron variants were determined using a live-virus assay 4 weeks after vaccination. In patients with temporary mycophenolic acid withdrawal, donor-specific anti-HLA antibodies and donor-derived cell-free DNA were monitored before withdrawal and at follow-up. SARS-CoV-2 specific antibodies significantly increased in kidney transplant recipients after additional COVID-19 vaccination. The effect was most pronounced in individuals in whom mycophenolic acid was withdrawn during vaccination. Higher SARS-CoV-2 specific antibody titers were associated with better neutralization of SARS-CoV-2 delta and omicron variants. In patients with short-term withdrawal of mycophenolic acid, graft function and donor-derived cell-free DNA remained stable. No acute rejection episode occurred during short-term follow-up. However, resurgence of prior anti-HLA donor-specific antibodies was detected in 7 patients.
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    Light engine and optics for HELIUM3D auto-stereoscopic laser scanning display
    (IEEE, 2011) Willman, Eero; Baghsiahi, Hadi; Day, Sally E.; Selviah, David R.; Fernandez, F. Anibal; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Akşit, Kaan; Ölçer, Selim; Erden, Erdem; Chellappan, Kishore Velichappattu; Ürey, Hakan; PhD Student; Other; Master Student; Researcher; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 8579
    This paper presents a laser-based auto-stereoscopic 3D display technique and a prototype utilizing a dual projector light engine. The solution described is able to form dynamic exit pupils under the control of a multi-user head-tracker. A prototype completed recently is able to provide a glasses-free solution for a single user at a fixed position. At the end of the prototyping phase it is expected to enable a multiple user interface with an integration of the pupil tracker and the spatial light modulator.
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    Peripapillary choroidal vasculature in pediatric eyes with type 1 diabetes mellitus
    (Kare Yayıncılık, 2022) N/A; N/A; Hasanreisoğlu, Murat; Kesim, Cem; Uzunay, Nur Sena; Taş, Ayşe Yıldız; Karslıoğlu, Melisa Zişan; Şahin, Afsun; Faculty Member; Teaching Faculty; Undergraduate Student; Faculty Member; Doctor; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; School of Medicine; School of Medicine; School of Medicine; N/A; School of Medicine; N/A; N/A; N/A; N/A; Koç University Hospital; N/A; 182001; 387367; N/A; 200905; N/A; 171267
    Objectives: choroidal vasculature change in children with diabetes mellitus is not investigated enough although it could reflect clinical outcome. Methods: pediatric Type 1 diabetes mellitus (T1DM) patients and healthy controls were retrospectively evaluated. Peripapillary retinal nerve fiber layer optical coherence tomography (OCT) images of the right eyes were analyzed. Choroidal parameters including total choroidal area, luminal area, stromal area, and choroidal vascularity index were measured through image binarization. Results: twenty eyes of 20 patients were compared with 46 eyes of 46 healthy controls. Mean total choroidal area, luminal area, and stromal area were 1.59±0.35, 1.10±0.24, and 0.50±0.13 mm2 in patients’ eyes and 1.52±0.49, 1.05±0.34, and 0.47±0.17 mm2 in healthy eyes. No difference was found in choroidal vascularity indices between patients and healthy eyes (68.8±3.9% vs. 69.4±4.4%, p=0.521). Temporal choroidal vascularity index was significantly higher than its nasal counterpart in healthy eyes (71.8±5.0% vs. 68.6±4.9%, p<0.001) which was not significant in patients’ eyes (70.7±4.0% vs. 68.9±5.1%, p=0.067). Temporal quadrant had the highest choroidal vascularity index score among all quadrants in healthy controls (all p<0.05), whereas no choroidal vascularity index difference between quadrants was detected in patients (p=0.75). Conclusion: peripapillary choroidal vasculature has shown subtle sectoral changes which did not reflect the overall peripapillary OCT section in pediatric T1DM patients when compared with healthy controls.
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    Foreign ownership, survival and growth dynamics in Turkish manufacturing
    (Routledge, 2014) Taymaz, Erol; Department of Economics; Yılmaz, Kamil; Faculty Member; Department of Economics; College of Administrative Sciences and Economics; 6111
    The chapter is organized as follows. Section 11.2 provides a brief overview of FDI flows to Turkey followed by brief information on the establishment-level Turkish manufacturing industry data used in empirical analysis. Section 11.3 presents the model and results of the firm survival dynamics. Section 11.4 presents the estimation model and results on the employment growth of domestic and foreign firms. Section 11.5 concludes the chapter.
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    Dimensional stability of 51CrV4 steel during bainitic phase transformation under tensile and compressive stresses
    (Elsevier, 2010) Lambers H.-G.; Maier H.J.; Department of Mechanical Engineering; Canadinç, Demircan; Faculty Member; Department of Mechanical Engineering; College of Engineering; 23433
    The effect of the prior austenitization treatment on the stress-strain response of a low alloy 51CrV4 steel in its supercooled austenitic state and its effect on the evolution of transformation plasticity strain during a subsequent isothermal bainitic transformation was investigated. One of the key findings is that the prior austenitization treatment strongly affects the evolution of transformation plasticity strains during the subsequent isothermal bainitic transformation under stress, such that higher transformation plasticity strains are present when the austenite grain size is increased. In addition, higher 0.2% offset yield strengths of the supercooled austenite are present following an incomplete austenitization treatment due to the existence of residual carbides. Overall, the current results clearly lay out the effect of the prior austenitization treatment on the stress-strain response of the supercooled austenite and the evolution of transformation plasticity during bainitic transformation.
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    Application QoS fairness in wireless video scheduling
    (Institute of Electrical and Electronics Engineers (IEEE), 2006) N/A; N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Özçelebi, Tanır; Tekalp, Ahmet Murat; Civanlar, Mehmet Reha; Sunay, Mehmet Oğuz; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 26207; 16372; N/A
    The video pre-roll delay for filling up the client buffer can not be too long for user utility and buffer limitations in wireless point-to-multipoint streaming systems. Cross-layer design that deals with both physical and application layer aspects jointly is necessary for this purpose. We present a cross-layer optimized multiuser video adaptation and user scheduling framework for wireless video communication, where Quality-of-Service (QoS) fairness among users is provided with maximum video quality and video throughput. Both protocol layers are jointly optimized using a single Multi-Objective Optimization (MOO) framework that aims to schedule the user with the least remaining playback time and the highest video throughput (delivered video seconds per transmission slot) with maximum video quality. Experiments carried out in the IS-856 (1×EV-DO) standard and ITU pedestrian and vehicular environments demonstrate the improvements over the state-of-the-art schedulers in terms of video QoS fairness, video quality and throughput. / İstemci arabelleğini doldurmak için videodan önce gösterilen reklam gecikmesi, kablosuz noktadan çok noktaya akış sistemlerinde kullanıcı yardımcı programı ve arabellek sınırlamaları için çok uzun olamaz. Bu amaç için hem fiziksel hem de uygulama katmanı özelliklerini birlikte ele alan çapraz katman tasarımı gereklidir. Kablosuz video iletişimi için, kullanıcılar arasında Hizmet Kalitesi (QoS) adaletinin maksimum video kalitesi ve video çıkışı ile sağlandığı, katmanlar arası optimize edilmiş çok kullanıcılı bir video uyarlaması ve kullanıcı planlama çerçevesi sunuyoruz. Her iki protokol katmanı, kullanıcıyı maksimum video kalitesiyle en az kalan oynatma süresi ve en yüksek video verimi (iletim yuvası başına iletilen video saniyesi) ile programlamayı amaçlayan tek bir Çok Amaçlı Optimizasyon (MOO) çerçevesi kullanılarak ortaklaşa optimize edilmiştir. IS-856 (lxEV-DO) standardında ve ITU yaya ve araç ortamlarında gerçekleştirilen deneyler, video QoS adaleti, video kalitesi ve verim açısından en son teknoloji zamanlayıcılara göre iyileştirmeler göstermektedir.
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    Investigation of ionizing radiation response in new resistance models of glioblastoma.
    (Amer Assoc Cancer Research, 2021) N/A; N/A; Değirmenci, Nareg Pınarbaşı; Önder, Tuğba Bağcı; Sur, İlknur Erdem; Selek, Uğur; PhD Student; Faculty Member; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Health Sciences; School of Medicine; School of Medicine; School of Medicine; N/A; 184359; N/A; 27211
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    Continuous spontaneous alternation and turn alternation in Artemia Sp.
    (The Regents of the University of California, 2015) Department of Psychology; Department of Psychology; Department of Psychology; Balcı, Fuat; Çarkoğlu, Can; Yılmaz, Meltem; Faculty Member; Undergraduate Student; Undergraduate Student; Department of Psychology; College of Social Sciences and Humanities; College of Social Sciences and Humanities; College of Social Sciences and Humanities; 51269; N/A; N/A
    Free-running spontaneous alternation refers to the animal's tendency to prefer the least recently visited locations in successive spatial choices, which is attributed to the animals' choice between stimuli based on prior experience. Turn alternation, which is observed in directional choices preceded by a forced turn in one direction, also reflects the animals' tendency to alternate between directional choices but this tendency has been assumed to rely on other cues (e.g., proprioceptive cues) derived from the prior responses (e.g., forced turn in one direction). Based on previous studies, the turn alternation appears to rely on more primitive (lower-form) information features and to be a more frequently observed empirical phenomenon than the spontaneous alternation. We investigated these two behavioral alternation tendencies in Artemia sp. Experiment 1 tested the continuous spontaneous alternation (cSAB) performance of Artemia sp. in two different mazes: t-maze (three options) and plus maze (four options). Experiment 2 tested the turn alternation performance of Artemia sp. counter-balancing the direction of initial forced-turn between subjects. Our results showed that Artemia sp. had nearly chance level spontaneous alternation performance in the t-maze and plus maze whereas a higher than chance level turn alternation performance. These results support the ubiquity of turn alternation tendency across species and point at the lack of spontaneous alternation in Artemia sp.
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    SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay
    (Elsevier, 2013) Etlik, Ozdal; Koksal, Vedat; Ocak, Zeynep; Baris, Saniye Tugba; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; Department of Molecular Biology and Genetics; College of Sciences; 111629
    Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T. discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.
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