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Publication Metadata only 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; 351800Seroconversion 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 Mycophenolic acid was withdrawn in 43 selected patients 5-7 days prior to vaccination and remained paused for 4 additional weeks after vaccination.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 The effect was most pronounced in individuals in whom mycophenolic acid was withdrawn during vaccination.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.Publication Metadata only Evolution of transformation plasticity in austenite-to-bainite phase transformation: a multi parameter problem(Elsevier Science Sa, 2012) Lambers, Hans -Gerd; Maier, Hans Jürgen; Department of Mechanical Engineering; Canadinç, Demircan; Faculty Member; Department of Mechanical Engineering; College of Engineering; 23433The current paper presents a thorough experimental analysis of the austenite-to-bainite phase transformation, and provides insight into microstructural changes associated with the observed transformation plasticity (TP). Specifically, the evolution of TP was studied in the presence of several parameters, namely pre-deformation, temperature and superimposed constant stresses, and the observed phenomena were linked to microstructural changes under these circumstances based on experimental data. One major finding is that the evolution of TP strains is governed both by the superimposed external stresses and the temperature dependence of internal stresses introduced by pre-deformation.Publication Metadata only Preface of the special issue on global multiobjective optimization(Springer, 2021) Miettinen, Kaisa; Department of Business Administration; Sayın, Serpil; Faculty Member; Department of Business Administration; College of Administrative Sciences and Economics; 6755N/APublication Metadata only Unguales plattenepithelkarzinom bei einem patienten mit mal de meleda(Wiley, 2016) Baykal, Can; Sarı, Şule Öztürk; Uyguner, Zehra Oya; Ekinci, Algun Polat; Demir, Özgür; Babuna, Goncagül; Büyükbabani, Nesimi; N/A; Kayserili, Hülya; Faculty Member; School of Medicine; 7945N/APublication Metadata only Counterexamples to regularity of Mane projections in the theory of attractors(Institute of Physics (IOP) Publishing, 2013) Eden, Alp; Zelik, Sergey V.; Department of Mathematics; Kalantarov, Varga; Faculty Member; Department of Mathematics; College of Sciences; 117655This paper is a study of global attractors of abstract semilinear parabolic equations and their embeddings in finite-dimensional manifolds. As is well known, a sufficient condition for the existence of smooth (at least C-1-smooth) finite-dimensional inertial manifolds containing a global attractor is the so-called spectral gap condition for the corresponding linear operator. There are also a number of examples showing that if there is no gap in the spectrum, then a C-1-smooth inertial manifold may not exist. on the other hand, since an attractor usually has finite fractal dimension, by Mane's theorem it projects bijectively and Holder-homeomorphically into a finite-dimensional generic plane if its dimension is large enough. It is shown here that if there are no gaps in the spectrum, then there exist attractors that cannot be embedded in any Lipschitz or even log-Lipschitz finite-dimensional manifold. Thus, if there are no gaps in the spectrum, then in the general case the inverse Mane projection of the attractor cannot be expected to be Lipschitz or log-Lipschitz. Furthermore, examples of attractors with finite Hausdorff and infinite fractal dimension are constructed in the class of non-linearities of finite smoothness.Publication Metadata only 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; 8579This 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.Publication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.Publication Metadata only Clinical results of anterior odontoid screw fixation for type II odontoid fractures(Turkish Neurosurgical Society, 2014) Keskin, Fatih; Gomleksiz, Cengiz; Sasani, Mehdi; Oktenoglu, Tunc; Suzer, Tuncer; Özer, Ali Fahir; Faculty Member; School of Medicine; 1022AIM: In this study, 31 patients with a diagnosis of Type II odontoid fractures were reported. All patients were treated with anterior transodontoid screw fixation and clinical outcomes were reported. MATERIAL and METHODS: In this study, the retrospective clinical analysis of 31 patients with traumatic type II odontoid fractures who were treated through anterior transodontoid fixation in Neurosurgery Department at VKV American Hospital between 1998 and 2012 was performed. The age, sex, cause of injury, diagnosis time, neurological examination before and after surgery, follow-up period were evaluated. The neurological status of patients was classified according to the Frankel scale. RESULTS: In 4 patients, 2 transodontoid screws were inserted. The mean hospital stay was 3.35 days. Posterior occipito-cervical fusion was done in 1 patient due to the lack of fusion in the first operation. No vascular injury, screw malposition, infection, neurologic deterioration, or complications were observed during the peroperative and postoperative stage. The mean postoperative follow-up period was 36 months after surgery. Radiological imaging of patients were performed at the early and late postoperative stage. CONCLUSION: We found satisfying fusion rates and better patient comfort during the postoperative period. We think that stabilization and fusion through a transodontoid screw is a minimal invasive method.AMAÇ: Çalışmada, Tip II odontoid fraktürü tanısı alan 31 olgu bildirilmiştir. Olguların hepsi anterior transodontoid vida fiksasyonu ile tedavi edilmiş ve klinik sonuçları bildirilmiştir. YÖNTEM ve GEREÇLER: Çalışma, VKV Amerikan Hastanesi Nöroşirürji Bölümü’nde 1998-2012 yılları arasında travmatik tip II odontoid kırığı nedeniyle anterior transodontoid fiksasyon ile cerrahi tedavi uygulanan 31 hastanın retrospektif klinik analizleri yapılmıştır. Tüm olguların yaş, cinsiyet, travma nedeni, teşhis zamanı, cerrahi girişim öncesi ve sonrasında nörolojik muayeneleri, takip süresi değerlendirilmiştir. Olguların nörolojik durumları Frankel skalasına göre sınıflandırılmıştır. BULGULAR: Dört hastaya 2 adet transodontoid vidası yerleştirildi. Hastanede kalış süresi ortalama 3,35 gün idi. 1 hastada postop takibinde füzyon oluşmaması nedeniyle ikinci bir operasyon ile posteriordan oksipitoservikal füzyon yapıldı. İşlem sırasında ve sonrasında damar yaralanması, vida malpozisyonu, enfeksiyon, nörolojik bozulma gibi komplikasyonlar izlenmedi. Hastalar ameliyat sonrasında ortalama 36 ay takip edildi. Hastaların erken ve geç dönemde radyolojik görüntülemeleri yapıldı. SONUÇ: Postoperatif dönemde hastaların takiplerinde tatmin edici füzyon oranı ve hasta konforunun daha iyi olduğunu saptadık. Tip II odontoid kırıklarının cerrahi tedavisinde minimal invaziv yöntem olan transodontoid vida ile fiksasyonun yüksek avantajlarından dolayı ilk seçenek olabileceğini düşünüyoruz.Publication Metadata only Beyond social mobility: Biographies, habitus and responses to changing 'Conditions of Existence' among university scholarship students(Sage, 2021) N/A; N/A; Nimer, Maissam; Researcher; Migration Research Program at Koç University (MIReKoç) / Göç Araştırmaları Uygulama ve Araştırma Merkezi (MIReKoç); N/A; N/A; 355744Wider access to higher education at a global level has been accompanied by growing literature on experiences of social mobility often using the concept of habitus as a theoretical tool to frame responses to changes in 'conditions of existence'. Drawing on the case study of a scholarship programme within an elite university in Lebanon, through in-depth interviews with students and university faculty and staff, this article elaborates on the typologies in responses that emerged as students position themselves in a new environment. These typologies, in contrast to the literature which presents them as a result of alterations in the habitus, appear to be related to each other and occur simultaneously within one person's trajectory. As such, instead of viewing these responses as degrees of incorporation of each set of schemes of perceptions from both fields, the context of origin and the new social context appear to be multi-faceted, and the interaction between them is complex. I argue, along the lines of Lahire's dispositional perspective, that the situation of contradictory experiences is not exceptional but characterizes all individuals to a certain extent, especially in the Lebanese context which is distinguished by its diversity in terms of regional and religious affiliations and in which class intersects with other types of identifications.Publication Metadata only Direct identification of A-to-I editing sites with nanopore native RNA sequencing(NATURE PORTFOLIO, 2022) Nguyen, Tram Anh; Heng, Jia Wei Joel; Kaewsapsak, Pornchai; Kok, Eng Piew Louis; Stanojevic, Dominik; Liu, Hao; Cardilla, Angelysia; Praditya, Albert; Yi, Zirong; Lin, Mingwan; Aw, Jong Ghut Ashley; Ho, Yin Ying; Peh, Kai Lay Esther; Wang, Yuanming; Zhong, Qixing; Heraud-Farlow, Jacki; Xue, Shifeng; Walkley, Carl; Ho, Ying Swan; Sikic, Mile; Wan, Yue; Tan, Meng How; N/A; Reversade, Bruno; Faculty Member; School of Medicine; 274182Inosine is a prevalent RNA modification in animals and is formed when an adenosine is deaminated by the ADAR family of enzymes. Traditionally, inosines are identified indirectly as variants from Illumina RNA-sequencing data because they are interpreted as guanosines by cellular machineries. However, this indirect method performs poorly in protein-coding regions where exons are typically short, in non-model organisms with sparsely annotated single-nucleotide polymorphisms, or in disease contexts where unknown DNA mutations are pervasive. Here, we show that Oxford Nanopore direct RNA sequencing can be used to identify inosine-containing sites in native transcriptomes with high accuracy. We trained convolutional neural network models to distinguish inosine from adenosine and guanosine, and to estimate the modification rate at each editing site. Furthermore, we demonstrated their utility on the transcriptomes of human, mouse and Xenopus. Our approach expands the toolkit for studying adenosine-to-inosine editing and can be further extended to investigate other RNA modifications.