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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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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 Mycophenolic acid was withdrawn in 43 selected patients 5-7 days prior to vaccination and remained paused for 4 additional weeks after vaccination.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 The effect was most pronounced in individuals in whom mycophenolic acid was withdrawn during vaccination.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 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 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.Publication Metadata only 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; 171267Objectives: 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.Publication Metadata only On the rate of convergence of a classifier based on a transformer encoder(IEEE-Inst Electrical Electronics Engineers Inc, 2022) Gurevych, Iryna; Kohler, Michael; Department of Computer Engineering; Şahin, Gözde Gül; Faculty Member; Department of Computer Engineering; College of Engineering; 366984Pattern recognition based on a high-dimensional predictor is considered. A classifier is defined which is based on a Transformer encoder. The rate of convergence of the misclassification probability of the classifier towards the optimal misclassification probability is analyzed. It is shown that this classifier is able to circumvent the curse of dimensionality provided the a posteriori probability satisfies a suitable hierarchical composition model. Furthermore, the difference between the Transformer classifiers theoretically analyzed in this paper and the ones used in practice today is illustrated by means of classification problems in natural language processing.Publication Metadata only Determination of thyroglobulin levels by radioimmunoassay method in anti thyroglobulin positive differentiated thyroid patients: one center clinical experience(Pergamon-Elsevier Science Ltd, 2020) Uçar, Burcu; Şen, Melis; Acar, Tayfun; N/A; Demirkol, Mehmet Onur; Faculty Member; School of Medicine; 196946It is very crucial to determine Tg accurately and precisely in thyroid cancer cases. Although there are many studies on the detection of Tg in thyroid cases in the literature, there are no sufficient clinical studies examining many cases with different features by using RIA methodology. Here, a radiometric and chromatographic method has been studied for the first time to eliminate the interference from anti-Tg positive patients. In this paper, radioimmunoassay (RIA) and immunoradiometric (IRMA) techniques were used for the analysis of 302 sera collected from patients for Tg and TgAb quantification. By the RIA technique, a reliable result was obtained by calculating the real Tg value quantitatively in 41 patients showing TgAb positivity out of 208 patients. Our findings show that the RIA assay is the most suitable approach for detection of changeable (low or undetectable) Tg value and metastases detected by post-therapeutic imaging in early-stage DTC cases showing preoperative and postoperative TgAb positivity. The new immunoradiometric method allows the real (%) Tg value to be reached in a part of TgAb-positive DTC. Even if TgAb positive in the metastatic and nonmetastatic DTC patient group. This allows the accurate clinical follow-up of patients.Publication Metadata only Impact of COVID-19 pandemic on academic research and being demotivated(AVES, 2020) N/A; Aydemir, Duygu; Ulusu, Nuriye Nuray; PhD Student; 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; N/A; 6807N/APublication Metadata only Prevalence of apis, vespula and polistes sensitivity in venom allergic patients in Turkey(Wiley, 2020) Dursun, A. B.; Sonmez, H.; Gelincik, A.; Yigit, O. O.; Albayrak, O.; Celebioglu, E.; Sahiner, U. M.; Buyuktiryaki, B.; Erdogan, T.; Firtina, S.; Taylan, D.; Soyer, O.; Karakaya, G.; Kalyoncu, A. F.; Sekerel, B.; N/A; Hela, Francesko; Öztürk, Ayşe Bilge; Saçkesen, Cansın; Albayrak, Özgür; Other; Faculty Member; Faculty Member; Researcher; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; N/A; School of Medicine; N/A; N/A; 147629; 182537; N/AN/APublication Metadata only Superior epididymal artery-based paraepididymal adipofascial flap(Lippincott Williams and Wilkins (LWW), 2023) Cinar, Fatih; Yalcin, Can Ege; Celik, Ugur; Demiroz, Anil; Baghaki, Semih; Cetinkale, Oguz; N/A; Ayas, Görkem; Undergraduate Student; School of Medicine; N/ABackground: Flap surgery is widely performed in reconstructive surgery. Experimental research is vital to improve flap viability. However, the number of flap models for animals is still limited. In this study, we define a new adipofascial flap in rats that can be used to investigate pedicled flap and/or adipofascial flap physiology.Methods: Eight Wistar male rats were used. Under deep anesthesia, paraepididymal adipofascial flaps were harvested. Flap perfusion was assessed using a near-infrared fluorescence imaging system. The length of the flap and the diameter of the flap pedicle were measured.Results: All animals (n = 8) had sufficient sizes of paraepididymal fat pad, and no animals were lost. The only postoperative complication was testicular hematoma, which was observed in 2 animals. The maximum length of the harvested paraepididymal adipofascial flap was 9.7 cm with a mean of 6.6 cm. The maximum width of the flap was 3.3 cm with a mean of 2.6 cm. The mean pedicle diameter of the paraepididymal adipofascial flap was 1.1 mm. Near-infrared fluorescence imaging revealed adequate perfusion in all flaps.Conclusions: The number of reported adipofascial flap models in animals is low, and they are mostly limited to flaps based on epigastric vessels. Superior epididymal artery-based paraepididymal adipofascial flap can be used as a pedicled flap model for studies focusing on adipofascial and/or pedicled flap physiology. Uncomplicated surgical technique and short operative time make this flap a valuable alternative to other flap models.