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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 Mycophenolic acid was withdrawn in 43 selected patients 5-7 days prior to vaccination and remained paused for 4 additional weeks after vaccination.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 The effect was most pronounced in individuals in whom mycophenolic acid was withdrawn during vaccination.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 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 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 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 Contact mechanics between the human finger and a touchscreen under electroadhesion(Natl Acad Sciences, 2018) Scaraggi, Michele; Persson, Bo N. J.; N/A; N/A; Department of Mechanical Engineering; Ayyıldız, Mehmet; Şirin, Ömer; Başdoğan, Çağatay; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 125489The understanding and control of human skin contact against technological substrates is the key aspect behind the design of several electromechanical devices. Among these, surface haptic displays that modulate the friction between the human finger and touch surface are emerging as user interfaces. One such modulation can be achieved by applying an alternating voltage to the conducting layer of a capacitive touchscreen to control electroadhesion between its surface and the finger pad. However, the nature of the contact interactions between the fingertip and the touchscreen under electroadhesion and the effects of confined material properties, such as layering and inelastic deformation of the stratum corneum, on the friction force are not completely understood yet. Here, we use a mean field theory based on multiscale contact mechanics to investigate the effect of electroadhesion on sliding friction and the dependency of the finger-touchscreen interaction on the applied voltage and other physical parameters. We present experimental results on how the friction between a finger and a touchscreen depends on the electrostatic attraction between them. The proposed model is successfully validated against full-scale (but computationally demanding) contact mechanics simulations and the experimental data. Our study shows that electroadhesion causes an increase in the real contact area at the microscopic level, leading to an increase in the electrovibrating tangential frictional force. We find that it should be possible to further augment the friction force, and thus the human tactile sensing, by using a thinner insulating film on the touchscreen than used in current devices.Publication Metadata only Response to microsurgical anatomy of lumbosacral spinal roots(Springer, 2015) Çavdar, Safiye; Faculty Member; School of Medicine; 1995Publication 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 Live birth following early follicular phase oocyte collection and vitrified-warmed embryo transfer 8 days later(Elsevier Sci Ltd, 2015) Hatirnaz, Safak; Hatirnaz, Ebru; N/A; Ata, Mustafa Barış; Faculty Member; School of Medicine; 182910A 30-year-old woman with premature ovarian insufficiency had two follicles measuring 17 mm and 14 mm on day 3 of her menstrual cycle. Serum oestradiol concentration was 210 pg/ml. Recombinant human chorionic gonadotrophin was given and 5 mg/day letrozole started orally. One metaphase II oocyte was collected 36 h later. A 4-cell embryo was vitrified on the second day after fertilization. Letrozole was stopped on cycle day 8 due to absence of any other visible antral follicles. Oestradiol valerate 6 mg/day was started and the endometrium was 9.2 mm on cycle day 11. The embryo was warmed and transferred on cycle day 13, the 8th day after oocyte retrieval. Luteal phase support with progesterone, oestradiol and low molecular weight heparin was started on the day of transfer and continued until the 10th gestational week. A healthy girl weighing 3200 g was born at term. Early follicular phase oocyte collection did not result in early opening of the implantation window. Apparently secretory transformation was not started until luteal phase support, enabling a cleavage stage embryo transferred 8 days later to implant. Either corpus luteum formation could be disrupted or the endometrium could remain unresponsive to progesterone during the early follicular phase.Publication Metadata only Strategies for controlled ovarian stimulation in the setting of ovarian aging(Thieme Medical Publ Inc, 2015) Seli, Emre; N/A; Ata, Mustafa Barış; Faculty Member; School of Medicine; 182910In the context of assisted reproduction, the term ovarian aging is often used to refer to declining potential of ovaries to produce oocytes in adequate number or quality in response to controlled ovarian stimulation (COS). Different aspects of COS have been modified with the intention to increase the number and quality of oocytes obtained for in vitro fertilization. In the setting of ovarian aging, suppression of the luteinizing hormone (LH) surge with gonadotropin-releasing hormone (GnRH) antagonist or short GnRH agonist protocol and stimulation with a daily gonadotropin dosage of300 IU/day seem to be appropriate first choices, and there is a strong need for well-designed randomized controlled trials investigating effects of addition of LH activity, estradiol priming, transdermal testosterone administration, and growth hormone supplementation. Given the lack of high-quality evidence showing effectiveness of one approach over another, other factors such as duration of stimulation, total gonadotropin consumption and cost of medication, patient friendliness, and possible side effect profiles must be considered in tailoring the COS protocol according to each individual's needs and desires.Publication Metadata only TNF-alpha inhibition prevents cognitive decline and maintains hippocampal BDNF levels in the unpredictable chronic mild stress rat model of depression(Elsevier, 2015) Şahin, Tuğce Demirtaş; Karson, Ayşe; Yazır, Yusufhan; Bayramgürler, Dilek; Utkan, Tijen; Department of Psychology; Balcı, Fuat; Faculty Member; Department of Psychology; College of Social Sciences and Humanities; 51269Previous findings have shown that patients with depression express higher levels of proinflammatory cytokines such as TNF-alpha and IL-6. We have recently found that Infliximab (a TNF-alpha inhibitor) decreased anhedonia and despair-like behavior in the rat unpredictable chronic mild stress (UCMS) model of depression suggesting that inflammation might play an important role in depression. An increasing number of studies suggest that inflammation is also associated with cognitive impairments. The current study aimed to investigate the effect of UCMS on the cognitive performance of rats and their hippocampal BDNF levels and the effect of chronic Infliximab (5 mg/kg/weekly, i.p.) treatment on these measures. Rats were subjected to different types of stressors daily for a period of 56 days to induce depression-like state. The UCMS resulted in impairments in spatial and emotional memory acquisition and retention with no effect on the level of locomotor activity. These behavioral effects of UCMS were accompanied by reduction in the level of BDNF in the CA1 and CA3 regions of the hippocampus. Chronic Infliximab treatment prevented the UCMS-induced cognitive impairments as well as the reduction in the levels of hippocampal brain-derived neurotrophic factor (BDNF). These results suggest that Infliximab improves the spatial and emotional memory impairments induced by chronic stress in rats likely through its effects on hippocampal function by modulating inflammation.