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Publication Metadata only 5-HT causes venodilatation to reduce blood pressure in the rat(Karger, 2016) Seitz, Bridget M.; Krieger-Burke, Theresa; Darios, Emma S.; Thompson, Janice M.; Watts, Stephanie W.; N/A; Orer, Hakan S.; Faculty Member; School of Medicine; 53477N/APublication Metadata only A 3-year-old child with multi-drug resistant epilepsy responding to pharmacological and nonpharmacological treatments(Taylor & Francis, 2022) Yıldırım, Canan; N/A; Coşkun, Yeşim; Doctor; N/A; Koç University Hospital; N/AIntroduction: Despite the development of new antiseizure drugs (ASDs), around one third of epilepsy patients become refractory to treatment or experience adverse events due to ASDs. Therefore, discovery of new ASDs and new therapy options are crucial to improve the quality of life. Herein, we report a 3-year-old child with multi-drug resistant epilepsy caused by perinatal asphyxia whose seizures were reduced by 90% after the introduction of ketogenic diet, vagal nerve stimulation (VNS) AspireSR (SR-seizure response) and oral cannabidiol.Case presentation: A 9-month-old female infant had a history of multidrug resistant epilepsy due to perinatal asphyxia. At admission, she was experiencing up to 20-25 seizures per day lasting for 2-3 minutes. In addition to antiseizure drugs (ASDs), she was put on ketogenic diet (KD), vagal nerve stimulation (VNS) aspire seizure response (AspireSR) was inserted and oral cannabidiol (CBD) was started sequentially. Using pharmacological and nonph armacological therapies, her seizures have been reduced by 90%.Conclusion: The concurrent use of pharmacological and nonpharmacological therapies may be beneficial to improve seizures in infants with multi- Furthermore, our patient is the youngest child inserted VNS AspireSR in Turkey.Publication Metadata only A case with new-onset neuromyelitis optica spectrum disorder following COVID-19 mRNA BNT162b2 vaccination(Lippincott Williams & Wilkins, 2022) Afşar, Nazire; N/A; N/A; N/A; Çalışkan, İlay; Buluş, Eser; Polat-Altıntaş, Sevgi; Master Student; Doctor; Researcher; N/A; N/A; 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; N/A; N/A; 150017Introduction: In the midst of the coronavirus disease of 2019 pandemic, active immunization by effective vaccination gained utmost importance in terms of global health. The messenger RNA (mRNA) vaccines are novel strategies requiring clinical surveillance for adverse events. Case Report: We report a 43-year-old previously healthy female with an optic neuritis attack 24 hours following immunization with the second dose of coronavirus disease of 2019 mRNA BNT162b2 vaccine. A second transverse myelitis attack together with an elevated anti-AQP-4 antibody titer confirmed the diagnosis of neuromyelitis optica spectrum disorder. Conclusion: Our case identifies the BNT162b2 vaccine as a possible trigger for neuromyelitis optica spectrum disorder. This rare and potentially coincidental event has no implications for vaccine administration practices. However, further research is needed to elucidate the effects of mRNA vaccines on humoral and cell-mediated immunity.Publication Metadata only A challenge for peptide coarse graining: transferability of fragment-based models(Wiley-V C H Verlag Gmbh, 2011) Villa, Alessandra; Peter, Christine; N/A; Department of Mechanical Engineering; Engin, Özge; Sayar, Mehmet; Master Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 109820Peptides are highly promising building blocks for design and development of novel materials with potential application areas ranging from drug design to biotechnology. The necessity to understand the structural and thermodynamic properties of these complex materials has led to a dramatic increase in the development of computational techniques geared specifically towards peptide-based systems. Both all-atom (AA) and coarse-grained (CG) simulations of such materials have become extremely important, where the latter is an indispensable tool for reaching the time and length scales relevant to the experiments. Here, we review different approaches and discuss the challenges in the development of CG models for peptides. In particular, we concentrate on the transferability of fragment-based CG models. We analyze the transferability of a solvent-free CG model developed to model hydrophobic phenylalanine dipeptides (FF) in water. Here, we employ the same CG strategy-with non-bonded potentials based on peptide fragments-to two other hydrophobic dipeptides, valine-phenylalanine (VF) and isoleucine-phenylalanine (IF). In line with the previously developed model, the dipeptides are described by seven beads and the potentials developed for FF (bonded and non-bonded) are directly applied to describe the phenylalanine and backbone atoms, while new potentials are developed to account for the valine and isoleucine sidechains. By comparing AA and CG intra and intermolecular samplings, we show the ability of the CG model to reproduce the conformational behavior and thermodynamic association properties of the corresponding atomistic systems.Publication Metadata only A clinical comparison of home-based and hospital-based exercise programs following arthroscopic capsulolabral repair for anterior shoulder instability(Human Kinetics Publ Inc, 2020) Atalar, Ata Can; Eren, Şule Meral; Uçak, Ayla; Çerezci, Önder; N/A; Eren, İlker; Canbulat, Nazan; Demirhan, Mehmet; Faculty Member; Faculty Member; Faculty Member; School of Medicine; School of Medicine; School of Medicine; Koc University Hospital; 168021; 58534; 9882Context: Ideal rehabilitation method following arthroscopic capsulolabral repair surgery for anterior shoulder instability has not been proven yet. Although rapid or slow protocols were compared previously, home- or hospital-based protocols were not questioned before. Objective: The aim of this prospective unrandomized controlled clinical trial is to compare the clinical outcomes of home-based and hospital-based rehabilitation programs following arthroscopic Bankart repair. Design: Non-randomized controlled trial. Setting: Orthopedics and physical therapy units of a single institution. Patients: Fifty-four patients (49 males and 5 females) with an average age of 30.5 (9.1) years, who underwent arthroscopic capsulolabral repair and met the inclusion criteria, with at least 1-year follow-up were allocated into 2 groups: home-based (n = 33) and hospital-based (n = 21) groups. Interventions: Both groups received identical rehabilitation programs. Patients in the home-based group were called for follow-up every 3 weeks. Patients in the hospital-based group admitted for therapy every other day for a total of 6 to 8 weeks. Both groups were followed identically after the eighth week and the rehabilitation program continued for 6 months. Main Outcome Measures: Clinical outcomes were assessed using Disabilities of Arm Shoulder Hand, Constant, and Rowe scores. Mann-Whitney U test was used to compare the results in both groups. Wilcoxon test was used for determining the progress in each group. Results: Groups were age and gender matched (P= .61, P = .69). Average number of treatment sessions was 13.8 (7.3) for patients in the hospital-based group. Preoperative Disabilities of Ann Shoulder Hand (27.46 [11.81] vs 32.53 [16.42], P= .22), Constant (58.23 [14.23] vs 54.17 [10.46], P = .13), and Rowe (51.72 [15.36] vs 43.81 [19.16], P= .12) scores were similar between groups. Postoperative scores at sixth month were significantly improved in each group (P = .001, P = .001, and P = .001). No significant difference was observed between 2 groups regarding clinical scores in any time point. Conclusions: We have, therefore, concluded that a controlled home-based exercise program is as effective as hospital-based rehabilitation following arthroscopic capsulolabral repair for anterior shoulder instability.Publication Metadata only A comparative evaluation of segmental analysis of macular layers in patients with early glaucoma, ocular hypertension, and healthy eyes(2020) Aksoy, F. E.; Altan, C.; Yılmaz, B. S.; Yılmaz, I; Tunç, U.; Kocamaz, M.; Paşaoğlu, I; N/A; Kesim, Cem; Doctor; Koç University Hospital; 387367Purpose: To compare macular layer thicknesses between early glaucoma, ocular hypertension, and healthy eyes and to evaluate the accuracy of spectralis optical coherence tomography (OCT) segmentation software in discriminating early glaucoma from ocular hypertension and healthy eyes. Methods: OCT scans were performed using the standard macular and peripapillary retinal nerve fiber layer (pRNFL) protocols on the Spectralis-OCT. The following macular thickness parameters were compared in the inner and outer circles of the Early Treatment Diabetic Retinopathy Study: total macular thickness (MT), retinal nerve fiber layer (mRNFL), ganglion cell layer (mGCL), inner plexiform layer (mIPL), inner nuclear layer (mINL), outer plexiform layer (mOPL), outer nuclear layer (mONL) and ganglion cell complex (mGCC: sum of mRNFL, mGCL, and mIPL). Sectors and layers with the best area under the receiver operating characteristic curve (AUC) were determined and compared between groups. Results: Of a total of 200 eyes included in this study, 64 eyes had primary open angle glaucoma, 69 had ocular hypertension, and 67 were healthy. Peripapillary RNFL was significantly thinner in the early glaucoma group (P < 0.05). For the macular variables, there was a significant reduction in the MT, mGCC, mRNFL, mGCL, and mIPL thicknesses in the early glaucoma group; while there were no statistically significant differences between the ocular hypertension and control groups (P > 0.05). For distinguishing early glaucoma from normal eyes, AUCs for mGCC, mGCL, and mRNFL were similar to the pRNFL; and for early glaucoma and ocular hypertension, AUCs for mGCC, mGCL mRNF and mIPL were comparable to the pRNFL. Conclusion: Macular segmentation can assist in the early diagnosis of glaucoma as a complementary study to pRNFL analysis.Publication Metadata only A computational biomechanical investigation of posterior dynamic instrumentation: combination of dynamic rod and hinged (dynamic) screw(Asme, 2014) Kiapour, Ali; Goel, Vijay K.; N/A; N/A; Erbulut, Deniz Ufuk; Öktenoğlu, Bekir Tunç; Özer, Ali Fahir; Researcher; Faculty Member; School of Medicine, College of Engineering; School of Medicine; 37661; 220898; 1022Currently, rigid fixation systems are the gold standard for degenerative disk disease treatment. Dynamic fixation systems have been proposed as alternatives for the treatment of a variety of spinal disorders. These systems address the main drawbacks of traditional rigid fixation systems, such as adjacent segment degeneration and instrumentation failure. Pedicle-screw-based dynamic stabilization (PDS) is one type of these alternative systems. The aim of this study was to simulate the biomechanical effect of a novel posterior dynamic stabilization system, which is comprised of dynamic (hinged) screws interconnected with a coiled, spring-based dynamic rod (DSDR), and compare it to semirigid (DSRR and RSRR) and rigid stabilization (RSRR) systems. A validated finite element (FE) model of L1-S1 was used to quantify the biomechanical parameters of the spine, such as range of motion, intradiskal pressure, stresses and facet loads after single-level instrumentation with different posterior stabilization systems. The results obtained from in vitro experimental intact and instrumented spines were used to validate the FE model, and the validated model was then used to compare the biomechanical effects of different fixation and stabilization constructs with intact under a hybrid loading protocol. The segmental motion at L4-L5 increased by 9.5% and 16.3% in flexion and left rotation, respectively, in DSDR with respect to the intact spine, whereas it was reduced by 6.4% and 10.9% in extension and left-bending loads, respectively. After instrumentation-induced intradiskal pressure at adjacent segments, L3-L4 and L5-S1 became less than the intact in dynamic rod constructs (DSDR and RSDR) except in the RSDR model in extension where the motion was higher than intact by 9.7% at L3-L4 and 11.3% at L5-S1. The facet loads were insignificant, not exceeding 12N in any of the instrumented cases in flexion. In extension, the facet load in DSDR case was similar to that in intact spine. The dynamic rod constructions (DSDR and RSDR) led to a lesser peak stress at screws compared with rigid rod constructions (DSRR and RSRR) in all loading cases. A dynamic construct consisting of a dynamic rod and a dynamic screw did protect the adjacent level from excessive motion.Publication Metadata only A LES/PDF simulator on block-structured meshes(Taylor & Francis Ltd, 2019) Pope, Stephen B.; N/A; Department of Mechanical Engineering; Türkeri, Hasret; Muradoğlu, Metin; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 46561A block-structured mesh large-eddy simulation (LES)/probability density function (PDF) simulator is developed within the OpenFOAM framework for computational modelling of complex turbulent reacting flows. The LES/PDF solver is a hybrid solution methodology consisting of (i) a finite-volume (FV) method for solving the filtered mass and momentum equations (LES solver), and (ii) a Lagrangian particle-based Monte Carlo algorithm (PDF solver) for solving the modelled transport equation of the filtered joint PDF of compositions. Both the LES and the PDF methods are developed and combined to form a hybrid LES/PDF simulator entirely within the OpenFOAM framework. The in situ adaptive tabulation method [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combust. Theory Model. 1 (1997), pp. 41-63; L. Lu, S.R. Lantz, Z. Ren, and B.S. Pope, Computationally efficient implementation of combustion chemistry in parallel PDF calculations, J. Comput. Phys. 228 (2009), pp. 5490-5525] is incorporated into the new LES/PDF solver for efficient computations of combustion chemistry with detailed reaction kinetics. The method is designed to utilise a block-structured mesh and can readily be extended to unstructured grids. The three-stage velocity interpolation method of Zhang and Haworth [A general mass consistency algorithm for hybrid particle/finite-volume PDF methods, J. Comput. Phys. 194 (2004), pp. 156-193] is adapted to interpolate the LES velocity field onto particle locations accurately and to enforce the consistency between LES and PDF fields at the numerical solution level. The hybrid algorithm is fully parallelised using the conventional domain decomposition approach. A detailed examination of the effects of each stage and the overall performance of the velocity interpolation algorithm is performed. Accurate coupling of the LES and PDF solvers is demonstrated using the one-way coupling methodology. Then the fully two-way coupled LES/PDF solver is successfully applied to simulate the Sandia Flame-D, and a turbulent non-swirling premixed flame and a turbulent swirling stratified flame from the Cambridge turbulent stratified flame series [M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames I: Non-swirling flows, Combust. Flame 159 (2012), pp. 2896-2911; M.S. Sweeney, S. Hochgreb, M.J. Dunn, and R.S. Barlow, The structure of turbulent stratified and premixed methane/air flames II: Swirling flows, Combust. Flame 159 (2012), pp. 2912-2929]. It is found that the LES/PDF method is very robust and the results are in good agreement with the experimental data for both flames.Publication Metadata only A microstructure-sensitive model for simulating the impact response of a high-manganese austenitic steel(Asme, 2016) N/A; N/A; Department of Mechanical Engineering; Mirzajanzadeh, Morad; Canadinç, Demircan; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 23433Microstructurally informed macroscopic impact response of a high-manganese austenitic steel was modeled through incorporation of the viscoplastic self-consistent (VPSC) crystal plasticity model into the ANSYS LS-DYNA nonlinear explicit finite-element (FE) frame. Voce hardening flow rule, capable of modeling plastic anisotropy in microstructures, was utilized in the VPSC crystal plasticity model to predict the micromechanical response of the material, which was calibrated based on experimentally measured quasi-static uniaxial tensile deformation response and initially measured textures. Specifically, hiring calibrated Voce parameters in VPSC, a modified material response was predicted employing local velocity gradient tensors obtained from the initial FE analyses as a new boundary condition for loading state. The updated micromechanical response of the material was then integrated into the macroscale material model by calibrating the Johnson-Cook (JC) constitutive relationship and the corresponding damage parameters. Consequently, we demonstrate the role of geometrically necessary multi-axial stress state for proper modeling of the impact response of polycrystalline metals and validate the presented approach by experimentally and numerically analyzing the deformation response of the Hadfield steel (HS) under impact loading.Publication Metadata only A mobile application for symptom management in patients with breast cancer(Oncology Nursing Society, 2022) Seven M.; N/A; N/A; Department of Computer Engineering; N/A; Paşalak, Şeyma İnciser; Bağçivan, Gülcan; Özkasap, Öznur; Selçukbiricik, Fatih; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Health Sciences; School of Nursing; College of Engineering; School of Medicine; 125009; 261422; 113507; 202015OBJECTIVES: To evaluate the effect of a symptom management mobile application on quality of life and symptom severity in women with breast cancer undergoing chemotherapy. SAMPLE & SETTING: This parallel randomized pilot study consisted of women with breast cancer admitted to oncology outpatient clinics between November 2019 and January 2021 in Turkey. METHODS & VARIABLES: Participants (N = 40) were randomly assigned to the intervention (n = 20) or control group (n = 20). The intervention group used the mobile application in conjunction with usual care. The control group received usual care. Participants were assessed during the first, third, and last chemotherapy cycles. Data were collected using the European Organisation for Research and Treatment of Cancer Quality-of-Life Questionnaire–Core 30 and the Edmonton Symptom Assessment System. RESULTS: During the study, the decrease in general health and physical functioning and the increase in the severity of depression/sadness in the intervention group were statistically lower than in the control group. IMPLICATIONS FOR NURSING: The use of a mobile application for symptom management may promote general well-being and physical function and may alleviate symptoms of depression/sadness in women with breast cancer undergoing chemotherapy. Further studies are needed to evaluate the application in clinical settings with larger groups.