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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 case of chordoma invading multiple neuroaxial bones: report of ten years follow up(Turkish Neurosurgery Society, 2013) Aydın, Ahmet Levent; Sasani, Mehdi; Öktenoğlu, Bekir Tunç; Solaroğlu, İhsan; Özer, Ali Fahir; Faculty Member; Faculty Member; School of Medicine; School of Medicine; 102059; 1022Aim: Chordoma is a rare, slow-growing primary malignant tumor of the axial skeleton, arising from the embryonic cells of primitive notochord. Chordomas may arise at different sites of the vertebral column simultaneously or more probably they may metastasise along the neural axis insidiously. Recurrence despite radical surgery and following adjuvant therapy is possible. MaterIal and Methods: A 46-year-old female patient presented weakness and numbness of the lower extremities. She was operated for clivus chordoma five years ago at another institute. Results: First the patient underwent surgery for resection of the tumor at the cervical region. a second surgery was performed to resect tumor on the foramen magnum and at the C1 level. Histologic examination of the removed vertebra confirmed the diagnosis of chordoma involving the vertebral body. Radiotherapy was administered after the second surgery. Follow-up neurological and radiological examinations revealed no abnormal neurological symptoms 2,5 years after second surgery. There were no distant organ metastases. ConclusIon: A patient with diagnosed chordoma of the spine must be investigated with MRI of other regions of the neuraxis to exclude second or even third source of chordoma metastases. In metastatic chordoma cases, radical or gross total resection should be performed for each lesion but if complete surgical resections are impossible, preoperative or postoperative radiation therapy should be planned to improve life expectancy. / AMAÇ: Kordoma, omurganın ender rastlanan, yavaş ilerleyen malign karakterli bir tümörüdür. Primitif notokordun embryo hücrelerinden köken alır. Omurganın farklı bölgelerinde, birbirinden bağımsız kordoma odakları eş zamanlı olarak gelişmeye başlayabilir. Fakat daha sıklıkla, birinci tümör odağından kaynaklanan metastatik kordoma lezyonları tüm nöral aks boyunca yayılabilir. Radikal cerrahiye ve ek onkolojik tedaviye rağmen rekürens sık görülür. YÖNTEM ve GEREÇLER: Bu sunumda tartışılan 46 yaşındaki kadın hasta, bacaklarında kuvvet ve his kaybı şikayetiyle kliniğimize başvurmuştur. Hasta, beş yıl önce, ayrı bir merkezde klivus kordoması tanısıyla opere edilmiştir. BULGULAR: Hasta öncelikle servikal bölgedeki tümör için opere edilmiştir. İkinci seansta foramen magnum ve C1 seviyesindeki tümör çıkarılmıştır. Patolojik inceleme sonucunda, omurga cismini tutan kordoma lezyonu tanısı konmuştur. İkinci cerrahi seansından sonra hasta radyoterapiye yönlendirilmiştir. Bu tedaviden ikibuçuk yıl sonra yapılan değerlendirmede, hastanın nörolojik muayenesinde progresyon gözlenmemiştir. SONUÇ: Omurganın herhangi bir lokalizasyonunda kordoma tanısı konulan bir hastada, tüm spinal bölge manyetik rezonans görüntüleme (MRG) tetkiki ile incelenmelidir. Bu hastalarda birden fazla kordoma odağına rastlanabilir. Birden fazla odak tespit edilmesi durumunda, her ayrı tümör odağı için rezeksiyon planlanmalıdır. Total rezeksiyonun mümkün olmaması durumunda, yaşam süresini uzatmak için operasyon öncesi ve sonrası dönemlerde radyoterapi uygulanmalıdır.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 comparative study on thyroid function in alzheimer's disease: results from a Turkish multi-centre study(Journal Neurological Sciences, 2015) Yılmaz, Gökhan; Erbayraktar, Zübeyde; Evlice, Ahmet; Genç, Metin; Aras, Sevgi; Avcı, Aslıhan; Yener, Görsev; Ulusu, Nuriye Nuray; Faculty Member; School of Medicine; 6807Alzheimer's disease is a very severe degenerative disease that affects brain function. Neuronal loss, accumulation of extracellular amyloid beta containing plaques and accumulation of intracellular (tau) neurofibrillary tangles are the hallmarks of this disease. We aim to investigate serum thyroid function tests in Alzheimer's disease, in addition to other dementias, and geriatric Turkish patients. We evaluated patients from Ankara, Dokuz Eylul, Cukurova University Hospitals. 357 female and male geriatric subjects were enrolled. All the cases were selected from three different geographical regions irrespective of sex and socioeconomic status. In this study, we evaluated the results of thyroid functions in Alzheimer disease patients as well as in other dementias and geriatric patients. In patients from Ankara, Central Anatolia region, no significant difference between groups regarding the routine control of biochemical parameters was observed. However, thyroid function results revealed that hypothyroidism in Alzheimer's disease patients from Mediterranean region, Adana and Aegean region, Izmir is a recurrent medical condition and is often an embedded side of the normal aging process. We concluded that currently, routine thyroid functions tests should be a part of all geriatric patients for screening presymptomatic Alzheimer's disease. There might be an interplay between reduced thyroid function and Alzheimer's disease that could be exploited for diagnostic purposes.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 critical analysis of low molecular weight heparin use during pregnancy in a tertiary referral centre(Taylor & Francis, 2014) Kutuk, M. S.; Ozgun, M. T.; Uludag, S.; Dolanbay, M.; Tas, M.; Terzioğlu, Ayşecan; Faculty Member; School of Nursing; 177870The aim of this study was to analyse low molecular weight heparin (LMWH) use during pregnancy in terms of patient evaluation, treatment indication and social and financial costs. This was a retrospective analysis of patients using LMWH in their pregnancies. A total of 147 women were included in the study. The most common indications were thrombophilia (55/147, 37.4%); recurrent pregnancy loss (RPL); (47/147, 32.0%) and previous single pregnancy loss (18/147, 12.2%). In the RPL group, 53.1% of patients were not evaluated with standard tests; 31.9% of women were incompletely evaluated and 15% were properly evaluated. Out of 104 women screened for thrombophilia, 32 (32/104, 30.8%) were tested during pregnancy. Despite published guidelines and increasing scientific evidence against their use in some indications, LMWHs are prescribed widely during pregnancy for a variety of indications. Public and healthcare providers' education to change this attitude should be implemented.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 metal nitride carbodiimide with a stuffed skutterudite-type structure: synthesis, crystal structure and ir spectra of (BA6N 5/6)2[NBN4][CN2]6(Walter de Gruyter, 2007) Reckeweg, Olaf; Disalvo, Francis J.; Department of Chemistry; Somer, Mehmet Suat; Faculty Member; Department of Chemistry; College of Sciences; 178882Coppery-red, transparent single crystals of (Ba6N 5/6)2[NbN4][CN2]6 [NbN4] [CN2]6 (Im3̄, no. 204, a = 1125.83(3) pm, Z = 2) are obtained by the reaction of Ba2N and ZnCN2 with the container walls of the arc-welded Nb ampoules at 1100 K. The title compound assumes a stuffed skutterudite-type structure in which edge-sharing (Ba6N5/6) octahedra form large voids which are occupied by either [NbN4] tetrahedra or by [N=C=N]2- units with symmetric C=N bond lengths of d = 121.8(6) pm but a bond angle deviating significantly from linearity (∠(N-C-N) = 175.3(9)°). The IR spectra corroborate this crystallographic result by the fact that all fundamental vibrations are visible in the IR spectrum [v1 = 1262 (symmetric stretching mode); v2 = 1957/2009 (antisymmetric stretching mode); v3 = 611/633/653 cm-1 (bending modes)], which is symmetry forbidden for [N=C=N]2- units having D∞h symmetry but expected for the C2v symmetry found in the title compound.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 multidisciplinary clinical approach to facioscapulohumeral muscular dystrophy orthopedic surgery in facioscapulohumeral dystrophy(Literatura Medica, 2018) N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; N/A; Çakmak, Özgür Öztop; Eren, İlker; Aslanger, Ayça Dilruba; Günerbüyük, Caner; Kayserili, Hülya; Oflazer, Piraye; Şar, Cüneyt; Demirhan, Mehmet; Özdemir, Yasemin Gürsoy; Faculty Member; Faculty Member; Doctor; Teaching Faculty; Faculty Member; Faculty Member; Doctor; Faculty Member; Faculty Member; School of Medicine; School of Medicine; N/A; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; School of Medicine; Koc University Hospital; 107818; 168021; N/A; 380939; 7945; N/A; N/A; 9882; 170592Background - Impaired shoulder function is the most disabling problem for daily life of Fascioscapulohumeral muscular dystrophy (FSHD) patients. Scapulothoracic arthrodesis can give a high impact to the functionality of patients. Here we report our experience with scapulothoracic arthrodesis and spinal stenosis surgery in FSHD patients. Patients and methods - 32 FSHD patients were collected between 2015-2016. Demographical and clinical features were documented. All the patients were neurologically examined. The Medical Research Council (MRC) and the FSHD evaluation scale was used to assess muscle involvement(1). Scapulothoracic arthrodesis and spinal stenosis surgeries were performed in eligible patients. Results - There were 16 male and 16 female (mean age 34.4 years; range 12-73) patients. 6 shoulders of 4 patients aged between 2132 years underwent scapulothoracic arthrodesis (two bilateral, one left and one right sided). Only one 63 years old female patient with severe hyperlordosis had spinal fusion surgery. All of the patients undergoing these corrective surgeries have better functionality in daily life, as well as superior shoulder elevation. Conclusion - Until the emergence and clinical use of novel therapeutics, surgical interventions are indicated in carefully selected patients with FSHD to improve arm movements, the posture and the quality of life of patients in general. Scapulothorosic arthrodesis is a management with good clinical results and patient satisfaction. In selected cases other corrective orthopedic surgeries like spinal fusion may also be considered.