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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 novel microfluidics-based point of care technique for viscoelastic hemostatic assay(IOS Press, 2021) Erten, Ahmet Can; Yalçın, Özlem; Torun, Berfin Irmak; Öz, Fatma; Faculty Member; Master Student; Master Student; School of Medicine; Graduate School of Sciences and Engineering; raduate School of Sciences and Engineering; 218440; N/A; N/AN/APublication Metadata only A structured mechanical risk sensitivity assessment system using red cell deformability and fragmentation parameters(Ios Press, 2021) Yalçın, Özlem; Uğurel, Elif; Göktaş, Polat; Göksel, Evrim; Çilek, Neslihan; Atar, Dila; Faculty Member; Researcher; Researcher; PhD Student; PhD Student; Undergraduate Student; School of Medicine; School of Medicine; School of Medicine; Graduate School of Health Sciences; Graduate School of Health Sciences; School of Medicine; 218440; N/A; N/A; N/A; N/A; N/AN/APublication Metadata only Activation of protein kinase a cascade increases deformability of sickle red blood cells(Ios Press, 2021) Connes, Philippe; Boisson, Camille; Renoux, Celine; Gauthier, Alexandra; Fort, Romain; Nader, Elie; Poutrel, Solene; Göksel, Evrim; Yalçın, Özlem; PhD Student; Faculty Member; School of Medicine; School of Medicine; N/A; 218440Publication Metadata only Application of the nonlinear methods in pneumocardiogram signals(Springer, 2020) Akilli, Mahmut; Ozbek, Mustafa; Zeren, Tamer; Akdeniz, K. Gediz; Department of Physics; Yılmaz, Nazmi; Teaching Faculty; Department of Physics; College of Sciences; 178427In this work, the pneumocardiogram signals of nine rats were analysed by scale index, Boltzmann Gibbs entropy and maximum Lyapunov exponents. The scale index method, based on wavelet transform, was proposed for determining the degree of aperiodicity and chaos. It means that the scale index parameter is close to zero when the signal is periodic and has a value between zero and one when the signal is aperiodic. A new entropy calculation method by normalized inner scalogram was suggested very recently. In this work, we also used this method for the first time in an empirical data. We compared the both methods with maximum Lyapunov exponents and observed that using together the scale index and the entropy calculation method by normalized inner scalogram increases the reliability of the pneumocardiogram signal analysis. Thus, the analysis of the pneumocardiogram signals by those methods enables to compare periodical and/or nonlinear aspects for further understanding of dynamics of cardiorespiratory system.Publication Metadata only Applications of deep learning to the assessment of red blood cell deformability(IOS Press, 2021) Turgut, Alper; N/A; Yalçın, Özlem; Faculty Member; School of Medicine; 218440BACKGROUND: Measurement of abnormal Red Blood Cell (RBC) deformability is a main indicator of Sickle Cell Anemia (SCA) and requires standardized quantification methods. Ektacytometry is commonly used to estimate the fraction of Sickled Cells (SCs) by measuring the deformability of RBCs from laser diffraction patterns under varying shear stress. In addition to estimations from model comparisons, use of maximum Elongation Index differences (Delta EImax) at different laser intensity levels was recently proposed for the estimation of SC fractions. OBJECTIVE: Implement a convolutional neural network to accurately estimate rigid-cell fraction and RBC concentration from laser diffraction patterns without using a theoretical model and eliminating the ektacytometer dependency for deformability measurements. METHODS: RBCs were collected from control patients. Rigid-cell fraction experiments were performed using varying concentrations of glutaraldehyde. Serial dilutions were used for varying the concentration of RBC. A convolutional neural network was constructed using Python and TensorFlow. RESULTS and CONCLUSIONS: Measurements and model predictions show that a linear relationship between Delta EImax and rigid-cell fraction exists only for rigid-cell fractions less than 0.2. The proposed neural network architecture can be used successfully for both RBC concentration and rigid-cell fraction estimations without a need for a theoretical model.Publication Metadata only Assessment of oxidant susceptibility of red blood cells in various species based on cell deformability(IOS Press, 2011) Simmonds, Michael J.; Meiselman, Herbert J.; Marshall-Gradisnik, Sonya M.; Pyne, Michael; Kakanis, Michael; Keane, James; Brenu, Ekua; Christy, Rhys; Başkurt, Oğuz Kerim; Faculty Member; School of Medicine; N/APublication Open Access Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies(BioMed Central, 2007) Keskin, Özlem; Faculty Member; Faculty Member; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; 26605Background: How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre- existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results: Here, two antibodies, a germline antibody of 36 - 65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM) is used in the calculations. Pre- existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion: Results suggest that the pre- equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.Publication Open Access Cloning, expression, purification, crystallization and X-ray analysis of inositol monophosphatase from Mus musculus and Homo sapiens(Wiley, 2012) Singh, Nisha; Halliday, Amy C.; Knight, Matthew; Lowe, Edward; Churchill, Grant C.; Lack, Nathan Alan; Faculty Member; School of Medicine; 120842Inositol monophosphatase (IMPase) catalyses the hydrolysis of inositol monophosphate to inositol and is crucial in the phosphatidylinositol (PI) signalling pathway. Lithium, which is the drug of choice for bipolar disorder, inhibits IMPase at therapeutically relevant plasma concentrations. Both mouse IMPase 1 (MmIMPase 1) and human IMPase 1 (HsIMPase 1) were cloned into pRSET5a, expressed in Escherichia coli, purified and crystallized using the sitting-drop method. The structures were solved at resolutions of 2.4 and 1.7 angstrom, respectively. Comparison of MmIMPase 1 and HsIMPase 1 revealed a core r.m.s. deviation of 0.516 angstrom.Publication Open Access Comparing interfacial dynamics in protein-protein complexes: an elastic network approach(BioMed Central, 2010) Zen, Andrea; Micheletti, Cristian; Nussinov, Ruth; Keskin, Özlem; Faculty Member; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; 26605Background: The transient, or permanent, association of proteins to form organized complexes is one of the most common mechanisms of regulation of biological processes. Systematic physico-chemical studies of the binding interfaces have previously shown that a key mechanism for the formation/stabilization of dimers is the steric and chemical complementarity of the two semi-interfaces. The role of the fluctuation dynamics at the interface of the interacting subunits, although expectedly important, proved more elusive to characterize. The aim of the present computational study is to gain insight into salient dynamics-based aspects of protein-protein interfaces. Results: The interface dynamics was characterized by means of an elastic network model for 22 representative dimers covering three main interface types. The three groups gather dimers sharing the same interface but with good (type I) or poor (type II) similarity of the overall fold, or dimers sharing only one of the semi-interfaces (type III). The set comprises obligate dimers, which are complexes for which no structural representative of the free form (s) is available. Considerations were accordingly limited to bound and unbound forms of the monomeric subunits of the dimers. We proceeded by first computing the mobility of amino acids at the interface of the bound forms and compare it with the mobility of (i) other surface amino acids (ii) interface amino acids in the unbound forms. In both cases different dynamic patterns were observed across interface types and depending on whether the interface belongs to an obligate or non-obligate complex. Conclusions: The comparative investigation indicated that the mobility of amino acids at the dimeric interface is generally lower than for other amino acids at the protein surface. The change in interfacial mobility upon removing "in silico" the partner monomer (unbound form) was next found to be correlated with the interface type, size and obligate nature of the complex. In particular, going from the unbound to the bound forms, the interfacial mobility is noticeably reduced for dimers with type I interfaces, while it is largely unchanged for type II ones. The results suggest that these structurally-and biologically-different types of interfaces are stabilized by different balancing mechanisms between enthalpy and conformational entropy.