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Citation Count: 225
2019 EACTS Expert Consensus on long-term mechanical circulatory support
(European Association for Cardio-Thoracic Surgery, 2019) Potapov,E.V.; Antonides,C.; Crespo-Leiro,M.G.; Combes,A.; Färber,G.; Hannan,M.M.; Gustafsson,F.
Long-term mechanical circulatory support (LT-MCS) is an important treatment modality for patients with severe heart failure. Different devices are available, and many - sometimes contradictory - observations regarding patient selection, surgical techniques, perioperative management and follow-up have been published. With the growing expertise in this field, the European Association for Cardio-Thoracic Surgery (EACTS) recognized a need for a structured multidisciplinary consensus about the approach to patients with LT-MCS. However, the evidence published so far is insufficient to allow for generation of meaningful guidelines complying with EACTS requirements. Instead, the EACTS presents an expert opinion in the LT-MCS field. This expert opinion addresses patient evaluation and preoperative optimization as well as management of cardiac and non-cardiac comorbidities. Further, extensive operative implantation techniques are summarized and evaluated by leading experts, depending on both patient characteristics and device selection. The faculty recognized that postoperative management is multidisciplinary and includes aspects of intensive care unit stay, rehabilitation, ambulatory care, myocardial recovery and end-of-life care and mirrored this fact in this paper. Additionally, the opinions of experts on diagnosis and management of adverse events including bleeding, cerebrovascular accidents and device malfunction are presented. In this expert consensus, the evidence for the complete management from patient selection to end-of-life care is carefully reviewed with the aim of guiding clinicians in optimizing management of patients considered for or supported by an LT-MCS device. © 2019 The Author(s).
Citation Count: 487
Advanced heart failure: a position statement of the Heart Failure Association of the European Society of Cardiology
(John Wiley and Sons Ltd, 2018) Crespo-Leiro,M.G.; Metra,M.; Lund,L.H.; Milicic,D.; Costanzo,M.R.; Filippatos,G.; Ruschitzka,F.
This article updates the Heart Failure Association of the European Society of Cardiology (ESC) 2007 classification of advanced heart failure and describes new diagnostic and treatment options for these patients. Recognizing the patient with advanced heart failure is critical to facilitate timely referral to advanced heart failure centres. Unplanned visits for heart failure decompensation, malignant arrhythmias, co-morbidities, and the 2016 ESC guidelines criteria for the diagnosis of heart failure with preserved ejection fraction are included in this updated definition. Standard treatment is, by definition, insufficient in these patients. Inotropic therapy may be used as a bridge strategy, but it is only a palliative measure when used on its own, because of the lack of outcomes data. Major progress has occurred with short-term mechanical circulatory support devices for immediate management of cardiogenic shock and long-term mechanical circulatory support for either a bridge to transplantation or as destination therapy. Heart transplantation remains the treatment of choice for patients without contraindications. Some patients will not be candidates for advanced heart failure therapies. For these patients, who are often elderly with multiple co-morbidities, management of advanced heart failure to reduce symptoms and improve quality of life should be emphasized. Robust evidence from prospective studies is lacking for most therapies for advanced heart failure. There is an urgent need to develop evidence-based treatment algorithms to prolong life when possible and in accordance with patient preferences, increase life quality, and reduce the burden of hospitalization in this vulnerable patient population. © 2018 The Authors. European Journal of Heart Failure © 2018 European Society of Cardiology
Citation Count: 15
Advanced Sensor and Detection Materials
(Wiley Blackwell, 2014) Tiwari A.; Demir, M.M.
Presents a comprehensive and interdisciplinary review of the major cutting-edge technology research areas-especially those on new materials and methods as well as advanced structures and properties-for various sensor and detection devices. The development of sensors and detectors at macroscopic or nanometric scale is the driving force stimulating research in sensing materials and technology for accurate detection in solid, liquid, or gas phases; contact or non-contact configurations; or multiple sensing. The emphasis on reduced-scale detection techniques requires the use of new materials and methods. These techniques offer appealing perspectives given by spin crossover organic, inorganic, and composite materials that could be unique for sensor fabrication. The influence of the length, composition, and conformation structure of materials on their properties, and the possibility of adjusting sensing properties by doping or adding the side-groups, are indicative of the starting point of multifarious sensing. The role of intermolecular interactions, polymer and ordered phase formation, as well as behavior under pressure and magnetic and electric fields are also important facts for processing ultra-sensing materials. The 15 chapters written by senior researchers in Advanced Sensor and Detection Materials cover all these subjects and key features under three foci: 1) principals and perspectives, 2) new materials and methods, and 3) advanced structures and properties for various sensor devices. © 2014 Scrivener Publishing LLC. All rights reserved.
Citation Count: 4
Advances in Model-Based Testing of Graphical User Interfaces
(Elsevier Academic Press inc, 2017) Belli, Fevzi; Beyazit, Mutlu; Budnik, Christof J.; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Graphical user interfaces (GUIs) enable comfortable interactions of the computer-based systems with their environment. Large systems usually require complex GUIs, which are commonly fault prone and thus are to be carefully designed, implemented, and tested. As a thorough testing is not feasible, techniques are favored to test relevant features of the system under test that will be specifically modeled. This chapter summarizes, reviews, and exemplifies conventional and novel techniques for model-based GUI testing.
Citation Count: 15
Aggregation of fillers blended into random elastomeric networks: Theory and comparison with experiments
(2006) Demir M.M.; Menceloglu Y.Z.; Erman, B.
A theoretical model describing aggregation of filler particles in amorphous elastomers is proposed. The model is based on a counting technique originally used in genome analysis to characterize the size and distribution of overlapping segments randomly placed on a DNA molecule. In the present model, the particles are first assumed to aggregate randomly upon mixing into the elastomer and then-sizes are calculated. The sizes and distributions of aggregates are also studied in the presence of attractive interparticle forces. Results of the proposed model are compared with experimental data on silica-filled end-linked poly(dimethyl-siloxane) networks. Comparison of the theory and experiment shows that the random aggregation assumption where no attractive forces exist between the particles is not valid and a significant attraction between the silica particles is needed in the theory to justify the experimental data obtained using atomic force microscopy. For filler content below 1.45 vol.-%, the model agrees, qualitatively, with experiment and shows the increase in cluster size with increasing amount of filler. It also explains the increase in the dispersion of aggregate sizes with increasing amount of filler. © 2006 WILEY-VCH Verlag GmbH & Co. KGaA.
Citation Count: 0
AMWC 2013: Advanced Materials World Congress (izmir, Turkey, September 16-19, 2013)
(2013) Demir, M.M.
[No abstract available]
Citation Count: 20
Apoptotic effects of non-edible parts of Punica granatum on human multiple myeloma cells
(Springer Science and Business Media B.V., 2016) Baran, Yusuf; Neergheen-Bhujun,V.S.; Rummun,N.; Baran,Y.
Multiple myeloma is of great concern since existing therapies are unable to cure this clinical condition. Alternative therapeutic approaches are mandatory, and the use of plant extracts is considered interesting. Punica granatum and its derived products were suggested as potential anticancer agents due to the presence of bioactive compounds. Thus, polypenolic-rich extracts of the non-edible parts of P. granatum were investigated for their antiproliferative and apoptotic effects on U266 multiple myeloma cells. We demonstrated that there were dose-dependent decreases in the proliferation of U266 cells in response to P. granatum extracts. Also, exposure to the extracts triggered apoptosis with significant increases in loss of mitochondrial membrane potential in U266 cells exposed to the leaves and stem extracts, while the flower extract resulted in slight increases in loss of MMP. These results were confirmed by Annexin-V analysis. These results documented the cytotoxic and apoptotic effects of P. granatum extracts on human U266 multiple myeloma cells via disruption of mitochondrial membrane potential and increasing cell cycle arrest. The data suggest that the extracts can be envisaged in cancer chemoprevention and call for further exploration into the potential application of these plant parts. © 2015, International Society of Oncology and BioMarkers (ISOBM).
Citation Count: 0
Application of the Law of Minimum and Dissimilarity Analysis to Regression Test Case Prioritization
(Ieee-inst Electrical Electronics Engineers inc, 2023) Ufuktepe, Ekincan; Tuglular, Tugkan; Tuğlular, Tuğkan; Bilgisayar Mühendisliği Bölümü
Regression testing is one of the most expensive processes in testing. Prioritizing test cases in regression testing is critical for the goal of detecting the faults sooner within a large set of test cases. We propose a test case prioritization (TCP) technique for regression testing called LoM-Score inspired by the Law of Minimum (LoM) from biology. This technique calculates the impact probabilities of methods calculated by change impact analysis with forward slicing and orders test cases according to LoM. However, this ordering doesn't consider the possibility that consecutive test cases may be covering the same methods repeatedly. Thereby, such ordering can delay the time of revealing faults that exist in other methods. To solve this problem, we enhance the LoM-Score TCP technique with an adaptive approach, namely with a dissimilarity-based coordinate analysis approach. The dissimilarity-based coordinate analysis uses Jaccard Similarity for calculating the similarity coefficients between test cases in terms of covered methods and the enhanced technique called Dissimilarity-LoM-Score (Dis-LoM-Score) applies a penalty with respective on the ordered test cases. We performed our case study on 10 open-source Java projects from Defects4J, which is a dataset of real bugs and an infrastructure for controlled experiments provided for software engineering researchers. Then, we hand-seeded multiple mutants generated by Major, which is a mutation testing tool. Then we compared our TCP techniques LoM-Score and Dis-LoM-Score with the four traditional TCP techniques based on their Average Percentage of Faults Detected (APFD) results.
Citation Count: 8
The case of a cyst hydatid localized within the interatrial septum
(2004) Karabay,Ö.; Önen,A.; Yildiz,F.; Yilmaz,E.; Erdal,A.C.; Şanli,A.; Açikel,Ü.
The ratio of cardiac involvement of Echinoccocus granulosus is 0.02-2% and although seen rarely, involvement of the interatrial septum has also been reported in the published literature. The present case was a 19-year-old male university student admitted to hospital with complaints of headache and dizziness. Computerized tomography of the cranium revealed a cystic mass located at the frontal region and enucleation of the cyst was performed during surgery. A cystic lesion 5 × 4 cm in size was detected within the interatrial septum on two-dimensional transthoracic echocardiography during the postoperative period and the patient was referred to our clinic. Open heart surgery was performed and a hydatid cyst that involved the interatrial septum was enucleated. The cyst wall was sutured to the interatrial septum. No complications developed during the postoperative period. The patient was discharged on the fifth day of hospitalization and medical therapy was started with albendazole. Copyright © 2004 by the Japanese Heart Journal.
Citation Count: 255
Cell proliferation and cytotoxicity assays
(Bentham Science Publishers B.V., 2016) Baran, Yusuf; Kiraz,Y.; Baran,Y.
Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes. © 2016 Bentham Science Publishers.
Citation Count: 47
Challenges in the preparation of optical polymer composites with nanosized pigment particles: A review on recent efforts
(2012) Demir M.M.; Wegner, G.
Blends of nanosized pigment particles and polymers are widely believed to offer the potential for the design of novel or at least improved materials. This review critically evaluates the recent literature with regard to the following issues: (a) why and how does the size of the particles matter, (b) what are the requirements to create compatibility between amorphous polymers and nanoparticles, (c) carbon allotropes as nanosized pigments, (d) bulk polymerization of monomer/pigment mixtures, (e) interaction of growing chains with the particles in the polymerization, (f) depletion flocculation as a mechanism to counteract homogeneous distribution of the particles in the polymer matrix and ways to suppress the undesirable flocculation, and (g) optical properties of the blends as well as methods of optical characterization. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Citation Count: 7
Characterization of Sb scaling and fluids in saline geothermal power plants: A case study for Germencik Region (Büyük Menderes Graben, Turkey)
(Elsevier Ltd, 2021) Tonkul S.; Baba A.; Demir M.M.; Regenspurg, S.
Turkey is located on the seismically active Alpine-Himalayan belt. Although tectonic activity causes seismicity in the Anatolian plate, it also constitutes an important geothermal energy resource. Today, geothermal energy production is heavily concentrated in Turkey's Western Anatolia region. Graben systems in this region are very suitable for geothermal resources. The Büyük Menderes Graben (BMG) is an area of complex geology with active tectonics and high geothermal potential power. Germencik (Aydın) is located in the BMG, where the geothermal waters include mainly Na-Cl-HCO3 water types. This study examined the stibnite scaling formed in the preheater system of the Germencik Geothermal Field (GGF). The formation of the stibnite scaling on the preheater system dramatically reduces the energy harvesting of the GGF. Considering the stibnite scaling in the surface equipment, the optimum reinjection temperature was determined as 95 °C to prevent stibnite scaling in the GGF. © 2021 Elsevier Ltd
Citation Count: 101
Chitosan fiber-supported zero-valent iron nanoparticles as a novel sorbent for sequestration of inorganic arsenic
(Royal Soc Chemistry, 2013) Horzum, Nesrin; Demir, Mustafa M.; Nairat, Muath; Shahwan, Talal; Demir, Mustafa
This study proposes a new sorbent for the removal of inorganic arsenic from aqueous solutions. Monodispersed nano zero-valent iron (nZVI) particles were nucleated at the surface of electrospun chitosan fibers (average fiber diameter of 195 +/- 50 nm) by liquid phase reduction of FeCl3 using NaBH4. The material was characterized using SEM, TGA, XPS, XRD, and FTIR. The diameter of iron nanoparticles was found to vary between 75-100 nm. A set of batch experiments were carried out to elucidate the efficiency of the composite sorbent toward fixation of arsenite and arsenate ions. The ion concentrations in the supernatant solutions were determined using inductively coupled plasma-mass spectrometry (ICP-MS). The results revealed that the chitosan fiber supported nZVI particles is an excellent sorbent material for inorganic arsenic uptake at concentrations ranging from 0.01 to 5.00 mg L-1 over a wide range of pH values. Based on XPS analysis, As(III) was found to undergo oxidation to As(V) upon sorption, while As(V) retained its oxidation state. By virtue of the successful combination of the electrospun fibers' mechanical integrity and the large reactivity of dispersed nZVI particles, the applicability of the resulting sorbent material in arsenic sorption holds broad promise.
Citation Count: 38
Clinical and laboratory features, complications and treatment outcome of brucellosis in childhood and review of the literature
(2011) Uluǧ,M.; Yaman,Y.; Yapici,F.; Can-Uluǧ,N.
Brucellosis, whether in an endemic region or not, remains a diagnostic puzzle due to occasional misleading unusual presentations and non-specific symptoms. The aim of this study was to evaluate the clinical and laboratory findings, complications and treatment outcome of brucellosis in children in southeastern Anatolia, Turkey. This study focuses on the frequency of clinical and laboratory findings and complications in cases with brucellosis. Of 22 patients, 8 (36.3%) were female and 14 (63.7%) were male. Fever, malaise, lack of appetite, arthralgia, and night sweating were the main presenting symptoms overall. Hematologic complications (n=13, 59.1%) were most common, followed by skeletal (n=7, 31.8%) and cutaneous system (n=1, 4.5%). Brucellosis may affect any organ system and imitate a variety of clinical entities. Diagnosis of brucellosis should be considered whenever there is a febrile illness associated with rheumatological complaints. Consequently, early recognition of the infection, prolonged antibiotic treatment and careful long-term follow-up should improve the patient outcome.
Citation Count: 7
Comparison of the body size and age structure of Lebanon lizard, Phoenicolacerta laevis (Gray, 1838) at different altitudes in Turkey
(Senckenbergische Naturforschende Gesellschaft, 2018) Üzüm,N.; Ilgaz,Ç.; Avci,A.; Candan,K.; Güler,H.; Kumlutaş,Y.
In this study, comparison of a life history traits (e.g. body size, age at maturity, longevity) of two populations of Phoenicolacerta laevis from different altitudes is being carried out (Anamur, 22 m a.s.l.; Andirin, 1.083 m a.s.l.) for the first time. We applied phalangeal skeletochronology to obtain the age of juveniles and adults. Age was determined by counting the lines of arrested growth (LAGs) in cross-sections. Males in both populations were the larger of the two sexes and a male biased sexual dimorphism was determined for both populations. Body size (SVL) was similar in both sexes and populations. Age of maturity was calculated to be 3 years of age for males and females in both populations. The average age of males and females was calculated as 6.62 ± 0.37 (Mean±SE) and 6.11 ± 0.26 years in Anamur, and 6.15 ± 0.51 and 5.26 ± 0.24 years in Andirin. There was statistically significant variation between sexes, but no significant difference in populations was found in relation to age. For both populations, a significant positive correlation was found between age and SVL in males and females. © Senckenberg Gesellschaft für Naturforschung, 2018.
Citation Count: 15
Controlling spontaneous emission of CdSe nanoparticles dispersed in electrospun fibers of polycarbonate urethane
(2009) Demir M.M.; Soyal D.; Ünlü C.; Kuş M.; Özçelik, S.
Luminescent fibrous composite films consisting of submicrometer diameter fibers were prepared by electrospinning of segmented polycarbonate urethane (PCU) in dimethyl formamide and tri-n-octylphosphine oxide (TOPO)-capped CdSe nanocrystals (5 nm in diameter) in toluene. Using a pair of conductive electrodes separated with an air gap, we successfully produced randomly deposited and uniaxially aligned electrospun fibers. The surface structure of the electrospun fibers was studied using atomic force microscopy (AFM) and was compared to the corresponding film prepared by casting. In cast film, tapping mode AFM imaging suggests that hard urethane segments organize into rodlike morphology dispersed in soft polycarbonate. When PCU/CdSe dispersions were subjected to electrospinning, copolymer domains were forced to arrange into lamella along the fiber axis due to elongational flow and high stretching. Molecular orientation in the domains of the composite fibers was confirmed by polarized infrared spectroscopy. We demonstrated that formation of the oriented domains by electrospinning develops a hierarchical structure, which consequently modifies spectral properties because new multiple sharp lines appeared in the photoluminescence (PL) spectra of the fibers. In contrast to randomly deposited fibers, the PL intensity of uniaxially aligned fibers was found to be angle dependent. We propose that the elongated internal structure within the fibers controls the spontaneous emission of CdSe nanoparticles dispersed throughout the electrospun mat. A discussion on the nature of the controlled spontaneous emission is provided. © 2009 American Chemical Society.
Citation Count: 0
Cytoplasmically localized tRNA-derived fragments inhibit translation in Drosophila S2 cells
(TUBITAK, 2022) Hamid,S.M.; Akgül,B.; Akgül, Bünyamin; Moleküler Biyoloji ve Genetik Bölümü; Moleküler Biyoloji ve Genetik Bölümü
Transfer ribonucleic acids (tRNAs) serve not only as amino acid carriers during translation but also as a template for the biogenesis of short fragments that can regulate gene expression. Despite recent progress in the function of tRNA-derived fragments (tRFs), their intracellular localization, protein partners, and role in regulating translation are not well understood. We used synthetic tRFs to investigate their localization and function in Drosophila S2 cells. Under our experimental setting, all synthetic tRFs tested were localized at distinct sites within the cytoplasm in a similar manner in Drosophila S2 cells. Cytoplasmically-localized tRFs were positioned in close proximity to GW182 and XRN1 proteins. Functionally, tRFs, which slightly suppressed proliferation in S2 cells, inhibited translation without any major shift in the polysome profile. These results suggest that 5’-tRFs are cytoplasmically-localized and regulate gene expression through inhibition of translation in Drosophila. © TÜBİTAK.
Citation Count: 44
Development of molecularly imprinted polymers (MIPs) as a solid phase extraction (SPE) sorbent for the determination of ibuprofen in water
(Royal Society of Chemistry, 2017) Olcer Y.A.; Demirkurt M.; Demir M.M.; Eroglu, A.E.
Ibuprofen is a well-known endocrine disrupter. In this study, highly selective molecularly imprinted polymers (MIPs) with different morphologies were synthesized via precipitation and bulk polymerization of methacrylic acid (MAA) and trimethylolpropane trimethacrylate (TRIM) in the presence of ibuprofen as a template. Non-imprinted polymers (NIPs) were also synthesized via the same procedure in the absence of ibuprofen. Spherical and monolithic MIPs were obtained using different experimental conditions, and the spherical MIP was shown to have better sorption towards ibuprofen. The optimum sample pH, sorbent amount, sample volume, and sorption time were determined to be 8.0, 25.0 mg, 10.0 mL, and 30.0 min, respectively. A methanol water mixture (MeOH:H2O, 80:20, pH 3.0) was employed as an eluent with >97% (±0.8, n = 3) desorption. The MIP demonstrated high selectivity towards ibuprofen in the presence of naproxen and ketoprofen. The validity of the proposed method was checked via spike recovery tests using drinking and tap water samples. The method worked efficiently for both water types, resulting in the recoveries of 97.2% (±0.3, n = 3) and 97.7% (±0.2, n = 3). © 2017 The Royal Society of Chemistry.
Citation Count: 11
Differential transform method and Adomian decomposition method for free vibration analysis of fluid conveying Timoshenko pipeline
(Techno-Press, 2017) Bozyigit,B.; Yesilce,Y.; Catal,S.
The free vibration analysis of fluid conveying Timoshenko pipeline with different boundary conditions using Differential Transform Method (DTM) and Adomian Decomposition Method (ADM) has not been investigated by any of the studies in open literature so far. Natural frequencies, modes and critical fluid velocity of the pipelines on different supports are analyzed based on Timoshenko model by using DTM and ADM in this study. At first, the governing differential equations of motion of fluid conveying Timoshenko pipeline in free vibration are derived. Parameter for the nondimensionalized multiplication factor for the fluid velocity is incorporated into the equations of motion in order to investigate its effects on the natural frequencies. For solution, the terms are found directly from the analytical solution of the differential equation that describes the deformations of the cross-section according to Timoshenko beam theory. After the analytical solution, the efficient and easy mathematical techniques called DTM and ADM are used to solve the governing differential equations of the motion, respectively. The calculated natural frequencies of fluid conveying Timoshenko pipelines with various combinations of boundary conditions using DTM and ADM are tabulated in several tables and figures and are compared with the results of Analytical Method (ANM) where a very good agreement is observed. Finally, the critical fluid velocities are calculated for different boundary conditions and the first five mode shapes are presented in graphs. © 2017 Techno-Press, Ltd.
Citation Count: 12
Differentially expressed tRNA-derived small RNAs co-sediment primarily with non-polysomal fractions in Drosophila
(MDPI AG, 2017) Akgül, Bünyamin; Yiğit,H.; Coşacak,M.İ.; Akgül,B.
Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos were fractionated on sucrose density gradients. Analysis of 12,553,921 deep-sequencing reads from unfractionated and fractionated Drosophila embryos has revealed that tRFs, which are detected mainly from the 5’ends of tRNAs, co-sediment with the non-polysomal fractions. Interestingly, the expression levels of a subset of tRFs change temporally following thematernal-to-zygotic transition in embryos. We detected non-polysomal association of tRFs in S2 cells as well. Differential tRF expression pattern points to developmental significance at the organismal level. These results suggest that tRFs are associated primarily with the non-polysomal complexes in Drosophila embryos and S2 cells. © 2017 by the authors.

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