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Publication Metadata only 18F-FDG PET / CT findings of Rosai Dorfman Disease with diffuse extranodal involvement(SPRINGER, 2020) Filizoglu, N.; Kesim, S.; Engur, C. O.; Oksuzoglu, K.; Ozguven, S.; Ones, T.; Turoglu, H. T.; Erdil, T. Y.Publication Open Access 2018 EULAR recommendations for physical activity in people with inflammatory arthritis and osteoarthritis(BMJ PUBLISHING GROUP, 2018-09) DURUÖZ, MEHMET TUNCAY; Osthoff, Anne-Kathrin Rausch; Niedermann, Karin; Braun, Juergen; Adams, Jo; Brodin, Nina; Dagfinrud, Hanne; Duruoz, Tuncay; Esbensen, Bente Appel; Guenther, Klaus-Peter; Hurkmans, Emailie; Juhl, Carsten Bogh; Kennedy, Norelee; Kiltz, Uta; Knittle, Keegan; Nurmohamed, Michael; Pais, Sandra; Severijns, Guy; Swinnen, Thijs Willem; Pitsillidou, Irene A.; Warburton, Louise; Yankov, Zhivko; Vlieland, Theodora P. M. VlietRegular physical activity (PA) is increasingly promoted for people with rheumatic and musculoskeletal diseases as well as the general population. We evaluated if the public health recommendations for PA are applicable for people with inflammatory arthritis (iAPublication Metadata only 25-HYDROXYVITAMIN D3 DEFICIENCY: PREVALANCE AND ITS IMPACT ON DISEASE ACTIVITY IN SMALL-MEDIUM VESSEL VASCULITIS(BMJ PUBLISHING GROUP, 2016) Korkmaz, F. N.; Ozen, G.; Unal, A. U.; Can, M.; Tuglular, S.; Direskeneli, H.Publication Metadata only 3-D optical profilometry at micron scale with multi-frequency fringe projection using modified fibre optic Lloyd's mirror technique(ELSEVIER SCI LTD, 2018) GÖRK, GÜLŞEN; Inanc, Arda; Kosoglu, Gulsen; Yuksel, Heba; Inci, Mehmet NaciA new fibre optic Lloyd's mirror method is developed for extracting 3-D height distribution of various objects at the micron scale with a resolution of 4 mu m. The fibre optic assembly is elegantly integrated to an optical microscope and a CCD camera. It is demonstrated that the proposed technique is quite suitable and practical to produce an interference pattern with an adjustable frequency. By increasing the distance between the fibre and the mirror with a micrometre stage in the Lloyd's mirror assembly, the separation between the two bright fringes is lowered down to the micron scale without using any additional elements as part of the optical projection unit. A fibre optic cable, whose polymer jacket is partially stripped, and a microfluidic channel are used as test objects to extract their surface topographies. Point by point sensitivity of the method is found to be around 8 mu m, changing a couple of microns depending on the fringe frequency and the measured height. A straightforward calibration procedure for the phase to height conversion is also introduced by making use of the vertical moving stage of the optical microscope. The phase analysis of the acquired image is carried out by One Dimensional Continuous Wavelet Transform for which the chosen wavelet is the Morlet wavelet and the carrier removal of the projected fringe patterns is achieved by reference subtraction. Furthermore, flexible multi -frequency property of the proposed method allows measuring discontinuous heights where there are phase ambiguities like 2 pi by lowering the fringe frequency and eliminating the phase ambiguity. (C) 2017 Elsevier Ltd. All rights reserved.Publication Metadata only 3D bio-printing of levan/polycaprolactone/gelatin blends for bone tissue engineering: Characterization of the cellular behavior(PERGAMON-ELSEVIER SCIENCE LTD, 2019) İNAN, AHMET TALAT; Duymaz, Busra Tugce; Erdiler, Fatma Betul; Alan, Tugba; Aydogdu, Mehmet Onur; Inan, Ahmet Talat; Ekren, Nazmi; Uzun, Muhammet; Sahin, Yesim Muge; Bulus, Erdi; Oktar, Faik Nuzhet; Selvi, Sinem Selvin; ToksoyOner, Ebru; Kilic, Osman; Bostan, Muge Sennaroglu; Eroglu, Mehmet Sayip; Gunduz, OguzhanPoly(epsilon-caprolactone) (PCL), gelatin (GT) and different concentrations of low molecular weight Halomonas levan (HLh) were combined and examined to develop physical networks serving as tissue scaffolds to promote cell adhesion for biocompatibility. Three-dimensional bioprinting technique (3D bioprinting) was employed during manufacturing the test samples and their comprehensive characterization was performed to investigate the physicochemical properties and biocompatibility. Physical properties of the printing materials such as viscosity, surface tension, and density were measured to determine optimal parameters for 3D bioprinting. The scanning electron microscope (SEM) was used to observe the morphological structure of scaffolds. Fourier-Transform Infrared Spectroscopy (FT-IR) and differential scanning calorimetry (DSC) were used to identify the interactions between the components. In-vitro cell culture assays using standard human osteoblast (Hob) cells showed increased biocompatibility of the printing materials with increasing HLh content. Thus, the formulations including the HLh are expected to be a good candidate for the production of 3D printed materials.Publication Metadata only 3D bioprinting applications in neural tissue engineering for spinal cord injury repair(ELSEVIER, 2020) GÜNDÜZ, OĞUZHAN; Bedir, Tuba; Ulag, Songul; Ustundag, Cem Bulent; Gunduz, OguzhanSpinal cord injury (SCI) is a disease of the central nervous system (CNS) that has not yet been treated successfully. In the United States, almost 450,000 people suffer from SCI. Despite the development of many clinical treatments, therapeutics are still at an early stage for a successful bridging of damaged nerve spaces and complete recovery of nerve functions. Biomimetic 3D scaffolds have been an effective option in repairing the damaged nervous system. 3D scaffolds allow improved host tissue engraftment and new tissue development by supplying physical support to ease cell function. Recently, 3D bioprinting techniques that may easily regulate the dimension and shape of the 3D tissue scaffold and are capable of producing scaffolds with cells have attracted attention. Production of biologically more complex microstructures can be achieved by using 3D bioprinting technology. Particularly in vitro modeling of CNS tissues for in vivo transplantation is critical in the treatment of SCI. Considering the potential impact of 3D bioprinting technology on neural studies, this review focus on 3D bioprinting methods, bio-inks, and cells widely used in neural tissue engineering and the latest technological applications of bioprinting of nerve tissues for the repair of SCI are discussed.Publication Open Access 3D printed artificial cornea for corneal stromal transplantation(PERGAMON-ELSEVIER SCIENCE LTD, 2020-06) ŞAHİN, ALİ; Ulag, Songul; Ilhan, Elif; Sahin, Ali; Yilmaz, Betul Karademir; Kalaskar, Deepak M.; Ekren, Nazmi; Kilic, Osman; Oktar, Faik Nuzhet; Gunduz, OguzhanThe aim of this study is to understand the optical, biocompatible, and mechanical properties of chitosan (CS) and polyvinyl-alcohol (PVA) based corneal stroma constructs using 3D printing process. Corneal stroma is tested for biocompatibility with human adipose tissue-derived mesenchymal stem cells (hASCs). Physico-chemical and chemical characterization of the construct was performed using scanning electron microscopy (SEM), fourier transforms infrared spectroscopy (FTIR). Optical transmittance was analyzed using UV-Spectrophotometer. Results showed fabricated constructs have required shape and size. SEM images showed construct has thickness of 400 mu m. The FTIR spectra demonstrated the presence of various predicted peaks. The swelling and degradation studies of 13%(wt)PVA and 13%(wt)PVA/(1, 3, 5)%(wt)CS showed to have high swelling ratios of 7 days and degradation times of 30 days, respectively. The light transmittance values of the fabricated cornea constructs decreased with CS addition slightly. Tensile strength values decreased with increasing CS ratio, but we found to support intraocular pressure (IOP) which ranges from 12 to 22 mm-Hg. Preliminary biostability studies showed that composite constructs were compatible with hASCs even after 30 days' of degradation, showing potential for these cells to be differentiated to stroma layer in future. This study has implications for the rapid and custom fabrication of various cornea constructs for clinical applications.Publication Open Access 3D Printed Polycaprolactone/Gelatin/Bacterial Cellulose/Hydroxyapatite Composite Scaffold for Bone Tissue Engineering(MDPI, 2020-08-29) ŞAHİN, ALİ; Cakmak, Abdullah M.; Unal, Semra; Sahin, Ali; Oktar, Faik N.; Sengor, Mustafa; Ekren, Nazmi; Gunduz, Oguzhan; Kalaskar, Deepak M.Three-dimensional (3D) printing application is a promising method for bone tissue engineering. For enhanced bone tissue regeneration, it is essential to have printable composite materials with appealing properties such as construct porous, mechanical strength, thermal properties, controlled degradation rates, and the presence of bioactive materials. In this study, polycaprolactone (PCL), gelatin (GEL), bacterial cellulose (BC), and different hydroxyapatite (HA) concentrations were used to fabricate a novel PCL/GEL/BC/HA composite scaffold using 3D printing method for bone tissue engineering applications. Pore structure, mechanical, thermal, and chemical analyses were evaluated. 3D scaffolds with an ideal pore size (similar to 300 mu m) for use in bone tissue engineering were generated. The addition of both bacterial cellulose (BC) and hydroxyapatite (HA) into PCL/GEL scaffold increased cell proliferation and attachment. PCL/GEL/BC/HA composite scaffolds provide a potential for bone tissue engineering applications.Publication Metadata only 3D printing of chitosan/ poly(vinyl alcohol) hydrogel containing synthesized hydroxyapatite scaffolds for hard-tissue engineering(ELSEVIER SCI LTD, 2019) KARTAL, İLYAS; Ergul, Necdet Mekki; Unal, Semra; Kartal, Ilyas; Kalkandelen, Cevriye; Ekren, Nazmi; Kilic, Osman; Chi-Chang, Lin; Gunduz, OguzhanIn recent years, 3D printed scaffolds becoming a widespread tool, which supports the repair mechanism of natural tissues. In order to support this knowledge, we used 3D printing methods to fabricated Chitosan (CH)/poly(vinyl alcohol)(PVA)-based scaffolds contains with a various ratio of hydroxyapatite (HA) (2.5, 5, 10, and 15 wt%). These composited scaffolds were further characterized for their chemical, morphological, mechanical, and biocompatibility properties. Scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), swelling test, and compressive strength test were performed to reveal structural, mechanical and chemical characteristics of scaffolds. Among others, 15 wt% HA contained group demonstrated significantly superior and beneficial features in printing quality. Also, the results reveal that scaffolds have similar elastic modulus to natural bone. Bone morphogenetic protein-2 (BMP-2) protein was added to the most successful mechanically produced sample. As a result, it was shown that Chitosan/PVA/HA (15 wt%) with BMP-2 tissue scaffold could form a three-dimensional natural extracellular scaffold suitable for human mesenchymal stem cells. Altogether, these results show that hydroxyapatite added scaffolds produced may be a promising approach for bone tissue engineering applications.Publication Open Access 3D printing of PVA/hexagonal boron nitride/bacterial cellulose composite scaffolds for bone tissue engineering(ELSEVIER SCI LTD, 2020-11) ŞENGÖR, MUSTAFA; Aki, Deniz; Ulag, Songul; Unal, Semra; Sengor, Mustafa; Ekren, Nazmi; Lin, Chi-Chang; Yilmazer, Hakan; Ustundag, Cem Bulent; Kalaskar, Deepak M.; Gunduz, OguzhanIn this study, a novel Polyvinyl Alcohol (PVA)/Hexagonal Boron Nitride (hBN)/Bacterial Cellulose (BC) composite, bone tissue scaffolds were fabricated using 3D printing technology. The printed scaffolds were characterized by fourier transform infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), tensile testing, swelling behaviour, differential scanning calorimetry (DSC), and in vitro cell culture assay. Results demonstrated that bacterial cellulose addition affected the characteristic properties of the blends. Morphological studies revealed the homogenous dispersion of the bacterial cellulose within the 12 wt%PVA/0.25 wt%hBN matrix. Tensile strength of the scaffolds was decreased with the incorporation of BC and 12 wt%PVA/0.25 wt%hBN/0.5 wt%BC had the highest elongation at break value (93%). A significant increase in human osteoblast cell viability on 3D scaffolds was observed for 12 wt%PVA/0.25 wt%hBN/0.5 wt%BC. Cell morphology on composite scaffolds showed that bacterial cellulose doped scaffolds appeared to adhere to the cells. The present work deduced that bacterial cellulose doped 3D printed scaffolds with well-defined porous structures have considerable potential as a suitable tissue scaffold for bone tissue engineering (BTE). (c) 2020 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http:// creativecommons.org/licenses/by/4.0/).Publication Open Access 3D structure syn/anti isomers of a valin hydrazone(INT UNION CRYSTALLOGRAPHY, 2017-12-01) Cela, Dorisa; Nepravishta, Ridvan; Mandaliti, Walter; Tatar, Esra; Senkardes, Sevil; Kucukguzel, Ilkay; Kucukguzel, S. Guniz; Paci, MaurizioPublication Metadata only 4TH VENTRICLE GLIOBLASTOMA(OXFORD UNIV PRESS INC, 2017) Unal, E.; Isik, S.; Gurbuz, M.; Kilic, K.Publication Metadata only 6 Sequencing of 16S rRNA Reveals a Distinct Salivary Microbiome Signature in Behcet's Disease(WILEY, 2016) Coit, Patrick; Mumcu, Gonca; Ozdemir, Filiz Ture; Unal, Ali Ugur; Alpar, Ugur; Bostanci, Nagihan; Ergun, Tulin; Direskeneli, Haner; Sawalha, AmrPublication Open Access A benchmarking project on the quality of previous guidelines about the management of malignant pleural effusion from the European Society of Thoracic Surgeons (ESTS) Pleural Diseases Working Group(OXFORD UNIV PRESS INC, 2017-08-01) BATIREL, HASAN FEVZİ; Bertolaccini, Luca; Bedetti, Benedetta; Brunelli, Alessandro; Marinova, Katerina; Raveglia, Federico; Rocco, Gaetano; Shargall, Yaron; Solli, Piergiorgio; Varela, Gonzalo; Papagiannopoulos, Kostas; Kuzdzal, Jaroslaw; Massard, Gilbert; Ruffini, Enrico; Falcoz, Pierre-Emmanuel; Martinez-Barenys, Carlos; Opitz, Isabelle; Batirel, Hasan F.; Toker, Alper; Scarci, MarcoOBJECTIVES: In the European Society of Thoracic Surgeons (ESTS) survey about management of malignant pleural effusions (MPE), 56% of respondents are not informed of any relevant clinical guidelines and 52%, who are aware of the existence of guidelines, declared that they are in need of updating or revision. The ESTS Pleural Diseases Working Group developed a benchmarking project on quality of previous guidelines on the management of MPE. METHODS: The Appraisal of Guidelines for Research and Evaluation (AGREE) II instrument was used to assess each guideline. Each item was scored on a 7-point scale. Scores for each domain were calculated. Economic data for the nations which have issued the guidelines were collected from the Organisation for Economic Cooperation and Development health statistics database. RESULTS: Six guidelines fitted the inclusion criteria and were assessed. Five out of 6 guidelines were produced by a multinational collaboration. Observers would recommend only 2 guidelines with minimal modification. Two areas that received the best score were clarity of presentation and scope and purpose (objectives and health questions target population). The applicability of guideline domain had the lowest score. Multivariate analysis demonstrated that clarity of presentation, international guidelines and publication through medical journal were related to improved scores. A strong correlation was observed between the measures of economic status. CONCLUSIONS: The quality of guidelines assessed by the AGREE II criteria was found to be extremely variable. Guidelines achieving higher AGREE II scores were more likely to come from the European Union with the direct involvement of scientific societies in their development. It was also recognized that some fundamental unanswered questions remain about the management of MPE.Publication Open Access A BETTER WAY TO DECREASE KNEE SWELLING IN PATIENTS WITH KNEE OSTEOARTHRITIS: INTERMITTENT PNEUMATIC COMPRESSION - A RANDOMIZED CONTROLLED CLINICAL TRIAL(BMJ PUBLISHING GROUP, 2017-06) DEMİRBÜKEN, İLKŞAN; Sari, Z.; Aydogdu, O.; Demirbuken, I.; Yurdalan, U. S.; Polat, G. M.Publication Metadata only A Case Of Adrenal Insufficiency Associated With Antituberculosis Treatment(AMER THORACIC SOC, 2016) Arikan, H.; Yildizeli, S. Olgun; Eryuksel, E.; Ceyhan, B. BagciPublication Metadata only A Case Of Malignant Mesothelioma Who Survived 9 Years Without Proper Treatment(AMER THORACIC SOC, 2016) Arikan, H.; Yildizeli, S. Olgun; Eryuksel, E.; Ceyhan, B. BagciPublication Metadata only A comparative investigation on the in vitro anti-inflammatory, antioxidant and antimicrobial potentials of subextracts from the aerial parts of Daphne oleoides Schreb. subsp oleoides(ELSEVIER SCIENCE BV, 2017) TAŞKIN, TURGUT; Balkan, Irem Atay; Taskin, Turgut; Dogan, Hacer Tugba; Deniz, Inci; Akaydin, Galip; Yesilada, ErdemDaphne oleoides Schreb. subsp. oleoides is an evergreen shrub which is known for its folkloric usage against various ailments such as arthritic and infectious diseases. The aim of the present study was to comparatively investigate the in vitro anti-inflammatory (nitric oxide inhibitory effects), antioxidant (DPPH center dot,ABTS(center dot+) and FRAP tests) and antimicrobial activities of the extract/subextracts from the aerial parts of D. oleoides Schreb. subsp. oleoides (Thymelaeaceae). The powdered aerial parts were first extracted with methanol and then partitioned into five subextracts (n-hexane, dichloromethane (CH2Cl2), ethyl acetate (EtOAC), n-butanol and remaining water) by succesive solvent extractions. The chemical compositions of the extracts were compared with regard to their total phenolic, total flavonoid contents and fatty acid compositions. The CH2Cl2 and n-hexane extracts exerted the highest inhibitory effect on NO production (61.67 +/- 13.97% inhibition at 50 mu g/ml and 67.91 +/- 11.17% inhibition at 100 mu g/ml, respectively) of LPS-induced Raw 264.7 cells. The EtOAC subextract showed the highest antioxidant effect evaluated by DPPH center dot (IC50: 0.35 +/- 0.12 mg/ml) and FRAP (4.54 +/- 10.01 mM FeSO4/mg extract) tests. The CH2Cl2 subextract was shown to contain the highest levels of flavonoids (0.837 +/- 10.035 mg QUE/mg extract) and was also found to be rich in phenolics (1.063 +/- 10.011 mg GAE/mg extract). Fatty acid analysis of the n-hexane extract revealed hexadecahoic acid and 9,15-octodecadienoic acids to be the major components. The n-hexane and CH2Cl2 subextracts exerted the'highest antimicrobial potential. (C) 2016 Elsevier B.V. All rights reserved.Publication Open Access A comprehensive simulation study on classification of RNA-Seq data(PUBLIC LIBRARY SCIENCE, 2017-08-23) Zararsiz, Gokmen; Goksuluk, Dincer; Korkmaz, Selcuk; Eldem, Vahap; Zararsiz, Gozde Erturk; Duru, Izzet Parug; Ozturk, AhmetRNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg. microarray data) or require a normal distribution assumption. Hence, these methods cannot be directly applied to RNASeq data since they violate both data structure and distributional assumptions. However, it is possible to apply these algorithms with appropriate modifications to RNA-Seq data. One way is to develop count-based classifiers, such as Poisson linear discriminant analysis and negative binomial linear discriminant analysis. Another way is to bring the data closer to microarrays and apply microarray-based classifiers. In this study, we compared several classifiers including PLDA with and without power transformation, NBLDA, single SVM, bagging SVM (bagSVM), classification and regression trees (CART), and random forests (RF). We also examined the effect of several parameters such as overdispersion, sample size, number of genes, number of classes, differential-expression rate, and the transformation method on model performances. A comprehensive simulation study is conducted and the results are compared with the results of two miRNA and two mRNA experimental datasets. The results revealed that increasing the sample size, differential-expression rate and decreasing the dispersion parameter and number of groups lead to an increase in classification accuracy. Similar with differential-expression studies, the classification of RNA-Seq data requires careful attention when handling data overdispersion. We conclude that, as a count-based classifier, the power transformed PLDA and, as a microarray-based classifier, vst or rlog transformed RF and SVM classifiers may be a good choice for classification. An R/BIOCONDUCTOR package, MLSeq, is freely available at https://www. bioconductor. org/packages/release/bioc/ html/MLSeq. html.Publication Metadata only A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis(SPRINGER, 2016) ÖZBEK SARICA, PEMRA; Sercinoglu, Onur; Ozcan, Gulin; Kabas, Zeynep Kutlu; Ozbek, PemraA single amino acid difference (Asp116His), having a key role in a pathogenesis pathway, distinguishes HLA-B*27:05 and HLA-B*27:09 sub-types as associated and non-associated with ankylosing spondylitis, respectively. In this study, molecular docking simulations were carried out with the aim of comprehending the differences in the binding behavior of both alleles at varying pH conditions. A library of modeled peptides was formed upon single point mutations aiming to address the effect of 20 naturally occurring amino acids at the binding core peptide positions. For both alleles, computational docking was applied using Autodock 4.2. Obtained free energies of binding (FEB) were compared within the peptide library and between the alleles at varying pH conditions. The amino acid preferences of each position were studied enlightening the role of each on binding. The preferred amino acids for each position of pVIPR were found to be harmonious with experimental studies. Our results indicate that, as the pH is lowered, the capacity of HLA-B*27:05 to bind peptides in the library is largely lost. Hydrogen bonding analysis suggests that the interaction between the main anchor positions of pVIPR and their respective binding pocket residues are affected from the pH the most, causing an overall shift in the FEB profiles.