PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 8Protective and Therapeutic Effects of Milrinone on Acoustic Trauma in Rat Cochlea(Springer, 2019) Ceylan, Seyit Mehmet; Uysal, Erdal; Altinay, Serdar; Sezgin, Efe; Bilal, Nagihan; Petekkaya, Emine; Gulbagci, Mustafa EmreObjectiveThe aim of this study was to investigate the potential protective and therapeutic effects of milrinone, a specific phosphodiesterase (PDE) III inhibitor, on acoustic trauma-induced cochlear injury and apoptosis.MethodsA total number of 30 healthy Wistar albino rats were evenly divided into five groups as follows: group 1 was assigned as control group; group 2 and 3 were assigned as low-dosage groups (0.25mg/kg) in which milrinone was administered 1h before acoustic trauma (AT) and 2h after AT, respectively; group 4 and 5 were assigned as high-dosage groups (0.50mg/kg) in which the drug was administered 1h before AT and 2h after AT, respectively. Except control group, all treatment groups received a single dosage of milrinone for 5days. Distortion product otoacoustic emissions (DPOAE) measurements were recorded before AT as well as at second and fifth post-traumatic days. At the end of fifth day, all rats were sacrificed and the cochlea of the rats was removed for histopathological evaluation. In addition, the groups were compared in terms of apoptotic index via caspase-3 staining.ResultsIn terms of signal-to-noise ratio (SNR), there was no statistically significant difference among the groups following AT (p>0.05). After 5days of milrinone treatment, the best SNR values were found in group 5, though all groups did not statistically differ (p>0.05). In histopathological evaluation, vacuolization, inflammation, and edema scores in all treatment groups were statistically lower than those of the control group (p<0.05). In group 2 and 4 where the drug was administered before AT, the inflammation and apoptosis index was lower than those of group 3 and 5 where the drug was administered after AT (p<0.0001).ConclusionWe reveal that milrinone has a protective effect on cochlear damage in the experimental acoustic model of rats. This protective effect was more apparent following the pre-traumatic milrinone administration, and is associated with its effect on decreasing inflammation and apoptosis. Based on DPOAE measurements following AT, especially in the group 5 (high-dosage group), milrinone may also have a therapeutic effect.Conference Object Citation - WoS: 24Effect of pH and Hydration on the Normal and Lateral Interaction Forces Between Alumina Surfaces(2006) Polat, Mehmet; Sato, Kimiyasu; Nagaoka, Takaaki; Watari, KojiNormal and lateral interaction forces between alumina surfaces were measured using Atomic Force Microscopy-Colloid Probe Method at different pH. The normal force curves exhibit a well-defined repulsive barrier and an attractive minimum at acidic pH and the DLVO theory shows excellent agreement with the data. The normal forces are always repulsive at basic pH and the theory fails to represent the measurements. Lateral forces are almost an order of magnitude smaller in the basic solutions. These differences, which have important implications in the study of stability and rheology, are attributed to the hydration of the alumina surface at basic pH. © 2013 Elsevier B.V., All rights reserved.Article Citation - WoS: 15Citation - Scopus: 18Search for Supersymmetry in pp Collisions at √s=13 TeV in the Single-Lepton Final State Using the Sum of Masses of Large-Radius Jets(Amer Physical Soc, 2017) Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Ambrogi, F.; Asilar, E.; Bergauer, T.; Woods, N.Results are reported from a search for supersymmetric particles in proton-proton collisions in the final state with a single lepton, multiple jets, including at least one b-tagged jet, and large missing transverse momentum. The search uses a sample of proton-proton collision data at root s = 13 TeV recorded by the CMS experiment at the LHC, corresponding to an integrated luminosity of 35.9 fb(-1). The observed event yields in the signal regions are consistent with those expected from standard model backgrounds. The results are interpreted in the context of simplified models of supersymmetry involving gluino pair production, with gluino decay into either on- or off-mass-shell top squarks. Assuming that the top squarks decay into a top quark plus a stable, weakly interacting neutralino, scenarios with gluino masses up to about 1.9 TeV are excluded at 95% confidence level for neutralino masses up to about 1 TeV.Article Citation - Scopus: 34Machine Learning Methods for Microrna Gene Prediction(Humana Press Inc., 2014) Saçar,M.D.; Allmer,J.MicroRNAs (miRNAs) are single-stranded, small, noncoding RNAs of about 22 nucleotides in length, which control gene expression at the posttranscriptional level through translational inhibition, degradation, adenylation, or destabilization of their target mRNAs. Although hundreds of miRNAs have been identified in various species, many more may still remain unknown. Therefore, discovery of new miRNA genes is an important step for understanding miRNA-mediated posttranscriptional regulation mechanisms. It seems that biological approaches to identify miRNA genes might be limited in their ability to detect rare miRNAs and are further limited to the tissues examined and the developmental stage of the organism under examination. These limitations have led to the development of sophisticated computational approaches attempting to identify possible miRNAs in silico. In this chapter, we discuss computational problems in miRNA prediction studies and review some of the many machine learning methods that have been tried to address the issues. © Springer Science+Business Media New York 2014.Article Citation - WoS: 37Mechanisms of Cellular Resistance To Imatinib in Human Chronic Myeloid Leukemia Cells(Taylor and Francis Ltd., 2007) Baran, Yusuf; Ural, Ali Uğur; Gündüz, UfukA major advancement in the treatment of chronic myeloid leukemia (CML) has been the development of imatinib, which has shown striking activity in the chronic phase and the accelerated phase, but less so in the blast phase of the disease. Despite high rates of hematologic and cytogenetic responses to therapy, the emergence of resistance to imatinib has been recognized as a major problem in the treatment of patients with CML. Various cellular mechanisms may be involved in the nature of cellular resistance. Increased amount of target, alteration in structure of target proteins, decreased drug uptake and increased detoxification are well-known mechanisms of resistance. On the other hand, in some cases, even if anticancer drugs reach their sites of action, bypassing drug efflux system of the cells, some cells still may survive via the dysregulation of apoptotic signalling. In this study, mechanisms of resistance to imatinib-induced apoptosis in human Meg-01 CML cells were examined. Continuous exposure of cells to step-wise increasing concentrations of imatinib resulted in the selection of 200- and 1000 nM imatinib-resistant sub-lines referred to as Meg-01/IMA-0,2 and Meg-01/1MA-1, respectively. MTT cell proliferation, cell cycle analyses and trypan blue dye exclusion analyses showed that Meg-0l/IMA-1 cells were resistant to imatinib-induced apoptosis as compared to parental sensitive cells. There was an increased expression of BCR/ABL, Bcl-2 and an increase in mitochondrial membrane potential (MMP) detected in resistant cells comparing to parental sensitive cells. There was no mutation detected in imatinib binding site of ABL kinase region. Various diverse mechanisms have been reported for their involvement in the multidrug resistance. In this study, it has been shown that the degree of BCR/ABL expression appears to be directly proportional to the levels of imatinib resistance. In addition, there have been BCR/ABL-independent mechanisms reported for deriving resistance against imatinib. Our results revealed that besides BCR/ABL overexpression, imatinib resistance also depends on the inhibition of apoptosis as a result of up-regulation of anti-apoptotic stimuli and down-regulation of pro-apoptotic stimuli through MMP but does not depend on any mutation on imatinib binding site of ABL kinase.Article Citation - WoS: 111Stabilization of Magnetic Iron Oxide Nanoparticles in Biological Media by Fetal Bovine Serum (fbs)(American Chemical Society, 2011) Wiogo, Hilda T. R.; Lim, May; Bulmuş, Volga; Yun, Jimmy; Amal, RoseA facile method of stabilizing magnetic iron oxide nanoparticles (MNPs) in biological media (RPMI-1640) via surface modification with fetal bovine scrum (FBS) is presented herein. Dynamic light scattering (DLS) shows that the size of the MNP aggregates can be maintained at 190 +/- 2 nm for up to 16 h in an RPMI 1640 culture medium containing >= 4 vol % FBS. Under transmission electron microscopy (TEM), a layer of protein coating is observed to cover the MNP surface following treatment with FBS. The adsorption of proteins is further confirmed by X-ray photoelectron spectroscopy (XPS). Gel electrophoresis and LC-MS/MS studies reveal that complement factor I-I, antithrombin, complement factor I, alpha-1-antiproteinase, and apolipoprotein E are the proteins most strongly attached to the surface of all MNP. These surface-adsorbed proteins serve as a linker that aids the adsorption of other serum proteins, such as albumin, which otherwise adsorb poorly onto MNPs. The size stability of FBS-treated MNPs in biological media is attributed to the secondary adsorbed proteins, and the size stability in biological media can be maintained only when both the surface-adsorbed proteins and the secondary adsorbed proteins are present on the particle's surface.Article Citation - WoS: 2Evaluation of Malassezia Species by Fourier Transform Infrared (ft-Ir) Spectroscopy(Ankara Microbiology Society, 2011) Ergin, Çağrı; Vuran, M. Emre; Gök, Yaşar; Özdemir, Durmuş; Karaarslan, Aydın; Kaleli, İlnur; Çon, Ahmet HilmiMalassezia species which are lipophilic exobasidiomycetes fungi, have been accepted as members of normal cutaneous flora as well as causative agent of certain skin diseases. In routine microbiology laboratory, species identification based on phenotypic characters may not yield identical results with taxonomic studies. Lipophilic and lipid-dependent Malassezia yeasts require lipid-enriched complex media. For this reason, Fourier transform infrared (FT-IR) spectroscopy analysis focused on lipid window may be useful for identification of Malassezia species. In this study, 10 different standard Malassezia species (M.dermatis CBS 9145, M.furfur CBS 7019, M.japonica CBS 9432, M.globosa CBS 7966, M.nana CBS 9561, M.obtusa CBS 7876, M.pachydermatis CBS 1879, M.slooffiae CBS 7956, M.sympodialis CBS 7222 and M.yamatoensis CBS 9725) which are human pathogens, have been analyzed by FT-IR spectroscopy following standard cultivation onto modified Dixon agar medium. Results showed that two main groups (M1; M.globosa, Robtusa, M.sympodialis, M.dermatis, M.pachydermatis vs, M2; M.furfur, M.japonica, M.nana, M.slooffiae, M.yamatoensis) were discriminated by whole spectra analysis. M.obtusa in M1 by 1686-1606 cm(-1) wavenumber ranges and M.japonicum in M2 by 2993-2812 cm(-1) wavenumber ranges were identified with low level discrimination power. Discriminatory areas for species differentiation of M1 members as M.sympodialis, M.globosa and M.pachydermatis and M2 members as M.furfur and M.yamatoensis could not be identified. Several spectral windows analysis results revealed that FT-IR spectroscopy was not sufficient for species identification of culture grown Malassezia species.Article Citation - WoS: 47Search for Heavy Neutrinos and W-R Bosons With Right-Handed Couplings in a Left-Right Symmetric Model in Pp Collisions at Root S=7 Tev(American Physical Society, 2012) Karapınar, GülerResults are presented from a search for heavy, right-handed muon neutrinos, N-mu, and right-handed W-R bosons, which arise in the left-right symmetric extensions of the standard model. The analysis is based on a 5: 0 fb(-1) sample of proton-proton collisions at a center-of-mass energy of 7 TeV, collected by the CMS detector at the Large Hadron Collider. No evidence is observed for an excess of events over the standard model expectation. For models with exact left-right symmetry, heavy right-handed neutrinos are excluded at 95% confidence level for a range of neutrino masses below the WR mass, dependent on the value of M-WR. The excluded region in the two-dimensional (M-WR, MN mu) mass plane extends to M-WR = 2.5TeV. DOI: 10.1103/PhysRevLett.109.261802Article Citation - WoS: 72Search for a Standard-Model Higgs Boson With a Mass in the Range 145 To 1000 Gev at the Lhc(Springer Verlag, 2013) Karapınar, Güler; CMS CollaborationA search for a standard-model-like Higgs boson in the H -> WW and H -> ZZ decay channels is reported, for Higgs boson masses in the range 145 < m(H) < 1000 GeV. The search is based upon proton-proton collision data samples corresponding to an integrated luminosity of up to 5.1 fb(-1) at root s = 7 TeV and up to 5.3 fb(-1) at root s = 8 TeV, recorded by the CMS experiment at the LHC. The combined upper limits at 95 % confidence level on products of the cross section and branching fractions exclude a standard-model-like Higgs boson in the range 145 < m(H) < 710 GeV, thus extending the mass region excluded by CMS from 127-600 GeV up to 710 GeV.Article Citation - WoS: 105Evidence of B-Jet Quenching in PbPb Collisions at √sNN=2.76 TeV(American Physical Society, 2014) Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Bergauer, T.; Smith, W. H.The production of jets associated to bottom quarks is measured for the first time in PbPb collisions at a center-of-mass energy of 2.76 TeV per nucleon pair. Jet spectra are reported in the transverse momentum (p(T)) range of 80-250 GeV/c, and within pseudorapidity |eta| < 2. The nuclear modification factor (RAA) calculated from these spectra shows a strong suppression in the b-jet yield in PbPb collisions relative to the yield observed in pp collisions at the same energy. The suppression persists to the largest values of p(T) studied, and is centrality dependent. The R-AA is about 0.4 in the most central events, similar to previous observations for inclusive jets. This implies that jet quenching does not have a strong dependence on parton mass and flavor in the jet p(T) range studied.