PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
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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 Tc-99m Erythromycin Lactobionate Inhalation Scintigraphy in Parenchymal Lung Diseases(Elsevier Science inc, 1999) Durak, H; Aktogu, S; Degirmenci, B; Sayit, E; Ertay, T; Dereli, SWe have investigated Technetium 99m erythromycin lactobionate (Tc 99m EL) clearance from the lungs after inhalation, in the presence of an alveolitis. Eighteen patients (6 sarcoidosis, 7 idiopathic fibrosis, and 5 miliary tuberculosis) were imaged after the patients inhaled 1,110 MBq of Tc 99m EL. Clearance half time for the first 45 min, for 24 h, and retention at 24 h correlated with percentage of lymphocytes in bronchoalveolar lavage fluid (BAL) (r =.729, r =.883, and r =.826, respectively). There was a positive correlation between peripheral penetration (PP) and forced expiratory volume in 1 s (FEV1) (r =.806) and forced vital capacity (FVC) (r =.781). Retention was more marked in sarcoidosis compared with tuberculosis (0.025 < p less than or equal to 0.05). Radioaerosol lung imaging may reflect the pulmonary function impairment in parenchymal lung diseases. Retention of Tc 99m EL may be related to number of BAL cells or presence of a lymphocytic alveolitis. Long residency time of Tc 99m EL in the lungs implies that erythromycin can also be administered by inhalation for therapeutic purposes. NUCL MED BIOL 26;6:695-698, 1999. (C) 1999 Elsevier Science Inc. All rights reserved.Article Citation - Scopus: 27Apoptotic Effects of Resveratrol, a Grape Polyphenol, Onimatinib-Sensitive and Resistant K562 Chronic Myeloid Leukemia Cells(2012) Can,G.; Cakir,Z.; Kartal,M.; Gunduz,U.; Baran,Y.Aim: To examine the antiproliferative and apoptotic effects of resveratrol on imatinib-sensitive and imatinib-resistant K562 chronic myeloid leukemia cells. Materials and Methods: Antiproliferative effects of resveratrol were determined by the 3-Bis[2-methoxy-4-nitro-5-sulphophenyl]-2H-tetrazolium-5- carboxanilide inner salt (XTT) cell proliferation assay. Apoptotic effects of resveratrol on sensitive K562 and resistant K562/IMA-3 cells were determined through changes in caspase-3 activity, loss of mitochondrial membrane potential (MMP), and apoptosis by annexin V-(FITC). Results: The concentrations of resveratrol that inhibited cell growth by 50% ( IC50) were calculated as 85 and 122 μM for K562 and K562/IMA-3 cells, respectively. There were 1.91-, 7.42- and 14.73-fold increases in loss of MMP in K562 cells treated with 10, 50, and 100 μM resveratrol, respectively. The same concentrations of resveratrol resulted in 2.21-, 3.30- and 7.65-fold increases in loss of MMP in K562/IMA-3 cells. Caspase-3 activity increased 1.04-, 2.77- and 4.8-fold in K562 and 1.02-, 1.41- and 3.46-fold in K562/IMA- 3 cells in response to the same concentrations of resveratrol, respectively. Apoptosis was induced in 58.7%-and 43.3% of K562 and K562/IMA-3 cells, respectively, in response to 100 μM resveratrol. Conclusion: Taken together these results may suggest potential use of resveratrol in CML, as well as in patients with primary and/or acquired resistance to imatinib.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: 139Granulocytic Sarcoma: a Systematic Review(e-Century Publishing Corporation, 2013) Yılmaz, Asu Fergün; Saydam, Güray; Şahin, Fahri; Baran, YusufGranulocytic sarcoma also called myeloid sarcoma is an extramedullary tumor of immature granulocytic cells. It is a rare entity, and mostly accompanied by acute myeloid leukemia. It is observed during the course of myeloproliferative disorders especially in chronic myeloid leukemia and myelodysplastic syndromes. In some rare circumstances, it is detected before clinical signs of leukemia or other diseases. When the bone marrow biopsy reveals no other hematologic malignancies, the granulocytic sarcoma is described as nonleukemic, primary or isolated. It is observed at any part of the body but the most common locations are soft tissues, bone, peritoneum and lymph nodes. Presenting signs or symptoms are mainly due to mass effect of the tumor and dysfunction of the organ, or the tissue that is affected. The diagnosis is performed by biopsy of the tumor. The tumor consists of immature granulocytic cells, which could be documented by H&E, immunohistochemistry, and flow cytometric methods. Fluorescence in-situ hybridization and molecular analysis are also performed. The optimal time and type of treatment is not clear. Surgery could be an option especially for tumors, which cause organ dysfunction and/or obstruction. Systemic treatment should be considered in all patients because without systemic treatment, relapses and progression to acute myeloid leukemia is the ultimate fate of the disease in many cases. Cytarabine-containing remission-induction chemotherapies have been the most applied therapeutic strategies, but it is not clear whether the consolidation therapies are required or not, and what kind of regimens are appropriate. The role of hematopoietic stem cell transplantation (HSC) as a consolidation regimen is not clear, but, after the relapse of the disease with or without bone marrow involvement, HSC transplantation should be considered in suitable patients after the reinduction performed by AML chemotherapies. There is only limited data about the role of radiotherapy in these patients. It could be used in patients with relapsed disease, organ dysfunction which should be quickly relieved and inadequate response to chemotherapy. The effect of radiotherapy on overall survival is not known. New prospective studies and clinical trials are needed to generate guidelines for the treatment of primary granulocytic sarcomas.Data Paper Citation - WoS: 3Citation - Scopus: 4Experimental data showing the thermal behavior of a flat roof with phase change material(Elsevier, 2015) Tokuç, Ayça; Başaran, Tahsin; Yesügey, Sadık CengizThe selection and configuration of building materials for optimal energy efficiency in a building require some assumptions and models for the thermal behavior of the utilized materials. Although the models for many materials can be considered acceptable for simulation and calculation purposes, the work for modeling the real time behavior of phase change materials is still under development. The data given in this article shows the thermal behavior of a flat roof element with a phase change material (PCM) layer. The temperature and energy given to and taken from the building element are reported. In addition the solid-liquid behavior of the PCM is tracked through images. The resulting thermal behavior of the phase change material is discussed and simulated in [1] A. Tokuç, T. Başaran, S.C. Yesügey, An experimental and numerical investigation on the use of phase change materials in building elements: the case of a flat roof in Istanbul, Build. Energy, vol. 102, 2015, pp. 91-104.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.