PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
Browse
17 results
Search Results
Now showing 1 - 10 of 17
Data Paper Citation - WoS: 2Citation - Scopus: 3Assessing Museums' Daylighting Adequacy Without Annual Measurement Campaign: Dataset of a Confrontation Between Measured and Simulated Illuminance Values Inside the Cetacean Gallery of the Charterhouse of Calci(Elsevier Ltd., 2020) Leccese, Francesco; Salvadori, Giacomo; Tambellini, Giuseppe; Kazanasmaz, Zehra TuğçeLighting Cultural Heritage is a complex task: light is necessary for the act of seeing, it can even enhance the visual experience [1,2], in addition proper lighting can significantly cut down energy consumptions [3], but on the same time it has detrimental effects on exhibits, especially daylight. In order to safeguard the exhibits from damages, national and international standards provide specific recommendations for exhibits' exposure, based on their photosensitivity category. These recommendations are the annual luminous exposure(LO) and the Maximum Illuminance Level (E-max), museums' curators have to verify that the display lighting conditions comply with the standards. Historical buildings are often converted into museums but, as their original purpose was different, the lighting conditions are often inadequate (e.g. too much uncontrolled daylight), therefore the lighting conditions' adequacy of the space should be assessed [4]. As the name suggest the annual luminous exposure requires an annual monitoring campaign, unfortunately it often happens that exhibits have been exposed incorrectly for prolonged periods, and therefore it is very important to evaluate the need of a fast intervention. In this casuistry a prolonged measurement campaign is not acceptable. Simulations can help running a great number of analysis while reducing the length and expenses of a measurements campaign, however their previsions must be validated. This paper provides the data acquired through measurements and simulations inside the Cetacean Gallery of the Monumental Charterhouse of Calci, near Pisa (Tuscany Region, Italy). The data comprehends horizontal and vertical illuminance measurements, recorded on December the 6th, and simulations run in Grasshopper with the plugins Honeybee+ and Ladybug. The data are related to the research article entitled "Application of climate-based daylight simulation to assess lighting conditions of space and artworks in historical buildings: the case study of Cetacean Gallery of the Monumental Charterhouse of Calci", published on the Journal of Cultural Heritage [5]. (C) 2020 The Author(s). Published by Elsevier Inc.Article Citation - WoS: 14Citation - Scopus: 18Separating Normosmic and Anosmic Patients Based on Entropy Evaluation of Olfactory Event-Related Potentials(Elsevier Ltd., 2019) Güdücü, Çağdaş; Olcay, Bilal Orkan; Schaefer, L.; Aziz, M.; Schriever, V. A.; Özgören, Murat; Hummel, T.Objective: Methods based on electroencephalography (EEG) are used to evaluate brain responses to odors which is challenging due to the relatively low signal-to-noise ratio. This is especially difficult in patients with olfactory loss. In the present study, we aim to establish a method to separate functionally anosmic and normosmic individuals by means of recordings of olfactory event-related potentials (OERP) using an automated tool. Therefore, Shannon entropy was adopted to examine the complexity of the averaged electrophysiological responses. Methods: A total of 102 participants received 60 rose-like odorous stimuli at an inter-stimulus interval of 10 s. Olfactory-related brain activity was investigated within three time-windows of equal length; pre-, during-, and post-stimulus. Results: Based on entropy analysis, patients were correctly diagnosed for anosmia with a 75% success rate. Conclusion: This novel approach can be expected to help clinicians to identify patients with anosmia or patients with early symptoms of neurodegenerative disorders. Significance: There is no automated diagnostic tool for anosmic and normosmic patients using OERP. However, detectability of OERP in patients with functional anosmia has been reported to be in the range of 50%.Article Citation - WoS: 11Citation - Scopus: 12Characterization of the Self-Assembly and Size Dependent Structural Properties of Dietary Mixed Micelles by Molecular Dynamics Simulations(Elsevier Ltd., 2019) Tuncer, Esra; Bayramoğlu, BesteThe bile salts and phospholipids are secreted by the gallbladder to form dietary mixed micelles in which the solvation of poorly absorbed lipophilic drugs and nutraceuticals take place. A comprehensive understanding of the micellization and structure of the mixed micelles are crucial to design effective delivery systems for such substances. In this study, the evolution of the dietary mixed micelle formation under physiologically relevant concentrations and the dependence of structural properties on micelle size were investigated through coarse grained molecular dynamics simulations. The MARTINI force field was used to model cholate and POPC as the representative bile salt and phospholipid, respectively. The micellization behavior was similar under both fasted and fed state concentrations. Total lipids concentration and the micelle size did not affect the internal structure of the micelles. All the micelles were slightly ellipsoidal in shape independent of their size. The extent of deviation from spherical geometry was found to depend on the micellar POPC/cholate ratio. We also found that the surface and core packing density of the micelles increased with micelle size. The former resulted in more perpendicular alignments of cholates with respect to the surface, while the latter resulted in an improved alignment of POPC tails with the radial direction and more uniform core density.Article Citation - WoS: 13Citation - Scopus: 13Cycloartane-Type Sapogenol Derivatives Inhibit Nf?b Activation as Chemopreventive Strategy for Inflammation-Induced Prostate Carcinogenesis(Elsevier Ltd., 2018) Debeleç Bütüner, Bilge; Öztürk, Mert Burak; Tağ, Özgür; Akgün, İsmail Hakkı; Yetik Anacak, Günay; Bedir, Erdal; Korkmaz, Kemal SamiChronic inflammation is associated to 25% of cancer cases according to epidemiological data. Therefore, inhibition of inflammation-induced carcinogenesis can be an efficient therapeutic approach for cancer chemoprevention in drug development studies. It is also determined that anti-inflammatory drugs reduce cancer incidence. Cell culture-based in vitro screening methods are used as a fast and efficient method to investigate the biological activities of the biomolecules. In addition, saponins are molecules that are isolated from natural sources and are known to have potential for tumor inhibition. Studies on the preparation of analogues of cycloartane-type sapogenols (9,19-cyclolanostanes) have so far been limited. Therefore we have decided to direct our efforts toward the exploration of new anti-tumor agents prepared from cycloastragenol and its production artifact astragenol. The semi-synthetic derivatives were prepared mainly by oxidation, condensation, alkylation, acylation, and elimination reactions. After preliminary studies, five sapogenol analogues, two of which were new compounds (2 and 3), were selected and screened for their inhibitory activity on cell viability and NFκB signaling pathway activity in LNCaP prostate cancer cells. We found that the astragenol derivatives 1 and 2 as well as cycloastragenol derivatives 3, 4, and 5 exhibited strong inhibitory activity on NFκB signaling leading the repression of NFκB transcriptional activation and suppressed cell proliferation. The results suggested that these molecules might have significant potential for chemoprevention of prostate carcinogenesis induced by inflammatory NFκB signaling pathway.Article Citation - WoS: 8Citation - Scopus: 7Secreted Wnt Antagonists in Leukemia: a Road Yet To Be Paved(Elsevier Ltd., 2018) Pehlivan, Melek; Çalışkan, Ceyda; Yüce, Zeynep; Sercan, Hakkı OgünWnt signaling has been a topic of research for many years for its diverse and fundamental functions in physiological (such as embryogenesis, organogenesis, proliferation, tissue repair and cellular differentiation) and pathological (carcinogenesis, congenital/genetic diseases, and tissue degeneration) processes. Wnt signaling pathway aberrations are associated with both solid tumors and hematological malignancies. Unregulated Wnt signaling observed in malignancies may be due to a wide spectrum of abnormalities, from mutations in the genes of key players to epigenetic modifications of Wnt antagonists. Of these, Wnt antagonists are gaining significant attention for their potential of being targets for treatment and inhibition of Wnt signaling. In this review, we discuss and summarize the significance of Wnt signaling antagonists in the pathogenesis and treatment of hematological malignancies.Data Paper Citation - WoS: 3Citation - Scopus: 3Small Rna Data Set That Includes Trna-Derived Fragments From Jurkat Cells Treated With Camptothecin(Elsevier Ltd., 2018) Coşacak, Mehmet İlyas; Erdoğan, İpek; Nalbant, Ayten; Akgül, BünyaminIn this article, we report a small RNA data set obtained from human T cell acute leukemia Jurkat cells, which were treated with the universal apoptotic agent camptothecin. Based on the Annexin-V labeling pattern, we sorted two Jurkat subpopulations in treated cells: one that is sensitive to the drug and the other being relatively more resistant. We report new original data that include the frequency of tRNA-derived fragments (tRF) in drug-sensitive and resistant cells. We also present partially analyzed data to show the origin of reads on tRNAs as well as the borders of the fragments. We believe that this data can benefit the science community working in the field of tRF and/or apoptosis.Article Citation - WoS: 11Citation - Scopus: 11Secondary Metabolites From Astragalus Karjaginii Boriss and the Evaluation of Their Effects on Cytokine Release and Hemolysis(Elsevier Ltd., 2017) Aslanipour, Behnaz; Gülcemal, Derya; Nalbantsoy, Ayşe; Yusufoğlu, Hasan; Bedir, ErdalA new cycloartane sapogenol and a new cycloartane xyloside were isolated from Astragalus karjaginii BORISS along with thirteen known compounds. The structures of the new compounds were established as 3-oxo-6α,16β,24(S),25-tetrahydroxycycloartane (1) and 6-O-β-D-xylopyranosyl-3β,6α,16β,24(S),25-pentahydroxycycloartane (2) by 1D- and 2D-NMR experiments as well as ESIMS and HRMS analyses. The presence of the keto function at position 3 was reported for the first time for cyclocanthogenol sapogenin of Astragalus genus. In vitro immunomodulatory effects of the new compounds (1 and 2) along with the n-BuOH and MeOH extracts of A. karjaginii at two different doses (3 and 6 μg) were tested on human whole blood for in vitro cytokine release (IL-2, IL-17A and IFN-γ) and hemolytic activities. The results confirmed that compound 2, a monodesmosidic saponin, had the strongest effect on the induction of both IL-2 (6 μg, 6345.41 ± 0.12 pg/mL (× 5), P < 0.001) and a slight effect upon IL-17A (3 μg, 5217.85 ± 0.72 pg/mL, P < 0.05) cytokines compared to the other test compounds and positive controls (AST VII: Astragaloside VII; and QS-21: Quillaja saponin 21). All tested extracts and molecules also induced release of IFN-γ remarkably ranging between 5031.95 ± 0.05 pg/mL, P < 0.001 for MeOH extract (6 μg) and 5877.08 ± 0.06 pg/mL, P < 0.001 for compound 1 (6 μg) compared to QS-21 (6 μg, 5924.87 ± 0.1 pg/mL, P < 0.001). Administration of AST VII and other test compounds did not cause any hemolytic activity, whereas QS-21 resulted a noteworthy hemolysis.Article Citation - WoS: 5Citation - Scopus: 7High-Speed Dynamic Atomic Force Microscopy by Using a Q-Controlled Cantilever Eigenmode as an Actuator(Elsevier Ltd., 2015) Balantekin, MüjdatWe present a high-speed operating method with feedback to be used in dynamic atomic force microscope (AFM) systems. In this method we do not use an actuator that has to be employed to move the tip or the sample as in conventional AFM setups. Instead, we utilize a Q-controlled eigenmode of an AFM cantilever to perform the function of the actuator. Simulations show that even with an ordinary tapping-mode cantilever, imaging speed can be increased by about 2 orders of magnitude compared to conventional dynamic AFM imaging.Article Citation - WoS: 14Citation - Scopus: 15Neuraminidase-1 Contributes Significantly To the Degradation of Neuronal B-Series Gangliosides but Not To the Bypass of the Catabolic Block in Tay-Sachs Mouse Models(Elsevier Ltd., 2015) Timur, Zehra Kevser; Akyıldız Demir, Seçil; Marsching, C.; Sandhoff, R.; Seyrantepe, VolkanTaySachs disease is a severe lysosomal storage disorder caused bymutations in the HEXA gene coding for? subunit of lysosomal β-Hexosaminidase A enzyme, which converts GM2 to GM3 ganglioside. HexA mice, depleted of the β-Hexosaminidase A iso-enzyme, remain asymptomatic up to 1 year of age because of a metabolic bypass by neuraminidase(s). These enzymes remove a sialic acid residue converting GM2 to GA2,which is further degraded by the still intact β-Hexosaminidase B iso-enzyme into lactosylceramide. A previously identified ganglioside metabolizing neuraminidase, Neu4, is abundantly expressed in the mouse brain and has activity against gangliosides like GM2 in vitro. Neu4 mice showed increased GD1a and decreased GM1 ganglioside in the brain suggesting the importance of the Neu4 in ganglioside catabolism. Mice with targeted disruption of both HexA and Neu4 genes showed accumulating GM2 ganglioside and epileptic seizures with 40% penetrance, indicating that the neuraminidase Neu4 is a modulatory gene, but may not be the only neuraminidase contributing to the metabolic bypass in HexA mice. Therefore, we elucidated the biological role of neuraminidase-1 in ganglioside degradation in mouse. Analysis of HexANeu1 and HexANeu4Neu1 mice models showed significant contribution of neuraminidase-1 on B-series ganglioside degradation in the brain. Therefore, we speculate that other neuraminidase/neuraminidases such as Neu2 and/or Neu3 might be also involved in the ganglioside degradation pathway in HexA mice.Article Citation - WoS: 11Citation - Scopus: 9Quantification of Staphylococcus Aureus in White Cheese by the Improved Dna Extraction Strategy Combined With Taqman and Lna Probe-Based Qpcr(Elsevier Ltd., 2014) Kadiroğlu, Pınar; Korel, Figen; Ceylan, ÇağatayFour different bacterial DNA extraction strategies and two different qPCR probe chemistries were studied for detection of Stapylococcus aureus from white cheeses. Method employing trypsin treatment followed by a commercial kit application and TaqMan probe-based qPCR was the most sensitive one detecting higher counts than standards in naturally contaminated samples.