TR-Dizin İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12469/4467
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Browsing TR-Dizin İndeksli Yayınlar Koleksiyonu by Publication Index "PubMed"
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Other Antibiyotikli kemik çimentosunun 0 ve 15. günlerde mekanik dayanımı: Surgical Simplex P kemik çimentosu ve teikoplanin ile biyomekanik çalışma(Türk Ortopedi ve Travmatoloji Derneği, 2002) Göğüş, Abdullah; Akman, Şenol; Göksan, Bora S.; Bozdağ, ErgünAmaç: Mekanik dayanım açısından 40 gr belirli bir kemik çimentosuna katılabilecek belirli bir antibiyotiğin maksimum dozu "0. gün" ve antibiyotik salınımı sonrası "15. gün" için araştırıldı. Çalışma planı: 40 g Surgical Simplex P kemik çimentosuna 0, 400, 800,1200,1600, 2000, 3200 ve 4000 mg teikoplanin katılarak sekiz deney grubu oluşturuldu. Kompresyon ve dört nokta eğme mekanik dayanım testleri için üçüncü kuşak sement hazırlama ve uygulama koşullarında örnekler elde edildi. Her bir konsantrasyon için "0. gün" ve "15. gün" için 10'ar örnek oluşturuldu. Örneklerin mekanik dayanım testleri ASTM ve ISO standartlarına göre "0. gün" ve 37∘ C su banyosunda antibiyotik salınımı sonrası "15. gün"de yapıldı. Değişik antibiyotik konsantrasyonları 0 mg kontrol grubu ile, ayrıca aynı antibiyotik konsantrasyonlarının 0. gün ve 15. gün mekanik test sonuçları karşılaştırıldı. Sonuçlar: Kompresyon testlerinde "0. gün" grubu içinde anlamlı farklılık bulunmadı; "15. gün" grubunda ise 800 mg'den itibaren anlamlı dayanım azalması saptandı. Her iki grupta tüm konsantrasyonlarda elde edilen mekanik dayanım değerleri ASTM alt limiti olan 70 MPa'nın üzerindeydi. Dört nokta eğme testinde "0. gün" grubunda 1200 mg'den itibaren, "15. gün" grubunda ise 400 mg'den itibaren anlamlı dayanım azalması saptandı. "15. gün" grubundan 4000 mg ISO'nun alt limiti olan 50 MPa'nın altında kalırken, 3200 ve 2000 mg gruplarında 50 MPa'ya çok yakın sonuçlar elde edildi. Çıkarımlar: Deney sonuçları, üçüncü kuşak çimento hazırlama ve uygulama koşullarında, 40 gr Surgical Simplex P kemik çimentosuna güvenle katılabilecek en yüksek teikoplanin dozunun 1600 mg olduğunu gösterdi.Article Citation - WoS: 1Citation - Scopus: 1Covid-19 Modeling Based on Real Geographic and Population Data(Tubitak Scientific & Technological Research Council Turkey, 2023) Baysazan, Emir; Berker, A. Nihat; Mandal, Hasan; Kaygusuz, HakanBackground/aim: Intercity travel is one of the most important parameters for combating a pandemic. The ongoing COVID-19 pandemic has resulted in different computational studies involving intercity connections. In this study, the effects of intercity connections during an epidemic such as COVID-19 are evaluated using a new network model. Materials and methods: This model considers the actual geographic neighborhood and population density data. This new model is applied to actual Turkish data by means of provincial connections and populations. A Monte Carlo algorithm with a hybrid lattice model is applied to a lattice with 8802 data points. Results: Around Monte Carlo step 70, the number of active cases in Turkiye reaches up to 8.0% of the total population, which is followed by a second wave at around Monte Carlo step 100. The number of active cases vanishes around Monte Carlo step 160. Starting with Istanbul, the epidemic quickly expands between steps 60 and 100. Simulation results fit the actual mortality data in Turkiye. Conclusion: This model is quantitatively very efficient in modeling real-world COVID-19 epidemic data based on populations and geographical intercity connections, by means of estimating the number of deaths, disease spread, and epidemic termination.Article Citation - WoS: 5Citation - Scopus: 5The Effect of Weekend Curfews on Epidemics: a Monte Carlo Simulation(Tubitak Scientific & Technical Research Council Turkey, 2021) Kaygusuz, Hakan; Berker, A. NihatThe ongoing COVID-19 pandemic is being responded with various methods, applying vaccines, experimental treatment options, total lockdowns or partial curfews. Weekend curfews are among the methods for reducing the number of infected persons, and this method is practically applied in some countries such as Turkey. In this study, the effect of weekend curfews on reducing the spread of a contagious disease, such as COVID-19, is modeled using a Monte Carlo algorithm with a hybrid lattice model. In the simulation setup, a fictional country with three towns and 26,610 citizens were used as a model. Results indicate that applying a weekend curfew reduces the ratio of ill cases from 0.23 to 0.15. The results also show that applying personal precautions such as social distancing is important for reducing the number of cases and deaths. If the probability of disease spread can be reduced to 0.1, in that case, the death ratio can be minimized down to 0.Article Citation - WoS: 14Citation - Scopus: 14Exploration of the Binding Pocket of Histone Deacetylases: the Design of Potent and Isoform-Selective Inhibitors(Tübitak, 2017) Auba, Budullahi İbrahim; Yelekçi, KemalHistone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. “Classical” HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivityNote Citation - Scopus: 1Isolated Left Ventricular Diverticulum in an Adult: Dynamic Contrast-Enhanced Mri Findings(2005) Duran, Cihan; Kantarcı, Mecit; Karaman, Kutlay[Abstract Not Available]Article Citation - WoS: 2Citation - Scopus: 2Modelling of C-Terminal Tail of Human Sting and Its Interaction With Tank-Binding Kinase 1(Tubitak Scientific & Technical Research Council Turkey, 2022) Ata Ouda Al-Masri, Rahaf; Audu-Bida, Hajara; Essiz, SebnemStimulator of interferon genes (STING) plays a significant role in a cell's intracellular defense against pathogens or self DNA by inducing inflammation or apoptosis through a pathway known as cGAS-cGAMP-STING. STING uses one of its domains, the C-terminal tail (CTT) to recruit the members of the pathway. However, the structure of this domain has not been solved experimentally. STING conformation is open and more flexible when inactive. When STING gets activated by cGAMP, its conformation changes to a closed state covered by 4 beta-sheets over the binding site. This conformational change leads to its binding to Tank-binding kinase 1 (TBK1). TBK1 then phosphorylates STING aiding its entry to the cell's nucleus. In this study, we focused on the loop modeling of the CTT domain in both the active and inactive STING conformations. After the modeling step, the active and inactive STING structures were docked to one of the cGAS-cGAMP-STING pathway members, TBK1, to observe the differences of binding modes. CTT loop stayed higher in the active structure, while all the best-scored models, active or inactive, ended up around the same position with respect to TBK1. However, when the STING poses are compared with the cryo-EM image of the complex structure, the models in the active structure chain B displayed closer results to the complex structure.