Bioengineering / Biyomühendislik
Permanent URI for this collectionhttps://hdl.handle.net/11147/4529
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Article Blank Frame and Intensity Variation Distortion Detection and Restoration Pipeline for Phase-Contrast Microscopy Time-Lapse Images(Aves, 2024) Ucar, Mahmut; Iheme, Leonardo O.; Onal, Sevgi; Pesen-Okvur, Devrim; Yalcin-Ozuysal, Ozden; Toreyin, Behcet U.; Unay, DevrimIn this study, we propose a preprocessing pipeline for the detection and correction of distorted frames in time-lapse images obtained from phase-contrast microscopy. The proposed pipeline employs the average intensities of frames as a foundational element for the analysis. In order to evaluate the degree of correction required for intensity variance, a normalization technique is applied to the difference between the average intensity of a specific frame and the median average intensity of all frames within the study. Our restoration method increases the histogram similarity between the distorted and non-distorted frames, preserves trans-passing pixels in regions of interest, and mitigates the development of additional distortions. The efficacy of the proposed method was evaluated using 15 395 time-lapse image frames from 27 experiments using our own dataset and 830 time-lapse images from four different experiments obtained from the cell tracking challenge. The results of the validation demonstrate a high degree of numerical and visual accuracy of the proposed pipeline.Article Novel Coronavirus Disease: Overview and Recent Situation(İstanbul Üniversitesi-Cerrahpaşa Sağlık Bilimleri Fakültesi, 2020) Öksel, Ceyda; Bilgi, Eyüp; Başlar, Muhammet Semih; Çeşmeli, Selin; Tomak, Aysel; Hanoğlu, Berçem DilanIn the last days of 2019, local hospitals in Wuhan city (population of 11 million) reported several pneumonia cases with unknown etiology among people linked to the Huanan Seafood Wholesale Market. The virus, which is thought to be the source of the unknown viral infection, was first identified as a new type of coronavirus on January 7, 2020. With the first case reported in Thailand about a week later, the virus’s spread outside the borders of China became apparent. In an alarmingly short time, the new type of coronavirus disease (called COVID-19) started to gain worldwide recognition with the detection of various COVID-19 cases in multiple countries, including Japan, South Korea, USA, Singapore, France, Germany, Italy, Spain, and England. As a result of its rampant spread and fatal clinical manifestations, the coronavirus outbreak was declared a pandemic on March 11, 2020, by the World Health Organization (WHO). Turkey announced its first confirmed case of COVID-19 on the same date that WHO characterized COVID-19 as a pandemic. As of April 2020, the COVID-19 pandemic has traveled to 209 countries and territories around the world, infecting more than 3 million people. Since specific treatment and vaccine for COVID-19 are not yet available, early case detection and preventive healthcare practices (isolation, social distancing, and personal hygiene) play a critical role in combating the COVID-19 outbreak. This review is intended to build an overall picture of the COVID-19 outbreak based on the available scientific knowledge.Article Kinetic and Structural Characterization of Interaction Between Trypsin and Equisetum Arvense Extract(Türk Biyokimya Derneği, 2014) Uslu, Mehmet Emin; Bayraktar, Oğuz; Ceylan, ÇağatayObjective: In this study the inhibitory effect of E. arvense extract on trypsin activity and the effect of trypsin on E. arvense extract were studied. In addition the nature of the interaction between the extract and trypsin was investigated. Methods: The inhibitory effect ethanol extract of E. arvense on trypsin activity was determined using trypsin enzyme assay. The structural effects of the extract-trypsin interaction for the extract were analyzed by FTIR. Finally, the HPLC analyses were carried out to analyze the individual components of the extract and the supernatant and soluble precipitate phases. Results: E. arvense extract was found to decrease total percent activity of trypsin to 5% in 24 hour at 24 °C. FTIR analyses indicated that the interaction between trypsin and E. arvense extract caused changes in the structure and hydrogen bonding behavior and composition of the extract proteins. These interactions also caused the extract lipids to accumulate in the insoluble precipitate phase. Most of the phenolics remained in the supernatant phase enhancing the inactivation of trypsin. However, the precipitated compounds were shown to be of apolar in nature as shown in the HPLC chromatograms. Conclusion: The methods that were used showed that the high phenolic content of E. arvense was the main reason for the inhibition of trypsin enzyme activity by denaturing the enzyme.