PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collections
Permanent URI for this collectionhttps://hdl.handle.net/20.500.13091/5
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Browsing PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collections by Scopus Q "Q4"
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Conference Object Citation - Scopus: 4Deep Learning-Based Brain Hemorrhage Detection in Ct Reports(IOS Press BV, 2022) Bayrak, Gıyaseddin; Toprak, M. Şakir; Ganiz, Murat Can; Kodaz, Halife; Koç, UralRadiology reports can potentially be used to detect critical cases that need immediate attention from physicians. We focus on detecting Brain Hemorrhage from Computed Tomography (CT) reports. We train a deep learning classifier and observe the effect of using different pre-trained word representations along with domain-specific fine-tuning. We have several contributions. Firstly, we report the results of a large-scale classification model for brain hemorrhage detection from Turkish radiology reports. Second, we show the effect of fine-tuning pre-trained language models using domain-specific data on the performance. We conclude that deep learning models can be used for detecting brain Hemorrhage with reasonable accuracy and fine-tuning language models using domain-specific data to improve classification performance. © 2022 European Federation for Medical Informatics (EFMI) and IOS Press.Article Citation - Scopus: 2Direct or Dna Extraction-Free Amplification and Quantification of Foodborne Pathogens(2025) Williams M.R.; Telli A.E.; Telli N.; Islam D.T.; Hashsham S.A.The use of direct nucleic acid amplification of pathogens from food matrices has the potential to reduce time to results over DNA extraction-based approaches as well as traditional culture-based approaches. Here we describe protocols for assay design and experiments for direct amplification of foodborne pathogens in food sample matrices using loop-mediated isothermal amplification (LAMP) and polymerase chain reaction (PCR). The examples provided include the detection of Escherichia coli in milk samples and Salmonella in pork meat samples. This protocol includes relevant reagents and methods including obtaining target sequences, assay design, sample processing, and amplification. These methods, though used for specific example matrices, could be applied to many other foodborne pathogens and sample types. © 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.Article Electrochemical Detection of Nucleic Acids Using Three-Dimensional Graphene Screen-Printed Electrodes(2025) Islam D.T.; Mobasser S.; Kotaru S.; Telli A.E.; Telli N.; Cupples A.M.; Hashsham S.A.Electrochemical approaches, along with miniaturization of electrodes, are increasingly being employed to detect and quantify nucleic acid biomarkers. Miniaturization of the electrodes is achieved through the use of screen-printed electrodes (SPEs), which consist of one to a few dozen sets of electrodes, or by utilizing printed circuit boards. Electrode materials used in SPEs include glassy carbon (Chiang H-C, Wang Y, Zhang Q, Levon K, Biosensors (Basel) 9:2-11, 2019), platinum, carbon, and graphene (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). There are numerous modifications to the electrode surfaces as well (Cheng FF, He TT, Miao HT, Shi JJ, Jiang LP, Zhu JJ, ACS Appl Mater Interfaces 7:2979-2985, 2015). These approaches offer distinct advantages, primarily due to their demonstrated superior limit of detection without amplification. Using the SPEs and potentiostats, we can detect cells, proteins, DNA, and RNA concentrations in the nanomolar (nM) to attomolar (aM) range. The focus of this chapter is to describe the basic approach adopted for the use of SPEs for nucleic acid measurement. © 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
