Electrical - Electronic Engineering / Elektrik - Elektronik Mühendisliği
Permanent URI for this collectionhttps://hdl.handle.net/11147/11
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Article Citation - WoS: 6Citation - Scopus: 7Time-Resolved Eeg Signal Analysis for Motor Imagery Activity Recognition(Elsevier, 2023) Olcay, Bilal Orkan; Karaçalı, BilgeAccurately characterizing brain activity requires detailed feature analysis in the temporal, spatial, and spectral domains. While previous research has proposed various spatial and spectral feature extraction methods to distinguish between different cognitive tasks, temporal feature analysis for each separate brain region and frequency band has been largely overlooked. This study introduces two novel approaches for recognizing cognitive activity: temporal entropic profiling and time-aligned common spatio-spectral patterns analysis. These approaches capture and use discriminative short-lived signal segments for motor imagery activity recognition. In Approach-1, we evaluated nine different measures to determine timing parameters that showed altered behavior associated with maximal inter-activity differences, which we then used in a machine-learning framework. In Approach-2, we used the best-performing signal characteristic measures from Approach-1 to determine the optimum latency of each channel at each frequency band for a CSP-based activity recognition strategy. We evaluated both approaches on two online available motor imagery EEG datasets and achieved average recognition accuracy levels of 86%. We compared our methods with four established BCI methods. The performance results show that our approaches exceeded the benchmark methods' performances, with notable improvements in the proposed time-aligned common spatio-spectral patterns approach. This study demonstrates that motor imagery recognition performance is improved when a temporal analysis is adopted alongside spatio-spectral neural feature analysis and that timing parameters associated with the maximal entropic difference of EEG segments to the cognitive tasks varied between different brain regions and subjects. © 2023 Elsevier LtdArticle Citation - Scopus: 13The Prognostic Value of Tumor-Stroma Proportion in Laryngeal Squamous Cell Carcinoma(Federation of Turkish Pathology Societies, 2013) Ünlü, Mehtat; Çetinayak, Hasan Oğuz; Önder, Devrim; Ecevit, Cenk; Akman, Fadime; İkiz, Ahmet ömer; Ada, Emel; Karaçalı, Bilge; Sarıoğlu, SülenObjective: Tumor-stroma proportion of tumor has been presented as a prognostic factor in some types of adenocarcinomas, but there is no information about squamous cell carcinomas and laryngeal carcinomas. Material and Method: Five digital images of the tumor sections were obtained from 85 laryngeal carcinomas. Proportion of epithelial tumor component and stroma were measured by a software tool, allowing the pathologists to mark 205.6 μm2 blocks on areas as carcinomatous/stromal, by clicking at the image. Totally, 3.451 mm2 tumor areas have been marked to 16.785 small square blocks for each case. Results: Median follow up was 48 months (range 3-194). The mean tumor-stroma proportion was 48.63+18.18. There was no difference for tumor-stroma proportion when tumor location, grade, stage and perinodal invasion were considered. Although the following results were statistically insignificant, the mean tumor-stroma proportion was the lowest (37.46±12.49) for subglottic carcinomas, and it was 52.41±37.47, 50.86+19.84 and 44.56±16.91 for supraglottic, transglottic and glottic cases. The tumor-stroma proportion was lowest in cases with perinodal invasion and the highest in cases without lymph node metastasis (44.72±20.23, 47.77±17.37, 50.05±17.34). Tumor-stroma proportion was higher in the basaloid subtype compared with the classical squamous cell carcinoma (53.76±14.70 and 48.63±18.38 respectively). The overall and disease-free survival analysis did not reveal significance for tumor-stroma proportion (p=0.08, p=0.38). Only pathological stage was an independent factor for overall survival (p=0.008). Conclusion: This is the first series investigating tumor-stroma proportion as a prognostic marker in laryngeal carcinomas proposing a new method, but the findings do not support tumor-stroma proportion as a prognostic marker.Article Citation - WoS: 7Citation - Scopus: 9Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences(Public Library of Science, 2013) Doğan, Tunca; Karaçalı, BilgeIdentifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.