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Sökning: WFRF:(Torkamani Ali) > Naturvetenskap

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1.
  • Brownstein, Catherine A., et al. (författare)
  • An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
  • 2014
  • Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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2.
  • Torkamani-Azar, Mastaneh, et al. (författare)
  • Prediction of Response Time and Vigilance Score in a Sustained Attention Task from Pre-trial Phase Synchrony using Deep Neural Networks
  • 2019
  • Ingår i: 2019 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).
  • Konferensbidrag (refereegranskat)abstract
    • A real-time assessment of sustained attention requires a continuous performance measure ideally obtained objectively and without disrupting the ongoing behavioral patterns. In this work, we investigate whether the phasic functional connectivity patterns from short-and long-range attention networks can predict the tonic performance in a long Sustained Attention to Response Task (SART). Pre-trial phase synchrony indices (PSIs) from individual experiment blocks are used as features for assessment of the proposed average cumulative vigilance score (CVS) and hit response time (HRT). Deep neural networks (DNNs) with the mean-squared-error (MSE) loss function outperformed the ones with mean-absolute-error (MAE) in 4-fold cross-validations. PSI features from the 16-20 Hz beta sub-band obtained the lowest RMSE of 0.043 and highest correlation of 0.806 for predicting the average CVS, and the alpha oscillation PSIs resulted in an RMSE of 51.91 ms and a correlation of 0.903 for predicting the mean HRT. The proposed system can be used for monitoring performance of users susceptible to hypo-or hyper-vigilance and the subsequent system adaptation without implemented eye trackers. To the best of our knowledge, functional connectivity features in general and phase locking values in particular have not been used for regression models of vigilance variations with neural networks. 
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