Dataset Information

ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.

ABSTRACT: ADVICE (Automated Detection and Validation of Interaction by Co-Evolution) is a web tool for predicting and validating protein-protein interactions using the observed co-evolution between interacting proteins. Interacting proteins are known to share similar evolutionary histories since they undergo coordinated evolutionary changes to preserve interactions and functionalities. The web tool automates a commonly adopted methodology to quantify the similarities in proteins' evolutionary histories for postulating potential protein-protein interactions. ADVICE can also be used to validate experimental data against spurious protein interactions by identifying those that have few similarities in their evolutionary histories. The web tool accepts a list of protein sequences or sequence pairs as input and retrieves orthologous sequences to compute the similarities in the proteins' evolutionary histories. To facilitate hypothesis generation, detected co-evolved proteins can be visualized as a network at the website. ADVICE is available at http://advice.i2r.a-star.edu.sg.

SUBMITTER: Tan SH

PROVIDER: S-EPMC441609 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

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ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.

Tan Soon-Heng SH Zhang Zhuo Z Ng See-Kiong SK

Nucleic acids research 20040701 Web Server issue

ADVICE (Automated Detection and Validation of Interaction by Co-Evolution) is a web tool for predicting and validating protein-protein interactions using the observed co-evolution between interacting proteins. Interacting proteins are known to share similar evolutionary histories since they undergo coordinated evolutionary changes to preserve interactions and functionalities. The web tool automates a commonly adopted methodology to quantify the similarities in proteins' evolutionary histories fo ...[more]

PMID: 15215353

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Project description:Background: Respiratory muscle electromyography (EMG) can identify whether a muscle is activated, its activation amplitude, and timing. Most studies have focused on the activation amplitude, while differences in timing and duration of activity have been less investigated. Detection of the timing of respiratory muscle activity is typically based on the visual inspection of the EMG signal. This method is time-consuming and prone to subjective interpretation. Aims: Our main objective was to develop and validate a method to assess the respective timing of different respiratory muscle activity in an objective and semi-automated manner. Method: Seven healthy adults performed an inspiratory threshold loading (ITL) test at 50% of their maximum inspiratory pressure until task failure. Surface EMG recordings of the costal diaphragm/intercostals, scalene, parasternal intercostals, and sternocleidomastoid were obtained during ITL. We developed a semi-automated algorithm to detect the onset (EMG, onset) and offset (EMG, offset) of each muscle's EMG activity breath-by-breath with millisecond accuracy and compared its performance with manual evaluations from two independent assessors. For each muscle, the Intraclass Coefficient correlation (ICC) of the EMG, onset detection was determined between the two assessors and between the algorithm and each assessor. Additionally, we explored muscle differences in the EMG, onset, and EMG, offset timing, and duration of activity throughout the ITL. Results: More than 2000 EMG, onset s were analyzed for algorithm validation. ICCs ranged from 0.75-0.90 between assessor 1 and 2, 0.68-0.96 between assessor 1 and the algorithm, and 0.75-0.91 between assessor 2 and the algorithm (p < 0.01 for all). The lowest ICC was shown for the diaphragm/intercostal and the highest for the parasternal intercostal (0.68 and 0.96, respectively). During ITL, diaphragm/intercostal EMG, onset occurred later during the inspiratory cycle and its activity duration was shorter than the scalene, parasternal intercostal, and sternocleidomastoid (p < 0.01). EMG, offset occurred synchronously across all muscles (p ≥ 0.98). EMG, onset, and EMG, offset timing, and activity duration was consistent throughout the ITL for all muscles (p > 0.63). Conclusion: We developed an algorithm to detect EMG, onset of several respiratory muscles with millisecond accuracy that is time-efficient and validated against manual measures. Compared to the inherent bias of manual measures, the algorithm enhances objectivity and provides a strong standard for determining the respiratory muscle EMG, onset.

Project description:ImportanceInterpretation of chest radiographs is a challenging task prone to errors, requiring expert readers. An automated system that can accurately classify chest radiographs may help streamline the clinical workflow.ObjectivesTo develop a deep learning-based algorithm that can classify normal and abnormal results from chest radiographs with major thoracic diseases including pulmonary malignant neoplasm, active tuberculosis, pneumonia, and pneumothorax and to validate the algorithm's performance using independent data sets.Design, setting, and participantsThis diagnostic study developed a deep learning-based algorithm using single-center data collected between November 1, 2016, and January 31, 2017. The algorithm was externally validated with multicenter data collected between May 1 and July 31, 2018. A total of 54 221 chest radiographs with normal findings from 47 917 individuals (21 556 men and 26 361 women; mean [SD] age, 51 [16] years) and 35 613 chest radiographs with abnormal findings from 14 102 individuals (8373 men and 5729 women; mean [SD] age, 62 [15] years) were used to develop the algorithm. A total of 486 chest radiographs with normal results and 529 with abnormal results (1 from each participant; 628 men and 387 women; mean [SD] age, 53 [18] years) from 5 institutions were used for external validation. Fifteen physicians, including nonradiology physicians, board-certified radiologists, and thoracic radiologists, participated in observer performance testing. Data were analyzed in August 2018.ExposuresDeep learning-based algorithm.Main outcomes and measuresImage-wise classification performances measured by area under the receiver operating characteristic curve; lesion-wise localization performances measured by area under the alternative free-response receiver operating characteristic curve.ResultsThe algorithm demonstrated a median (range) area under the curve of 0.979 (0.973-1.000) for image-wise classification and 0.972 (0.923-0.985) for lesion-wise localization; the algorithm demonstrated significantly higher performance than all 3 physician groups in both image-wise classification (0.983 vs 0.814-0.932; all P < .005) and lesion-wise localization (0.985 vs 0.781-0.907; all P < .001). Significant improvements in both image-wise classification (0.814-0.932 to 0.904-0.958; all P < .005) and lesion-wise localization (0.781-0.907 to 0.873-0.938; all P < .001) were observed in all 3 physician groups with assistance of the algorithm.Conclusions and relevanceThe algorithm consistently outperformed physicians, including thoracic radiologists, in the discrimination of chest radiographs with major thoracic diseases, demonstrating its potential to improve the quality and efficiency of clinical practice.

Dataset Information

ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.

Publications

ADVICE: Automated Detection and Validation of Interaction by Co-Evolution.

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