Fully-Automated Deep Learning Tool for Sarcopenia Assessment on CT: L1 Versus L3 Vertebral Level Muscle Measurements for Opportunistic Prediction of Adverse Clinical Outcomes

Author(s):  
Perry J. Pickhardt ◽  
Alberto A. Perez ◽  
John W. Garrett ◽  
Peter M. Graffy ◽  
Ryan Zea ◽  
...  
Author(s):  
Humberto Farias ◽  
Mauricio Solar ◽  
Daniel Ortiz

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
John-William Sidhom ◽  
Alexander S. Baras

AbstractSARS-CoV-2 infection is characterized by a highly variable clinical course with patients experiencing asymptomatic infection all the way to requiring critical care support. This variation in clinical course has led physicians and scientists to study factors that may predispose certain individuals to more severe clinical presentations in hopes of either identifying these individuals early in their illness or improving their medical management. We sought to understand immunogenomic differences that may result in varied clinical outcomes through analysis of T-cell receptor sequencing (TCR-Seq) data in the open access ImmuneCODE database. We identified two cohorts within the database that had clinical outcomes data reflecting severity of illness and utilized DeepTCR, a multiple-instance deep learning repertoire classifier, to predict patients with severe SARS-CoV-2 infection from their repertoire sequencing. We demonstrate that patients with severe infection have repertoires with higher T-cell responses associated with SARS-CoV-2 epitopes and identify the epitopes that result in these responses. Our results provide evidence that the highly variable clinical course seen in SARS-CoV-2 infection is associated to certain antigen-specific responses.


IEEE Access ◽  
2020 ◽  
Vol 8 ◽  
pp. 201450-201457 ◽  
Author(s):  
Zeeshan Abbas ◽  
Hilal Tayara ◽  
Kil to Chong
Keyword(s):  

2020 ◽  
Vol 36 (10) ◽  
pp. 3248-3250
Author(s):  
Marta Lovino ◽  
Maria Serena Ciaburri ◽  
Gianvito Urgese ◽  
Santa Di Cataldo ◽  
Elisa Ficarra

Abstract Summary In the last decade, increasing attention has been paid to the study of gene fusions. However, the problem of determining whether a gene fusion is a cancer driver or just a passenger mutation is still an open issue. Here we present DEEPrior, an inherently flexible deep learning tool with two modes (Inference and Retraining). Inference mode predicts the probability of a gene fusion being involved in an oncogenic process, by directly exploiting the amino acid sequence of the fused protein. Retraining mode allows to obtain a custom prediction model including new data provided by the user. Availability and implementation Both DEEPrior and the protein fusions dataset are freely available from GitHub at (https://github.com/bioinformatics-polito/DEEPrior). The tool was designed to operate in Python 3.7, with minimal additional libraries. Supplementary information Supplementary data are available at Bioinformatics online.


2020 ◽  
Vol 135 ◽  
pp. 110921 ◽  
Author(s):  
Yi-Wei Wang ◽  
Lei Huang ◽  
Si-Wen Jiang ◽  
Kan Li ◽  
Jun Zou ◽  
...  

2020 ◽  
Vol 77 (1) ◽  
pp. 35 ◽  
Author(s):  
Michael P. Ewbank ◽  
Ronan Cummins ◽  
Valentin Tablan ◽  
Sarah Bateup ◽  
Ana Catarino ◽  
...  

Author(s):  
Rowland W. Pettit ◽  
Robert Fullem ◽  
Chao Cheng ◽  
Christopher I. Amos

AI is a broad concept, grouping initiatives that use a computer to perform tasks that would usually require a human to complete. AI methods are well suited to predict clinical outcomes. In practice, AI methods can be thought of as functions that learn the outcomes accompanying standardized input data to produce accurate outcome predictions when trialed with new data. Current methods for cleaning, creating, accessing, extracting, augmenting, and representing data for training AI clinical prediction models are well defined. The use of AI to predict clinical outcomes is a dynamic and rapidly evolving arena, with new methods and applications emerging. Extraction or accession of electronic health care records and combining these with patient genetic data is an area of present attention, with tremendous potential for future growth. Machine learning approaches, including decision tree methods of Random Forest and XGBoost, and deep learning techniques including deep multi-layer and recurrent neural networks, afford unique capabilities to accurately create predictions from high dimensional, multimodal data. Furthermore, AI methods are increasing our ability to accurately predict clinical outcomes that previously were difficult to model, including time-dependent and multi-class outcomes. Barriers to robust AI-based clinical outcome model deployment include changing AI product development interfaces, the specificity of regulation requirements, and limitations in ensuring model interpretability, generalizability, and adaptability over time.


Author(s):  
Jin Yang

The chapter explores the use of social media in educational settings and assesses its potential as a learning tool in facilitating deep learning and knowledge development. Guided by Vygotsky and Bakhtin's theory of dialogic learning, the chapter argues, by discussion, that social media may facilitate deep learning and knowledge development due to social media's convenient discursive space and heightened interactivity. Specifically, social media's discursive space may provide a platform that is egalitarian and democratic to all who have access to it. The breakdown of traditional communication barriers in this discursive space can be significant in engaging students in dialogic learning. Social media's heightened interactivity embodied in social, procedural, expository, explanatory, and cognitive dimensions may shorten psychological distances, lighten class-managing load, expedite learning materials' delivery, expand the learning space without time constraint, and encourage cross-pollination of ideas and viewpoints. The chapter discusses the profound opportunity that social media may have to enhance knowledge development.


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