PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients.
Reads0
Chats0
TLDR
In this paper, the authors applied principal component-analysis-based unsupervised feature extraction (PCAUFE) to the RNA expression profiles of 16 COVID-19 patients and 18 healthy control subjects.Abstract:
Coronavirus disease 2019 (COVID-19) is raging worldwide. This potentially fatal infectious disease is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, the complete mechanism of COVID-19 is not well understood. Therefore, we analyzed gene expression profiles of COVID-19 patients to identify disease-related genes through an innovative machine learning method that enables a data-driven strategy for gene selection from a data set with a small number of samples and many candidates. Principal-component-analysis-based unsupervised feature extraction (PCAUFE) was applied to the RNA expression profiles of 16 COVID-19 patients and 18 healthy control subjects. The results identified 123 genes as critical for COVID-19 progression from 60,683 candidate probes, including immune-related genes. The 123 genes were enriched in binding sites for transcription factors NFKB1 and RELA, which are involved in various biological phenomena such as immune response and cell survival: the primary mediator of canonical nuclear factor-kappa B (NF-κB) activity is the heterodimer RelA-p50. The genes were also enriched in histone modification H3K36me3, and they largely overlapped the target genes of NFKB1 and RELA. We found that the overlapping genes were downregulated in COVID-19 patients. These results suggest that canonical NF-κB activity was suppressed by H3K36me3 in COVID-19 patient blood.read more
Citations
More filters
Journal ArticleDOI
Review on the Evaluation and Development of Artificial Intelligence for COVID-19 Containment
TL;DR: In this paper , a comprehensive review of artificial intelligence with specific attention to machine learning, deep learning, image processing, object detection, image segmentation, and few-shot learning studies were utilized in several tasks related to the COVID-19 pandemic.
Journal ArticleDOI
Skin-Interfaced Wearable Sweat Sensors for Precision Medicine.
Jihong Min,Jiaobing Tu,Changhao Xu,Heather Lukas,Soyoung Shin,Yiran Yang,Samuel A Solomon,Daniel Mukasa,Wei Gao +8 more
TL;DR: Wearable sensors hold great potential in empowering personalized health monitoring, predictive analytics, and timely intervention toward personalized healthcare as discussed by the authors , and a comprehensive review of wearable sweat sensors and outlines state-of-theart technologies and research that strive to bridge these gaps.
Journal ArticleDOI
Application of principal component analysis on temporal evolution of COVID-19
TL;DR: The authors applied principal component analysis (PCA) to the daily time series of the COVID-19 death cases and confirmed cases for the top 25 countries from April of 2020 to February of 2021.
Journal ArticleDOI
A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers
Adriano Barbosa-Silva,Milena Magalhaes,Gilberto Ferreira da Silva,Fabricio Alves Barbosa da Silva,Flávia Raquel Gonçalves Carneiro,Nicolas Carels +5 more
TL;DR: This report focused on the up-regulated genes of crucial cell signaling pathways, which are key hallmarks of unregulated cell division and apoptosis and analyzed the genes of the WNT pathway and seven cross-linked pathways that may explain the differences in aggressiveness among cancer types.
Journal ArticleDOI
PCA-based sub-surface structure and defect analysis for germanium-on-nothing using nanoscale surface topography
TL;DR: In this paper , a principal component analysis (PCA)-based database is constructed to correlate surface images with empirically determined sub-surface structures, and from this database, the morphology of buried sub-sub-surface structure is determined only using surface topography.
References
More filters
Journal ArticleDOI
Targeting the NLRP3 inflammasome in inflammatory diseases
Matthew Mangan,Matthew Mangan,Edward James Olhava,William R. Roush,H. Martin Seidel,Gary D. Glick,Eicke Latz +6 more
TL;DR: Recent advances in the understanding of NLRP3 activation and regulation are reviewed, the evolving landscape ofNLRP3 modulators are highlighted and opportunities for pharmacologically targeting NL RP3 with novel small molecules are discussed.
Journal ArticleDOI
Systems biological assessment of immunity to mild versus severe COVID-19 infection in humans.
Prabhu S. Arunachalam,Florian Wimmers,Chris Ka Pun Mok,Ranawaka A.P.M. Perera,Madeleine K D Scott,Thomas Hagan,Natalia Sigal,Yupeng Feng,Laurel Bristow,Owen Tak-Yin Tsang,Dhananjay Wagh,John A. Coller,Kathryn L. Pellegrini,Dmitri Kazmin,Ghina Alaaeddine,Wai Shing Leung,Jacky Man Chun Chan,Thomas Shiu Hong Chik,Chris Yau Chung Choi,Christopher Huerta,Michele Paine McCullough,Huibin Lv,Evan J. Anderson,Srilatha Edupuganti,Amit A. Upadhyay,Steve E. Bosinger,Steve E. Bosinger,Holden T. Maecker,Purvesh Khatri,Nadine Rouphael,Malik Peiris,Bali Pulendran +31 more
TL;DR: In the peripheral blood mononuclear cells of COVID-19 patients, the authors observed reduced expression of human leukocyte antigen class DR (HLA-DR) and proinflammatory cytokines by myeloid cells as well as impaired mammalian target of rapamycin (mTOR) signaling and interferon-α (IFN-α) production by plasmacytoid dendritic cells.
Journal ArticleDOI
Presymptomatic Transmission of SARS-CoV-2 - Singapore, January 23-March 16, 2020.
Wycliffe E. Wei,Zongbin Li,Calvin J Chiew,Sarah E. Yong,Matthias Paul Han Sim Toh,Vernon J. Lee +5 more
TL;DR: Evidence of presymptomatic transmission of SARS-CoV-2 underscores the critical role social distancing, including avoidance of congregate settings, plays in controlling the COVID-19 pandemic.
Journal ArticleDOI
Imbalance of Regulatory and Cytotoxic SARS-CoV-2-Reactive CD4 + T Cells in COVID-19.
Benjamin J Meckiff,Ciro Ramírez-Suástegui,Vicente Fajardo,Serena J Chee,Anthony Kusnadi,Hayley Simon,Simon Eschweiler,Alba Grifoni,Emanuela Pelosi,Daniela Weiskopf,Alessandro Sette,Alessandro Sette,Ferhat Ay,Grégory Seumois,Christian H. Ottensmeier,Christian H. Ottensmeier,Christian H. Ottensmeier,Pandurangan Vijayanand,Pandurangan Vijayanand,Pandurangan Vijayanand +19 more
TL;DR: In hospitalized COVID-19 patients, a strong cytotoxic TFH response was observed early in the illness which correlated negatively with antibody levels to SARS-CoV-2 spike protein, and these analyses provide insights into the gene expression patterns of Sars-Cov-2-reactive CD4+ T cells in distinct disease severities.