Hadley Wickham1, Mara Averick1, Jennifer Bryan1, Winston Chang1, Lucy D’Agostino McGowan8, Romain François1, Garrett Grolemund1, Alex Hayes12, Lionel Henry1, Jim Hester1, Max Kuhn1, Thomas Lin Pedersen1, Evan Miller13, Stephan Milton Bache3, Kirill Müller2, Jeroen Ooms14, David Robinson5, Dana Paige Seidel10, Vitalie Spinu4, Kohske Takahashi9, Davis Vaughan1, Claus Wilke6, Kara Woo7, and Hiroaki Yutani11

/pdf/welcome-to-the-tidyverse-2gqeyze158.pdf

Welcome to the Tidyverse

fastai is a deep learning library which provides practitioners with high-level components that can quickly and easily provide state-of-the-art results in standard deep learning domains, and provides researchers with low-level components that can be mixed and matched to build new approaches. It aims to do both things without substantial compromises in ease of use, flexibility, or performance. This is possible thanks to a carefully layered architecture, which expresses common underlying patterns of many deep learning and data processing techniques in terms of decoupled abstractions. These abstractions can be expressed concisely and clearly by leveraging the dynamism of the underlying Python language and the flexibility of the PyTorch library. fastai includes: a new type dispatch system for Python along with a semantic type hierarchy for tensors; a GPU-optimized computer vision library which can be extended in pure Python; an optimizer which refactors out the common functionality of modern optimizers into two basic pieces, allowing optimization algorithms to be implemented in 4–5 lines of code; a novel 2-way callback system that can access any part of the data, model, or optimizer and change it at any point during training; a new data block API; and much more. We used this library to successfully create a complete deep learning course, which we were able to write more quickly than using previous approaches, and the code was more clear. The library is already in wide use in research, industry, and teaching.

Fastai: A Layered API for Deep Learning

Examples are discussed to show the differences among discriminant analysis, logistic regression, and multiple regression. Chapter 6, “Multivariate Analysis of Variance,” presents advantages of multivariate analysis of variance (MANOVA) over univariate analysis of variance (ANOVA), discusses assumptions of MANOVA, and assesses validations of MANOVA assumptions and model estimation. The authors also discuss post hoc tests of MANOVA and multivariate analysis of covariance. Chapter 7, “Conjoint Analysis,” explains what conjoint analysis does and how it is different from other multivariate techniques. Guidelines of selecting attributes, models, and methods of data collection are presented. Chapter 8, “Cluster Analysis,” studies objectives, roles, and limitations of cluster analysis. Two basic concepts: similarity and distance are discussed. The authors also discuss details of five most popular hierarchical algorithms (singlelinkage, complete-linkage, average-linkage, centroid method, Ward’s method) and three nonhierarchical algorithms (the sequential threshold method, the parallel threshold method, and the optimizing procedure). Profiles of clusters and guidelines for cluster validation are studied as well. Chapter 9, “Multidimensional Scaling and Correspondence Analysis,” introduces two interdependence techniques to display the relationships in the data. The book describes clearly and intuitively the differences between the two techniques and how these two techniques are performed. Chapters 10–12 cover topics in SEM. Chapter 10, “Structural Equation Modeling: An Introduction,” introduces SEM and related concepts such as exogenous, endogenous constructs, and so on, points out the differences between SEM and other multivariate techniques, overviews the decision process of SEM. Chapter 11, “Confirmatory Factor Analysis,” explains the differences between exploratory and confirmatory factor analysis, discusses how to construct, validate, and assess the goodness of fit of a measurement model in SEM by confirmatory factor analysis. Chapter 12, “Testing a Structural Model,” presents some methods of SEM in examining the relationships between latent constructs. The book is an excellent book for people in management and marketing. For the Technometrics audience, this book does not have much flavor of physical, chemical, and engineering sciences. For example, partial least squares, a very popular method in Chemometrics, is discussed but not as detailed as other techniques in the book. Furthermore, due to the amount of materials covered in the book, it might be inappropriate for someone who is new to multivariate analysis.

The Grammar of Graphics

The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) coronavirus is a major public health challenge. Rapid tests for detecting existing SARS-CoV-2 infections and assessing virus spread are critical. Approaches to detect viral RNA based on reverse transcription loop-mediated isothermal amplification (RT-LAMP) have potential as simple, scalable, and broadly applicable testing methods. Compared to RT quantitative polymerase chain reaction (RT-qPCR)-based methods, RT-LAMP assays require incubation at a constant temperature, thus eliminating the need for sophisticated instrumentation. Here, we tested a two-color RT-LAMP assay protocol for detecting SARS-CoV-2 viral RNA using a primer set specific for the N gene. We tested our RT-LAMP assay on surplus RNA samples isolated from 768 pharyngeal swab specimens collected from individuals being tested for COVID-19. We determined the sensitivity and specificity of the RT-LAMP assay for detecting SARS-CoV-2 viral RNA. Compared to an RT-qPCR assay using a sensitive primer set, we found that the RT-LAMP assay reliably detected SARS-CoV-2 RNA with an RT-qPCR cycle threshold (CT) number of up to 30, with a sensitivity of 97.5% and a specificity of 99.7%. We also developed a swab-to-RT-LAMP assay that did not require a prior RNA isolation step, which retained excellent specificity (99.5%) but showed lower sensitivity (86% for CT < 30) than the RT-LAMP assay. In addition, we developed a multiplexed sequencing protocol (LAMP-sequencing) as a diagnostic validation procedure to detect and record the outcome of RT-LAMP reactions.

/pdf/a-colorimetric-rt-lamp-assay-and-lamp-sequencing-for-h88h9zodh3.pdf

A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples.

Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia2. Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation. Analysis of bronchoalveolar lavage fluid samples from patients with SARS-CoV-2-induced respiratory failure suggests that SARS-CoV-2 infects alveolar macrophages to cause release of T cell chemoattractants, thereby inducing local inflammatory cytokine release and further T cell activation, ultimately resulting in a positive feedback loop that drives alveolar inflammation.

/pdf/circuits-between-infected-macrophages-and-t-cells-in-sars-3dd0qab0tq.pdf

Vitalie Spinu

Papers

Welcome to the Tidyverse

Make Dealing with Dates a Little Easier

Make Dealing with Dates a Little Easier [R package lubridate version 1.7.10]