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ATRPred: A machine learning based tool for clinical decision making of anti-TNF treatment in rheumatoid arthritis patients
Rheumatoid arthritis (RA) is a chronic autoimmune condition, characterised by joint pain, damage and disability, which can be addressed in a high proportion of patients by timely use of targeted biologic treatments. However, the patients, non-responsive to the treatments often suffer from refractoriness of the disease, leading to poor quality of life. Additionally, the biologic treatments are expensive. We obtained plasma samples from N = 144 participants with RA, who were about to commence anti-tumour necrosis factor (anti-TNF) therapy. These samples were sent to Olink Proteomics, Uppsala, Sweden, where proximity extension assays of 4 panels, containing 92 proteins each, were performed. A total of n = 89 samples of patients passed the quality control of anti-TNF treatment response data. The preliminary analysis of plasma protein expression values suggested that the RA population could be divided into two distinct molecular sub-groups (endotypes). However, these broad groups did not predict response to anti-TNF treatment, but were significantly different in terms of gender and their disease activity. We then labelled these patients as responders (n = 60) and non-responders (n = 29) based on the change in disease activity score (DAS) after 6 months of anti-TNF treatment and applied machine learning (ML) with a rigorous 5-fold nested cross-validation scheme to filter 17 proteins that were significantly associated with the treatment response. We have developed a ML based classifier ATRPred (anti-TNF treatment response predictor), which can predict anti-TNF treatment response in RA patients with 81% accuracy, 75% sensitivity and 86% specificity. ATRPred may aid clinicians to direct anti-TNF therapy to patients most likely to receive benefit, thus save cost as well as prevent non-responsive patients from refractory consequences. ATRPred is implemented in R.
Journal Article
100 great street photographs
Over the past few decades, the long tradition of street photography has been wholly transformed by the proliferation of digital cameras, the Internet, and smartphones. A new generation of photographers have embraced this modern technology to capture the world around us in a way that is un-staged, of-the- moment, and real. Exploring this rich seam of emergent and exciting street photography, the 100 photographs featured in this book-the majority of which are previously unpublished and taken in the last few years-are presented on double-page spreads along with commentary about the work and its creator. Curated by David Gibson, a street photographer and expert in the genre, this stunning book offers a truly global collection of images. Gibson's insightful introduction gives an insider's overview of street photography, illuminating its historic importance and its renaissance in the digital age.
Book
Enantioselective remote C–H activation directed by a chiral cation
Chiral cations have been used extensively as organocatalysts, but their application to rendering transition metal–catalyzed processes enantioselective remains rare. This is despite the success of the analogous charge-inverted strategy in which cationic metal complexes are paired with chiral anions. We report here a strategy to render a common bipyridine ligand anionic and pair its iridium complexes with a chiral cation derived from quinine. We have applied these ion-paired complexes to long-range asymmetric induction in the desymmetrization of the geminal diaryl motif, located on a carbon or phosphorus center, by enantioselective C–H borylation. In principle, numerous common classes of ligand could likewise be amenable to this approach.
Journal Article
Street photography : a history in 100 iconic images
This visually arresting book charts a global history of street photography, from its inception to today, through the most candid, immediate and provocative images captured by the genre's biggest names.
Book
Talk at the Brink
In October 1962, the fate of the world hung on the American response to the discovery of Soviet nuclear missile sites in Cuba. That response was informed by hours of discussions between John F. Kennedy and his top advisers. What those advisers did not know was that President Kennedy was secretly taping their talks, providing future scholars with a rare inside look at high-level political deliberation in a moment of crisis.Talk at the Brinkis the first book to examine these historic audio recordings from a sociological perspective. It reveals how conversational practices and dynamics shaped Kennedy's perception of the options available to him, thereby influencing his decisions and ultimately the outcome of the crisis.
David Gibson looks not just at the positions taken by Kennedy and his advisers but how those positions were articulated, challenged, revised, and sometimes ignored. He argues that Kennedy's decisions arose from the intersection of distant events unfolding in Cuba, Moscow, and the high seas with the immediate conversational minutia of turn-taking, storytelling, argument, and justification. In particular, Gibson shows how Kennedy's group told and retold particular stories again and again, sometimes settling upon a course of action only after the most frightening consequences were omitted or actively suppressed.
Talk at the Brinkpresents an image of Kennedy's response to the Cuban missile crisis that is sharply at odds with previous scholarship, and has important implications for our understanding of decision making, deliberation, social interaction, and historical contingency.
eBook
Changing world : cold data for a warming planet
The terrifying effects of a warming planet are impossible to ignore, but sometimes it's hard to pick through the facts and to understand exactly what's happening and how. This book of bright, bold infographics illuminates the realities of climate change in hard numbers, digestible data and vivid visualizations. How will rising sea levels affect us? What is the impact of meat on the planet? What industries create the most emissions? How do renewable energies compare to one another? What are the most effective things we as individuals can do to help the planet? Without sugar-coating or fear-mongering, this is a book that conveniently unpacks inconvenient truths in a way that is accessible to readers young and old.
Book
Hyping the Hypothetical: Talk and Temporality in US Supreme Court Oral Arguments
The US Supreme Court conducts much of its business through talk, including during oral arguments, where a central activity is the consideration of hypotheticals posed by justices. Using conversation analysis, I examine a key segment of the oral arguments for Citizens United v. FEC, one that arguably changed the course of campaign finance history. I identify the conversational devices employed to advance and contest one particular hypothetical, involving an imagined ban on books, subject to a speech-exchange system that differentially empowers justices to dictate both the terms of the discussion and the time afforded the advocate to respond to any particular question. The article offers the first disciplined qualitative analysis of interaction during oral arguments, illustrates the place of temporality in legal reasoning and argumentation, and makes several contributions to conversation analysis: it advances the study of institutional talk to a new legal setting, identifies some ways in which the machinery of talk can be harnessed for rhetorical effect, and demonstrates the analytical utility of prior knowledge of what a participant arrives to an encounter equipped to say.
Journal Article
One week to change the world : an oral history of the 1999 WTO protests
\"One week in late 1999, more than 50,000 people converged on Seattle. Their goal: to shut down the World Trade Organization conference and send a message that working-class people would not quietly accept the runaway economic globalization that threatened their livelihoods. Though their mission succeeded, it was not without blowback. Violent confrontations between police and protestors resulted in hundreds of arrests and millions of dollars in property damage. But the images of tear gas and smashed windows that flashed across TVs and newspapers were not an accurate representation of what actually happened that week.\"-- Provided by Amazon
BOOK
Optimal background matching camouflage
Background matching is the most familiar and widespread camouflage strategy: avoiding detection by having a similar colour and pattern to the background. Optimizing background matching is straightforward in a homogeneous environment, or when the habitat has very distinct sub-types and there is divergent selection leading to polymorphism. However, most backgrounds have continuous variation in colour and texture, so what is the best solution? Not all samples of the background are likely to be equally inconspicuous, and laboratory experiments on birds and humans support this view. Theory suggests that the most probable background sample (in the statistical sense), at the size of the prey, would, on average, be the most cryptic. We present an analysis, based on realistic assumptions about low-level vision, that estimates the distribution of background colours and visual textures, and predicts the best camouflage. We present data from a field experiment that tests and supports our predictions, using artificial moth-like targets under bird predation. Additionally, we present analogous data for humans, under tightly controlled viewing conditions, searching for targets on a computer screen. These data show that, in the absence of predator learning, the best single camouflage pattern for heterogeneous backgrounds is the most probable sample.
Journal Article