An antibody-escape calculator for mutations to the SARS-CoV-2 receptor-binding domain

A key goal of SARS-CoV-2 surveillance is to rapidly identify viral variants with mutations that reduce neutralization by polyclonal antibodies elicited by vaccination or infection. Unfortunately, direct experimental characterization of new viral variants lags their sequence-based identification. Here we help address this challenge by aggregating deep mutational scanning data into an "escape calculator" that estimates the antigenic effects of arbitrary combinations of mutations to the virus's spike receptor-binding domain (RBD). The calculator can be used to intuitively visualize how mutations impact polyclonal antibody recognition, and score the expected antigenic effect of combinations of mutations. These scores correlate with neutralization assays performed on SARS-CoV-2 variants, and emphasize the ominous antigenic properties of the recently described Omicron variant. An interactive version of the calculator is at https://jbloomlab.github.io/SARS2_RBD_Ab_escape_maps/escape-calc/, and we provide a Python module for batch processing.

Interaction is Necessary for Distributed Learning with Privacy or Communication Constraints

Local differential privacy (LDP) is a model where users send privatized data to an untrusted central server whose goal it to solve some data analysis task. In the non-interactive version of this model the protocol consists of a single round in which a server sends requests to all users then receives their responses. This version is deployed in industry due to its practical advantages and has attracted significant research interest. Our main result is an exponential lower bound on the number of samples necessary to solve the standard task of learning a large-margin linear separator in the non-interactive LDP model. Via a standard reduction this lower bound implies an exponential lower bound for stochastic convex optimization and specifically, for learning linear models with a convex, Lipschitz and smooth loss. These results answer the questions posed by Smith, Thakurta, and Upadhyay (IEEE Symposium on Security and Privacy 2017) and Daniely and Feldman (NeurIPS 2019). Our lower bound relies on a new technique for constructing pairs of distributions with nearly matching moments but whose supports can be nearly separated by a large margin hyperplane. These lower bounds also hold in the model where communication from each user is limited and follow from a lower bound on learning using non-adaptive statistical queries.

Mastering the content and aspect terminology of the French language on the basis of co-working with students of materials for distant content

Introduction. The relevance of the research is determined by the demand for the development of new content of training programs, including through the creation of educational and control materials based on them together with students in the process of mastering theoretical grammar. The purpose of the article is to optimize the process of teaching theoretical language disciplines using the capabilities of electronic resources, as well as to develop students' skills to create control and measurement materials, including those based on electronic constructors/products. Materials and methods. The study involved 45 students of the French-English department of the Faculty of Foreign Languages of the Bryansk State University in 2015/2016/2017. The dynamics of learning outcomes in the course of step-by-step training was established both on the basis of a subjective assessment of students ' responses by the teacher (I and II training models), and on the basis of electronic reports and training program schedules reflecting the assessments of subjects in different ranges (III training model). The results of the study. It is established that the interactive version of the study of thematic material in the electronic learning system (ESO) in the organizational mode "student – task co-developer" (model III-the creation of interactive tasks by students based on lecture material) is characterized by a fairly high level of indicators: 100% coverage of subjects and almost the same indicator of independence in the process of completing tasks. In accordance with the electronic reporting provided by the graphic material, 95-100% of the subjects have good and excellent indicators (4.5/5 – on a five-point scale; 8.5/10-on a ten-point scale). Discussion and conclusion. The peculiarities of mastering theoretical grammar on the basis of interactive resources of training programs can be taken into account by other researchers in the field of methods of teaching theoretical disciplines. In the future, the study of this topic can be continued in collaboration with developers of electronic products for philologists.

Data visualisation using R, for researchers who don't use R

In addition to benefiting reproducibility and transparency, one of the advantages of using R is that researchers have a much larger range of fully customisable data visualisations options than are typically available in point and-click software, due to the open-source nature of R. These visualisation options not only look attractive, but can increase transparency about the distribution of the underlying data rather than relying on commonly used visualisations of aggregations such as bar charts of means. In this tutorial, we provide a practical introduction to data visualisation using R, specifically aimed at researchers who have little to no prior experience of usingR. First we detail the rationale for using R for data visualisation and introduce the “grammar of graphics” that underlies data visualisation using the ggplot package. The tutorial then walks the reader through how to replicate plots that are commonly available in point-and-click software such as histograms and boxplots, as well as showing how the code for these “basic” plots can be easily extended to less commonly available options such as violin-boxplots. The dataset and code used in this tutorial as well as an interactive version with activity solutions, additional resources and advanced plotting options is available at https://osf.io/bj83f/. This is a pre-submission manuscript and tutorial and has not yet undergone peer review. We welcome user feedback which you can provide using this form: https://forms.office.com/r/ba1UvyykYR. Please note that this tutorial is likely to undergo changes before it is accepted for publication and we would encourage you to check for updates before citing.

Ludwig van Beethoven’s “Fidelio”: Participation of the Public in Graham Vick and Tobias Kratzer’s Productions

Relevance of the study. Versions of the only opus magnum of the German genius in modern filmmaking practice are associated with various sources: from myth, historical documentary to modern political thriller. The performances of Fidelio by the German Tobias Kratzer on the stage of the London Royal Opera and the British Graham Vick with the Birmingham Opera Company directed the vector of directorial innovations into the mainstream of the actual problem in the field of art — communication. Both directors brought the image of an opera audience onto the stage.Main objective of the study is to analyze the aforementioned opera productions from the point of view of the public participation, which presupposes the use of the stage experience of performance, documentary and Immersion Theater.Research methodology. Expending the experience of scientists who have developed the classification of the concepts of the public and the audience, the structural vector of these concepts in the form of a link in the recipient-performer-creator chain is revealed. In the versions from Vick and Kratzer, the public and the audience not only actively influence the artistic processes, but also become their participants. A watershed between the concepts of the public and the audience, important for comparing these artifacts, is revealed which required, provided the reason to use a comparative research methodology.The results of directorial artifacts. Vick interprets “Fidelio” as a performer-director. His fourth interactive version of the opera features Birmingham residents. Kratzer accentuates the historical traditionally theatrical barriers between performers and spectators and first gives the opportunity to relive the events of the costumed “Fidelio”, designed for a suggestive public reaction, which gives impetus to an unexpected evolution. At first, the audience, passively reflecting the events, acquires a certain breakthrough in consciousness in the finale and begins to act on a par with the protagonists of the opera. For Kratzer and Vick, the argument for including the image of the audience in the production was the historical fact (the creation of an opera during the French Revolution) and the coverage of the connections between Beethoven’s opera narrative and the social realities of modern society. Vick associated “Fidelio” with modern outbursts of totalitarianism. For Kratzer, the key idea is ideal love, inherent in Beethoven’s ideas of humanism, loyalty and moral duty. Vick’s Theater connects the type of audience as a spontaneous community. Kratzer focuses on the centuries-old culture of opera lovers united by common interests. The approbation of various forms of integration of performance and opera shows how important the artistic, social, didactic and psychological results of participation are. The public develops, evolves and becomes a professional audience.

Responsible Gambling: Who is Responsible?

A Critical Gambling Studies blog entry on responsible gambling. The interactive version of this blog is available at: https://criticalgamblingstudies.blogspot.com/2020/09/responsible-gambling-who-is-responsible.html

Gambling and Social Theory - Part 1

A Critical Gambling Studies blog entry on gambling and social theory. The interactive version of this blog is available at: https://criticalgamblingstudies.blogspot.com/2020/06/gambling-and-social-theory-part-1.html

Stars from the GTSh10 catalogue in the Shajn's Plan

We examine objects from the GTSh10 catalogue among the studied stars as a part of implementing the Plan of Academician G.A. Shajn in order to replenish the database of photometric and spectral observations of red dwarfs. We consider a question concerning the cross-identification of data from the GTSh10 interactive version and the Shajn's Plan catalogues, as well as an access to the archive of photographic observations. The article is illustrated with examples of working with the obtained list by means of the Virtual Observatory in order to analyze the state of objects and/or to refine their photometric and spectral characteristics in the middle of the past century.

Upgrade of the “ActiveTectonics” on-line database of Pliocene-Quaternary fautls in the Baikal Region and adjacent areas

<p>Studying and mapping of faults in the Earth’s crust is one of the priority objectives in structural geology and tectonophysics. Generally, faults are associated with mineral deposits, thermal springs, and earthquakes, and fault zones are areas of the most dangerous geological processes and various geophysical anomalies. In this regard, databases of faults are highly demanded by both science and practical applications. In this work, we present an on-line geospatial database containing faults, which were active in the Pliocene‐Quaternary within the territory between 96–124°E to 49–58°N. The locations of the faults were mapped with using MapInfo GIS based on the extensive analysis of cartographic, published and own structural materials. The data about each fault were input via ActiveTectonics Information System developed by us. The interactive version of the database put out in the open (http://www.activetectonics.ru/) in Russian and English and anyone may get available information about a fault by a click. The geoportal is constantly developing and constitutes a base for the creation of an automated system for modeling geological hazards (seismic soil liquefaction, secondary rupturing, subsidence and slope processes) in the Baikal region.</p><p>Currently, as part of the modernization of the ActiveTectonics geographic information product, we are developing models and schemes of data and metadata to create a detailed geospatial database of seismogenic ruptures of the Baikal region. A modern user-friendly interface is being developed to automate the data collection process.</p><p>The creation of such a publicly accessible catalog of seismogenic ruptures will be useful for applied and fundamental research.</p><p>The reported study was partly funded by RFBR and the Government of the Irkutsk Region, project number 20-45-385001.</p>