Millions of new viral sequences have been identified from metagenomes, but the quality and completeness of these sequences vary considerably. Here we present CheckV, an automated pipeline for identifying closed viral genomes, estimating the completeness of genome fragments and removing flanking host regions from integrated proviruses. CheckV estimates completeness by comparing sequences with a large database of complete viral genomes, including 76,262 identified from a systematic search of publicly available metagenomes, metatranscriptomes and metaviromes. After validation on mock datasets and comparison to existing methods, we applied CheckV to large and diverse collections of metagenome-assembled viral sequences, including IMG/VR and the Global Ocean Virome. This revealed 44,652 high-quality viral genomes (that is, >90% complete), although the vast majority of sequences were small fragments, which highlights the challenge of assembling viral genomes from short-read metagenomes. Additionally, we found that removal of host contamination substantially improved the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions. The quality of viral genomes assembled from metagenome data is assessed by CheckV.

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CheckV assesses the quality and completeness of metagenome-assembled viral genomes.

Precise nanomedicine has been extensively explored for efficient cancer imaging and targeted cancer therapy, as evidenced by a few breakthroughs in their preclinical and clinical explorations. Here, we demonstrate the recent advances of intelligent cancer nanomedicine, and discuss the comprehensive understanding of their structure-function relationship for smart and efficient cancer nanomedicine including various imaging and therapeutic applications, as well as nanotoxicity. In particular, a few emerging strategies that have advanced cancer nanomedicine are also highlighted as the emerging focus such as tumor imprisonment, supramolecular chemotherapy, and DNA nanorobot. The challenge and outlook of some scientific and engineering issues are also discussed in future development. We wish to highlight these new progress of precise nanomedicine with the ultimate goal to inspire more successful explorations of intelligent nanoparticles for future clinical translations.

Precise nanomedicine for intelligent therapy of cancer

SARS-CoV-2 is responsible for the coronavirus disease 2019 (COVID-19) pandemic, infecting millions of people and causing hundreds of thousands of deaths. The Spike glycoproteins of SARS-CoV-2 mediate viral entry and are the main targets for neutralizing antibodies. Understanding the antibody response directed against SARS-CoV-2 is crucial for the development of vaccine, therapeutic, and public health interventions. Here, we perform a cross-sectional study on 106 SARS-CoV-2-infected individuals to evaluate humoral responses against SARS-CoV-2 Spike. Most infected individuals elicit anti-Spike antibodies within 2 weeks of the onset of symptoms. The levels of receptor binding domain (RBD)-specific immunoglobulin G (IgG) persist over time, and the levels of anti-RBD IgM decrease after symptom resolution. Although most individuals develop neutralizing antibodies within 2 weeks of infection, the level of neutralizing activity is significantly decreased over time. Our results highlight the importance of studying the persistence of neutralizing activity upon natural SARS-CoV-2 infection.

Cross-Sectional Evaluation of Humoral Responses against SARS-CoV-2 Spike.

A single dose of the SARS-CoV-2 vaccine BNT162b2 elicits Fc-mediated antibody effector functions and T cell responses.

With the recent approval of highly effective COVID-19 vaccines, functional and lasting immunity to SARS-CoV-2 is currently under investigation as antibody levels in plasma were shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we evaluate the presence of SARS-CoV-2-specific memory B cells in convalescent individuals. Here we report a longitudinal assessment of humoral immune responses on 32 donors up to 8 months post-symptom onset. Our observations indicate that anti-Spike and anti-RBD IgM in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity also declines rapidly when compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells which remain stable. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for the prevention of secondary infections and vaccine efficacy.

Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset.

RAWGraphs is an open source web application for the creation of static data visualisations that are designed to be further modified. Originally conceived for graphic designers to provide a series of tasks not available with other tools, it evolved into a platform that provides simple ways to map data dimensions onto visual variables. It presents a chart-based approach to data visualisation: each visual model is an independent module exposing different visual variables that can be used to map data dimensions. Consequently, users can create complex data visualisations. Finally, the tool is meant to produce outputs that are open, that is, not subjected to proprietary solutions, which can be further edited.

RAWGraphs: A Visualisation Platform to Create Open Outputs

Figure 1: A summary of the main functions of the XAI Primer. The design space is structured into three layers, namely: the cluster layer (a), the item layer (b) and the network layer (c) that can be explored in an open-ended and serendipitous way. Guided tours (d) provide focused reading of the space by automatically panning and zooming. The exploration modes panel (e), the collection panel (f), the search bar (g) and the minimap (h) complete the interface, respectively allowing users to navigate across views, collect and download lists of items, search for authors or projects, orient them in space and highlighting the same items in the space.

xai-primer.com — A Visual Ideation Space of Interactive Explainers

In this paper we present the outcomes of a research aimed at designing a new visual model for the analysis and presentation of data of genetic criticism carried out in collaboration between researchers in information design and literary scholars of the project [name of the project redacted for blind review]. The design process involved three moments: gathering of information for the definition of design requirements, prototyping the networks and conducting preliminarily evaluations, and producing and evaluating ten network visualizations. The presented process is rich in insights about the collaboration between design researchers and scholars involved in digital humanities.

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Designing network visualizations for genetic literary criticism

This paper presents the design report of an experimental data visualization art-work that deals with sexual harassment in academic environments. The visualiza-tion employs a qualitative dataset of stories of abuse and aims at nurturing emo-tional involvement by creating connections with the people behind the data. In the paper, we outline our theoretical background, considering previous research on anthropomorphic and artistic visualizations. Successively, we disclose our de-sign approach and discuss the visualizations’ capability to nurture reflection, stimulate conversations, and empower the community of people fighting against sexual harassment in academia and beyond. 

Tommaso Elli

Papers

RAWGraphs: A Visualisation Platform to Create Open Outputs

xai-primer.com — A Visual Ideation Space of Interactive Explainers

Designing network visualizations for genetic literary criticism

Visualizing stories of sexual harassment in the academy: Community empowerment through qualitative data