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

In this paper we suggest a different approach that considers visualizations in the wider domain of communication and defines a model capable of taking into account the context in which visualizations act as communication tools. In this perspective we consider visualizations as transformation processes within the Data-Information-Knowledge (DIK) continuum. In the paper we discuss the continuum, and apply the transformation process model to the main disciplines of visualization. Visualizations represent powerful cognitive tools that surround our everyday life [1]. By doing this we are able to think about visualization from a multidisciplinary perspective, exploring the role of visualizations in design practice, as artifacts that are used in facing problems of various degrees of complexity and nature. The contribution of the model is mainly addressed to orientate and nurture the reflective practice and to formalize the strategic more than the technical role of visualizations in the design discipline.

From Data to Knowledge - Visualizations as Transformation Processes within the Data-Information-Knowledge Continuum

Manual analysis of security-related events is still a necessity to investigate non-trivial cyber attacks. This task is particularly hard when the events involve slow, stealthy and large-scale activities typical of the modern cybercriminals' strategy. In this regard, visualization tools can effectively help analysts in their investigations. In this paper, we present BURN, an interactive visualization tool for displaying autonomous systems exhibiting rogue activity that helps at finding misbehaving networks through visual and interactive exploration. Up to seven values are displayed in a single visual element, while avoiding cumbersome and confusing maps. To this end, animations and alpha channels are leveraged to create simple views that highlight relevant activity patterns. In addition, BURN incorporates a simple algorithm to identify migrations of nefarious services across autonomous systems, which can support, for instance, root-cause analysis and law enforcement investigations.

/pdf/burn-baring-unknown-rogue-networks-384sa56lqm.pdf

BURN: baring unknown rogue networks

For the last few years , computers and the Internet have been changing the way research is conceived, conducted, and communicated, transforming scholarly publication and collaboration, and supporting the creation, the storage, the analysis, and the dissemination of data and information. While natural, medical, and social sciences have a long and established tradition with these technologies, most of the humanities disciplines have found it difficult if not impossible to integrate computational tools, based mostly on quantitative approaches, with their research methods. In the last 20 years however, new research areas and activities have emerged from the intersection between humanities and computing. Today, what is known as digital humanities represents a heterogeneous set of studies and practices that aims at understanding the implications and the opportunities that digital technologies can provide as media, tools, or objects of study in the humanities (Schreibman et al. in A companion to digital humanities. Blackwell, Oxford, 2004; Gold in Debates in the digital humanities. University of Minnesota Press, Minneapolis, 2012; Berry in Understanding digital humanities. Palgrave Macmillan , New York, 2012). These new relationships between the digital and the humanities are rapidly demanding for new modes of observation and interpretation. Information visualizations and interfaces appear as essential tools to explore and make sense out of big and heterogeneous amounts of data (Manovich 2013). But, in a context where most of the methods and the technologies are still adopted from other disciplines, the biggest challenge seems to be imagining new genuine research tools capable of embedding and valorizing the humanities endeavor (Drucker in Culture Machine 12:1–20, 2011). The work presented here aims at deepening the relationships between designers, humanities scholars, and computer scientists through the outlining of new research tools and processes based on humanistic data and digital environments. Furthermore, it explores the possibilities and challenges set forth by information and data visualizations as tools to support scholarly activities.

Information Visualizations and Interfaces in the Humanities

This paper describes the design of Knot, a digital tool for exploring historical social networks, developed within a multidisciplinary research context involving designers, humanities scholars and computer scientists. The goal of the tool is to provide scholars and researchers with an environment for exploring multi-dimensional and heterogeneous data, allowing them to discover and create explicit and implicit relationships between people, places and events. What distinguishes our approach to traditional network exploration and analysis is an emphasis on the construction of the network graph through the visual interface, rather than on its static observation. Knot aims to explore new opportunities for interface design and information visualization within the definition of novel research practices in the humanities, bringing together scholars, HCI, design, and computer science communities.

Giorgio Caviglia

Papers

RAWGraphs: A Visualisation Platform to Create Open Outputs

From Data to Knowledge - Visualizations as Transformation Processes within the Data-Information-Knowledge Continuum

BURN: baring unknown rogue networks

Information Visualizations and Interfaces in the Humanities

Knot: an interface for the study of social networks in the humanities