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The 500-ns CG-MD simulation trajectory towards SARS-CoV-2 virus.

This model has been invalidated.

Figure S1. Phylogenetic reconstruction of SARS-CoV-2 sequences distinguished between general population and healthcare workers. Samples correspond to the period of November 17th, 2021 and February 21st, 2022. The phylogenetic tree was reconstructed with 1,000 iterations for Ultra-Fast Bootstrap and SH-like approximate likelihood ratio test (SH-aLRT). Reference (SARS-CoV-2 reference genome - NC_045512).

Top 4 models per each simulation strategy of docking from the manuscript.

Effect of driving pressure guided mechanical ventilation on postoperative pulmonary function in elderly patients with non COVID-19

Supplementary Tables of Scientific Paper

Dataset of Scientific Paper

The set includes data related to the paper "The vibe of musical and social reward: Listening to beat-based music acts as a surrogate for socioemotional support during the Covid-19 pandemic"

Deliverable report 3.2 describes the findings on the analysis of the Science-Policy-Society (SPS) collaboration system on specific casesthrough a Net-Map analysis. Net-Map is an interview-based mapping tool to visualize implicit knowledge and understand the interplay of complex formal and informal networks, power relations, and actors/stakeholders’ goals; uncover sources of conflicts as well as potentials for cooperation; facilitate knowledge exchange and learning processes; and develop visions and strategies to achieve common goals. The development of the Net-Map analysis tool is described. Due to the Covid-19 pandemic, the interviewbased mapping tool was adapted to fit in an online setting. Online meeting applications such as Microsoft Teams® and MIRO® were implemented to map the stakeholders and their relations in the society-policyscience (SPS) collaboration system in risk analysis of emerging food safety issues and to identify constraints in relations, resources, and capabilities. Food safety scenarios based on gobal challenges were selected based on the in-depth expert interviews (Deliverable 3.1). These were food safety concerns regarding emerging mycotoxins and recycled food contact materials (FCM). Several steps in mycotoxin risk analysis are incomplete due to e.g. lack of occurrence or toxicokinetic/toxicity data, lack of analytical techniques and lack of scientific knowledge. Therefore, this case of emerging mycotoxins was used to perform a Net-Map analysis to identify stakeholders involved in this risk analysis and how they interact. For the FCMs, the focus was put on packaging consisting of recycled paper or cardboard, as they have become increasingly important in the light of sustainability and circular economy. However, food safety challenges are related to these materials, making it a good model case to apply the Net-Map tool on. A Net-Map guidance protocol, including a standardized data reporting format, was distributed among the food safety hub (HUB) leaders. Pilot workshops with FS4EU consortium partners were held, enabling further refinement of the protocol. The final protocol has been made publicly available through the FS4EU website and can be applied in many other contexts. Next, four Net-Map workshops were carried out in the respective home countries of the HUB leaders. In Belgium (West HUB) and Finland (North HUB) the case of FCMs was implemented, while participants of Italy (South HUB) and the Czech Republic (East HUB) worked on the emerging mycotoxins case. First, stakeholders and their main goals in mycotoxin/FCM risk analysis were identified. The next step was to characterise how the stakeholders were linked in the system, followed by an assessment on how influential the stakeholders were. Finally a discussion took place on constraints compromising the risk analysis. The workshops resulted in complex Net-Maps, visualizing how the SPS collaboration system regarding risk analysis of the aforementioned food safety issues is set up in each country. The most prominent stakeholders who take up a central role in the risk analysis process were identified. Many linkages between stakeholders were revealed, going from information sharing (legally required or voluntary), data requesting or communicating to the public. Moreover, in every country, constraints related to these linkages could be identified. These constraints, such as lack of resources or communication issues can be used to define needs for improvements in the current SPS collaboration system. While the initial results are already very interesting to discuss, further validation and verification of the obtained conclusions is needed.

Count matrices to accompany the manuscript "­­Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C ­­Nucleic acid biomarkers of immune response and cell and tissue damage in children with COVID-19 and MIS-C ". Summary: Differential host responses in coronavirus disease 2019 (COVID-19) and multisystem inflammatory syndrome in children (MIS-C) remain poorly characterized. Here we use next-generation sequencing to longitudinally analyze blood samples from pediatric patients with acute COVID-19 (n=70) or MIS-C (n=141) across three hospitals. Profiling of plasma cell-free nucleic acids uncovers distinct signatures of cell injury and death between COVID-19 and MIS-C, with increased multi-organ involvement in MIS-C encompassing diverse cell types including endothelial and neuronal cells, and an enrichment of pyroptosis related genes. Whole blood RNA profiling reveals upregulation of similar pro-inflammatory pathways in COVID-19 and MIS-C, but also MIS-C specific downregulation of T cell-associated pathways. Profiling of plasma cell-free RNA and whole blood RNA in paired samples yields different yet complementary signatures for each disease state. Our work provides a systems-level view of immune responses and tissue damage in COVID-19 and MIS-C and informs the future development of new disease biomarkers. Overview: cfRNA_gene-count-matrix.tsv: tab delimited cell-free RNA-seq gene count matrix wbRNA_gene-count-matrix.tsv: tab delimited whole blood RNA-seq gene count matrix cfDNA_methylation-matrix.tsv: tab delimited cell-free DNA whole genome bisultie-seq methylation matrix Reference genome: GENCODE v38 primary assembly