Trend analysis of COVID-19 mis/disinformation narratives-A 3-year study.

To tackle the COVID-19 infodemic, we analysed 58,625 articles from 460 unverified sources, that is, sources that were indicated by fact checkers and other mis/disinformation experts as frequently spreading mis/disinformation, covering the period from 1 January 2020 to 31 December 2022. Our aim was to identify the main narratives of COVID-19 mis/disinformation, develop a codebook, automate the process of narrative classification by training an automatic classifier, and analyse the spread of narratives over time and across countries. Articles were retrieved with a customised version of the Europe Media Monitor (EMM) processing chain providing a stream of text items.

A New Online Resource to Monitor New or Emerging Plant Pests: MEDISYS Media Monitoring and the Case of Xylella fastidiosa.

The European Food Safety Authority has established a horizon scanning exercise for plant pests by automated monitoring of open-source media. The news sources are screened using the publicly accessible MEDISYS (Medical Information System) platform of the Joint Research Centre of the European Commission. Here, we report the example of monitoring for Xylella fastidiosa, a highly polyphagous plant-pathogenic bacterium.

Event-Based Surveillance During EXPO Milan 2015: Rationale, Tools, Procedures, and Initial Results.

More than 21 million participants attended EXPO Milan from May to October 2015, making it one of the largest protracted mass gathering events in Europe. Given the expected national and international population movement and health security issues associated with this event, Italy fully implemented, for the first time, an event-based surveillance (EBS) system focusing on naturally occurring infectious diseases and the monitoring of biological agents with potential for intentional release. The system started its pilot phase in March 2015 and was fully operational between April and November 2015.

Interfacing a biosurveillance portal and an international network of institutional analysts to detect biological threats.

The Early Alerting and Reporting (EAR) project, launched in 2008, is aimed at improving global early alerting and risk assessment and evaluating the feasibility and opportunity of integrating the analysis of biological, chemical, radionuclear (CBRN), and pandemic influenza threats. At a time when no international collaborations existed in the field of event-based surveillance, EAR's innovative approach involved both epidemic intelligence experts and internet-based biosurveillance system providers in the framework of an international collaboration called the Global Health Security Initiative, which involved the ministries of health of the G7 countries and Mexico, the World Health Organization, and the European Commission. The EAR project pooled data from 7 major internet-based biosurveillance systems onto a common portal that was progressively optimized for biological threat detection under the guidance of epidemic intelligence experts from public health institutions in Canada, the European Centre for Disease Prevention and Control, France, Germany, Italy, Japan, the United Kingdom, and the United States.

Factors influencing performance of internet-based biosurveillance systems used in epidemic intelligence for early detection of infectious diseases outbreaks.

Background: Internet-based biosurveillance systems have been developed to detect health threats using information available on the Internet, but system performance has not been assessed relative to end-user needs and perspectives.

Method And Findings: Infectious disease events from the French Institute for Public Health Surveillance (InVS) weekly international epidemiological bulletin published in 2010 were used to construct the gold-standard official dataset. Data from six biosurveillance systems were used to detect raw signals (infectious disease events from informal Internet sources): Argus, BioCaster, GPHIN, HealthMap, MedISys and ProMED-mail.

Evaluation of epidemic intelligence systems integrated in the early alerting and reporting project for the detection of A/H5N1 influenza events.

The objective of Web-based expert epidemic intelligence systems is to detect health threats. The Global Health Security Initiative (GHSI) Early Alerting and Reporting (EAR) project was launched to assess the feasibility and opportunity for pooling epidemic intelligence data from seven expert systems. EAR participants completed a qualitative survey to document epidemic intelligence strategies and to assess perceptions regarding the systems performance.

ECVAM and new technologies for toxicity testing.

The development of alternative empirical (testing) and non-empirical (non-testing) methods to traditional toxicological tests for complex human health effects is a tremendous task. Toxicants may potentially interfere with a vast number of physiological mechanisms thereby causing disturbances on various levels of complexity of human physiology. Only a limited number of mechanisms relevant for toxicity ('pathways' of toxicity) have been identified with certainty so far and, presumably, many more mechanisms by which toxicants cause adverse effects remain to be identified.

Event-driven architecture for health event detection from multiple sources.

Early detection of potential health threats is crucial for taking actions in time. It is unclear in which information source an event is reported first and, information from various sources can be complementing. Thus, it is important to search for information in a very broad range of sources.

Toxicogenomics applied to in vitro carcinogenicity testing with Balb/c 3T3 cells revealed a gene signature predictive of chemical carcinogens.

Information on the carcinogenic potential of chemicals is primarily available for High Production Volume (HPV) products. Because of the limited knowledge gain from routine cancer bioassays and the fact that HPV chemicals are tested only, there is the need for more cost-effective and informative testing strategies. Here we report the application of advanced genomics to a cellular transformation assay to identify toxicity pathways and gene signatures predictive for carcinogenicity.

Comparative analysis of structural and dynamic properties of the loaded and unloaded hemophore HasA: functional implications.

A heme-acquisition system present in several Gram-negative bacteria requires the secretion of hemophores. These extracellular carrier proteins capture heme and deliver it to specific outer membrane receptors. The Serratia marcescens HasA hemophore is a monodomain protein that binds heme with a very high affinity.

A novel in vitro metabolomics approach for neurotoxicity testing, proof of principle for methyl mercury chloride and caffeine.

There is a need for more efficient methods giving insight into the complex mechanisms of neurotoxicity. Testing strategies including in vitro methods have been proposed to comply with this requirement. With the present study we aimed to develop a novel in vitro approach which mimics in vivo complexity, detects neurotoxicity comprehensively, and provides mechanistic insight.

ECVAM's approach to intellectual property rights in the validation of alternative methods.

In this article, we discuss how intellectual property rights affect the validation of alternative methods at ECVAM. We point out recent cases and summarise relevant EU and OECD documents. Finally, we discuss guidelines for dealing with intellectual property rights during the validation of alternative methods at ECVAM.

Influence of chemical shift tolerances on NMR structure calculations using ARIA protocols for assigning NOE data.

Large-scale protein structure determination by NMR via automatic assignment of NOESY spectra requires the adjustment of several parameters for optimal performance. Among those are the chemical shift tolerance windows (delta), which allow for the compensation of badly matching chemical shifts in the assignment-list and peak-lists, and the maximum number of assignment possibilities allowed per peak (n(max)). Here, we test the influence of different values for Delta and n(max) on the performance of automated assignment of NOESY spectra by ARIA.

NOE assignment with ARIA 2.0: the nuts and bolts.

The assignment of nuclear Overhauser effect (NOE) resonances is the crucial step in determining the three-dimensional structure of biomolecules from nuclear magnetic resonance (NMR) data. Our program, Ambiguous Restraints for Iterative Assignment (ARIA), treats Noe assignment as an integral part of the structure determination process. This chapter briefly outlines the method and discusses how to carry out a complete structure determination project with the new version 2.

Correction of spin diffusion during iterative automated NOE assignment.

Indirect magnetization transfer increases the observed nuclear Overhauser enhancement (NOE) between two protons in many cases, leading to an underestimation of target distances. Wider distance bounds are necessary to account for this error. However, this leads to a loss of information and may reduce the quality of the structures generated from the inter-proton distances.

Refinement of protein structures in explicit solvent.

We present a CPU efficient protocol for refinement of protein structures in a thin layer of explicit solvent and energy parameters with completely revised dihedral angle terms. Our approach is suitable for protein structures determined by theoretical (e.g.

ARIA: automated NOE assignment and NMR structure calculation.

Motivation: In the light of several ongoing structural genomics projects, faster and more reliable methods for structure calculation from NMR data are in great demand. The major bottleneck in the determination of solution NMR structures is the assignment of NOE peaks (nuclear Overhauser effect). Due to the high complexity of the assignment problem, most NOEs cannot be directly converted into unambiguous inter-proton distance restraints.

The CCPN project: an interim report on a data model for the NMR community.

A recent workshop discusses the progress toward integrating NMR data into a unifying data model.

Improving the quality of protein structures derived by NMR spectroscopy.

Biomolecular structures provide the basis for many studies in several research areas such as homology modelling, structure-based drug design and functional genomics. It is an important prerequisite that the structure is reliable in terms of accurate description of the experimental data, and in terms of good quality of local- and overall geometry. Recent surveys indicate that structures solved by NMR-spectroscopy normally are of lower precision than high-resolution X-ray structures.

Structure of the histone mRNA hairpin required for cell cycle regulation of histone gene expression.

Expression of replication-dependent histone genes requires a conserved hairpin RNA element in the 3' untranslated regions of poly(A)-less histone mRNAs. The 3' hairpin element is recognized by the hairpin-binding protein or stem-loop-binding protein (HBP/SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage generating the mature mRNA 3' end.