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Abstract Infectious bursal disease (IBD) is an avian viral disease caused in chickens by infectious bursal disease virus (IBDV). IBDV strains (Avibirnavirus genus, Birnaviridae family) exhibit different pathotypes, for which no molecular marker is available yet. The different pathotypes, ranging from sub-clinical to inducing immunosuppression and high mortality, are currently determined through a 10-day-long animal experiment designed to compare mortality and clinical score of the uncharacterized strain with references strains. Limits of this protocol lie within standardization and the extensive use of animal experimentation. The aim of this study was to establish a predictive model of viral pathotype based on a minimum number of early parameters measured during infection, allowing faster pathotyping of IBDV strains with improved ethics. We thus measured, at 2 and 4 days post-infection (dpi), the blood concentrations of various immune and coagulation related cells, the uricemia and the infectious viral load in the bursa of Fabricius of chicken infected under standardized conditions with a panel of viruses encompassing the different pathotypes of IBDV. Machine learning algorithms allowed establishing a predictive model of the pathotype based on early changes of the blood cell formula, whose accuracy reached 84.1%. Its accuracy to predict the attenuated and strictly immunosuppressive pathotypes was above 90%. The key parameters for this model were the blood concentrations of B cells, T cells, monocytes, granulocytes, thrombocytes and erythrocytes of infected chickens at 4 dpi. This predictive model could be a second option to traditional IBDV pathotyping that is faster, and more ethical.

We detected highly pathogenic avian influenza A(H5N1) clade 2.3.4.4b virus in a domestic cat that lived near a duck farm infected by a closely related virus in France during December 2022. Enhanced surveillance of symptomatic domestic carnivores in contact with infected birds is recommended to prevent further spread to mammals and humans.

From 2020 up to summer 2023, there was a substantial change in the situation concerning the high pathogenic avian influenza (HPAI) virus in Europe. This change concerned mainly virus circulation within wildlife, both in wild birds and wild mammals. It involved the seasonality of HPAI detections, the species affected, excess mortality events, and the apparent increased level of contamination in wild birds. The knock-on effect concerned new impacts and challenges for the poultry sector, which is affected by repeated annual waves of HPAI arriving with wild migratory birds and by risks due to viral circulation within resident wild birds across the year. Indeed, exceeding expectations, new poultry sectors and production areas have been affected during the recent HPAI seasons in France. The HPAI virus strains involved also generate considerable concern about human health because of enhanced risks of species barrier crossing. In this article, we present these changes in detail, along with the required adjustment of prevention, control, and surveillance strategies, focusing specifically on the situation in France.

The reconstruction of particle trajectories is a key challenge of particle physics experiments, as it directly impacts particle identification and physics performances while also representing one of the main CPU consumers of many high-energy physics experiments. As the luminosity of particle colliders increases, this reconstruction will become more challenging and resourceintensive. New algorithms are thus needed to address these challenges efficiently. One potential step of track reconstruction is ambiguity resolution. In this step, performed at the end of the tracking chain, we select which tracks candidates should be kept and which must be discarded. The speed of this algorithm is directly driven by the number of track candidates, which can be reduced at the cost of some physics performance. Since this problem is fundamentally an issue of comparison and classification, we propose to use a machine learning-based approach to the Ambiguity Resolution. Using a shared-hits-based clustering algorithm, we can efficiently determine which candidates belong to the same truth particle. Afterwards, we can apply a Neural Network (NN) to compare those tracks and decide which ones are duplicates and which ones should be kept. This approach is implemented within A Common Tracking Software (ACTS) framework and tested on the Open Data Detector (ODD), a realistic virtual detector similar to a future ATLAS one. This new approach was shown to be 15 times faster than the default ACTS algorithm while removing 32 times more duplicates down to less than one duplicated track per event.

Particle tracking is among the most sophisticated and complex part of the full event reconstruction chain. A number of reconstruction algorithms work in a sequence to build these trajectories from detector hits. Each of these algorithms use many configuration parameters that need to be fine-tuned to properly account for the detector/experimental setup, the available CPU budget and the desired physics performance. Few examples of such parameters include the cut values limiting the search space of the algorithm, the approximations accounting for complex phenomena or the parameters controlling algorithm performance. The most popular method to tune these parameters is hand-tuning using brute-force techniques. These techniques can be inefficient and raise issues for the long-term maintainability of such algorithms. The opensource track reconstruction software framework known as “A Common Tracking Framework (ACTS)” offers an alternative solution to these parameter tuning techniques through the use of automatic parameter optimization algorithms. ACTS come equipped with an auto-tuning suite that provides necessary setup for performing optimization of input parameters belonging to track reconstruction algorithms. The user can choose the tunable parameters in a flexible way and define a cost/benefit function for optimizing the full reconstruction chain. The fast execution speed of ACTS allows the user to run several iterations of optimization within a reasonable time bracket. The performance of these optimizers has been demonstrated on different track reconstruction algorithms such as trajectory seed reconstruction and selection, particle vertex reconstruction and generation of simplified material map, and on different detector geometries such as Generic Detector and Open Data Detector (ODD). We aim to bring this approach to all aspects of trajectory reconstruction by having a more flexible integration of tunable parameters within ACTS.

C++ is a vital part of particle physics as it allows for high level abstractions while offering state of the art performance. In this article we will first introduce the C++ 20 concepts, a major C++ usability enhancement. We will then introduce Kiwaku, a new multidimensional arrays library taking advantage of the most advanced C++ features at the time of writing, providing the user with intuitive API while retaining state of the art performance. Multidimensional arrays are a basic building block for many scientific experiments and simulations, and particle physics is no exception. Using examples borrowed from Covfie and ACTS libraries, and using data from the ATLAS CERN experiment, we will show how Kiwaku offers good usability while having a negligible impact on performance compared to using classic C++ std::arrays.

Abstract Quantitative mechanical properties of biological tissues can be mapped using the shear wave elastography technique. This technology has demonstrated a great potential in various organs but shows a limit due to wave attenuation in biological tissues. An option to overcome the inherent loss in shear wave magnitude along the propagation pathway may be to stimulate tissues closer to regions of interest using alternative motion generation techniques. The present study investigated the feasibility of generating shear waves by applying a Lorentz force directly to tissue mimicking samples for magnetic resonance elastography applications. This was done by combining an electrical current with the strong magnetic field of a clinical MRI scanner. The Local Frequency Estimation method was used to assess the real value of the shear modulus of tested phantoms from Lorentz force induced motion. Finite elements modeling of reported experiments showed a consistent behavior but featured wavelengths larger than measured ones. Results suggest the feasibility of a magnetic resonance elastography technique based on the Lorentz force to produce an shear wave source.

We detected 3 genotypes of highly pathogenic avian influenza A(H5N8) virus in France during winter 2016–17. Genotype A viruses caused dramatic economic losses in the domestic duck farm industry in southwestern France. Our phylogenetic analysis suggests that genotype A viruses formed 5 distinct geographic clusters in southwestern France. In some clusters, local secondary transmission might have been started by a single introduction. The intensity of the viral spread seems to correspond to the density of duck holdings in each production area. To avoid the introduction of disease into an unaffected area, it is crucial that authorities limit the movements of potentially infected birds.

This study proposes a geopolitical analysis of opinion dynamics based on a statistical exploration of a press dataset covering 2014–2019. This exploration questions three case studies of geopolitical and international interest: international migration, political borders, and pandemics. Through the framework of geopolitical agenda, the aim of this study is to question the “crisis” status of changes in the media coverage of the three topics in a cross-analysis and multilingual analysis of 20 western European newspapers. It concludes that there is a prevalence of national agendas.

If the agenda-setting terms of discussion of international mobility in 2015 were « refugee crisis », the absence of any abrupt change in the migration system suggests that the « crisis » stemmed from media representations. Taking a corpus of online Press materials, with a global and multi-lingual scope, our analysis practises reading at a distance, and a geographical approach, in order to broach the spatial and temporal dimensions of the media’s highlighting of migration. The temporal variations in information flow concerning migration prove to be linked to the quantitative changes in the spatial content of the representations of the migratory situation (the geographical coverage concentrated on the EU and the Eastern Mediterranean). Due to these links, examined here with attention to the production of geographical imaginaries and to differences of scale, a global geopolitical upheaval in migration was identified.

The capacity of individuals to cope with threatening situations depends directly on their capacity to anticipate what will come next. The media should play a key role in that respect, but an extensive analysis of earthquake media coverage by the international news reveals systematic biases. Exploring a corpus of 320 888 news articles published by 32 worldwide newspapers in 2015 in English, Spanish or French, we found that the press covers a very small number of events: 71 % of the news about seismic events was dedicated to only 3 earthquakes (among the 1559 magnitude 5+ events). A combination of frequency and content analysis reveals a typical framing of the “earthquake news”. Except for the “Nepal quake”, the duration of the coverage is usually very short. Thus, the news tends to focus on short-term issues: the event magnitude, tsunami alerts, human losses, material damage and rescue operations. Longer-term issues linked to the recovery, restoration, reconstruction, mitigation and prevention are barely addressed. Preventive safety measures are almost never mentioned. The news on impacts shows a peculiar appetency for death counts, material damage estimates and sensationalism. News on the response tends to emphasize the role played by the international community in helping the “poor and vulnerable”. The scientific content of the coverage is often restricted to mentions of the magnitude, with the concept of the seismic intensity being largely ignored. The notion of the “seismic crisis” also seems unclear, with aftershocks sometimes being treated as isolated events. Secondary hazards are barely mentioned, except in the case of tsunami alerts. Together, these biases contribute to fatalistic judgments that damage cannot be prevented. If scientific messages are to be communicated, they should be broadcast a few hours after an event. Why not take the opportunity to familiarize people with the real timeline of seismic disasters?

The avibirnavirus infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (Gallus gallus). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1. These viruses were serially passaged at controlled multiplicities of infection in several biological systems, including primary chickens B cells, the main cell type targeted by IBDV in vivo. Passages were also performed in the absence or presence of a strong selective pressure using the antiviral nucleoside analog 7-deaza-2′-C-methyladenosine (7DMA). Next Generation Sequencing (NGS) of viral genomes after the last passage in each biological system revealed that (i) a higher viral diversity was generated in segment A than in segment B, regardless 7DMA treatment and viral strain, (ii) diversity in segment B was increased by 7DMA treatment in both viruses, (iii) passaging of IBDV in primary chicken B cells, regardless of 7DMA treatment, did not select cell-culture adapted variants of rvv, preserving its capsid protein (VP2) properties, (iv) mutations in coding and non-coding regions of rCu-1 segment A could potentially associate to higher viral fitness, and (v) a specific selection, upon 7DMA addition, of a Thr329Ala substitution occurred in the viral polymerase VP1. The latter change, together with Ala270Thr change in VP2, proved to be associated with viral attenuation in vivo. These results identify genome sequences that are important for IBDV evolution in response to selection pressures. Such information will help tailor better strategies for controlling IBDV infection in chickens.

The Euro Spatial Diffusion Observatory (ESDO) database records face-to-face questionnaire surveys conducted between March 2002 and December 2011 in France, in December 2003 in Belgium and in December 2005 in Germany. The data provides information on the coins contained in the respondents' wallets at the time of the survey, classified by country of origin and value. A series of control variables provide information on the socioeconomic profile of the respondents and the location of their place of residence at the NUTS 3 level. In total, more than 22,500 people opened their wallets and about 300,000 coins were registered allowing the tracking of euro coins circulation from their country of introduction on January 1, 2002 (or later for countries that joined the euro zone afterwards) to their place of observation at the time of the survey.

Avian influenza virus (AIV) outbreaks occur frequently worldwide, causing a potential public health risk and great economic losses to poultry industries. Considering the high mutation rate and frequent genetic reassortment between segments in the genome of AIVs, emerging new strains are a real threat that may infect and spread through the human population, causing a pandemic. Therefore, rapid AIV diagnostic tests are essential tools for surveillance and assessing virus spreading. Real-time reverse transcription PCR (rRT-PCR), targeting the matrix gene, is the main official standard test for AIV detection, but the method requires well-equipped laboratories. Reverse transcription Loop-Mediated Isothermal Amplification (RT-LAMP) has been reported as a rapid method and an alternative to PCR in pathogen detection. The high mutation rate in the AIV genome increases the risk of false negative in nucleic acid amplification methods for detection, such as PCR and LAMP, due to possible mismatched priming. In this study, we analyzed 800 matrix gene sequences of newly isolated AIV in the EU and designed a highly efficient LAMP primer set that covers all AIV subtypes. The designed LAMP primer set was optimized in real-time RT-LAMP (rRT-LAMP) assay. The rRT-LAMP assay detected AIV samples belonging to nine various subtypes with the specificity and sensitivity comparable to the official standard rRT-PCR assay. Further, a two-color visual detection RT-LAMP assay protocol was adapted with the aim to develop on-site diagnostic tests. The on-site testing successfully detected spiked AIV in birds oropharyngeal and cloacal swabs samples at a concentration as low as 100.8 EID50 per reaction within 30 minutes including sample preparation. The results revealed a potential of this newly developed rRT-LAMP assay to detect AIV in complex samples using a simple heat treatment step without the need for RNA extraction.

Infectious Bronchitis virus (IBV) continues to cause significant economic losses for the chicken industry despite the use of many live IBV vaccines around the world. Several authors have suggested that vaccine-induced partial protection may contribute to the emergence of new IBV strains. In order to study this hypothesis, three passages of a challenge IBV were made in SPF chickens sham inoculated or vaccinated at day of age using a live vaccine heterologous to the challenge virus. All birds that were challenged with vaccine heterologous virus were positive for viral RNA. NGS analysis of viral RNA in the unvaccinated group showed a rapid selection of seven genetic variants, finally modifying the consensus genome of the viral population. Among them, five were non-synonymous, modifying one position in NSP 8, one in NSP 13, and three in the Spike protein. In the vaccinated group, one genetic variant was selected over the three passages. This synonymous modification was absent from the unvaccinated group. Under these conditions, the genome population of an IBV challenge virus evolved rapidly in both heterologous vaccinated and non-vaccinated birds, while the genetic changes that were selected and the locations of these were very different between the two groups.

Abstract Background Growing and finishing performances of pigs strongly influence farm efficiency and profitability. The performances of the pigs rely on the herd health status and also on several non-infectious factors. Many recommendations for the improvement of the technical performances of a herd are based on the results of studies assessing the effect of one or a limited number of infections or environmental factors. Few studies investigated jointly the influence of both type of factors on swine herd performances. This work aimed at identifying infectious and non-infectious factors associated with the growing and finishing performances of 41 French swine herds. Results Two groups of herds were identified using a clustering analysis: a cluster of 24 herds with the highest technical performance values (mean average daily gain = 781.1 g/day +/− 26.3; mean feed conversion ratio = 2.5 kg/kg +/− 0.1; mean mortality rate = 4.1% +/− 0.9; and mean carcass slaughter weight = 121.2 kg +/− 5.2) and a cluster of 17 herds with the lowest performance values (mean average daily gain =715.8 g/day +/− 26.5; mean feed conversion ratio = 2.6 kg/kg +/− 0.1; mean mortality rate = 6.8% +/− 2.0; and mean carcass slaughter weight = 117.7 kg +/− 3.6). Multiple correspondence analysis was used to identify factors associated with the level of technical performance. Infection with the porcine reproductive and respiratory syndrome virus and the porcine circovirus type 2 were infectious factors associated with the cluster having the lowest performance values. This cluster also featured farrow-to-finish type herds, a short interval between successive batches of pigs (≤3 weeks) and mixing of pigs from different batches in the growing or/and finishing steps. Inconsistency between nursery and fattening building management was another factor associated with the low-performance cluster. The odds of a herd showing low growing-finishing performance was significantly increased when infected by PRRS virus in the growing-finishing steps (OR = 8.8, 95% confidence interval [95% CI]: 1.8–41.7) and belonging to a farrow-to-finish type herd (OR = 5.1, 95% CI = 1.1–23.8). Conclusions Herd management and viral infections significantly influenced the performance levels of the swine herds included in this study.

Abstract In 2013, PED emerged for the first time in the United States (US). The porcine epidemic diarrhea virus (PEDV) spread quickly throughout North America. Infection with PEDV causes watery diarrhea and up to 100% mortality in piglets, particularly for highly pathogenic non-InDel strains circulating in the US. PEDV is mainly transmitted by the fecal–oral route. Transmission via the venereal route has been suspected but not previously investigated. The aim of the study was to determine if PEDV could be detected in semen from infected specific pathogen-free (SPF) boars inoculated with a PEDV US non-InDel strain suggesting venereal transmission may occur. Two boars orally inoculated with PEDV showed clinical signs and virus shedding in feces. Transient presence of the PEDV genome was detected by RT-qPCR in the seminal (5.06 × 102 to 2.44 × 103 genomic copies/mL) and sperm-rich fraction of semen (5.64 × 102 to 3.40 × 104 genomic copies/mL) and a longer duration of viral shedding was observed in the sperm-rich fraction. The evidence of PEDV shedding in semen raises new questions in term of disease spread within the pig population with the use of potentially contaminated semen.

The period that begins with the reflections and debates around the new constitution in Tunisia is also the one of territorial reform. Questions about it and, more generally, about the recasting of local authorities and equalization rules has emerged as a major political and social issue. This article shows that what is played out in this country cannot free itself on the one hand from the territorial grids that have existed for several decades, on the other hand from the urban fact that takes more and more importance in the structuring of activities and wealth. This article finally stresses the need to take account of the representations and perceptions of the populations to carry out such a reform.

Abstract Pigs infected by porcine epidemic diarrhea virus (PEDV) are affected by severe diarrhea, vomiting and dehydration. The severity of clinical signs depends on the virus strain. Two genetically different PEDV strains are known to infect pigs, the PEDV S-InDel strains which circulate on all continents and the highly virulent PEDV S-non-InDel strains found in Asia and in America. We have previously demonstrated the presence of PEDV RNA in semen from boars experimentally infected with an S-non-InDel PEDV strain. If naturally infected boars may shed PEDV in semen, this would have important consequences for the breeding sector. Thus we sought to determine whether PEDV has been circulating in populations of breeding boars from French artificial insemination (AI) centers. The current study reports on a serological survey conducted on one hundred and twenty boars from six AI centers, representing 18.6% of the total population of breeding boars in French AI centers in 2015. All of them were found negative for PEDV antibodies, showing no evidence of PEDV circulation in French AI centers at that time.

From 2020 up to summer 2023, there was a substantial change in the situation concerning the high pathogenic avian influenza (HPAI) virus in Europe. This change concerned mainly virus circulation within wildlife, both in wild birds and wild mammals. It involved the seasonality of HPAI detections, the species affected, excess mortality events, and the apparent increased level of contamination in wild birds. The knock-on effect concerned new impacts and challenges for the poultry sector, which is affected by repeated annual waves of HPAI arriving with wild migratory birds and by risks due to viral circulation within resident wild birds across the year. Indeed, exceeding expectations, new poultry sectors and production areas have been affected during the recent HPAI seasons in France. The HPAI virus strains involved also generate considerable concern about human health because of enhanced risks of species barrier crossing. In this article, we present these changes in detail, along with the required adjustment of prevention, control, and surveillance strategies, focusing specifically on the situation in France. [ABSTRACT FROM AUTHOR]