Land Parcel Identification System (LPIS) Anomalies' Sampling and Spatial Pattern: Towards convergence of ecological methodologies and GIS technologies

To date, the Land Parcel Identification System (LPIS) has often been proposed as the foundation for effective spatial management of agriculture and the environment and many land managers have suggested incorporating it in most of the instruments for sustainable agriculture. The LPIS is originally used for registration of agricultural reference parcels considered eligible for annual payments of European Common Agricultural Policy (CAP) subsidies to farmers. Its intrinsic quality depends on the frequency and magnitude of the discrepancies in area, since some parcels can be under- or over-declared by farmers compared with reference registered within the LPIS. General application of the LPIS therefore depends on our capacity to ¿ first identify and explain the causes of these area discrepancies perceived as anomalies by national CAP payment agencies ¿second, to propose future improvements in its overall quality. From a set of images used during the 2005 Control with Remote Sensing (CwRS) campaign, using the geographic information system (GIS) and ecological methodologies we assessed the quality of the LPIS by identifying the diversity of the existing anomalies. To that end, the ecological sampling method was adapted to the specific case of image-based detection of anomalies. The observed anomalies assemblages obtained from a set of European Member States representing the four types of LPIS were analysed to establish the spatial pattern of the anomalies. We showed that the twelve zones surveyed can be grouped into four different clusters, each individually correlated with the presence of certain categories of LPIS anomaly. Some clusters were more particularly related to the presence of natural and anthropogenic landscape features, whereas others were typified by anomalies which stemmed from the process for creating and updating the LPIS, which accounted for 20% of the anomalies detected. Finally, we also showed that, even if useful for establishing procedures to manage the LPIS, the LPIS typology used in the European Union had no effect on the anomalies assemblage or on the spatial pattern; consequently, the type of LPIS no longer needs to be considered and LPIS anomalies assemblages could be pooled across Europe. In the light of the results obtained, different proposals are made to improve LPIS quality by: ¿ identifying the critical points along the LPIS management chain; ¿ using landscape ecological methodologies to explain the causes of the clusters observed; and ¿ extrapolating the whole results in the CwRS risk analysis to perform ex-ante LPIS anomalies risk map. Keywords: Land Parcel Identification System, Control with Remote Sensing, orthophoto, quality assessment, diversity, spatial pattern, landscape structureJRC.G.3-Agricultur

The GGELS Project: European Greenhouse Gases Emissions from Livestock Production Systems LPS Regional Zoning for the Survey of Related Manure Management Practices

According to the Administrative Arrangement (AA) No. AGRI-2008-02451 signed between DG AGRI and DG JRC in 2008, the final expectation of the GGELS project is a more precise quantification of the greenhouse gases emission (GHG) from livestock production in Europe by considering GHG emission all along the production chains. To later analyse and plan European GHG mitigation scenario for the livestock sectors, a particular effort of description of the Livestock Production Systems (LPS) in place in Europe is necessary, livestock production is differing largely over Europe according to the local farming particularities and to the specific practices in vigour. The previous statements asked for considering spatial as well as strategic diversity of LPS existing in Europe and for the classification of LPS. For that, Work Package 2 (WP2) of the GGELS project has to focus on the conceptualisation and build up of a new LPS typology allowing policy makers to precisely identify LPS diversity. Regarding the main scales at which LPS datasets are available to date, LPS typology is planed to be performed at NUTS2 level (region level) in EU27. The dimensions to be considered in the LPS typology must reflect the strategies decided by the breeders according to market and regional (mainly biotic) constraints met in regions; these dimensions have also to point out the major livestock production steps responsible for GHG emission variation between regions such as manures management practices. Concerning manures management practices, since no specific information existed at region level, while JRC expertise on this issue was insufficient, it has been decided to launch a call for tender to select academic parties for a specific study on this issue following a questionnaire approach. To facilitate this task, DG JRC decided to perform a preliminary classification of the NUTS2 zones according to the remaining dimensions plus other regional descriptors such as regional meteorological particularities, economic intensity of the LPS, stocking density or again the potential autonomy to feed reared animals from local crops production. For that, official statistics contained inside databases of the CAPRI (Common Agricultural Policy Regional Impact Analysis) Modelling System have been used to describe diversity and particularities of the LPS (by specie) in every one of the European regions. Independently, by using Crop Growth Monitoring System (CGMS) datasets, classification of the climatic conditions met in Europe have been mapped. All classifications were performed using multivariate statistical procedures such as Principal Components Analysis (PCA) and two-way Hierarchical Ascendant Classification (HAC). Results of the by-specie LPS classifications have been then confronted to the clusters describing climate conditions in regions to interpret LPS diversity. In parallel, other statistics such as regional farm types repartition provided by Eurostat were used to verify of the pertinence of the results obtained from the purely statistical method applied. Then, clusters verified were interpreted by relating all dimensions together to give a picture as reliable as possible of the reality following a more subjective approach; finally, to ease the comprehension of the reader, by-specie LPS clusters were mapped in a GIS environment. Despite possible improvements, the preliminary zoning performed here allowed us to identify and describe reliably the specificities of the LPS in every one of the European regions (EU27). From this, we proposed a by-specie and by-LPS type sampling of the regions. This was undertaken to help the academic party to decide later of the minimum sample size necessary to obtain reliable information on the regional manures¿ management practices in vigour regarding the particularities of the LPS pointed out in this report.JRC.G.3-Agricultur

Evaluation of the Livestock Sector's Contribution to the EU Greenhouse Gas Emissions - Phase 1 (GGELS)

This interim report constitutes the third and final deliverable of the study "Evaluation of the livestock sector's contribution to the EU greenhouse gas emissions - Phase 1 (GGELS)", in accordance with the terms of reference of the Administrative Arrangement (AA) No. AGRI-2008-0245. It reports on Work Packages 2, 3 and 4. A report on Work package 1 constituted the project¿s first deliverable, which was accepted in October 2008. It is thus not covered in this report. This report aims to provide DG AGRI, as well as other possible users of the GGELS project results, with a clear though exhaustive insight in the work preformed during GGELS Phase 1 and the intermediate results produced. GGELS being a multi-disciplinary research project spanning across three JRC institutes and 5 actions, this GGELS Phase 1 report is largely a collection of output produced by the different partners. Each of these contributions constitutes a separate section in this report.JRC.G.3-Monitoring agricultural resource

Physics informed Neural Networks applied to the description of wave-particle resonance in kinetic simulations of fusion plasmas

The Vlasov-Poisson system is employed in its reduced form version (1D1V) as a test bed for the applicability of Physics Informed Neural Network (PINN) to the wave-particle resonance. Two examples are explored: the Landau damping and the bump-on-tail instability. PINN is first tested as a compression method for the solution of the Vlasov-Poisson system and compared to the standard neural networks. Second, the application of PINN to solving the Vlasov-Poisson system is also presented with the special emphasis on the integral part, which motivates the implementation of a PINN variant, called Integrable PINN (I-PINN), based on the automatic-differentiation to solve the partial differential equation and on the automatic-integration to solve the integral equation

The CCR5 antagonist maraviroc exerts limited neuroprotection without improving neurofunctional outcome in experimental pneumococcal meningitis.

One-third of pneumococcal meningitis (PM) survivors suffer from neurological sequelae including learning disabilities and hearing loss due to excessive neuroinflammation. There is a lack of efficacious compounds for adjuvant therapy to control this long-term consequence of PM. One hallmark is the recruitment of leukocytes to the brain to combat the bacterial spread. However, this process induces excessive inflammation, causing neuronal injury. Maraviroc (MVC)-a CCR5 antagonist-was demonstrated to inhibit leukocyte recruitment and attenuate neuroinflammation in several inflammatory diseases. Here, we show that in vitro, MVC decreased nitric oxide production in astroglial cells upon pneumococcal stimulation. In vivo, infant Wistar rats were infected with 1 × 104 CFU/ml S. pneumoniae and randomized for treatment with ceftriaxone plus MVC (100 mg/kg) or ceftriaxone monotherapy. During the acute phase, neuroinflammation in the CSF was measured and histopathological analyses were performed to determine neuronal injury. Long-term neurofunctional outcome (learning/memory and hearing capacity) after PM was assessed. MVC treatment reduced hippocampal cell apoptosis but did not affect CSF neuroinflammation and the neurofunctional outcome after PM. We conclude that MVC treatment only exerted limited effect on the pathophysiology of PM and is, therefore, not sufficiently beneficial in this experimental paradigm of PM

Nebulized Bacteriophages for Prophylaxis of Experimental Ventilator-Associated Pneumonia Due to Methicillin-Resistant Staphylococcus aureus.

OBJECTIVES There is a need for alternative strategies to combat and prevent antibiotic-resistant bacterial infections. Here, we assessed the potential for bacteriophage prophylaxis in the context of experimental ventilator-associated pneumonia due to methicillin-resistant Staphylococcus aureus in rats. DESIGN Nebulized phages (aerophages) were delivered to the lungs of rats using a modified vibrating mesh aerosol drug delivery system. Animals were intubated and ventilated for 4 hours, at which point they were infected with methicillin-resistant S. aureus strain AW7 via the endotracheal tube, extubated, and then monitored for 96 hours. SETTING Ventilator-associated pneumonia. SUBJECTS Male Wistar rats. INTERVENTIONS A single application of aerophages prior to ventilation at one of two concentrations (~1010 plaque forming units/mL or ~1011 plaque forming units/mL). MEASUREMENTS AND MAIN RESULTS 1) Animal survival at 96 hours, 2) enumeration of bacteria and phages in the lungs and spleen, and 3) lung tissue histopathology. Animals that received aerophages prior to ventilation and methicillin-resistant S. aureus challenge showed a higher survival rate compared with untreated controls (60% for animals that received 3 × 10 plaque forming units; 70% for animals that received 3 × 10 plaque forming units; 0% for controls; p < 0.01 for each treatment versus untreated). Surviving animals that received aerophage prophylaxis had fewer methicillin-resistant S. aureus in the lungs compared with untreated control animals that succumbed to pneumonia (1.6 × 10 colony forming units/g vs 8.0 × 10; p < 0.01). CONCLUSIONS Prophylactically administered nebulized bacteriophages reduced lung bacterial burdens and improved survival of methicillin-resistant S. aureus infected rats, underscoring its potential in the context of ventilator-associated pneumonia

Searching for synergy: combining systemic daptomycin treatment with localised phage therapy for the treatment of experimental pneumonia due to MRSA.

OBJECTIVE Bacteriophages (or phages) are viruses which infect and lyse bacteria. The therapeutic use of phages (phage therapy) has regained attention in the last decades as an alternative strategy to treat infections caused by antimicrobial-resistant bacteria. In clinical settings it is most likely that phages are administered adjunct to antibiotics. For successful phage therapy it is therefore crucial to investigate different phage-antibiotic combinations in vivo. This study aimed to elucidate the combinatorial effects of systemic daptomycin and nebulised bacteriophages for the treatment of experimental pneumonia due to methicillin-resistant Staphylococcus aureus (MRSA). RESULTS Using a rat model of ventilator-associated pneumonia caused by MRSA, the simultaneous application of intravenous daptomycin and nebulised phages was not superior to aerophage therapy alone at improving animal survival (55% vs. 50%), or reducing bacterial burdens in the lungs, or spleen. Thus, this combination does not seem to be of benefit for use in patients with MRSA pneumonia

Efficacy assessment of a novel endolysin PlyAZ3aT for the treatment of ceftriaxone-resistant pneumococcal meningitis in an infant rat model.

BACKGROUND Treatment failure in pneumococcal meningitis due to antibiotic resistance is an increasing clinical challenge and alternatives to antibiotics warrant investigation. Phage-derived endolysins efficiently kill gram-positive bacteria including multi-drug resistant strains, making them attractive therapeutic candidates. The current study assessed the therapeutic potential of the novel endolysin PlyAZ3aT in an infant rat model of ceftriaxone-resistant pneumococcal meningitis. METHODS Efficacy of PlyAZ3aT was assessed in a randomized, blinded and controlled experimental study in infant Wistar rats. Meningitis was induced by intracisternal infection with 5 x 107 CFU/ml of a ceftriaxone-resistant clinical strain of S. pneumoniae, serotype 19A. Seventeen hours post infection (hpi), animals were randomized into 3 treatment groups and received either (i) placebo (phosphate buffered saline [PBS], n = 8), (ii) 50 mg/kg vancomycin (n = 10) or (iii) 400 mg/kg PlyAZ3aT (n = 8) via intraperitoneal injection. Treatments were repeated after 12 h. Survival at 42 hpi was the primary outcome; bacterial loads in cerebrospinal fluid (CSF) and blood were secondary outcomes. Additionally, pharmacokinetics of PlyAZ3aT in serum and CSF was assessed. RESULTS PlyAZ3aT did not improve survival compared to PBS, while survival for vancomycin treated animals was 70% which is a significant improvement when compared to PBS or PlyAZ3aT (p<0.05 each). PlyAZ3aT was not able to control the infection, reflected by the inability to reduce bacterial loads in the CSF, whereas Vancomycin sterilized the CSF and within 25 h. Pharmacokinetic studies indicated that PlyAZ3aT did not cross the blood brain barrier (BBB). In support, PlyAZ3aT showed a peak concentration of 785 μg/ml in serum 2 h after intraperitoneal injection but could not be detected in CSF. CONCLUSION In experimental pneumococcal meningitis, PlyAZ3aT failed to cure the infection due to an inability to reach the CSF. Optimization of the galenic formulation e.g. using liposomes might enable crossing of the BBB and improve treatment efficacy

Neuro-axonal injury in COVID-19: the role of systemic inflammation and SARS-CoV-2 specific immune response

Background: In coronavirus disease-2019 (COVID-19) patients, there is increasing evidence of neuronal injury by the means of elevated serum neurofilament light chain (sNfL) levels. However, the role of systemic inflammation and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)–specific immune response with regard to neuronal injury has not yet been investigated. Methods: In a prospective cohort study, we recruited patients with mild–moderate (n = 39) and severe (n = 14) COVID-19 and measured sNfL levels, cytokine concentrations, SARS-CoV-2-specific antibodies including neutralizing antibody titers, and cell-mediated immune responses at enrollment and at 28(±7) days. We explored the association of neuro-axonal injury as by the means of sNfL measurements with disease severity, cytokine levels, and virus-specific immune responses. Results: sNfL levels, as an indicator for neuronal injury, were higher at enrollment and increased during follow-up in severely ill patients, whereas during mild–moderate COVID-19, sNfL levels remained unchanged. Severe COVID-19 was associated with increased concentrations of cytokines assessed [interleukin (IL)-6, IL-8, interleukin-1 beta (IL-1β), and tumor necrosis factor-alpha (TNF-α)], higher anti-spike IgG and anti-nucleocapsid IgG concentrations, and increased neutralizing antibody titers compared with mild–moderate disease. Patients with more severe disease had higher counts of defined SARS-CoV-2-specific T cells. Increases in sNfL concentrations from baseline to day 28(±7) positively correlated with anti-spike protein IgG antibody levels and with titers of neutralizing antibodies. Conclusion: Severe COVID-19 is associated with increased serum concentration of cytokines and subsequent neuronal injury as reflected by increased levels of sNfL. Patients with more severe disease developed higher neutralizing antibody titers and higher counts of SARS-CoV-2-specific T cells during the course of COVID-19 disease. Mounting a pronounced virus-specific humoral and cell-mediated immune response upon SARS-CoV-2 infection did not protect from neuro-axonal damage as by the means of sNfL levels