dataesr/scientific-paragraphs-categorization huggingface dataset:
g. , bivalve molluscs such as Bathymodiolus azoricus, which is phylogenetically close to the deeper-dwelling B. puteoserpentis, and which naturally inhabits hydrothermal vent environments but which can survive at atmospheric pressure rendering it tractable for laboratory experiments). Ultimately, the precise selection of appropriate canary species will be habitat dependent, and still requires much more comprehensive datasets of the resident biological communities in potential mining locations, particularly in the case of nodule fields at abyssal depths. Using the WOE approach it will be possible to identify high-risk resources or high-risk communities within a license block during contractor exploration or contractor Environmental Impact Assessments prior to exploitation licenses being issued by the regulating authority-the ISA in the case of the mining within the Area.
ACKNOWLEDGMENTS The research leading to these results has received funding from the  European Union Seventh Framework Programme  ( FP7/2007(FP7/ -2013 ) ) under the  MIDAS  project, grant agreement n • 603418. This publication reflects only the views of the authors; the  European Commission  is not liable for any use that may be made of the information contained herein. Martins is financed by  SFRH/BPD/73481/2010  grant and had the support of  Fundação para a Ciência e Tecnologia (FCT) , through the strategic project  UID/MAR/04292/2013  granted to MARE. Brown is supported through an  IMarEST Stanley Gray Fellowship. Canals and  Sanchez-Vidal  acknowledge the support received from the  Spanish  funded projects NUREIEV (ref. CTM2013-44598-R ) and NUREIEVA (ref. CTM2016-75953-C2-1-R ), including ship time.
Considering the integration time of realistic simulations, this limitation is also due to the paramount importance of the mechanical energy dissipation, which has to be guaranteed in order to produce physically acceptable solutions. Adapting the choices made to express the distribution of the pressure law, which is also generally formulated, in some sense, by mean of staggered discretizations of the vertical direction, the multilayer equations formulated in this work are closely connected to those used in the majority of operational oceanic simulation softwares like HYCOM  [11] , ROMS  [49]  or NEMO  [37] , in isopycnal coordinates (i. e. when the flow is represented along the lines of constant density). These softwares have been developed on staggered grids, sharing an Arakawa C-grid type as a general basis with orthogonal curvilinear coordinates to take into account irregular lateral boundaries.
Some reference solutions for the multilayer shallow water model with the Coriolis force are of course provided by more sophisticated operational softwares like HYCOM  [11] , ROMS  [49]  or NEMO  [37] , but with the inconvenience of not being necessary exactly based on the same physical model as the one concerned here. A first academic test case is considered, involving two-dimensional oscillating layers around a steady state in the linear small amplitude limit. It is investigated for this test case the inequality conditions for the stabilization constants γ and α ensuring the linear stability, as well as those which guarantee the strict decrease of the mechanical energy between each time step. At the end, the a priori best pair verifying the two stability conditions with a minimum of dissipation will be extracted and the resulting scheme compared to the classical HLLC approximate Riemann solver (see  [55]  with the wave speed estimates of  [57] ).
| Data collection The field sampling took place 22 months after the experimental setup, that is, in December 2015. The paired plots had a similar species composition at the beginning of the experiment (time of the fence setting). Within each plot, we identified all the species of the associated communities and estimated their relative cover using a 10*10 cm mesh (see Garcia, Meneses, Naoki, & Anthelme, 2014, for details). We measured plant functional traits on the nurses themselves and on all the species of the associated community: LDMC, leaf thickness, and maximum height. The LDMC characterizes plant resource acquisition strategies and is negatively correlated with maximum relative growth rate, because of a trade-off between resource acquisition speed and nutrient conservation  (Diaz et al.
ACKNOWLEDGMENTS We thank  Mary Carolina García Lino ,  Ariel Lliully ,  Arthur Sanguet ,  Marine Segond , and  Pierre Vincent  for their invaluable help in the field, and we are grateful to  Marine Segond  for her help with the leaf analysis. We also thank  Étienne Baron ,  Grégoire Freschet , and  Cyrille Violle  for their helpful advices about the measurements of functional traits. This work was funded by the  Fond Français pour l'Environnement Mondial (FFEM)  and the  Fondation pour la Recherche sur la Biodiversité (FRB)  (" Modeling BIOdiversity and land use interactions under changing glacial water availability in Tropical High Andean Wetlands "-BIOTHAW, AAP-SCEN-2011-II).
Some of the published papers describe the use of alternatives for the reduction of disease risk. The literature review has identified gaps in knowledge that limit the use of alternatives to antimicrobials in animal husbandry in the EU. For example, there are very few cases in which data on the same agent used as an alternative to antimicrobials are reported in more than one study, and most of these studies demonstrate the efficacy of these agents, but very few are clinical trials or provide robust data to demonstrate the efficacy according to the authorisation guidelines as feed additives or veterinary medicines. A positive impact on animal health parameters has been demonstrated for some of the alternatives considered. These include organic acids, probiotics, competitive exclusion, synbiotics, passive immunisation, bacteriophages, immunomodulators, Zinc oxide, clay minerals and teat sealants.
Evidence on the efficacy of these alternatives, associated risks and specific knowledge gaps are listed in the Opinion. For ToR 4 (to assess the potential impact of such alternative measures on the occurrence of antimicrobial resistance in bacteria from food-producing animals and food), EFSA and EMA concluded that due to the limitation in data availability, the potential impact of the alternative measures on the occurrence of AMR in bacteria from food-producing animals and food cannot be conclusively established. Measures which reduce the need to use antimicrobials, such as improved biosecurity, control and/or eradication of infectious diseases and the alternatives identified above, are likely to reduce development of AMR indirectly. Some substances which are used as alternatives to antimicrobials (e.
g. proliferative enteropathy by L. intracellularis, swine dysentery, ileitis, Salmonella spp. ); • sows: urogenital disorders (e. g. leptospirosis), post-partum dysgalactia syndrome, Actinobacillus pleuropneumoniae in gilts. In Denmark, as reported in the Vetstat database  (Dupont et al. , 2016) , the use of antimicrobials in intensive swine production is higher for weaner pigs compared to sows, piglets and finishers. Such use is mostly related to gastrointestinal disorders; for example, 58% of the standardised animal daily doses in Danish pig production in 2014 were for gastrointestinal diagnoses. Secondly, antimicrobials are used for respiratory problems. Such use was also observed in Spain  (Moreno, 2014b). A different picture was observed in Sweden, with the highest consumption recorded for suckling piglets  (Sj € olund et al.
Monitoring of antimicrobial use at national level, on farms and by prescriber In Europe, 29 countries provided their antimicrobial sales data for 2014 to ESVAC. In addition to provision of data to the ESVAC project, the EC PUAVM Guidelines recommend that MSs collect data on use by animal species and age group. These databases are a vital tool that underpins the benchmarking of antimicrobial use, for measuring the effectiveness of reduction of use policies and ultimately, when analysed in conjunction with AMR monitoring data, for making inferences about the impact of antimicrobial use on AMR.
DANMAP (see above) was established to follow the impact of withdrawing antimicrobial growth promoters in the pig and poultry sectors between 1997 and 2000, but more broadly to monitor antimicrobial consumption and study its association with AMR in animals and humans. It was established as a collaborative effort of all stakeholders involved in the farm-to-fork chain, including commercial and public, and human and animal health sectors. The veterinary medicines database VetStat was established in 2000 to monitor antimicrobial consumption and is hosted by the Danish Veterinary and Food Administration. Veterinarians, feed mills and pharmacists send information electronically to VetStat, which includes the supplier and prescribing veterinarian identity, farm-identity, name of product, quantity prescribed and administered, animal species, age group and diagnostic group.
The Netherlands In 2010, the independent Netherlands Veterinary Medicines Authority (SDa) was set up to collect data on antimicrobial consumption on farms, establish benchmark indicators for the individual major livestock sectors and analyse trends in consumption. The SDa is a public-private partnership between government, stakeholders from the major livestock sectors (pigs, broilers, veal calves and dairy cattle) and the Royal Dutch Veterinary Association (KNMvD). Veterinarians enter prescription information in a Practice Management System and this is transferred to a central database. The information includes veterinarian and farm details, quantity supplied and animal species treated. Data are then transferred to databases held by private livestock quality assurance systems. The sectors calculate consumption as the number of days per year on a farm that animals have been administered antimicrobials.
4%, compared to the goal to achieve a 75% reduction by 2020. It was suggested that new requirements for veterinarians to perform antimicrobial susceptibility testing prior to use of CIAs, and to register use of all antimicrobials in the national database, might help to reinforce responsible use principles in future. A study conducted in 2012-2013 on 47 farrow-to-finish pig farms in Belgium showed that 3rd-and 4th-generation cephalosporins were the 4th ranking antimicrobials used, with a proportion of 10. 8% of the total antimicrobial consumption  (Sj € olund et al. , 2016). For fluoroquinolones and colistin this proportion was 5. 3% and 17. 5% (2nd ranking), respectively. Another study on 61 pig farms in Flanders, performed between December 2010 and May 2014, studied the potential reduction in antimicrobial consumption that could be achieved by optimisation of herd management, biosecurity status, vaccination strategy, anthelmintic therapy and advice on prudent use of antimicrobials  (Postma et al.
g. for cheese or yoghurt. A second example involves certification schemes for monitoring antimicrobial use in pigs, poultry and fattening calves, based on systematic recording of antimicrobial use or deliveries recorded in the database of the certification body (QA Germany). Some multinational food manufacturers, retailers and restaurant chains have recently announced new policies to serve meat from animals grown without use of medically important antimicrobials. This has led to a pressure on animal farming companies, mainly chicken producers, to rear the majority of animals for such influential customers (e. g. major supermarket chains) without supplementation by antimicrobials important to human medicine, and with antimicrobials use limited to treating clinical disease outbreaks. Some animal farming companies or farm cooperatives use their labelling to communicate about products obtained without, or with limited use of, antimicrobials.
, 2015; Szulkin et al. , 2015). Breeding for disease resistance or resilience is now widespread in the livestock industry, being applied on an extensive or nationwide basis as part of the selection index in a number of countries. The earliest and most notable examples are the disease recording routines in Scandinavian countries  (Koeck et al. , 2010) , where selection is applied in cattle to increase milk production, reproductive performance, and resistance to mastitis, ketosis and 'other' diseases. Health data collected via veterinary systems are integrated into the national electronic database system, and used for genetic evaluation  (Heringstad et al. , 2000). Health data recorded by dairy producers can be used to establish an evaluation system for genetic selection for improved disease resistance  (Koeck et al.
). The resulting clustering effect with multiple technical replicates from the same sample and multiple samples from the same store was not included in the statistical analyses, either in the original studies  (Cui et al. , 2005; Miranda et al. , 2007; Miranda et al. , 2008a,b) , or in the systematic review. The fifth study included did not demonstrate any effect of farming type  (Lestari et al. , 2009). Due to some methodological flaws identified in the three systematic reviews and the large uncertainties in the results, the RONAFA WG elected to perform an additional extensive literature review. Details of the search strategy, queried databases and selection criteria used to identify relevant studies are provided in Appendix G. In addition, all primary papers included in the three systematic reviews were screened.
Genotyping of pathogens Molecular analysis with polymerase chain reaction (PCR) is needed to demonstrate the presence of virulence or resistance genes in organisms (genotyping), sometimes in combination with plasmid profiling to detect horizontal transferable mechanisms. With multiplex PCR and microarrays different genes can be simultaneously identified, and advanced PCR techniques enables to quantify genes to improve the relevance of found genes and species-specific virulence factors  (Aarts et al. , 2006; Batchelor et al. , 2008). These systems can have a little workload and can have very short turn on hands (minutes) and turnaround time (hours). Detection and accuracy relies on and is limited to a well-managed and up-to-date database with DNA information the needs continuously updated to detect upcoming mutations and mobile genetic elements.
Spectrometry The most recent wave in routine microbiology is the implementation of MALDI-TOF and related spectrometry assays for rapid diagnosis of pathogens. By comparisons of protein profiles with a databank, identification of the bacterial species from pure culture is possible within minutes  (Dingle and Butler-Wu, 2013) , although standardisation by bacterial species needs to be done  (Martiny et al. , 2013). A standard culture is still required, but recent advances show promising results for direct identification on clinical samples  (Nilsen, 2012; Johansson et al. , 2014). These assays are not restricted to a limited number of organisms (including non-bacterial infective agents like yeasts), and some are able to identify clonal relatedness and antimicrobial resistance mechanisms (e. g.
Details of the search terms used, databases queried and selection criteria used are provided in Appendix G. Specific criteria were used to select the papers for further review from those identified from the literature search; the aim was to select studies on the efficacy of the alternative measure on health parameters (e. g. reduced morbidity or mortality) and, preferably, reporting a comparison of with an antimicrobial treatment. Reduction in human zoonotic pathogens (e. g. Salmonella spp. and Campylobacter spp. ) was generally not considered further when discussing alternatives to antimicrobials. The majority of the papers identified by the search failed to meet one or more of the inclusion criteria. Most of the articles focussed on the effect of the potential alternative to antimicrobials on performance and did not include health parameters as endpoints of the studies.
In addition, structure and process indicators for infection prevention and control and for antimicrobial stewardship in various healthcare settings have been developed are being implemented in the HAI-Net modules. The results of the two above searches were merged into one single database, and all duplicates were removed, resulting in a database including 1,505 references. Titles and abstracts of the references were screened in order to identify relevant papers to be reviewed in detail. When screening the references, papers were considered relevant if: • they were about experimental studies comparing the effect of the above alternatives with the effect of antimicrobials, or reviews on the subject; or • they investigated the effect of the above alternatives on the health status of food-producing animals (papers were excluded if they were pure assessment of the growth or production quality); or • they compared the effect of the above alternatives with the effect of antimicrobials for growth promotion but included as end points the assessment of some health parameters of the animals (e.
G. 2. Literature search on the association between AMR and organic farming compared to conventional farming As indicated in Sections 2. 2 and 4. 2. 3. 10, a literature search was conducted to identify available evidence concerning the possible association of AMR and organic compared to conventional farming. The searches were conducted using combinations of terms covering three main question components: (1) organic farming, (2) bacterial and antimicrobial resistance and (3) animal populations. The search string used is reported in Table  G. 3. The search was conducted in the following database: PubMed. The search was conducted for years 1975-2016. A total of 125 references (1 November 2016) was retrieved and screened for studies of interest. Relevance screening was conducted by one reviewer person whereas quality assessment and data extraction were conducted by three reviewers.
Some tumour tissue samples were obtained after pancreatic resection (duodeno-pancreatectomy) from patients diagnosed with pancreatic adenocarcinoma (Gastroenterology and Digestive Surgery departments, Timone Hospital, Marseille, France; CRO2 Agreement DC20131857) between February 2007 and February 2016. All specimens were re-evaluated by an expert pathologist. PanINs, tumour or control pancreatic tissues from Pdx1-Cr,Ink4a fl/fl LSL-Kras G12D mice  (Leca et al, 2016)  were fixed in 4% (wt/vol) formaldehyde for immunochemistry. Gene expression microarrays. Gene expression microarrays from xenografted tumours issued from 55 PDAC tissue samples (see above) were performed as previously described  (Duconseil et al, 2015). All array data are available on the Gene Expression Omnibus (http://www-ncbi-nlm-nih-gov.
Cell surface cadherin extinction was assessed by both immunofluorescence (Figure  3A ) and western blot (Supplementary Figure  S1 ). Spheroid formation assay. Spheroid formation assay was used to investigate the effect of cadherins on the cell À cell adhesion properties as previously described  (Terciolo et al, 2017). Isolated cells were seeded onto U-bottom untreated tissue culture 96-well plates at a concentration of 5000 cells per well in 100 ml DMEM containing 10% FCS and 0. 24% methylcellulose. Spheroids were grown for 24 h and pictures were taken using an Olympus microscope (objective Â 4). The size of the spheroids was quantified by measuring the area occupied by cells using ImageJ software (rsb. info. nih. gov/ij/). 3D-invasion assay. Cells were cultured for 72 h as described above to obtain compact spheroids.
The latter were embedded into 1. 6 mg ml À 1 of bovine collagen I matrix (Advanced Biomatrix) diluted in 0. 12% methylcellulose and covered with serum-free medium. Spheroids were then incubated for 24 h in a temperature and CO 2 controlled chamber mounted on an inverted microscope Olympus IX83. Images were captured every 60 min using an orca-flash4 camera (Hamamatsu) with a Â 4 objective. The size of the spheroids was quantified by measuring the area occupied by cells using ImageJ software (rsb. info. nih. gov/ij/). In this experiment, cell invasion is independent of cell proliferation since cell treatment with mytomicin C did not alter the results obtained in 3D invasion (data not shown). 2D-invasion assay. Owing to their inability to form spheroids, the 3D invasion assay was unachievable for CRCM08 cells.
The cell tracks were obtained using ImageJ software. The values for the assessment of migration speed, velocity and directionality were obtained using ImageJ software. Migration speed was determined by the ratio between the total distance and duration of cell migration. Cell velocity corresponds to the distance between the positions of the cells at the beginning and the end of the experiment divided by time. Cell directionality is the ratio between cell velocity and cell speed. Fluorescent-gelatin degradation assay. Coverslips coated with FITC-conjugated gelatin (Sigma) were prepared as described by  (Steffen et al, 2008). Isolated cells were plated on FITC-conjugated gelatin at 70 000 cells cm À 2 for 16 h and then fixed in 4% paraformaldehyde. The areas of degraded matrix were observed with an SP5 Leica confocal microscope equipped with LAS AF Lite software.
ImageJ software was used to evaluate the number of invadopodia per cell. At least 150 cells from three different coverslips were chosen randomly and analysed. Subcutaneous and orthotopic xenografts of pancreatic cancer cells. All experimental procedures involving animals were performed in accordance with the French Guidelines and approved by the ethical committee of Marseille (agreement 50-31102012). BxPC-3 cells were harvested by mild trypsinisation, washed twice in PBS, and then suspended in Matrigel at 2 Â 10 6 cells per 100 ml. To induce tumours, cell suspension was injected subcutaneously (s. c. ) into the flank of 6-8-week-old female NMRI-Foxn1nu/ Foxn1nu mice (Charles River Laboratories, L'Arbresle, France; six mice per group). Injected mice were monitored daily and killed 3 weeks after inoculation.
Samples were then washed and mounted in ProLong Gold (Invitrogen, Illkirch, France). After dewaxing and antigen retrieval, paraffin-embedded 4 mm sections of human pancreatic tumour biopsies were treated and subjected to double immunostaining, as described above. Images were captured and analysed using a SP5 Leica confocal microscope equipped with LAS AF Lite software. The intensity and distribution patterns of specific immunofluorescence staining were evaluated by two blinded, independent observers using a semi-quantitative score (graded as 0 ¼ none, 1 ¼ weak, 2 ¼ moderate, 3 ¼ strong staining, and 4 ¼ saturated signal). This analysis was performed without any knowledge of anatomopathological evaluation, the diagnosis or the standard performed pathological haematoxylin reaction of each specimen.
Similar results were obtained with a type I collagen 2D invasion, an assay that did not require cell-cell contacts (Figure  4C ). Interestingly, CRCM110 cells were more invasive than CRCM08 cells that express only cadherin-3. All in all, our data indicate that both cadherin-1 and cadherin-3 take part in intercellular-dependent and -independent invasion through type I collagen. Cell invasion is a complex and multifactorial process that requires cell adhesion, extracellular matrix proteolysis and cell migration. We therefore set out to dissect the role of each cadherin during these crucial events. Collective cell migration (i. e. , cell-cell contact dependent cell migration) was assessed by wound healing assay. While BxPC-3-cadh-1 þ /cadh-3 þ cells resulted in 30% of closed wound at 6 h, there was a significant increase of cell migration for BxPC-3-cadh-1 À /cadh-3 þ cells (Figure  5A ).