dataesr/scientific-paragraphs-categorization huggingface dataset:
Immunofluorescence microscopy. IFAs on intracellular parasites on HFFs cells were conducted as described previously  29. Note that RON labelling in the rhoptries have been performed after methanol fixation while RON labelling at the moving junction have been performed after formaldehyde 4% fixation, followed by 0, 1% saponin permeabilization. The antibodies used and their dilution for IFA are listed in Supplementary Table  S2. Samples were observed with a Zeiss Axioimager epifluorescence microscope. Images were acquired with a Zeiss Axiocam MRm CCD camera driven at the 'Montpellier resources imagerie' facility and processed using Zeiss Zen software. Adjustments for brightness and contrast were applied uniformly on the entire image. Transfection and selection of transformants. 20 × 10 6 T. gondii tachyzoites were transfected by electroporation at 2.
Acknowledgements We Thanks  Damien Jacot  and the flow cytometry facility,  CMU, Geneva  for their work with sorting parasites. We thank  Boris Striepen ,  Michael Cipriano  and  Sebastian Lourido  for plasmids. This research was supported by the  ANR  ( ANR-16-CE15-0010-01 ),  Laboratoire d'Excellence (LabEx)  (ParaFrap  ANR-11-LABX-0024 ), by the  Fondation pour la Recherche Médicale  (Equipe FRM  DEQ20130326508 ) to ML. A. G. has been supported by  ParaFrap  ( ParaFrap   ANR-11-LABX-0024 ) and is a recipient of  FRM  (award no. FDT20160435387 ). M. L. gratefully acknowledges the " Montpellier Ressources Imagerie " technical platform for access to their microscopes and cell sorters. ML and SB are INSERM researchers.
Real-Time Reverse Transcription Polymerase Chain Reaction (PCR) Total RNA from a section of thoracic aorta was extracted with Trizol Reagent (Euromedex) and purified using the RNeasy kit, according to the manufacturer's instructions (Qiagen, Hilden, Germany). First strand cDNA was synthesized according to the manufacturer's instructions (Roche, Basel, Switzerland). Quantitative polymerase chain reaction analysis was then performed with N ,N -dimethyl-N-[4-[(E)-(3-methyl-1,3-benzothiazol-2-ylidene)methyl]-1-phenylquinolin-1-ium-2-yl]-N-propylpropane-1,3-diamine (SYBR) green PCR technology (ABGene, Portsmouth, NH, USA) (Table  S1 ). Relative quantification was achieved with MyiQ (Bio-Rad, Hercules, CA, USA) software according to the manufacturer's instructions. Data were normalized by hypoxanthine phosphoribosyltransferase (HPRT) and β-actin levels and expressed as percentage relative to controls.
Statistical Analysis Data are expressed as mean ± SEM. Normality of distributions was verified by means of the Kolmogorov-Smirnov test. Data were analyzed using a one-way analysis of variance, followed by a Newman-Keuls to assess specific differences among groups or conditions. All analyses was done with SPSS version 20. 0 (IBM SPSS Statistics) and amtwo-tailed p-value of <0. 05 was considered statistically significant.
Quantification of chemokines and cytokines in serum A panel of chemokines and cytokines, CxCL1 (KC), CxCL2 (MIP-2), CCL5 (RANTES), TNFα, and IFN-γ were measured in mouse serum (1:2 dilution in assay buffer) with ProcartaPlex Multiplex Immunoassays (eBioscience) according to the manufacturer's instructions. Samples were processed with xMAP Technology by MagPix Luminex using 50-bead count and analyzed with eBioscience Procarta Plex Analyst software. q-PCR and RT-PCR DNA was extracted from blood, urine, and kidney using a NucleoSpin tissue kit. Leptospira was quantified using TAMRA probe and primers (Eurofins) to Leptospira 16s rRNA by qPCR. Total RNA was extracted from tissues using an RNeasy mini kit and reverse transcribed using a high-capacity cDNA reverse transcription kit. cDNA was subjected to real-time PCR using primer and TAMRA probes previously described  [11].
Flow cytometry Single cell suspensions of lymphoid tissues were prepared as described  [11]. Live/dead cell stain was used to eliminate dead cells. Cells were incubated in Fc blocking for 15 min at 4˚C in staining buffer and incubated with the appropriate marker for surface staining in the dark for 30 min at 4˚C. Surface markers for T cells (CD3, CD4, CD8, CD62L, CD44) were described previously  [11]. The surface marker for B cells was CD-19 conjugated with PercP Cy5. 5. For myeloid cells the following lineage surface markers (Tonbo) were used (1:200): CD3 conjugated with pacific blue, MHC-II conjugated with allophycocyanin, CD11b conjugated with phycoerythrin Cy7, CD11c conjugated with allophycocyanin Cy7, and Ly6C conjugated with FITC. Cells were acquired on a BD-LSR II flow cytometer and analyzed using Flow Jo software.
1 surgical cases per 100,000 inhabitants recorded for 2003-2010 by the Ministry of Health of Morocco), and the high incidence of CE in cattle (42. 9%) and in sheep (11. 0%) reported by El  Berbri et al. (2015b) , were suggestive of the importance of dog infection in this province. Despite the rate of infection in dogs probably being the best indicator of the degree of transmission of Eg in a region  (Barnes et al. , 2012; Craig et al. , 2003) , data for Eg infection in dogs are lacking for this region. For these reasons, surveys in dogs were undertaken as part of a large collaborative project funded by the EU under FP7, entitled the "Integrated Control of Neglected Zoonoses" (ICONZ, www. iconzafrica. org) conducted in this region. Investigations on CE included (1) prevalence of infection in livestock (cattle and small ruminants) as part of abattoir surveys, (2) Eg prevalence in dogs, (3) evaluation of knowledge, attitudes and practices with regards to the presence, transmission factors, impact, and control of CE and, (4) piloting a control intervention.
Research design Dog sampling was conducted in 23 rural communes and in all of the 5 municipalities. For each of the rural communes and municipalities, one to two douars (villages) were randomly selected from the list of villages in each commune obtained from the Caïd (an appointed commune government official). At village level, 5-20 households were randomly selected from lists of households in each village obtained from the Cheikhs (locally appointed village heads). The inclusion criteria established by  Gemmell (1973)  were used in this study. All dogs two months older and younger than 10 years, except pregnant females, were selected to undergo AH purgation. For households owning more than one dog, only one dog was randomly selected for purgation. For each dog sampled, data on age, sex, and village/commune of origin was recorded.
Statistical analysis WinPepi ® v11. 42  (Abramson, 2013a,b)  software was used for the statistical analysis of risk factors. Data were categorised according to age and sex of dog, whether the dog was from a rural (commune) versus urban (municipality) area and presence/absence of rural or urban abattoir in commune or municipality respectively. Comparison of proportions of infected dogs across variables was firstly undertaken by calculating 95% confidence intervals (CI) using Fisher's exact method. Overlap of confidence intervals means that no conclusion can be drawn on a difference in infection rate between different categories. Odds ratios (with Fisher's exact 95% CI) and Pearson's chi-square were also calculated.
Acknowledgements This research was supported by  European Union   Seventh Framework Program  ( FP7/2007-2013)  under grant agreement no. 221948 , ICONZ (Integrated control of Neglected Zoonoses). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the  European Commission. We would like to thank the ONSSA, the local authorities of  Sidi Kacem Province , the local veterinarians and veterinary technicians and the farmers for their help in carrying out the fieldwork. We are grateful to  Professor Ian Maudlin  for a critical reading of the manuscript.
Evolution and dispersion history on Earth of organisms can best be studied through biological markers in molecular epidemiological studies. The biological diversity of the cestode Echinococcus multilocularis was investigated in different cladistic approaches. First the morphological aspects were explored in connection with its ecology. More recently, molecular aspects were investigated to better understand the nature of the variations observed among isolates. The study of the tandemly repeated multilocus microsatellite EmsB allowed us to attain a high genetic diversity level where other classic markers have failed. Since 2006, EmsB data have been collected on specimens from various endemic foci of the parasite in Europe (in historic and newly endemic areas), Asia (China, Japan and Kyrgyzstan), and North America (Canada and Alaska).
Biological data on the isolates and metadata were also recorded (e. g. host, geographical location, EmsB analysis, citation in the literature). In order to make available the data set of 1,166 isolates from classic and aberrant domestic and wild animal hosts (larval lesions and adult worms) and from human origin, an open web access interface, developed in PHP, and connected to a PostgreSQL database, was developed in the EmsB Website for the Echinococcus Typing (EWET) project. It allows researchers to access data collection, perform genetic analyses online (e. g. defining the genetic distance between their own samples and the samples in the database), consult distribution maps of EmsB profiles, and record and share their new EmsB genotyping data. In order to standardize the EmsB analyses performed in the different laboratories throughout the world, a calibrator was developed.
Introduction The description of diversity among isolates for a given species is a major field of investigation for the understanding of its past and present history on Earth. This kind of data collection needs to be shared among the scientific community working in this field, to ensure experience and knowledge is brought together and thus enhanced. The GenBank sequence database is the best example of an open access genetic and proteomic data source (http://www. ncbi. nlm. nih. gov/genbank/). Dedicated databases are also available on more focused topics in the field of biology, such as the North-East India microbial database NEMiD  [1]. This database gathers biological characteristics, sampling details and molecular data aspects relating to soil organisms. The InSatDb is a database putting together annotated microsatellite targets of five fully sequenced insects  [2].
From this database, the Web interface allows us, inter alia, to find genotyping targets. In the field of host-parasite relationships, the data about the genetic diversity of a parasite associated with host data such as species identity, geographical location, or the level of severity of the disease induced are more powerful when they are gathered in scalable databases. These data, put together in a common database, are more useful because they provide information about the genetic variations between parasite specimens, the pathogenicity of parasite strains circulating in the environment and, when coupled with Geographical Information Systems (GIS) can depict the spread and emergence of host and parasite strains or genotypes over space and time. The microsatellite EmsB was described for the first time in the cestode Echinococcus granulosus for genotyping studies on this infectious agent  [3] , causing cystic echinococcosis, one of the most important cestode diseases with a huge public health impact globally  [4, 5].
Compared to EmsB, few studies, such as other microsatellite investigations or haplotype network experiment, have been additionally done that could help to further explore the genetic diversity in E. multilocularis,  [26, 27]. So far, EmsB genotyping appears to be the most convening marker, because producing raw data is simple using a single PCR followed by a fragment size analysis (FSA) (see S1 File EmsB Guidelines sections I to V). Thanks to geographical mapping of the data set constituted from all previous studies performed on the EmsB genotyping, and using a statistical analysis quantifying genetic distance among isolates, this approach may yield in the future, the potential to trace back the contamination event of a patient. These attempts are, however, partly obscured by the heterogeneous geographical distribution of EmsB-related information and the rather small amount of data considering the large areas of investigation.
It is therefore a priority to set-up an open and collaborative information system allowing EmsB profiles to be collected at an international level. The aim of the present paper is to introduce the EmsB database (DB) application, named EWET-DB, as well as the EmsB Website for Echinococcus Typing database, that allows us to build a reference collection dedicated to Echinococcus genetic data by recording, sharing and providing access to the EmsB data.
The EmsB data EmsB genotyping was performed in different projects in order to describe the genetic diversity of Echinococcus multilocularis. First of all, the EU EchinoRisk project (QLK2-CT-2001-01995) aimed to assess the risk related to alveolar echinococcosis in Europe and propose a prevention framework. The first collection of isolates from different hosts (human, rodent, monkey and fox) and from different endemic foci (Europe, Asia and North America) was constituted to assess the genetic discriminative power of the EmsB marker  [13]. Secondly, various studies were conducted to better understand the genetic variations of the parasite at different geographical levels through the EmsB data, from a regional  [11, 24]  to a micro-local level  [13]. At this latter level, the over-discrimination was avoided because rodents from the same field presented common profiles, and were probably infected by the same fox or the same strain circulating locally.
Toolbox for EmsB data analyses In order to use the EmsB data generated by FSA, a new approach was developed. For a given sample, the EmsB data were considered as an EmsB profile. This profile was first normalized to make it suitable for analysis, and for comparison, the genetic distance calculation was performed according to a specific protocol. In the present paper an additional tool was developed, known as the calibrator, to allow us to monitor the control of quality of profiles obtained by different FSA automaton models. This tool was developed to control the quality of EmsB profiles and the process of calculating genetic distance. Profile normalization. From each E. multilocularis specimen, a PCR was performed to amplify the EmsB targets. The PCR products were labeled during the amplification.
Reproducibility was previously tested using different Taq Polymerases and was then statistically validated  [13]. A FSA was then performed on a sequencer machine, in order to separate the PCR products according to their size in base pairs (bp) and obtain the fluorescence intensity value for each size or peak (see S1 File EmsB Guidelines section VI). First the lowest peak values (under 10% of the highest peak) had to be removed as they were considered as artefacts, and data had to be transformed by normalization of the profiles (for each allele, the fluorescence intensity value was divided by the sum of intensities of the whole peaks retained; see S1 File EmsB Guidelines section VI). Genetic distance calculation. To study E. multilocularis genetic diversity and spatio-temporal relationships, the evaluation of the genetic distance among samples was performed.
Distance calculation was achieved by using hierarchical clustering analysis. First, a distance matrix among isolates was computed based on the Euclidean distance (see S1 File EmsB Guidelines section VII). Then, linkage between isolates was formed using the Unweighted Pair-Group agglomerative Method using Arithmetic mean (UGPMA) and a dendrogram of distance was generated. UGPMA allows an object (EmsB profile) to join a group of objects at the mean of the Euclidean distance between this object and all members of the group  [30]. Multiscale bootstrap resampling is used to compute p-values of each group, thereby providing information about the likelihood of each node of the dendrogram, thanks to the pvclust R package  [31]. EmsB calibrator. In order to control the EmsB quality obtained by the different working groups, a calibrator was designed in the present study.
FSA of the labeled EmsB PCR products in the various surveys were performed using different analyzers, e. g. ABI PRISM 310 Genetic Analyzer  [7, 24, 32] , Applied Biosystems 3130 Genetic Analyzer  [8, [11] [12] [13] , Applied Biosystems 3730 DNA Analyzer  [10] , Applied Biosystems 3500 Genetic Analyzer  [32]  (Life Technologies, Foster City, CA), or Beckman CEQ 8000  [3, 8, 13]  (Beckman Coulter, Fullerton, CA). With these different analyzers, a shift in the fragment size reading can be observed because of different labeling dyes used, between amplicons and standard molecular weight, influencing migration of the different components during capillary electrophoresis  [7, 33]. Based on the EmsB sequence (GenBank access code number AY680860. 1), a plasmid construction was made with four EmsB microsatellites, corresponding to (CA) 9 to 11 (GA) 11 repeats respectively, two microsatellites having the same size (including flanking regions) with 190 bp, a second with 192 bp and the last one with 194 bp.
EWET-DB to manage EmsB data In order to manage the gathered EmsB data and their associated metadata in a rigorous and systematic way, a database was developed with an open access web interface (Fig  2). Database characteristics and functionalities. The database was developed in PHP and connected to a PostgreSQL database. The different applications of the EWET web site are presented in Fig 3. The homepage of the EWET application (Fig 4 ) gives a general introduction to the EmsB microsatellite database. The "search" page can be used to consult isolate data (including EmsB data) and to consult the distribution map from the database using different criteria (host, country, province, year of sampling, etc. ) (Fig  5 ). After registering and selecting isolates, the "analyses" page allows us to calculate genetic distances among samples, generate dendrograms.
The results of the analysis can be obtained from the "Download" button. The "export" page allows us to download data from a selection of isolates, and contains the EmsB guidelines providing full details of the microsatellite and the description of the online analyses (S1 File EmsB Guidelines). R scripts are likewise available for users who wish to obtain more details on the analyses or to perform the analysis without the EWET application. EWET members can access and download the EmsB data and the all dataset, and record their isolates once they have registered. They can choose whether they would like their data to be shared or kept private. Data quality. Data recorded in the database were standardized as much as possible by using frameworks recognized by the International community, such as species names, geographical locations and coordinates.
Data set description The compilation of published EmsB data allowed us to generate a data set composed of 1166 isolates from adult or larval stage of the parasite E. multilocularis, from definitive and intermediate hosts (red foxes, domestic dogs, wild and domestic cats, raccoon dogs, humans, rodents ). The origin of the samples are available in the dataset, all samples taken from published works. Approval from an ethical committee or institutional review board was not necessary for these researches, because of the nature of the samples (parasite material). previously performed on an ABI-310 machine  [24]  were performed again on an ABI-3500 machine, as recommended by the manufacturer, to compare data with other versions. Using the electrophoregram pictures available for the EmsB profiles it is possible to visually compare samples, and the original intensity of each locus recorded provides data quality control.
Secondly, the calibrator study has allowed us to observe the non-proportionality (from a mathematical point of view) between the number of copies of a given microsatellite size and the fluorescence intensity. With the ABI-3130, the microsatellite in two copies (188 bp) presented a fluorescence intensity that was four-times higher than the second peak (190 bp), and five-times higher than the third peak (192 bp), both representing a microsatellite in one copy (Fig  6 ). The intensity of fluorescence has to be taken into account in the comparison of EmsB profiles but not in the interpretation of the number of microsatellite copies. Profile normalization and electrophoregram picture. From the published data, original fluorescence intensity values were gathered from archives for part of the data set.
EWET-DB database description The data model. The first step was to design the data model (Fig  7 )  [35]. The isolate is the central entity of the data model. Information about the isolate was gathered from the literature, computer and paper archives, as were the sampling author and sampling date, the host species, The data model consists of three main parts (Fig  7) : zone 1 describes the host of the isolate (e. g. taxonomical classification and spatial information); zone 2 was dedicated to the isolate and gave genotyping results; zone 3 provides administrative elements such as genotyping or sampling authors, laboratories, used devices and publications linked to the isolate. Application architecture. A postgreSQL database was created from this model and the existing data was successfully integrated.
The EWET application allows us to centralize and record all the data concerning isolates genotyped for the EmsB microsatellite in a unique database. It makes these data available with remote access for the scientific community (https://ewet-db. univ-fcomte. fr). It ensures the quality of the data and provides easy access to tools for calculating EmsB (distance matrix, dendrogram, comparison, maps), thanks to the dedicated interfaces (Fig  3 ). Users need to connect to access functionalities like "Analyses" and "Export". EWET application private isolate and data records. The submission interface offers two functionalities: (i) comparison between the data collection and new data without recording, saved as private isolates (only accessible by the author) and (ii) record new data (for public consultation) in the data collection, saved as new isolates (in the "Creator" part of the Website).
The more data the author provides, the more the information is relevant for the community. The author of the submission and all other authors involved in the sampling and analyses agree to make their data publicly available on the EWET-DB. When the submission is complete, the data enter a quality control process before being published with a unique EWET code on the EWET website. Data quality. The quality control of EmB data was improved in different ways in order to create a reference collection. Data recorded in the present database are standardized as far as possible by using reference lists (Reference data in  Fig 7)  recognized by the community, such as taxonomic classification according to Wilson and Reeder's Mammal Species of the World online database  [21] , name of the geographical position and coordinates (decimal degree), obtained thanks to the Getty Thesaurus of Geographic Names (TGN), available online (http:// www.
getty. edu/research/tools/vocabularies/tgn/), and the name and code of the country from the ISO 3166, the International Standard for country codes, and ORCID code author (http:// orcid. org). The submission of new EmsB data is first controlled by the data manager, who validates the data and sends the corresponding EWET-code to authors. Secondly, the standardization of genotyping data is performed using the EmsB-calibrator developed in the present study. The calibrator must be run with all new EmsB genotyping submissions. Identification of data. The automatic EWET-code "id_isolate" allocates a unique code to identify all EmsB isolates genotyped and allows the authors to pinpoint their own data. Each EmsB sequence receives a code corresponding to a compilation of (i) the order number of registration in the database, (ii) the 3 letters of the ISO Code 3166-1.