dataesr/scientific-paragraphs-categorization huggingface dataset:
T he Corynebacterium ulcerans tox gene was first described in 1926, isolated from a human throat  (1). The tox gene present in C. ulcerans has 95% similarity compared to the tox gene present in Corynebacterium diphtheriae  (2). This gene encodes diphtheria toxin present in lysogenic ␤-corynephages described in C. ulcerans 0102 but not in C. ulcerans 809 (both strains available at GenBank)  (3). However, the virulence of C. ulcerans does not necessarily depend on the production of diphtheria toxin; some strains have been reported to produce a powerful and severe dermonecrotic toxin similar to phospholipase D from Corynebacterium pseudotuberculosis (4). This repertoire of potent toxins shared by C. ulcerans, C. diphtheriae, and C. pseudotuberculosis, along with levels of genomic DNA relatedness and taxonomic analyzes of 16S rRNA gene sequences, particularly highlights the close phylogenetic relationship, putting these three species in a distinct cluster of the genus Corynebacterium  (5).
The SOLiD platform was used to perform the genome sequencing, using a fragment library. The predicted genome coverage was approximately 1,900ϫ based on C. ulcerans genomes available in GenBank (http://www. ncbi. nlm. nih. gov/genbank/). The de novo assembly strategy was performed through SOAPdenovo version 2. 04  (8)  and Velvet version 1. 0. 13 (9). The assembly generated 258 contigs with 2,428,683 bp. The contigs were submitted to GenBank for automatic annotation. The genome has 2,270 coding sequences, 12 rRNA genes, 49 tRNA genes, 272 pseudogenes, and a GϩC content of 53. 60%. This genome is part of further studies of comparative genomics, pathogenicity, and vaccine and drug targets of the species. Nucleotide sequence accession numbers. The C. ulcerans whole-genome shotgun (WGS) project has the project accession number LGSY00000000.
Data collection Behaviour was recorded by direct observation 6 h postmixing and 24 h post-mixing. Social behaviour and general activity were recorded by scan sampling adapted from the methodology proposed by the Welfare Quality® (WQ®) protocol for growing pigs on farm  [10]  which is briefly described here. Pigs were scored as either active or inactive. The behaviours recorded from active pigs are shown in Table  1. Observations took place on two consecutive days (day 0, 6 h post-mixing and day 1, 24 h post-mixing), with two observations blocks per day for each pen (from 10 am to 12 pm and from 2 pm to 4 pm). Within an observation block, each pen was observed 5 times with a 2. 5 min interval between two scans. The number of pigs engaged in each social behaviour category (social negative and social positive) and four general active behaviours (feeding, drinking, exploration and "other") were recorded.
Statistical analysis The pen was the statistical unit for all data. Behavioural data were analysed by means of nonparametric generalized estimating equation models using the GENMOD procedure for repeated measures. The models accounted for the effect of the treatment and the day as well as their interaction day x treatment. A Mann-Whitney Wilcoxon test was used to test whether the prevalence of wounded animals in the control and the PAP block treatments were significantly different. A P-value of 0. 05 was considered significant for all analyses. The data was analyzed using the statistical package SAS (SAS. 9. 2. Institute Inc. , Cary, NC, USA).
No significant effect could be observed in the spleen (Figure  4A , Right panel). This response was accompanied by a decrease of CFU numbers in CLN in treated mice (Figure  4A , FIGURE 3 | The intradermal inoculation pathway induces a strong local inflammatory response in CLN. C57BL/6 mice (n = 5 per group) were infected using the routes of infection described in the methods section. At 8 and 29 days post-infection, mice were sacrificed and organs were weighed and analyzed for their bacterial loads by plating homogenates on nutrient agar. Data represent mean of CLN (Left panel) and spleen (Right panel) weight (A) or CFU per organ (B) from three independent experiments. Analysis significance was determined using ANOVA ( * p < 0. 05; * * p < 0. 005; * * * p < 0. 001; * * * * p < 0. 0001). (C) C57BL/6 mice (n = 5 per group) were infected using different routes of infection as described in methods section.
ACKNOWLEDGMENTS The authors would like to thank  Hugues Lelouard ,  Johnny Bonnardel , and  Clara Degos  for providing and supporting in establishment of protocols and for valuable discussions. We deeply thank  Dr. Ignacio Moriyon  for providing the Brucella strains as well as  Dr. Philippe Pierre  for the J558L GM-CSF producing cell line. Also, we are very grateful to the  BSL-3 core facilities  staff at the  Immunophenomique Center (CIPHE).
Acknowledgements This study was conducted as part of the  Chair of Excellence "Equine Immunology" of the University of Caen Basse-Normandie , a program supported by the  Region council of Basse-Normandie (France)  and the  European Regional Development Fund. SF is supported by the  Institut Français du Cheval et de l'Equitation and R egion Basse-Normandie. Conflict of Interest: The authors report no conflict of interest.
Study Design, Data Collection, and Definitions A retrospective study was conducted at the Centre de Diagnostic et de Traitement de la Lèpre et de l′Ulcère de Buruli (CDTLUB) in Pobè, Benin, which has one of the largest databases for cases of Buruli ulcer confirmed by polymerase chain reaction (PCR)  [14]. We first conducted a preliminary analysis of 545 Buruli ulcer patients treated at the CDTLUB in Pobè from 2010 to 2013. For the selection of medical records, we used several key words defined on the basis of publications in this field: spontaneous healing, spontaneous clearance, scar, old ulcer, scarring lesion. During this review step, medical records containing at least 1 of the chosen key words were selected. If the clinical records were incomplete (eg, lack of photographic monitoring, patients lost to follow-up), the patient was excluded.
Cohort Presentation We selected 26 patients (sex ratio M/F =1. 4), on the basis of our criteria, from the database of the CDTLUB. Median patient age at diagnosis was 13. 5 years (5-70 years), with female patients tending to be older than male patients (Figure  1 ). The age distribution of male and female patients was similar to that for the entire population of 545 Buruli ulcer patients from 2010 to 2013 (Figure  1 ). Almost all the patients (25 of 26) had category 3 lesions (World Health Organization nomenclature) presenting as single lesions of more than 15 cm in diameter or osteomyelitis, or multiple lesions, and/or lesions at critical sites. In 85% of patients  (22 of 26) , lesions were present on the lower limbs (59% for the total cohort, P <. 05, Fisher test). Three patients presented multiple active Buruli ulcer lesions (2 patients with 2 lesions, 1 patient with 3 lesions).
Acknowledgments Members of the  Franco-Beninese Buruli Research Group are as follows: Quentin B. Vincent (Laboratory of Human Genetics of Infectious Diseases ,  Necker Branch ,  Institut National de la Recherche Médicale [INSERM] U1163  and  Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France) ;  Laurent Abel (Laboratory of Human Genetics of Infectious Diseases ,  Necker Branch ,  INSERM U1163  and  Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, Paris, France  and.
Data handling and statistical analysis The sample sizes decided for the studies were not determined by use of a power analysis calculation. Instead, the group size used was equivalent to that used in previous studies assessing VFI and palatability  [20, 22]. For the VFI studies, the primary outcome measure of interest was the amount of energy consumed (expressed both as KJ and Kcal per kg of MBW), whilst secondary outcomes included the weight of food consumed (in grams), and also BW (in kg) measured before and after each protocol (as described above). For the palatability studies, the primary outcome measure was the amount of each diet consumed in grams. In all studies, complete data were available for all animals participating, except for one cat in the Feline VFI study whereby malfunction of the electronic food scales meant that the data could not be used.
Data were recorded in a computer spreadsheet (Additional file 1; Excel For Mac version 15. 28, Microsoft Inc. ) and analysed using the Statistical Analysis Systems institute package (SAS version 9; SAS Institute Inc. ). For the canine VFI, a linear mixed model assessing the fixed effects of diet (C1, C2) and meal (M1, M2, M3, M4), and their related interaction, on the food and energy intake of dogs. The variable 'dog' was defined as a random term. In a similar manner, a linear mixed model was used to assess the fixed effect of diet (F1, F2) on the food and energy intake of cats, with the variable 'cat' being included as a random term. Given the design of the palatability studies, the fixed effects of diet (C1, C2 for dogs; F1, F2 for cats) and either meal (M1, M2) for dogs or day (D1, D2) for cats with their related interaction were assessed on food intake.
Purpose: To establish a training data set of digital images and to investigate the scoring criteria and dose assessment of the dicentric assay within the European network of biodosimetry (RENEB), a web based scoring inter-comparison was undertaken by 17 RENEB partners. Materials and methods: Two sets of 50 high resolution images were uploaded onto the RENEB website. One set included metaphases after a moderate exposure (1. 3 Gy) and the other set consisted of metaphases after a high dose exposure (3. 5 Gy). The laboratories used their own calibration curves for estimating doses based on observed aberration frequencies. Results: The dose estimations and 95% confidence limits were compared to the actual doses and the corresponding z-values were satisfactory for the majority; only the dose estimations from two laboratories were too low or too high.
Materials and methods To establish the two galleries with a moderate and a high dose, digital images of Giemsa stained first mitoses in high resolution mode (1280 * 1024 pixels) were captured automatically with the Autocapture software module of MetaSystems (Altlussheim, Germany) in 63x magnification (with oil immersion). The aim was to obtain information about the scoring criteria and dose assessment of the participating laboratories. It was not possible to use 50 images arbitrarily generated from a slide of an irradiated sample, as many images could be rejected for several reasons and the remaining images would be difficult to compare. Therefore, it was decided to establish the galleries manually, using only good quality images that were selected by an experienced scorer. To simulate the yield of dicentrics and the correlated Poisson distribution of dicentrics for a moderate and high dose exposure, the parameters of a pooled dose effect curve established in the frame of the MULTIBIODOSE project (multidisciplinary biodosimetric tools to manage high scale radiological casualties, www.
multibiodose. eu) were applied. The parameters of the pooled curve (by means: C ¼ 0. 0016, alpha ¼ 0. 0269, beta ¼ 0. 0588, by weighted means C ¼ 0. 0004 ± 0. 0064; alpha ¼ 0. 0195 ± 0. 0353 and beta ¼ 0. 0562 ± 0. 0192) described the dose effect curve Y ¼ C þ alpha *D þ beta *D 2 (Y ¼ aberration fre- quency, D ¼ dose [ Gy], C ¼ spontaneous frequency, alpha ¼ linear and beta ¼ quadratic coefficient) for dicentric chromosomes of eight European laboratories after gamma irradiation  (Romm et al. 2012 ) (Table  1 ). The images were provided to the participating laboratories using a gallery creator software (www. jalbum. net) to integrate two galleries in the RENEB homepage in the form of a browser based web application for examining microscopy images. The images in the galleries were 800 Â 705 pixels in size, with 256 grey levels.
Access to the images was available with free standard internet browsers (Figure  1 ); no special software was needed by the partners for image analysis. The results were recorded with a standardized scoring sheet. The instruction was to analyse all images (if possible) and to perform dose estimations (including 95% confidence interval) with the gamma dose effect curve of the laboratory. Each laboratory used its standard procedures, including one or more scorers per institution analysing the images. The interindividual variation in cell proliferation was handled as in conventional scoring and only first mitoses were analysed. The dose estimations were calculated with the free software CABAS 2. 0  (Deperas et al. 2007 ) and/or Dose Estimate 4. 2 or 5. 1  (Ainsbury et al. 2010). One laboratory (lab 6) used its own statistical program, which had an impact on the resulting 95% percent confidence interval.
As differences in rejection criteria may have some impact on the resulting frequency of dicentrics  (Yoshida et al. 2007; Ainsbury et al. 2009) , further investigations about the applied criteria regarding cell rejection and/or dicentric selection in not preselected image galleries would be of great interest to make a step forward in harmonization of the method. With the knowledge of experienced scorers a wide field of training modules could be developed as a training program for new staff members or as appropriate quality assurance and quality control program within individual laboratories or RENEB as network. Hereby the use of modules with digital images could be extended to other assays like, e. g. , the cytokinesis-block micronucleus (CBMN) assay, the fluorescence insitu hybridization (FISH) translocation assay, the c-H2AX foci assay and the premature chromosome condensation (PCC) assay.
We investigate this trade-off for livestock-exchange markets in France, for which we have access to extensive data. The construction of network models of livestock markets requires the use of records of animal movements. In the European Union (EU), for instance, exhaustive tracing of livestock movement is available in many nationally maintained datasets, originally for cattle since the 1990s (Council Directive 92/102/ EEC of 27 November 1992 on the identification and registration of animals) and more recently for swine (Council Directive 2008/71/EC of 15 July 2008 on the identification and registration of pigs). In other countries, data with such levels of detail may not be available because, for example, the data may have been aggregated to comply with privacy laws, or routine data collection may not be implemented at the farm level.
In this study, we aim to identify efficient strategies for preventing epidemics with minimal disruption to markets and limited cost to the stakeholders such as regulators and business owners. We introduce a market-based categorization for aggregating the holdings based on economic as well as structural network summaries, namely position along the supply chain and market share or leadership. To study the economic-epidemiological implications of our categorization, we analyse two datasets recording cattle and swine livestock movement in France during 2005-2009 and 2010, respectively ( §2). We show that the market categories that we propose describe livestock exchange intuitively and provide insights on the underlying trading patterns ( §3. 1). Using these categories, which are easy to implement because they are empirically defined, we evaluate the joint economic-epidemiological risks of epidemic outbreak and associated regulatory measures ( §3.
French livestock-exchange data described as trade networks We analyse and compare trade networks derived from two datasets recording livestock exchange in France: the BDNI for cattle (managed by the French Ministry in charge of Agriculture (FMA)) over years 2005-2010, and BDPorc for swine (managed by the French professional union BDPorc) in 2010. Each dataset details movements of animals occurring in France among all economic agents involved in the supply chain, from strictly breeding farms to slaughterhouses with various categories of structural wholesalers in between (e. g. breeding-fattening farms, strictly fattening farms, dealers). Data on imports and exports are also available. Traceability is imposed by the regulator at different scales: on individual animals in the case of cattle, and on batches (sets of animals shipped from a seller to a demander during a transaction) in the case of swine.
Hence, we extract individual-level transactions directly from the cattle dataset. Moreover, we reconstruct individual-level transactions for pigs based on a simple matching process (see the electronic supplementary material, section B. 2 of  [28] , for details). Our core network-based analyses are carried out at the microeconomic business scale, i. e. agricultural holdings, as far as national livestock exchange is concerned. The datasets allow us to distinguish three groups of holdings: farms, i. e. agents aiming to produce livestock; trading agents such as assembling centres, i. e. agents aiming to exchange livestock; and the rest of the world, a single entity aggregating all agents located outside of France, which we use to assess the importance of international restrictions on trade, as e.
As an example, wholesaling leaders are surveyed preferentially when we set: z suppliers ¼ z demanders. 0, z nichers ¼ 0 and z leaders. 0. In the case when two or more agents take the same value of R, we choose their relative orders uniformly at random. Note that the variability resulting from this ranked ordering is weak, as confirmed by assessments of each strategy over 100 random replicate targeting for both datasets.
Practical implementation of the MCDA Multiple criteria decision analyses are carried out over time period T , which we set to start in 2009 for cattle and 2010 for swine. To account for potential delays in the collection of data necessary to calculate flow polarity fp a (2. 1) and flow share fs a (2. 2), we explore two contrasting cases: the real-time scenario or the deferred scenario, respectively, where the regulator has access to real-time data or deferred data, respectively, so fp a and fs a can be calculated based on T or based on T À dt (with dt representing the delay of data collection), respectively. We set dt ¼ 1 year, a deliberately large value for data collection. For each strategy explored, the relative decrease in the LSCC size is evaluated at increasing values of F n. For each value of F n , we keep track of the proxy for prevention effectiveness (the relative decrease in the LSCC size (2.
Analyses and representation of trade networks using market categories Considering the French datasets for livestock movements of cattle and swine, we categorize agents with similar market characteristics, according to position along the supply chain, quantified by flow polarity (figure  1a, c ), and market leadership, quantified by flow share (figure  1b, d ). Agents with similar ranks in flow polarity and flow share belong to the same market category (figure  2a ). Since market categories are relatively invariant over time (electronic supplementary material, section B. 1, figure  S1 ), we focus our subsequent analyses based on 2009 for cattle and 2010 for swine. We notice suppliers and demanders are overly represented in the cattle and swine markets, respectively (figure  1a ). Since demanders act as epidemiological dead-ends, our analyses suggest that the cattle market is riskier than the swine market, a result in agreement with  [12].
Data accessibility. French livestock-and swine-exchange data were, respectively, provided by the French Ministry in charge of Agriculture (FMA) (contact point: bicma. sdspa. dgal@agriculture. gouv. fr) and the professional union BDPorc (contact point: administrateur@bdporc. fr), which operates under contract for the FMA. Data collection and analyses are subject to a confidentiality agreement available upon request from the designated contact points.
Acknowledgements. Many thanks to  Julien Fosse ,  Etienne Geoffroy ,  Bhagat Lal Dutta ,  Francois Moutou ,  Emilie Moyne ,  Marco Pautasso  and  Stephane Robin  for helpful comments and insights. We are grateful to the  French Ministry in charge of Agriculture  and to the professional union BDPorc for granting us access to the cattle and swine datasets, respectively. We are also grateful to the  INRA MIGALE bioinformatics platform  (http://migale. jouy. inra. fr)for providing computational resources. This article is dedicated to the memory of Anne-Therese Domanska-Lefebvre.
Patients and Methods This was an observational, retrospective, single-center case-series of children hospitalized in PICU from November 2008 to June 2016. Cases were identified and reviewed from among all the hospitalized poisoned children for which Tramadol overdose was confirmed. We defined as overdose an excessive dose taken by the child. The usual dose is 1 to 2 mg/kg every 6 hours, not to exceed 8 mg/kg/24 hours with a maximum dose of 400 mg/day if the child's weight exceeds 50 kg. Intoxication was confirmed by quantitative blood sample and questioning the child and/or parents. Inform consent was waived according to French law. Cases were identified combining PICU database with International Classification of Disease Codes (ICD10 codes version 2010) with T40 codes (Poisoning by narcotics and psychodysleptics [hallucinogens]): T40.
2 (Other opioids, Codeine Morphine), T40. 4 (Other synthetic narcotics Pethidine), T40. 6 (Other and unspecified narcotics) and T40. 9 (Other and unspecified psychodysleptics [hallucinogens]). Patient data were extracted from the medical charts and recorded from informatics medical records and hospital reports. The review of the medical literature was made by using PubMed key concepts: children/paediatric tramadol intoxication / overdose. drowsiness. Pupils were middle and reactive. Since a febrile headache was reported, the patient received antibiotics and an antiviral treatment. Infectious, metabolic and traumatic causes were excluded. She presented a moderate hepatic cytolysis. Cerebral imaging (scanner and Magnetic Resonance Imaging) and an electro-encephalography (EEG) were not conclusive.
Handheld laser methane detector Another approach to monitor exhaled air CH 4 concentration is the use of handheld laser CH 4 detectors (LMD) to measure CH 4 concentration in the air between the animal"s nose or mouth and the LMD  (Chagunda, 2013; Ricci et al. , 2014). Measurements of CH 4 concentration are taken manually by a portable apparatus approximately 1-3 m from the animal and are based on infrared-absorption spectroscopy for CH 4. The sequence of data acquisition consists of short periods of 2-4 continuous min. The resulting data consist of a series of peaks which represent the animal"s respiratory cycle. Only peaks reflecting the increase in CH 4 concentration due to exhalation or eructation are used in the analysis  (Ricci et al. , 2014). The measured concentrations are adjusted for distance and background concentrations by the LMD.
(2015)  assessed the duration and number of GreenFeed measurements required for estimating daily CH 4 emission from cattle with a pre-specified accuracy and confidence level. This analysis was based on a feedlot situation using 24 beef steers over 64 d with an average of two GreenFeed visits/d. These authors found that it was not possible to define CH 4 emission of a treatment group within 5% of the 64-d mean with 95% confidence using 10 animals, and it would require more than three months of data collection using 20 animals. Arbre et al. (2016)  evaluated the repeatability (R) of CH 4 measurements in two different trials using cattle. The It is important to note that these calculations were based on the actual number of cattle that visited GreenFeed and that this level of replication changes with contrasting environments, including intensive vs.