dataesr/scientific-paragraphs-categorization huggingface dataset:
Establishment of a general database There are already many databases in different fields and many large companies have their own databases, plus the ECHA database, which contains information for all REACH registered substances. Unfortunately, most databases have different formats and the data is not easily extracted; this represents a hindrance, but does not prevent their use within the framework of ITS. A new platform should permit the use of data while respecting confidentiality claims and preserving intellectual property rights, including datasets which are not fully publicly visible. The usefulness of such a database is measured by the success in encouraging scientists to fill it with their data. Scientific funding bodies might provide economic compensation for such additional efforts to the benefit of the scientific community.
Data analysis In both experiments, the first two parameters were snail survival on day 30 p. e. and the prevalence of C. daubneyi infection calculated in relation to the number of snails surviving on day 30 p. e. For each parameter, the differences were analyzed using a v 2 test. Two other parameters in the first experiment were the number of free rediae and that of free cercariae counted in dissected snails. In the second experiment, the shell growth of infected snails at their death, the total number of shed cercariae, and the number of shedding waves for each infected snail  [30]  were also considered. Individual values recorded for these last five parameters were averaged and standard deviations were established for each snail group. Normality of these values was analyzed using the Shapiro-Wilk test  [39].
According to results given by this test, one-way analysis of variance (ANOVA) or the Kruskal-Wallis test was used to establish levels of significance. In the first experiment, the differences between survival rates, prevalence of infection and the numbers of larval forms were analyzed for each snail population considered separately. In the second experiment, the influence of snail population on the characteristics of C. daubneyi infection was evaluated by comparing differences between the five parameters for each snail group (1 or 2 mm). All statistical analyses were performed using Statview 5. 0 software (SAS Institute Inc. , Cary, NC, USA).
Cats were also excluded if SBP >200 mmHg was recorded, unless the investigator estimated that the cat could be enrolled in the study. Other reasons for exclusion were presence of clinically relevant liver failure or impaired hepatic function and unstable CKD that was expected to worsen markedly during the study. The dose of amlodipine was determined from data found in literature. In previous studies, most cats received an initial single dose of 0. 625 mg amlodipine daily. This dosage regimen was chosen mainly for practical reasons as this corresponds to 1/8 of the 5 mg tablet registered for human use. The amlodipine product used in this study was a chewable chicken flavored tablet designed for cats. Placebo tablets were equal in size and shape, contained the same excipients but no active ingredient.
Statistical Methods The target number of cats in the study was 72 with group sizes of 36 giving 90% power to detect superiority, assuming 70% and 30% response rates in amlodipine and placebo groups respectively. Block randomization was used with different block size for cats with CKD than for cats without CKD. Comparison between groups was made using Wilcoxon rank sum test for numeric data and Fisher's exact test for categorical data. The change from baseline SBP at the end of blinded efficacy period (Day 28) was evaluated as a dichotomous variable, where a responder was defined as decrease of SBP to <150 mmHg or decrease from baseline of at least 15%. This was the primary efficacy variable and factors influencing its attainment were analyzed with a logistic regression model, where baseline SBP, CKD (present or absent), and concomitant ACE inhibitor use (yes or no) were used as covariates.
Acknowledgments The authors thank all the veterinarians, owners of cats, and study team members who participated in the study. Conflict of Interest Declaration: Authors declare potential conflicts of interest. M. Huhtinen  and  J. Aspegr  en are employees of the sponsor Orion Corp. C. Zemirline is employee of the sponsor Ceva-Sogeval;  Prof. Elliott  has the following interest disclosures: Consultancy:  Pfizer Animal Health/Zoetis, Ceva Animal Health, Boehringer Ingelheim UK Ltd, V etoquinol Magny-Vernois, Orion Corp. , Elanco Animal Health, Idexx Laboratories, Inc ,  Niche Generics Ltd. , Triveritas Ltd. , Virbac Ltd. Advisory   board membership: International Renal Interest Society  (supported by  Novartis) European Emesis Council  (sponsored by  Pfizer Animal Healthnow Zoetis) Cardiorenal Board-Ve´toquinol Magny-Vernois, Idexx Renal Advisory Board , Research Grants or contracts:  Ve´toquinol Magny-Vernois ,  Novartis Pharmaceuticals UK Ltd ,  Pfizer Animal Health Ltd (now Zoetis ),  Royal Canin SAS ,  Boehringer Ingelheim UK Ltd, Waltham Centre for Pet Nutrition, Ceva Animal Health, Orion Corp.
Results (Figure 1A) The results on the domestic horses living in naturalistic conditions confirm data from feral animals and other natural conditions: Only 10 play bouts (social play) were observed over the 52 hrs observations, in three of the five individuals. Within these 10 bouts, 6 were observed in December, 2 in April and 1 in June and July respectively. There was no relation with age nor sexual status (1 out of 2 stallions, 2 out of 3 geldings involved). The results were very different for the riding center horses: 22 of the 29 horses (only two mares out of 6 but 20 geldings) have played at least once (3+ 5 SE in 2 hrs, 1 to 20 times). One horse played 20 times in 2 hrs, which is more than the play rate observed in foals in natural conditions. There was no correlation with age (Spearman correlation rs = 0.
Data were collected in a randomized order twice a day (morning and afternoon), outside of feeding times. Breeding facility (Institute of Beijing Xierxin Biology Resource, China)  (Camus et al. , 2014). This facility produces macaques for pharmacological and medical laboratories. Weaning was done early at 6 months and the density of macaques was high. The animals lived in stable (> 1 year) single male groups (one male with eight or nine females) in an indoor/outdoor enclosure (14m 2 ). They were fed with monkeys pellets twice a day and fruit once a day. Thirty five females (9. 06 years old ± 0. 6) from 8 different stable groups were observed in both conditions and their behaviors were recorded using a scansampling method, in which behavioral parameters were assessed every 6 min, during 2 hr sessions, resulting in 240 scans per female.
For each group, data were collected in a randomized order twice a day (morning and afternoon) on 6 consecutive days. Following a 4-hr habituation phase performed one day before the beginning of the observations, macaque behavior was voice-recorded and scored live, by one trained observer, outside of feeding and cleaning times. The observations were performed during 2 months: September and October 2010. For both populations, the observation methods were the same: scan sampling in the morning and in the afternoon, outside of feeding time and with the same observer (SC) in China and Nantes, but with another additional observer in Nantes (CR) (inter-observer reliability: Spearman rank order correlation rs = 0. 86, p < 0. 05). Four categories of play were distinguished: social play, object play, water play and movement play.
Socially-housed female macaque behavior was scored following the same protocol, whatever the facility, and recorded live by one (in Xierxin and Haikou; SC) or two (in Fangcheng Gang SC and CR) trained observers (inter-observer reliability: Spearman correlation rs = 0. 86). Colored medals were added to the monkeys' collar to facilitate the identification of the females using gentle restraint. The observations occurred outside of the feeding and cleaning times. For each group, the data were collected using exactly the same protocol as the one described earlier resulting in 216 scans per female in Xierxin and 240 scans per female in Fang Chen Gang and Haikou. Different types of stereotypies were observed, such as motor stereotypies, oral stereotypies and manual stereotypies (Table  3 ).
Acknowledgements We thank  M. Bourjade ,  S. Swessel-Robert ,  C. Coste  and  Q. Li  for helping with analyses and data collections,  A. Rossard  and  P. Bec  for taking care of the Paimpont primates, F. Joubaud helped with literature data. This work was supported by  CCMSA  (horses' observations) and by  Motac Neuroscience Ltd  (macaques' observations). We are most grateful to the managers and staff of the different facilities that opened their door to our studies: Riding schools,  Fang Cheng Gang ,  Xierxin  and  Hannan Jingang  primate breeding facilities, Planète sauvage (in particular M. Boye). We are grateful to  Dr. A. Chapelain  for correcting the English of this manuscript. We thank  Dr. Stan Kuczaj  to offer us the opportunity to write this paper.
Observation procedure To render data comparable with existing literature on group coordination, we sampled collective movements in only one functional context: that of maintenance behaviour. All movements sampled were from one foraging site to another, or to natural shelters (see  [37]  for details about ecological contexts). In consequence, if several individuals were found to contribute to group coordination, it will not be underpinned by mixed contexts. Group movements in response to external cues such as predator shapes (foxes, dogs. ) or fleeing responses (for instance from motorbikes on a few occasions) were not considered for data collection. In the same vein, stallions frequently use "herding behaviour" during the breeding season, by which they approach group members from the back and push them away from a rival in the context of stallion rivalry  [45].
This often results in group movements that do obviously not serve the aim to move from point A to point B, but rather to move away from point A. Thus, collective movements were observed outside the breeding season to limit the effect of stallion competition on family movements (88 hrs in 2004 and 120 in 2006). Two observers approached horses on foot at a distance of about 20 m and data were collected over four consecutive hours using tape recorders. The first observer continuously recorded the occurrence of agonistic interactions and the walking order of horses when travelling. The second monitored any moving horse and recorded all the following behaviours and their time of occurrence: pre-departure behaviour (moving away, staying peripheral (i. e. without any neighbour within a distance of at least three horse body-lengths), following an individual that is moving away, joining a peripheral individual or pausing; see Bourjade et al.
We tested for potential relationships between the dominance rank of individuals and their tendency to lead within each group. Social hierarchies were assessed by the occurrence of unidirectional agonistic interactions. We verified their linearity through a rank order analysis carried out with Matman (Noldus): BO group, h' = 0. 60, p = 0. 002; AD group, h' = 1, p = 0. 023. Dominance ranks were strongly related to age in both groups (Spearman rank correlation coefficient test: BO group, r s = -0. 96, p < 0. 001; AD group, r s = -0. 97, p = 0. 001), with older individuals being higher-ranked than others. Age was retained in analyses as an intrinsic feature of individuals. Non-parametric tests were used to analyse the data on leadership according to the age of individuals. All tests were two-tailed and performed with R 3.
Questionnaire sent to French equine veterinary surgeons The survey was emailed to French veterinarians referenced as having an equine activity in the veterinary professional directory (access to the email database was provided by M. Neveux, Les Editions du Point Vétérinaire). The database contained 940 email addresses. The survey was provided online using the INRA survey interface implemented with the Limesurvey V. 1. 91+ software (http:\\www. limesurvey. org/fr). A summary of the questionnaire is provided in online supplementary information 1. Briefly, 23 questions distributed in six different topics aimed at describing the considered practice and the associated parasitological epidemiology according to each practitioner. The four remaining parts were dedicated to the perception of resistance to anthelmintics by veterinarians, the drenching procedures and strategies they applied and the detailed use of FEC or coproculture, that is, incubation of nematode eggs in faeces to have infective larvae hatched.
Statistical analyses Correlations between factors were computed using the 'rcorr' function implemented in the Hmisc R package (http:\\www. r-project. org). To evaluate the effect of some factors ( practice size, veterinarian's age, proportion of equines in practice, number of horses in practice) on the reported use of anthelmintics, a sustainability index was constructed to rank veterinarians and identify putative clustering patterns. One point was added to veterinarian's index for the application of each of the sustainable management practices, that is, test of efficacy before drug use and FEC-based drenching. Sustainability of annual rotation between anthelmintic classes has been questioned  (Barnes and others 1995)  and was therefore not given an extra point. On the contrary, one point was subtracted for both the application of a systematic drenching calendar and the lack of FEC-based approach.
For the villages visited in 2006 and 2007 in Northwest Senegal, oral informed consent was given and recorded on paper by assigning ID numbers, name, age, gender and village of residence to those for whom consent was obtained. The data were anonymized prior to analyses. All schistosomiasis positive children were treated with a single dose of praziquantel at 40 mg/kg bodyweight. In schools or classes where the percentage of Schistosoma infections was more than 50%, mass treatment of all children was carried out at the end of the study according to WHO guidelines  [36].
Parasite collection and epidemiological background Three genetic datasets were prepared (Table  1 ). The first genetic dataset, hereafter referred to as DSEQ, comprised the cox1 sequences that were generated in this study from the villages Richard Toll  (1993 and 1994) ,  Ndombo (1997 and 2006) , Assoni (2011) and the villages Wayowayanko and Farako in Southwest Mali (1993) (Table  1 ) (see section 'Molecular analyses' for details on sequencing). Miracidia from the village Assoni were collected within the framework of this study (see below), while all other samples were adult worms provided by the Schistosomiasis Collection at the Natural History Museum in London (SCAN)  [37]  (SCAN numbers: 2800,  2916, 2953, 3108, 3109, 3421, 3445, 3464, 3465, 3815, 4580). Note that sequences could not be generated for miracidia sampled in 2007 in Northwest Senegal as there was insufficient DNA.
Our sequence data were therefore complemented with previously published GenBank sequences from miracidia obtained from Northwest Senegal in the villages Temey and Nder in 2007, from Southeast Senegal in the village Kolda in 2009, and from seven other countries in Africa (Fig  1a  and Table  1 )  [38]. Sequences of cercariae and adults worms from Webster and colleagues  [38]  were not included here as they might be clones from each other, possibly introducing a bias in estimates of diversity. In contrast, sequences generated from worms in this study were included because the microsatellite genotyping allowed us to identify and exclude clones (see below). The second genetic dataset, hereafter referred to as DMS1, comprised parasites that were genotyped at nine microsatellite markers (see section 'Molecular analyses' for details on microsatellite genotyping), and that were either miracidia collected within the framework of this study or adult worms provided by SCAN  [37]  (see Table  1  for details on sample origin and sample type).
As adult worms may be genetically identical (i. e. clones), microsatellite genotypes obtained from worms were visually inspected to identify identical multilocus genotypes. When such identical genotypes were found within a sample, all but one were removed from the dataset. In addition, miracidia were collected within the framework of this study from eight children aged 5-14 in 2011 in the village Assoni in the Region of Kédougou (Southeast Senegal) (Fig  1b ). Six of these children were treated eight months prior to this study. The village is situated near tributaries of the Tiokaye River, itself a tributary of the Gambia River. Assoni was enrolled as pilot village in the national control program of Senegal, namely 'le Programme Table  1. Details of the three genetic datasets that were used in this study.
Region Water  National de Lutte contre les bilharzioses' (PNLB)  [41]. The prevalence of S. mansoni infection in Assoni among children aged 6-14 years was initially 100% in 2006 (i. e. before treatment), but decreased to 50% in 2013 after three treatment rounds  (2008, 2010, 2012)  with praziquantel to those children that were diagnosed positively for S. mansoni infection  [41]. Similar to above, eggs from positive stool samples were isolated after filtration, hatched and miracidia were individually pipetted onto Whatman FTA indicator cards in a volume of 3 μl of water  [40]. The third genetic dataset, hereafter referred to as DMS2, includes the same genotypes as DMS1, but complemented with previously published S. mansoni genotypes from miracidia that were collected in the village Kokry-Bozo in 2007 in Southwest Mali within the framework of the study of Gower and colleagues  [42].
Main local watercourses are irrigation channels fed by the Niger River. The prevalence of S. mansoni infection in Kokry-Bozo at the time of sampling was 88%  [42]. Samples were obtained from children that had not been treated previously and miracidia were genotyped at the Department of Infectious Disease Epidemiology (Faculty of Medicine, Imperial College London)  [42]. The genetic data of 104 miracidia were provided as raw genotyping chromatogram files that were scored within our lab using GENEMAPPER v4. 0 (Applied Biosystems). Six microsatellite markers (CA11-1, S9-1, SMD25, SMD28, SMD89, SMDA28) were shared among the study of Gower and colleagues  [42]  and our study (see section 'Molecular analyses'); hence DMS2 only contained six loci. All genotypes were imported into ALLEOGRAM v2. 2  [43]  for binning of allele lengths.
Genealogical relationships between all sequences were explored by constructing two haplotype networks based on statistical parsimony  [53]  in the package 'pegas'  [54]  as implemented in the R software  [55]. Haplotypes were first identified using the function haplotype and used to construct a network with the function haploNet. The number of sequences that represented a given haplotype was logarithmically transformed to narrow high and small values, and used to determine the size of its corresponding pie diagram. A first network included all sequences from the DSEQ dataset. A second network included only sequences from Senegal and Mali.
Population genetic analyses using microsatellite markers (DMS1 and DMS2) First, the genetic diversity of parasite populations was quantified by estimating the proportion of heterozygous individuals (i. e. observed heterozygosity, Ho), the expected proportion of heterozygous individuals assuming Hardy-Weinberg Equilibrium (unbiased expected heterozygosity, Hs) and the number of alleles corrected for sample size (allelic richness, AR). Ho and Hs were estimated in GENETIX v4. 05  [56]  while AR was estimated in the R package 'hierfstat'  [57]. The inbreeding coefficient F IS was estimated by f  [58]  in GENETIX; the significance of f was tested using 10,000 permutations and corrected for multiple testing using Bonferroni corrections. Analyses were done per village, year and region. Second, the ancestry of individual parasites was inferred using a Bayesian Markov Chain Monte Carlo (MCMC) clustering analysis as implemented in STRUCTURE v2.
2. 3  [59]. The program assigns individuals to K populations that are each characterized by a set of allele frequencies. Individuals could be assigned to two or more populations if their genotypes indicate that they are admixed. As K is unknown, the model is run multiple times, each time with a different K-value (from 1-10). Sampling locations (i. e. village) were included in the model as a prior (LOCPRIOR = 1), as they can assist clustering when the amount of genetic markers is low  [60]. Note that the LOCPRIOR model will not falsely identify genetic structure when there is none and will ignore sampling information when the ancestry of individuals is uncorrelated with sampling locations  [60]. Five replicate runs were initiated assuming the admixture model and correlated allele frequencies for datasets DMS1 and DMS2; each run consisted of 10 6 MCMC chains, initiated by 10 5 burn-in steps.
All jobs were run parallel on multiple cores using the R package 'ParallelStructure'  [61]. The optimal K value was identified by the maximum LnP(D), which is the log likelihood of the observed genotype distribution in K clusters. Third, population genetic structure was visualized by exploring the distribution of genotypes of DMS1 and DMS2 in hyperspace using a Factorial Correspondence Analysis (FCA) as implemented in GENETIX and results were visualized using the R software. FCA visualizes genotypic (dis)-similarities among individual parasites. Fourth, genotypic (dis)-similarities were studied among groups of parasites by estimating the F ST analogue θ  [58]. This was done pairwise between regions and villages in GENETIX for DMS1 and DMS2. Significant population differentiation was tested for all estimates by 1,000 permutations of individuals among localities, and Bonferroni correction was applied for multiple testing.
Characteristics of the datasets The DSEQ dataset comprised a total of 657 cox1 sequences of which 121 were generated in this study (Table  1 ). After alignment and trimming, sequence fragments of 420 bp long were retained for further analyses. The DMS1 dataset comprised a total of 542 S. mansoni parasites that were successfully genotyped for all nine microsatellite loci, among which 154 originated from the village Assoni in Southeast Senegal and 388 from several villages across Northwest Senegal (Table  1 ). Sample sizes for Northwest Senegal ranged from five genotypes in Ndombo in 2006 to 98 genotypes in Rhonne in 2007 (Table  1 ). The DMS2 dataset comprised a total of 758 S. mansoni parasites that were successfully genotyped for all six microsatellite loci. A total of 73 out of 104 genotypes were successfully scored for the Kokry-Bozo sample from Southwest Mali.
However, population bottlenecks followed by genetic drift could also produce divergent populations  [72] , which could apply to the sample from Ndombo that was obtained Table  4. Pairwise F ST estimates between Schistosoma mansoni samples from Mali and Senegal. Estimates were obtained for microsatellite dataset DMS1 (below diagonal) and DMS2 (above diagonal). Note that samples with less than 10 parasites were not included to avoid biased estimation, and that samples from Richard Toll from 1993 and 1994 were pooled. after laboratory passage  [73, 74]. Altogether, these findings support the hypothesis that the widespread dominant population of S. mansoni in Northwest Senegal is more likely the result of an admixture between multiple introductions (scenario 2) than the result of a single introduction (scenario 1).
Acknowledgments We thank  Prof. J. Webster  for access to the raw microsatellite data of  Kokry-Bozo (Mali)  and the Schistosomiasis Collection team at the  Natural History Museum in London (SCAN ) for providing S. mansoni worms. We are grateful to all villagers in Senegal for their cooperation and thank the  Senegalese field team (M Diop ,  A Fall ,  N Sy ,  M Wade ,  A Yague ) for their dedicated help with the fieldwork.