dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements The authors thank the technicians of the Vasco research team, UMR AGIR, and those of the Auzeville experimental unit for field crops, for their kind support during this study. We are grateful to  Gilles Tison  ( UE Auzeville, INRA ) for his availability to discuss and program field experiment and  Christine Le Bas  ( INRA, Orléans ) for her suggestions concerning methods to determine the soil water potential. This study was funded by a starter grant of the  INRA's Environment and Agronomy Division  to the first author.
Background Patients with cervical dystonia (CD) typically require regular injections of botulinum toxin to maintain symptomatic control. We aimed to document long-term patient satisfaction with CD symptom control in a large cohort of patients treated in routine practice. Methods This was a prospective, international, observational study (NCT01753349) following the course of adult CD treated with botulinum neurotoxin type A (BoNT-A) over 3 years. A comprehensive clinical assessment status was performed at each injection visit and subjects reported satisfaction in two ways: satisfaction with symptom control at peak effect and at the end of treatment cycle. Results Subject satisfaction remained relatively stable from the first to the last injection visit. At 3 years, 89. 9% of subjects reported satisfaction with symptom control at peak effect and 55.
Methods INTEREST IN CD2 (NCT01753349) was a 3-year multicentre longitudinal cohort study following the course of adult idiopathic CD patients treated with BoNT-A. Baseline analyses have previously been reported  [22]. The study was conducted in compliance with the International Society for Pharmacoepidemiology (ISPE) Guidelines for Good Pharmacoepidemiology Practices (GPP)  [23] ; it began on 10 December 2012 and the last visit occurred on 25 September 2017. Independent Ethics Committee/Institutional Review Board approval was obtained prior to each centre initiation. Written informed consent was obtained prior to subject enrolment and performance of any study procedures.
completely satisfied; 2. rather satisfied; 3. neither satisfied nor dissatisfied; 4. rather dissatisfied; 5. completely dissatisfied). Clinical outcomes including the Toronto Western Spasmodic Torticollis Rating Scale (TWSTRS)  [24]  and Tsui scale (tremor component)  [25]  were also assessed as secondary measures. Data were collected using an electronic case report form (eCRF) with sections for patterns of dystonia (e. g. , rotation, laterocollis etc. ), injection parameters (muscles selected, injected dose, injected volume, number of injection sites, use of injection guidance technique), TWSTRS, and Tsui tremor scale scores. At the start of the study, a survey was sent to all sites to ascertain whether they reinjected according to fixed re-injection intervals (hospital rules/usual practice), a flexible schedule (depending on patient needs) or a mix of both.
Safety No safety assessments were planned in this study; hence no safety data were recorded in the clinical database. However, in compliance with the European Medicines Agency guideline on good pharmacovigilance practices (GVP Module VI), investigators were required to report all serious adverse events (sAEs) and all study drug-related non-serious adverse events (AEs) occurring with aboBoNT-A to the sponsor's pharmacovigilance department. Safety data for other BoNT-A were to be reported in line with national requirements but were not available for analyses. We made an effort to review all aboBoNT-A safety data reported and cross-checked with this study.
Study exposure to BoNT-A treatment The mean ± SD length of study exposure was 34. 20 ± 9. 90 months and number of treatment cycles was 8. 65 ± 3. 25. At baseline, 689 subjects received aboBoNT-A, 247 subjects received onaBoNT-A and 59 subjects received incoBoNT-A. Injection practices were generally in line with BoNT-A prescribing information (Table  2 ). As previously reported for baseline interim data  [22] , the most frequently injected muscle groups at baseline/first visit were the splenius capitis, sternocleidomastoid, trapezius, levator scapulae, semispinalis capitis, and scalene group. These six muscle groups remained the most frequently injected muscles throughout the study. Most subjects were reinjected at intervals of 12-16 weeks (58. 6%) and switches between BoNT-A preparations were uncommon (14.
Acknowledgements The INTEREST IN CD2 study is sponsored by  Ipsen Pharma. We confirm that we have read the Journal's position on issues involved in ethical publication and affirm that this work is consistent with those guidelines. The authors wish to thank all participating sites, principal investigators, sub-investigators, study coordinators and patients who contributed to the INTEREST IN CD2 study. We thank  Anita Chadha-Patel PhD  of  ACP Clinical Communications Ltd (Hertfordshire, UK ) for providing medical writing support, which was funded by  Ipsen (Paris, France)  in accordance with Good Publication.
Participants Thirty-four young and 35 older adults participated in this study. The data of 5 young and 5 older adults were excluded, because they used psychotropic medication (1 young), were nonnative Dutch speakers (4 young), or performed an incorrect version of the learning task (5 older). The remaining 29 young adults (6 male, 5 left-handed) ranged in age from 19 to 29 years  (M 22. 41, SD 2. 86) , the 30 older adults (14 male, 3 left-handed) from 65 to 79 years  (M 70. 13, SD 3. 95). All participants were free of neurological and psychiatric disorders, did not take psychotropic medication, did not have a history of brain damage, and had a normal or corrected-tonormal vision. Older adults did not show signs of depression as assessed with the Geriatric Depression Scale 15 (score of 5 or lower;  Burke, Roccaforte, & Wengel, 1991; Yesavage et al.
Computational model estimation of the role of working memory in reinforcement learning The computational model served two primary functions in the context of our study: (i) validating our hypothesis that performance depended more on working memory in the shortdelay condition than in the long-delay condition; (ii) confirming that older adults relied on average more on an RPE-based reinforcement-learning process than young adults did. Thus, we fitted the computational model to the choice data of the short-and long-delay conditions separately and we examined the two sets of estimated values for the RLWM arbitration parameter in the two age groups. While the arbitration parameters did not differ between age groups, F(1,57) = 1. 756, p =. 190, η p 2 =. 030, we observed a salient age-condition interaction, F(1,57) = 10.
To do so, we used the parameter values obtained when fitting the model to the complete dataset. Interestingly, O-span scores correlated with perseveration in the young but not in the older group (young: r S = -. 43, p =. 019; old: r S = -. 10, p =. 590; z = 1), whereas it correlated with WM decay in the older but not in the young group (young: r S = -. 170, p =. 36; old: r S = -. 362, p =. 049). Note however that these correlation coefficients did not differ significantly across groups, all p > 0. 1, hence requiring confirmation in a larger sample. Finally, it must be noted that within the parameters governing the update and maintenance of stimulus-response associations only the decay rates of the RL module were unaffected by age per se, p = 0. 24 (Figure  4(c) ): the learning rate of the RL module was higher in young as compared to older adults, t(57) = 5.
However, complex models tend to have low statistical power (lower precision) and to exhibit estimation issues when applied to sparse datasets, meaning that special care needs to be taken at the sampling design stage. In particular, we demonstrate a case of weak identifiability, that is a case where the parameters are in theory all separately estimable, but their relative contributions to the variance in the data becomes impossible to separate as the data get sparser  (Auger-Méthé et al. , 2016; Barker et al. , 2018; Fan et al. , 2018; Garrett and Zeger, 2000). A straightforward example of weak identifiability is when attempting to discriminate two categories of individuals based on their size. The discriminatory power (model identifiability) weakens as the difference between the two categories decreases below to the within-category variance, i.
Three types of detection data for unmarked animals The first type of detection data is distance to the observer -our model is a generalization of the distance sampling model. In our implementation, distance may be recorded exactly, or binned into classes of approximate distance. Importantly, when counting animals that are grazing the distant opposite slope of a valley, distance is not always relevant as an information about detection probability, i. e. , the visibility is sometimes good enough that all the animals have almost the same detection probability. Therefore, it is interesting to be able to combine distance sampling with other sources of information about detection, in a flexible way that allows the joint analysis of locations where distance is the main source of information about detection, and locations where distance conveys little information.
The 8 sites were treated as spatial replicates in the analysis. These parameters values were purposely chosen so that the expected population count slightly increased over the years, whereas the actual population size decreased. Accordingly, the IPS methodology failed to detect the underlying population decrease (Table  2 ). This scenario was also expected to challenge the N-mixture approach, because the nonindependence of animals in groups and the two-step detection process (availability and detection) violated the binomial variance assumption. In addition, the simulated counts were quite small especially at the end of the simulation, which the relatively large simulated effort (24 replicates per year) may not adequately compensate for. We tentatively analyzed the simulated datasets with the N-mixture methodology.
ACKNOWLEDGEMENTS We thank  Q. Richard  for the capture-recapture analysis of the chamois data. We warmly thank the computing lab at  IN2P3. This work was supported by the  French National Park  system. We thank all French national park staff for their collective insight into mountain ungulate monitoring, and in particular  R. Bonet ,  M. Canut ,  J. Cavailhes ,  M. Delorme ,  T. Faivre ,  G. Farny ,  L. Imberdis ,  A. Jailloux ,  R. Papet ,  E. Sourp. For the mouflon and chamois studies we thank wildlife technicians  J. Appolinaire ,  J. Duhayer , and  C. Itty. For the cat study we thank the  French Polar Institute (IPEV)  for financial support (Program n°279) and all field workers ( Y Chervaux ,  F. Egal , A. Lec'hvien and  C. Brunet ). A very warm thank you generally goes to everyone who contributed to the field efforts over the years.
A 2013 Cochrane review concluded that there was insufficient evidence to support the routine use of magnesium for treating in people experiencing AWS  [18]. In this meta-analysis, among studies that tested oral magnesium, dosages ranged from 312 mg to 499mg of magnesium per day, unfortunately with important clinical and methodological variations between trials  [18]. There is a current ongoing naturalistic randomized multicenter double-blinded trial comparing oral magnesium supplementation to placebo in addition to usual care among inpatients with alcohol withdrawal syndrome (NCT03033823). The main objectives are to examine the efficacy of such supplementation for decreasing intensity of AWS among inpatients requiring pharmacological treatment of their AWS, and to examine if this strategy can reduce benzodiazepine consumption related to AWS treatment.
It has also demonstrated possible inconsistencies in nomenclature and allowed for taxonomic congruency of newly recognised genetic strains between studies. Using methodologies previously outlined  [14] , original and previously published mitochondrial and nuclear data were synthesized into haplotype collections without a primary focus on species membership  [4]. The use of multiple markers and methods to assign Primary Species Hypotheses (PSH), and the addition of further analyses (microsatellite markers) to assign Secondary Species Hypotheses (SSH), form a robust basis for delimitation of true evolutionary units. These methods and the naming and cataloguing of the genetic diversity of the Pocillopora, provide a collated reference dataset of genetic marker information on the phylogenetics of Pocillopora including microsatellite data.
This accessioned dataset provides a powerful referencing tool for aligning localised genetic diversity of Pocillopora, even if species designations are not yet known, so as to avoid pre-emptive designations based on morphology alone. Scleractinia of the Maputaland reef complex (MRC) in South Africa exist at the margins of the Western Indian Ocean (WIO) reef coral range and are the most diverse hermatypic coral communities in South Africa. These coral communities are linked to the WIO centre of diversity by Mozambican Channel eddies that move warm water southward from the Equator transporting coral larvae southward  [15]. This and the favourable stable East African marine environment may account for the comparatively diverse coral assemblages found on this high latitude reef environment. Pocillopora species occupy a conspicuous component of the MRC, covering about 1% of total reef cover, with hard coral abundance having increased in the last 15 years  [16].
These phenomena could have an effect on the perceived southward attenuation in genetic diversity in Pocillopora. Species delineation of Pocillopora using genetics has improved in the past few years, with novel and complete datasets  [3] [4] [5] [7] [8] [9] 11, 12, [26] [27] [28] [29] [30] , and methods available for scientists to use  [3] [4] [5] 7, [9] [10] [11] [12] 29, [31] [32] [33] [34]. Using these methods, the objective was to produce DNA sequences for the mitochondrial ORF and D-loop, the nuclear HSP70A and ITS2 and microsatellite data, a priori of morphological designation. Our aims were four-fold: First; to elucidate Pocillopora species diversity, primarily based on the ORF gene defining Primary Species Hypotheses (PSH), second; to test for the presence of hybridisation within the Pocillopora community on the South-West margin of distribution in the Indian Ocean using two nuclear and two mitochondrial markers, third; to define Secondary Species Hypotheses (SSH) and the presence of cryptic species, using 13 microsatellite markers, and finally forth: elucidate the degree of genetic diversity within each Pocillopora species found using all markers.
Each amplification reaction was performed in a total volume of 10 μL: 1X of MasterMix Applied (Applied Biosystems), 0. 025 μM of forward primer tagged with the M13-tail, 0. 25 μM of reverse primer, 0. 25 μM of fluorescent dyed M13-tail and 2 ng/ μL of genomic DNA. The thermocycling program was: [94˚C for 5 min], 7 × [94˚C for 30 s, 62˚C (-1˚C at each cycle) for 30 s, 72˚C for 30 s], 30 × [94˚C for 30 s, 55˚C for 30 s, 72˚C for 30 s], 8 × [94˚C for 30 s, 56˚C for 30 s, 72˚C for 30 s] for the final hybridization of fluorescent dyed M13-tail + 72˚C for 5 min. PCR products were genotyped using an ABI 3730XL sequencer at the Plateforme Gentyane (INRA, Clermont-Ferrand, France). Allelic sizes were determined with GENEMAPPER 4. 0 (Applied Biosystems) using an internal size standard (Genescan LIZ-500, Applied Biosystems).
Ultrametric phylogenies using BEAST 2. 0 were completed using the GTR+I+G model for each marker  [45]. Four MCMC chains were run for 20×10 6 generations and sampled every 20×10 3 generations. Parameter convergence (ESS values were at least 800 for all trees) was verified using Tracer  [46] , and tree convergence topology was checked using AWTY  [47]  for all Bayesian analyses. The consensus trees (maximum clade credibility tree; 10% burn-in) were constructed with TREEANNOTATOR 1. 7  [48]. Maximum Likelihood (ML) methods were conducted using phyML  [49] , using the same substitution models calculated in MrModeltest  [43] , and results were used for the Automatic Barcode Gap Discovery (ABGD) species delimitation method by analysing the distribution of pairwise differences within a dataset. Trees were rooted using two sister genera within the Pocilloporidae; Stylophora  [50]  and Seriatopora  [51] , accession numbers: KX618661-KX618678 (for ORF, CR, and ITS2) and JX869141-JX869151 for HSP70A, after a BLAST search  [52].
SSH delimitation using microsatellite data Genotyped individuals were assigned to an SSH with reference to a comprehensive published dataset  [4]. The sixteen PSHs identified were used as a point of reference for species clusters in our data set. Population structure was assessed using Bayesian clustering analysis in the program Structure 2. 3. 4  [63]. The analysis was run for the whole dataset using five MCMC simulations per run, with 10 6 iterations and 5×10 5 steps as burn-in, to test possible clusters (K) between one and ten. Structure harvester was used to determine the most likely combination of homogenous clusters  [64].
Mitochondrial DNA phylogenetic analysis and species delineation Bayesian, ultrametric and ML phylogenies for the ORF were congruent using single and multiple individuals per haplotype for the ABGD analysis when using GTR and HKY model parameters. The time-calibrated ORF phylogram formed three significantly distinct and robust clades, for each of the three haplotypes, and correlated with the a priori morphotypes (Fig  2 ). Calculated divergence time for ORF27 from ORF39 and ORF46 was approximately 2 million years ago (MYA) with a 13 bp difference, while ORF39 and ORF46 shared a divergence time Divergence times using the CR were identical to the ORF. CR could not be compared to previous studies due to shorter sequence lengths in this dataset. Nevertheless, the 1 bp insert at position 322 is enough to determine that at least one unique D-loop haplotype exists in the studied colonies.
Nuclear DNA phylogenetic analysis The nuclear HSP70A data were congruent with the ITS2 dataset, even though only half the HSP70 gene was used (S2 Fig). The concatenated nDNA (ITS2+HSP70A) dataset resulted in 56 haplotypes (S1 Fig). These data were not included in our argument as they were mostly congruent with the primary data (the ORF and ITS2 gene, and the microsatellite data). These data were excluded as they were mostly not comparable, nor were they used consistently across previous studies. Thus, for the sake of continuity and reducing redundancy, we report these results as a supplementary addition to the study. SSH09a was composed of 16 ITS2 haplotypes (two shared: one each with SSH13a and SSH13b). SSH13a was composed of six haplotypes (one shared with SSH09a). SSSH13b was composed of 10 haplotypes (one shared with SSH09a).
Use of mitochondrial, nuclear, and microsatellite markers for Pocillopora in South Africa Nuclear DNA data suggests a unique haplotype profile, but low diversity at the population level when compared with other lower latitude populations. Fifty-seven colonies of Pocillopora were sampled for species-level diversity in South Africa for the first time. The MRC marks the southwestern margin of hermatypic coral diversity in the WIO bioregion, where a paucity of research on coral biogeography exists. Recent insight  [3]  has highlighted the concordance of the ORF marker with holobiont, transcriptomic, SNP, and conspecificity data. Added to this, a collection of data now exists for the marker in the form of a collated list of haplotypes  [4]. Thus, species assessment using the ORF marker was appropriate for delineation in South African Pocillopora and demonstrates the efficacy of this marker and suggests its use as a principal barcode marker.
This data also corroborates and illustrates the reproducibility of our methods developed and employed by many studies over different regions  [3, 4, 7, 10, 13, 30, [32] [33] [34] 37]. The failure of the CR primers  [11]  to amplify the much longer CR gene across our dataset suggests mutations within the primer annealing sites. The CR exhibits phylogenetic congruency with the considerably shorter ORF gene. The ITS2 marker was easier to amplify than the HSP70A and B regions. Evidence of this was apparent by the high failure rate of the HSP70B marker in this study, and we were forced to use only half the gene region (HSP70A). Although the ITS2 gene has been reasoned to be a poor barcode marker, it may have merit in identifying.
Acknowledgments We are grateful to members of the  Marine Evolution Lab (MAREVOL)  that assisted in sampling:  Kerry Etsebeth ,  Carolina Barausse ,  Kirsty Wiggill , and  Jessica Chiazzari. We are also thankful to  David Obura , and Louis Celliers who aided in identifying species in the field, and  Louis Celliers  for aiding in confirming previous information on species identification. Thanks go to  Kerry Sink ,  Mari-Lise Franken  and  Prideel Madjiet  and SANBI for logistical and funding support. We acknowledge the  Plateforme Gentyane of the Institut National de la Recherche Agronomique  ( INRA, Clermont-Ferrand, France ) for genotyping and technical support. Lastly, thanks to the three anonymous reviewers, their advice and comments have greatly improved the overall quality of this manuscript.
This work was supported by a personal grant to BC from the  National Research Foundation of South Africa , and a portion of the laboratory work was funded by  SANBI  as part of the  SeaKeys  project ( FBI Marine grant ). HM funded the microsatellite laboratory work through personal university stipend. AM funded the bulk of laboratory work and field work. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data samples and selections The data samples have been collected under particular beam conditions where proton bunches moving towards the detector do not cross any bunch moving in the opposite direction at the nominal pp interaction point. Events with J/ψ or D 0 candidates must have a reconstructed primary vertex within the fiducial region -200 mm < z PV < 200 mm, where high reconstruction efficiencies are achieved and calibration samples available. In order to suppress residual pp collisions, events with activity in the backward region are vetoed, based on the number of hits in VELO stations upstream of the interaction region. Events with at least one primary vertex are selected where the primary vertex is reconstructed from at least four tracks in the VELO detector. The J/ψ candidates are obtained from two oppositely signed muons forming a good-quality vertex.
Differential cross-sections and yields The J/ψ differential cross-sections per target nucleon obtained for the pHe dataset, as functions of the rapidity in the centre-of-mass frame y * and transverse momentum p T , are shown in the two top plots of Fig. 1. These results are compared with HELAC-ONIA predictions  [11] , for pp (blue dashed lines) and pHe (green boxes) collisions. The pp (pHe) calculations use CT14NLO (nCTEQ15) parton densities. Since the predictions underestimate the measured total cross-section, they are rescaled by a factor 1. 78 in Fig. 1  to compare the shape of the distributions. Data are also compared with phenomenological parametrisations, interpolated to the present data energies, based on Refs. [12, 13]. Solid and dashed red lines are obtained with linear and logarithmic interpolations, respectively, between experimental results obtained in pAu collisions at √ s NN = 38.