dataesr/scientific-paragraphs-categorization huggingface dataset:
However, where required expertise was not available within the group, external experts were consulted. In addition, because observational studies need large numbers of patients, this core dataset will need to be implemented in many research facilities. Although this might prove to be a challenge, we think that, as many of the items from the core dataset are already registered in clinical practice, this will not become a problem. Although we had a very experienced patient representative, who also was the Chair of the Dutch Association for People with Atopic Dermatitis, it would have been desirable to include more patient representatives in this consensus process. Finally, for a number of domain items no underlying systematic reviews of the evidence were available. This meant that, in this study, expert opinion played a larger role than, for example, in the HOME initiative.
Category When to measure Follow-up frequency while on therapy 4 weeks, 3 months and then every 3 months Follow-up frequency while off therapy Every 6 months Visit window +/À1 month encouraged that the larger TREATgermany dataset appears feasible to local investigators in its current form. 21 his core dataset will allow the international dermatology community to generate, compare and pool data of patients with AE on phototherapy and systemic therapy across country borders to answer important questions on long-term effectiveness, safety and cost-effectiveness of these therapies; which can only be addressed with very large patient numbers (e. g. on rare adverse events). We are working on a standardized data collection/storage platform to facilitate uniform data collection, pooling and analyses.
Acknowledgments The authors would like to thank the following for providing their valuable expertise:  Olivier Chosidow ,  Kathleen Mcelhone ,  Matthias Augustin  and  Peter Wolf  (patient-reported satisfaction with AE care received),  Matsutaka Furue  (use validated diagnostic criteria),  Ellen Smets  and  Pythia Nieuwkerk  (adherence to treatment between appointments),  Judith Sluiter  and  Angela de Boer  (days lost from usual activities),  Eric Simpson  (patient-reported symptoms and investigator/physician global assessment),  Sonja St€  ander and  Gil Yosipovitch  (patientreported symptoms).
Ancillary study (see online supplementary information for details). Determine the evolution of the plasmatic glutamate levels during the study (at visits 0, 2, 3 and at the last follow-up visit). The data will be compared in the two treatments arms. First, the prognostics value of glutamate levels correlated with CRC TNM scores in CRC patients will be assessed. Second, we will investigate a possible correlation between blood glutamate levels and the intensity of neuropathic disorders. This investigation may open up new avenues for research.
Statistical analysis All analyses will be performed using Stata software (V. 13, StataCorp, College Station, Texas, USA). The analysis will be performed on unblinded data in accordance with the International Conference on Harmonisation-Good Clinical Practice guidelines. Continuous variables will be presented as mean and SD or median and quartiles range, according to statistical distribution. These variables will be compared using the unpaired t-test or the Mann-Whitney U test when appropriate, according to assumptions of t-test: (1)  the Shapiro-Wilk test will be used to assess normality and (2) the Fisher-Snedecor test to assess homoscedasticity. Categorical data will be presented as exact numbers and percentages. A two-sided p-value of <0. 05 will be considered for statistical significance for all analyses.
Unblinding will be allowed only in cases of serious adverse effects. If required, the sponsor will inform the pharmacist and investigator, by email within 24 hours of unblinding, whether riluzole or placebo corresponds to the number allocated. dissemination Approval We will submit all substantial modifications of the protocol and/or informed consent form to the ethics committee and/or competent authority for approval. The sponsor will notify the ethics committee and the competent authority of study termination. This study is registered in EudraCT and clinicaltrials. gov. The current protocol is V. 1. 1 (11 July 2018).
Data collection and quality management At each participating centre, delegated site staff will be responsible for data entry and coding, and the secure storage of data. The patient's data will be pseudoanonymised. The data will be collected and managed using an electronic case report form. A clinical research associate, commissioned by the sponsor (UNICAN-CER-AFSOS group), will verify the data and monitor the study according to UNICANCER's standard operating procedures, good clinical practice and French laws. All participants, investigators, clinical research associates and pharmacists of each clinical centre will be blinded to study treatment. Biostatisticians will be blinded to treatment during all analysis. An IDMC will be constituted for the study. The committee will consist of at least two clinicians, with expertise in OIPN, and a statistician/methodologist.
Patient and public involvement The objective of the Federation of the Patient Committees for Clinical Research in Cancerology is to reviews trial documents provided to patients in oncology clinical studies. The committee makes recommendations to improve the quality of information given to patients. The 'Ligue Nationale Contre le Cancer' and the French NCI (INCa) coordinate this committee. The relevant trial documents for this study have been reviewed by this committee. In addition, the study has been registered in the EudraCT and the clinicaltrial. gov public registries. The study results will be published on these registries, when available. In addition, the study information will be available for patients on the 'Ligue Nationale Contre le Cancer' and INCa websites.
Acknowledgements We would like to thank the  Federation of the Patient Committees for Clinical Research in Cancerology  for reviewing the study documents. Contributors NK, TS, VP, DB, FB, IK, JB, AE and DP led and contributed to the conceptualisation and implementation of this research protocol. BP and FB led to the development of the statistical analysis plan. NK, DB, VP and DP participated in the design of the protocol for interventions and assessments. All the authors have read and approved the final manuscript. A steering committee that will include at least the coordinator (DP), the methodologist/statistician (BP), the project leader at  UNICANCER  and the supportive care representative (VP) will meet regularly to manage the trial.
Microscopy One gram of faeces was either suspended in 10 mL of distilled water or concentrated using the diethyl ether-PBS concentration method as previously described  (Castro-Hermida et al. , 2005). The supernatant was removed and the pellet was resuspended in distilled water up to 500 μL. Cryptosporidium oocysts were detected from 20 μL of both concentrated and non-concentrated oocyst solutions via direct immunofluorescence assay (DFA) using the commercial Merifluor Cryptosporidium/Giardia immunofluorescence assay (Meridian Diagnostics, Inc. , Milano, Italy) as indicated by the manufacturer, and including previously described modifications  (Mammeri et al. , 2018). Stained slides were observed with a Leica fluorescent microscope using the Leica Application Suite software (version 4. 5. 0; Leica Microsystems; Inc.
DNA sequence analysis PCR products of the two target genes (18S rRNA and gp60) were sequenced on both strands using internal primer sets by Eurofins Genomics (France) and Genoscreen (France), respectively. Consensus sequences were edited using the BioEdit Sequence Alignment Editor software and compared with published GenBank sequences using the freely-available Basic Local Alignment Search Tool (BLAST) from the National Center for Biotechnology Information (NCBI) (http://blast. ncbi. nlm. nih. gov/Blast. cgi). Representative nucleotide consensus sequences generated in this study were deposited into the GenBank database under accession numbers as indicated in Table  1. C. parvum subtypes were recognised based on the number of trinucleotide repeats (TCA or TCG) or rare (R) repeats in the gp60 sequence as previously described  (Sulaiman et al.
Acknowledgements Mohamed Mammeri is the grateful recipient of a  Cifre (Industrial Research Training Agreement) grant. He would like to thank  Phileo  ( Lesaffre Animal Care, France ) and the  ANRT (National Association for Technical Research), Ministry of Research (France). The authors are grateful to  Aurélie Heckmann  and  Amandine Blaizot  for their help in creating the map, and to  Dr. Grégory Karadjian  for help with submitting sequences to NCBI. The authors are especially grateful for all the veterinarians who participated in the collection of faecal samples:  Dr. Valérie Wolgust ,  Dr. Catherine Bardot ,  Dr. Caroline Pagneux ,  Dr. Edwige Bornot ,  Dr. Radu Blaga , and  Dr. Typhaine Hebert.
Acknowledgments Foremost, the authors are deeply saddened by the unexpected passing of Ruth on October 25, 2018. Ruth was an exceptional scientist and pioneer in the field of coral reef biology who worked tirelessly on a 'super coral' that would be better poised against the damaging effects of climate-change, such as ocean acidification and ocean warming. Her life and work is a testament to what can be achieved through scientific innovation and infectious optimism. This work was supported in part by the  IAEA Environment Laboratories  and the  U. S. Department of State  through the  Junior Professional Officer program  (ML). The IAEA is grateful for the support provided to its Environment Laboratories by the  Government of the Principality of Monaco. PWS thanks  Ms Theresa Fregoso  ( USGS -Santa Cruz, CA USA ) for graphics assistance.
, 2017; Reniers, Vanschoenwinkel, Rabet, & Brendonck, 2013; Vanschoenwinkel et al. , 2012). This has been explained as a consequence of relatively recent range expansion from a small number of refugia after the Pleistocene glacials. Two studies have been undertaken to investigate specific aspects of the phylogeny of B. schaefferi, one based on allozymes and CO1  (Gandolfi et al. , 2015)  and 4. Overall, the studied B. schaefferi dataset comprises high levels of genetic differentiation, without a clear morphological signal. Phylogenetic searches and pairwise genetic distances suggest that the studied lineages belong to a complex of four morphologically cryptic species. Since these four evolutionary old clades persist (±2 million years), despite overlapping geographic ranges and since they span a variety of ecological conditions, they should be considered as separate evolutionary significant units for conservation.
| Sampling procedure Samples were collected from a total of 68 temporary ponds in Europe, northern Africa and one site in Bahrain (Asia). Most specimens were field collected between 1980 and 2016 and conserved in ethanol of variable strength. Upon reception of the samples at KU  Leuven (2012 Leuven ( -2016)) , all ethanol was substituted by pure grade absolute ethanol and samples were subsequently stored in a fridge at 4°C. Specimens from Morocco (Timahdite, Ifrane, Ighergharen, and unknown localities), around Alger in Algeria, El Battan in Tunisia, unknown locality in Malta, and Vars and Les Cannet-des-Maures in France (for accession numbers see Table  1 ) were obtained after hatching field-collected sediment with B. schaefferi egg banks in the laboratory.
| Phylogenetic and phylogeographical reconstructions All generated B. schaefferi CO1 sequences were assembled and visually checked for quality using SeqScape v2. 5. Consensus sequences were edited in BioEdit Sequence Alignment Editor  (Hall, 1999). All sequences that contained insertions and/or deletions (15 in total) were removed from the CO1 alignments to avoid the risk of co-amplified nuclear mitochondrial pseudogenes interfering with the analyses  (Song et al. , 2008). The newly generated sequences of B. schaefferi, together with existing B. schaefferi sequences from GenBank  (Gandolfi et al. , 2015) , one sequence of Branchipus blanchardi Daday 1908 (KP702861. 1) and one outgroup taxon (CO1: Branchipodopsis drakensbergensis GU139737. 1 and ITS1: Branchipodopsis wolfi MN325155), were aligned with the CLUSTALW multiple alignment tool in BioEdit.
All sequences were uploaded to GenBank (for accession codes see Table  1 ). The most probable evolutionary model for both markers was determined in PhyML  (Lefort, Longueville, & Gascuel, 2017)  based on both the Bayesian information criterion and Akaike information criterion (AIC). For CO1, the AIC selected for a general time reversible model (GTR) with discrete γ model (+G; γ = 1. 83) with invariable sites (I = 0. 57) which was used to assemble the Bayesian inference (BI) and maximum likelihood (ML) tree. To assemble neighbour joining (NJ) trees, we used a Tamura Nei evolutionary model (TN93;  Tamura & Nei, 1993)  with a discrete γ distribution, which was the best scored available model for the NJ method. For ITS1, the Bayesian information criterion selected a Kimura 2-parametric model (K2P;  Kimura, 1980) , which was used for constructing the ML and NJ tree.
, 2010)  according to the GTR + G + I evolutionary model for the CO1 and K2P model for ITS1 with 1,000 bootstrap replicates. The MP analyses for CO1 were performed in PAUP* v4. 0  (Swofford, 2001)   on the studied CO1 fragment. The 4×-rule states that the lineages can be considered as separate species when the mean distance between them is at least four times larger than the mean divergence within the lineages  (Birky et al. , 2005). The ABGD method separates species based on the barcode gap that occurs when the divergence between individuals of the same species is lower that the divergence between the individuals of the different species  (Puillandre et al. , 2012). To run the ABGD method, we used the online version (http:// wwwabi. snv. jussi eu. fr/publi c/abgd/abgdw eb. html) following the default settings.
and for ITS1 in MEGA. The settings included Heuristic search, Tree-Bisection-Reconnection, 1,000 saved trees, and 100 bootstrap replicates. The number of polymorphic and parsimony informative sites was also determined in PAUP*. NJ analyses were performed in MEGA X including 1,000 bootstrap replicates and partial deletion TA B L E 1 Overview of newly generated and GenBank sequences of Branchipus schaefferi with details on the localities 3), DJ(1,3), DL(1-3), DM(1-2), DN(1-2), DS(1-3), FS(1alignment gaps, missing data, and ambiguous bases were allowed at any position). Bayesian inference was performed in MrBayes (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck, 2003; Ronquist et al. , 2012). Markov Chain Monte Carlo analysis ran for 2 × 10 6 generations with a sampling frequency of 1,000 generations and a 25% burn-in.
Zsófia Horváth,  Olivier Baron ,  Jean-Pierre Besson ,  Jean-François Cart ,  Pierre Olivier Cochard ,  Eric Gallerne ,  Pascal Lluch ,  Fabien Massinissa Garaoun ,  Olivier Peyronel ,  Eric Quéinnec ,  François Thiéry ,  Olivier Vannucci ,  Bartłomiej Gołdyn , and  Michał J. Czyż  for providing B. schaefferi specimens. We thank  Bart Hellemans  for extensive assistance in the molecular lab and  Simon Vitecek  for help with the data analysis. Research visits of D. L. to  KU Leuven  were financially supported by short-term mobility grants of the  University of Vienna  ( KWA grant), OeAD (Erasmus + internship ), and  ÖFG  grant for international communication. D. L. receives financial support from a  DOC  fellowship, awarded by  Austrian Academy of Science (ÖAW)  at the  WasserCluster Lunz  and  University of Vienna.