dataesr/scientific-paragraphs-categorization huggingface dataset:
The PC laboratory was financed by the  Institut National de la santeet de la Recherche Medicale , the  Centre National de la Recherche Scientifique , the  Ministère de la Recherche et Author summary Technologie  and the  Fondation pour la Recherche Medicale (FRM). It has received support under the  PIA  launched by the  French Government  and implemented by the  ANR , with the references:  ANR-10-LABX-54   MEMOLIFE  and  ANR-11-IDEX-0001-02 PSL Ã Research University. PT and ET were supported by doctoral grants from  Universite Ṕaris Sciences et Lettres and Sorbonne Universites , respectively, and by the  Labex Memolife  and the FRM, respectively. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Grhl2 knockout models display both cranial and spinal neural tube defects (NTDs), whereas the Axial defects (Axd) model, a Grhl2 overexpressing model, has spinal defects. Grhl2 is expressed in the non-neural ectoderm or surface ectoderm, a monolayer of cells covering and wrapping around the neural folds that ultimately will give rise to the epidermis. We investigated the molecular and cellular mechanisms by which either excess or insufficient Grhl2 expression can cause NTDs. We performed RNA-seq experiments on both knockout and overexpressing models (Axd) and identified multiple pathways regulated inversely in both models. Genes encoding proteins of the junctional apical complex were highly regulated in both datasets. We further validated a number of adherens junction molecules (such as E-cadherin) and tight junction molecules (a number of claudins) to be regulated by Grhl2 in the caudal neural tube.
[11, 29] Consequently, the acquisition of large genetic datasets in each of these classes is expected to provide insight into the ancestral poriferan genetic toolkit. However, the taxon sampling of transcriptomic and genomic data from sponges is currently quite poor (Figure  1 , see also http://www. spongebase. net, resource accessed in April 2018). Indeed, although transcriptomic and partial genomic data exist from individual researchers, those data are unfortunately not always made publicly available. In all, there are only four genome drafts publicly available so far that are complete enough to provide reliable estimates of gene content and genome size: these are from two demosponges Amphimedon queenslandica and Tethya wilhelma,  [5, 30]  one homoscleromorph Oscarella pearsei,  [31, 32]  and one calcareous sponge Sycon ciliatum.
] [103]  More complete and updated taxonomy can be found on the Word Porifera Database. [104] The names of species are written as follows: 1) in red, when transcriptomic and genomic analyses are already published (whether the corresponding databases are publicly available or not)  [30, 33, 40, 43, 83, 105]  ; 2) in violet, when transcriptome analyses are already published (whether the corresponding databases are publicly available or not) and there is a known Ã on-going genome project  [71, 106]  ; 3) in blue, when transcriptome analyses are already published (whether the corresponding databases are publicly available or not) and there is NO known Ã on-going genome project  [13, 49, 52, 55, 56, 59, 107]  ; 4) in gray, when there are known Ã on-going transcriptome and/or genome projects but not yet published sequence analyses (except on symbiotic content).
Figure1. Phylogenetic relationships among the main sponge taxa according to molecular phylogenetic studies. [29, 60, [101] [102] [103] More complete and updated taxonomy can be found on the Word Porifera Database. [104] The names of species are written as follows: 1) in red, when transcriptomic and genomic analyses are already published (whether the corresponding databases are publicly available or not) [30, 33, 40, 43, 83, 105]  ; 2) in violet, when transcriptome analyses are already published (whether the corresponding databases are publicly available or not) and there is a known Ã on-going genome project [71, 106]  ; 3) in blue, when transcriptome analyses are already published (whether the corresponding databases are publicly available or not) and there is NO known Ã on-going genome project [13, 49, 52, 55, 56, 59, 107]  ; 4) in gray, when there are known Ã on-going transcriptome and/or genome projects but not yet published sequence analyses (except on symbiotic content).
Acknowledgements The authors thank the following colleagues for providing sponge pictures of Oscarella lobularis:  Christian Marschal  ( IMBE, France ); of Oscarella pearsei:  Jennyfer Mora Mitchell  ( University of Denver, USA ); of Oopsacas minuta: Fr ed eric Zuberer ( OSU Pyth eas, France ); of Geodia barretti:  Paco Cardenas  ( Upsalla University, Sweden ); of Tethya wilhelma:  Oliver Voigt  ( LMU, Germany ); of Ephydatia muelleri and Aphrocallistes vastus: Sally leys ( University of Alberta, Canada ); of Amphimedon queenslandica:  Bernard Degnan  ( University of Queensland, Australia ); of Sycon ciliatum:  J erôme Mallefet  ( Catholic University of Louvain, Belgium ). G. W. acknowledges funding by  LMU Munich's Institutional Strategy LMU  excellent within the framework of the  German Excellence Initiative , and the  German Research Foundation (DFG)  grant  Wo896/19-1  within the  Priority Program SPP 1991 "TaxonOMICS,"  and from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  764840  ( ITN IGNITE ).
S. P. L. acknowledges funding from  NSERC   Discovery Grant   2016-05446. C. B. and E. R. thank the grant from  A Ã MIDEX  (n  ANR-11-IDEX-0001-02 ) funded by the  "investissements d'Avenir" French Government program , managed by the  French National Research Agency (ANR) , for the funding of two on going genome sequencing projects.
Objectives and outcome measures The primary objective of ETNA-VTE-Europe is to quantify the long-term rate of VTE recurrence in a large, real-world population of acute symptomatic VTE patients prescribed edoxaban as part of their initial treatment regimen. Accordingly, the primary outcome measure will be the proportion of such patients who experience recurrent symptomatic VTE on one or more occasions within the 18 months following their index VTE, regardless of the length of edoxaban exposure. The co-primary objective is to collect and evaluate real-world safety data regarding adverse drug reactions (ADRs) in patients treated with edoxaban across the currently approved indications. Therefore, ETNA-VTE-Europe data will be combined with 18-month safety data from the Edoxaban Treatment in routine cliNical PrActice for patients with non-valvular Atrial Fibrillation in Europe (ETNA-AF-Europe) study, a parallel European PASS evaluating the safety and effectiveness of edoxaban in real-world treatment of atrial fibrillation (AF)  [10].
Documentation and assessment Data for this study will be sourced from medical records and, when in line with routine clinical practice, from telephone calls between the patient and treating physician. As a non-interventional study, no patient contact, examinations, laboratory tests or procedures are compulsory, and will only be carried out at the discretion of the treating physician, as and when deemed appropriate and without registry influence. A standardised electronic case report form (eCRF) will be completed by the site shortly after enrolment and again after every interaction with a patient over the subsequent 18 months. The eCRFs will be uploaded to the secure, internet-based Medidata Rave EDC system. Given that the edoxaban SmPC recommends 5 days of parenteral anticoagulation following VTE before starting edoxaban treatment  [7] , baseline is defined as the first day of heparin/fondaparinux administration after the index acute VTE event.
The first data entry, which will be completed following enrolment and within 2 weeks of the index VTE, will include details of baseline patient characteristics, comorbidities, VTE-related parameters, past and current therapy, and other relevant assessments made according to site protocol (Table  1 ). Memory aids will be provided to all patients at enrolment, with space to record edoxaban-related treatment changes, use of concomitant medication, adverse events, hospitalisation, physician contact, and productivity loss. This aid can be used to assist with recall during subsequent visits/telephone calls, but are voluntary and will not be formally assessed. In each country, all patients will be followed until the last patient for that particular country has completed the 18-month documentation period, in line with EMA requirements.
At this point, a last-patient-out (LPO) questionnaire, requesting a minimum of vital status, will be issued for each patient enrolled in the respective country. Upon completion of the ETNA-VTE-Europe registry, data will be extracted for the following time points: baseline, 1, 3, 6, 12 and 18 months. Details of the parameters to be evaluated at each time point are outlined in Table  1. The current status, change/events since baseline and change/events since the previous time point will be assessed for each parameter, as appropriate. In addition, recurrence of symptomatic VTE and death since the 18month time point will be retrospectively documented at the time of LPO per country.
Quality control ETNA-VTE-Europe will be conducted in accordance with the Guidelines for Good Pharmacoepidemiology Practice (GPP) and the EMA Guideline on Good Pharmacovigilance Practices (GVP) Module VIII (management and reporting of adverse reactions to medicinal products; EMA/813938/2011 rev 1)  [16, 17]. Automated checks for plausibility and integrity will be carried out at data entry to permit correction or confirmation by the site. Furthermore, approximately 30% of sites will be randomly selected to undergo on-site monitoring, during which random source data verification will be performed. In particular, monitoring activities will closely assess the completeness and correctness of safety data. Patients with missing observations for a particular time point and/or parameter will be omitted from the corresponding analyses.
(5) Physician judgment only. (6) Timing, diagnosis and interventions. (7) I. e. death, stroke, bleeding events, systemic embolism, non-valvular atrial fibrillation, and malignancies. (8) Admittance and discharge dates, clinical event, and use of the emergency room and/or intensive care unit. (9) If assessed. (10) Including blood pressure, heart rate, height and weight. (11) As per the Guideline on Good Pharmacovigilance Practices (GVP) Module VI (Management and reporting of adverse reactions to medicinal products; EMA/873138/2011 Rev. 1)  [16] ; coding according to the standardised Medical Dictionary for Regulatory Activities (MedDRA). *Defined as the first day of heparin administration after the index acute VTE event. [11]. Items in bold reflect differences compared to ETNA-VTE-Europe edoxaban (regardless of treatment discontinuation) and a relative precision of 15% for a two-sided 95% confidence interval (95% CI), data for 1964 patients will be required to assess with sufficient accuracy the primary outcome.
Given an expected dropout rate of 25%, enrolment of 2700 patients should result in an adequate sample size for evaluation at 18 months. In order to obtain a dataset as large as possible for co-primary outcome assessment, safety data from ETNA-VTE-Europe will be combined with 18-month safety data from ETNA-AF-Europe, a sister European PASS study of edoxaban in approximately 13,100 patients with NVAF  [10]. Together, these studies will enrol approximately 15,800 patients, with an overall expected 18-month dropout rate of 20%. Consequently, data for approximately 12,640 patients should be available at 18 months to assess the incidence rates of interest and their 95% CIs. A key aim of this combined analysis is to provide sufficient statistical power to capture uncommon ADRs with low incidence rates; for those that occur at rates of 0.
Statistical analysis Owing to the non-interventional study design, all ETNA-VTE-Europe data analysis will be explorative and descriptive only. In addition to the Europe-wide analysis, safety and effectiveness data will be presented for each individual country and region (Austria, Switzerland and Germany [DACH]; the United Kingdom and Ireland [UK/IE]; Belgium and the Netherlands [BE/NL]; and Italy). Comparisons between patients in particular edoxaban exposure categories (current use, recent use [within the last 3 days], and past use [> 3 days ago], as well as use within the last 30 days) will also be performed, with outcome data additionally presented for all patients permanently discontinuing edoxaban. Furthermore, subgroup analyses comparing patients with/without the following baseline characteristics are planned: renal impairment, hepatic impairment, DVT only (vs.
PE with/ without DVT), age ≥ 75 years, male gender, initial 30 mg edoxaban dose (vs. 60 mg), and active cancer. To provide context to our results, the outcomes of ETNA-VTE patients will be appraised relative to those of PREFER in VTE patients treated with a DOAC, PRE-FER in VTE patients treated with a vitamin-K antagonist (VKA), Hokusai-VTE patients treated with edoxaban, and Hokusai-VTE patients treated with warfarin. These evaluations will be performed on an entirely visual basis, with no joint statistical models planned. Given the oneyear follow up of the PREFER in VTE and Hokusai-VTE studies, only 12-month data from ETNA-VTE-Europe will be considered for these purposes  [12, 13]. Data will be analysed and presented using descriptive statistics. Categorical variables will be reported as absolute numbers and percentages, and continuous variables will be presented as means with standard deviations or medians with interquartile ranges and minimum/maximum values, alongside the number of missing and nonmissing observations.
Data gathered from the ETNA-VTE-Europe study with minimal selection criteria will address this knowledge gap, with several pertinent subgroup analyses already planned. The gathered data will also provide a snapshot of the types of patients being prescribed edoxaban, the doses used, and the durations of treatment in a real-life setting. This will permit appraisal of the appropriateness of such therapeutic decisions as well as acting as a marker for evaluation of subsequent trends of prescription. An additional limitation of current studies is that data are only available for up to 12 months of edoxaban therapy  [6]. Considering that a number of patients will require longer-term anticoagulation in clinical practice  [8] , those continuing edoxaban dosing beyond 12 months will find themselves in uncharted waters.
The 18-month follow-up period planned for ETNA-VTE-Europe patients will provide clinicians and patients with valuable information regarding the safety and net clinical benefit of extended treatment. In particular, trends in rare ADRs such as liver events and major bleeding will be of interest, given their low frequency in the Hokusai-VTE trial  [6]. Combination of ETNA-VTE-Europe data with those from the ETNA-AF-Europe sister study will provide an even larger population from which to assess these safety outcomes  [10]. Thus, the present PASS is a responsible and important part of the early post-marketing phase, designed to address several of the knowledge gaps highlighted in the EMA risk-management plan for edoxaban  [9]. The single-arm design of the ETNA-VTE-Europe study reflects its key aim of characterising the real-world safety and effectiveness of edoxaban.
Lambrachaeus ramifer Aniptumnus vietnamicus  Ng and Clark, 2008  is another related species, similar to L. malardi for distal aspect of male G1 (several specimens from Vietnam attributed by Raoul Serène to 'Parapilumnus malardi' have been assigned to A. vietnamicus by  Ng and Clark (2008). GEOGRAPHIC AND DEPTH RANGES -WIO (?IWP), Mayotte (present study), Madagascar (type locality); intertidal, subtidal. This species is probably widespread in IWP although rarely reported. It is invasive in the Levantine Sea and in the English Channel (but not established there). De Man (1913 , 1914)  has described this crab from specimens collected between barnacles fixed on ship hull mooring at Saint-Vaast-la-Hougue, English Channel, coming from Madagascar. The record in the Levantine sea is indicated as 'from  Türkay, 2015 , personal database' in WoRMS (2018).
The two pelagic species reported are Charybdis smithii, observed in large oceanic swarms, and the 'oceanic crab' Planes major. The results of Table  3  show that the deep fauna is poorly represented in the present inventory in Mayotte region. The three main oceanic campaigns having collected deep Decapoda in the region are shown below (Figure  22 ) with these campaigns being also presented in BasExp (2018). While the Decapoda collection found in 1977 has been already studied in several contributions those undertaken in 2009 and 2017 require investigation. Undoubtedly they will create many new records for the region. The total number of crab in the region can be estimated by comparison with more global inventories in the IO, these including the deep species that are poorly represented in the present contribution:  For WIO French overseas territories the database of  Legall and Poupin (2018)   From these examples it appears that the estimation of the total number of crabs in Mayotte region is still speculative.
It is, however, realistic to consider that the number of crabs in this region may be about twice as for the present inventory; that is ~ 600 species. This figure is consistent with other IWP regions, e. g. Australia, the 'Zoological catalogue'  (Davie, 2002)  with 969 species; Taiwan, 'Annotated checklist'  (Ng et al. , 2001)  with 548 species including the caveat that 'the brachyuran fauna for Taiwan and its associated islands will probably approach 700 species when more surveys and studies have been completed'; Japan and adjacent seas  (Sakai, 2004)  with 'some 1250 species and subspecies of brachyuran crabs'; French overseas territories of New Caledonia and French Polynesia (database of  Legall and Poupin, 2018)  with 640 and 480 valid species, respectively; and the Hawaiian Islands  (Castro, 2011) , which are more isolated and probably have an impoverished fauna, with 284 'reliably identified' species.
ACKNOWLEDGMENTS Financial support for this study has been obtained from the  Direction de l'Agriculture et de la Forêt of Mayotte (DAF)  and  Total Foundation. Supplementary assistance for this research has been given by the  École Navale, Brest  and the  Muséum national d'Histoire naturelle, Paris (MNHN). In MNHN Paris the registration of the collection was begun by  R. Cleva ,  R. Kebir  and  J. Poupin , using the old handwritten catalogs (e. g. B32251). It was continued and computerized (e. g. MNHN-IU-2009-1069 ) by  P. Martin Lefèvre  with assistance of  R. Kebir ,  A. Sato  and  S. Soubzmaigne. Photographs of some species were obtained via several collaborators, by alphabetical order:  Lionel Bigot ,  Matthias Deuss ,  François Fromard ,  Yvon Gildas ,  Christian Hily ,  Matthieu Leray ,  J.
knowledge, such a mechanism of ribosome splitting has not been reported in the context of antibiotic resistance. In this study, we assessed the role of lmo0762 in antibiotic resistance. We showed that lmo0762 confers resistance to lincomycin and erythromycin, two antibiotics that block translation. Thus, we renamed it hflXr, for hflX resistance. We analyzed its expression regulation, and showed that an attenuation mechanism leading to premature transcription termination controls hflXr expression. This attenuation mechanism relies on the 14-aa ORF encoded by rli80, which strikingly contains the arginineleucine-arginine (RLR) motif, a signature feature for macrolide resistance gene leader peptides  (22). Moreover, by analyzing the polysome profiles of bacteria grown in the presence of erythromycin, we provide data suggesting that HflXr promotes recycling of blocked 70S ribosomes and thus translation.
Results lmo0762 Is an Antibiotic Resistance Gene. In a previous study, we analyzed the expression profile of all Listeria genes in the presence of subinhibitory concentrations of lincomycin and discovered that lmo0762 is induced (ref. 13  and Fig. 1A ; data are publicly available in the European Nucleotide Database, accession no. PRJEB25942). This gene is located downstream of a small RNA, rli80, and while rli80 appears to be transcribed in both the absence (black) or the presence (green) of lincomycin, lmo0762 is primarily transcribed in the presence of the antibiotic. To verify lmo0762 induction by lincomycin at the protein level, we created a strain in which a Flag tag was introduced at the C terminus of the Lmo0762 protein. We extracted total proteins from this strain after growth in the absence or presence of subinhibitory concentration of the antibiotic, and performed a Western blot using an anti-Flag antibody (Fig.
S5 ). Interestingly, other phyla also harbor a duplication in the hflX genes, e. g. , α-, β-, γ-, and δ-proteobacteria and Archaea. These events occurred independently from the one of Firmicutes, highlighting the importance of hflX gene duplication. The analysis of 163 pangenomes from bacteria revealed that the genes of this family, when present, are in the core genome (98% in >90% of the strains, SI Appendix, Fig. S6 ). Finally, the analysis of genetic neighborhood of the two subfamilies showed much higher conservation for lmo1296 than for hflXr (Datasets S1 and S2). Based on these elements, it is tempting to speculate that the ancient duplication of hflX led to two proteins with specialized functions in Firmicutes, explaining why duplicates cooccur, one of which being involved in antibiotic resistance (hflXr).
4A , brown dashed squares). We analyzed the RNAseq profile of the rli80-lmo0762 locus in these different mutant strains, in the absence and presence of lincomycin (Fig. 4B  and SI Appendix, Fig. S9C , data available in the ENA database, accession no. PRJEB25942). In agreement with the above hypothesis, mutating the anti-terminator region or the ORF start codon, both of which are predicted to stabilize the off conformation of rli80, prevented activation of lmo0762 expression during lincomycin exposure and led to lower mRNA abundance in qRT-PCR assay (SI Appendix, Fig. S10 ). In contrast, mutating the anti-antiterminator region (i. e. , the strain that we previously named const), which is predicted to maintain the on conformation of the riboregulator, led to constitutive readthrough and expression of hflXr, regardless of the presence of lincomycin, as well as enhanced antibiotic resistance (Fig.
1A. further investigations will be required to reconcile these data with our results. WT ΔhflXr WT ΔhflXr Erythromycin No antibiotic Interestingly, L. monocytogenes encodes another hflX homolog, lmo1296, which is not involved in antibiotic resistance. Many Firmicutes possess two copies of hflX, and similar independent duplications are observed in other clades of prokaryotes (Fig. 2B ). Given that many Firmicutes possess a hflX gene that belongs to the subfamily of hflXr, it seems reasonable to think that the antibiotic resistance mechanism that we described in Listeria for hflXr could be conserved in many other bacteria. This duplication represents an example of how bacteria can employ common stress response factors as antibiotic resistance genes. In addition, our work is now strengthened by two recently published studies where functional metagenomic databases constructed from antibiotic-rich environments pointed to hflX from Simkania negevensis and Emergencia timonensis as a putative resistance gene  (23, 33).