dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments This study has been supported by an unrestricted operating grant (Troncy) from the  Scientific Council of VetAgro Sup , a  Canadian Institutes of Health   Research-Strategic and Training Initiative in Health Research: Gasotransmitter REsearch And Training (GREAT) Program  grant, a  Canada Foundation for Innovation  (# 9483 , Troncy) supporting materials, and internal grant from  French Agriculture Ministry  ( EA 4173 ).
The division of Hexactinellida into the two subclasses Amphidiscophora and Hexasterophora  [20, 21]  is well supported by the mutually exclusive occurrence of amphidiscs and hexasters in these groups (Fig. 2i, j ), and is also highly corroborated by molecular data  [3]. Amphidiscophora contains a single extant order, Amphidiscosida (Hyalonematidae, Pheronematidae, Monorhaphididae). Hexasterophora currently comprises four orders: Hexactinosida (Aphrocallistidae, Auloplacidae, Craticulariidae, Cribrospongiidae, Dactylocalycidae, Euretidae, Farreidae, Fieldingiidae, Tretodictyidae), Aulocalycoida (Aulocalycidae, Uncinateridae), Lychniscosida (Aulocystidae, Diapleuridae), and Lyssacinosida (Euplectellidae, Leucopsacidae, Rossellidae). Members of the first three orders have socalled dictyonal frameworks, which are rigid internal skeletons composed of fused hexactins, whereas members of Lyssacinosida have internal skeletons composed of mostly unfused spicules, a condition called lyssacine that is also characteristic of Amphidiscophora (Fig.
In this study, we have increased molecular taxon sampling of the four markers established by Dohrmann et al. [3, 16]  by 12 additional genera, which include representatives of one additional order (Aulocalycoida), and three additional families (Aulocalycidae, Craticulariidae, Uncinateridae). Furthermore, we compiled morphological character matrices from all described extant genera of the two subclasses. Molecular and morphological datasets were first analyzed separately and then combined to incorporate the unsequenced genera into the molecular phylogeny by using "total-evidence" approaches in maximum-parsimony (MP), maximum-likelihood (ML), and Bayesian analysis frameworks, as well as a "morphology-based phylogenetic binning" approach recently developed by Berger and Stamatakis  [22]. Comparisons of the results of these four ).
Morphological data assembly and phylogenetic analysis Analyses of morphological data were performed on genus-level, i. e. , monophyly of all genera was assumed a priori. Although a simplifying assumption, it is reasonable because most hexactinellid genera are morphologically well delineated. Furthermore, almost half of them (59/126 = 46. 8%; counted May 2016) are monospecific (see Appendix 1). In any case, a comprehensive analysis on species-level would have been too time-consuming and is left for future projects. A genus-level matrix comprising 105 taxa and 154 morphological characters was recently compiled by Henkel et al. [23]  to reconstruct hexactinellid phylogeny, with a focus on Hexasterophora. This matrix was kindly provided to us by Daniela Henkel and used as a starting point for building our own morphological datasets.
The final Amphidiscophora matrix has 13 taxa and 29 characters, and the final Hexasterophora matrix has 114 taxa and 108 characters; these datasets can be found in Nexus format in Additional files 1 and 2 and as tables with annotated character lists in Additional files 3 and 4 (all Additional files are available at figshare [https:// doi. org/10. 6084/m9. figshare. 3120130. v3]). Phylogenetic analysis of the morphological data matrices was performed under maximum parsimony (MP) as implemented in TNT v1. 1  [57] , using "new technology" searches (sectorial search, ratchet, drift, and tree fusing; init. addseqs = 100, find min. length = 10) with implied weighting (default function, concavity constant K = 3. 0), which is a technique to down-weight overly homoplastic characters  [58]. Preliminary analyses under equal weighting were also performed but generally produced longer trees that were less congruent with morphology-based taxonomy and/or molecular evidence (results not shown).
Molecular data assembly and phylogenetic analysis The datasets of Dohrmann et al. [16]  consisting of 18S ribosomal DNA (rDNA), 28S rDNA, mitochondrial (mt) 16S rDNA and mt cytochrome oxidase subunit I (COI) fragments (see  [3, 16] )were supplemented with subsequently published hexactinellid sequences  [17, 18, 70] ; sequences for 16 additional specimens were newly generated for this study (Table  1 ). DNA was extracted by boiling small pieces of tissue for 20 min in 20% Chelex (Sigma-Aldrich) (detailed protocol available upon request from MD). Polymerase chain reaction (PCR) was performed with GoTaq (Promega) or MyTaq (Bioline) according to manufacturers' instructions. Thermal regimes and primers are described in  [3, 16]. PCR products were purified either with ExoSAP-IT (Affymetrix) in case of clear single bands, or otherwise cut out from 1% agarose gels and cleaned with a "freeze-squeeze" method adopted from  [71]  or a QIAquick Gel Extraction kit (QIAGEN).
Sanger sequencing was performed with BigDye Terminator chemistry (Applied Biosystems) at the sequencing facility of the University of Alabama, Birmingham, AL, USA and the Sequencing Service of the Department of Biology at LMU Munich. Chromatograms were edited using Codon Code Aligner (Codon Code Corporation) or Geneious 6. 1. 6 (Biomatters) and consensus sequences manually aligned to the datasets described above. In addition, 16S rDNA and COI sequences from Lophophysema eversa, Tabachnickia sp. (Amphidiscophora: Hyalonematidae), and Vazella pourtalesii (Lyssacinosida: Rossellidae) were extracted from mt genome sequencing To check for conflicting phylogenetic signal between markers, single-gene alignments were first analyzed separately in RAxML 8. 0. 26  [67] , after removal of unalignable regions and sites with excessive numbers of gaps.
Phylogenies were inferred from the supermatrix using ML and Bayesian methods as follows. For ML analyses, we used RAxML under the models and options described above, assuming a single topology and set of branch lengths across partitions but independent model parameters for each partition. For Bayesian analyses, we used MrBayes 3. 2. 4 [62]  under a model-partitioning scheme analogous to the ML analyses. For 18S and 28S rDNA stem-encoding regions we employed the Doublet model (based on  [78] ). Structure information was converted from dot-bracket format to MrBayes format using a perl script written by Oliver Voigt (see  [79] ). We ran 2 × 4 MCMC chains in parallel for 5 × 10 6 generations, sampling every 100th. Convergence was checked in Tracer 1. 6  [66]  and 50% of samples were discarded as burn-in before calculating the MRC.
Combined analysis of molecular and morphological data ("total evidence") To investigate whether addition of morphological characters to the molecular dataset would influence tree topologies, we first conducted analyses restricted to those genera with molecular data. For this purpose we split the supermatrix into submatrices representing Hexasterophora and Amphidiscophora, respectively (see above), excluded all but one species each of genera represented by multiple species, and renamed the remaining terminal taxa to match the taxon names in the morphological dataset. Species retained from multi-species genera were chosen as to minimize missing data; those were C. weddelli for Caulophacus, R. nuda for Rossella, N. asconemaoida for Nodastrella, B. spinosus for Bathydorus, E. sp. 1 for Euplectella, I.
panicea for Iphiteon, D. pumiceus for Dactylocalyx, H. calyx for Heterochone, A. vastus for Aphrocallistes, A. australia for Aspidoscopulia, T. n. sp. 2 for Tretopleura, and H. sp. 3 for Hyalonema. Iphiteon and Semperella were included as outgroups for Amphidiscophora and Hexasterophora, respectively. Morphological characters for the outgroups were all coded as absent (0) in order to mimick the conditions of the morphological analyses (see above). Molecular and morphological partitions were then concatenated in SeaView and analyzed in RAxML and MrBayes as described above (using 10% burnin in the MrBayes analyses, and not accounting for ascertainment bias of the morphological partition in the RAxML analyses due to software limitations). To facilitate comparison, the taxonreduced molecular supermatrices were also analyzed separately in RAxML.
Next, we attempted to reconstruct complete genuslevel phylogenies of the two subclasses. For this purpose we first concatenated the taxon-reduced molecular supermatrices with the complete morphological matrices (resulting in datasets with ~62 and ~65% missing data for Amphidiscophora and Hexasterophora, respectively), and analyzed those datasets in RAxML and MrBayes as described above. Second, we analyzed the data with MP in TNT under the same settings as used for the morphology-only analyses (see above; gaps were treated as missing data). Because TNT does not support mixed data types, we first recoded the sequence data such that A was replaced with 0, C with 1, G with 2, and T with 3; all ambiguous characters (N, R, Y etc. ) were recoded as gaps (-). For comparability with the ML analysis, we performed bootstrapping  [80]  with 550 (Hexasterophora) and 1000 (Amphidiscophora) pseudoreplicates (init.
Ancestral state reconstruction For the purpose of more in-depth investigations of character evolution across Hexactinellida, we first merged the morphological data sets of Amphidiscophora and Hexasterophora, resulting in a matrix of 124 characters for 125 taxa (plus outgroup coded as 0 for all characters; see above) (Additional file 12). We then also included six additional characters that were not used for the purpose of phylogeny reconstruction because they are too prone to homoplasy or overly simplistic representations of complex morphological features (extended matrix in Additional file 13): 1) pinular hexactins (hexactins with a bushy distal ray), 2) basiphytous attachment to the substrate (attachment by a siliceous plate), 3) lophophytous attachment to the substrate (attachment by anchoring spicules), 4) general presence of synapticular fusion (fusion of spicules through siliceous bridges [see Fig.
Sceptrulophora. In this study, we have added five additional sceptrule-bearing species to the molecular dataset: Tretopleura n. sp. 1 and 2 (Uncinateridae; Fig. 1c ), Laocoetis perion (the sole extant survivor of the paleontologically important Craticulariidae), the recently described euretid Homoieurete macquariense  [44] , and the tretodictyid Cyrtaulon sigsbeei. In the ML tree, Laocoetis is the sister taxon to a clade containing all sampled sceptrulophorans except Tretodictyum, Hexactinella, and Psilocalyx (Tretodictyidae sensu stricto [s. str. ] hereafter). However, BS for this arrangement is very low, and in the Bayesian tree the position of this longestranging hexactinellid genus (since the Late Jurassic  [86] ) with respect to Tretodictyidae s. str. and the remaining sceptrulophorans remains unresolved.
Pending further evidence, and given that recognizing the LD clade as a Linnean taxon is problematic (see below), we here treat Dactylocalycidae as Hexasterophora inc. sed. (Appendix 2). The enigmatic dictyonal genus Heterorete (Fig. 1b ; currently in Euretidae) is here included for the first time in a molecular phylogenetic study. As this taxon lacks sceptrules and uncinates it is not too surprising that it comes out closer to Lyssacinosida than to Sceptrulophora. One reason (but see also above) for our inability to confidently infer the exact position of this genus is likely the low gene coverage (Table  1 ); additional, better preserved specimens are needed to obtain more sequence data from this important taxon. Regardless of its exact position, however, our results clearly reject an affinity of Heterorete to Sceptrulophora, and it is best treated as Hexasterophora inc.
Phylogenies inferred from combined molecular and morphological data Combined analyses restricted to genera with sequence data Not surprisinglygiven the small number of informative characters available for this subclassaddition of morphological data to the Amphidiscophora matrix had no effect on the tree topology; only some BS values slightly decreased (not shown). In contrast, addition of morphological characters to the Hexasterophora matrix had some noticeable effects: In the ML tree (Additional file 25: Figure  S11 ), the exact positions of Asconema, Rossella, and Atlantisella within Rossellidae and Euplectellidae, respectively, changed (albeit with poor BS), Dactylocalycidae came out monophyletic (also with weak support), and support for monophyly of Lyssacinosida (sensu novo [s. nov. ]), Euplectellidae, Tretodictyidae s.
A possible synapomorphy of Hyalonematidae and Pheronematidae to the exclusion of Monorhaphis is the presence of anchorate basalia (attachment spicules with anchor-like distal ends). However, molecular data of Monorhaphis are required to further test its phylogenetic position within Amphidiscophora. The remaining part of the Hyalonematidae topology is congruent with the morphology-based tree (Fig. 4 ) in showing a sister-group relationship of Hyalonema and Lophophysema. However, the positions of Compsocalyx and Chalaronema are reversed, character support for which remains unclear. In any case, for a comprehensive understanding of character evolution within Hyalonematidae, all subgenera of Hyalonema need to be included in future studies, given the molecular evidence for nonmonophyly of this genus (see above).
Furthermore, the major division in Hexasterophora appears to be between Sceptrulophora and a clade containing all taxa that lack sceptrules and uncinates (and not between dictyonal and lyssacine taxa). For the latter we here propose the name "Anuncinataria". This name is to be preferred over "Asceptrulophora" because uncinates also occur in most species of Amphidiscophora and hence the lack of uncinates might be a derived feature of this group. Even if uncinates evolved convergently in Amphidiscophora and Sceptrulophora (see section Maximum-likelihood ancestral state reconstruction and  [93] ), the absence of uncinates has at least some diagnostic value. However, we refrain from erecting a Linnean taxon for Anuncinataria for three reasons: 1) no meaningful positive morphological diagnosis can be provided for this clade; 2) super-or suborders would have to be introduced, but the number of ranks should be kept at a minimum; and 3) it is very important that the monophyly of this proposed group is first further tested with molecular data from Lychniscosida and Myliusia.
As discussed in  [14] , morphological support for this branching order remains unclear. Aulocalycidae is here reconstructed as sister to Leucopsacidae + Rossellidae, in contrast to the ML phylogenies inferred from the molecular supermatrix and the total-evidence matrix restricted to sequenced genera (Fig. 7 , Additional file 25: Figure  S11 ), where Aulocalycidae (Euryplegma) and Leucopsacidae were reconstructed as sister groups (albeit with weak support). Molecular data from additional aulocalycids will be required to disambiguate between these two hypotheses. However, the latter one is intriguing because Leucopsacidae have choanosomal megascleres exclusively as hexactins, as is the case for all dictyonal taxa as well, whereas the majority of lyssacine hexasterophorans have choanosomal spicules dominated by diactins (see Additional file 14).
The presence of this construction type in the LCA of Hexasterophora was also not supported under the three alternative topologies when the Mk1 model was used (range 0. 26-0. 48); however, the aMk2 model supported its presence by pl of 0. 75-0. 83. These observations demonstrate that a robust resolution of this part of the topology, especially by including sequence data from Lychniscosida and Myliusia, will be required to more confidently reconstruct the evolution of non-sceptrulophoran dictyonal frameworks. Furthermore, the distinct construction type of dactylocalycid frameworks (Fig. 2c ) suggest that they might have evolved convergently (see Additional file 14), regardless of phylogenetic considerations. On the other hand, a possible link between dictyonal and lyssacine hexasterophorans are the socalled basidictyonal frameworks occuring in both groups, which are structures of fused spicules involved in the attachment of basiphytous species to the substratum  [2].
These updates are timely and bring the Linnean classification of glass sponges in closer agreement with their phylogeny, similar to what was recently proposed for Demospongiae  [99]. We further compiled morphological character matrices including all extant genera of Amphidiscophora and Hexasterophora and analyzed these alone and in combination with the molecular data. We compared MP, ML, and Bayesian approaches, as well as "morphology-based phylogenetic binning"  [22]  and found that MP consistently outperformed the other methods in terms of congruence with well-founded taxonomic and phylogenetic hypotheses. Bayesian analyses performed second best, whereas ML and binning gave largely dubious results. Phylogenies based only on morphological data were partly congruent with the molecular tree (e.
g. , paraphyly of Hexactinosida, monophyly of many families), but also conflicted in many areas (e. g. , monophyletic Aulocalycoida nested within Sceptrulophora). The total-evidence trees were largely congruent with the molecular phylogeny and suggest that the major division of Hexasterophora is not between lyssacine and dictyonal taxa, but instead between taxa with and without sceptrules and uncinates, i. e. , between Sceptrulophora and a clade we call Anuncinataria. Besides Lyssacinosida (including Aulocalycidae), Dactylocalycidae, and Heterorete, Anuncinataria also includes Myliusia (formerly Euretidae) and Lychniscosida, a species-poor relict group that was highly diverse in the Jurassic and Cretaceous. Inclusion of sequence data from the latter two taxa will be crucial to further test the monophyly of Anuncinataria.
In general, placement of the unsequenced genera in our total-evidence phylogeny should not be taken as the last word but as a starting point; these are working hypotheses that need to be further tested by filling the gaps in the molecular dataset. Also, the morphological character matrices should not be viewed as static, but as a resource that is subject to constant revision. Character mapping and ML ancestral state reconstruction (ASR) on the total-evidence tree allowed us to gain deeper insights into the evolution of skeletal structures in Hexactinellida. Our results suggest that evolution of the dictyonal body plan was more complex than previously thought. Besides from the obvious implication that the dictyonal skeletons of Aulocalycidae evolved convergently from a lyssacine condition and that the peculiar construction types of Uncinateridae and Auloplacidae evolved independently from a more regular type, we found that dictyonal skeletons with parallel ray fusion might have been present in the ground pattern of Hexasterophora and got secondarily lost in the stem lineage of Lyssacinosida.
Scope: Four families are included in Lyssacinosida: Euplectellidae Gray, 1867, Leucopsacidae Ijima, 1903, Rossellidae Schulze, 1885, and Aulocalycidae Ijima, 1927. Two monospecific genera with uncertain family assignment (Lyssacinosida inc. sed. ) are also included: Clathrochone Tabachnick, 2002 and Hyaloplacoida Tabachnick, 1989. Remarks: Aulocalycidae is here included in Lyssacinosida on the basis of molecular evidence (e. g. , Fig. 7 ), which is consistent with earlier taxonomic hypotheses (reviewed in  [87] ) and finds some morphological support from the widespread occurrence of synapticular fusion in this taxon (see main text for discussion). This result is based on sequence data from a single species, Euryplegma auriculare Schulze, 1886; the phylogenetic position of the remaining six genera currently included in Aulocalycidae (see Appendix 1) awaits to be determined with molecular data.
Specimen information and sequence accession numbers for newly sampled species Notes: B. C. British Columbia, Canada, MR Macquarie Ridge, NZ New Zealand (specimen supplied by NIWA Invertebrate Collection, NIWA, Wellington), HURL Hawaiian Undersea Research Laboratory (samples collected with submersible PISCES), HBOI Harbor Branch Oceanographic Institution (samples collected with submersible Johnson-Sea-Link II; most subsamples taken during August 2011 PorToL Integrative Taxonomy Workshop at Ft. Pierce, FL, USA), QM Queensland Museum, Brisbane, Australia, NIWA National Institute of Water and Atmospheric Research, New Zealand, RBCM Royal British Columbia Museum, RMNH Naturalis, Leiden, The Netherlands (samples provided by R. W. M. van Soest), MIRIKY French Expedition MIRIKY 2009. Underwater photographs of Heterorete sp.
Acknowledgements MD and HMR thank the organizers of the August 2011 PorToL Integrative Taxonomy Workshop ( Christina Diaz ,  Bob Thacker ,  Shirley Pomponi ,  Malcolm  and  April Hill ,  Joe Lopez ,  Dennis Lavrov ,  Allen Collins , and  Niamh Redmond)  for their invitation to participate and funding to attend. We are indebted to  Shirley Pomponi  and  John Reed  for access to HBOI specimens,  Rob van Soest  for providing Cyrtaulon and additional Dactylocalyx specimens, and  Philippe Bouchet  ( MNH Paris ) for access to Laocoetis material. We thank  Daniela Henkel  for the morphological character matrix used in [23], and  Dennis Lavrov  and  Karri Haen  for providing mtDNA sequences before public release. Dorte Janussen  and an anonymous reviewer are thanked for critical comments on an earlier version of the manuscript.
MD acknowledges  Gert Wörheide  ( LMU ) for providing work space and computational resources. The  Willi Hennig Society  is acknowledged for making TNT available free of charge. Funding MD was supported by a  Smithsonian   Institution Postdoctoral Fellowship  and by the  Deutsche Forschungsgemeinschaft  ( DFG grants   DO 1742/1-1, 2 ). Additional funding for molecular work was provided by a  US National Science Foundation Porifera Tree of Life  grant to  Allen Collins  ( Smithsonian Institution ). Collection of the Hawaii sponges was funded by a grant from the  Papahanaumokuakea Marine National Monument  (administered by the  National Marine Sanctuaries Program ). MK was supported by  New Zealand Foundation for Research, Science and Technology  ( C01X0224 ,  SFAS033 ),  Ministry of Fisheries  ( ZBD2004-01 ),  NOAA Satellite Operations Facility  ( NRAM053 ),  CSIRO Wealth from Oceans Flagship, and Coasts and Oceans Research Programme 2 Marine Biological Resources: Discovery and definition of the marine biota of New Zealand  (2014/2015 and 2015/2016 SCI).
Preterm birth places newborn infants in an adverse environment that leads to brain injury linked to neuroinflammation. To characterise this pathology, we present a translational bioinformatics investigation, with integration of human and mouse molecular and neuroimaging datasets to provide a deeper understanding of the role of microglia in preterm white matter damage. We examined preterm neuroinflammation in a mouse model of encephalopathy of prematurity induced by IL1B exposure, carrying out a gene network analysis of the cell-specific transcriptomic response to injury, which we extended to analysis of protein-protein interactions, transcription factors, and human brain gene expression, including translation to preterm infants by means of imaging-genetics approaches in the brain. We identified the endogenous synthesis of DLG4 (PSD95) protein by microglia in mouse and human, modulated by inflammation and development.