dataesr/scientific-paragraphs-categorization huggingface dataset:
A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT measured samples is explicitly given (Figure  8 ;  Jouniaux et al. (2000) ;  Bernard et al. (2007) ;  Kolzenburg et al. (2012) ;  Kendrick et al. (2013) ;  Heap et al. (2014b) ;  Farquharson et al. (2015) ). Although more felsic in composition -SiO 2 ranges between ~58 and 61%  (Bernard et al. , 2007; Farquharson et al. , 2015)  -the microstructure of these rocks is similar to those of this study (see Figure  8  of  Farquharson et al. (2015) ). Phenocryst content does not vary considerably between studies; reported phenocryst contents are 44% for Montagne Pelée  (Jouniaux et al. , 2000) , ~30% for Volcán de Colima  (Kendrick et al. , 2013; Heap et al. , 2014b) , and 30-55 vol. % for Merapi  (Erdmann et al. , 2016). As there are no obvious discontinuities in the combined dataset (i.
e. no obvious breaks or gaps in the data; Figure  8 ), we now include all Type 1 samples in our analysis. Applying a single empirical power law to the amalgamated dataset, we find This relationship approaches that proposed for other dome-forming rocks  (Mueller et al. , 2005). We note that the data are not well constrained by this power law below φ c = 10 vol. % (Figure  8 ). This is due to outlying samples below φ c = 5 vol. % that may deviate from a simple microstructural control on permeability; these data are omitted for the BIC analysis of the combined dataset. Piecewise linear regression of the data suggests that applying three power laws is warranted for all data above φ c = 5 vol. % and modified BIC analysis confirms the statistical existence of two changepoints at φ c = 10. 5 and 31 vol.
A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT porosity where vesicles form a more complete flow path and passing fluids only occasionally rely on microcrack connections. Domain 4, beginning at φ c = 31 vol. %, is predominantly associated with pumiceous samples (Figure  8 ). In these rocks, fluids travel through a connected vesicle network. While the power law describing this final domain predicts decreasing permeability with increasing connected porosity ( ), we hazard that this is an artefact of our dataset, which is limited to connected porosities below 63 vol. % and, therefore, highly vesicular pumiceous samples are under-represented. Indeed, studies on pumice confirm that porosity and permeability are positively correlated  (Eichelberger et al. , 1986; Klug and Cashman, 1996; Rust and Cashman, 2004; Wright et al.
Acknowledgements Funding for research costs was provided by the  ANR  project  DoMerapi  ( ANR-12-BS06-0012 ). Additional funding for A. R. L. Kushnir was provided by a  Postgraduate Scholarship-Doctoral  ( CGS D3 ) provided by the  Natural Sciences and Engineering Research Council of Canada (NSERC)  (number  CGSD3-444207-2013 ). M. J. Heap acknowledges  IDEX Attractivité grant  ("VOLPERM"), funded by the  Université de Strasbourg. We thank  S. Byrdina  for collecting and providing us with the 2013 samples. We acknowledge  J. I. Farquharson  for discussions and for his role in the development and maintenance of the benchtop permeameter at  EOST (Strasbourg). F. Wang  is acknowledged for measuring the connected porosities of the Type 1 samples used in this study. I. Di Carlo  is thanked for SEM assistance.
Even for these very long wavelengths, which are the largest observable with CMB anisotropies, the difference with the R2 -2 R model is negligible during MD, and only shows up as a difference of at most (1-2)% percent near the recent epoch, x = 0 (although scalar perturbations in the Weyl model will start to show an instability in the cosmological future, x > 0). This means that, compared to the pure R2 -2 R model, the addition of the Weyl-square term has basically no effect on SNe, BAO, and structure formation data while, in the CMB, it only affects the late integrated Sachs-Wolfe (ISW) effect, just at the level of order (1-2)% percent. The late ISW effect only contributes to the very low multipoles, and even for these multipoles it is sub-leading with respect to the (non-integrated) Sachs-Wolf effect.
Such a contradictory result can limit the validity of the conclusion by Sargsyan et al. [1]. Moreover, both the above mentioned theoretical models have investigated the neutron transfer effect on fusion process through fusion excitation function. However, the barrier distribution (BD) provides deeper understanding about the intrinsic degrees of freedom involved in the fusion than the fusion excitation function alone. From the existing experimental fusion excitation function  [3] , we have extracted the BD and studied the coupling effect using CCFULL program  [4] , incorporating ∼ 10% error in the data. But the uncertainty in the data forbids us from resolving the influence of various coupling channels on fusion enhancement as reported earlier  [5]. In the present article, we have reported a precise measurement of quasielastic (QE) excitation function for the 28 Si+ 154 Sm system at large backward angles.
Data analysis and results The counts of elastic, inelastic and transfer events, from particle identification spectra, have been considered for the QE events as per definition. After centrifugal correction, the obtained QE cross sections, σ qe (E, θ), normalized to rutherford cross section, i. e. , dσ qe /dσ R (E) for θ lab =170 • and 140 • , have been shown in fig. 1  (left). The statistical error is found to be less than 1% at lower energies and around 2% at higher energies. The BD, D qe (E), as shown in fig. 1  (right), has been extracted from QE excitation function using the method given in ref. [6]. Similarity in BD structure from QE measurements at two different angles give a check on the consistency of the extracted experimental BD, as shown in fig. 1 (right). To quantitatively understand the experimental BD, quantum coupled channel (QCC) calculations have been performed using CCFULL code  [4].
S2 ; compiled by  52  ), using the seacarb package in R  53  , with dissolution assumed to be controlled only by SST at a constant salinity of 35. EDC3 gas age was converted to LR04 using a published conversion  54. Carbon isotopic composition of planktic forams were used as a rough proxy for relative nutrient (~ phosphate) availability corrected for the effect of temperature, using the relationships of  55. See Fig. S3  for time series. Smear slides were prepared using a trial and error approach to attain the optimum coccolith density. SYRACO analysis was carried out in CEREGE.
Acknowledgements This study was conducted at the  University of Oxford (UK)  with laboratory work at CEREGE (France). HLOM was funded by PhD studentship NE/I019522/1 in association with UKOARP. REMR acknowledges  NERC  grant  NE/H017119/1  and  ERC  grant  SP2-GA-2008-200915. LB is grateful for financial support from  EU   Seventh Framework program Past4Future  and from the  Agence Nationale de la Recherche  under project  ANR-12-B06-0007  (CALHIS). PF was funded by  Marie-Curie Reintegration  grant ( PERG-GA-2010-272134 -MILLEVARIABILI ), funded by the  EU PNRA 2013/AZ2. 06and GEOSMART, funded by the  Italian National Antarctic Research Programme. We thank  Marius Müller  for advice on experimental design,  Yves Gally  for running the SYRACO software,  William Hutchison  for help with GMT,  Jean-Charles Mazur  for laboratory assistance, and to  Ian Probert  for providing strains.
Introduction Cyclotron-resonant loss of trapped electrons via scattering by lightning whistler waves was first indirectly evidenced as whistler-associated perturbations of subionospheric very low-frequency (VLF) signals  (Helliwell et al. , 1973)  and then directly detected  (Voss et al. , 1984 (Voss et al. , , 1998) )  as lightning-induced electron precipitation bursts associated with ducted whistlers. In a subsequent study,  Inan et al. (2007)  show that large regions of enhanced background precipitation are produced and maintained by high rates of lightning within a localized thunderstorm. Analysis of the DEMETER (Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions) spacecraft particle data showed that energetic electron precipitation exhibits a seasonal dependence consistent with lightning-induced electron precipitation.
ATDnet data were available for 2004 to 2011, whereas EUCLID-Météorage data were available for 2007 to 2008. WWLLN data have an average resolution over Europe; this led us to generally prefer the local ATDnet database for reported cases. However, ATDnet data do not provide intensity and polarity lightning features; therefore, we determined causative lightning peak currents from the EUCLID-Météorage database for cases reported for 2007 to 2008.
Observations DEMETER data were used to search for LEP bursts over Europe for the entire mission period, i. e. , from 2004 to 2010. Such an example of short bursts of electron fluxes up to 200 keV, detected on 9 October 2007, is displayed in Fig. 2a  in the IDP data (first and third panel from the top), with strong whistlers in ICE data (second panel from the top) associated with strong lightning peak intensity (fourth panel from the top). Figure  2b  shows the simultaneous position of lightning and the satellite. High-frequency lightning thunderstorms are present during that day, with 148 lightning strokes between 20:48:00 and 20:49:30 UT. Two active cells trigger electron precipitation over Germany, with one located offshore of Corsica, the other in southern Italy. This precipitation of electrons presents flux enhancements over a wide energy range in IDP spectra and a clear peak in integral fluxes (90.
Discussion Complementary measurements of energetic electrons and VLF waves performed simultaneously on board DEMETER allowed us to unambiguously determine the occurrence of electron short bursts associated with whistlers. More rarely, we were able to relate these events to lightning whose position is given by ground-based networks. In about 60 cases, the identification of the exact position of the lightning, not only that of the storm cell, was possible based on relative timings. The analysis of the database clearly shows that the electron precipitation in the energy range of 90 to 200 keV is located north of the parent lightning in a wide region with an average difference in latitude reaching up to 7. 7 ± 3. 6 •. This result is in good agreement with models of wave propagation and of their interaction with the electrons from the radiation belt, either considering ducted or non-ducted whistlers  (Inan and Carpenter, 1986; Lauben, 1998; Lauben et al.
Materials We provide rock physical property data for two volcanic rock samples collected during the 1-18 November 2013 NA039 E/V Nautilus cruise carried at KeJ. Both samples were collected using a remotely operated vehicle (ROV). The first sample (NA039-13) was a black, plagioclase-phyric basaltic andesite with granule fractures collected from a columnar-jointed outcrop (Fig. 2 ) within the crater of KeJ (12. 29932 N; 61. 6379 W; collection site shown on Fig. 1 ). The second sample (NA039-056) was a gray, massive, plagioclase-phyric basaltic andesite containing bio-encrustation and a manganese crust. The second sample was collected on the wall of the horseshoe-shaped structure on which abuts the eastern flank of the KeJ edifice (12. 29816 N; 61. 6323 W; collection site shown on Fig. 1 ).
3 ). We assume here a simple effective pressure (P eff ) law P eff = P c , -αP p and that poroelastic constant α equals 1; P eff is therefore considered to be 7 MPa for our experiment. A recent study has shown that α is very close to 1 for porous andesites, thus validating our assumption  (Farquharson et al. 2016a). A load cell and a displacement transducer recorded axial load and axial displacement, respectively. These values were converted to axial stress and strain using the sample dimensions. All the experiments were performed at room temperature. In this study, we consider compressive stresses and strains as positive. Table  1  summarizes the data collected during the laboratory experiments.
Acknowledgments We would first like to thank  Bettina Scheu  ( LMU, Munich ) for stimulating collaboration. We would also like to thank  Robert Ballard  and  Katherine Croff Bell  of the  Ocean Exploration Trust  for providing the opportunity to collect the rock samples during the NA039 E/V Nautilus cruise. We thank  Sarah Fuller , the data manager for the NA039 E/V Nautilus cruise, for describing the rock samples. Finally, we thank the  National Science Foundation  grant  OCE-0956368  for providing the support for the curation and distribution of the geological samples at the  University of Rhode Island. Michael Heap acknowledges funding from an  Initiative d'Excellence (IDEX)  BAttractivitéĝ rant (VOLPERM), funded by the  University of Strasbourg. We also thank  Thierry Reuschlé ,  Jamie Farquharson , and  Alex Kushnir  for experimental support at  Université de Strasbourg.
Total-evidence dating (TED) allows evolutionary biologists to incorporate a wide range of dating information into a unified statistical analysis. One might expect this to improve the agreement between rocks and clocks but this is not necessarily the case. We explore the reasons for such discordance using a mammalian dataset with rich molecular, morphological and fossil information. There is strong conflict in this dataset between morphology and molecules under standard stochastic models. This causes TED to push divergence events back in time when using inadequate models or vague priors, a phenomenon we term 'deep root attraction' (DRA). We identify several causes of DRA. Failure to account for diversified sampling results in dramatic DRA, but this can be addressed using existing techniques.
Inadequate morphological models also appear to be a major contributor to DRA. The major reason seems to be that current models do not account for dependencies among morphological characters, causing distorted topology and branch length estimates. This is particularly problematic for huge morphological datasets, which may contain large numbers of correlated characters. Finally, diversification and fossil sampling priors that do not incorporate all the available background information can contribute to DRA, but these priors can also be used to compensate for DRA. Specifically, we show that DRA in the mammalian dataset can be addressed by introducing a modest extra penalty for ghost lineages that are unobserved in the fossil record, for instance by assuming rapid diversification, rare extinction or high fossil sampling rate; any of these assumptions produces highly congruent divergence time estimates with a minimal gap between rocks and clocks.
Recent work has shown that this is not always the case in practice. In fact, TED is often reported to result in divergence time estimates that are more uncertain and more at odds with the fossil record than those from node dating or a combination of TED and node dating  [6, 7]. The aim of this paper is to examine why this might be the case. For several reasons, we chose to focus on the radiation of mammals, more specifically on the radiation of the Eutheria (crown-group and stem-group placentals). There may be no other group with so much data available for a TED analysis, and so much controversy surrounding the divergence time estimates. Recently, an exceptional morphological ( phenomic) dataset (the O'Leary et al. dataset) was published for fossil and recent mammals  [8]. With 4541 characters in total, scored for 46 extant and 40 fossil taxa, this may be the largest phenomic dataset published to date: it includes 1284 cranial characters, 1451 dental characters, 925 postcranial characters and 881 soft characters (including behavioural and other characters).
The abundance of placental fossils in the Palaeogene and the absence of them in the Cretaceous provide one of the strongest pieces of evidence supporting the explosive radiation scenario (  [8]  but see  [12] ), whereas the high rates of molecular evolution around the K -Pg boundary required by such a scenario is one of the most powerful arguments against it (  [13]  but see  [14] ). The O'Leary et al. dataset  [8]  has not been subjected yet to TED analysis. However, a TED analysis of the placental radiation based on a similar dataset was recently published  [15]. The phenomic dataset in the latter study comprised 421 characters coded for 102 taxa, most of them fossils. The divergence time estimates obtained when these morphological data were analysed alone or in combination with molecular data under an unconstrained TED model were unrealistically old (around 164 Ma), suggesting that the placental radiation might be a suitable target for investigating why TED misbehaves in some cases.
Using a slightly modified version of the O'Leary et al. dataset, we show here that there is a tendency for TED divergence time estimates, under certain conditions, to be pushed back to very old strata and to be very imprecise. We term this phenomenon 'deep root attraction' (DRA). By exploring various prior models, we characterize the causes of DRA. DRA occurs when there are model errors or conflicts in the data that are difficult to reconcile, and ghost lineages carry little cost. A major driver of DRA appears to be inadequacies of current morphological models, a problem that is difficult if not impossible to address. However, by increasing the cost of ghost lineages, we show that it is possible to address DRA and obtain a stable TED solution that is robust to variation in prior assumptions.
Methods (a) Data The dataset of O'Leary et al. [8]  includes 46 recent taxa and 40 fossil taxa. We were worried that it would be difficult to model rstb. royalsocietypublishing. org Phil. Trans. R. Soc. B 371: 20150136 the radiation of mammals into stem forms of monotremes, marsupials and placentals because these early events involve few lineages and long time periods according to both molecular and palaeontological studies. Therefore, we removed all extant and fossil taxa outside of the Eutheria (placentals plus stem-group placentals). The fossil Eomaia scansoria was placed outside of Theria (placentals þ marsupials) in the analysis of O'Leary et al. [8]  but it has previously been considered a member of Eutheria or Placentalia in analyses that densely sample stem therians  [18, 19] , and we therefore included it in our dataset.
To improve the fit between the data and our model of diversified sampling, we removed a very recent split among extant taxa by deleting Galeopterus variegatus from the dataset. Similarly, we omitted the very young  (16. 4 Ma)  fossil Hapalops elongatus. The diversified sampling model  [20]  assumes that all deep splits in the tree have been sampled. The actual age of the most recent split in the tree, beyond which no more lineages are sampled, is inferred from data. Spurious young speciation events can seriously distort the inference of BD parameters under this model because they erroneously extend the period during which the process is assumed to be completely sampled. The resulting dataset included 74 eutherian or potentially eutherian taxa, 33 fossils and 41 extant taxa. The character data comprised 4541 discrete morphological characters and 36 860 DNA sites from 27 nuclear genes, including 22 protein-coding genes and five untranslated regions (UTRs)  [8].
(e) Tip sampling assumptions For both the BD and FBD priors, we explored three different assumptions concerning tip sampling, namely that the tips represent: (i) a complete sample, (ii) a random sample or (iii) a diversified sample of the entire tree  [5, 20]. Given that there are approximately 5000 described species of placentals, we considered the 41 extant taxa in our dataset to represent approximately 1% of the total diversity of the group in the randomized and diversified tip sampling scenarios.
(h) Markov chain Monte Carlo sampling All analyses were performed with pre-release versions of MRBAYES v. 3. 2. 6 (svn revision 1067 and following)  [26] , the source code of which is available from the program website (http://mrbayes. net). The code is now part of the latest MRBAYES release. To improve topological convergence when fossils are included, we added a couple of topology moves that specifically rstb. royalsocietypublishing. org Phil. Trans. R. Soc. B 371: 20150136 target fossil subtrees but that are, otherwise, identical to existing topology moves. For each model, we ran four independent analyses, each using four Metropolis-coupled chains. We ran the chains for 10 -30 M generations each and sampled them every 500 generations, discarding 25% of the samples as burn-in. When fossils were included in the analysis, tree samples were summarized both with fossils included and with fossils first pruned away from all tree samples.
Results (a) Conflict between morphology and molecules The non-clock analyses demonstrate strong conflict between the molecular and the morphological signal in the eutherian dataset (figure  1 ). Whereas the total-evidence (figure  1a ) and molecular (figure  1b ) trees both retrieve the four mammalian superorders that have been recognized in most recent analyses (Xenarthra, Afrotheria, Laurasiatheria and Euarchontoglires), the morphological tree (figure  1c ) presents quite different groupings, often consistent with results from classical morphological cladistic analyses of placental relationships  [29]. The morphological evidence sprinkles the afrotherian taxa across the tree, and even if we disregard the Afrotheria, the Euarchontoglires and Laurasiatheria remain intermixed. Among the Laurasiatheria, the pangolin (Manis) occupies a basal position in the tree together with Xenarthra (anteaters, sloths and armadillos).
(c) Tip sampling effects The assumption concerning the tip sampling procedure has a major influence on the divergence time estimates obtained under BD models (figure  3 ). When fossils are not included in the analysis, the root date is not affected much for the studied dataset, but the estimates of the most recent divergence times differ substantially. The effect is most clearly seen in the estimated age of the split between the whale (Caperea) and the dolphin (Tursiops), the most recent of all speciation events (arrows in figure  3 ). If tips are assumed to represent a complete sample of lineages, then the split is estimated to (all posterior age distributions are summarized using the median, followed by the 95% region of highest posterior density) 13  (5, 26)  Ma (figure  3a ). If we account for the fact that the tips only represent approximately 1% of all known species, but still assume that they represent a random sample, the same split is estimated to 16  (5, 27)  Ma (figure  3b ).
The same pull towards unrealistic deep-root scenarios occurs under the uniform clock tree prior, which must also be described as vague or uninformative about divergence times. Without fossils, the estimated crown age of Placentalia under this prior is 84 (64, 151) Ma, which is not unreasonable. However, inclusion of fossils in the analysis, without changing any of the prior settings, moves the estimate back to 284 (203, 374) Ma, which would imply more than 200 Myr of evolution of crown placentals without leaving a trace in the fossil record. We term the pull towards deep-root scenarios that we observe under TED with vague or erroneous priors DRA. To explore the causes of DRA in the study dataset, we examined four informative diversification models that put less prior probability on deep-root scenarios with long ghost lineages: a model with a low expected extinction rate, a model with a high expected fossil sampling rate, a model combining both of these expectations and a model assuming a high net diversification rate (up to the time of the last speciation event observed in the diversified tree; after that event, the tree is no longer informative about diversification rates because of the absence of speciation events).