dataesr/scientific-paragraphs-categorization huggingface dataset:
The incident angle is converted to approximate offset assuming the Moho interface at 9. 5 km and the crustal velocity of 6 km/s. b) Normalised PmP AVO for the four different models for MTZ as shown in Fig. 3 : sharp (black line), gradient (red line), staircase (green line) and layered (blue line). c) Normalised PmP AVO for different thicknesses of gradient MTZ starting from 100 m to 2000 m. The gap between 7 and 14 km is due to interference with seafloor reflection. (For interpretation of the references to colour in this figure legend, the reader is referred to the web version of this article. ) range of 15 to 30 km (green arrows), and also by Streamer 2 recording a duplicate of the 0-15 km offset range. Each vessel will shoot at 100 m interval in an alternate mode. As data recording will be continuous, the two vessels data could be arranged in such a way that a continuous offset range from 0 to 45 km can be achieved at 100 m shot interval.
Mithal and Mutter [1989]  have shown using expanding spread profile, where MCS technology was used, one could record Moho reflections continuously starting from zero offset to post-critical distance. Guo et al. [2020a]  have recently demonstrated that the full elastic waveform inversion of Pg arrivals could retrieve information about the lower crustal layer. Neves and Singh [1996]  have indicated that full waveform inversion of continuous MCS seismic data from zero offset to critical angle could provide complete information about the sub-surface with a resolution of the quarter of the wavelength. Therefore, 2D elastic full waveform inversion of 0-45 km MCS type data should provide complete information about the lower crust, the MTZ and the structure of the upper mantle. One should note that wide-angle reflection amplitude from the lower crust and the MTZ do not simply depend on the P-wave velocity but also depends on the S-wave velocity, and therefore, elastic, not acoustic, waveform inversion should be used to characterise the lower crust and the MTZ.
4. The amplitude variation with an offset (AVO) analysis of MTZ models suggests that the critical distance increases linearly with the increase in the thickness of the MTZ. 5. When the thickness of the MTZ is less than ~1. 75 times the dominant seismic wavelength, two high-amplitude peaks for PmP reflections occur at critical distances associated with P-and S-wave velocities. 6. For a thicker MTZ only one large peak at large offset is observed, suggesting that AVO analyses could provide information about the MTZ. Our study indicates that a continuous recording of 0-45 km offset data using MCS technology with a source spacing of 100-150 m combined with elastic full-waveform inversion should provide a complete information about the elastic properties of the lower crust, MTZ and upper mantle.
Acknowledgements This project was funded by the  European Research Council  Advanced Grant agreement No. 339442  TransAtlanticILAB. Venkata Vaddineni  provided OBS data shown in Fig. 1. We are thankful to  Natsue Abe  and  Keishi Okazaki  for providing the lithology and velocity logs shown in Fig. S3. Constructive comments from two anonymous reviewers have helped to improve the manuscript significantly. This is the  Institut de Physique du Globe contribution. This paper is dedicated to  Professor Adolph Nicolas  who provided valuable insight about the magma chamber, lower crust and MTZ during memorable field trips. One of us (SS) would like to thank  Françoise Boudier  and  David Jousselin  for leading the field trip to Oman in January 2020, that allowed to prepare the composite figure shown in Fig.
Furthermore, our experiments show that only native tRNAs are properly distinguished by tRip; whereas the corresponding unmodified transcripts form complexes with the enzyme indiscriminately (Figure  4A ). Apart from their primary sequence, tRNAs are characterized by the presence of numerous posttranscriptional modifications. Many modifications are located in the corner of the tRNA 3D structure, which is precisely the region protected by tRip in footprint experiments (Figure  1C  and Supplementary Figure  S2 ). In particular, these post-transcriptional modifications are important for proper tRNA folding and stability (Reviewed in  (37) (38) (39) ). Therefore, we searched the Modomics database  (40)  with the tRNAs tested herein against all vertebrate cytosolic tRNAs harboring known post-transcriptional modifications.
48. Schimmel, P. (  2018 ). The emerging complexity of the tRNA world: mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell  Biol 19, 45-58. 49. Shikha, S. , Brogli, R. , Schneider, A. , and Polacek, N. (2019). tRNA Biology in Trypanosomes. Chimia 73, 395-405. 50. Warrenfeltz, S. , Basenko, E. Y. , Crouch, K. , Harb, O. S. , Kissinger, J. C. , Roos, D. S. ,  Shanmugasundram, A. , and Silva-Franco, F. (2018). EuPathDB: The Eukaryotic Pathogen Genomics Database Resource. Methods Mol Biol 1757, 69-113. (8, 20, and 40 µM). The control lane contains 2 µM tRNA in the absence of tRip. tRNAs were eluted from the gel and radiolabeled. Three examples of hybridized tRNA arrays are shown; they correspond to H. sapiens crude tRNA (Unselected) as well as the bound and free tRNA of the four tRNAs per tRip dimer condition.
FUNDING This work was performed under the framework of the  Interdisciplinary Thematic Institute IMCBio , as part of the  ITI 2021-2028 program  of the  University of Strasbourg ,  CNRS  and  Inserm. It was supported by  IdEx Unistra  ( ANR-10-IDEX-0002 ), by  SFRI-STRAT ' US  project ( ANR 20-SFRI-0012 ), and  EUR   IMCBio  (IMCBio  ANR-17-EURE-0023 ) under the framework of the  French Investments for the Future Program  », by previous  Labex NetRNA  ( ANR-10-LABX-0036 ), by the  CNRS  and the  Université de Strasbourg  to  Magali Frugier  and the  Fondation pour la Recherche Médicale (FRM)  (grant number  FDT201704337050 ) to  Marta Cela , and by a  SC INBRE grant  from the  National Institute of General Medical Science -NIH  ( P20GM103499 ) to  Renaud Geslain.
ACKNOWLEDGEMENT We are grateful to Laura Antoine, Annika Breidenstein and Caroline Paulus for their technical assistance as well as Ansley Elkins and Professor Tamara Hendrickson for providing comments on this manuscript. S1 : List of the probes used in human tRNA microarrays. Each probe hybridizes to one or more tRNAs. These tRNAs are generally present in the genome in several copies; each copy is reported as indicated in the genomic tRNA database (51). Some tRNAs may contain up to 8 point-mutations when compared to the probes.
The contigs corresponding to the mitochondrial DNA (mtDNA) genome were identified by local BLASTN v2. 9. 0  (Camacho et al. 2009 ) searches using the C. graminicola mitochondrial genome Gen-Bank CM001021. 1  (O'Connell et al. 2012)  as the query sequence. The completeness of the assembly was assessed using BUSCO v3. 1  (Simão et al. 2015)  while statistics were evaluated with QUAST v5. 0. 2  (Gurevich et al. 2013). The MAKER2 v2. 0 annotation pipeline  (Holt and Yandell 2011)  was used to annotate the genome of C. lupini RB221. Transcriptomic data of the same isolate grown in liquid culture and during plant infection are available in the European Nucleotide Archive, bioproject accession number PRJEB40331  (Dubrulle et al. 2020b ). All libraries were merged and assembled using rnaSPAdes v3.
8. 2. (Bushmanova et al. 2019 ) and aligned to the genome with HISAT v2. 1. 0 (Kim et al. 2019)  to select only those belonging to C. lupini RB221. The transcript sequences were used as biological evidence in MAKER2. Three different ab initio gene annotation programs were trained for use with MAKER2. GeneMark-ES v4. 10 (Borodovsky and Lomsadze 2011) was self trained for each of the four genomes. AUGUSTUS v3. 3  (Stanke et al. 2006 ) was trained using the transcript sequences. Transfer RNA (tRNA) were predicted with tRNAscan-SE v1. 3. 1  (Lowe and Eddy 1997). Putative functions were assigned to the annotations using BLASTP v2. 9. 0  (Camacho et al. 2009)  to identify homologs in a database constructed of proteins from the UniProt database (release 2013_12). Secreted proteins were identified using SignalP v.
, 2018;; Huo et al. 2021 ) revealed that 47 clusters (48 proteins) were unique to C. lupini; among those, 39 lacked similarity with any other sequence available in the NCBI nonredundant protein sequence database (e-value cutoff = 10 -3 ) and, therefore, were classified as species specific. These genes may be associated with the peculiar capability of C. lupini to infect lupins and, therefore, selected for further analyses. The genome sequence of C. lupini presented here will be useful for further research into the biology and evolution of these destructive pathogens.
grant number  RBRE160116CR0530019 , funded by the  regions of Bretagne and Pays de la Loire (France)  and the  European Union (FEADER) ; by  Ascochyta Colletotrichum Lupin Pois chiche CASDAR (AsCoLuP ) number 19AIP5913; The  National Council for the Improvement of Higher Education  ( PROEX/CAPES 8887. 508683/2020-00 ); and the  Ministerio de Ciencia and Innovaci on of Spain  (grant  RTI2018-093611-B-I00 ).
Data Availability The strain sequenced in this work has been deposited in the CABI culture collection (IMI 504893) and in the UBO Culture Collection (UBOCC-A-117274). The data generated in this study are publicly available from the NCBI GenBank database at Bioproject ID PRJNA360503 and Biosample ID SAMN06211573. The genome sequences have been deposited in GenBank under the accession CP019471-CP019482. The genome can also be accessed on the JGI MycoCosm website.
Methods Data collection. The experimental protocol was approved by the UCSF Institutional Review Board. Six participants were included in the study (Supplementary Table  1 ) and all provided written informed consent. Five had medically refractory seizures requiring surgical management due to temporal lobe epilepsy, for which the anterior lobe was resected from a lateral approach, eventually accessing the lateral ventricle and exposing the ventricular hippocampal surface. The other participant (Participant 5) had a circumscribed antero-lateral temporal lobe tumor that required a similar anterior temporal surgery, and resultant exposure of the hippocampus which was presumably normal (unaffected on MRI and intraoperative visual inspection). Intraoperative monitoring was performed as part of routine clinical care, with the experimental use of grids with high-density interelectrode spacing (see below) instead of standard clinical grid or strip spacing.
The recordings occurred under general anesthesia (combinations of dexmedetomidine, propofol, and fentanyl) in Participants 1-4. Participants 5 and 6 were in awake state during the recordings due to clinical factors (intraoperative stimulation mapping procedures) and participated in a behavioral task. We utilized a 32-contact microgrid manufactured through micro-electromechanical system technology by Lawrence Livermore National Laboratories (Fig. 1a ), configured as a polymer-metal-polymer stack. Electrodes were cosputtered thin film 60/40 platinum/iridium on gold traces (1. 22 mm diameter, 2 mm center-to-center) in a 4 × 8 two-dimensional layout (approximately 110 mm 2 coverage). Additional rectangular contacts uniformly lined the perimeter of the recording contacts (Fig. 1a ) and were shorted together for use as a single recording reference with no subsequent re-referencing (to ensure the original amplitude and phase data were maintained  44  ).
Briefly during intraoperative downtime, the microgrid was carefully placed parallel to the long axis on the lateral hippocampus (its ventricular surface; Fig. 1b ) to achieve conformal surface contact. Irrigated gauze was placed over top to ensure stability during the subsequent recordings. The cable connector edge was always positioned anteriorly toward the temporal pole regardless of laterality. Referential recordings were obtained using a multichannel amplifier (Tucker Davis Technologies using TDT OpenEx software 2. 31) with a fiber-optic connection digitized at 24. 4 kHz, for approximately 8-22 min per participant and divided into 2-8 recording blocks for data handling purposes or to separate adjustments in grid placement. Contacts that extended just beyond the hippocampal surface, or were otherwise noted to have low signal or excessive artifact, were excluded from analysis (0-4 channels per participant).
Signal processing and analysis. All analyses were performed in Matlab (Natick, MA) version R2019a. For each participant, the segment of the recording selected as a baseline period was screened to be largely artifact-free. Segments with epileptiform discharges or artifact (excessive cable movement, electrode pops, etc. ) were identified using automated line-length detection methods  45  followed by manual screening by a trained epileptologist (J. K. ), and these segments were excluded from all analyses. To identify unique oscillation peaks in spectral profiles, each recording channel was pre-filtered (255 Hz low-pass) then downsampled to 512 Hz. Each participant's recording underwent Morlet (Gabor) wavelet transformation of the entire recording block with 211 logarithmically spaced frequencies between 1 and 32 Hz using the cwt.
We compared the proportion of timepoints going toward/away from the temporal pole (ratio) by frequency using a Spearman correlation. We compared anterior-posterior amplitude gradients (mean z-scored amplitude across timepoints from the 16 electrodes in the anterior half of the grid minus the same from the posterior half) between the two direction conditions using a paired t-test (11 instances). We trained a 5-fold cross-validated SVM model (fitcsvm. m function file in Matlab) using the corresponding amplitude on each electrode as predictors (i. e. , up to 32 features). To avoid overfitting, we verified models had far more observations than features (Supplementary Table  4 ), avoided hyperparameter optimization, and utilized 5-fold cross-validation. Amplitude (similar to the power, or strength) of the frequency at any given timepoint is independent of its phase, and only the latter was used to calculate the TW angle.
In addition to being commonplace in the intraoperative setting for clinical language mapping purposes, the ease of initial instruction and rapid pace of trials also facilitated behavioral data acquisition during our limited-duration recordings. Visual stimuli were pictures of objects  51  displayed on a laptop monitor via Microsoft PowerPoint (version: 2010) presentation equipped with a simultaneous acoustic tone (exactly 440 Hz) at onset to enable audio data (24 kHz sampling) including speech (microphone near participant's mouth) to be time-locked with the neural data (same amplifier). The audio recording thus provided a unified solution for marking both stimulus and speech onsets through automated detection of the audio envelope with subsequent manual verification using the audio recording spectrogram.
Acknowledgements We are tremendously grateful to the six participants. We also thank  Dawn Hilken  and  Jeanie Pebbles  for technical support, as well as  Josh Chartier ,  John Burke ,  Matt Leonard ,  Honghui Zhang , and  Joshua Jacobs  for analytic insight and helpful comments. The project was funded by  NINDS  grants  R25NS070680  and  K23NS110920  (J. K. );  R01-DC012379 ,  R00-NS065120  and partially funded by the  Defense Advanced Research Projects Agency (DARPA)  grant  DP2-OD00862  (E. C. ), also under Cooperative Agreement Number  W911NF-14-2-0043  (E. C. , K. S. , J. Z. , D. H. , J. P. , M. T. , K. L. , A. T. , and R. H. ) issued by the  Army Research Office  contracting office in support of  DARPA 's  SUBNETS program. The views, opinions, and/or findings expressed are those of the authors and should not be interpreted as representing the official views or policies of the  Department of Defense  or the  U.
Code availability Data processing and analyses were performed in Matlab R2019a, and all code is available from the corresponding author upon reasonable request. Custom automated-detection software for artifact (electrical, or interictal discharge) is publicly available from the Kleen Lab (https://github. com/Kleen-Lab), and circular-linear regression analysis was adapted from publicly available code from the Jacobs Lab (http://github. com/jacobslab/Travelingwave-analysis). Hippocampal mesh reconstructions for illustrations were obtained from publicly available template brain structures from Freesurfer (https://surfer. nmr. mgh. harvard. edu/).
General methodology We calculated 15 descriptors (five for each of the three types) of catchment response to storm events and assessed their variability as a function of karst occurrence. To this end, we grouped elementary catchments into three different geology types, based on relative areas of their main geological formations. Catchments underlain by only karstified rock are in the karst group (K), whereas catchments containing only non-karstified rock are in the non-karst group (NK). Any catchment with a combination of both karstified (>10 %) and non-karstified rocks is in the mixed group (M). The karstifiable nature of rocks was assessed with the BDLISA (Base de Donnée des Limites des Systèmes Aquifères) database (Sect. 3. 1. 2). Descriptors were calculated for the 20 strongest storm events for all catchments (Sect.
Flow assessment at the elementary catchment scale The 15 descriptors were calculated on elementary catchments for 20 selected strongest storm events. For the sake of representativeness, this selection was based on both rainfall and streamflow records. From the available data time series spanning several decades (see Sect. 3. 1 for more details), the 10 strongest precipitation and 10 strongest streamflow events were extracted. Care was taken not to select the same events via the two extraction methods. https://doi. org/10. 5194/hess-25-1259-2021 Hydrol. Earth Syst. Sci. , 25, 1259-1282, 2021 Streamflow is measured at several gauging stations along a given river, defining elementary catchments. For the most upstream station of a river, the elementary catchment corresponds to the ordinary topographic catchment.
Temporal data Temporal data used in this paper are the following: -Hourly streamflow data from the French public streamflow database "Banque Hydro" (http://www. hydro. eaufrance. fr/, last access: 10 April 2020), managed by the French Regional Environment Directions (Direction Régionale de l'Environnement, de l'Aménagement et du Logement, DREAL). These data are produced by interpolation of water-depth measurements at a variable infra-hourly time step and converted into streamflow values. -Hourly rainfall data are from Comephore  (Tabary, 2007)  covering 1997 to 2005 and Antilope  (Champeaux et al. , 2011)  from 2006 to 2018. Both data sets are measurement reanalyses edited by the French public meteorological service Météo-France (http://www. meteofrance. fr/, last access: 3 February 2020).
Spatial data Spatial data used in this paper are the following: - -BDLISA database (https://bdlisa. eaufrance. fr/, last access: 3 April 2020), which describes the properties of hydrogeological entities and aquifers in France, edited by the French Geological Survey (Bureau de Recherches Géologiques et Minières, BRGM). -Map of available soil-water capacity from INRAE (Le Bas, 2018), used for estimating effective rainfall (Appendix C).
Boundaries of topographic catchments, from the French National Watershed Database (Base Nationale des Bassins Versants, BNBV). It was edited by the French Central Service for Hydrometeorology and Support on Flood Forecasting (Service Central d'Hydrométéorologie et d'Appui à la Prévision des Inondations, SCHAPI) and the French Research Institute for Agriculture, Food, and the Environment (Institut National de Recherche en Agriculture, Alimentation et Environnement, INRAE).
Acknowledgements. The authors thank the Editor  Jim Freer  and three anonymous reviewers for their constructive comments. Financial support. The work was funded by the  French Governmental Administration for Risk Prevention (DGPR) , the  Service Central d'Hydrométéorologie et d'Appui à la Prévision des Inondations (SCHAPI)  and the  French Geological Survey (BRGM). Review statement. This paper was edited by  Jim Freer  and reviewed by three anonymous referees.
Data availability. Hourly streamflow data were gathered from the "Banque hydro" database using a script available at https://doi. org/10. 5281/zenodo. 3744183 (Hakoun and Manlay, 2020). Author contributions. RM and JBC were involved in conceptualization, funding acquisition and supervision. MLM gathered the data and designed the methodology with the help of JBC, RM and YC. MLM prepared the article with the help of all co-authors.
, 2009 ; but see  Chapman et al. , 2017; Dawson et al. , 2017; Seebens et al. , 2020). A major goal of invasion science today is to quantify the global flows of alien species between their donor and recipient regions and to identify the socio-economic drivers of those intercontinental species exchanges. The growing availability of large databases containing data on the native and invaded ranges of alien species has made progress possible in mapping the global flows of plants  (van Kleunen et al. , 2015) , amphibians and reptiles  (Capinha et al. , 2017). This research has shown that some donor regions were overrepresented relative to what would be expected based on the available source pools of these regions (i. e. the number of native species that could potentially be exported). These asymmetric exchanges of alien species among continents may be linked to different human activities, such as accidental transport, pet and horticultural trade or environmental factors.
In general, such studies retrace the invasion history of individual well-studied species. Although evidence for complex invasion histories with recurrent bridgehead effects is accumulating, population genetic surveys are labour-intensive and require an extensive sampling effort and are therefore not suitable to assess whether secondary introductions are widespread in general. Using a dataset of ant interceptions at air and maritime ports, previous studies have found that the vast majority of introductions across all alien ant species arise via secondary transport  (Bertelsmeier et al. , 2018; Suhr et al. , 2019). Given that the bridgehead effect is such a widespread phenomenon, we hypothesize that it has the potential to distort our view of global species exchanges between donor and recipient regions, which classically map flows as direct introductions from the native to the introduced range (e.
| Species distributions and flows To determine the number of alien ant species that are established in each country, we used the geo-referenced database Antmaps (an authoritative database maintained and updated regularly by experts based on new records from the peer-reviewed scientific literature). The Antmaps database includes information on the native and alien ranges of 252 ant species. We did not consider occurrence records that may be dubious (needing taxonomic verification). We kept both indoor and outdoor locations because all parts of the species' distribution are the consequence of human-mediated dispersal. Populations that occurred at indoor locations were also a possible source of new invasions, for example, if material such as potted plants and soil are moved from an indoor location to a different location.