dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work was supported by the  Japanese Society for the Promotion of Science (JSPS) KAK-ENHI  (Grant Numbers  JP26247037 ,  JP23340076 ) in Japan, by  Istituto Nazionale di Fisica Nucleare (INFN)  in Italy and by the  joint research program  of the  Institute for Cosmic Ray Research (ICRR) ,  University of Tokyo. Parts of this work were performed using the computer resource provided by  ICRR ,  CERN  and  CNAF (INFN).
Growth of adhered cells Biofilm maturation was evaluated after the adhesion step (24 hours without any flow of medium to allow the microalgae adhesion). For this purpose, a flow (90 or 15 µL/min) was activated with ASW supplemented with Guillard's F/2 medium (2%) using a Watson Marlow 205U peristaltic pump (Watson Marlow, Falmouth, UK). Biofilm was observed after 24, 48, 72, 96 and 120 hours. Images were taken every micrometer throughout the whole biofilm thickness. The Zen software (Zeiss) was used to process data of 3D image with maximal intensity projection. The average thickness of the biofilm (µm) and the biovolume (µm 3 /µm 2 ) were measured using COMSTAT software  (Heydorn et al 2000). Results were representative of 27 randomly fields.
Use of culture in flow-cells to evaluate antibiofilm/ anti-bioadhesion compounds The use of bioassays to evaluate anti-biofilms compounds is essential to screen potential substances and understanding their mode of action. Among bioassays developed, the use of multiwell plates is particularly common  (Trepos et al. 2014 , Hellio et al. 2015). However, biofilms developed in flow-cells could also be useful to evaluate the anti-microalgal biofilm activity of compounds (Table  1 ). Data obtained with both bioassays are listed in Table  2  and it appeared clearly that study in flow cells led deeper analysis. In this context, a reference compound has been tested using both bioassays: multi-well plates and flow-cell system. A hemibastadin analog named dibromohemibastadin-1 was selected. It has been shown an anti-bacterial biofilm and anti-quorum sensing activities without toxic activity  (Le Norcy et al.
Impact of DBHB on adhesion strengths in flow-cells The use of flow-cells allowed the determination of the impact of DBHB on the adhesion strengths of microalgae. For that, after 72 hours of adhesion in flow cells with DBHB, a continuous flow (330 µL/min, 8. 10 -3 Pa) was applied during 30 minutes. The concentration of 16 µM was applied to be lower than the MIC (80µM). The number of adhered cells on glass slide was quantified before and after activation of flow and the removal percentage was determined. These data provided key information about adhesion strengths of cells on the glass surface which increased with time as observed in previous studies  (Schultz et al. 2000 , Holland et al. 2004 , Finlay et al. 2013 , Alles and Rosenhahn 2015 , Nolte et al 2017). Concerning C. closterium, a significant (p<0.
Acknowledgements: The authors acknowledge the financial support for the PhD of T. Le Norcy:  Région Bretagne (ARED LACTOPAI)  and the  Université de Bretagne occidentale. Authors are gratefully acknowledged to  Prof Peter Proksch  ( Institute of Pharmaceutical Biology and Biotechnology, University of Düsseldorf, Germany ) for allowing the study on DBHB by the synthesis of the molecule. Declaration of interest: none.
Data analysis Data were analyzed using SAS (version 9. 4, SAS institute Inc. , USA). An analysis of variance was computed for all the collected parameters and the mean comparisons were performed for the quantitative variable to evaluate the level of variability among the varieties and replication using the least significance difference at p<0. 05 level. Thereafter, correlation analysis was also computed to estimate the relatedness among variables, especially the relationship between the virus single or co-infection on the storage root and upper ground biomass yield.
Statistical analyses The 4 soil mesocosms that contained dead earthworms were removed from the data processing. Statistical analyses were performed using the R software 3. 2. 3 (R. Core Team, 2017). Significance was evaluated at P < 0. 05. Data met the conditions of normality and homoscedasticity. The differences between the initial biomass of the six earthworm species were assessed by one-way ANOVA, followed by Tukey HSD tests for post hoc pairwise comparisons ("agricolae" package). Litter mass loss was first analyzed by one-way ANOVA, followed by Tukey HSD tests for post hoc pairwise comparisons, to assess the differences between litter mass loss in the presence of mono-specific assemblages of strict-and epi-anecic earthworms and the control treatment (i. e. without earthworm). Second, a three-way ANOVA was applied, followed by Tukey HSD tests for post hoc pairwise comparisons, to test the effects of earthworm assemblages, earthworm pairs, and blocks on litter mass loss.
Acknowledgements We thank the  Institut National de la Recherche Agronomique (Arras, France)  for mineral soil analyses and  Météo France  for meteorological data. We also thank  Clément De Graaf ,  Clément Bertran ,  Albin Fertil ,  Alan Schneider  and  Anaïs Rancon  for their technical assistance in the laboratory. We sincerely thank  Kevin Richard Butt  and  Claudia Wiegand  for helpful comments.
We also consolidated a Ti-6Al-4V alloy (i. e. , a Ti6Al4V-0 vol. % TiB composite) at 1100 • C for 60 min for comparison with the tensile properties and microstructure of the Ti6Al4V-TiB composites. The chemical compositions of the Ti6Al4V-TiB composites were identified with X-ray diffraction (XRD; RINT Ultima II, Rigaku Corporation, The Woodlands, TX, USA) and a field emission electron probe micro analyzer (FE-EPMA; JXA-8530F, JEOL Ltd. , Tokyo, Japan). The XRD patterns were obtained with a counting time of 4/s, a step size of 0. 02 • using CuKα radiation, a voltage of 40 V and a current of 40 A. We determined the scanning range between 30 • and 50 • , with Ti, TiB 2 , and TiB having peaks at different angles, by the powder data files from the International Centre for Diffraction Data for 00-044-1294 (Ti), 00-035-0741 (TiB 2 ) and 00-006-0641 (TiB)  [14] [15] [16].
Song recordings Humpback whale song recordings were collected near Raoul Island, Kermadecs (figure  1 ) in September and October 2015 during a dedicated humpback whale research voyage. A hydrophone (HTI 96MIN, frequency response 2 Hz to 30 kHz) suspended to approximately 10 m deep in water depths of approximately 60 m from a 5 m RIB was used to collect acoustic recordings when humpback whales were observed. The recordings were made on a Zoom or a Microtrack II digital recorder (WAV format, 16 bit, sampling rate 44. 1 kHz). A total of 12 recordings were collected over 13 days, all within 5 km of Raoul Island. To maximize data quality and reduce uncertainty, we excluded all lowquality sections of recordings where songs were unclear (electronic supplementary material, tables S1 and S2). This resulted in a disparity between the number of recordings and the total number of 'individual' singers, as we were conservative in linking sections of song together within a recording (see below).
One recording from Niue was taken from a video collected using an underwater camera (Canon EOS 10D Digital SLR, audio extracted at a sampling rate of 44. 1 kHz, 16 bit, WAV file format). All other recordings were made using a hand-held hydrophone (HighTech HTI 96MIN) suspended to approximately 10 m deep in water depths of 30 m to greater than 1 km connected to a digital recorder (M-Audio Microtrack 24/96 or Microtrack II, or a Zoom H2 or H4, recording at 44. 1 kHz, 16 bit, WAV file format) from a designated research vessel or a platform of opportunity. While we endeavoured to analyse all available recordings to capture as much singer variability as possible, the available data represent a snapshot in time of a small (but broadly representative, due to strong song matching  [9] ) sample of singers from each location.
Each stereotyped string of units that were identified as a phrase was allocated a letter (e. g. A, B, C). Phrases containing similar sounds in the same order were grouped into the same theme number (e. g. 1, 2, 3). The qualitative assignment of phrase types (and higher-level theme groupings) was validated through clustering of unit sequences (see below). When multiple singers were present in a recording or a royalsocietypublishing. org/journal/rsos R. Soc. open sci. 6: 190337 singer was silent for more than 3 min before the song continued, it was not always possible to confirm the same singer was resuming. To avoid ambiguity, the subsequent phrases were labelled with a letter (e. g. KI01S1a) and the strings of phrases were analysed separately. This resulted in 39 'individual' singers in the Kermadec dataset from the 12 initial recordings (electronic supplementary material, table  S1 ).
The LSI produces a measure of similarity (between 0 and 1) among multiple sequences of varying lengths and provides an overall understanding of the similarity of all sequences  [29]. The LD has been shown to outperform other methods of comparing acoustic sequences by consistently reconstructing the already-known contextual information, for example, clustering humpback whale songs by population  [30]. All LSI analyses were run in R  [31]  using custom-written code (available at https://github. com/ ellengarland/leven). Detailed methods for calculating the LD, LSI and applying a weighting system are provided in Garland et al. [29]. The LSI was initially run here with all unit sequence data (i. e. the sequence of units making up each phrase, hereafter called a 'phrase string') from every singer and clustered to validate the qualitative assignment of each phrase string to a phrase type (and higherlevel theme grouping).
Acknowledgements. We thank  Blue Planet Marine ,  Conservation International , the crew of the RV Braveheart, the research team- Rémi Dodémont ,  Becky Lindsay ,  James Tremlett , the  Raoulies  and our colleagues at the  South Pacific Whale Research Consortium , for supporting research in the Kermadec Islands. Many thanks to  Ngāti Kuri  and  Te Aupoūri  for allowing us to work with their taonga. Research was conducted under a Department of Conservation Permit # 44388-MAR  to R. C. The  BRAHSS  project thanks  Rebecca Dunlop ,  Doug Cato  and the numerous staff and volunteers who have assisted with acoustic data collection. Thanks to  Patrice Plichon  and the  Province Sud , as well as  Véronique Perard ,  Rémi Dodémont  and  Solene Derville  from  Operation Cétacés  for their help with data collection in New Caledonia.
5 mL (15 ± 2 nm), 13 mL (11 ± 2 nm) and 14. 5 mL (below 5 nm). Oligomer size was determined after merging 20 independents particles by "ImageJ v 1. 51" software. Vol: Elution volume. In order to study their in-cell Ni(II)-binding capability and behavior, RrCooJ and its truncated version RrCooJ-∆ were overproduced in E. coli in growth medium supplemented with a range of Ni(II) concentrations from 0 to 2. 5 mM NiSO4. As a control, the impact of nickel was evaluated on a strain of E. coli transformed with an empty vector. The growth of the control culture was strongly affected by nickel, decreasing remarkably between 0. 5 mM and 1. 5 mM, and stopping for concentrations higher than 1. 5 mM. The presence of RrCooJ or RrCooJ-∆ increases the nickel resistance of E. coli, resulting in a constant growth even at high concentration of metal (Figure  4a ).
5 mL (15 ± 2 nm), 13 mL (11 ± 2 nm) and 14. 5 mL (below 5 nm). Oligomer size was determined after merging 20 independents particles by "ImageJ v 1. 51" software. Vol: Elution volume. In order to study their in-cell Ni(II)-binding capability and behavior, RrCooJ and its truncated version RrCooJ-∆ were overproduced in E. coli in growth medium supplemented with a range of Ni(II) concentrations from 0 to 2. 5 mM NiSO 4. As a control, the impact of nickel was evaluated on a strain of E. coli transformed with an empty vector. The growth of the control culture was strongly affected by nickel, decreasing remarkably between 0. 5 mM and 1. 5 mM, and stopping for concentrations higher than 1. 5 mM. The presence of RrCooJ or RrCooJ-∆ increases the nickel resistance of E. coli, resulting in a constant growth even at high concentration of metal (Figure  4a ).
Circular Dichroism (CD) Spectroscopy CD spectra were recorded using a J-1500 circular dichroism spectrometer (JASCO Analytical Instruments, Easton, PA, USA). A stock solution of 10 mM NiSO4 was used to monitor metaldependent secondary structure content upon Ni(II) titration (from 0 to 7 molar equivalents of NiSO4). Spectra were recorded from 190 to 250 nm using a 1 mm cuvette, with ten accumulations to increase the signal-to-noise ratio. Proteins were thawed and diluted to 4 µM dimer in CD buffer (5 mM potassium phosphate pH 7. 0, containing 0. 5 mM TCEP). For the determination of the secondary structure elements, the spectra were analyzed using the BeStSel online software  [12]. The guanidine hydrochloride denaturation experiments were performed via additions of different concentrations of.
Circular Dichroism (CD) Spectroscopy CD spectra were recorded using a J-1500 circular dichroism spectrometer (JASCO Analytical Instruments, Easton, PA, USA). A stock solution of 10 mM NiSO 4 was used to monitor metal-dependent secondary structure content upon Ni(II) titration (from 0 to 7 molar equivalents of NiSO 4 ). Spectra were recorded from 190 to 250 nm using a 1 mm cuvette, with ten accumulations to increase the signal-to-noise ratio. Proteins were thawed and diluted to 4 µM dimer in CD buffer (5 mM potassium phosphate pH 7. 0, containing 0. 5 mM TCEP). For the determination of the secondary structure elements, the spectra were analyzed using the BeStSel online software  [12]. The guanidine hydrochloride denaturation experiments were performed via additions of different concentrations of GuCl on 4 µM dimer samples (apo-and Ni-RrCooJ), followed by 2 h of incubation.
Acknowledgments: This work used the platforms of the  Grenoble Instruct Centre (ISBG ;  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB). The electron microscope facility is supported by the  Rhône-Alpes Region , the  Fondation Recherche Medicale (FRM) , the fonds  FEDER , the  Centre National de la Recherche Scientifique (CNRS) , the  CEA , the  University of Grenoble, EMBL , and the  GIS-Infrastrutures en Biologie Santé et Agronomie (IBISA). We thank  Daphna FENNEL  and  Dr Guy SCHOEHN , from the  Electron Microscopy platform of the Integrated Structural Biology of Grenoble  (ISBG,  UMI3265 ).
Funding: This work was supported by "the  ITERLIS PhD program ,  CEA Life sciences" for MA's PhD funding, the "FUNBIOCO" project (IDEX-UGA ,  Initiatives de Recherche stratégiques)  and the " COSYNBIO " project (Projets exploratoires, Cellule energie-CNRS). This work has been partially supported by  Labex ARCANE  and  CBH-EUR-GS  ( ANR-17-EURE-0003 ). The research leading to these results has received funding from the networking support from the  COST Action FeSBioNet  (Contract  CA15133 ).
Aqueous phase characterization All standards and reagents, were prepared with ultra-pure water, and were of analytical grade from Fluka, Sigma-Aldrich or Merck. The glass and plastic parts were firstly washed with 5% HNO3 then with ultra-pure water (18 MΩ. cm -1 ). The Eh and pH data were recorded automatically every 10 seconds using an Aligent 34970A BenchLink Data Logger through the Eh and pH electrodes (Mettler-Toledo Xerolyt Solid). Measured Eh value was corrected for the reference electrode's voltage (+207 mV) relative to the standard hydrogen electrode (SHE), and corresponded to the Ag/AgCl (3 M KCl) reference electrode. The pH electrodes were calibrated using the measured data of three-point using pH buffers of 4, 7 and 10 at 25 o C at the start and the end of experiment displaying that the electrode response were not shifted significantly.
, 2012)   PCR products were conceived on an agarose gel, and the 16S rRNA band excised and purified using the Wizard® SV Gel and PCR Clean-Up System (Promega, USA). The sequencing process of PCR 16S rRNA amplicons were merged, denosed, quality trimmed and demultiplexed using USEARCH  (Edgar, 2013). These sequences were then clustered into operational taxanomic units (OTUs) using the UPARSE algorithm with a similarities higher than 97%  (Edgar, 2013) , and then checked for Chimera detection using UCHIME  (Edgar, 2011). A summarized database of high quality sequences derived from the NCBI database was described in the OTUs table  (Table 1 ), and the full data shown in Table  S-3 (Supporting Information).
X-ray absorption near edge structure (XANES) Solid-phase samples were collected from the two reactors at the end of the redox cycles indicated in Fig. 1a-b. X-ray absorption near edge structure (XANES) was used to characterize both As and S speciation. S K-edge XANES data were collected at the XAFS beamline of the Elettra synchrotron (Trieste, Italy), whereas As K-edge XANES data were done at the bending magnet beamline BM08-LISA of the European Synchrotron Radiation Facility (ESRF, Grenoble, France). Sulfur K-edge (2472 eV) measurements were performed using a Si(111) monochromator calibrated relative to the white line of a Na2S2O3(s) standard (Sigma-Aldrich) at 2471. 64 eV. Spectra were collected in fluorescence mode using a solid-state Si detector. A commercial elemental sulfur reference was measured in fluorescence mode before each scan for accurate energy calibration.
, 2018)  Both of As and S XANES data analysis were performed using the Athena software  (Ravel & Newville, 2005)  and the relative contributions of the different compounds to the sample spectra were achieved by linear combination fitting (LCF). A homemade program based on a Lenvenberg-Marquardt alogorithm was used to improve the fit quality following the method of Resongles et al. (2016), which was described in detail in  Phan et al. (2018).
22μm pore size membranes. The supernatants were then analyzed by HPCL (PerkinElmer 2000 pump and auto-sampler, UV-vision detectors and software AZUR V6. 0 software) using a C18 column (Nucleosil 100-5PAH) and isocratic elution in methanol 95% at a flow rate of 0. 4 mL/min. The detection was performed at a wavelength of 265 nm.
Thermodynamic modeling Thermodynamic calculations were performed using the PHREEQC program version 3. 3. 10 (Parkhurst & Appelo, 2013). The following calculations were performed: (i) thermodynamic aqueous species distribution during the anoxic and oxic half cycles, and (ii) the saturation indices (SI = log IAP/Ksp) at each sampling point with respect to solid arsenic, sulfur and iron phases. The WATEQ4F database for the As species was updated according to the data reported in the literature  (Helz & Tossell, 2008). The added species included As(III) species (HnAsO3 n-3 (As(III) -arsenite), HnAsO4 n-3 , HnAsSO2 n-3 (MTA(III) -monothioarsenite), HnAsS2O n-3 (DMAs(III) -dithioarsenite), HnAsS3 (TTA(III) -trithioarsenite), and As(V) species (HnAsO4 n-3 (As(V) -arsenate), HnAsSO3 n-3 (MTA(V) -monothioarsenate), HnAsS2O2 n-3 (DTAs(V) -dithioarsenate), HnAsS3O n-3 (TTA(V)trithioarsenate) and HnAsS4 n-3 (TeTA(V) -tetrathioarsenate)).
Solid As speciation To determine the effect of redox cycling on solid arsenic speciation, X-ray absorption spectra were recorded at the As K-edge and the bulk As concentration was analyzed using total digestion on sediments sampled at the end of each half-cycle for both reactors, and on the initial sediment. It is worth noting that Linear Combination Fitting XANES analysis is able to detect only species that are present in amounts higher than 5 -10%, and to distinguish only species with sufficiently different spectral features. Arsenic K-edge XANES data suggested the presence of four distinct As species (Fig. 3 , Fig. 4 ). The initial sediment included O-bound As(V), O-bound As(III), S-bound As(III), and arsenian pyrite (i. e arsenic-substituted pyrite) (Fig. 3 ). The bulk As concentrations in the same samples were analyzed using total digestion and ICP.
Acknowledgements The authors acknowledge the financial support of the doctoral scholarship from  University Grenoble Alpes and Geochemistry group (ISTerre) , which is part of  Labex OSUG@2020  ( ANR10 LAB56 ). This study has been conducted under the framework of  CARE-RESCIF  initiatives. We would like to thank  Prof. Douglas Kent  and  Dr. Guillaume Morin  for their help and advice during the writing and review process. We give special thanks to  Y. Wang  from  EPFL  for help with collecting sediment and fieldwork in Vietnam,  L. Spadini  and  M-C Morel  in LTHE for IC and S8 analysis. Aqueous As species were analyzed on  Plateforme AETE -HydroSciences/OSU OREME, Montpellier, France. We also acknowledge  Dr. Francesco D'Acapito  and  Dr. Giovanni Ignazio Lepore  for the assistance during XAS measurements at the LISA beamline at the  ESRF  ( BM08 ),  Dr.
For the first Am-U/Am shell, the distances obtained by EXAFS are slightly lower than those expected by XRD, but within the uncertainty limits. The refined Debye-Waller U 4+ O 2 U 3 5+/6+ O 8 U 3 5+/6+ O 8 U 3 5+/6+ O 8 U 3 5+/6+ O 8 Fig. 2  XANES spectra collected at the L III edge of uranium. XANES spectra and their second derivatives for the four (U,Am)O 2 oxides are compared to the spectra of the standard compounds factors are generally low because the data were recorded at 15 K. At such temperatures, the thermal contribution can be neglected and the Debye-Waller factors can be attributed only to the structural disorder. The obtained values are always larger for the oxygen shells than for the cation shells, as expected from the higher mobility of oxygen compared to that of uranium/ americium.
Acknowledgements We are thankful to  M. Bataille ,  P. Coste  and  L. Ramond  for helping with the manufacture of the oxide pellets. E. Epifano  thanks the  SETAM  project for financial support of the Ph. D and the  GENTLE European project  (Grant agreement no:  323304 ) for founding the internship at the  JRC Karlsruhe. We acknowledge the  KIT  synchrotron light source for provision of the CAT-ACT beamline instrumentation and the  European Synchrotron Radiation Facility  for provision of synchrotron radiation facilities at the  Rossendorf Beamline.
The percussion of carcasses was identified on 22 zones. The macro-traces were comparable to those observed on the experimental tools that served as butcher axes in forceful disarticulation, or to break the ribs at the sternum or the spine. Finally, a small number of pieces presented edge damage that could testify to cutting actions and percussion on the same edge. If we consider the pieces for which an interpretation of the traces could not be established (Annex 5; table 48), the number of active zones reflecting butchery activities could be greatly increased, since 62 additional active zones could have been used for cutting and eight for percussion (Annex 5; table  48 ). Furthermore, some of the active zones that were used for scraping hard material (41 pieces, i. e. 8 %) could potentially be attributed to butchery activities, but their identification required data to be taken into account from the study of faunal remains at the different sites concerned.