dataesr/scientific-paragraphs-categorization huggingface dataset:
Species ecological preferences and strategies To analyse how the ecological preferences and ecological strategies of riparian plants varied between old and recent surveys, as well as with environmental conditions, we collected data for each species from two sources of information (Appendix S2). Ellenberg's indicator values  (Ellenberg et al. , 1992)  for light (L), nutrient availability (N) and soil moisture (F) were extracted from the Baseflor database  (Julve, 1998)  and used to characterize variations in habitat preferences of species. Among the 448 species encountered, these values were unavailable for two species, one with a single occurrence in our data set (i. e. , singleton species) and one identified at the genus level. Grime's values  (Grime, 1977)  for respectively Competitors, Stress tolerators and Ruderals, i.
Environmental data At the centre of each quadrat of the recent survey plots, the coordinates (longitude, latitude and altitude) were measured using a GPS receiver with centimetric accuracy. From these measurements, the elevation difference and distance from the centre of the main riverbed, used hereafter as connectivity parameters, were characterized in a GIS (ArcGIS 10. 7. 1 Esri Inc. ). First, we determined for each plot the position of the nearest point located on main stream bed of the Rhône or Ain River (from the Carthage® database) and then calculated the distance between the center of the plot and this point. Second, we extracted from a Digital Elevation Model (RGE alti®, 5 m resolution) the elevation of the plot and the elevation of the nearest main stream bed point and determined the elevation difference by subtracting these two values.
Acknowledgements The study was supported by the  Agence de l'eau Rhône Méditerranée Corse and INRAE. The authors thank  Laurent Bergès  for advice regarding methodology and statistical analysis,  Eric Mermin  and  Julien Pierre  for their help on field, and  Remi Bogey  ( Réserve Naturelle Nationale du Haut-Rhône ) and  Anne-Sophie Pingon  ( Grand Parc Miribel-Jonage ) for facilitating access to the study sites.
4. 0). 47  In the GFN2-xTB calculations the implicit ethanol solvation was performed using the ALPB (from Analytical Linearized Poisson-Boltzmann) method. 48  The periodic calculations with the GFN2-xTB were performed with the DFTB+ code (version 21. 2). 49  Accurate DFT calculations of periodic systems are performed using the Meta-Generalized Gradient Approximation, non-local SCAN+rVV10 exchange-correlation functional,  50  as implemented in the Vienna ab initio Package (VASP, version 6. 0). 51  The plane wave kinetic energy cutoff was 500 eV. The projector augmented wave (PAW) method was used to describe the interactions between atomic cores and valence electrons. 52, 53  Finally, the AIMD simulations were carried out with CP2K code,  54  with a 1 fs timestep. The PBE exchange-correlation functional was employed, 55 using double-ζ basis sets with Goedecker-Teter-Hutter (GTH) pseudopotentials, 56 with 1, 4, 5, 6, and 12 valence electrons for H, C, N, O, and Zn atoms respectively.
The number of Zn 2+ cations and Im -ligands are shown using the (z, l) notation. The energy is calculated from the linear regression reported in Figure  6. Color code as in Figure  1. -  , calculated with three types of calculations, namely the periodic meta-GGA exchange-correlation functional SCAN+rVV10, with the GFN2-xTB method, and with the non-periodic, hybrid exchange-correlation functional ωB97X/6-311++G(d,p). Each line represents a fitting of the cluster energies corresponding to a particular value of z (with different number of ligands, l). The black circles correspond to the energies of the clusters with z > 8. Red empty circles correspond to the energies of the crystalline materials calculated with the GFN2-xTB method (zni, cri, coi, ZIF-1, ZIF-4, ZIF-6, ZIF-8, SALEM-2, and ZIF-10).
Acknowledgments S. H. acknowledges funding from the  Agencia Estatal de Investigación  and the  Ministerio de Ciencia, Innovación y Universidades, of Spain  ( PID2019-110430 G B-C22 ), and from the  EU FEDER Framework   2014-2020  and  Consejería de Conocimiento, Investigación y Universidad of the Andalusian Government  ( FEDER-UPO-1265695 ). S. R. G. B. was supported by grants  FJC2018-035697-I  funded by  MCIN/AEI/10. 13039/501100011033  ( Ministerio de Ciencia e Innovación; Agencia Estatal de Investigación)  and  POSTDOC_21_00069  funded by  Consejería de Universidades, Investigación e Innovación, Junta de Andalucía. We are thankful to  C3UPO  for the HPC facilities provided.
Treg deficiency was associated with a reduced expression of Foxp3, the master transcription factor known to maintain the Treg phenotype stability and suppressive functions. Transcriptomic profiling of Treg revealed activation of the tumor necrosis facto (TNF)-α pathway, which was linked to increased serum TNF-α concentrations that were twice as high as in controls. Treg transcriptomic profiling also suggested that post-translational mechanisms possibly accounted for Foxp3 downregulation and Treg dysfunctions. Since TNF-α participates in the rupture of immune tolerance during wAIHA, its inhibition could be of interest. To this end, the effects of fostamatinib, a SYK inhibitor, were investigated in vitro, and we showed that besides the inhibition of erythrocyte phagocytosis by monocytes, fostamatinib is also able to dampen TNF-α production, thus appearing as a promising multitargeting therapy in wAIHA (clinicaltrials gov.
RNA sequencing, gene ontology terms, Treg signature and index computations Fluorescent-activated cell sorting (FACS) of Treg (FVS780 -CD3 + CD4 + CD25 hi CD127 -) from four primary wAIHA and four sex-and age-matched HC were used for RNA sequencing (RNAseq). RNAseq was processed in one batch. Only protein-coding transcripts and genes were included in the downstream analysis. Genes with a P value below 0. 05 and normalized read count greater than 25 were considered as significantly differentially expressed. RNAseq data are available in the Gene Expression Omnibus database (accession number: GSE195791). Treg transcriptomic identity was assessed by referring to the Treg signature genes. 19  Tumor necrosis factor (TNF) index was calculated for each subject by averaging the normalized expression of all genes belonging to TNF pathway (normalized expression vs.
Statistics Statistical analyses and graphs were performed with Prism v9. 3. 0 (GraphPad Software), R Studio (1. 4. 1717) and Heatmaper. Data are reported as the median with interquartile range (IQR) and were compared using Mann-Whitney test for independent data, Wilcoxon signed-rank test for paired conditions, and Spearman's rank correlation test for correlation analyses, unless otherwise specified. P value <0. 05 was considered significant.
The activation of these mechanisms positively correlates with the engagement of the TNF-α pathway in Treg, whose serum concentration is increased. Targeting TNF-α could be a novel approach complementary to current treatments to restore immune tolerance in wAIHA. Along this line, fostamatinib could be a promising treatment as it reduces both the production of TNF-α and the phagocytosis of RBC by monocytes. This investigation was supported by a research grant (2012-A001154-39) from the GIRCI Est (Groupement Interrégional pour la Recherche Clinique et l'Innovation), by the French Ministry of Health and Solidarity (Referral Centers for Rare Monocytes from 7 healthy controls were cultured 24 hours alone or in conditions mimicking hemolysis, i. e. , in the presence of heme or red blood cells (RBC) labeled with CellTrace and either coated with immunoglobulin (Ig)G anti-glycophorin A (RBC/monocytes ratio: 5/1) or in the presence of isotype control (RBC-Ig).
Acknowledgments We thank  Y. Duffourd  and  Dr. H. Begue  for their valuable advice for RNA-sequencing analysis. We thank  Dr. A. Legrand ,  N. Pernet  and  S. Monier , from the flow cytometry core facility ( INSERM UMR1231, Université de Bourgogne Franche-Comté) , for their technical support for flow cytometry and cell sorting.
Electrophysiology For whole-cell voltage-clamp recordings of autaptic cultures, cells were held at -70 mV, and holding voltage was increased to 0 mV (2 ms) to depolarize cells (MultiClamp 700B amplifier, Axon Instruments, Molecular Devices) under the control of the Clampex program 10. 1 (Molecular Devices). Recordings were done at room temperature. The flow of extracellular solution was maintained during recordings, and pharmacological solutions were applied if required. Hypertonic sucrose solution (0. 5 M in external solution) was used to trigger the fusion of the readily releasable pool of vesicles (RRP). NBQX (HelloBio) and bicuculline (Tocris) were used to inhibit AMPA and GABA receptors, respectively. Miniature excitatory post-synaptic currents (mEPSCs) were recorded in the presence of 300 nM tetrodotoxin (TTX; Tocris).
The recording rate was 10 kHz. Microelectrodes were made by using a Sutter 2,000 filament-based horizontal puller and were used only if they had pipette resistances of 2. 5-4. 5 MΩ. Serial resistance was compensated by 35-60%, and cells with serial resistances below 12 MΩ were analyzed. All chemicals were purchased from Sigma-Aldrich unless mentioned otherwise. All autaptic electrophysiology data were analyzed using Axograph (Ver. 1. 5. 4) software (Axograph Scientific). Recordings of S-SCAM KD and control autaptic neurons were performed from DIV11 to DIV14. Whole-cell patch clamp recordings of conventional dissociated cultured hippocampal neurons were made at 37 • C ± 0. 5 • C using a HEKA EPC-10 USB amplifier and the software Patchmaster (HEKA Electronics). During recordings, cultures were continuously perfused with an extracellular solution consisting of (in mM): NaCl 125.
0, KCl 2. 5, NaHCO 3 25. 0, NaH 2 PO 4 1. 25, CaCl 2 2. 0, MgCl 2 1. 0, glucose 20. 0 (pH 7. 4), with the addition of 1 µM TTX. The intracellular solution consisted of (in mM): 150 K + -D-Gluconate, 10 NaCl, 3 Mg-ATP, 0. 3 Na-GTP, 10 Hepes, and 0. 05 EGTA (pH 7. 3). Cells were voltage-clamped at -70 mV, and a liquid junction potential of 13 mV was corrected online. Recordings were discarded if the series resistance was >10 M. Recordings were digitized at 20 kHz and filtered at 2. 9 kHz. mEPSCs in conventional cultures were detected by the software MiniAnalysis (Synaptosoft). Recordings of S-SCAM KD and control neurons in conventional cultures were performed at DIV9-10.
cDNA libraries were amplified and sequenced by using the cBot and HiSeq2000 from Illumina (SR; 1 × 50 bp; ∼30-40 million reads per sample). Sequence images were transformed with Illumina software BaseCaller to bcl files, which were demultiplexed to fastq files with CASAVA v1. 8. 2. Quality check was done via FastQC (v. 0. 10. 0, Babraham Bioinformatics). Read alignment was performed using STAR v2. 3. 0 to the Rattus norvegicus v5 reference genome. Data were converted and sorted by Samtools 1. 2, and reads per gene were counted via htseq version 0. 6. Data analysis was performed using R (3. 2. 1), and differential gene expression was performed using DESeq2 (v1. 8. 1). Candidate genes were filtered to a minimum FDR-corrected p-value <0. 05. Sequence data have been deposited in NCBI's Gene Expression Omnibus and are accessible through GEO Series accession number GSE228093.
For functional analysis, Gene Ontology (GO;  Ashburner et al. , 2000)  enrichment was tested using g:Profiler  (Reimand et al. , 2007)  against a statistical domain scope of all annotated genes. Significance was assessed using the g:SCS threshold. To decrease redundancy in GO terms, an upper limit of term size was set to 1,000. To investigate the interaction between differentially expressed gene products, we used STRING  (Szklarczyk et al. , 2015). The displayed genes were limited to those in the same functional network as S-SCAM (Magi2) and only those with a high confidence interaction score (minimum of 0. 77). qPCR Methods for qPCR were basically the same as described  (Becker et al. , 2012). In brief, total RNA was extracted using Nucleozol  Cat. No. 740404. 200 ) directly from the culture plates, and 1 µg RNA was transcribed using the Omniscript RT kit  (Qiagen, Cat.
Microscopy Images were acquired using a SPOT-cooled CCD camera (Visitron Systems) attached to a Zeiss Axiovert 200M. Images were collected using 40× and 63× Plan-Neofluar oil objectives, and digital images were analyzed with Metamorph software. Image acquisition and analysis were done in a blind manner. For measuring puncta number and intensity per given neuron, four to five dendritic segments were used, using the proximal 25 µm of dendrites starting from the soma and their average values.
Quantification of synaptic puncta Dissociated neurons were plated on poly-L-lysine-coated 13mm glass coverslips in 24-well plates. Cells were fixed and stained with neuronal markers Bassoon or Synaptophysin as presynaptic markers and PSD95 as a post-synaptic marker. Image analyses were conducted in Opera Phenix at 60× magnification using Harmony software. Proximity localization of post and presynapse was quantified using OpenView software  (Tsuriel et al. , 2006). Postsynapses were automatically detected using the BoxpunctaEx function. An 8 × 8 pixel box was placed around the maximum of each postsynapse. Proximity-localized presynapses were detected using the MatchSet function. The number of synapses was counted along the selected dendritic segment.
Spine analysis Confocal images were acquired using a laser-scanning confocal microscope (Leica TCS SP5, Leica Microsystems CMS, Germany) equipped with 488 nm (Ar) and 561/633 nm (He-Ne) lasers for excitation of the respective Alexa fluorophores and a 63×/1. 4 NA oil-immersion objective. The spine analysis was conducted using the Dendritic Spine Counter 1. 4. 7 plugin in Fiji/ImageJ software. The average spine size was calibrated manually, allowing for automatic detection of spines along the dendrite. The automatically generated results were adjusted manually if necessary. The dendrite was traced using the Polyline tool, and the number and classes of spines were quantified along the tranced stretch.
Single-particle measurements were performed in the epifluorescence mode using Nikon Ti-E inverted microscope with a Nikon CFI Plan Apo 60× oil objective (NA = 1. 4). The excitation was provided by light emitting diodes (SpectraX, Lumencor) at 550 nm. The fluorescence signal was recorded with a Hamamatsu Orca Flash 4 camera. The exposure time was set to 100 ms per image frame. Single-particle analysis was performed using the Fiji software. Particle locations were detected through a Fiji routine applied to a projection (maximum intensity) of all obtained frames per experiment. After the automatic background subtraction, the mean intensities of circular regions of interest with a diameter of 50 pixels around the found particle locations were then measured. At least three image sequences (500 × 500 pixels) per condition were analyzed.
A total of 20 μg mL -1 of neutravidin or streptavidin-Cy3 (Amersham) in DPBS was added for 20 min. Cells were washed with 0. 1% BSA/DPBS and incubated with 1 × 10 -9 m of PEMA-ZI-biotin-NPs in 0. 1% BSA/DPBS for 20 min at room temperature. Cells were washed two times with 0. 1% BSA/DPBS and imaged in the epifluorescence mode using Nikon Ti-E inverted microscope with a Nikon CFI Plan Apo 60× oil objective (NA = 1. 4). The fluorescence signal was recorded with a Hamamatsu Orca Flash 4 camera. The excitation was provided by light emitting diodes (LED, SpectraX, Lumencor). Acquisition settings for Rhodamine B were: excitation at 550 nm; emission filter was 600/50 nm; the excitation power of LED was 8% and exposure time of 500 ms. Bright-field images were recorded simultaneously. The images were recorded using NIS Elements and then processed with Fiji software.
Acknowledgements T. Y. and E. C. D. S. contributed equally to this work. This work was supported by the  European Research Council   ERC Consolidator grant Bright-Sens 648528 ,  ERC PoC AmpliFISH 899928 ,  SATT Conectus Alsace (Maturation grant NanoAntenna). A. C. and A. R. acknowledge support form  FRC Emerging Investigators grant. The authors thank  Ilya Aparin  for help with some step of synthesis. PACSI platform is acknowledged for help with NMR and Mass analysis, while PIQ platform for providing access to fluorescence microscopy. C. Crucifix  from the  FRISBI  platform is acknowledged for help with electron microscopy.
Acknowledgements The workshop was organised by the IPBES task force on scenarios and models, supported by the IPBES technical support unit on scenarios and models, based at  PBL Netherlands Environmental Assessment Agency. The workshop was hosted by the  Institute for Global Environmental Strategies (IGES) , with support from the research team on " Predicting and Assessing Natural Capital and Ecosystem Services through an Integrated Social-Ecological Systems Approach (PANCES) " based at the  University of Tokyo , the  Research Institute for Humanity and Nature (RIHN) , and the  United Nations University , with generous financial support from the  Ministry of the Environment of Japan. We sincerely appreciate the valuable comments and suggestions made by  Laetitia Navarro  and two anonymous reviewers, which helped us in improving the quality of the manuscript.
The  UK Natural Environment Research Council  award number  NE/R016429/1  as part of the  UK-SCAPE programme delivering National Capability. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the  US Government. Funding was provided by  Instituto Nacional de Ciência e Tecnologia em Biodiversidade e Produtos Naturais  [Grant no. PIA APOYO CCTE AFB170008 ] that all relevant data are included in the article and/or its supplementary information files.
I G U R E 8 Mycobactin-dependent iron uptake. The proteins encoded by PA1909 and the MFS transporter are not represented, as there is no data proving their involvement in iron acquisition by mycobactin or their biological role F I G U R E 9 Structures of hydroxamate-type siderophores. The hydroxamate functions are shown in red Pseudomonas aeruginosa AND ITS MULTIPLE STRATEGIES 13 14622920, 0, Downloaded from https://ami-journals. onlinelibrary. wiley. com/doi/10. 1111/1462-2920. 16328 by Cochrane France, Wiley Online Library on [08/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License.
F I G U R E 8 Mycobactin-dependent iron uptake. The proteins encoded by PA1909 and the MFS transporter are not represented, as there is no data proving their involvement in iron acquisition by mycobactin or their biological role F I G U R E 9 Structures of hydroxamate-type siderophores. The hydroxamate functions are shown in red Pseudomonas aeruginosa AND ITS MULTIPLE STRATEGIES 13 14622920, 0, Downloaded from https://ami-journals. onlinelibrary. wiley. com/doi/10. 1111/1462-2920. 16328 by Cochrane France, Wiley Online Library on [08/03/2023]. See the Terms and Conditions (https://onlinelibrary. wiley. com/terms-and-conditions) on Wiley Online Library for rules of use; OA articles are governed by the applicable Creative Commons License.
Interestingly comparison of prt6 vs prt6 erfVII with Col-0 vs prt6 erfVII showed a very high level of similarity of differentially (both up and down)-regulated genes (Fig. 3a ) suggesting that ERFVIIs are at least partially active in Col-0 under normoxia. Analysis of Gene Ontologies demonstrated that the major functional groups associated with ERFVII genetic activity in the comparison of prt6 to prt6 erfVII were related to biological processes of response to hypoxia (Fig. 3b , Supplementary Data 4, 5). Analysis of genes previously shown through meta-analysis of available transcriptome datasets to be differentially regulated in response to hypoxia  37  showed that almost half were shared with transcripts differentially regulated in prt6 compared to prt6 erfVII (Fig. 3c ). The majority of a set of 49 core hypoxia-responsive transcripts, previously shown to be upregulated in diverse cell populations of A.
3 3xHA and RAP2. 12 3xHA bands were visible on Coomassie-stained SDS-PAGE gels at the expected sizes of the two  proteins (Supplementary Fig. 5a ). Excision, destaining and trypsin digestion of these bands, followed by LC-MS/MS analysis and database searching, identified them unambiguously as originating from RAP2. 3 and RAP2. 12 12 based on the presence of 9 matching peptides from each protein (Supplementary Fig. 5b , Supplementary Data 12). Examination of the MS and MS/MS data revealed the same extensive alterations at the amino termini of both proteins, including methionine excision, and arginylation. In addition, a Cys-sulfonate (SO 3 -) modification only at position 2 was also observed. High quality MS/MS spectra containing a clear series of b and y fragment ions were recorded for the two tryptic peptides to confirm this observation (Fig.
In combination with previous datasets analysing the role of individual or combinations of ERFVIIs  19, 40, 57  , these data highlight the overall importance of ERFVIIs in regulating the expression of the genome in response to low oxygen, as a response to inhibition of the PCO N-degron pathway. Direct visualisation of ERFVII abundance through immunolocalization and Western blot analysis allowed an investigation of the relative influences of environmental and genetic factors. Stabilisation of RAP2. 3 3xHA in the presence of bortezomib and addition of polyubiquitin moieties demonstrate that degradation of ERFVIIs requires the proteasome (Fig. 4a , b, Supplementary Fig. 4 ). Genetic removal of PRT6 activity also resulted in stabilisation, though not as strongly as with bortezomib, and addition of bortezomib to prt6 seedlings revealed high molecular weight products, suggesting the activity of other E3 ligases in regulating ERFVII stability.
Each sample was then imaged using a voltage and current of 112 kV and 168 µA, respectively, at a voxel size resolution of 23 µm. The scanner stage rotated through 360 degrees at a rotation step increment of 0. 125 degrees over a period of 48 minutes, acquiring a total of 2880 projection images using a fast (no image averaging) multiscan of three sections with an exposure time of 333 ms. Each scan was reconstructed using DatosRec software (Waygate Technologies (a Baker Hughes business), Wunstorf, Germany). Radiographs were visually assessed for sample movement before being reconstructed in 32-bit depth volumes with a beam hardening correction of 8, no filtration was applied to the image. Reconstructed sections were processed in VGStudioMAX (version 2. 2. 0; Volume Graphics GmbH, Heidelberg, Germany) with manual alignment of the 3 sections to combine to a single 3D volume.
Seedling transcriptome analyses For RNA-seq analysis, seedlings of Col-0, prt6-1 and prt6 erfVII were grown under continuous light on 1/2 strength MS agar. Four biological replicates of 7-day-old seedlings of each genotype were harvested and frozen in liquid nitrogen. RNA was extracted using RNeasy plant mini kit Qiagen as per manufacturer's instructions. RNA  Low quality reads and adaptor sequences were removed from raw reads using default parameters of skewer v0. 2. 2 software 66. Filtered reads were mapped onto the reference genome (TAIR10) using the default parameters of Hisat2 v2. 1. 0 software  67. Only uniquely and correctly mapped reads were kept in bam files for the further analysis. Read counts for each gene are calculated using featureCounts v1. 6. 0. PCA was used to identify that the biological replicates are close enough to each other.