dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic analysis Fungal genes homologous to GUN1 were searched by BLAST in GenBanK and Mycocosm  (Benson et al. , 2013; Grigoriev et al. , 2014) , using the default parameters with the GUN1 protein sequence as query. For a selection of Ascomycota, Basidiomycota and Mucoromycota species, hits with an e-value lower than 10 -5 were selected. Research for other homologs was carried out for each selected species on OrthoDB  (Kriventseva et al. , 2019). The alignment was performed with MAFFT  (Katoh et al. , 2005)  and manually refined using Jalview  (Waterhouse et al. , 2009). The phylogenetic tree was built using the maximum likelihood method (PhyML software using the default parameters)  (Guindon and Gascuel, 2003). The tree was visualized on the iTOL server  (Letunic and Bork, 2007). Bootstrap values are expressed as percentages of 100 replicates (Figure  S4 ).
A boosted decision tree (BDT)  [49] , using the AdaBoost algorithm from the TMVA package  [50] , combines information from: the χ 2 of the vertices of the B 0 , K * 0 and tau candidates; the χ 2 of the flight-distances of the B 0 and the tau candidates. The BDT is trained using simulated signal samples and the upper sideband of the same-sign data sample as a background proxy. A k-folding approach  [51]  is used to exploit the training samples without biasing the output of the classifiers. For the threshold optimisation, the background yield in the signal region is extrapolated from a fit with a decreasing exponential function to the candidate m corr distribution in the region 11 to 18 GeV/c 2 , dominated by combinatorial background. The second stage is a multivariate selection dedicated to the rejection of charmed mesons mis-identified as tau leptons.
Determination of efficiencies The efficiencies for the different steps of the selection chain are evaluated separately for each year of data taking. With the exception of the particle identification efficiency, they are estimated with simulation. The reliability of the simulation is checked using B 0 , D -and D + s mesons from the normalisation channel B 0 → D -D + s (with D -→ K + π -π - and D + s → K + K -π + ) as proxies for two-and three-prong particle vertices, selected with the additional requirement that the B 0 candidate mass lies within ±50 MeV/c 2 from its nominal value. All the variables used in the multivariate selections are found to be well described by simulation. Residual discrepancies are assessed as a systematic uncertainty. The particle identification variables are not perfectly described in simulation.
Therefore, the particle identification efficiency is evaluated using data calibration samples. A pure sample of pions and kaons is obtained from the decay D * + → (D 0 → Kπ)π + while muons are selected from the decay J/ψ → µ + µ -, without relying on PID selection criteria  [56]. The efficiencies of the PID requirements can then be computed in intervals of the kinematic variables of the final-state-particles momentum and pseudorapidity  [57]. Intervals are chosen making a compromise between the stability of the efficiency within the interval and statistical uncertainty. The event occupancy, parameterised by the number of tracks per event, is also taken into account, relying on same-sign events in the case of signal and on the observed distribution for the normalisation channel. The distribution of the selection efficiency as a function of the kinematic variables m 2 K * 0 µ ± and m 2 τ ∓ µ ± , normalised to unity, is shown in Fig.
(1969)  was afterwards followed by other authors  (Selte et al. , 1971; Keller et al. , 2015) , who refined the magnetic structure on the basis of powder data. In none of the refinements of the magnetic structure was the concept of magnetic superspace groups employed. However, in an entry for the magnetic structure of CrAs in the database MAGNDATA  (Gallego et al. , 2016) , the magnetic superspace group P2 1 2 1 2 1. 1 0 (00)00ss is given as the one corresponding to the reported structure by  Watanabe et al. (1969)  and  Selte et al. (1971). The double-helix model includes restrictions that are not forced by the symmetry of P2 1 2 1 2 1. 1 0 (00)00ss. To our knowledge, a determination of the magnetic structure of CrAs based on group-theoretical considerations, including a comparison of all symmetry-allowed models for its magnetic structure, was performed neither by  Watanabe et al.
Pressure was applied using a stationary wheel-driven hydraulic press. The initial pressure at room temperature was determined to be 0. 17 GPa. The loaded cell was inserted into an orange-type cryostat and cooled to 2 K. Based on earlier experiences, the pressure drop upon cooling amounts to approximately 30% for this temperature decrease  (Lelievre-Berna, 2023). Accordingly, the first data collection was performed at 0. 12 GPa and 2 K. The measurement consisted of a series of ! scans. Data collection out of the horizontal reflection plane was possible due to the lifting counter range of the detector, À12. 5 to 25. Afterwards, the cell was warmed to room temperature and compressed to 1. 2 GPa. After cooling it to 2 K, this corresponds to a pressure of about 0. 84 GPa. Under these conditions, the same set of nuclear and magnetic reflections, like at 0.
Therefore, we used RT-qPCR to study the osmolarity-dependent response of proVWX. We designed eleven primer pairs to evaluate the transcriptional profile across the operon and its flanking genes (Supplementary Data 1A and 1B). The transcriptional profile across proU shows that the central proW gene has lower transcript levels than the flanking proV and proX genes and that the transcript level of the terminal proX gene is higher than that of proV, in agreement with genome-wide RNA-seq studies  80. This trend was observed at 0. 08 M NaCl, 0. 3 M NaCl, and upon a hyperosmotic shock (Fig. 1a-c  and Supplementary Fig. 1a-c ; Supplementary Tables  1  and 2 ). Mechanistically, the decline in relative expression between proV and proW may be accounted for by transcription termination at the junction of the two genes, while the sharp increase in expression between proW and proX may arise because of the presence of an internal promoter between the two genes.
Indeed, with Term-seqa technique used to identify transcription termination sites  81  the presence of a termination site downstream of proW1 at chr:2806395-2806398 was detected in our study and at chr:2806397-2806401 in an earlier report  82  (Accession number: NC_000913. 3https://www. ncbi. nlm. nih. gov/nuccore/556503834) (Supplementary Fig. 2 , Supplementary Data 1A). Despite its positioning downstream of proW1 (Supplementary Data 1A), the terminator may have had an impact on the proW1 RT-qPCR signal. Our Term-seq studies also identify a termination site between proW and proX downstream of a putative hairpin structure (Supplementary Fig. 2 , Supplementary Data 1A), however, this site was not detected in Term-Seq studies performed by others  82. TSS mapping using differential RNA sequencing  83  identifies a TSS within proW at chr:2806878 (NC_000913.
Strains and plasmids Bacterial strains used in this study were derived from Escherichia coli MG1655 using a two-step genome editing method based on the λ-red recombinase system 119 as described in 120. Chemically competent bacteria were transformed with pKD46 119 , a temperature-sensitive plasmid encoding the λ-red proteins under an arabinose-inducible promoter. Electrocompetent pKD46+ cells were prepared from a culture grown at 30 °C in LB medium (1. 0% bactotryptone (BD), 0. 5% yeast extract (Alfa Aesar), 170 mM NaCl, pH 7. 5) supplemented with 10 mM arabinose, for plasmid maintenance and to induce the expression of the λred proteins, respectively. The cells were transformed with a kanR-ccdB cassette 120 encoding kanamycin resistance and the ccdB toxin under a rhamnose-inducible promoter  119.
The cassette was designed to carry ~1. 5 kb extensions on either side homologous to the flanks of the genomic region to be edited. KanR-ccdB was amplified from plasmid pKD45 119 and the homology regions from genomic DNA. The complete construct was assembled using overlap extension PCR (oePCR). Recombinants were selected for on LB agar (1. 0% bactotryptone (BD), 0. 5% yeast extract (Alfa Aesar), 170 mM NaCl, 1. 5% bacteriological agar (Oxoid), pH 7. 5) supplemented with 40 μg/mL kanamycin at 37 °C and verified using colony PCR and Sanger sequencing (BaseClear B. V. ). The mutant allele construct with ~1. 5 kb homology regions was assembled into a plasmid using Gibson assembly 121. The allele was amplified and used to replace the genomic kanR-ccdB cassette via the λ-red recombinase system. Recombinants were selected for on M9 agar plates (42 mM Na 2 HPO 4 , 22 mM KH 2 PO 4 , 19 mM NH 4 Cl, 8.
RT-qPCR Primer design. Primers for RT-qPCR experiments were designed using the Escherichia coli K-12 MG1655 sequence (Accession number: NC_000913. 3https://www. ncbi. nlm. nih. gov/nuccore/556503834). In silico specificity, screening was performed on SnapGene® Viewer 5. 2. RT-qPCR primers were ordered as dried pellets from Sigma-Aldrich. The oligonucleotides were dissolved in 1X TE pH 8. 0 to a final concentration of 100 μM and stored at 4 °C. The list of primers used for the RT-qPCR assay and corresponding amplicon details are provided in Supplementary Data 1B. Primer annealing sites and amplicon positions in the proVWX operon are provided in Supplementary Data 1A and 1B. The specificity of primer pairs was experimentally determined with Sanger sequencing (BaseClear B. V. ) of the amplified PCR product (Supplementary Data 1B and 2) and with melting curves (Supplementary Fig.
2 ng/μL with 10 mM Tris, pH 8. 0. The libraries were individually pipetted into a 96-well plate for 3C-qPCR. 3C libraries were stored at 4 °C and placed at room temperature during reaction set-up to avoid freeze-thaw cycles. Library stocks were stored at -20 °C. 3C-qPCR  98, 99  Primer and TaqMan probe (hydrolysis probe) design. Primers and TaqMan probes for 3C-qPCR experiments of the proVWX operon were designed using the Escherichia coli K-12 MG1655 sequence (Accession number: NC_000913. 3https://www. ncbi. nlm. nih. gov/nuccore/ 556503834) on SnapGene® Viewer 5. 2. The program was also used for in silico specificity screening. For the fragments of interest for 3C-qPCR test reactions and cross-linking controls, primers and TaqMan probes were designed on opposite DNA strands within 100 bp of the downstream NlaIII site, with TaqMan probes positioned closer to the restriction site than the primers.
) using 1 ng of the 3C libraries, corresponding to ~2 × 10 5 genome equivalents, as the template. A detailed reaction composition is provided in Supplementary Table  14. Experiments were set-up manually in Hard-Shell® 96-well PCR plates (Catalogue number HSP9635, Bio-Rad) and run on a C1000 Touch™ thermal cycler heating block (Catalogue number: 1841100, Bio-Rad) with a CFX96™ Real-time system (Catalogue number: 1845097, Bio-Rad) using the program outlined in Supplementary Table  15. Standard, Test, and No Template Control samples were processed in the same manner. qPCR data analysis RT-and 3C-qPCR data was processed using the Bio-Rad CFX Manager™ Version 3. 1 program (Bio-Rad) and analysed with Microsoft Excel (Microsoft 365). All the raw data files, and the exported. csv files are available as Supplementary material (Supplementary Data 3 and 4 for RT-qPCR, and Supplementary Data 5, 6 and 7 for 3C-qPCR).
Electrophoretic mobility shift assay Purified H-NS was serially diluted in low salt binding buffer (130 mM NaCl, 20 mM Tris, 10% glycerol, 8 mM β-mercaptoethanol, and 3 mM benzamidine, pH 7. 2). The dilutions were mixed with an equivalent volume of 400 nM DRE mut or DRE wt (Supplementary Fig. 4 ; Supplementary Data 1A) in nuclease-free water (Catalogue number: AM9932,ThermoFisher Scientific) and incubated for 20 minutes at 25 °C followed by 10 minutes at 4 °C. The samples were resolved on a polyacrylamide gel (Mini-Protean® TGX™ precast gels, 4-15%, Catalogue number: 4561086, Bio-Rad) at 30 V at 4 °C. Experiments were performed in triplicate. The polyacrylamide gels were stained for 45 minutes in a solution of 10X GelRed (Catalogue number: 41003, Biotium) and thereafter imaged with GelDoc™ XR+ (Catalogue number: 10000076955, Bio-Rad) using Bio-Rad's ImageLab software.
Acknowledgements This research was supported by grants from the  Netherlands Organisation for Scientific Research  [ VICI 016. 160. 613/533  and  OCENW. G-ROOT. 2019. 012 ](RTD) and the  Human Frontier Science Program  ( HFSP ;  RGP0014/2014 ) (RTD, DWH, and DCG). We thank  James Haycocks  for his help in setting up the Chromosome Conformation Capture technique in Article https://doi. org/10. 1038/s41467 -023-43322 -y Nature Communications | (2023) 14:7478.
Data availability All data generated in this study have been deposited in the 4TU Repository (https://doi. org/10. 4121/21065275). Hi-C data are also available from the NCBI GEO repository under accession number GSE214511. The RT-qPCR and 3C-qPCR data generated in this study are also provided in the Supplementary Information files. Source data are provided with this paper. E. coli reference genomes U00096. 2 (https:// www. ebi. ac. uk/ena/browser/view/U00096) and NC_000913. 3 (https:// www. ncbi. nlm. nih. gov/nuccore/556503834) were used in this study. Source data are provided with this paper.
Code availability SnapGene Viewer (RRID:SCR_015053) is a freely available program developed by Dotmatics (Boston, Massachusetts, U. S. A. ) for viewing and annotating sequence files. Bio-Rad CFX Manager™ (RRID:SCR_017251) Version 3. 1 is an experiment setup and data analysis software for all CFX Real-Time PCR Detection Systems (Bio-Rad Laboratories, Inc. , Hercules, California, U. S. A. ).
Bio-inspired algorithm for contact surface morphogenesis A bio-inspired algorithm for contact surface morphogenesis was proposed based on the equivalent biological process (see algorithm 1). This algorithm considers the mechanical equivalents of biological concepts, the normalization, and the dimensionless analysis explained in the previous sections. It was implemented in a computational framework based on the finite element method (FEM). For the implementation, the finite element analysis (FEA) software tool EDF Code Aster was employed. The algorithm has as input the magnitude of the loading F = 100N/mm 2 and the material properties of the pieces, E = 100GPa and ν = 0. 3. The rest of parameters: The ones related to initial geometry, l = 5mm, R u = l, and R l = ∞; and those of the bio-inspired process are treated in section 3.
The themes were defined independently by researchers of different backgrounds (an anthropologist, a psychiatrist, and four surgeons) so that we could compare various perspectives with our own backgrounds and pay systematic attention to our own effects as researchers at each stage of the process  (Malterud, 2001). Consensus was established in meetings attended by two other surgeons to finalize the triangulation. The analysis process was performed using NVIVO software (QSR International, Melbourne, Australia). The Ethics Committee of the French College of Neurosurgery and the Data Protection Authority (CNIL, Commission Nationale de l'Informatique et des Libertés) approved the study (IRB number: IRB00011687), and the trainees interviewed provided their written consent. Our research protocol follows the Consolidated Criteria for Reporting Qualitative Research (COREQ) statement  (Tong et al.
Acknowledgments We would like to thank  Ellie McArthur  for translating the oral quotations of the participants, and Editage for the English language edition of the manuscript. We are very grateful to  Marion Pastor  for the transcription and formatting of the interviews, and to  Jeremy Viallard  for the realization of the figures. We'd like to extend our heartfelt thanks to all the young colleagues who gave up their time for this project.
Data analysis Statistical analyses were performed using R version 4. 1. 1 (R Core Team 2021), with differences considered signi cant at p < 0. 05. All graphs were plotted using the ggplot2 package  (Wickham 2016 ). Signi cant differences were analysed for ne roots (i. e. FRB, FRP, FRT and FRCI) among depths, among distances and between sites, and for hedge leaf litter (LB and LCI) among distances and between sites. The Shapiro-Wilk test was used to verify the normality of data distribution, followed by analysis of variance (ANOVA) and Tukey's HSD test for the analyses.
Acknowledgement The authors thank  Sylvain Busnot ,  Yannick Benard ,  Mikael Faucheux ,  Florian Gaillard ,  Clotilde Blancfene ,  Vincent Stubbe ,  Virginie Parnaudeau  and  Nolwenn Poulaillon  for their assistance in eld sampling. They are grateful to the  AFAC -agroforestry (French Association  for Rural Trees -agroforestry) and the RMQS team ( French national soil monitoring programme ) for the additional data they provided. They are also grateful to the farmers who allowed sampling and monitoring in their elds. This research was funded by  ADEME  (the  French Environment and Energy Management Agency)  and  CASDAR (Special   Allocation Account for Agricultural and   Rural Development)  in the  RESP ' HAIES  project. All authors contributed to the study conception and design, the material preparation and the data collection and analysis.
Acquisition of Mid-Infrared Spectra during Coagulation MIR spectra were recorded by using a Tensor II Series Fourier transform spectrometer (Bruker, Billerica, MA, USA) mounted with a thermostated ATR ZnSe accessory (6 reflections, incident angle 45 • ). Measurement range located between 3800 and 900 cm -1 has been considered in this study at a resolution of 4 cm -1. The spectra acquisition was performed with the OPUS software version 7. 5 (Bruker, Billerica, MA, USA). To improve the signal-to-noise ratio, 32 scans were recorded per spectrum. Before spectral acquisition and according to the manufacturer's reference, 0. 25 µL/mL of commercial rennet (CHY-MAX ® M-Chr. Hansen) was added to the 10 mL of milk mixtures (CaM, CaM3:CM1, CaM1:CM1, CaM1:CM3 and CM (v/v)) previously heated at 40 • C.
After gentle mixing by hand (10 s), milk was immediately deposited on a ZnSe ATR accessory warmed at 40 • C. The temperature was maintained during the coagulation experiment by using a Specac temperature controller series 4000 (Eurolabo, Paris, France). During coagulation, the MIR spectra were recorded on the same sample formulation each 5 min for 115 min (i. e. , giving a total of 24 spectra). Three replicates were performed per formulation. The spectra were subjected to smoothing by the savgol algorithm (polynomial order: 2, sliding: 11-point spectral window)  [36]  and subjected to a Standard Normal Variate (SNV) correction by using the PLS toolbox 8. 5. 2 (Eigenvector Research, Manson, WA, USA) in MATLAB 8. 0. 0. 783 (R2012b) (The MathWorks, Natick, MA, USA).
Two-Dimensional Correlation Spectroscopy The two-dimensional correlation spectroscopy-mid-infrared spectra (2DCOS-MIR) were calculated after treatment of the collections of coagulation time-dependent dynamic spectra using an in-house software program in MATLAB. The synchronous and asynchronous 2DCOS spectra were calculated by the generalized 2DCOS algorithm after considering coagulation time (0 to 115 min) as the external perturbation. This technique provides better resolution by simplifying the spectral data, allowing for more distinct band assignments, and offering the potential to explore the sequential order of the measured intensity changes  [37]. As previously reported by Noda and Ozaki  [37]  and Boukria et al. [38] , the reference spectra were chosen as the average spectrum. The 2DCOS spectral intensities are organized as a function of wavelength variables.
Statistical Analysis The Tukey test was performed to investigate significant difference (p < 0. 05) between means of the physicochemical properties on the one hand, and on the other, of the textural properties of the five milk formulations (CaM, CaM3:CM1, CaM1:CM1, CaM1:CM3, and CM (v/v)) using SPSS Statistics 26. 0. 0 (SPSS Armonk, NY: IBM Corp. ) and Microsoft ® Office Excel 2013 (Microsoft Corporation, Santa Rosa, CA, USA). The mean difference between auto-peak spectra intensity identified on the 2DCOS synchronous maps of milk formulations was statistically evaluated by one-way analysis of variance (ANOVA) through LSD test (p < 0. 05) using Microsoft ® Office Excel 2013 (Microsoft Corporation, Santa Rosa, CA, USA).
Partial Least Square Discriminant Analysis PLS-DA is a supervised classification method. The objective of the method is to separate groups of individuals as best as possible. Its fundamental principle is to create new variables Y, of dimension n × k, formed by the indicators of the groups where n and k represent the number of individuals and groups, respectively. For each MIR wavelength range cited above (1 and 2), the 2DCOS spectra calculated on the five milk formulations (CaM, CaM3:CM1, CaM1:CM1, CaM1:CM3, and CM (v/v)) were concatenated to build a new 3D-2DCOS data cube. This data cube was then analyzed by PLS-DA after unfolding. Before performing PLS-DA, data were split into two data sets. The data recorded during the year 2019 (24 spectra × 5 milk mixtures × 3 repetitions) was used for calibration and cross-validation steps (venetian blinds, number of data splits: 5) and the samples analyzed in the year 2021 (24 spectra × 5 milk mixtures × 3 repetitions) were used for external validation.
Statistical analysis Descriptive statistics were expressed as median and range or mean ± standard error of the mean (SEM), and performed using GraphPad Prism 9. 0 (GraphPad Software, CA, USA). Inter-and intra-rater reliabilities were evaluated by comparing the scores between the groups and at 2 separate time points (test-retest) respectively, using the 2-way random for inter-rater (or 2-way mixed for intra-rater), absolute agreement, single measures intraclass correlation coefficient (ICC). The following guidelines were used for ICC interpretation: < 0. 4 was considered poor, 0. 4-0. 59 fair, 0. 6-0. 74 good and ≥ 0. 75 excellent  (15).
Available resources Here, a summary overview of main references and suggestions for practical tools is provided. Reference review papers on cyclostratigraphy and astrochronology are:  Strasser et al. , 2006; Hinnov, 2013; 2018; Meyers, 2019; Sinnesael et al. , 2019; Laskar 2020. Laskar (2020)  in particular gives an overview from the theoretical perspective of the astronomical solutions. Weedon (2003)  is a timeseries analysis and cyclostratigraphy handbook introducing many key concepts in an accessible way. The 'www. cyclostratigraphy. org' website is designed to be an educational online platform providing cyclostratigraphy training by experts for the broader stratigraphic community, and hosts a cyclostratigraphy figure repository, Cyclo-podcast and newsletter. Often used software packages for spectral and time-series analyses are 'ACycle'  (Li et al.
Acknowledgements Matthias Sinnesael thanks  Thijs R. A. Vandenbroucke ,  Phillipe Claeys  and numerous colleagues for supporting his work on Ordovician cyclostratigraphy and astrochronology. Editor  David Harper , reviewer  Graham Weedon  and one anonymous reviewer are thanked for constructive comments. This work contributes to International Geoscience Programme projects IGCP 652 (Reading geologic time in Paleozoic sedimentary rocks) and  IGCP 7353 (Rocks and the Rise of Ordovician Life).