dataesr/scientific-paragraphs-categorization huggingface dataset:
Our initial prediction focused on whether the time-scales at which the reproductive benefits of dominance accrue depend on how individuals achieve high rank. However, we realized that there was no straightforward way to assess this prediction. The species in our dataset have vastly different lifespans and associated inter-birth intervals, so the time-scale needs to be considered on a relative rather than an absolute scale. The values for the relative duration of a study (number of years studied divided by the maximum lifespan of the species) show that 90% of effect sizes are from studies that lasted less than 10% of the lifespan of the species (median 3%). In all of the 19 species in which studies spanned more than 10% of the lifespan, females acquire rank by nepotism. We did not find any consistent pattern of relationship between effect size and study duration dependent on the system of dominance acquisition.
Discussion Our results provide support for three of our four pre-registered objectives. First, we find that in social mammals, dominant females have higher reproductive success than lower-ranking females. While there appears to be a publication bias in the dataset we put together, the overall positive effect of higher rank on reproductive success is strong, thus unlikely to result only from such bias, and instead reflects a genuine biological phenomenon. Second, positive effects of dominance rank are present across all life history measures and among plural breeders, where data for all measures of reproductive success exist, are highest for life-time reproductive success. This suggests that even if dominants might face some trade-offs (e. g. higher stress levels  Cavigelli et al. (2003) ), obtaining a high ranking position in a social group generally leads to fitness benefits, though how females obtain these benefits (e.
Figure1. Phylogenetic distribution of the effect sizes in our dataset. Most effect sizes came from studies of primates (green: 254 effect sizes from 35 different species), followed by ungulates (blue: 74 effect sizes from 21 different species), rodents (yellow: 63 effect sizes from 17 species), and carnivores (purple: 51 effect sizes from 12 species), plus a single effect size each from hyraxes (red) and marsupials (aqua). Effect sizes (averaged when multiple values exist for a given species) vary even among closely related species, though there are slight differences among Orders (e. g. carnivores generally have high effect sizes, for more details see below).
Acknowledgements We thank our  PCI Ecology Recommender ,  Matthieu Paquet , and our reviewers,  Bonaventura Majolo  and two anonymous reviewers, for their valuable feedback both on our preregistration and the manuscript, that greatly improved this piece of research. We are grateful to the members of the  Department of Human Behavior, Ecology and Culture  at the  Max Planck Institute for Evolutionary Anthropology  for feedback during the early stages of this project. This article is the contribution n°ISEM 2022-180 SUD. A preprint version of this article has been peer-reviewed and recommended by  Peer Community In Ecology  (https://doi. org/10. 24072/pci. ecology. 100101).
Smears were analyzed microscopically after Papanicolaou, May-Grünewald Giemsa, Ziehl, Grocott, and Perls staining by one experienced pathologist blinded to the patient treatments. Cell count in BAL fluid (BALF) was expressed as percentages of the total calculated on a 300-cell sample. Tracheal aspirates were sampled every 24 or 48 h to detect bacterial infection. Within 24 h of BAL, peripheral white blood cells counts and CD3+, CD4+, CD8+, CD19+, CD16+, and CD56+ lymphocyte subsets were quantified using FACS-Canto™ flow cytometry (Becton Dickinson, Erembodegem, Belgium). Clinical and routine biological data were collected from the patients' records. Results are presented as median [percentiles 25th-75th] for the quantitative parameters and percentages for categorical variables. Data were compared using Mann-Whitney and Fischer's exact tests, as appropriate.
Still, salinity measurements conducted in surface waters at the beginning of our study showed contrasted salinity between the two selected fringe and riverine sites at low tide (Online Resource 1). French Guiana coast is mesotidal with semi-diurnal tides  (Ray et al. 2020). Litterbags were therefore submerged twice a day during our assay, where tide elevation ranged from 1. 11 to 3. 04 m above hydrographic reference for Sinnamary and Kourou rivers and from 0. 92 m and 3. 06 m for Mahury. These data were collected from the Service Hydrographique et Oceanique de la Marine for the Iles du Salut harbor which was closest to the corresponding Sinnamary and Kourou study sites and the Degrad de Cannes harbor for Mahury sites (SHOM: www. shom. fr). Experimental sites map figure was obtained using QGIS Geographic Information System software (QGIS Association, QGIS.
Statistical analyses To analyze the effects of distance from the sea (i. e. , fringe (F) or riverine (R) mangrove) on initial t 0 leaves C and N contents, LA, physiological indices and catabolic indices of epiphytic microbes, linear-mixed-effect models (LMMs) (R package "lme4") were applied including the type of mangroves as fixed factor and the river as random factor. When necessary, data were transformed using the "best-Normalize" package  (Peterson and Cavanaugh 2020)  to meet the assumptions of normality and homoscedasticity of variances. Differences were tested using generalized linearmixed-effect models (GLMMs) with binomial distribution (lme4 package) for C:N ratio since transformation did not allow normality and homoscedasticity.
The same approach was used to test the effects of litter transplants (i. e. , RR, RF, FF, and FR) and decomposition time (i. e. , 30 and 45 days) on t 1 and t 2 leaf litter C and N contents, EEAs, microbial catabolic diversity indices, and PLFA biomarker abundances while AFDM remaining, total PLFA abundance, and total bacterial PLFA abundance differences where tested using GLMMs since transformation did not allow normality and homoscedasticity. All implemented LMMs and GLMMs are shown in Online Resource 3 for each variable. In the case of a significant litter transplant effect, a Tukey HSD post hoc test was used to test which types of transplants are different from others. The used R scripts are shown in Online Resource 4 with EEAs (Online Resource 5) and AFDM remaining (Online Resource 6) datasets as an example.
Acknowledgements We are grateful to the  Ecologie, Evolution, et Interactions des Systèmes amazoniens laboratory (USR LEEISA, Cayenne)  and to the  Ecologie des Forêts de Guyane laboratory (UMR EcoFoG, Cayenne) , in particular to  Antoine Gardel ,  Yann Rousseau  and  Christophe Duplais  for making their facilities available during our missions in French Guiana. We are also grateful to the  Common Services of Biological and Chemical Analysis and of Chemical Ecology and Metabolomics (Mediterranean Institute of marine and terrestrial Biodiversity, IMBE, Marseille ) technical facilities for producing a part of the data used in this study. We thank all members of the  DFME team from IMBE, Marseille.
As the high-pressure high-temperature synthesis has become a well established technique for materials discovery, extending investigations to the TPa regime has long been desired. Here we report a methodology for high-pressure high-temperature synthesis experiments that extends the limits of high-pressure crystallography to the terapascal range. To achieve the desired pressures, we combined toroidal  7, 8  and double-stage  3, 17, 18  anvil designs. A rheniumnitrogen alloy and rhenium nitride Re 7 N 3 were synthesized in three different experiments in the Re-N system (Supplementary Table  1 ) in a laser-heated dsDAC. Their full structural and chemical characterization was performed in situ using single-crystal XRD. The dsDACs were prepared following the procedure outlined below. Conventional Boehler-Almax-type single-bevelled diamond anvils with 40-μm culets were milled by focused ion beam (FIB) in order to produce a toroidal profile on the surface of the culet and to shape a miniature culet of about 10 μm in diameter in its centre (Extended Data Fig.
5 ), indicating phase transformation(s) and/or chemical reaction(s) in the samples. However, interpreting the powder diffraction data turned out to be impossible, as the patterns were dominated by the diffraction lines from the gasket and untransformed Re, owing to the relatively large X-ray beam and a small sample size. Single-crystal diffraction data were of poor quality that precluded their analysis. The dsDACs with temperature-quenched material were transported to ID11 at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) and investigated using both powder and single-crystal XRD (see Methods). Despite the nominally small size of the X-ray beam, the reflections from the gasket were present even in the patterns collected from the centre of the sample chamber. Two-dimensional (2D) diffraction maps of still XRD images revealed powder diffraction of the Re gasket and untransformed material that enabled the analysis of the pressure distribution both within and around the sample (Extended Data Fig.
2 ). In dsDAC #1, for example, pressure at the sample/gasket boundary did not exceed approximately 160 GPa, and pressure at all points within the sample chamber was almost the same, of about 900 GPa (Extended Data Fig. 2 ). Our observations regarding the pressure distribution (Extended Data Fig. 3 ) in the sample chamber are consistent with those previously reported for toroidal-type anvils  7, 8  and give the pressure magnification factor (the ratio of the pressures on the primary and secondary anvils) of about 6, in accordance with previous publications on ds-DACs  17, 28. Apart from powder diffraction rings, the diffraction patterns collected at ID11 from certain locations in the sample area show numerous spots (Fig. 1 ). At these positions we collected single-crystal datasets upon rotation of the DAC around the ω axis from -38° to 38° with an angular step of 0.
2 ). Three prisms are connected through shared edges forming triads, which are stacked along the 6 3 axis. Each triad is rotated by 60° with regard to upper and lower neighbours in the columns (Fig. 2 ). The columns are connected to each other by the common vertices of the prisms. Crystal structures built of combined triads of prisms are well known among carbides, borides, phosphides and nitrides  29. Moreover, there are a number of binary compounds with the A 7 X 3 stoichiometry (A and X are different chemical elements), and especially hexagonal ones with Th 7 Fe 3 -type structure (more than 70 entries in the ICSD database)  30  , the same as that of the Re 7 N 3 compound. We noticed that in Re 7 N 3 , the shortest and average distances between the Re-Re nearest neighbours (approximately 2.
Methods Diffraction data were acquired at ID11 beamline at ESRF. Experiments with dsDAC #1 were performed using a Frelon 4M detector, wavelength 0. 3099 Å, beam size 0. 45 × 0. 45 μm 2 at FWHM; data for dsDAC #2 and dsDAC #3 were collected with Eiger2 CdTe 4M detector, wavelength 0. 2882 Å, beam size 0. 5 × 0. 5 μm 2 at FWHM. 2D mappings of still XRD images (without ω oscillations) were performed with an exposure time up to 10 s; single-crystal datasets were collected via DACs rotation around the ω axis from -38° to 38° with an angular step of 0. 5° and an acquisition time of 10 s per step. For the powder diffraction studies, calibration of instrument model and integration of diffraction patterns were made in the DIOPTAS  35  software using CeO 2 powder standard (NIST SRM 674b). Integrated patterns from powder XRD experiments were processed using the Le Bail technique implemented in JANA2006  36  software.
XRD imaging of the sample chamber was reconstructed using XDI  37  programme and map of still images converted from 'edf' to 'tif' format. For the single-crystal XRD, integration of the reflection intensities and absorption corrections were performed in CrysAlisPro software  38. A single crystal of orthoenstatite (Mg 1. 93 ,Fe 0. 06 )(Si 1. 93 ,Al 0. 06 )O 6 (space group Pbca, a = 8. 8117(2) Å, b = 5. 18320(10) Å, c = 18. 2391(3) Å) was used as calibration standard for refinement of the instrument model of the diffractometer. Diffraction images were converted from 'edf' to the native CrysAlisPro format 'ESPERANTO' with Freac software  38. Detailed information of integration parameters as well as of the data-reduction output files and indicators of the XRD data quality are given in ref. 19.
The crystal structures were solved using SHELXT or the superflip method in JANA2006 and Olex2  36, 39, 40. Crystal structures were refined by least-squares minimization of adjustable parameters. We performed isotropic refinement of atomic displacement parameters due to limited dataset collected in DAC. Reflections coming from parasite diffraction produced by diamonds and crystallized pressure media were eliminated during the refinement procedure. The software Diamond  41  was used for visualization of molecular graphics. The electronic structure, total energy and forces calculations of the studied rhenium nitrides were carried out in the framework of density functional theory (see Supplementary Information section 'Computational details'). We used supercells of different sizes with an underlying fcc crystal structure and various amounts of either N or C to simulate the Re-N and Re-C cubic phases with NaCl (B1)-type structure (see Supplementary Information section 'Re-based solution phase').
Acknowledgements We thank  S. Petitgirard  ( ETH Zürich, Zurich, Switzerland ) for help in the FIB preparation of samples. We acknowledge  A. Kurnosov ,  D. Wiesner ,  S. Übelhack  and  S. Linhardt  for technical assistance. D. L. thanks the  Alexander von Humboldt Foundation and Article Department of Energy (DOE) Office of Science User Facility  operated for the  DOE Office of Science by Argonne National Laboratory  under contract no. DE-AC02-06CH11357. Theoretical analysis of chemical bonding was supported by the  Russian Science Foundation  (project no. 18-12-00492 ). Support from the  Knut and Alice Wallenberg Foundation  ( Wallenberg Scholar  grant no. KAW-2018. 0194 ),the  Swedish Government Strategic Research Areas in Materials Science on Functional Materials at Linköping University  (Faculty Grant  SFO-Mat-LiU no.
1. 53 k, see electronic supplementary material, figure  S2  for definition of measurements). All statistical analysis was performed in R (v. 4. 0. 3). ANOVAs, t-tests, Pearson's χ 2 and generalized linear models were performed within the R set of core functions (stats 4. 0. 3). All code and data are available in the electronic supplementary material. The estimation of pairwise sequence identity of the inr genes coding sequences was done with Muscle (v. 3. 8. 425 (alignment in Geneious (v. 2021. 1. 1) using standard parameters.
Data accessibility. The data used in this manuscript can be found in the file named 'Data_file_Gudmunds_etal_20211221. xslx'. To analyse these data, the R-script 'R_code_Gudmunds_etal_20211221. R' can be used. Available from the Dryad Digital Repository: https://doi. org/10. 5061/dryad. zs7h44jbz [40]. The data are provided in the electronic supplementary material  [41]. Authors' contributions.
Acknowledgements. We are grateful to  Kevin Nielsen  who helped with the shifting experiment and to  Mattias Vass  for help with water strider maintenance. We are grateful to  David Armisen  and  Jesper Boman  for comments on the manuscript and  Severine Viala  for sharing initial density data. We also thank  John Spence ,  Chang Han , the associate editor and one anonymous reviewer for comments that greatly improved the manuscript.
The first step of the process is the definition of the purpose and scope of the TPS. The second step is the definition of the weighted criteria and associated target values, to facilitate the selection of the tests to be included in the TPS. The use of weighted criteria allows an impartial evaluation of the validation data available. Once the criteria have been defined, it is possible to proceed with a comprehensive analysis of the validation data available. When validation data are lacking, tests may be selected for preliminary validation studies, which are conducted in the laboratory of the TPS organiser by authorised personnel supervised by the person responsible for the TPS organisation. After completion of the preliminary studies, the organiser analyses the results and selects the tests to be included in the TPS based on the previously defined criteria.
Collection of Available Validation Data After these 'rules' for the selection of the tests have been decided upon, the validation data should be collected to support the selection of the tests. Available In many cases the validation data for tests are not comparable (e. g. , different sample types, units, volumes), and sometimes crucial information is missing or is not available (e. g. , sample preparation and concentration). It is important to also evaluate the reported information about the number of tested targets and non-targets and the controls performed, and to compare these between the different tests available. In all of these cases, the expertise of the TPS organiser is invaluable to be able to judge the results reported and the other relevant information. The biggest designated database of validation data for plant pests is the EPPO database on diagnostic expertise (available at: https://dc.
eppo. int/), which contains a significant number of validation datasheets for pests that are considered important in the EPPO region. Laboratories are invited to submit their validation data to this database to help other laboratories when selecting tests, and to contribute to the better diagnostics of certain pests. In addition, the availability of the data can prevent duplication of work across different laboratories, so other laboratories can focus on the pests or tests for which there are no validation data available. Other more specialised databases where validation data can be found are the database of the ISHI-VEG validation reports of the International Seed Federation (available at: https://www. worldseed. org/our-work/phytosanitary-matters/seed-health/ishi-vegvalidation-reports/) and the database of the International Seed Testing Association (ISTA) (available at: https://www.
2021 ; EPDIA Quality Charter available at https://www. epdia. eu). The EPDIA database can be searched according to different parameters, such as pests, methods and tests. The EPDIA database contains basic information on the kits (tests), and also validation data sheets provided by the manufacturers and validation data sheets about the availability of their kits in the EPPO database for diagnostic expertise. The database of the EPDIA is available at: https://pestdiagnosticdatabase. eu/. As mentioned above, for some pests there are a huge number of tests available, including those from commercial providers and from scientific publications. Therefore, the collection of validation data is a time-consuming process that should be planned in advance. For example, for the TPS that was organised for the detection and identification of TSWV, collection of the available validation data took 3 months.
TSWV is in the second place on the list of the top 10 economically most important plant viruses  (Scholthof et al. 2011; Rybicki 2015) , and has a wide host range of >1000 plant species (which include some important vegetables, such as tomato and pepper, and a variety of ornamental plants). This virus has been in the spotlight of diagnosticians and researchers worldwide. Therefore, it was expected that there would be numerous tests available for its detection and identification. After a thorough search through all of the available resources, a total of 76 tests was found, and all available validation data for these were collected. This process included searching the websites of commercial providers, communicating with them to clarify missing data, analysing the available validation data from databases, and collection of the available research articles in which detection of TSWV was included.
Definition of a List of Tests Subjected to Preliminary Studies There are numerous sources available that can be used to collect tests for any particular pest (see Sect. 3. 2. 3). Data from all of the available tests should be collected systematically according to the criteria presented in Table  3. 2, and their performance should be judged based on those predefined weighted criteria. For this step, the experience and critical judgement of the TPS organiser is crucial to define the tests for preliminary studies. Where there are not enough data collected to make an informed decision on test selection, the TPS organiser can use additional available resources to better define the performance criteria of some tests; e. g. , for PCR-based tests, in-silico analysis can be carried out to check the specificity of the primers and probes, to make an informed decision on test selection.
2016). The molecular tests such as RT-PCR and real-time RT-PCR were developed based on amplification of different genomic parts. Molecular tests are usually more sensitive compared to biological and serological tests; however, they can also cross-react with other orthotospovirus species or they do not detect all TSWV isolates. Consequently, the main challenge for the detection and identification of TSWV was the selection of the appropriate method and test. The process and reasoning for the test selection for the TPS on TSWV was the following. The ELISA method was taken into consideration because it is widely used and 13 tests were evaluated. Some of these tests were excluded because the commercial provider had stopped production of the test or was in the process of changing the antisera, or because the TPS organiser could not obtain the required information on the validation data despite direct communication with the company.
In addition, IC-RT-PCR is not widely used in diagnostic laboratories in the EU (i. e. , there were no EU research publications, and this was not included in the EPPO and IPPC diagnostic protocols for TSWV detection). From the five available TaqMan real-time RT-PCRs, four were selected for the preliminary studies based on the availability of validation data and based on the results of in-silico analysis (Table  3. 3). One commercial TaqMan real-time RT-PCR test was not selected for the preliminary studies because the protocol was available in Russian only. In the TPS on TSWV, the validation data collected for the tests varied across companies and publications. For some tests, extensive validation data were available, for others, there were little or none. Therefore, comparisons of the different tests based on the available validation data was very difficult.
Evaluation of the Tests Selected for the Preliminary Studies The tests selected for the preliminary studies are evaluated internally by the TPS organiser, to provide missing validation data for the selection of the final tests to include in the TPS, and to identify any difficulties for the TPS organisation. The number of samples included in the preliminary studies can be different than those for the TPS, based on resources, availability of isolates/strain/populations, and the diagnostic parameters for which data are required. Therefore, performance characteristics, such as, inclusivity, exclusivity and selectivity, which usually require many samples to be prepared, can be determined in preliminary studies based on a panel of different isolates/strains/populations of the target organism, with non-target pests that might cross-react with the target organism, and if appropriate with healthy plant samples (i.