dataesr/scientific-paragraphs-categorization huggingface dataset:
This limitation is the direct consequence of the lack of underpinning long-term datasets. This deficiency restricts our understanding of processes overarching several decades, such as climate change, the temporal patterns of exotic invasions, or continuous anthropogenic pressure, and likely prevents timely action to mitigate them  (Poisot et al. 2015 , Tulloch et al. 2016). Moreover, species co-occurrence networks may also depend on the seasonal dynamics of species of which we have little information. In this study, we did not focus on differences resulting from taxonomical or functional grouping but these, most likely, exist. Whereas this approach would plausibly be a fruitful area of research, a complete dataset of traits is crucial and, besides taxonomy, a phylogenetic tree would also be desirable.
Funding statement This work was funded by a  Research Program Contract for the Center for Ecology, Evolution and Environmental Changes  ( cE3c ), through programmatic funding with a contract to GP ( FCT-UIDP/00329/2020 ) and research pluriannual funds for cE3c ( FCT-UIDB/00329/2020 ). MB was supported by contract  DL57/2016/CP1375/CT0001.
For example, infection may alter hosts' behaviour in ways that make them more or less easily bitten by mosquitoes  [19, 37]. In the present study, we compared the number of mosquito bites received by uninfected and Plasmodium-infected birds in semi-natural conditions, using experimental infections allowing for testing during the acute and the chronic phases. For this experiment, we used Plasmodium relictum, the most common avian malaria parasite in our study population  [38, 39]  and in most parts of Europe (MalAvi database;  [40] ), and its natural vector Culex pipiens.
Genotyping Amplified fragments were separated by capillary electrophoresis using a 3100 Genetic Analyzer ® (Applied Biosystems). Genotypes were evaluated on the GeneMapper ® software v. 4. Samples with more than two alleles in at least one of the markers, which could be caused by mixed blood meals (mosquito feeding on two or more birds) or contamination during lab procedures, were discarded (68/786 mosquitoes). Identity analyses were performed with Cervus© software v. 3. 0. 7  [45] , with the minimum number of matching loci set at four and two fuzzy matches allowed. We identified 687 blood meals over the 786 tested mosquitoes.
), suggesting that our models accounted for key ecological gradients influencing coral competitive performances in our study system. Restricting data to the most abundant taxa resulted in similar patterns (electronic supplementary material, figures S5 and S6), confirming the prevalence of the identified mechanisms among dominant species. A total of 1073 competitive interactions were recorded encompassing 41 taxa and eight morphotypes (electronic supplementary material, table  S1 )  [35]. All surveys were performed by the same observer using SCUBA, occasionally assisted by another diver. Analyses and graphing were coded in R statistical software complemented by the mgcv package  [45]  (electronic supplementary material, appendix S2). Over-dispersed variables were log-transformed, and model diagnostics were performed by checking the assumptions of residual normality and homoscedasticity.
The mass spectrometer was operated in data dependent acquisition mode. Full MS scans were captured in the Orbitrap (scan range 400-1500 m/z) with a resolution of 120,000. Dynamic exclusion was set at 10 ppm with a duration of 80 s, and the intensity threshold was fixed at 5 × 10 4. MS2 was performed using High Collision Dissociation (HCD) in the Orbitrap at a resolution of 30,000. Polysilaxolane ions m/z 445. 12002, 519. 13882, 593. 15761, and 667. 1764 were used for internal calibration. Protein identification was performed using X!TandemPipeline C + + 0. 4. 17  10  and the Bos taurus UniProtKB database (version 2019, 46,697 entries). Data filtering was achieved according to a peptide E-value < 0. 01, protein log (E-value) < -4 and a minimum of two identified peptides per protein. The peptide and protein False Discovery Rates (FDR) were estimated at 0.
Statistical analyses. Statistical analyses were performed using R software v4. 0. 2 (R Core Team, 2020, http:// www. R-proje ct. org) with the lme4 package version 1. 1-23. Analyses of variance of the major milk protein data were performed using a mixed model that included day, diet and their interaction as fixed effects, and the cow as a random effect. The restriction effect was calculated by comparison with pre-restriction values except for RP-HPLC analysis on M trial, where pre-restriction values were used as co-factors and feed restriction effects were calculated by comparison with the control group. A trial effect was analyzed for pre-restriction data using a linear model. Analyses of variance of the proteomic data were performed using a mixed model that included diet as a fixed effect and the cow as a random effect.
Feed restriction effects were calculated by comparison with pre-restriction values. The threshold for statistical significance was set at P < 0. 05 and trend-level significance was defined as 0. 05 ≤ P < 0. 10. Moreover, for statistical analysis of proteomic data, proteins showing numbers of spectra lower than 5 in all the samples or fold change above or below 1. 5 were removed. Exploration of in silico metabolic pathways. Enrichment analyses were carried out using the PAN-THER overrepresentation test  13  with the GO ontology database (https:// doi. org/ 10. 5281/ zenodo. 52288 28; Released 2021-08-18). The Bos taurus database (22,798 proteins) was used as the reference list and Fisher's test was performed with a false discovery rate (FDR) cut-off point set at 0. 05. Hierarchy sorting was used to identify families of gene ontology (GO) terms.
5 ). All 232 proteins were found in H milk samples, 50 of them were only found during the feed restriction and two of them were only found before the feed restriction period. 194 proteins were found during M trial, 26 of them were only found during feed the restriction and 2 before the feed restriction period (Fig. 5 ). The differences of milk protein abundances led to a good discrimination between feed conditions for H trial whereas individual variations had more influence during M trial (Fig. 6 ). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD033969  15. In the M trial, statistical analyses led to the identification of eight proteins whose abundance varied significantly during feed restriction (P < 0.
The abundance of 39 proteins decreased and that of 77 increased during feed restriction. Seven of the eight differentially abundant proteins in the restriction period of the M trial were in common with the differentially abundant proteins found during the restriction period of the H trial. The one that was exclusive of H trial during restriction was a fragment of β-LG D, a rare genetic variant. Biological processes affected by feed restriction. Gene Ontology (GO) analyses were only performed on data from the H trial because too few proteins varied under feed restriction during the M trial to perform a relevant GO analysis. The GO analyses of the H trial showed that the major cellular processes affected by feed restriction were related to carbohydrate, protein and lipid metabolisms as well as immune system processes (Table  2 ).
Acknowledgements The authors are very grateful to the staff at the  Herbipôle (INRAE ,  UE1414 ,  Marcenat, France)  and  IEPL (INRAE, UMR PEGASE ,  Le Rheu , France) experimental farms for animal care and sampling. Yannick Faulconnier  ( INRAE ,  UE 1213 , France) is thanked for the collection of milk samples, and  Céline Henry  ( Micalis Institute, PAPPSO, France ) for her assistance with understanding and describing the  LC-MS/MS  method as well as  Lucile Hervé  ( INRAE, UMR PEGASE, France ) for her contribution in conducting the M trial.
| Study population We used data from a multicenter, multinational prospective diagnostic management outcome study. We screened outpatient pregnant women presenting at one of the participating centers with a clinical suspicion of PE, as defined as acute onset of new or worsening shortness of breath or chest pain without another obvious cause. Exclusion criteria were: age below 18 years, allergy to iodinated contrast agent, impaired renal function (defined by a creatinine clearance below 30 ml/min as per the Cockcroft-Gault formula), diagnosis made prior to presentation, indication for or already on full dose anticoagulation, and inaccessibility for follow-up. The study was performed in two countries (France and Switzerland) and 11 centers actively included patients. The study was approved by the ethics committee according to legislation at each study site.
| Study analysis Although neonatal screening was performed in both countries, results were not systematically collected in the French participating centers, so this analysis is restricted to babies born from women included in the Swiss participating centers. Results of Guthrie tests were obtained at follow-up or when data were not available at follow-up, through the National Central Swiss Laboratory (Zürich, Switzerland). Results are provided as negative when the TSH measurements were below 15 U/ml. The actual TSH value is given in case of abnormal results. Women using medications that could have an influence on the babies' thyroid function (levothyroxine, amiodarone) were excluded. The analysis was performed using babies as a unit. We estimated the proportion of newborns with an abnormal TSH result using exact proportions along with the 95% confidence interval (CI).
High-frequency outputs have also been saved over the last 50 years of the simulation for the analyses of extreme events and to provide the boundary conditions for future regional simulations. This reference simulation is called CMIP6. PMIP. IPSL. IPSL-CM6A-LR. lig127k. r1i1p1f1 in the ESGF database. Because of the combined effects of eccentricity and precession changes, the length of seasons relative to the insolation forcing is different between the LIG and the PI periods. However, both simulations use a fixed present-day calendar to compute online monthly averages, which is aligned with our current definition of seasons in terms of number of days for each month. As a consequence, this adds artificial biases in the analysis due to phase lag in the seasonal cycle, especially in boreal autumn  (Joussaume and Braconnot, 1997; Timm et al.
To evaluate the ability of IPSL-CM6A-LR to simulate the Last Interglacial climate, we compare the simulated surface temperature changes with the new data synthesis provided by  Otto-Bliesner et al. (2021). We use temperature reconstructions representing annual or summer surface conditions (Fig. 2 ). Marine proxies generally display more heterogeneous LIG-PI changes than model outputs. In summer, the IPSL-CM6A-LR model simulates the surface warming well, but it does not reproduce local cooling in the Labrador and Norwegian seas. This mismatch appears to be a general feature across CMIP5  (Lunt et al. , 2013; Masson-Delmotte et al. , 2013)  and CMIP6  (Otto-Bliesner et al. , 2021)  models. This has been attributed to uncertainties or simplifications in the specified boundary conditions. Indeed, the PMIP4-CMIP6 protocol consists of setting the ice sheets to their modern configuration and neglects the freshwater inputs to the North Atlantic from ice melting in the LIG simulation.
We choose the same sign convention for all fluxes; i. e. positive fluxes point downward. They act to warm the surface when they are positive except for F BOT , which cools the sea ice when positive. Ocean, atmosphere and sea ice transport is computed as the residual of the surface heat fluxes, the bottom heat flux and the heat storage term. From Eqs. (3), (  8 ) and (10), we can write AHT = AHS + F SFC -F TOA (11) OHT = OHS -F SFC × f oce + F BOT (12) IHT = IHS -F SFC × f ice -F BOT. ( 13 ) These equations give coherent zonally averaged profiles for the PI simulation with a zero northward atmospheric and oceanic heat transport at the North Pole (Fig. 4 ). To validate this approach, we also compared the mean annual OHT computed as a residual with the OHT computed online by the model (AHT and IHT are not stored in the CMIP6 database).
However, while the distribution of liquid droplets and ice crystals in cold mixed phase clouds is closer to observations, low-level clouds remain too abundant over high-latitude regions. The increase in low-level clouds seems to be compensated for by the decrease in the mid-to high-level clouds and finally does not impact the LW CRE. As shown in  Kageyama et al. (2021) , while the insolation received at the top of the atmosphere is similar for all models following the PMIP4 lig127k protocol, the amplitude of the anomaly of the annual cycle of the downwelling shortwave radiation varies across PMIP4 models. The atmospheric energy budget can be analysed only for eight models (out of the initial 17 models) for which data were available. Even with this reduced dataset, the diversity of responses suggests that cloud feedback is not consistent in these climate models.
, 2021). In winter, model and observations are in better agreement except for two sites in the Labrador Sea. At these locations, the model shows seasonal or perennial sea ice, while marine sediment cores provide evidence of ice-free conditions all year round  (Kageyama et al. , 2021). On the basis of a simple linear regression model, we try to identify the relationship between surface temperature biases in the historical and the lig127k simulations. The aim is to determine if the model biases found in  Boucher et al. (2020)  are correlated with those of the lig127k simulation. Surface temperature biases are analysed at the core site location (Fig. 2 ). As in  Boucher et al. (2020) , near-surface air temperatures simulated by the historical simulation are compared with ERA-Interim dataset for the period 1980-2009  (Dee et al.
, 2011)  and sea surface temperature with WOA13-v2 dataset for the period  1975 -2004 (Locarnini et al. , 2013)). For the annual average, the lack of data points limits the in-Clim. Past, 18, 607-629, 2022  https://doi. org/10. 5194/cp-18-607-2022 terpretation of the linear regression and we cannot conclude on the impact of the model biases in the lig127k simulation (Fig. 18 ). For the summer average, the correlation coefficient is low (r 2 = 0. 18), which indicates that the model biases have only a limited influence on the lig127k. This result depends largely on the uncertainties of the reconstructions, which can be very large for some points. The uncertainty associated with the surface temperature biases during the Last Interglacial is plotted in Fig. 2. It is estimated from the data uncertainty (±1σ ) and the standard deviation of the model outputs computed following a Gaussian distribution.
However, accounting for the evolution of the Greenland ice sheet was not included in the PMIP4-CMIP6 protocol of the lig127k simulation followed here. Investigating the energy budget of other PMIP4-CMIP6 lig127k simulations would allow to evaluate whether their temperature response to lig127k forcings is related to the same processes in terms of energy budget and to compare the strengths of these processes, especially in models which simulate a near-complete loss of Arctic sea ice in summer  (Kageyama et al. , 2021). just" monthly model outputs that were used to draw the figures in this paper are also available for download online at https://doi. org/10. 5281/zenodo. 5777277 (Sicard et al. , 2021). Author contributions. MS, MK and SC designed the study. PB performed the lig127k simulation.
Competing interests. The contact author has declared that neither they nor their co-authors have any competing interests. Disclaimer. Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Special issue statement. This article is part of the special issue "Paleoclimate Modelling Intercomparison Project phase 4 (PMIP4) (CP/GMD inter-journal SI)". It is not associated with a conference. Acknowledgements. This work was granted access to the HPC resources of IDRIS under allocations 2016-A0030107732, 2017-R0040110492 and 2018-R0040110492 (project gencmip6) made by GENCI (Grand Equipment National de Calcul Intensif). It also benefited from the ESPRI (Ensemble de Services Pour la Recherche à l'IPSL) computing and data centre (https://mesocentre.
Marie Sicard is funded by a scholarship from the Commissariat à l'énergie atomatique et aux énergies alternatives (CEA) and the Convention des Services Climatiques from IPSL. Masa Kageyama is supported by the Centre national de la recherche scientifique (CNRS). Sylvie Charbit and Pascale Braconnot are supported by the CEA. Jean-Baptiste Madeleine is supported by Sorbonne Université (SU).
Financial support. support Marie Sicard is funded by a scholarship from the Commissariat à l'énergie atomatique et aux énergies alternatives (CEA) and the Convention des Services Climatiques from IPSL. Masa Kageyama is supported by the Centre national de la recherche scientifique (CNRS). Sylvie Charbit and Pascale Braconnot are supported by the CEA. Jean-Baptiste Madeleine is supported by Sorbonne Université (SU).
Length-force characteristics Passive muscle force as a function of muscle length was obtained by the mean force between the second twitch and the tetanus and to a second order exponential (Equation  5 ). Active muscle force was calculated by subtracting passive force at each muscle length from total muscle force. The active length-force was fitted by a polynomial function (Equation. 6). y = e b0 + b1x + b2 (Equation  5 ) y = b0 + b1x + b2x 2 + b3x 3 + b4x 4 + bnx n (Equation  6 ) Matlab scripts were used for evaluation of the force data, and for calculation of number of sarcomeres in series (version R2017a, The MathWorks, Inc. , Massachusetts, USA). The public domain software ImageJ (version 1. 52e, US National Institutes of Health, Maryland, USA) was used to assess the quantity of endomysium, perimysium, number of myofiber, type, fiber CSA and mean sarcomere lengths.
Interaction effects and gender main effects were explicitly described when present, otherwise only group main effects were reported. General estimating equations was used to determine the relationship of righting time and Neurological Score and righting reflex with age and age*gender within the spastic mice group. These statistics did not include WT mice, as their score was constantly zero. Two-way ANOVA were used to calculate all the other parameters. All statistical analyses were performed using SPSS (IBM SPSS statistics 25, New York, USA). Prism (version 8. 2. 0, GraphPad software Inc, California, USA) was used in order to plot the figures. Effects were considered significant at p<0. 05. Data is presented as mean ± SEM.
These results suggest that the function of Bx genes in activating the transcription of ac/sc genes (  22 ) is conserved between Diptera and Gerromorpha. As observed for the gene tx, only one of the two copies (BxA) is implicated in regulating leg length in addition to its role in bristle development. Next, we asked whether the two Bx paralogs perform a similar function in M. mulsanti that has a lower-leg bristle density. Whereas the depletion of BxB resulted in empty socket cells due to nonelongated bristles in M. mulsanti embryos (Fig. 3A ), we failed to observe any phenotypes for double-stranded (ds)-BxA RNAi in this species. When we assessed the expression profile of Bx paralogs (Fig. 3 B  and C ) in our comparative transcriptomics datasets, we discovered that BxA is not significantly expressed during embryogenesis in M.
We trimmed those lists by first removing lowly expressed transcripts (mean expression < 1 TPM) and then removing transcripts that are not differentially expressed between midand late embryogenesis in at least two legs. This analysis identified 7,578 and 7,166 transcripts that are differentially expressed between G. buenoi and M. mulsanti during midembryogenesis and late embryogenesis, respectively. BLAST searches led to the identification of 1,234 homologous sequences between G. buenoi and M. mulsanti (SI Appendix, Fig. S6 B  and C ). Among these 1,234 genes, we performed RNAi experiments for the genes showing higher fold-change and still expressed during postembryogenic stages at least in G. buenoi. The rationale is that bristle density significantly increases at stages N4 and N5 in G. buenoi contrary to M.
This nuclear function of Simiate might underlie its direct or indirect implication in leg growth in the Gerromorpha. These findings raise the hypothesis that increased bristle density evolved in concert with increased leg length, both of which are characteristic to the Gerromorpha  (5). To further test this hypothesis, we reanalyzed our dataset of bristle density measurements in Gerromorpha L2 tarsi (Fig. 1 ) by adding the mean length of the tarsus L2 and the entire leg L2. We found that leg bristle density increases linearly with tarsus length (Pearson R 2 = 0. 24) (Fig. 7H ). We also performed the same analysis of correlation for the control and knockdown individuals in G. buenoi. Our data showed that tarsus L2 bristle density positively correlates with tarsus L2 length (Pearson R 2 = 0.
Only cells in anaphase or telophase were analyzed to ensure that the spindles had finished rotation before fixation. For each cell division, the angle α PD between the local PD axis of the leg and the separating chromosomes was measured using the angle tool in Fiji. Angles were always measured as acute angles. To obtain the orientation of cell division in the relation to the PD axis, the angle α PD was transformed as follows: α division = 90°Àα PD. Angular histograms were plotted using an in-house R script available at the Dryad digital depository database (https://doi. org/10. 5061/dryad. fbg79cns8).
Results: We sequenced 17 representative plastomes and integrated three published plastome data together to conduct comparative and phylogenetic analyses. We found that Mahonia and Berberis share a large IR expansion (~ 12 kb), which is recognized as a typical character of Berberideae. Repeated sequences are revealed in the species of Mahonia, which are valuable for further population genetic studies. Using a comparative plastome analysis, we determined eight hypervariable regions whose discriminative power is comparable to that of the whole plastid genomes. The incongruence of the ITS and the plastome tree topologies may be ascribed to ancestral hybridization events and/or to incomplete lineage sorting. In addition, we suggest that leaf epidermal characters could help to distinguish closely related species in Mahonia.
Notably, after the migration to East Asia, the genus Mahonia probably underwent a radiation event, leading to the current Eastern Asian biodiversity center  [8, 18]. Phylogenetic analyses based on molecular datasets provide reasonable phylogenetic hypotheses  [21] [22] [23] [24]. However, it is disputable that using just a single line of evidence is sufficient to delimit species boundaries  [25]. Therefore, multiple evidence (such as including plastome datasets, morphological traits, ecological traits) should be applied to modern systematics  [26] , in particular with respect to recently diverging lineages, such as Mahonia. Complete plastome data have proven to be effective in resolving phylogenetic relationships at a wide range of taxonomic levels  [16]. The phylogenetic incongruence between the plastome tree and the nrDNA tree indicated that frequent hybridization has occurred between Mahonia and Berberis  [2].