dataesr/scientific-paragraphs-categorization huggingface dataset:
Data collection A total of 15 chicks were recorded 4 times each between the ages of 2 and 46 d: Age 1: 2-5 d; Age 2: 14-15 d; Age 3: 30-31 d; Age 4: 43-46 d. The 2 main vocalizations produced by houbara chicks (CCs and SCs) were recorded while each chick was isolated for a short time (<15 min) in a box without any visual or vocal interactions with other chicks. Vocalizations were recorded using a Gras 46AE microphone (frequency response: 3. 15 Hz -20 kHz, ± 2 dB) connected to a Marantz PMD661 recorder (frequency response: 20 Hz -24 kHz, ±1 dB; sampling frequency: 44. 1 kHz). To elicit CCs, chicks were in visual contact with the bird keeper and were stimulated by presenting them with food (mealworm given with a clamp). To elicit SCs, chicks were kept alone without any external stimulation. Then, the microphone was presented, either handheld (CCs) or mounted on a tripod (SCs), at head height and less than 1 m from the chick.
For the SC at Age 1, the frequency gap (GSC) was not included in the analysis because all measurements for this parameter were equal to zero. We also performed a cross-validation DFA using the cross-validation leave-one-out method to assess the reliability of the DFA re sults. In order to reduce biases associated with scaling, all values were standardized using the Fisher z-transformation. DFAs were performed using the R package 'MASS'  (Venables & Ripley 2002). We also conducted 2 series of generalised linear mixed models (GLMMs) using the 'lmer()', 'lme()' and 'glmmTMB()' functions of the 'lme4', 'nlme' and 'glmmTMB' packages  (Brooks et al. 2017 , Kuznetsova et al. 2017 , Pinheiro et al. 2021). Due to an excess of 0 values in the data, we applied a negative binomial or Tweedie distribution for the frequency gaps of CCs and SCs (GCC and GSC) using the function 'glmmTMB()'.
2017 ) and compared. Adjusted repeatability corresponds to the fraction of the total variance in the population that can be attributed to variation among individuals while controlling for the variance explained by the fixed effect weight. Repeatability was assessed with the 'rptR' package, as it allows estimation of CIs based on parametric bootstrapping associated with the repeatability estimates (n = 1000 data samples). When the effect of weight was not significant, we assessed individuality based solely on the PIC previously computed. We then conducted a second series of models complementary to the first. Here, we aimed to test for the effect of chick age on the acoustic parameters of CCs and SCs. Chick age (range: 2-46 d) was systematically included as a continuous fixed effect, and chick identity was included as a random effect.
Acknowledgements. This study was funded by the  Emirates Center for Wildlife Propagation (ECWP) , a project of the  International Fund for Houbara Conservation (IFHC). We are grateful to  H. H. Sheikh Mohammed  bin  Zayed Al Nahyan ,  Crown Prince  of  Abu Dhabi  and Chairman of the  IFHC and S. E. Mohammed Al Bowardi, Deputy Chairman of IFHC , for their support. This study was conducted under the guidance of  Reneco International Wildlife Consultants , a consulting company managing ECWP. We are thankful to  Frédéric Lacroix , managing director, and  Gwénaëlle Levèque , project director, for their supervision. We sincerely thank all ECWP's fieldworkers involved in the collection of data. We are particularly grateful to  Cécile Landsman ,  Mathieu Guillemin ,  Thibault Dieuleveut  and  Maël Lelièvre  for their contributions to the recordings.
Although the stratigraphic origin of the specimens could not be directly assessed, the occurrence of similar fossil wood preserved in volcanoclastic sediments in the Tournaisian formations above the collection site indicates that the Tournaisian is the most plausible one  (Hueber & Galtier 2002; Decombeix et al. 2011b). The four specimens were prepared as classical thin sections in the transverse, tangential, and radial planes  (Hass & Rowe 1999). Observation and photography were conducted using a Sony XCD-U100CR digital camera attached to an Olympus SZX12 stereomicroscope and an Olympus BX51 compound microscope. Images were captured using Archimed imaging software (Microvision Instruments, Evry, France). When necessary, the multifocus tool included in Archimed was used to provide a better image.
Measurements were carried out using ImageJ software (U. S. National Institutes of Health, Bethesda MD, United States). Unless stated otherwise in the text, all average values and percentages are based on a minimum of 50 measurements. Images were processed using Photoshop (Adobe Systems, San Jose CA, United States). The specimens and corresponding slides are deposited in the AMAP Research Unit, Collections de Paléobotanique, Université de Montpellier, under accession numbers MSM08-14 (six slides), MSM08-20 (six slides), MSM08-171 (five slides), and MSM08-172 (eight slides).
Acknowledgements We are grateful to the editor,  Cyrille Prestianni , and the anonymous reviewer for their insightful suggestions to improve our manuscript. This work was conducted during  B. Laloux 's master project in 2015 at  UMR AMAP and Biodiversity Research Centre, Earth and Life Institute, UCLouvain  (co-supervised by  A. -L. Decombeix  and  R. Wesselingh ). Technical support for the observation of the specimens was kindly provided by the  Unité des Eaux et Forêts (Earth and Life Institute, UCLouvain). We thank  J. Talent ,  B. Meyer-Berthaud  and  J. Galtier  for their help in the field and during this project. AMAP (botAny and Modelling of Plant Architecture and vegetation) is a joint research unit which associates Montpellier University (UM),  CNRS  ( UMR 5120 ),  CIRAD  ( UMR 51 ),  INRAe  ( UMR 931 ) and  IRD  ( R123 ).
Selection of the target gene Sequences from the high coverage viral genome database were obtained from the GISAID (https://www. gisaid. org/) in July -August 2021. A total of 3200 genomes originating from Indonesia were used in this study. A multiple sequence alignment was performed on these sequences using the MAFFT version 7  (Katoh et al. , 2019)  to obtain a consensus sequence with a threshold above 95%. The S gene sequence (Spike) was obtained from the consensus sequence and translated into protein. A pairwise alignment of that protein was performed with the Receptor Binding Domain (RBD) sequence to look for RBD in the obtained sequence. Alignment with SARS-CoV-1 was also performed to find the differences between SARS-CoV-1 and SARS-CoV-2 sequences. Finally, the superimposition of this system.
Target gene validation We used molecular docking to identify residues that play an important role in the interaction of RBD with ACE-2 in humans. Homology modeling was carried out between protein sequences obtained from the consensus compared to the databases using the Swiss Model  (Waterhouse et al. , 2018). Molecular Docking was performed using Cluspro 2. 0 server  (Kozakov et al. , 2017)  and the proteinprotein interaction was checked using Ligplot version 4. 5. 3  (Wallace et al. , 1996).
Acknowledgment This study was financially supported by the  LPDP Research Mandatory   COVID-19  (No. 8/FI/P. KCOVID-19. 2B3/X/2020 ) coordinated by  Akhirta Atikana. This study is also part of the research collaboration between the  Research Center for Biotechnology, BRIN , and the  Faculty of Health Sciences, Esa Unggul University. The support from the  Deputy of Life Sciences , BRIN and  Dekan Fakultas Ilmu-ilmu Kesehatan ,  Esa Unggul University , are greatly appreciated.
Study area and data collection Our study area consisted of the "communes" selected in previous works on the badger-cattle bTB system in the South-West of France  [24, 25]. This study area was restricted to a 3754 km 2 area of 335 "communes" (Figure  1 ), straddling the border of Pyrénées-Atlantiques and Landes. A maximum of three SB0821 strains per official declaration of infection per farm, collected between 2002 and 2017, were included in the study. All SB0821 badger strains collected during our study period by "Sylvatub" were included. The sampling date considered was either the date of slaughter for cattle strains or the date of capture recorded by "Sylvatub" for badger strains. Cattle information was provided by the "Base de données nationale d'identification" (BDNI), in which every bovine is registered in France.
Genomic data Upon reception at the NRL, liquid culture media (7H9 + ADC) was employed to grow the M. bovis strains. After a heating step, the lysate obtained was sent for purification and Illumina sequencing (paired-end 2*150 bp) to the Paris Brain Institute (ICM). At the ICM, sequencing quality was controlled using FASTQC with an acceptability Phred score threshold of 30. Sequence alignment and Single Nucleotide Polymorphism (SNP) calling were computed at the NRL using the AF2122/97 reference strain on Bionumerics software, version 7. 6 (AppliedMath, Belgium). SNPs identified were selected according to strict criteria of wgSNP module: (i) they had to be present on at least 5 reads in both forward and reverse direction, (ii) 12 base pairs had to separate them, (iii) they were not present in repetitive regions of the genome and (iv) ambiguous SNPs (at least one unreliable (N) base, ambiguous (non ATCG) base or gap) were not included.
SNPs were then used to reconstruct a maximum parsimony tree on Bionumerics in order to identify genetic outliers. We estimated pairwise distances between sequences using the dist. dna function available in the ape package version 5. 0  [26]  on R4. 0. 3. The model considered was the F84 model  [27]  since it closely resembles the HKY model  [28]  that was previously used on M. bovis strains  [17, 29]. Distances were estimated between all, badger and then cattle sequences.
Bayesian evolutionary model We used a Bayesian evolutionary model consisting of a structured coalescent population model, in order to capture the transition between two pathogen populations defined by their host-species, using BEAST2 (Bayesian Evolutionary Analysis by Sampling Trees) v2. 6. 3  [30]. The probability of nucleotide substitutions was described by the substitution model and the molecular clock modeled the evolution of substitution rates across branches. Moreover, the pathogen sub-population structure was inferred using the marginal approximation implemented in the Mascot package v2. 1. 2 [21]. We needed to select the most appropriate substitution and molecular clock models. Models were finally compared using the Bayes Factor (BF) after estimating their marginal likelihoods with the "Nested Sampling" algorithm implemented in the NS package v1.
All models were tested in BEAST2 software after annotation on BEAUti interface  [30]. We set the site model frequencies parameter to empirical and the constant effective population prior to a lognormal distribution (mean: 0, standard deviation: 1); other parameters kept their default settings. We selected a chain length of 300 million iterations, a burn-in period of 10% and a sampling frequency of 1 in 30 000. Four replicates were performed and combined in LogCombiner v. 2. 6. 3 with a lower sampling frequency of 1 in 120 000. We checked for convergence i. e. stationary distribution of the MCMC (Markov chain Monte Carlo), and independence of sampling (Effective Sample Size (ESS) above 200 for each parameter), on TRACER v1. 7. 1  [36]. To summarize the posterior sampled trees, a maximum clade credibility (MCC) tree was built via Tree Annotator using the common ancestor heights option  [37].
Genomic data From 167 SB0821 strains, 171 SNPs were identified. Pairwise distances between sequences ranged from 0 to 0. 145 for all and cattle strains (median: 0. 042) and from 0 to 0. 108 for badger strains (median: 0. 036). Among these 167 SB0821 strains, 146 were isolated from cattle and 21 from badgers (Figure  2 ). In 2002, SB0821 strains were first detected in cattle, which preceded our first SB0821 badger strain (2013).
Data Collection ProCEAS ® was connected to the airways from the beginning of the procedure, and data were recorded continuously to the end of EVLP (Figure  1 ). ProCEAS ® sampled small quantities of gas (200 ml min -1 ) extracted from the ventilation circuit. The eCO values were given by the difference between the maximum values (end of expiratory phase) and the minimum values (end of inspiratory phase). This made it possible to measure the production of eCO regardless of its content in the ambient air used by the ventilator when FiO 2 was set to 21%. ECO data were averaged over a period of 5 min following each recruitment maneuver. Hemodynamic parameters and pulmonary mechanics (compliance, pulmonary pressure, and vascular resistance) were recorded by the XPS ™ device. The quantifications of the perfusion fluids were conducted manually.
Samples of perfusate fluid were collected after each recruitment maneuver to measure blood gases, glucose, and lactate levels. At the very end of the procedure, a sample of perfusate was taken for later cytokines measurements. The following cytokines (Interleukine (IL) 1-β, 6, 8, 10 and Tumor Necrosis Factor α (TNFα) were assayed by the MagPix device and Xponent software (Luminex Corp), using a porcine cytokine/chemokine magnetic bead panel (Milliplex MAP kit, Millipore Corp. ), according to manufacturers' instructions.
The comparison of the data between groups was made by a nonparametric test (Mann Withney U test). For the analysis of distribution between groups we used an exact Fischer test. We also performed a ROC curve with the hope to determine a clinically relevant eCO threshold to predict the evolution of the transplanted lungs. Differences with a p < 0. 05 were considered as significant. These analyses were carried out using Statview software except for the ROC curve obtained with R version 3. 6. 1 (R Foundation for Statistical Computing).
RESULTS We included 21 bi-pulmonary graft procedures from December 2018 to July 2019. The characteristics of donors and recipients are summarized in Tables  1, 2. Raw data of the study are available, as a single Table, in Supplementary Materials. During the EVLP procedure, only 2 grafts were rejected for transplantation by the surgical team. These two rejected lungs had absorbed large amounts of perfusion fluid during the procedure; their compliance had decreased significantly and their PO 2 /FiO 2 ratio was less than 350 mmHg. eCO measurement was possible in all of the 21 EVLP procedures and, as expected, did not perturb their progress. The ProCeas allows monitoring in real-time eCO during the entire EVLP as plotted in Figure  2 , where four recruitments periods, spaced by interrecruitment periods, were performed.
The gustatory function was screened via "taste strip" and the results compared to sex and age differentiated normative data. The diagnosis of qualitative taste disorders such as salty, bitter or metallic taste disorder was based on patient's self-report. To avoid conditions which could create temporary or permanent impairment of gustatory function, patients presenting untreated hypothyroidism, inflammation of the oral cavity or renal disorder were excluded. At least 30 min before the test volunteers were asked to drink only water and to not smoke. GSTA1 and GSTP1 were titrated following an ELISA protocol using commercial kits (Abbexa, Cambridge, UK). Descriptive analysis of the GSTA1 and GSTP1 ELISA data in each group was performed. However, the small number of subjects belonging to the ageusia group did not allow us to perform a robust comparison test considering all 3 groups.
Nitrogen was used for spray stabilization, and collision-induced dissociation experiments were performed in the higher energy collision dissociation (HCD) cell and as the damping gas in the C-trap. The following ionization parameters were applied: electrospray voltage 3 kV, heater temperature 350 • C, capillary temperature 350 • C, sheath gas (N 2 ) 60 arbitrary units (arb), auxiliary gas (N 2 ) 20 (arb), and S-lens RF level at 70 (arb). Full scan data were acquired at a mass resolving power of 60,000 FWHM. The m/z scan range was 100-1000.
GST crystals were soaked a few minutes in their mother liquor supplemented with isothiocyanate (allyl isothiocyanate, hexyl isothiocyanate or iberin) at high concentration (approximately 20 mM) with or without 5 mM glutathione. To minimize crystal handling, cryoprotection was performed during the same soaking time by adding 20% glycerol to the soaking drop. Crystals were flash frozen in liquid nitrogen and shipped to SOLEIL synchrotron. Diffraction experiments were performed on the SOLEIL synchrotron beamline PROXIMA1. The crystals of GSTP1:iberin, GSTA1:hexyl isothiocyanate and GSTA1:allyl isothiocyanate diffracted to 1. 73 Å, 2. 03 Å and 2. 46 Å, respectively. Datasets were indexed and integrated with XDS and scaled with pointless. The three structures were solved by molecular replacement with the coordinates of the previously solved GSTA1 (PDB 6YAW) and GSTP1 (PDB 5X79) as search models.
The structures were manually adjusted using COOT and refined using PHENIX. Careful inspection of electron density maps allowed identification and building of ligands into their binding sites. Restraint files were generated for iberin, allyl isothiocyanate and the glutathione adduct of hexyl isothiocyanate with the GRADE webserver (https://grade. globalphasing. org). Structures were validated using Molprobity  (Chen et al. , 2010). Coordinates and structure factors were deposited in the Protein Data Bank under accession codes 7BIA (GSTP1:iberin), 7BIB (GSTA1:hexyl isothiocyanate) and 7BIC (GSTA1:allyl isothiocyanate).
Funding This work was funded by the  French "Agence Nationale de la Recherche " ( ANR-08-BLAN-0145-01 , " Galodude ",  ANR  " LOCOGAZE "  ANR-15-CE32-0007-01 ,  MOTOC "  ANR-22-CE16-0004-02 , and  LOCOGATE "  ANR-22-CE37-0002-02 ), the  Fondation Pour la Recherche Médicale  ( DEQ20170336764 ), the  LMU-Bordeaux Research Cooperation Program , the  German Science Foundation  ( STR 478/3-1  and  CRC 870 ,  B12 , reference number:  118803580 ), and the  German Federal Ministry of Education and Research  (grant codes  01 EO 0901  and  01 GQ 1407 ). Financial support was also provided by the  Bayerisch-Französisches Hochschulzentrum (BFHZ)  and the  Center for Advanced Studies at the Ludwig-Maximilians-University Munich  through an  LMU CAS visiting fellowship.
monocytogenes genomes publicly available on the NCBI database. We examined the PMSC occurrence rate (per 100bp) in the agr operon compared to genes from several other gene categories including, two-component systems, the sigB operon, genes used for MLST analysis, metabolic genes and virulence genes (Fig. 6 ). As expected, results for the sigB operon and other genes used as controls (MLST genes, sigma factors & metabolic genes, rsbR1 paralogues, virulence genes) were similar to our earlier observations. The PMSC rate for agrC was comparable to the highest observed in sigB operon and was substantially higher in the case of agrA (Fig. 6 ). In clear contrast, PMSCs in all other two-component systems encoding genes were very rare, with resD as the sole exception. ResD is known important for mediating carbohydrate-based repression on virulence genes as well as controlling respiration in L.
Samples were visualized in SEM (Hitachi S2600N). Three biological replicates were made. In silico analysis of premature stop codon occurrence rates. Methodology for this analysis was directly adapted from our previous study  (Guerreiro, Wu, et al. , 2020)  however, with 40,080 genome sequences available from the NCBI database analysed (accessed April 19 th 2021). Briefly, a BLAST DNA database was constructed for each genome and Blastn match for each gene of interest was extracted and translated in silico. For the genes determined as present in the genome, lengths of deduced translation products were calculated as percentage values relative to the length of reference protein sequence from L. monocytogenes EGD-e strain. PMSC is defined as <90% of reference protein length and its occurrence as a rate corrected for gene length.
11°C. s -  until 95°C was reached; and cooling for 30 s at 40°C. Cycle quantification was calculated by using LightCycler 480 software version 1. 5. 1 (Roche) and the Pfaffl relative expression formula  (Pfaffl, 2001; Pfaffl et al. , 2002). 16S rRNA expression was used as a reference. Three biological replicates were performed. Results were converted to Log2 expression normalized relative to the WT strain. Growth kinetics. Several L. monocytogenes strains were grown to stationary phase in BHI medium at 30°C were adjusted to an initial OD600 of 0. 05 and grown in fresh BHI medium at 30°C. Measurements of the OD600 of each culture were made every hour for 8 hours. Growth rates were calculated with GrowthRates 4. 3 software  (Hall et al. , 2014). Two biological replicates were made. Biofilm formation.
L. monocytogenes strains were grown overnight in BHI at 30°C. Cultures were diluted 1:100 into 50 mL conical bottom flasks containing 5 mL fresh BHI and further incubated for 24 hours. Liquid cultures were discarded, washed twice with PBS and dried at RT for 30 min. Flasks were dyed with 1% Crystal Violet (Sigma-Aldrich ® ) for 30 min at RT and further washed twice with PBS and once with deionized water. Flasks were dried overnight at RT and pictures were taken. Two biological replicates were made. Blue bars represent parental strain and white coloured colonies, while red and green represent sigB -and agr -, respectively. Data were generated from two independent biological replicates. For strains details refer to Table  S1. Statistical analysis was performed using a paired student t-test (*, p-value of <0.
05; **, p-value of <0. 01). (G) Growth curves were performed at 30°C in BHI using wild type, ΔsigB, ΔagrA and colonies isolated during the in vitro evolution experiment at 30°C. (H) Growth rates were calculated from growth curves from (G). All competitions were initiated with a 1:1 ratio of white:grey colonies. Data were generated from two independent biological replicates. Statistical analysis was performed using a paired student t-test in comparison to the passage 0 (*, p-value of <0. 05).
Acknowledgments: The authors would like to thank members of the PATHSENSE network (https://www. pathsense. eu/ ) for helpful discussions throughout this study. This project has received funding from the  European Union 's  Horizon 2020 research-andinnovation program  under  Marie Skłodowska-Curie  grant agreement no. 721456. Jialun Wu  was funded by the  Department of Agriculture, Food  and the  Marine  ( 17/F/244 ).
Implementation ONTdeCIPHER is an open-source pipeline coded in python3 compatible with Ubuntu distributions and macOS. It uses the Snakemake  (Köster et al. , 2012)  features to perform reproducible and scalable data analysis (see Supplementary information Fig. S1 ) and seamlessly adapts to server, cluster, grid and cloud environments. ONTdeCIPHER's dependencies and environments are installed and managed using the Conda package and environment management system. Currently, ONTdeCIPHER can be run locally or on an HPC. ONTdeCIPHER includes 13 tools (see Supplementary information Table  S1 ) validated by the bioinformatics community to perform key downstream analyses on raw sequencing data from amplicon-based ONT sequencing. In addition, it comes with a python master script (run_deCiPHER. py) allowing the user to run the various pipelines' steps via a command line.