dataesr/scientific-paragraphs-categorization huggingface dataset:
1. Field observations revealed that beetles produced larger galleries (∼5-6 mm in diameter) than termites (<3 mm in diameter), while earthworms produced intermediate galleries (∼3-4 mm). Further, anecic earthworm species are also wellknown to make large and vertical burrows open to the surface  (Capowiez et al. , 2011). From these observations, galleries made by earthworms, beetles, and termites were manually isolated from the total macroporosity based on their body size and shape (Figure  1 ) and using the option "volume edit" in the Avizo 8. 1 software. Galleries were then described by measuring their (i) diameter, (ii) verticality (orientation or angle between the maximum Feret diameter of the object and the XY plane), (iii) tortuosity (the ratio between the actual branch length >10 mm of the object and the Euclidean distance along the skeleton), (iv) sphericity (the ratio between the volume and surface of the object), (v) total length of galleries (sum of branches with length >10 mm after skeletonization), (vi) number of branches (number of branches with length >10 mm after.
Statistical Analyses Prior to analysis, the homogeneity of variances was inspected using Levene's test, and data were log-transformed if needed. One-way analysis of variance (ANOVA) and least significant difference (LSD) tests were performed to assess differences between means. To visually resume the information from the soil total macroporosity and galleries properties, an ordination method (principal component analysis, PCA) was applied using "ade4" packages in R. Partial least squares regression (PLSR) analysis was performed to predict important total macropores variables associated with soil hydraulic conductivity using the "pls" package  (Mevik and Wehrens, 2007). All statistical calculations were carried out using R version 3. 5. 1. Differences among treatments were declared significant at the <0.
DATA AVAILABILITY The datasets for this manuscript are not publicly available because the datasets generated during and/or analyzed during the current study are available from the corresponding author upon request. Requests to access the datasets should be directed to sougueh. cheik@ird. fr. this study were made available through the support of Dr. Yvan Capowiez from the department Environnement Méditerranéen et Modélisation des Agro-Hydrosystèmes (EMMAH) at French National Institute for Agricultural Research (INRA). We are grateful to Dr. Nguyen Ngoc Hie, vice director of Bach Maï Hospital for providing us with access to the medical scanner. We also thank Lucian Elles and Hien for their help during fieldwork.
Soil preparation and measurement The database used in the present study is composed of laboratory made soil surfaces prepared with two different soils and a various range of sieved clods, in order to evaluate the segmentation method in various roughness conditions. In order to do so, two trays of 50 x 50 cm 2 were prepared with loose silt loam soil for 10 cm depth. One of them had a nearly planar surface (P) and the other one was shaped with gentle furrows every 8 cm (F). Then air-dried clods collected in the field were set upon the two soil surfaces, with various sizes and spacing to reproduce different roughness conditions (Figure  1 ). These trays were subjected to controlled rainfalls with a laboratory rainfall simulator similar in design to the one presented in  (Foster et al. , 1979 ) also described in  (Vannier et al.
5a. This pattern could be detected using the quantiles of coordinates xc and yc of the data points of clod contour at minimum, 12. 5%, 87. 5% and maximum. We had a wrong pattern if two quantiles were equal for xc or yc. Then, the inclination and height of the mean plane were refined when needed. The second test of goodness of intersection (Fig. 4 , line 6) checked for requirement of the local surface to be extended in one or more than one direction. As illustrated in Fig. 5b , a too small local surface due to inadequate extensions of detected clod, caused straight borders in the clod contour. These lines were detected by thresholding the percentage of abscissa (or ordinates) equal to their minimum or maximum value. The local surface was then extended a little in the direction given by straight borders and the test repeated until no extension was required.
Gap Closures, Genome Analysis, and Comparisons Detection of contigs harboring ICE-related CDSs was performed by comparison with the previously reported genome sequences of M. fermentans PG18 (GenBank accession number: AP009608), M. agalactiae 5632 (FP671138), M. bovis PG45 (CP002188), M. bovis Hubei (CP002513), and M. mycoides subsp. capri GM12 (CP001668) using MolliGen  (Barre et al. , 2004). The characterization of ICEHo 4788, carried by a single contig, allowed detection of contigs carrying fragments of ICEHo in the other fully sequenced strains. Gap closure between contigs carrying ICE sequences was performed by PCR and Sanger sequencing. ICE maps were drawn using Clone Manager 9 Basic Edition (Scientific & Educational Software, Denver, CO, United States). The ICE-related CDSs were analyzed using BLAST 3  , InterPro 4  , MolliGen 5  , Artemis Comparison Tool 6  , EMBOSS Needle 7  , TMHMM Server v.
PCR for detection of the specific M. hominis ICE modules was carried out in a volume of 50 µL using the Expand Long Template PCR system (Roche). Thermal cycling reactions consisted of an initial denaturation step for 2 min at 95 • C followed by 15 cycles of denaturation for 10 s at 95 • C, annealing for 30 s at 57 • C, and extension for 2 min at 68 • C, and 20 cycles of denaturation for 15 s at 95 • C, annealing for 30 s at 57 • C, and extension for 2 min + 20 s for each successive cycle at 68 • C, with a final extension for 7 min at 68 • C. All PCR products were sent to Eurofins Genomics (Ebersberg, Germany) for sequencing. Sequencing data were analyzed using BioEdit § 7. 2. 5 software (Isis Pharmaceuticals, Carlsbad, CA, United States).
Detection of MICEs in M. hominis We first searched for the minimal ICE backbone composed of CDS1, CDS5, CDS17, and CDS22 using the Molligen database in the 12 fully sequenced M. hominis genomes. Three isolates, i. e. , 331, 3299, and 5096, had none of the four CDSs. Two isolates, i. e. , 2674 and 5060, had three CDSs (CDS1, CDS5, and CDS22), but they occurred at different loci suggesting that they were vestigial ICE remnants. The minimal ICE backbone was detected in the remaining seven isolates, suggesting the presence of complete ICEs. A full ICE, designated as ICEHo 4788, was identified in isolate 4788 and was carried by a single contig. Its organization and composition were defined and ICEHo 4788 was then used as a reference to analyze and assemble other isolates, in which ICE elements were distributed over several contigs.
When compared to ICEA-III  (Marenda et al. , 2006) , only 10 distinct homologous CDSs were found in ICEHo 4788 (Figure  1 , Table  3 , and Supplementary Table  S2 ). Overall, the percentages of similarity and identity between CDSs of ICEHo 4788 and ICEA-III were lower than those between ICEHo 4788 and ICEF-II (Table  3  and Supplementary Table  S2 ). Using TMHMM and InterPro softwares, six CDSs (CDS5, CDS14, CDS15, CDS16, CDS17, and CDS19) were shown in ICEHo 4788 to harbor transmembrane domains in comparison to eight CDSs previously described in ICEF-II (CDS4, CDS5, CDS7, CDS14, CDS15, CDS16, CDS17, CDS19)  (Calcutt et al. , 2002)  and seven in ICEA-III (CDS5, CDS7, CDS14, CDS15, CDS16, CDS17, CDS19)  (Marenda et al. , 2006). Marked differences were observed with M. fermentans, as six ICEF-II CDS homologs were lacking in ICEHo 4788 (CDS2, CDS4, CDS6, CDS7, CDS8, CDS13) and eight ICEHo 4788 CDSs had no homology with ICEF-II CDSs, nor with CDSs described previously in MICEs.
Analysis of the Specific M. hominis ICE Module Further analysis of the specific M. hominis ICE module highlighted that in MhoH, MhoG, MhoF, and MhoJ, an absolutely conserved sequence of 23 aa (SSLSDFDKTPTDLKDSKVINEYN) was present within the last 40 residues of the sequences (Figure  1 ). This conserved sequence was also detected in CDS11 and CDS21, but a Prosite search failed to retrieve functional motifs. The conserved sequence contained a large number of charged amino acids, with five D/E and three K residues, and was also found in a hypothetical protein from Candidatus Mycoplasma girerdii (MGM1_3750). The C-terminal part of the proteins containing this conserved motif was predicted to be disordered using SPINE-D, Phyre2, and IsUnstruct v2. 02, and was enriched in putative phosphorylation sites (prediction using DEPP R server) (Supplementary Figure  S4 ).
Prevalence of ICEHo in a Collection of 120 M. hominis Clinical Isolates To define the prevalence of ICEHo in the M. hominis strains, the four CDSs that are part of the minimal ICE backbone (CDS1, CDS5, CDS17, and CDS22) and the specific M. hominis ICE module were searched by PCR in a panel of 120 M. hominis clinical isolates (Table  6 ). A complete ICEHo was considered present when the four CDSs and the specific M. hominis ICE module were detected. The data showed that 45% of the isolates possessed the four CDSs and the specific M. hominis ICE module, suggesting the presence of complete ICEHos. In 35% of isolates, none of the four CDSs or the specific M. hominis ICE module were detected, suggesting the absence of ICEHo. The remaining 20% of clinical isolates harbored one, two or three CDSs, suggesting the presence of potential ICEHo remnants (Table  6 ).
e. , 45% in a collection of 120 M. hominis clinical isolates. This prevalence may have been slightly underestimated because six additional strains (5%) harbored the specific M. hominis ICE module and three of the four backbone CDSs. We cannot exclude the possibility that the fourth CDS would not have been detected by PCR due to slight modifications of the gene sequence. In addition, CDS1, CDS5, CDS17, CDS22 and the specific M. hominis ICE module are also present in two previously published genome datasets for two other clinical isolates, M. hominis PL5 (GenBank JRXA01000000) and M. hominis TO0613 (GenBank CP033021). Overall, this 45% prevalence was equivalent to that of 47% (78/166) found in a collection of four ruminant mycoplasma species  (Tardy et al. , 2015). It should also be noted that CDS22 from ICEHo 4788 has a match in the genome of U.
Overall, ICEHos showed a similar structure except for the occurrence of MhoA as a pseudogene, which was only present in ICEHo 4788 (Supplementary Figure S1). All ICEHos contained a 4. 0-5. 1-kb module composed of five to six juxtaposed CDSs, i. e. , MhoJ, MhoH, MhoG, MhoF, MhoE, and MhoC, the synteny of which varied slightly among the strains, as shown in Figure 1B. All of the genes forming this module were specific to M. hominis ICEs (see below for detailed description) as they had no homologs in other MICEs. ICEHo 4235-I of 30. 5 kb at position 397,452-428,015 and ICEHo 4235-II at position 778,637-809 029 (GenBank accession number CP038014). The two copies showed 99. 0% sequence identity and were in opposite orientation within the genome of M. hominis 4235. In M. hominis strain 35, the presence of two ICEHo copies, namely ICEHo 35-I of 30.
3 kb (position 449,355-479,744) and ICEHo 35-II of 29. 1 kb (position 312,315 to 341,498) (GenBank accession number CP035543) was also confirmed. These two copies were in the same orientation within the genome and showed 90. 0% sequence identity. M. hominis ICEHo May Occur as Multiple CopiesSouthern blot hybridization data using labeled CDS1 and CDS22 probes and EcoRV-digested chromosomal DNA suggested the presence of a single chromosomal ICEHo in M. hominis strains 3631, 132, 4016, 4788, and 5012, and the presence of at least two ICEHo copies in strains 4235 and 35 (Supplementary FigureS2).
Data analysis Statistical analyses were performed in R-3. 5. 0 (R Core Team 2018). To analyze and model comparative functional responses, we used the FRAIR-0. 5. 100 package  (Pritchard 2017 ). Rogers  ' (1972)  Type II equation was used to describe the functional response of both species as food resources were not replaced as they were consumed: N e = N o (1 -exp(a(N e h -T))) where N e is the number of food pellets consumed, N o is the initial number of food pellets, a is attack rate, h is handling time, and T is experimental duration (which was set at 1 in the present study as we wished to compare FR parameters for both species over the same period of time). Maximum feeding rate was thus calculated as 1/h. Models were bootstrapped (n = 2000) to generate 95% confidence intervals for each species' functional response curve.
Acknowledgements We thank  Muaaz Tariq  for assistance with animal husbandry and experimental setup. We appreciate helpful comments from  Drs Gregor Kalinkat  and  Jonathan Jeschke  and an anonymous reviewer. TH was supported by  NSERC Undergraduate Scholarship , HJM by  NSERC   Discovery Grant  and  Canada Research Chair , and XC and HJM by a  Joint Grant of Yunnan Provincial Science and Technology Department -Yunnan University Major Project  ( 2018FY001-007 ).
Statistical analysis Data were analyzed by means of ANOVA using the GLM procedure of SAS 9. 01 (SAS Institute Inc, Cary, USA). The model for nutritional data included the treatment (Untreated, MH, HPP), storage time (1, 7, 14, 21 and 28 days) and replicate as fixed effects. For the sensory data, the model included the treatment, storage time, taste session and replicate as fixed effects. Non-significant interactions (P>0. 05) were removed from the model. Mean differences were tested using the Tukey test (P<0. 05).
Nutritional quality: Vitamin C, total phenols, flavonoids and sugars The vitamin C content was very low, 4. 3, 3. 1 and 2. 3 mg 100 ml -1 in untreated, HPP and MH smoothies, respectively (Table  2 ) and it was due mainly to the dehydroascorbic acid. These results were expected because the smoothies were made with vegetables that, in general, are not very rich in vitamin C; for example, zucchini has 15 mg 100 g -1 , pumpkin 12 mg 100 g -1 or carrot 7 mg 100 g -1 of vitamin C (Spanish food composition database [BEDCA]), and also, as reported by  González-Tejedor et al. (2017) , due to the mincing and blended procedure followed to prepare vegetable smoothies, low ascorbic acid levels were detected, because the ascorbic acid oxidation to dehydroascorbic acid is rapidly catalysed by the enzyme ascorbate oxidase.
Epidemiological survey of foamy virus among mandrills in Gabon and Cameroon We previously identified roughly a hundred mandrills infected with a specific SFV strain  (Calattini et al. 2004; Mouinga-Ondeme et al. 2010 , 2012). DNA samples of 11 of these animals were still available: 10 from Gabon and 1 from Cameroon (Table  1 ). DNA quality was attested by a b-globin PCR, and SFV status was confirmed by the SFV pol-integrase PCR, as previously described in  Calattini et al. (2004)  and  Mouinga-Ondeme et al. (2010 , 2012). All samples were found positive for SFV pol, including the MSP115 sample (GenBank accession number: MK014762), which had been previously found as serologically positive, but negative with the PCR assay  (Mouinga-Ondeme et al. 2010). Complete SFV env sequences were obtained from four of these samples (two from South Gabon animals, and two from North Gabon) by the nested PCR technique (see primers used in Supplementary Table  S1 ).
Recombination within the env alignment Alignments of pol and env genes were prepared for phylogenetic analyses, and potential recombination was assessed using seven programmes, including RDP, GENECONV, Chimaera, MaxChi, BootScan, SiScan, and 3Seq, implemented in the Recombination Detection Program 4 package  (Martin et al. 2015). Two RHs were detected by all seven programmes in the env alignment at a P value <0. 05, both of which were located within the Env SU-coding region (Fig. 1 ). From the 5 0 end, the first and second hotspots lie approximately between 631 and 768 nt, and between 1,369 and 1,521 nt of the alignment, respectively. These RHs can be mapped to 7,775-7,909 nt and 8,564-8,716 nt of the prototype foamy virus (PFV; GenBank accession number Y07725) genome in their respective order, dividing the env genes into three parts: 1, the sequence region corresponding to the leader peptide (LP) and the 5 0 portion of the SU (env LP/5 0 SU ), 2, the central SU coding region, specifically the receptor binding domain (RBD) (env cenSU ), and 3, the coding region for the 3 0 end of the SU and the transmembrane domain (TM) (env 3 0 SU/TM ).
The known fifteen N-glycosylation sites in PFV  (Luftenegger et al. 2005)  were recovered, suggesting that the prediction is effective. The majority of the predicted N-glycosylation sites were shared between the two variants. Nevertheless, three sites, which were located in the RBD mapping to aa 350/1, 410 and 423 of the PFV Env protein (accession number: CAA69004, reported in the GenBank file Y07725), are unique to variant I, and are shared among SFVs of different host species. Furthermore, we also identified one unique site for variant II, mapping to aa 412/3 of the PFV Env protein (accession number: CAA69004). These findings suggest that the two env variants might allow viruses to interact with different host receptors.
Genomic sequence Evolutionary timescale (million years)   1 ). Nevertheless, it has been demonstrated with larger datasets that the Ogooue Ŕiver is indeed a major gene-flow barrier that can lead to the diversification of SFVmsp  (Telfer et al. 2003; Mouinga-Ondeme et al. 2010 ) and mandrill monkeys  (Telfer et al. 2003) , separating both hosts and viruses into two phylogenetically distinct populations. Similar observations have also been reported for simian immunodeficiency virus  (Souquiere et al. 2001) , and simian T-cell leukemia virus infecting mandrills  (Makuwa et al. 2004 ). Our results are comparable to these previous findings, and we believe that they truly reflect geographical isolation of the North and South Gabon SFVmsp. Furthermore, our analyses of these three genomic regions estimated their divergence dates to be between 0.
Instead, we found that the rest of the genome of the two SFV variants is phylogenetically indistinguishable. This means that the recombinants do not survive for very long, and that the recombination must have happened multiple times with great frequency and relatively recently. Combining these observations, this ghost virus lineage hypothesis implies that the ghost viruses are present in all of the investigated OWMA populations, codiversify with their hosts, and recombine with the other SFVs. It also implies that the recombinants die young, but are continually resupplied due to frequent recombination. The natural follow-up question is then; what are these elusive ancient ghost viruses? Could it be an ancient endogenous virus, which potentially could explain frequent recombination and the long-term co-speciation patterns that we observed in both clades? We searched various NCBI nucleotide/genomic databases by using tBLASTn with Env cenSU protein sequences as probes, but the search only returned FV sequences.
Funding This study received funding from the  CNRS  ( UMR 3569 ), the  Institut Pasteur, France , the  'Centre international de Recherches Medicales de Franceville' (CIRMF) in Gabon and through the 'Investissement d'Avenir' as part of a 'Laboratoire d'Excellence' (LabEx) French  research programme:  Integrative Biology of Emerging Infectious Diseases  ( ANR10-LBX-62 IBEID ) (A. G. ). Lea Richard was financially supported by the  ANR-14 ,  SHAPES  project. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data analysis All determinations were conducted in triplicates and results for each measured parameter were expressed as mean ± SEM. Variations of total phenol and flavonoid contents and the arginase inhibitory activity among extracts were determined by the analysis of variance (ANOVA) procedure (p b. 05), followed by Duncan's multiple range test using the SAS program version 9. Correlations between the total phenol or flavonoid contents and the arginase inhibitory activity were determined with the PROC CORR procedure using SAS version 9.
Black curtains surrounded the aquarium with a small slit that allowed us to observe fish without disturbing them. The position of the focal fish was then continuously recorded for 10 min using software for tracking behaviour (Observer 2. 01). The large compartment was divided with vertical marks every 2 cm; time spent shoaling was defined as time spent by the focal fish within the 2 cm closest to the stimulus shoal  (Cote et al. 2010a ). When the assay was complete, individuals were returned to their individual home aquarium and water was changed in the centre compartment of the sociability arena to exclude confounding effects on sociability by accumulation of conspecific chemical cues in the water.
The % time that the fish spent moving was the % frames in which the fish moved > 1 body length in the previous second. Area explored incorporates both the distance an individual moved and the spatial pattern of those movements. Given x-y coordinates from each frame, we tracked each individual's continuous path (assuming that movements between frames were straight). Explored area was calculated (in Matlab R2007) as the percentage of the arena that fell within 5 cm of the fish's path. At the end of each observation day, mosquitofish were weighed to the nearest 0. 001 g. The individuals used here display significant rank order consistency over 4-5 months in all four behaviours assayed and these behaviours are all correlated with the exception of sociability and activity  (Cote et al. 2011). We therefore performed a principal component analysis to define possible personality trait dimensions  (Cote et al.
Statistics The sociability score for one individual and the boldness score for one individual are missing. We thus excluded these individuals from the analysis. Also, five individuals never emerged from shelter during the novel environment assay and could not be assessed for exploration/activity. As a consequence, they were excluded from the PCA (see above) and survival analyses, leaving two hundred seventeen fish to be analysed. We analyzed survival during predation assays using a generalized linear mixed model with a logit-link, a binomial error distribution and a bobiqa optimizer in R 2. 13. 0 and with the experimental group as a random effect (package lme4 in R 3. 4. 4, Bates et al. 2013). We first standardized each explanatory variable to zero mean and unit variance  (Lande and Arnold 1983).
Acknowledgements We thank  Demetri Dokos  and the  Sacramento-Yolo Mosquito  and Vector Control District to provide us with mosquitofish, three reviewers and the editor. This research programme has been supported by a  Fyssen Foundation  fellowship to J. C. and by a postdoctoral fellowship from the  Swedish research council  to T. B. The  laboratoire Evolution et Diversité Biologique (CNRS, UPS ,  UMR 5174 ), part of the  "Laboratoire d'Excellence (LABEX) " entitled  TULIP  ( ANR -10-LABX-41 ) also supported J. C.
, 2012 Bartiromo et al. , , 2013)). In total, six pieces were embedded in Epon resin: three blocks were made from three treated samples; three blocks from three untreated samples. From these, 300 ultrathin 60-70 nm thick uncoated sections were made: 210 for untreated sample (170 were mounted on 300 Mesh copper grids, 20 with 75 Mesh hexagonal copper grids, 20 with single slot Nickel or copper grids) and 90 for treated sample collected on uncoated 300 Mesh copper grids. Of the sections, 270 are transversal, i. e. perpendicular to the leaf length, while 30 are longitudinal, i. e. parallel to the leaf length. Ultrathin sections were selected, observed and photographed with a Philips CM 120 at 80 kV, at the Centre de Technologie des Microstructures (CTμ) of Lyon-1 University, France. In order to check for chemical elements the Energy Dispersive Spectroscopy (EDS) analyses was performed on the TEM using SIRIUS SD ENSOTECH coupled with IDFIX software, acceleration voltage 120 kV, spot sizes 1-3, processing time 120 s, constant of time 4 μs.