dataesr/scientific-paragraphs-categorization huggingface dataset:
Agar-grown colonies were microscopic and translucent with a mean diameter of 1 μm. Bacterial cells were Gram-positive cocci, ranging in length from 300 to 500 nm. Strain FC2 was catalase and oxidase negative. The 16S rRNA gene was sequenced using the fD1-rP2 primers as previously described  [4] , using a 3130-XL sequencer (Applied Biosciences, Saint Aubin, France). Strain FC2 exhibited a 91% sequence identity with Peptoniphilus coxii strain RMA 16757 T (GenBank Accession number GU938836)  [5] , the phylogenetically closest species with standing in nomenclature (Fig. 1 ), which putatively classifies it as a new genus member of the family Peptoniphilaceae in the phylum Firmicutes. Strain FC2 presents a 16S rRNA gene sequence divergence >5% with its phylogenetically closest species with standing in nomenclature  [6] , so we propose the creation of the new genus 'Urinacoccus' gen.
nov. (u. ri. na. coc'cus, N. L. masc. n. composed of u. ri. na, L. N. gen. fem. urina, from urina, the Latin name of urine and coc'cus. L. N. gen. masc. coccus, from coccus, the Latin name of bacterium having a spherical or spheroidal shape) as strain FC2 is a coccus and was first isolated from a paediatric urine sample. We propose the new species 'Urinacoccus massiliensis' sp. nov. (mas. sil. ien'sis. L. Adj. gen. fem. massiliensis, of massilia, the Latin name of Marseille) because strain FC2 was first found in the city of Marseille. MALDI-TOF spectrum accession number. The MALDI-TOF spectrum of 'Urinacoccus massiliensis' strain FC2 T is available at: http://mediterranee-infection. com/article. php? laref=256&titre=urms-database. Nucleotide sequence accession number. The 16S rRNA gene sequence was deposited in GenBank under Accession number LN881616.
evasion indirectly provides a gateway at the host-tick interface for pathogens such as Borrelia spp. and tick-borne encephalitis virus. A profile during viral infection showed that nymphal I. scapularis salivary gland lipocalin genes are differentially expressed when compared to mock infections  14. There are currently over a dozen salivary lipocalins from various arthropod species structurally resolved in the Protein Databank (PDB)  15. The hard tick Rhipicephalus appendiculatus has two salivary lipocalins that are structurally resolved, bind different ligands and have separate functions, namely, Ra-HBP2 and Japanin. The Ra-HBP2 has been proposed for therapeutic use since it sequesters two histamine molecules, with different affinities, thereby reducing inflammatory responses  16. Japanin reprograms dendritic cells (antigen-presenting cells) so they no longer respond to a wide spectrum of stimuli that are specific pathogenic markers for immune recognition  17.
Results and Discussion Identifying three lipocalins from the European tick disease vector, Ixodes ricinus. The most frequent transcripts from the I. ricinus salivary gland transcriptome shotgun assembly (TSA: GADI00000000. 1) are lipocalins (5. 76% of the entire transcriptome) and most (~90%) are putative histamine-binding proteins  26  according to the Conserved Domain Database (CDD)  27  and Pfam  28. This designation by CDD and Pfam suggest that these lipocalins possess the histamine-binding protein fold, but not necessarily an affinity for histamine  29. Instead, Mans et al. 29  proposed a degenerated pattern motif, CD[VIL]X (7,17)EL[WY]X (11,30)C, to search for tick monoamine-binding lipocalins. Using the degenerated motif in a Pattern Hit Initiated (PHI)-BLAST resulted in ~200 sequences for monomine or monotonin in the non-redundant tick TSA database, mainly from I.
29. Many identified I. ricinus lipocalins are also highly glycosylated  31  ; however, according to Schwarz et al. 26  , only three of the eight have glycosylation sites. These include, JAA70260 (4 sites), JAA70156 (1 site) and JAA67401 (1 site). The Illumina data from the Schwarz et al. 26  publication was compiled to initially evaluate the expression patterns of the eight identified I. ricinus lipocalins. The Illumina reads for the lipocalins in Fig. 1  show the four independent cDNA libraries from the I. ricinus salivary gland transcriptome -two nymphal stages (EN and LN) and two adult stages (EA and LA). The specifics of these I. ricinus cDNA libraries can be found in Schwarz et al. 26. Except for the JAA70189 gene, the remaining seven lipocalin genes show extremely low Illumina reads during adult blood-feeding (Fig.
ricinus lipocalins with other tick lipocalins, we performed a second phylogenetic analysis that included 1748 tick lipocalins available in GenBank. After applying some selection criteria to the lipocalins (see methods), the final alignment contained 803 sequences. The NJ phylogenetic tree obtained from this analysis is shown in Fig. 3. The full phylogenetic tree is available in newick format in Supplemental File S1. As in the previous analysis (Fig. 2 ), JAA67401 and JAA65433 clustered together, however, they cluster with other lipocalins from Ixodes, Amblyomma, Rhipicephalus and Ornithodoros ticks, and not Japanin (Cluster 1, Fig. 3  and Supplemental Figure  S2 ). The lipocalins from Ornithodoros in Cluster 1 were previously shown to bind ricinoleic acid (AAT65682 [OmCI]), LTB4 (AAN76829 [TSGP2]) and LTB4 and thromboxane A2 (AAN76830 [TSGP3] and AAA29432 [moubatin]), but not histamine.
Sequences are labeled with species names, GenBank accession numbers and PDB ID (when crystal structures were available). and Monotonin (Fig. 4 ). The substitutions, however, may prevent the three I. ricinus lipocalins maintaining monoamines within their binding cavity or may provide alternative binding modes. Mans et al. 29  proposed a conserved Asp residue found in Monotonin (Asp101), Monomine (Asp94) and Ra-HBP2 (Asp120) at the L site that may act as a marker for monoamine-binding. This Asp residue is conserved (Asp112) in JAA67401 and JAA65433, but not JAA70189, which has a Phe substitution at position 125 (Fig. 4 ). On the same JAA70189 beta-hairpin loop as Phe125, however, there is an Asp120 exposed toward the solvent. The superimposed structure in Fig. 4  of JAA67401 (red) and JAA65433 (orange) depict their 71% identity; the remaining 29% (in blue) are generally in the beta-sheets and beta-hairpin loops near the open-end composed of residues oriented towards the solvent.
Concluding remarks A new approach is presented here to predict the substrate(s) for highly divergent, uncharacterized proteins. Biophysical simulations, such as the stochastic approach employed by the PELE software, permit a robust analysis on the all-atom energy landscape exploration and interaction between a ligand and its target protein. The computational cost of testing high numbers of putative substrates (as is the case for lipocalins) renders PELE impractical. Therefore, we combined bioinformatics, phylogeny and structural analysis to reduce the number of putative candidates tested by PELE. By combining such methods with biophysics, disparate assumptions and calculations are used hence convergent results have a low probability of being by chance. Accurate substrate prediction for uncharacterized proteins is a step forward during the high-throughput sequencing era.
Materials and Methods Sequences. The protein sequence dataset for the global tree of lipocalins comprised 146 sequences. These lipocalins included 113 sequences analyzed by Ganfornina et al. 1  , 30 new sequences reported since 2000 with experimentally determined 3D structures, and 3 lipocalins described herein from the tick, I. ricinus. For the tick tree we used 1748 tick lipocalin sequences available in GenBank. From these initial sequences, those with less than 160 amino acids were removed since this is the average length of lipocalins, resulting in 1463 sequences. An alignment with such divergent sequences as that of lipocalins is challenging and no gap-free positions were obtained. Therefore in order to improve the alignment area, after the initial alignment using MAFFT, we removed from the alignment those sequences with many gaps using MaxAlign  44.
We did not use PAGAN (see below) at this stage, as it would be computationally expensive. The selection using MaxAlign resulted in an alignment of 788 sequences. Since MaxAlign excluded tick lipocalins with known ligands, we used the "add" option from the MAFFT package  45  to include them. The final tick lipocalins alignment contained 803 sequences. The accession numbers of these sequences are provided in Supplemental File S1.
Global tree of lipocalin amino acid sequences. The three alignments produced by the methods described in the previous section were used to infer maximum likelihood (ML), neighbor joining (NJ) and maximum parsimony (MP) phylogenetic trees. The best-fit model of sequence evolution was selected based on the Corrected Akaike Information Criterion (AICc) and the Bayesian Information Criterion (BIC) as implemented in Molecular Evolutionary Genetics Analysis software MEGA 6  49. Accordingly, the WAG+ G 50 substitution model was chosen for subsequent phylogenetic analyses. The ML, MP and NJ methods implemented in MEGA 6  49  , were used to obtain the best tree topologies from each method. All sites of the alignments were used in the tree. The proportion of Gamma distributed sites was estimated in MEGA 6  49.
These PDBs included Japanin (PDB: 4BOE) and Ra-HBP2 (PDB: 1QFT) from R. appendiculatus, Monotonin from the soft tick A. monolakensis (PDB: 3BRN), and the bilin-binding protein (BBP; PDB: 1BBP) from the butterfly P. brassicae. The three I. ricinus salivary lipocalins were modelled using the Robetta server  52. All structures were optimized using the Schrödinger's Maestro Protein Preparation Wizard  53  and any steric clashes identified were removed via minimization -default conditions in the Schrodinger's Maestro package. The Protein Preparation Wizard analyzes the input structure for clustering hydrogen bonds with sampling at the highest degree of hydrogen bonding in equilibrium. A total of 100000 Monte Carlo orientations are performed for each cluster. The algorithm determines an optimized structure according to electrostatic and geometric scoring functions.
Metropolis Monte Carlo exploration simulations for ligand screening. The Metropolis Monte Carlo-based PELE server was used for the biophysical simulations. The PELE software can demonstrate, step-by-step, the entrance or exit pathway of a ligand to/from the active site of a protein. Since lipocalins maintain ligands within their eight-stranded beta-barrel, the PELE software can demonstrate the efficiency by which a particular lipocalin can maintain a specific ligand within the binding cavity. The PELE server provides ready-made scripts that can be accessed at https://pele. bsc. es/ and its many applications are thoroughly explained elsewhere  24. The PELE software implements an anisotropic network model (ANM)  54  for perturbations of the alpha-carbon backbone causing structural conformational changes.
Molecular dynamics studies on lipocalins indicate that the overall conformation of the beta-barrel is maintained while larger changes occur for the open-end beta-hairpin loops  55. Confirmed by NMR, these large conformational changes are present for open-end beta-hairpin loops in bound and unbound lipocalin structures  56. Some regions were omitted from ANM calculations to minimize extraneous perturbations outside the open-end beta-hairpin loops. There are examples of Normal Mode Exploration at the PELE website (https://pele. bsc. es/) for more details. Briefly, the PELE algorithm performs three stages. First, localized ligand translations (or perturbations) and alpha-carbon protein backbone perturbations are performed. Small translations (tra_r 0. 6) were used for a more local exploration (see binding refinement script at the PELE website (https://pele.
Statistical analysis of ligand exploration simulations. A two-way ANOVA was performed to test the differences in the response variable of the distance (in Å) from the active site and binding energy (in kcal/mol), as calculated by PELE, and for the categorical explanatory variables 'lipocalin' and 'ligand'. An ANOVA, which assumes the data are normally distributed, was chosen as the appropriate statistical test because i) it is robust to deviations from normality, even in small sample sizes, and ii) in very large sample sizes, as in our data, the central limit theorem (CLT) validates normal-based methods, such as ANOVA  62, 63. However, frequency distribution histograms were also examined to confirm that there were no radical departures from normality. The tests and plots were performed using the R statistical package  64.
Relative quantitative RT-PCR analyses. Total RNA was isolated from eggs, larvae, nymphs (non-infected and infected with B. afzelii CB43) and adult tick homogenates as well as from dissected tissues (salivary glands, guts and ovaries) from semi-engorged I. ricinus females, as previously described  65. For the qPCR, the single-stranded cDNA that was reverse-transcribed using 0. 5 μ g of total RNA served as a template for an expression profile analyses using the LightCycler 480 (Roche) and SYBR green chemistry. The cDNA preparations from developmental stages, B. afzelii CB43 infection and dissected tissues were made in independent biological triplicates. The qPCR statistics was analyzed and the histograms were generated using GraphPad Prism 6 for Windows (GraphPad Software, San Diego, USA). An unpaired Student's t-test was used for sample group comparisons and for evaluating statistical significance (P-value < 0.
Acknowledgements This work was supported by the  European Union Seventh Framework Programme  ( FP7/2077-2013  under grant agreement no. 316304  to JJV) and with financial support from the  Ministry of Education, Youth and Sports of the Czech Republic  under the  Národní program udržitelnosti I program  (project  LO1218  to JJV), by the  Ministère de l'Education Supérieure et de la Recherche of France  (to ACC), and by the  Grant Agency of the Czech Republic  (grant #s  13-12816P  to RS and  14-36098G  to PTB).
Acknowledgements We thank  P. Paoletti ,  V. Klippenstein ,  S. Edelstein ,  D. Baigl ,  S. Supplisson ,  S. Zhu  and  J. Lehmann  for suggestions. We also thank  Dr. Philippe Rondard  at the  University of Montpellier  for the generous gift of the HA-GluN1 construct. We are grateful to the  Proteomic Resource Center at the Curie Institute  for providing technical resources. Financial support was provided by the  Chinese Scholars Council  ( CSC fellowship  to M. T. ) and the  Agence Nationale de la Recherche of France  ( ANR-JCJC grant  to S. Y. ). Other financial support was provided by  National Natural Science Foundation of China  ( 31528007  to S. Y. ).
FUNDING GC is funded by the  Fondation ARC pour la recherche sur le cancer , the  European Research Council  ( ERC-2010-StG 243312 , RETROGENOMICS), the  French Government (National Research Agency, ANR)  through the  "Investments for the Future" (LABEX SIGNALIFE ,  ANR-11-LABX-0028-01 ), and the  Fondation pour la Recherche Médicale  ( FRM DEP20131128533 ).
The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell's neutral theory of biodiversity can still be estimated. We find that parameters can be inferred provided that PCR noise on taxa abundances does not exceed a certain threshold. However, inference is seriously biased by the presence of artifactual taxa.
In this study, we ask how the parameter estimates of Hubbell's neutral theory, one of the most prominent quantitative biodiversity models of the last decade  3, 8, 9  , are affected by noise in taxa-abundance datasets. We focus on the type of noise generated in DNA-based surveys, and specifically in DNA metabarcoding surveys (see below)  6  , currently the most popular method for environmental DNA analysis. Nevertheless, our results can apply more generally. DNA metabarcoding is a multi-taxa extension of the DNA-based identification of single specimen from tissue samples using a universal DNA-barcode sequence  10. It consists in amplifying a short DNA barcode by PCR from the DNA extracted from an environmental sample (e. g. soil, water, bulk sample of organisms), and sequencing the product by high-throughput sequencing.
Some studies have also applied neutral models to environmental DNA data to interpret the composition of microbial communities. Sloan et al. 26, 27  and Woodcock et al. 28  developed a continuous approximation to Hubbell's model adapted to large-sized bacterial populations. They focused on estimating the rate of immigration into the local community independently of assumptions on the regional pool of taxa, by comparing taxa occurrence in multiple samples  26, [29] [30] [31] [32]  or by measuring the turnover of taxa over time  33. The composition of many microbial communities was found to be compatible with stochastic immigration of taxa of equivalent fitness from a regional pool, at odds with the classic assumption that deterministic niche sorting explains the assemblage of microbial communities  34, 35.
This type of noise can be regarded as simulating the noise generated in the sequencing step. To illustrate our modelling choices with empirical data, we produced a benchmark dataset obtained by mixing the DNA of 16 plant species in known quantities. The experiment and its results are detailed in the Supplementary Methods. After following standard data curation protocols, we found that the dataset contained 33% of artifactual MOTUs and displayed a lognormally distributed multiplicative noise on relative abundances of log standard deviation σ log = 1. 2. We reported these values on the figures as examples of realistic noise intensities. Simulating noise in DNA sequence reads: 'biological' noise. Irrespective of experimental noise, variability in the number of barcode copies per individual may cause bias in the interpretation of read abundances.
For each set of parameters and noise intensity, we generated 100 simulated samples. We reported the mean and standard deviation of the relative biases θ θ θ -( )/ and Î I log ( / ) 10 over the 100 realizations. In the absence of dispersal limitation, the Ewens distribution permits the inference of θ by likelihood maximization. The maximum-likelihood estimator of θ, hereafter referred to as the Ewens estimator, is implicitly given by θ θ = ∑ + = -ˆT j /( ) j J 0 1 as a function of the number T of taxa and the number J of individuals  58. In the dispersal-limited case, the Etienne distribution provides an exact likelihood expression for the simultaneous inference of θ and I 23 , as implemented in the software Tetame  62. As noted previously in the literature, the likelihood landscape of the Etienne formula often displays two local maxima  25, 63.
Discussion Although they provide an unparalleled amount of information, biodiversity studies based on environmental DNA also have limitations. One of them is that the abundance of sequence reads corresponding to a given molecular taxonomic unit does not necessarily reflect the true population abundance of the corresponding taxon. Our analysis offers a quantitative assessment of the importance of this issue in attempting to relate environmental DNA datasets with theoretical model predictions. Our goal was to assess when amplicon-based DNA read abundance data can offer biological insights into Hubbell's neutral theory's predictions. We selected Hubbell's model over other models predicting taxa-abundance distributions because it incorporates a number of key features for any biodiversity model such as demographic stochasticity and dispersal limitation  65.
Estimating the parameters θ and m of the neutral model is useful in interpreting biodiversity patterns even if the community is not governed by purely neutral mechanisms  62. Indeed, θ is closely related to Fisher's biodiversity index, and is an unbiased index of biodiversity, while m quantifies how the local sample is connected to its surroundings. We simulated taxa abundance datasets from a neutral model and 'noised' them using a range of plausible noise types and intensities. We showed that the parameters θ and I could still be reliably estimated by maximum likelihood inference from the simulated sequence reads, provided that artifactual MOTUs are rare, and that lognormal noise on relative read abundances is below a log standard deviation threshold that depends on θ. We also showed that under our modelling assumptions, neutral inference is unbiased for assemblages of multicellular organisms and for variable barcode copy numbers.
However, these methods do not guarantee a complete filtering of artifactual MOTUs from empirical datasets. In particular, chimeric sequences formed at the PCR stage may be misconstrued as MOTUs. Because these sequences are generated by rare PCR replication errors, they should be predominantly represented by few reads. Thus one strategy for removing artifactual MOTUs consists in ignoring all MOTUs below an empirically set abundance threshold. However, in doing so, we lose the information on the relationship between the number of reads and the number of MOTUs. Hence we suggest that a more satisfactory method to mitigate this problem is to take a sufficiently small subsample of the sequence reads so as to trim out the artifactual MOTUs. The presence of artifactual MOTUs in our simulated taxa assemblages manifests itself by a break in the slope of the ranked log-abundance curve (Fig.
1a , see also Fig. S3  in Supplementary Methods). Thus, the adequate subsample size for an empirical dataset may be chosen so as to trim out the MOTUs with abundances below an observed break in the ranked log-abundance curve. Another finding of our study is that for the same proportion of artifactual MOTUs, the θ estimate has a similar relative bias across θ values and the I estimate a similar relative bias across I values. Therefore, if artifactual MOTUs cannot be entirely excluded in an environmental DNA dataset, conclusions should be based on ratios of neutral parameter estimates among samples rather than on absolute values. We modelled PCR noise using a lognormally distributed multiplicative noise term. We found a threshold noise value beyond which the inference of the neutral parameters becomes biased.
This threshold was found to be lower for larger θ values. For instance, the empirical noise intensity σ log = 1. 2 measured on our benchmark dataset was near or below the threshold σ log,th for θ values up to ca. θ = 20, while for larger θ values, it was responsible for a moderate underestimation of θ (20% for θ = 500) and for a serious overestimation of I. Nevertheless, our benchmark dataset was here used for illustrative purposes, and noise intensity may differ in other datasets. In metabarcoding studies, noise intensity likely depends on the barcode, taxonomic group and wet laboratory protocol. Therefore we strongly advise to include at least one benchmark dataset as part of any environmental DNA study to quantify noise intensity. Empirical noise assessments can then be compared to our simulation results.