dataesr/scientific-paragraphs-categorization huggingface dataset:
Annotation of metabolic features Annotation of the discriminating features was done in four steps: 1) The m/z values of all the features were searched against the human metabolite database (HMDB, www. hmdb. ca, as of 25th May 2016) using [M + H] + and [M + Na] + as adducts and ± 8 ppm for molecular weight tolerance, with the metabolite origin set to Toxin/ Pollutant, Exogenous, and Endogenous. 2) Features with HMDB hits were grouped based on retention time similarity and intensity correlation across the samples to assist in identifying ions originating from the same metabolite. 3) Quality of the chromatographic peaks and spectra were inspected and the plausibility of HMDB candidates was assessed based on retention time, isotope pattern and adduct formation. 4) Identification was confirmed by reanalysis of representative samples and pure standards when available and comparison of the retention times and the MS/MS spectra acquired at 10 V, 20 V, and 40 V collision energies.
When standards were not available, MS/MS spectra were acquired and compared against those in mzCloud (www. mzcloud. org) or Metlin (metlin. scripps. edu). The level of identification was based on the recommendations of the Chemical Analysis Working Group of Metabolomics Standards Initiative. (Sumner et al. , 2007)  In our discussion we mainly refer to Level 1 (highest). For the features that could not be identified, the presence of chlorine atoms was studied. A compound exchange file (. cef) was generated for all the discriminant features in Mass Profiler Professional and exported to MassHunter Qual software for formula generation. The presence of 1-3 Cl atoms were required in addition to C (n = 2-50), H (n = 1-100), O (n = 0-10), N (n = 0-10), and S (n = 0-1), with maximum allowed mass error of 5 ppm and minimum score value of 50.
Acknowledgments This work was supported by the grant  FP7  of the  European Commission  ' Enhanced exposure assessment and omic profiling for high priority environmental exposures in Europe'  ( EXPOsOMICS grant   308610  to PV). The Centre for Environment and Health is supported by the  Medical Research Council and Public Health England  ( MR/ L01341X/1 ). Marc Chadeau-Hyam  acknowledges support from  Cancer Research UK ,  Population Research Committee Project grant ('Mechanomics ' project # 22184  to MC-H).
Except for these grains, kinematics are inhibited after 50 cycles. Porosity changes at the interface X-ray images are analysed looking at the grey levels in order to assess the effect of cycles on porosity. The study is carried out using the open-source image processing software Fiji (see  Schindelin et al. , 2012). Three phases are identified in the images as shown in Fig. 4 (c): pores (low grey level), intact grains (high grey level) and fines produced by grain crushing. These fines are smaller than the pixel size, therefore, they cannot be resolved at the spatial resolution of the images. However, they can be associated with an intermediate mean grey level. Choosing appropriate values for the grey level thresholds, the percentage of voxels belonging to each phase is estimated within 5-voxels-thickness hollow cylinders centred on the pile axis.
ACKNOWLEDGEMENTS The authors gratefully acknowledge  Pascal Charrier ,  Christophe Dano ,  Matías Silva  and  Edward Andò , from Laboratoire  3SR , for their contributions. They also thank the three reviewers for their extremely valuable suggestions. Laboratoire 3SR is part of the  LabEx Tec 21 (Investissements d 'Avenirgrant agreement number  ANR-11-LABX-0030 ).
*Represents the P-value <0. 05, when healthy controls group compared to cancer group in the automated system and ++ represents the P-value <0. 05 when cancer after treatment group in the automated system compared to cancer after treatment group in the semiautomated system. patients samples were acquired pre-diagnosis and thus pretreatment. It was only after obtaining the pathology report from the consultant at the clinic that cancer or other disease states could be confirmed. It is possible that both susceptibility and cancer status could be involved but this can only be ascertained by a long-term cohort study over several decades or in a mortality and morbidity study with pooled data bases linked to statistics from cancer registries. In terms of identifying those at risk of having or developing cancer, this uncertainty has no effect on the functionality of the assay because of its empirical nature and the power of the assay is based on this concept.
Optical sections were captured at 0. 3 lm Z steps using a Prior Proscan stepping motor with an EM-CCD camera (Cascade II, Photometrics) connected to a spinning-disk confocal head (CarvII, Beckton Dickinson) mounted on an inverted microscope (Eclipse TE2000S, Nikon). Each image is a maximum-intensity projection of all sections. Images were recorded using METAMORPH software package (Universal Imaging) and processed using IMAGEJ (http://imagej. nih. gov) and Adobe Photoshop.
Study funding Research reported in this publication was supported by the  Agence Nationale de la Recherche  ( ANR-16-CE16-0011  MC, AB, NBB), the  Fondation Maladies Rares , and  DESIRE  (grant agreement  602531 ). The project was also supported by the  European Network on Brain Malformations  ( COST Action   CA16118 ). The authors have no conflict of interest to declare. Disclosure N. Vegas ,  M. Cavallin ,  C. Maillard ,  N. Boddaert ,  J. Toulouse ,  E. Schaefer  report no disclosures. T. Lerman-Sagie  has served on the editorial boards of the  Journal of Child Neurology, Harefuah , and the  European Journal of Paediatric Neurology. D. Lev  has received research support from the  Sackler School of Medicine (Tel Aviv University). M. Barth  and  S. Moutton  report no disclosures. E. Haan  has received research support from the  Lipedema Foundation (USA).
The recomposition of fragments captured semi-randomly from the flows of data produced by our online activities is one of the artist's major interests, with a view to divesting the narrative of any trace of intentionality and showing how the emergence of meaning is inherently affected by contingency. Just as, according to Chatonsky, machines make a translation of the world into lines of code beyond meaning, so this idea of a non-human consciousness, a "something" which discovers the ruins of our world, in other words, this fiction, also attempts to think the world without humankind. This conception is endebted to Quentin Meillassoux's work, but Chatonsky additionally seeks to think beyond narrative in discarding its causal logic. The excavation of a data centre poses the question of the archive in the perspective of a problem specific to the architecture of databases which only produce sense if there is a computer programme interface to allow the previously atomised data to to be linked up, and this in turn immediately poses the problem of potentially absurd combinations, in a non-human context.
Divination by dreams 9 In Chatonsky's works, the juxtaposition of fragments from online sources or databases is generated only by the blind logic of a programme whose idiocy guarantees its malleability. Memories Center,  19  whose title once again refers to the data centres where the traces of our online activities are stored, uses 20,000 narratives of dreams put into a database by two Californian researchaers. Chatonsky describes his work as follows: "a computer programme [which] produces new dream sequences, reads them and captures images on the Internet corresponding to chosen keywords. " The relevance of the keywords is determined by the length of the chain of characters, and not by any semantic filter. These words determine the choice of three images through Markov chains: the associations produced depend on a semi-random process similar to the logic of dreams, characterised by juxtaposition or assembly unconstrained by intentionality or respect for the principle of non-contradiction.
From the point of view of the reader/spectator, it is narrativity that is destroyed, with the result that he or she either supplements the absent logical links with the logic of filmic montage, post hoc ergo propter hoc ("after this, therefore because of this"), or else the sequence is abandoned to meaninglessness. 12 In order to expand on how the work creates not contingency, but an effect of contingency, I shall return to the issue of the atomisation of data involved in the construction of a database. The linking of dream fragments with images is not the product of chance in the sense of something totally undetermined, but rather of an unfathomable determinism. The way in which the selection of elements proceeds through an arborescence is comparable to Lucretius's theory of the clinamen, or swerve, of atoms, which occurs in too short a time to be thinkable: it is an infraempirical "event.
" Deleuze's analysis in Logic of Sense is relevant to the new relation to time proposed by Chatonsky: "the clinamen is utterly different from a sideways movement which happens to alter the path of a vertical fall. It has always been present […]. The clinamen is the originary determination of the direction of the atom's movement. "  22 This is why the flow has neither origin nor end, or at least the nontotalisable circulation of data on the network tends to produce this interpretation. 13 Moreover, due to the combinatory capacities of the machine, and its generative power, which seems infinite to us because it exceeds our powers of comprehension, every dream becomes potentially the equivalent of all the others. To which should be added that whereas the database of dream narratives contains 20,000 sequences, the quantity and nature of the images stored online is unlimited.
The work's principle is therefore a continuous process of filmic montage. The process of reading, the time of narration and the fictionalisation of the whole, are produced only at the moment of reception. The relation between the different intermingling flows is immediately problematic. It is impossible to embrace in a single look the narrator as he tells a story which interferes with the reconstitution of sentences from the single words which emerge in the centre screen, and at the same time the moving images distract the viewer laterally. The atomisation of data, which is an inherent property of databases, together with the multiplication of narrative flows-written, visual and sound-quickly saturates the reader's/viewer's perceptual and cognitive capacities, producing a hallucinatory effect, as though the work were a form of machine-driven divination.
2001 ) and with anthropometric indices of central adiposity  (Siani et al. 2001). In the present study, we analyzed data collected in the Olivetti participants to determine whether the carriers of the Gly40Ser mutation of the glucagon receptor exhibit an abnormal potassium handling. We hypothesized that a less sensitive glucagon receptor in the kidney might lead to a less efficient secretion of potassium in the collecting duct and thus, to a less efficient urinary excretion of potassium.
Subjects and Methods The Olivetti Heart Study is an epidemiological investigation of cardiovascular risk factors carried out in southern Italy. The study started in 1975 with periodical follow-up for 30 years and involved the Olivetti factories male workforce (Olivetti Heart Study official website: www. olivettiheartstudy. org). Most of the data presented in the present article were collected during the 2002-2004 follow-up visit during which a total of 940 men (age range 25-75 years) were examined. The local Ethics Committee approved the study protocol, and participants provided informed written consent.
For the purpose of this analysis, a complete database for the serum and urinary potassium parameters at the 2002-2004 follow-up examination was available for 25 carriers of the G allele. We then selected in the same cohort the highest possible number of age-and weight-matched CC controls for each of the 25 carriers of the G allele. This resulted in 4 CC noncarriers for each of the G allele carriers.
Acknowledgements A. M. , V. S. , S. W. , F. N. and C. S. acknowledge the financial support of the  European Community  within the  Seventh Framework Programme  ( FP7)  under Grant Agreement No. 295775  (Project SoTherCo). S. C. , M. Q. and X. F. thank  Kurt Hansen  for all the support in the experiments. S. C. thanks  Thomas Smitshuysen  from  DTU CEN  and  Ebba Schnell  for their help in the SEM measurement. The authors acknowledge  David Wyon  for the proofreading work.
, 2012). Previous studies have shown that environmental chemicals, such as perfluorinated compounds and flame retardants, can competitively bind to TTR  (Hamers et al. , 2008; Weiss et al. , 2009; Weiss et al. , 2015) , which may alter TH bioavailability. Environmental chemicals can also induce thyroid disruption through activating or inhibiting the TR  (Zoeller, 2005). Of the 8306 chemicals analysed in the US EPA ToxCast database, 1815 (22%) were reported to be active in the stable TR reporter gene GH3. TRE-Luc assay in antagonist mode, with only 39 (0. 5%) active in agonist mode  (US EPA, 2015). In contrast to single chemicals, fewer studies have applied in vitro assays indicative of thyroid activity to environmental water samples  (Ishihara et al. , 2009; Jugan et al. , 2009; Escher et al.
Data Analysis Log-logistic concentration-effect curves were used to determine the concentration causing 50% inhibition (IC50) or 50% effect (EC50) for the model compounds and water extracts. The EC50 and IC50 values for the model compounds were reported in nanomolar units, while the EC50 and IC50 values for the water extracts were reported in units of relative enrichment factor (REF), which considers both sample enrichment by SPE and dilution in the assay  (Escher and Leusch, 2012). The effect in the water extracts were expressed as bioanalytical equivalent concentrations, which were calculated by dividing the EC50 or IC50 value of the reference compound by the EC50 or IC50 of the water extract. MMI equivalent concentrations (MMIEQ) were reported for the TPO inhibition assay and T4 equivalent concentrations (T4EQ) were reported for the other assays.
The two TTR displacement assays were generally less sensitive compared to the reporter gene assays and XETA, and there was a 2 to 10 times difference in the corresponding agonist IC50 values for the FITC and ANSA assays. Five model compounds previously reported to act as antagonists were run in all in vitro assays. Only the ultraviolet filter THBP and antithyroid pharmaceutical MMI had an effect in the TPO inhibition assay. The pesticide PCP and industrial compound ETU were previously reported to be active in this assay in the US EPA ToxCast database, but only at concentrations 6. 2 and 3. 9 times higher than tested in the current study, respectively  (US EPA, 2015). MMI is a potent TPO inhibitor and has been shown to induce thyroid disruption in vivo  (Degitz et al. , 2005) , though no effects were observed in the other in vitro assays indicative of TH transport and TR mediated action.
Lymphocyte Populations in the Spleen Spleens were dissociated in RPMI 1640 medium. Red blood cells were lysed with NH 4 Cl 140 mM (eBioscience, San Diego, CA, United States) before counting nucleated cells with a hemocytometer. To evaluate lymphocyte sub-populations, 10 6 splenocytes were incubated for 15 min at 4 • C in the dark with a mixture of four anti-mouse monoclonal antibodies: ECD anti-CD19 (clone 6D5, Beckman Coulter, Marseille, France), APC anti-CD3ε (clone 17A2, eBioscience), PE anti-CD4 (clone RM4-5, eBioscience) and PE-Cy7 anti-CD8α (clone 53-6. 7, eBioscience). Immunophenotyping was carried out using a five-color FC500 flow cytometer (Beckman Coulter). Data were analyzed using the FlowJo v7. 6. 5 software (Tree Star Inc. , Ashland, OR, United States).
Quantification of Cytokines Mouse sera and culture supernatants were thawed just before analysis. Cytokines (IFNγ, IL-12p70, IL-4, IL-5, IL-6 and TNFα) were quantified using the Bio-Plex R Instrument (Bio-Rad, Ivry sur Seine, France) and the ProcartaPlex Mouse Essential Th1/Th2 Cytokine Panel (Affymetrix, Santa Clara, CA, United States). Concentrations were determined using the Bio-Plex R software and expressed in pg/ml. The sensitivity of this kit is 0. 09 pg/ml for IFNγ, 0. 21 pg/ml for IL-12p70, 0. 03 pg/ml for IL-4, 0. 32 pg/ml for IL-5, 0. 21 pg/ml for IL-6 and 0. 39 pg/ml for TNFα.
Splenic Lymphocyte Populations To understand why splenic mass is decreased in CUMS mice, we determined the number of nucleated cells in that organ. Table  3  shows that this number was the same in both groups of mice. Furthermore, no statistically significant difference was observed between total lymphocyte percentages (Table  3 ). To precise these data, we determined the percentages of major splenic lymphocyte sub-populations by immunophenotyping. CD19 was used to identify B cells, CD3 to identify T cells, CD3 + CD8 to identify cytotoxic T cells and CD3 + CD4 to identify helper T cells. Cells positive for each phenotypic marker, or a combination thereof, were quantified within the viable lymphocyte gate. Our data show that the percentages of CD19 + B cells, CD3 + T cells, CD3 + CD4 + helper T cells and CD3 + CD8 + cytotoxic T cells did not vary between the two experimental groups (Table  3 ).
8) Specific medical conditions improvement (blood/ heart diseases 3,5 ,anticancer properties 3,5 ). (Gray et al. , 2005; Owusu-Kwarteng et al. , 2017) , using cell cytotoxicity assays, with Ped-2E9-murine hybridoma lymphocytes and CHO-based assays, as well as PCR methods. Hemolysin and lecithinase toxins, emetic toxins, diarrheal toxin, B component (dermonecrotic), EntFM (enterotoxic, induces vascular permeability), CytK (necrotic enteritis) and toxin genes bceT, cytK, nheA, nheB, nheC, hblA, hblC, hblD, entFM are typically found in a number of B. cereus strains  (Gray et al. , 2005; Hwang & Park, 2015). It is worth mentioning, that available genetic data for B. cereus (whole genome sequence from GenBank, 2018; Table  5 ) show numerous intrinsic similarities with Bacillus anthracis and Bacillus thuringiensis  (Ivanova et al.
Many probiotic Bacillus species are available in their type strains version, biochemically and genetically characterized, with additional detailed information regarding cultivation conditions, safety, risk groups and a list of references. Examples of probiotic Bacillus sp. type strains, with identity numbers in different microorganism collections and chosen information, covering available genome and 16s rRNA gene nucleotide sequence data with GenBank accession numbers, are given in Table 5  (GenBank, 2018).
Acknowledgements of Financial Support This work was supported by  GRUPA INCO S. A. , ul. Wspólna 25,  00-519 Warsaw, Poland ,  NCBiR  grant  POIG. 01. 04. 00-02-181/13  and  Polish Ministry of Science and Higher Education  funds DS 530-8645-D746-18 available for University of Gdansk, Faculty of Chemistry,  Department of Molecular Biotechnology.
Multilocus sequence typing (MLST) was performed using MLST version 2. 0 from the Center for Genomic Epidemiology (5). PAL0. 1 (PAO1 clade) is a Verona integrinencoded metallo-beta-lactamase (VIM-2)-producing strain that belongs to the sequence type 111 (ST-111), a clonal strain responsible for nosocomial infection epidemics worldwide (6, 7). PAL1. 1 (PA14 clade) shares an acquired resistance genotype commonly observed worldwide among clinical P. aeruginosa strains (8) belonging to ST-2613. Data availability. The whole-genome shotgun project of PAL0. 1 and PAL1. 1 has been deposited in DDBJ/EMBL/GenBank under the accession no. QFRL00000000 and QFRM00000000, respectively. The SRA accession no. is SRP155966.
Characterization In the conversion/complexation experiments, the determination of reactants, intermediates and products quantities was carried out using a Shimadzu high-performance liquid chromatography (HPLC) (Shimadzu Europa, Duisburg, Germany) instrument equipped with a LC-20ADXR pump, a DGU-20A5R degasser, a SIL-20ACXR autosampler, a SPD-MD20A diode array detector, a CTO-20AC oven and a CBM-20A communicator module piloted by a LabSolution software (LC Driver Ver1. 0, Shimadzu Europa, Duisburg, Germany). The column was an Aminex HPX-87H (300 mm × 7. 8 mm, 9 µm; Bio-Rad, Hercules, CA, USA). The mobile phase was 5 mM H 2 SO 4 , using isocratic mode with 0. 4 mL. min-1. The chosen wavelength for HMF and levulinic acid detection were 284 nm and 266 nm, respectively. The chosen wavelength for detection of formic acid, D-Glucose and D-Fructose was 195 nm.
Funding: This research received no external funding. Acknowledgments: This research was funded by  IFP Energies nouvelles for funding these studies. Chevreul Institute  ( FR 2638 ),  Ministère de l'Enseignement Supérieur et de la Recherche ,  Région Hauts-de-France  ( CPER ALIBIOTECH ),  REALCAT platform ('Future Investments' program  (PIA), with the contractual reference ' ANR-11-EQPX-0037  ) and  FEDER  are acknowledged for supporting and funding partially this work.
Mitochondrial and nuclear datasets To be able to build an alignment consisting of sequences of comparable length (and therefore comprehensive datasets), we obtained sequences of similar length to these downloaded from Genbank. Newly generated 662 mitochondrial and 63 nuclear sequence data from WCM in Poland were combined with previously published 85 Cox1 and 46 28S rDNA D2 regions of WCM and outgroup Trisetacus species data  [36, 39, 48, 50]  for analysis (see Additional file 1: Table  S1  for sample details and Genbank accession numbers). Trisetacus genus is a taxon belonging to the Eriophyoidae associated with coniferous plants, for which genetic differentiation according to host plants has been recorded  [50]. Sequences were aligned using the MAFFT algorithm (https://www. ebi. ac. uk/Tools/msa/ mafft/).
Altogether 747 Cox1 (662 + 85; 603 bp) and 109 28S D2 (63 + 46; 595 bp) sequences were analyzed and evaluated. They were obtained from mite specimens from 25 plant species (13 plant species collected in Poland in the course of this study plus 12 plant species from earlier sample collections) and eight countries (Additional file 1: Table  S1 ). Sequences from both mitochondrial and nuclear datasets were collapsed to haplotypes using FABOX 1. 41 DNA collapse tool  [51]  resulting in a batch of 291 unique Cox1 haplotypes, 39 unique D2 sequences, and 84 unique concatenated Cox1 + D2 sequences. Alignment reliability and product authenticity of Cox1 sequences was validated by translating aligned DNA sequences into amino acids and assessing the alignments for premature stop codons. A simplified Cox1 sequence dataset with a representative set of 158 sequences (for each WCM lineage a maximum of five sequences from the same country and same host) was used for the construction of phylogenetic trees.
This selection was based on preliminary trees and aimed to simplify the phylogenetic tree as well as to keep the general tree structure. Cox1 and D2 sequences obtained from the same DNA isolate were concatenated resulting in a dataset consisting of 109 concatenated haplotypes that were collapsed to 84 unique concatenated sequences. Partition congruence was analyzed using the incongruence length difference test (ILD) with 100 partition homogeneity test replicates implemented in PAUP* 4. 0a147  [52].