dataesr/scientific-paragraphs-categorization huggingface dataset:
Phytochemical constituents such as tannins, flavonoids, alkaloids and several other aromatic compounds are secondary metabolites of plants which are used as defense mechanisms against predation by many microorganisms, insects and herbivores  [36]. Regarding the absence of data on antibacterial properties, the Minimum Inhibitory Concentration (MIC) method was used to determine the antibacterial activity. Our results suggest moderate effect on Gram-positive bacteria while Gram-negative bacteria were found to be less sensitive to the extracts. A possible explanation for these observations may lie in the significant differences in the outer layers of Gram-negative and Gram-positive bacteria. Gram-negative bacteria possess an outer membrane and a unique periplasmic space not found in Gram-positive bacteria  [37].
Image processing and 3D Reconstruction Sample and grid preparation for cryo-EM experiments is detailed in the Supplementary Methods. Images of both holoenzyme and DNA-bound enzyme embedded in vitreous buffer were recorded at 59 000Â magnification on a Tecnai G2 Polara F30 cryo-EM operated at 100 keV with an Eagle 4k Â 4k CCD camera (FEI). Images were recorded in low dose conditions with a specimen dose of 20 electrons/A ˚2 per CCD frame and a pixel size of 1. 92 A ˚/pixel. Data collection was performed automatically using the EPU software (FEI). Images were acquired in a defocus range of À1 to À3 mm. Particles were selected from individual CCD frames in a semiautomated mode using e2boxer in the EMAN2 package  (35, 36)  at a box size of 192 pixels. The contrast transfer function parameters for each micrograph were determined using EMAN2 (http://blake.
Holoenzyme map 3D reconstruction Before cryo-EM data collection, several 3D maps were generated by random conical tilt from negatively stained particles and aligned in 3D, reflecting the sample heterogeneity. The 3D models corresponding to different orientations of the particle were averaged to populate the missing cone of information present in each individual 3D model. The most populated conformation corresponded to an elongated particle about 17-nm high and 9-nm large. A low-resolution map of this conformation was then determined from a data set of cryo-negatively stain particles. The cryo-EM data set without any staining was then analyzed by an iterative protocol consisting of a reference-based classification of particles followed by class averaging and 3D model reconstruction  (36, 37).
Single-particle cryo-EM of the Holoenzyme and DNA-bound complex To maximize the stability of a homogeneous complex, the GyrBA-fus protein was incubated with ADPNP to form the holoenzyme complex and cross-linked using glutaraldehyde. MALDI mass spectrometry analysis showed that cross-linking does not affect the dimeric conformation observed by native mass spectrometry (Supplementary Figure  S3A ). Trypsin digestion experiments coupled to MALDI mass spectrometry show that the same regions are prone to protease digestion in cross-linked and noncross-linked samples indicating that the trapped dimer conformation is preserved in our experiment (Supplementary Figure  S3B ). A data set of 62 322 molecular images was collected from frozen hydrated samples and was analyzed using single particle methods to reconstruct a 3D model from the most populated subset of 20 500 particles corresponding to the holoenzyme.
Furthermore, our structural data on the DNA gyrase show an asymmetric disposition of the CTD b-pinwheel domains, which are both stabilized by the presence of DNA (Figure  3C ). The positions of the b-pinwheel domains induce a smaller $70 DNA bend angle outside the cleavage domain than previously reported in crystal structures of DNA binding-cleavage domains with 34 bp oligonucleotides ($150 )  (6, 16). In our intact protein, the DNA gyrase CTD pinwheels direct the DNA outside the DNA binding-cleavage domain, preventing the DNA ends from moving upward as observed for CTD-less constructs in crystallographic studies. Such a small bend angle ($75 ) could also be observed for the TopoIV, whose CTD displays a partial pinwheel fold. In contrast, the reported mean bend angle measured in FRET and AFM studies are within the range of 150 for full-length eukaryotic Topo2A enzymes, with a CTD sharing no structural homology with the bacterial Topo2A (50).
ACKNOWLEDGEMENTS We are grateful to  S. Ludtke  for his assistance with the EMAN2 package and  J. M. Garnier  for his help with generating the initial expression plasmids. We thank  P. Oudet ,  J. C. Thierry  and  E. Howard  for discussions on the DNA topoisomerase mechanism. We thank  F. Rey ,  P. Arimondo  and  E. Westhof  for suggestions on the manuscript.
FUNDING Marie Curie International Reintegration Grant  from the  European Community   FP7 program ; doctoral grant from the  Alsace Region and CNRS ; the  Fondation pour la Recherche Me´dicale ; Instruct, part of the  European Strategy Forum on Research Infrastructures (ESFRI)  supported by national member subscriptions as well as the  French Infrastructure for Integrated Structural Biology (FRISBI)  [ ANR-10-INSB-05-01 ]. Funding for open access charge:  Fondation ARC pour la Recherche sur le Cancer.
Electrophysiological studies Sciatic nerve action potential (NAP) recording was performed as previously described  [24, 25]. Briefly, sciatic nerves were rapidly dissected from decapitated rats under urethane anesthesia (25%, 0. 5 ml/100g) and immerged in saline medium (NaCl 133, KCl 2, CaCl 2 1, MgCl 2 2, HEPES 10 and glucose 10 pH 7. 4) 5 to 10 min before recording. The sciatic nerve was put on chlorinated silver electrodes mounted in a classical homemade electrodes holder chamber. Square-shaped stimulating pulses of 0. 1ms duration generated by Clampex routine of the Pclamp software package (Axon Instruments, CA, USA) were applied to the distal end of the nerve through Digidata 1322A interface (Axon Instruments, CA, USA). Bipolar sciatic nerve action potentials (NAP) were recorded at the proximal end of the nerve (∆x=19 mm distance from the stimulus point) using an ISO-DAM8A differential amplifier (Word Precision Instruments, UK) with a bandwidth of 10 -10,000 Hz.
The signal was digitized (500 kHz) with the Digidata 1322A. Artifact of stimulation was obtained in isolation using a double pulse protocol allowing the second stimulation to occur in refractory period. This stimulus artifact was subtracted from recorded NAPs before analysis with Pclamp software. Nerve conduction velocity (CV) was calculated using the latency between the beginning of stimulus artifact and the NAP onset (∆t Latency ) or the NAP peak (∆t Peak ) for the fastest and relatively slower fibers group respectively according to the equations: CV Latency = ∆x / ∆t Latency CV Peak = ∆x / ∆t Peak Data obtained from the different conditions were compared using one way ANOVA statistical test followed by Bonferroni's Multiple Comparison Test. Statistical significance was fixed as usually at p<0.
5, respectively. The preparations were examined under a multichannel confocal laser-scanning microscope (Leica Confocal Systems, Paris, France) assisted by a pentium IV PC (Leica Microsystems). The number of CNPase or NF200 immunoreactive fibers was determined in a counting square of 200 x 200 µm 2 on sagittal sections of sciatic nerves isolated from each experimental group. Quantification of NF200 immunoreactivity was performed on sciatic nerve sagittal sections by using ImageJ software. Results were expressed as % of control (+ SEM). The number of PGP9. 5 positive-intraepidermal nerve fibers (IENF) was quantified as previously described  [50, 52] : all ascending nerve fibers that cross into the epidermis were counted, no minimum length was required and secondary branching into the epidermis was excluded from quantification.
Statistical analyses One or two-way repeated measures ANOVAs followed by Newman-Keuls post hoc comparisons were used. The data which did not exhibit a Gaussian distribution were analyzed by the non-parametric Mann-Whitney U test. The statistical significance of differences between sciatic nerve conduction velocities or NAP amplitude peaks was assessed by one way ANOVA statistical test followed by Bonferroni's Multiple Comparison Test. Data were analyzed with Statistica Software 5. 1 (Statsoft, Maisons-Alfort, France). A p-value of less than 0. 05 was considered significant.
Effects of PAC on NF200 expression in peripheral nerve axons To determine whether PAC treatment alters the structural organization of peripheral axons, we used immunohistochemical procedure to compare the expression of the key neuronal cytoskeleton protein NF200  [55]  in PACtreated and control rat sciatic nerve axons. Our results showed an intense NF200-like immunoreactivity in several processes in vehicle-treated or control rat sciatic nerves (Figure  3A ). PACtreatment drastically decreased NF200-immunofluorescence in sciatic nerve axons (Figure  3B ). Quantitative analysis using the counting score method combined with ImageJ software calculation revealed a 33% decrease of NF200-immunostaining in PAC-treated sciatic nerve axons compared to controls (p<0. 001) (Figure  4A ).
Sequencing and Assembly Statistics As shown in Table  1 , normalized and non-normalized libraries sequencing runs lead respectively to 724,119 and 581,370 reads of 344 and 315 mean bases length. In both cases, assembly using Newbler produced a similar number of contigs (69,975 and 57,962) covering about half of the reads. In the present study, non-assembled reads were not used for further analysis, and were not considered for prediction of new toxin compounds, but this major pool of single reads could be of great interest for future investigation. This also shows that despite deep sequencing and as mentioned in previous studies  [20] , the function of a significant part of the transcriptome is still unknown. Comparison of the two data sets (Supplementary Figure  1 ) shows that it is necessary to annotate only 1105 contigs to access 80% of the non-normalized dataset versus 13,221 contigs for the normalized one.
Analysis of Highly Expressed Transcripts and Detection of Unknown Proteins We focused our attention on the 57 most abundant gene transcripts (Figure  5 ), constituting more than 50% of reads. Surprisingly, we could not retrieve similar sequences from the GenBank database for the most abundant transcript recovered in this study, suggesting that this may be a new toxin type. SignalP program predicted a putative signal peptide for these transcripts, suggesting that this product is likely to be expressed in the venom glands. The mature sequence is 173 amino acids in length and includes two highly conserved cysteine residues. We were able to uncover at least 10 different isoforms from 34 full-length sequences. If similarly secreted, the high level of expression of this transcript in the venom gland suggests a "toxic" role for this new compound.
Bioinformatic Processing of the 454 Reads and Annotation of the Dataset Sequences were trimmed to remove adapters and low quality regions. Reads were assembled using Newbler 2. 3 (454 Life Science). An identity threshold of 98% was chosen for contig assembly with a minimal overlap of 40 bp. Open reading frames were predicted using GeneMark. hmm-E [26]  and matching contigs and singletons of at least 60 amino acids in length were further annotated by similarity search on the NR database of GenBank, specifying an e-value cut-off of 1E-05. Snake venom gland-specific transcripts were then selected from best-BLAST hit descriptions using a list of keywords of all known toxin protein families described so far  [18, 27]  in a broad range of venomous taxonomic groups. As most toxin sequences originate from duplication events of common cellular genes, retrieving toxin sequence by simple key-word search is highly prone to a false positive detection.
To avoid this major pitfall, we trimmed putative toxins from the original list. We choose to select hits showing a best bidirectional BLAST hit on NR database. To analyze the diversity of the toxin repertory, stringent parameters were applied as following: exclusion of (i) truncated sequences, (ii) sequences with ambiguous positions, and (iii) sequences lacking a signal peptide after a SignalP software screening  [28]. Nonetheless, we applied less stringent parameters for weakly expressed toxin families as we were sometimes unable to identify full-length sequences (see below). Information and datasets resultant from this project can be accessed from DDBJ/EMBL/GenBank under following accession numbers: Bioproject PRJNA210890, Biosample SAMN02230181, Sequence Read Archive (SRA) SRR931902 and Transcriptomic Shotgun Assembly SUB296805 and SUB291519.
Functional Annotation of Contigs To characterize the major transcripts of the venom gland transcriptome, we have chosen to describe the most abundant transcripts representing 80% of the dataset using reads from non-normalized library. Although the relationship between the number of transcripts and the corresponding amount of protein expressed is not always linear, analysis of transcripts covering 80% of reads assembled into contigs can nevertheless highlight the key molecular components of venom production as well as the main compounds of the venom cocktail. The distribution of functional categories for COGs, KOs, NOGs, and Subsystems at the highest level supported by these functional hierarchies was processed after the BLAST step against NR protein database.
Prediction of Non-Matching Sequences Several studies have shown that transcriptomes include a large number of uncharacterized sequences whose function is still unknown. These sequences can cover several categories of transcripts including mainly non-coding RNAs  [20]. We were particularly interested in the presence of transcripts which do not show strong similarities (e-value threshold set to 1E-05) with proteins or sequences already identified. For this, we combined the use of homemade software, which analyzes BLAST results, Signal P outputs and an optional detection of cysteine patterns. In the case of a venom gland, the detection of a transcript corresponding to a secreted protein suggests that the protein is most likely a toxin as the common core of the vertebrate genome is relatively well characterized.
Diversity Analysis Using Evolutionary Networks Phylogenetic analysis of toxins remains the gold standard to estimate sequence diversity and evolutionary processes. Unfortunately such analysis can lead to unresolved topologies for the following reasons: (1) the toxins are mainly small peptides, and (2) they are often very diverse. Consequently, alignments produced for a given family are generally of low quality and the number of positions available to produce informative phylogenetic analysis supported is insufficient. This gives rise to the production of non-informative topologies. In order to the nature of these sequences, we chose to adopt a network analysis. To form the data set, we imported the curated sequences of toxins available on Uniprot (named ToxProtDB,  [29] ) and we produced a non-redundant data set using cd-hit clustering software  [30].
In addition, Fast, Unconstrained Bayesian Approximation (FUBAR) approach implemented in HyPhy package  [38, 39]  was employed to provide additional support to the aforementioned analyses and to detect sites evolving under pervasive diversifying and purifying selection pressures. We also employed Mixed Effects Model Evolution (MEME)  [39]  to detect sites evolving under the influence of episodic diversifying selection. To clearly depict the pro-portion of sites under different regimes of selection, an evolutionary fingerprint analysis was carried out using the ESD algorithm implemented in datamonkey  [40]. We also employed branch-site REL (BSR) test  [41]  implemented in HyPhy to identify lineages diversifying under the influence of episodic selection pressure.
Acknowledgments To  Yvan Ineich  ( National Museum of Natural History, Paris, France ) for snake species identification. BGF was funded by the  Australian Research Council (ARC)  and the  University of Queensland. KS was funded by the  Ph. D. grant ( SFRH/BD/61959/2009 ) from F. C. T (Fundacao Fundação para a Ciencia Ciência e a Tecnologia).
pseudotuberculosis strains IP31758, IP32953, and YPIII (accession no. NC_009708. 1, NC_006155. 1, and NC_010465. 1, respectively). The average GϩC content of the draft genomes is 47. 53%. The comparative genomic analysis among strains B-6796 (C-2), B-6862 (797), B-6863 (1384), B-6864 (8421-S), B-6865 (2430-1), and B-6866 (2430-2) and other available Y. pseudotuberculosis and Y. pestis isolates (i) will provide information on the speciation and evolution of Y. pestis and (ii) might explain the means and mechanisms of the global spread of Y. pseudotuberculosis clone ST19 O:3. A detailed report of a full comparative genomic analysis will be included in a future publication. Nucleotide sequence accession numbers. The draft genome sequences for the strains B-6796, B-6862, B-6863, B-6864, B-6865, and B-6866 have been included in the European Nucleotide Archive at EMBL-EBI (http://www.
ACKNOWLEDGMENTS We are very grateful to  Irina Surovtsova  for feedback and valuable support. The research leading to these results received funding from  Cosmetics Europe  and the  European Community 's  Seventh Framework Program  ( FP7/2007-2013)  under grant agreement  N2 66835  and partly by grant agreement  N˚267038  as well as through the  German BMBF virtual liver funding initiative  (grant agreement  N˚0315762 ). In the final preparation of this manuscript our colleague and friend Jose Manuel Zaldivar unexpectedly died. We are deeply indebted with him due to his courage and energy in the development of central ideas contained in this manuscript.
Conclusion A toolbox to characterize the fate of colloids in mucus was developed. First, our mucus model was characterized. Pig intestinal mucus is a thixotropic, shear-thinning (non-Newtonian) gel, and its viscosity is hydration-dependent. The diffusion through the mucus and the stability of nanoparticles in this medium were then evaluated. These tools also allowed us to demonstrate that LNCs improved Ptx transport through the mucus layer in comparison to Taxol ® and that LNCs were stable for 3 hours at 37°C after contact with mucus. These data also established that LNC sizes smaller than 110 nm did not influence diffusion but that concentration did. These new data confirm that LNCs are a suitable vector for oral delivery of biopharmaceutical classification system class IV drugs such as Ptx.
These data suggested a possible deregulation of DDA metabolism in tumour cells compared with normal cells. We subsequently quantified DDA in human breast tumours and in the adjacent normal tissue from patients. We determined that the mean amount of DDA was fivefold lower in human breast tumours (15±6 ng per g of tissue) compared with matched normal tissue (72 ± 28 ng per g of tissue) (Fig. 2 ). DDA is a selective inhibitor of ChEH. We previously reported that ligands of the AEBS were potent inhibitors of ChEH 4 , which is associated with their capacity to induce tumour cell differentiation and death  5, 9, 10. We investigated whether DDA could be an inhibitor of ChEH activity because we had previously shown that ring B oxysterols inhibited ChEH  4. As shown in the thin-layer chromatography autoradiogram in Fig.
Acknowledgements This work was funded by the  'Institut National de la Santeet de la Recherche Medicale', the 'Universitede Toulouse III', the 'Institut Claudius Regaud', the 'Ministere Franc¸ais de la Recherche ' through a 3-year doctoral fellowship (G. S. ), the  'Association pour la Recherche contre le Cancer ' though a 1-year doctoral fellowship (G. S. ), Partial funding came from the  'Fondation de France ' grant  20349 , the  'National Institute on Environment Health Sciences ' Grant  PA2 ES011269  and  R01 ES002710CM. B. D. H. is a George and  Judy Marcus Senior Fellow  of the  American Asthma Foundation. We thank the staff of the tumour bank of  Claudius Regaud Institute  ( Dr P. Rochaix  and  L. Puydenus ) for their technical support and helpful discussions, and  F. Capilla  for IHC technical support.
Aims: The aim of the study was to investigate the efficacy and safety of as-needed use of nalmefene 18 mg versus placebo in reducing alcohol consumption in patients who did not reduce their alcohol consumption after an initial assessment, i. e. the pooled subgroup of patients with at least a high drinking risk level (men: >60 g/day; women: >40 g/day) at both screening and randomization from the two randomized controlled 6-month studies ESENSE 1 (NCT00811720) and ESENSE 2 (NCT00812461). Methods: Nalmefene 18 mg and placebo were taken on an as-needed basis. All the patients also received a motivational and adherence-enhancing intervention (BRENDA). The co-primary outcomes were number of heavy drinking days (HDDs) and mean total alcohol consumption (g/day) in Month 6 measured using the Timeline Follow-back method.
This article describes a post hoc analysis of the efficacy, safety and tolerability of as-needed nalmefene (18 mg) in the subgroup of patients with at least a high drinking risk level at both screening and randomization, based on the two doubleblind, randomized, placebo-controlled 6-month nalmefene efficacy studies: ESENSE 1  (Mann et al. , 2013; NCT00811720)  and ESENSE 2  (Gual et al. , 2013; NCT00812461).
Statistical analyses For the current post hoc subgroup analysis, three datasets were used: The target population, comprising all patients with at least a high drinking risk level (men: alcohol consumption >60 g/day; women alcohol consumption >40 g/day), as defined by the World Health Organization  (WHO, 2000)  at both screening and randomization, was used for the description of the baseline characteristics of the study sample. The target safety population, comprising all patients in the target population, but excluding from the dataset those with no recorded study medication intake and all study medication returned, was used for all safety analyses. The target efficacy population, comprising all patients in the target safety population with at least one valid postbaseline assessment of HDDs and total alcohol consumption, was used for all efficacy analyses.
Zeta potential and particle size The zeta potential was measured using a Malvern Zetasizer Nano ZS (Malvern Instruments, Worcestershire, UK) based on quasi-elastic light scattering at 25°C following 1/50 (v/v) dilution in a 1 mM NaCl solution. The values reported represent the average of three measurements. The size distribution of the powder was measured by light diffraction using a Mastersizer 2000 equipped with a Scirocco dry dispenser (Malvern Instruments, Orsay Cedex, France) at a dispersing pressure of 2 bar. Each sample was measured in triplicate. Data are expressed in terms of the particle diameter, at 10%, 50%, and 90% of volume distribution (D10, D50, and D90, respectively). The volume distribution span, which is the distribution width measurement relative to the median diameter, was calculated as follows: Span D90 D10 D50 = - (2) X-ray diffraction X-ray powder diffraction patterns were measured using a D4 Endeavor ® diffractometer (Bruker, Billerica, MA.
Acknowledgments The authors would like to thank the  Chilean Council for Science and Technology, (CONICYT-FONDECYT ) (Project  11080101 ). B Tobar-Grande is supported by the  International Cooperation Agency of Chile (AGCI). Institut Galien Paris-Sud  is a member of the  Laboratory of Excellence LERMIT  supported by a grant from  ANR  ( ANR-10-LABX-33 ). We would also like to thank  Margarita González  and  Mario Rodríguez  for their fruitful technical discussions concerning this work.
Acknowledgements We are grateful to all the women who participated in the study, particularly to those involved in STOPPAM project. We thank all the medical staffs of Akodeha, Come Central and  Ouedeme Pedah  health centres, for their valuable contributions. We also thank  Nadine Fievet  for facilitation of the field work,  Parfait Houngbegnon  for help in data analysis and  Jerome Clain  for critical review of the manuscript.