dataesr/scientific-paragraphs-categorization huggingface dataset:
A score >1. 9 enabled the identification at the species level and a score < 1. 7 did not enable any identification. Sequencing the 16S rRNA gene is needed to achieve the identification if the bacterium is not referenced in the database. The 16S rRNA gene amplification and sequencing were performed as previously described  (Morel et al. , 2015). For similarity level thresholds of 98. 65% and 95%, a new species or a new genus was suggested, respectively, as proposed by  Kim, Oh, Park, & Chun, (2014).
| Phylogenetic tree A custom python script was used to automatically retrieve all species from the same order of the new genus and download 16S sequences from NCBI, by parsing NCBI eutils results and NCBI taxonomy page. It only keeps sequences from type strains. In case of multiple sequences for one type strain, it selects the sequence obtaining the best identity rate from the BLASTn alignment with our sequence. The script then separates 16S sequences in two groups: one containing the sequences of strains from the same family (group a) and one containing the others (group b). It finally only keeps the 15 closest strains from group a and the closest one from group b. If it is impossible to get 15 sequences from group a, the script selects more sequences from group b to get at least nine strains from both groups.
Spectral database search was performed using MS Search 2. 0 operated with the Standard Reference Database 1A (NIST, Gaithersburg, USA) and the FAMEs mass spectral database (Wiley, Chichester, UK). Susceptibility to antibiotics was tested using Müller Hinton agar medium (bioMérieux) according to EUCAST 2015 recommendations (http://www. eucast. org). The following antibiotics were tested: doxycycline, cefoxitin, ciprofloxacin, clindamycin, erythromycin, fosfomycin, linezolid, oxacillin, penicillin, pristinamycin, rifampicin, teicoplanin, trimethoprim-sulfamethoxazole, vancomycin, colistin, and metronidazole.
68 nmol/L. The libraries were normalized at 3 nmol/L and pooled. After a denaturation step and dilution, the pool of libraries was loaded onto the reagent cartridge and then onto the instrument along with the flow cell. Automated cluster generation and sequencing run were performed in a single 2 × 251-bp run. Genome assembly was performed in pipelines that allow us to make assembly with different assembly's softwares, on trimmed or not trimmed data. Velvet  (Zerbino & Birney, 2008) , Spades  (Bankevich et al. , 2012) , and Soap Denovo  (Luo et al. , 2012)  were used on trimmed (MiSeq software and Trimmomatic  (Bolger, Lohse, & Usadel, 2014 ) software) and on not trimmed data (only MiSeq software). For each of the six assemblies performed, GapCloser  (Luo et al. , 2012)  was used to reduce gaps.
| Genome annotation and comparison The prediction of open reading frames (ORFs) was performed by Prodigal (http://prodigal. ornl. gov/) with default parameters but the predicted ORFs were excluded if they were spanning a sequencing gap region (containing N). The predicted bacterial protein sequences were searched against the clusters of orthologous groups (COG)  (Galperin, Makarova, Wolf, & Koonin, 2015)  using BLASTP (E-value 1e -03 , coverage 0. 7, and identity percent 30%). If no hit was found, it was searched against the NR database using BLASTP with E-value of 1e -03 coverage 0. 7 and identity percent of 30%, and if the sequence length was smaller than 80 amino acids, we used an E-value of 1e -05. tRNA genes were found by the tRNAScanSE tool, whereas ribosomal RNAs were found using RNAmmer  (Lagesen et al.
, 2007; Lowe & Eddy, 1997). Using Phobius, the lipoprotein signal peptides and the number of transmembrane helices were predicted  (Käll, Krogh, & Sonnhammer, 2004). ORFans were identified if all the BLASTP performed did not give positive results (Evalue smaller than 1e -03 for ORFs with sequence size larger than 80 aa or E-value smaller than 1e -05 for ORFs with sequence length smaller 80 aa). The XEGEN software (Phylopattern) allowed us to automatically retrieve genomes from the 16S RNA tree  (Gouret, Thompson, & Pontarotti, 2009). For each selected species, the complete genome sequence, proteome sequence, and Orfeome sequence were retrieved from the FTP of NCBI. The proteomes were analyzed with proteinOrtho  (Lechner et al. , 2011). Then for each couple of genomes, a similarity score (mean value of nucleotide similarity between all couple of orthologues between the two genomes studied) was computed by AGIOS software (Average Genomic Identity Of gene Sequences)  (Ramasamy et al.
, 2014 ). An annotation of all proteome was done to determine the predicted genes functional classes' distribution according to the clusters of orthologous groups of proteins. The Multi-Agent software system DAGOBAH, which includes Figenix libraries for provide pipeline analysis and Phylopattern for tree manipulation, was used to perform the annotation and comparison processes  (Gouret et al. , 2011). Genome-to-Genome Distance Calculator (GGDC) analysis T A B L E 1 Classification and general features of Hugonella massiliensis strain AT8 T according to the MIGS recommendations  (Field et   These evidence codes are from http://www. geneontology. org/GO. evidence. shtml of the Gene Ontology project  (Ashburner et al. , 2000). If the evidence is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgments.
| Phenotypic and biochemical features Strain AT8 T presents small, smooth, shiny, circular colonies with a diameter of 2-5 mm. Strain AT8 T is gram-positive, nonmotile, and nonspore forming (Fig. S1 ). Cells are rod-shaped with a mean diameter of 0. 8-1. 2 μm (Fig. S2 ). Growth was obtained at temperatures ranging from 28 to 55°C and pH ranging from 6. 5 to 8 with an optimum growth at 37°C and pH 7 after 48 hr incubation. The isolate did not require NaCl for growth; an optimal growth was observed at 0 or 0. 5% of NaCl. No growth was observed at 1 and 1. 5% of NaCl. Strain F I G U R E 1 Phylogenetic tree highlighting the position of Hugonella massiliensis strain AT8 T relative to other close strains. Sequences were aligned using Muscle v3. 8. 31 with default parameters and phylogenetic inferences were obtained using neighbor-joining method with 500 bootstrap replicates, within MEGA6 software.
| Strain identification and phylogenetic analysis The spectra of strain AT8 T obtained by MALDI-TOF MS did not match with any strains in our database (Bruker, continuously incremented with our data) suggesting that our isolate could be a new isolate. We added the spectrum from strain AT8 T to URMITE database (Figure  S3 ) (http://www. mediterranee-infection. com/article. php?laref=256&titre=urms-database). PCR-based identification of the16S rDNA of strain AT8 T (Accession number: LN881601) demonstrated 92% of 16S rRNA gene sequence similarity with the reference Eggerthella lenta (DSM 2243), the phylogenetically closest validated species (Figure  1 ). This value is under the threshold that allows the identification of a new genus, as established by  Kim et al. , (2014). Consequently, strain AT8 T is considered as the type strain of the first isolate of a new genus named Hugonella gen.
| Genome properties The genome of H. massiliensis strain AT8 T (Accession number:   4 , Figure  3 ) and is composed of nine scaffolds with 12 contigs. The draft genome was shown to encode 1,849 predicted genes, among which 1,781 were protein-coding genes, and 68 were RNAs (six genes are 5S rRNA, six genes are 16S rRNA, six genes are 23S rRNA, 50 genes are tRNA genes). A total of 1,438 genes (80. 74%) were assigned as putative function (by cogs or by NR blast). Ninety genes (5. 05%) were identified as ORFans. The remaining genes were annotated as hypothetical proteins (201 genes = 11. 29%) (Table  4 ). Table  5  represents the gene's distribution into clusters of orthologous groups (COGs).
The genome of H. massiliensis strain AT8 T is 2,091,845 bp with 63. 46% of G+C content. The 16S rRNA and genome sequences are deposited in EMBL-EBI under accession numbers LN881601 and FAUL00000000, respectively. MALDI-TOF Spectrum of strain AT8 T is available in: (http://mediterraner-infection. com/article. php?laref=256&titre=urms-database). The habitat of the microorganism is the human gut. The type strain AT8 T (=CSUR P2118 = DSM 101782) was isolated from the stool specimen of an obese French individual as part of a culturomics study.
The author's work in this field is supported by  Medical Research Grant  (MRC) grants  G0901839  and  MR/L00299X/1  and partially undertaken in the  MRC Centre for Reproductive Health  which is funded by  MRC Centre  grant  MR/N022556/1. The authors declare that there is no conflict of interest that could prejudice the impartiality of the present research. Key words: cryopreservation / gonadotoxicity / fertility preservation / tissue culture / ivm: artificial ovary.
Closed-Loop Supply Chain PhotoCopier Co. utilises a closed-loop supply chain. The company manages its own distribution network to distribute remanufactured photocopiers and take back used products. The forecast of cores arrival is conducted by looking at historical data available within the company. For this reason, cores arrive at the facility more predictably. Several advantages of offering PSS to customers as a part of a remanufacturing programme include: (1) cores arrival becomes more predictable; (2) employees who remanufacture the photocopiers do not need to acquire new skills as they are remanufacturing the same product models; and (3) easier identification of problems due to product history availability.
Early Identification of Damaged Parts Using the information that is available from the EHMS, Jet Engine Co. is able to identify any damaged parts, so that it can order new parts for replacement. As mentioned previously, the data available in the EHMS is captured by sensors attached to the jet engines. Meanwhile, in PhotoCopier Co. , the parts commonly damaged in photocopiers are documented, and the company can prepare the new parts for replacement in advance, before the cores arrive at the company facility. No. Benefit of PSS PhotoCopier Co. Jet Engine Co. 1. Substitution for cores sorting. Forecasting supported by historical data. EHMS supported by database.
4 g 5-ASA,  47  The efficacy of oral, non-colonic release budesonide for active UC was the subject of a previous Cochrane database systematic review of three trials. Budesonide was less likely to induce clinical remission than oral 5-ASA [RR 0. 72, 95% CI 0. 57-0. 91], with no benefit over placebo [RR 1. 41, 95% CI 0. 59-3. 39]. 33  This review has been updated,  48  supporting the use of budesonide MMX predominantly in left-sided UC, and as adjunctive treatment to 5-ASA; studies with improved power are needed to assess standard formulation budesonide in active UC. Tw  phase 3 induction trials of the novel MMX 9-mg budesonide preparation also failed to demonstrate a benefit over placebo in mild to moderate extensive UC, as opposed to significant efficacy in left-sided colitis. [34] [35] [36]  There is some evidence for a therapeutic benefit of probiotics when added to standard therapy to induce remission, 49 particularly VSL#3.
186 Infliximab at either dose [5 or 10 mg/kg] achieved clinical remission in a significantly greater proportion of patients at Week 8 than placebo, although the response for the subgroup of IM-refractory patients was not reported. A Cochrane database systematic review, of seven trials of IFX for treating patients with moderate to severe UC refractory to corticosteroids and/or IMs, concluded that IFX [three intravenous infusions at 0, 2, and 6 weeks] was more effective than placebo at inducing clinical remission at Week 8 [RR 3. 22, 95% CI  2. 18-4. 76]. 202 This review did not report the benefit in the patient subgroup refractory to IM therapy. 5 All patients recruited had failed or were intolerant to IM therapy, although only 5/25 patients treated with adalimumab and 15/28 patients treated with IFX were taking concomitant IM therapy at baseline.
6% for those dosed with vedolizumab every 8 weeks [p = 0. 001 vs placebo]; 50% for those dosed every 4 weeks [p < 0. 001 vs placebo]; 18% for those on placebo]. Ongoing concomitant treatment with IMs did not substantially affect the efficacy of vedolizumab. As described in section 11. 3. 1, data on second-line therapy with a second anti-TNF after failure of an initial anti-TNF are limited [see statement 11G]. For vedolizumab, GEMINI-1 included 48% of patients with a history of previous anti-TNF therapy; in exploratory subanalyses, outcomes were not significantly different in this group of patients, suggesting that patients with a history of anti-TNF failure may have a comparable outcome to anti-TNF naïve patients. The OCTAVE 1 and 2 trials of tofacitinib 199 included patients who had failed azathioprine.
12 vs 0. 22; p = 0. 02], and UC-or drug-related [0. 14 vs 0. 24; p = 0. 005] hospitalisations by Week 52 were significantly lower in patients receiving adalimumab in comparison with placebo in the combined patient cohort of the ULTRA 1 and 2 trials. 285 Fou-year follow-up data from ULTRA 1 and 2, along with the long-term extension study ULTRA 3, have been reported. 286 For the 199 patients followed to Week 208, the remission rate was 24. 7%. The efficacy of subcutaneous golimumab for maintenance of remission in moderate to severe UC was evaluated in the PURSUIT-M trial. 189 Anti-TNF naïve patients who responded in the induction studies [n = 464] were re-randomised to placebo or injections of.
Methotrexate Data on MTX for maintenance of remission in UC are few. The single placebo-controlled RCT was principally designed for induction of remission in refractory, active UC and used an oral dose of 12. 5 mg/week, which is probably sub-therapeutic. 309 The proportion of patients who relapsed after first remission [MTX 64% vs placebo 44%] or who maintained remission at 9 months [MTX 36% vs placebo 54%] were not significantly different. An open-label study compared MP, MTX, and 5-ASA in 72 steroid-dependent IBD patients, including 34 with UC. 271  Patients were randomly assigned in a 2:2:1 ratio to receive MP 1 mg/kg, MTX 15 mg/week orally, or 5-ASA 3g/day. All patients who achieved remission at Week 30 were then included in a maintenance study for 76 weeks. A significantly higher proportion of patients achieved remission in the MP group [79%] than in the 5-ASA group [25%], with no statistical differences compared with the MTX group [58%].
Acknowledgments Working groups [lead author shown first]:  WG1 :  Fernando Magro ,  Johan Burisch ,  Jimmy Limdi ,  Sandro Ardizzone ,  Cord Langner ;  WG2 :  Franck Carbonnel ,  Dominik Bettenworth ,  Konstantinos Karmiris ,  Torsten Kucharzik ,  Shaji Sebastian ,  Helen Tavares de Sousa ;  WG3 :  Axel Dignass ,  Tim Raine ,  Uri Kopylov ,  Konstantinos Katsanos ,  Tamas Molnar ;  WG4 :  Paolo Gionchetti ,  Peter Hindryckx ,  Ailsa Hart ,  Manuel Barriero de Acosta ,  Henriette Vind Thaysen ;  WG5 :  Florian Rieder ,  Kristina Gecse ,  Gianluca Pellino ,  Edyta Zagórowicz ,  Alessandro Armuzzi. Reviewers, on behalf of GuiCom:  Glen Doherty  [Ireland] and  Gionata Fiorino  [Italy]; and on behalf of the Governing Board:  Julian Panes  [Spain] and  Gerassimos Mantzaris  [Greece].
Indeed, the pathway allows two opposite processes to occur concomitantly, including the conversion of acetyl-CoA into acetate and the reverse conversion of acetate into acetyl-CoA. The two unidirectional fluxes were measured and were significant. They were in the range of glucose uptake, and were 3-4 times higher than the net flux of acetate production or utilization. The overall result (acetate production or consumption) is the net balance between the two opposite processes. The net direction of the Pta-AckA pathway upon excess glucose, i. e. net production or net utilization of acetate, is controlled thermodynamically and is basically determined by the extracellular concentration of the compound. The experimental data and the kinetic model of the Pta-AckA pathway presented in this work are consistent and indicate that acetate is produced when its external concentration is below a threshold value of 8 mM.
Glc , Glc , Ace , Ace , AcCoA , and AcCoA 0 1 0 1 0 1 represent the abundances of the corresponding isotopic species relative to the total metabolite pool. The system of ODEs defined by Eqs 1-7 was implemented in Fortran, and simulations were performed using the lsoda function of the deSolve package of R (v2. 15, www. r-project. org), as detailed previously  41. Free parameters (fluxes: μ, qS, v3, v4; and initial concentrations: Glc 0 , Glc 1 , Ace 0 , Ace 1 ) were estimated using the nlsic algorithm developed by Sokol et al. 42  , by fitting the time-course concentrations of biomass, labeled glucose, and labeled and unlabeled acetate. Sensitivity analyses were carried out using the Monte-Carlo method (with 1,000 iterations). The relative standard deviations on the estimated parameters were below 10%.
The scripts used to perform  13  C-flux calculations are distributed in Supplementary Information under an open source license to ensure reproducibility and reusability. Statistical differences in fluxes between the wild-type and mutant strains were calculated using Student's paired t-tests with two tailed distributions. In silico analyses of the Pta-AckA pathway. Gibbs energy of the Pta-AckA pathway (ΔG Pta-AckA ) was calculated for a wide range of acetate levels (10 μ M to 100 mM) using the following equation: and ∆ =∆ + ⋅ ⋅ Π - - G G R ∆ =-⋅ ⋅ ⋅ - ( ) G R T K K ln ( 10 ) Pta AckA e q Pta eq AckA 0 where R is the universal gas constant (R = 8. 3143 J. K -1. mol -  ), T is the temperature (T = 310 K), Π is the mass action ratio (calculated from reactant concentrations, eq. 9), and K eq is the equilibrium constant of the reaction (K eq AckA = 174 and K eq Pta = 0.
0281)  43. Reactant concentrations were fixed at the values measured in this study (ATP = 2. 4 ± 0. 5 mM, ADP = 0. 61 ± 0. 18 mM) or elsewhere (P = 10 mM; CoA = 1. 22 mM; AcCoA = 0. 61 mM)  44. To investigate the impact of changes of acetate concentration on the flux through the Pta-AckA pathway, a kinetic model of this pathway was constructed. Rate laws and parameter values were taken from the literature  43  , and concentrations of phosphate, CoA, acetylCoA, ADP and ATP were set to their experimental values. The robustness of these simulations to parameter uncertainties was evaluated using a Monte-Carlo analysis (with 20,000 iterations), where all the concentrations and parameters were uniformly sampled within ± 10%, ± 20%, ± 30% and ± 40% of their experimental value. The R scripts used to perform these simulations and generate the figures are provided in Supplementary Information.
Acknowledgements The authors are grateful to the members of the  MetaSys team (LISBP, Toulouse, France)  for fruitful discussions. We thank  MetaToul (Metabolomics & Fluxomics facilities, Toulouse, France , http://www. metatoul. fr),which is part of the national infrastructure MetaboHUB- ANR-11-INBS-0010  (The  French National Infrastructure for Metabolomics and Fluxomics , www. metabohub. fr), for access to NMR and MS facilities. The support of  Lindsay Peyriga ,  Edern Cahoreau  and  Matthieu Guionnet  is gratefully acknowledged. B. E. received the support of the  INRA (Institut National de la Recherche Agronomique) , the  INSA (Institut National des Sciences Appliquées)  [program "Chaire d' excellence"], and the  French Agence Nationale de la Recherche  ( ANR, Project  n°  ANR-06-BYOS-0003-03 ).
chemical specificity and dynamic range. Mass spectrometry imaging offers label-free imaging capabilities and for certain analytes has sub-femtomole sensitivity. 4 e quest for sub-cellular resolution metabolic imaging using mass spectrometry has led to significant advances in instrumentation. Recent developments in high-resolution mass spectrometers, for example the Orbitrap™ mass analyser  7  with a mass resolving power in the range of 10 5 -10 6 , a mass accuracy of < 1 ppm and MS/MS capability allow direct identification of metabolites from databases such as LIPID MAPS. 8 An elegant atmospheric pressure matrix assisted laser-desorption ionisation (AP-MALDI) mass spectrometer (MS) source that combines an Orbitrap MS with a tightly focused laser beam was recently reported  9  ; the authors demonstrated sampling regions down to 1.
28 The high mass resolving power at low molecular weight and high mass accuracy enabled putative annotation of the chemical formula of the signals. These features also allowed the use of the LIPID MAPS database to putatively annotate 127 lipid species including fatty acids, sterols, glycerophospholipids and sphingolipids (Supplementary Figs. 10,  11 and Supplementary Tables  2 3 4 5 6 7 8 ). The localization of 29 glycosphingolipid sulfatides were putatively annotated and mapped. Both hydroxylated and non-hydroxylated sulfatides with chain lengths ranging from 14 to 26 carbons with varying degrees of fatty acid saturation were identified. The presence and assignment of C24(OH) sulfatide [(3'-sulfo)Gal β-Cer(d18:1/24:0(2OH))] was confirmed with in situ tandem MS (Fig. 4a ). Sulfatide lipids are abundant in the extracellular membrane of myelin and are responsible for the efficient conduction of electrical signals in the nervous system.
The cells have been tested for mycoplasma within GlaxoSmithKline and are not listed in the database of commonly misidentified cell lines. These were grown on indium tin oxide (ITO) glass slides (Bruker, Germany) with Ham's F-12 Nutrient Mixture media containing GlutaMax and Phenol Red (Gibco, USA) and 15 % dialyzed, heatinactivated fetal bovine serum (Gibco, USA). 5 mg/mL stock solutions of amiodarone hydrochloride (Sigma-Aldrich, CAS 19774-82-4, purity 98 %) were prepared in 50:50 water/ MeOH. The stock solutions were added to the growth media for a final media concentrations of 1. 56 µg/mL, 6. 25ug/mL and 9. 38ug/mL. The cells were incubated (5 % CO2 and 37 °C) in the drug containing media for 72 hrs. Control cells were incubated alongside the dosed cells. To prepare the cells for analysis in the 3D OrbiSIMS, the media was removed and the cells were washed three times with 150 mM ammonium formate solution (Sigma-Aldrich, USA).
Spectra were summed across an analysis area of 20 μm x 20 μm until the entire cell was consumed. The Orbitrap analyser was operated in positive ion mode at the 240,000 at m/z 200 mass resolution setting [512 ms transient time]. Mass spectra information was collected for a mass range from 60 to 1000 Da. The total ion dose ranged from 1. 3 x 10 14 to 7. 8 x 10 14 ions/cm 2. To demonstrate the capability for depth profiling and 3D imaging we obtained negative ion data from the NPL organic multilayer reference material for three modes: mode 3 (single beam, 5 keV Ar2000 + , Orbitrap MS); mode 9 (analysis with 30 keV Bi3 and ToF MS, sputtering 5 keV Ar2000 + ) and mode 10 (5 keV Ar2000 + sputtering and Orbitrap MS analysis and 30 keV Bi3 with ToF MS imaging). For all three modes, a 5 keV Ar2000 + beam with a current of 41 pA was used for sputtering a 250 μm × 250 μm region of the sample.
Data analysis The 3D OrbiSIMS was controlled by software provided by SurfaceLab Version 6. 7 (ION-TOF, Germany), which utilized the Thermo Fisher provided application programming interface (API) for both control of the Orbitrap MS portion of the instrument as well as online retrieval of the data. Both ToF-SIMS and Orbitrap MS image analyses were performed using SurfaceLab Version 6. 7 (ION-TOF, Germany), OriginPro 2016 and MATLAB 2016a. Chemical structures were drawn in ChemDraw 14. 0. All Orbitrap MS images, depth profiles and linescans were created with a tolerance between ±2 and ±15 ppm, depending on the width of the signal peak, which increases proportional to the square root of its mass. This is the reciprocal of the resolving power at a given mass x 10 6. The resolving power is plotted in Supplementary Fig.