dataesr/scientific-paragraphs-categorization huggingface dataset:
Similar to the situation found in the 4. 0 µm, the FTS values of the CAVIAR consortium and of the two Tomsk datasets are largely overestimated, by about a factor of 5 in the present case. In our opinion, as the three sets of FTS values are reported with very large error bars (up to ±94 % for the CAVIAR value), they should be considered as upper limit values corresponding to the detectivity threshold of the FTS setups.
Acknowledgements. This project is supported by the  LabexOSUG@2020  ( ANR10 LABX56 ) and the  LEFE-ChAt program  from  CNRS-INSU. The research leading to the results at 3. 33 µm has received funding from the  European Community 's  Seventh Framework Program ERC-2011-AdG  under grant agreement no. 291062  ( ERC ICE&LASERS ), as well as  ERC-2015-PoC  under grant agreement no. 713619  ( ERC OCEAN-IDs ). Edited by: Frank Hase Reviewed by: two anonymous referees.
In practice, we used the emcee Python implementation, an affine invariant sampling algorithm, which is freely available and widely used in the astrophysical community 3. We also used the corner Python library to produce plots of the parameter distribution and correlation matrix. In this approach, the parameter space is explored using typically 24 Markov chains for typically 1000 to 5000 steps, including a burn-in phase of ∼ 300 steps (see Figs. A1  and A2 ). In our case, the prior probability was a uniform distribution for each parameter, with boundaries inferred from physical and chemical considerations. The kinetic temperature T kin varies between 6 and 15 K, while the log10 of the density, HC 3 N column density, and isotopic ratio, were taken in the intervals [4 : 7],  [11 : 15] , and [2 : 3] respectively.
Properties of the HC 3 N and HC 15 3 N lines obtained through Gaussian fitting. The rest frequency were taken from the CDMS database. ‡ Peak intensity (main beam temperature). † For HC 3 N, three integrated intensity values are provided: main component, sum of the two weaker hf lines, and the total (main+hf) flux. For HC 15 3 N, only the main component is detected. The statistical uncertainties (in brackets) are given in units of the last digit at the 1σ level. Upper limits are 1σ.
ACKNOWLEDGMENTS We thank the anonymous referee for a careful reading and general comments which helped to improve the manuscript. We wish to thank  Martin Legrand  and  Luc Lefort  who participated into the multi-line analysis and the implementation of the MCMC/Radex code during their internship in our group in May-July 2017. PHB acknowledges the  Institut Universitaire de France  for financial support. AF acknowledges the financial support from the  CNRS Programme National PCMI (Physique et Chimie du Milieu Interstellaire).
X-ray Crystallographic Studies All the crystal structures were measured by single-crystal X-ray diffraction and the diffraction data were collected on a Bruker Apex II CCD diffractometer operating at 50 kV and 30 mA using Mo Kα radiation (λ = 0. 71073 Å). All the crystal structures were solved by direct method with SHELXS program and refined with SHELXL or OLEX2 program  [24, 25]. The final refinements of all non-hydrogen atoms were performed through full-matrix least-squares methods with anisotropic thermal parameters on F 2. The hydrogen atoms on non-carbon atoms were located from difference Fourier maps and the hydrogen atoms riding on the carbon atoms were determined by theoretical calculation and refined isotropically. Crystallographic parameters and hydrogen bonds are listed in Tables  1  and 2.
Data Processing and Gene Ontology Terms Enrichment Analysis Data analysis was performed with MaxQuant (version 1. 5. 6. 5 for the SILAC analyses, version 1. 6. 0. 16 for the label-free analyses; ref. 24)  using the Andromeda search engine  (25)  with default search settings including a false discovery rate set at 1% on both the peptide and protein level. Spectra were searched against the human proteins in the Uniprot/Swiss-Prot database (database release version of January 2017 containing 20,172 human protein sequences for the SILAC analyses; database release version of September 2017 containing 20,237 human protein sequences for the label-free analyses, www. uniprot. org) supplemented with the sequence of listeriolysin O (RefSeq WP_003722731. 1) with a mass tolerance for precursor and fragment ions of 4.
From the SILAC analyses, for each protein the H/L ratio normalized by median subtraction is reported in Suppl. Table  S1. For the label-free analysis, matching between runs was enabled with a matching time window of 1 minute and an alignment time window of 20 minutes and proteins were quantified by the MaxLFQ algorithm integrated in the MaxQuant software  (26). Further data analysis of the labelfree samples was performed with the Perseus software (version 1. 5. 5. 3) after loading the proteingroups file from MaxQuant. Proteins only identified by site and reverse database hits were removed and protein LFQ intensity values were log2 transformed. Replicate samples were grouped, proteins with less than three valid values in at least one group were removed, and missing values were imputed from a normal distribution around the detection limit leading to a list of 2,972 quantified host proteins in the analysis with LLO treatment (Suppl.
Analysis of host gene expression in response to LLO treatment. Total RNAs from HeLa cells treated or not with 3 nM LLO for 20 min were extracted using RNeasy kits (QIAGEN). Quality of RNAs was monitored on Agilent RNA Nano LabChips (Agilent Technologies). RT on 5 µg of total RNA using oligo(dT) primers and in vitro transcription of the cDNA in presence of biotin were performed by using a GeneChip Amplification One-Cycle Target Labeling kit according to Affymetrix (Santa Clara, CA) standard protocols. Fragmented, biotin-labeled cRNA samples were hybridized on Array Type GeneChip Human Genome U133 Plus 2. 0. For each condition, three biological replicates were hybridized. The cell intensity files were generated with GeneChip Operating Software (GCOS). Data analysis was performed by using SPlus ArrayAnalyser software (Insightful, Seattle, WA).
LLO reshapes the host cell proteome In order to characterize host proteome alterations induced by LLO, we used shotgun proteomics on HeLa cells treated or not with the LLO toxin. We performed a first analysis using SILAC (stable isotope labelling by amino acids in cell culture)  (20). The SILAC approach is based on differential isotope labelling of proteins during cell culture by metabolic incorporation of essential amino acids (predominantly lysine and arginine) that carry light or heavy isotopes. After mixing light and heavy-labelled cell lysates, proteins are subjected to trypsin digestion. The resulting peptide mixture is then separated and analyzed by tandem mass spectrometry (MS/MS). Proteins are identified by searching the recorded spectra against protein databases, and quantification is obtained by comparing light and heavy intensity for each peptide.
ACKNOWLEDGMENTS Work in P. C. 's laboratory received financial support from  Institut Pasteur ,  INSERM ,  INRA , the  French National Research Agency (ANR)  ( ERANET Infect-ERA PROANTILIS ANR-13-IFEC-0004-02 ), the  French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases"  ( ANR-10-LABX-62-IBEID ), the  European Research Council (ERC)  ( H2020-ERC-2014-ADG 670823-BacCellEpi ), the  Fondation le Roch les Mousquetaires  and the  International Balzan Prize Fondation. J. M. was supported by a fellowship from  Paris Diderot University ; P. C. is a  Senior International Research Scholar  of the  Howard Hughes Medical Institute  and D. R. is a Research Associate from INSERM.
DATA AVAILABILITY The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral. proteomexchange. org) via the PRIDE partner repository  (41)  with the dataset identifier PXD009339 (username: reviewer87694@ebi. ac. uk ; password: gcQ7GPXO). Moreover, identified spectra of the label-free analysis were uploaded to MS Viewer and are accessible via following search keys: vgjqpmehba, label-free experiment LLO; owrygieix2, label-free experiment LLO + MG132.
S pectra were obtained using an aluminum anode (Al Ka = 1486. 6 eV) operated at 72 Wa nd as pot size of 400 mm. Survey scans and high-resolution scans of the separate regions were measured at constant pass energies of 200 eV and 50 eV,r espectively. T he background pressure of the ultra-high vacuum (UHV) chamber was 2 10 À8 mbar. S ample charging was compensated for by the use of an electron flood gun, and binding energy calibration was done by setting the peak as reference for all samples to ab inding energy (BE) of 284. 8 eV,w hich corresponds to ac ombination of phenyl (sp2) and adventitious carbon (sp3), according to previously reported procedures. Fitting of the spectra (BE, FWHM, peak shape, asymmetry,n umber of species) was carried out with CasaXPS software, version 2. 3. 16. Fourier-transformed infrared (FTIR) spectroscopy measurements were recorded on aP erkinElmer System 2000 instrument (16 scans, 4cm À1 resolution, DTGS detector,c ell with KBr windows).
Acknowledgements This project has received funding from the  European Union   Horizon2 020 research and innovation program  under the  Marie-Sklodowska-Curie grant agreement   641887 ( DEFNET). S. Dissegna (  Te chnical UniverstätM ünchen,T UM ),  W. S. Lamme  ( UtrechtU niversity,U U ) and L. C. E. Pompe(  UU ) are gratefully acknowledged fort he TEM measurements. We thank  H. C. de Waard  ( UU ) for analysis of the elemental content of metals and carbon in the different samples. B. S. gratefully acknowledges the  Netherlands National Science Foundation (NWO)  for her personal VENI grant. M. F. g ratefully acknowledgest he  Marie Sklodwoska-Curie  program agreement No. 7 48563. B. M. W. a cknowledges financial support from The  Netherlands Organisation forS cientific Research( NWO) Gravitation Program (Netherlands Center for Multiscale Catalytic Energy Conversion, MCEC).
18 However, the degree of polymerization (DP) obtained in these enzymatic and chemical approaches was limited to 4 and 8, respectively. Recently, mannoside phosphorylases have been discovered, as a new class of mannoside-synthesizing enzymes. 19 These bacterial enzymes, which act on β-1,2,  20  1,3 21 or 1,4-(hetero)mannosides,  19, 22  are classified in the CAZy database as belonging to the GH130 family,  23  which today contains more than 1500 members, of which only 16 have been functionally characterized. The physiological role of mannoside phosphorylases is the degradation of mannosides by phosphorolysis. This reaction being reversible, these enzymes can synthesize β-mannosides in vitro from α-D-mannose 1phosphate (αMan1P) and various acceptors. Therefore, they represent an attractive prospect as green catalysts for the selective synthesis of β-mannosides with a specific linkage composition and high level of purity.
The mannoside phosphorylase that has been found to synthesize the longest β-1,4-mannooligosaccharides (DP 12) in vitro is Uhgb̅ MP, a rather unstable enzyme produced by an uncultured human gut bacterium in order to degrade human N-glycans. 22 One of its homologues, the TM1225 protein from Thermotoga maritima MSB8, which shares a 61% identity with Uhgb̅ MP, was the first GH130 member to be structurally characterized. Although its crystallographic structure (PDB accession number 1VKD) was established in 2004, this protein has still not been biochemically characterized. 6] [27]  Thermotoga maritima MSB8 is a hyperthermophile bacterium, isolated from sediments collected near a submarine hot spring in the Bay of Naples,  28  which feeds on several plant and algal cell wall constituents, such as β-mannans.
■ MATERIAL AND METHODS Production and Purification of the Recombinant TM1225 Enzyme. The gene encoding the TM1225 protein from Thermotoga maritima strain ATCC 43589/MSB8/DSM 3109/JCM 10099 (TM1225, Genbank accession number AAD36300. 1, PDB 1VKD) was synthesized and cloned into the pET28a vector by the Biomatik Company (Biomatik, Ontario, Canada) between restriction sites NcoI and XhoI. The resulting plasmid sequence is provided in the Supporting Information. The recombinant enzyme was produced as the fusion protein (His) 6 -TM1225 by Escherichia coli BL21 star cells carrying the pET28a-tm1225 plasmid. For the sake of simplicity, (His) 6 -TM1225 will hereafter be referred to as TM1225. The culture was performed for 24 h at 20 °C in the ZYM-5052 autoinductible medium supplemented with 50 μg mL -1 kanamycin, and inoculated at A 600 nm 0.
The extinction coefficient of the purified TM1225 fused to the N-terminal His 6 tag was 75145 mol -1 cm -1 , a value estimated with the Protparam software (https://web. expasy. org/protparam/). In Vitro Phosphorolysis and Reverse Phosphorolysis. In order to determine TM1225 specificity, the phosphorolysis and reverse phosphorolysis reactions were performed during 24 h at 37 °C in 50 mM Tris-HCl buffer at pH 7. 0, using 1. 0 μg mL -1 of purified TM1225. Phosphorolysis was performed in the presence of 10 mM inorganic phosphate and 10 mM 1,4-β-D-mannooligosaccharides as substrates (mannobiose (M2), mannotriose (M3), mannotetraose (M4) and mannopentaose (M5) from Megazyme, Ireland). Reverse phosphorolysis was performed using αMan1P (sodium salt hydrate, Sigma-Aldrich, reference M1755) at 10 mM as the mannosyl donor, with 10 mM D-mannose as acceptor.
1 H and  13  C NMR. The freeze-dried reaction media was resuspended in deuterated water. Deuterium oxide was used as the solvent, and sodium 2,2,3,3-tetradeuterio-3-trimethylsilylpropanoate was selected as the internal standard. 1 H and  13  C NMR spectra were recorded on an Advance 500-MHz spectrometer (Bruker) operating at 500. 13  MHz for 1 H NMR and 125. 75 MHz for  13  C using a 5 mm z-gradient TBI probe. The data have been acquired at 298 K, and processed using TopSpin 3. 0 software. The various signals were assigned by comparison with those obtained from standards (αMan1P and 4-O-β-D-mannopyranosyl-D-mannose) as described. 22 ransmission Electron Microscopy (TEM). Drops of 10 μg mL -1 carbohydrate suspensions were deposited onto glow-discharged carbon-coated grids and negatively stained with 20 mg mL -1 uranyl acetate.
■ CONCLUSION Thermotoga maritima, a thermophilic bacterial species that feeds on numerous plant polysaccharides, is a goldmine in the search for thermostable enzymes of biotechnological interest. In this study, we characterized the function of TM1225, which became, in 2004, the first GH130 member to have its 3D structure released in the Protein Data Bank, although its function was still a matter of speculation. Here, we have demonstrated that TM1225 is a β-1,4-D-mannoside phosphorylase able to act on chains with a DP ≥ 2 according to our previous prediction based on structural comparison analyses,  51  but not with other hypotheses regarding its physiological role. 30 We further demonstrated the ability of TM1225 to synthesize in vitro β-1,4-D-mannoside chains up to DP 16, a length that had never been reached through chemical  12, 18, 52, 53  or enzymatic synthesis using glycosynthases.
■ ACKNOWLEDGMENTS The HPLC analyses were performed using the ICEO facility, which is dedicated to the screening, discovery and characterization of new enzymes. ICEO, part of the Integrated Screening Platform of Toulouse (PICT, IBiSA), is supported by grants from the Reǵion Midi-Pyreńeés, the European Regional Development Fund and the Institut National de la Recherche Agronomique (INRA). We are grateful to MetaSys, the Metabolomics and Fluxomics Center at the Laboratory for the Engineering of Biological Systems and Processes (Toulouse, France) for the NMR experiments, and to the NanoBio-ICMG Platform (FR 2607, Grenoble), for granting access to the Electron Microscopy facility. We cordially thank Nelly Monties and Angeline Rizzo for their technical support. This work was financed by the Agence Nationale de la Recherche (project ASPIRE, grant number ANR-14-CE27-0011-02, and project Oligomet, grant number ANR-16-CE20-0006) and by the European Union's framework programme Horizon 2020 (LEIT-BIO-2015-685474, Metafluidics).
Further, to study the star-formation around the bipolar H II regions, we explore their stellar, protostellar, and dense clump components using data from the Two Micron All Sky Survey (2MASS), UKIRT Infrared Deep Sky Survey (UKIDSS), and Visible and Infrared Survey Telescope for Astronomy (VISTA), Spitzer, and Herschel surveys (details about these datasets are given in Paper I). In the following, we briefly outline our methodology for identifying and studying various components of the bipolar H II regions. Further details can be found in Paper I.
6. The small red dots in the Class I zone are for sources of unknown nature; they have no 24 µm measurements, because they are either saturated or not detected at 24 µm. Of the IRAC-identified Class I YSOs that have 24 µm detections, we find that 28 are Class I (the two indicators agree), 25 are flat-spectrum, and 12 are Class II based on their [8]-  [24]  colours. This analysis shows the difficulty in disentangling Class I and Class II YSOs based on GLIMPSE data only, and thus the need for high-resolution longer-wavelength observations. Nonetheless, we can say that roughly 80% of the IRAC-classified Class I sources should be protostellar (i. e. Class I and flat-spectrum). The lifetime of Class I and flatspectrum sources are of the order 10 5 yr; therefore, the presence of such sources suggests recent star formation activity in the region.
Acknowledgements. We thank the anonymous referee for helpful and constructive comments. The authors would first like to thank the  Herschel Hi-GAL team  for their continuing work on the survey. Observations were obtained with the  Herschel-PACS  and Herschel-SPIRE photometers. PACS was developed by a consortium of institutes led by  MPE (Germany) , including  UVIE (Austria) ;  KU Leuven, CSL, IMEC (Belgium) ;  CEA ,  LAM (France) ;  MPIA (Germany) ;  INAF-IFSI/OAA/OAP/OAT ,  LENS ,  SISSA (Italy) ;  IAC (Spain). This development was supported by the funding agencies  BMVIT (Austria) ,  ESA-PRODEX (Belgium) ,  CEA/CNES (France) ,  DLR (Germany) ,  ASI/INAF (Italy) , and  CICYT/MCYT (Spain). SPIRE has been developed by a consortium of institutes led by  Cardiff Univ. (UK)  and including  Univ.
This publication makes use of data from The  UKIRT Infrared Deep Sky Survey or UKIDSS  which is a next generation near-infrared sky survey using the wide field camera (WFCAM) on the United Kingdom Infrared Telescope on Mauna Kea. This publication also made use of data products from the  Two Micron All Sky Survey  (a joint project of the  University of Massachusetts  and the  Infrared Processing and Analysis Center / California Institute of Technology , funded by  NASA  and  NSF. This paper also uses data observations made with the Spitzer Space Telescope (operated by the  Jet Propulsion Laboratory, California Institute of Technology  under a contract with NASA). We thank the  French Space Agency (CNES)  for financial support.
34 µM of SYTO-9 and 19. 97 µM of propidium iodide in PBS (LIVE/DEAD® BacLight TM Bacterial Viability Kits L-7007, Molecular Probes Inc. ) for a minimum of 15 min at room temperature. The attached stained cells were then assessed by confocal laser scanning microscopy (Olympus FluoView TM FV1000). Twelve images across the glass bottom were acquired and the surface coverage of the biofilm was analyzed using image analysis software (Fiji/ImageJ). Statistical analysis was performed using one-way ANOVA followed by Dunnett post hoc analysis on Prism (GraphPad). To evaluate the capacity of Fe 2+ as reducing agent for the catalytic conversion of nitrite to NO from CuDTTCT-containing films, we studied the impact of Fe 2+ on the production of NO under various conditions of aqueous media that are relevant to the water industriesthe phosphates-and carbonate-containing and pH-adjustable nitrifying bacteria growth medium (NBGM) and phosphate buffered saline (PBS).
Acknowledgements This research was supported under  Australian Research Council's Linkage Projects funding scheme  ( LP110100459 ). We would like to thank  Chemson Pacific Pty. Ltd. for the provision of polyvinyl chloride and  Australian Water Quality Centre (SA Water)  and  Western Australia Water Corporation  for the financial support. The authors would also like to thank  Dr Jay Hyun-Suk Oh  and  A/Prof Scott A. Rice  ( Nanyang Technological University ) for the assistance on the NO generation experiment. The authors also acknowledge the support from  Mark Wainwright Analytical Centre.
X-ray Data Collection and Structure Solution Single-crystal X-ray high-resolution and highly redundant data collection of meloxicam sodium monohydrate compound was performed on a Rigaku Micro Max-HF rotating anode diffractometer equipped with a Pilatus 200K hybrid pixel detector using MoKα radiation. The data collection was carried out at 90(2) K under a stream of nitrogen using the Oxford 700 Plus Cryo-systems gas flow apparatus. Data reduction and absorption correction were performed using the CrysAlisPro 1. 171. 39. 12f package,  [6]  the internal R(I) factor was 4. 4 % for all reflections. The crystal was mounted using a capton micro-loop. A high resolution data set was collected upto (sin ϑ / λ)max = 1. 2 Å -1 , the completeness being 98 % at sin ϑ / λ = 1. 11 Å -1. The unit cell parameters refinement, data reduction and absorption correction have been carried out using 1.
171. 39. 12f package. [6] For data averaging the program XPREP Version 2014/02 has been used. [7] Molecular graphics has been computed using Olex2. [8] The structure has been solved with the SIR2014,  [9]  structure solution program using VLD algorithm and refined with the ShelXTL Version 2014/7  [10]  under the ShelXle interface. [11] Further details of crystal data and measurement conditions are given in Table  1.
Multipolar Experimental Refinement The experimental electron density distribution was performed with the help of multipolar atom formalism  [12]  incorporated in the MoPro Software  [13]  which has been utilized to estimate the electron density distribution of small molecules from high resolution X-ray single crystal diffraction data. The core and valence spherical scattering factors were calculated using the wave functions for isolated atoms from Su and Coppens  [14]  and the anomalous dispersion coefficients were taken from Kissel et al. [15]  The charge density was refined against diffraction intensities truncated at s < 1. 2 Å -1. For the H atoms, the values of anisotropic Uij thermal parameters were fixed to those obtained from the SHADE3 server. [16] The H-X distances of H atoms were restrained to the values obtained from neutron diffraction studies  [17]  with a restraint sigma σd of 0.
01 Å. Distance X-H similarity restraints were also applied to chemically equivalent groups. The S atoms were treated up to hexadecapole level, the C,N,O atoms up to octapole level, the H atoms with one dipole among H-X bond, while the Na cation was set to monopolar with a charge of +1e. For the water molecule, local symmetry constraint was applied to the multipoles of the oxygen atom and the two H atoms were set equivalent. The charge density of the water atoms was restrained (σr = 0. 01) to that of the ELMAM2 databank. [18] The hydrogen atoms of water molecule were set isotropic with Uiso=1. 5Ueq(O) riding on the equivalent B-factor of the oxygen atom. For the non-H atom, enhanced rigid-bond restraints  [19]  were applied on the anisotropic thermal parameters. Expansion/contraction coefficients κ and κ' of H atoms were restrained to be similar (σ = 0.