dataesr/scientific-paragraphs-categorization huggingface dataset:
First, qPCR experiments on genomic DNA using different chicken populations estimated a relative copy number of 23 ± 1. 5 of these paralogs in the chicken genome. Second, analysis of genome DNA resequencing and RNA-Seq data confirmed the massive duplication of FFAR2. Although having strong identity (above 98. 5%), 9. 8-11. 9 substitutions between FFAR2 nucleotide sequences (each containing approximately 1,000 nucleotides) were detected. This is more than the 5 SNP/kb previously estimated for the entire chicken genome  (Wong et al. 2004). This is also much more than the approximately 2. 7 SNP/kb observed in coding regions between broilers and red jungle fowl  (Wong et al. 2004 ). This suggests that FIG. 7. -Gene conversion events in the FFAR2 cluster. Each line represents a gene and each ribbon represents a gene conversion event between two genes of the FFAR2 cluster.
2013)  were conserved among paralogs, suggesting that most of these paralogs are functional. In mammalian genome, FFAR2 gene is located in a locus that also contains genes encoding two other types of the FFAR family (FFAR1, FFAR3), HAMP coding for hepcidin, involved in the regulation of iron metabolism, and USF2, the upstream transcription factor involved in lipid homeostasis. By exploring the chicken genome by reciprocal tBLASTn analysis on genome and EST database, we did not find traces of FFAR1 and FFAR3 genes in chicken. This suggests that the only one study that has reported the expression of a chicken FFAR to date, which was claimed to be FFAR1  (Suh et al. 2008) , would refer rather to FFAR2. The hepcidin gene is absent from chicken, fish, and reptile genomes. Although chicken USF2 sequence is available for chicken (http://www.
(2009) ,  Kučera & al. (2010) ,  Mereďa & al. (2011 ), Lakušić & al. (2013) ,  Šingliarová & al. (2013) ,  Janković & al. (2016)  and  Tomović & al. (2016). The aim of this study is to present quantitative data on the floristics (a critical inventory), chorology (chorological groups) and life forms of the Balkan endemic vascular flora of Montenegro. We also aim to determine the degree of floristic similarity between geographical subregions of the country.
Selection of taxa "Taxa" are here counted as species and subspecies. A species with no or one subspecies is counted as one taxon, while a species with two subspecies is counted as two taxa, and so on. A checklist of Balkan endemic vascular plant taxa in Montenegro was made based on data from studies on floristics, taxonomy, morphology, phytocoenology and karyology. The Conspectus florae montene grinae  (Rohlena 1942 ) and its supplement  (Pulević 2005)  and the catalogue of the vascular flora of Montenegro  (Stešević & Caković 2013)  were used as the basis for the inventory. Taxonomy and nomenclature follow contemporary checklists and Floras  (Tutin & al. 1964 (Tutin & al. -1980 (Tutin & al. , 1993;; Jalas & Suominen 1972 -1994; Greuter & al. 1984 Greuter & al. -1989;; Jalas & al. 1996 Jalas & al.
, 1999;; Strid & Tan 1997; Kurtto & al. 2004 Kurtto & al. , 2007;; Greuter & Raab-Straube 2008) , online databases  (IOPI 1996 (IOPI -2007;; Euro+Med 2006+; The Plant List 2013; IPNI 2013+)  and in some cases older basic floras  (Pančić 1875; Rohlena 1942).
Acknowledgements We would like to thank  Dmitar Lakušić  and  Ivana Janković  ( Institute of Botany and Botanical Garden, Faculty of Biology, University of Belgrade ) for helping us to resolve the taxonomic status of species of Edraianthus (DL) and for making databases of species of Campanula available (IJ); our colleagues  Danka Caković  and  Danijela Stešević  ( Faculty of Sciences of the University of Montenegro ) for providing us with certain herbarium and literature data; and the  Ministry of Education, Science and Technological Development of the Republic of Serbia  (Grant  173030 ), which supported this research. We would also like to thank  Boštjan Surina  ( Natural History Museum Rijeka, Croatia and University of Primorska, Slovenia ) and an anonymous reviewer for their comments on an earlier draft of this paper.
3 ). Based on the carbonate system parameters data collected during the 2013 MedSeA cruise, an Eastward increasing trend of A T was remarked in parallel with the salinity one  [15]. Our results indicate the presence of significant correlations between A T and S in the Mediterranean Sea globally, its main basins and many of its sub-basins as well. Table  1  presents the Model II linear regression between these two parameters in each basin and sub-basin and at different depth layers (surface, intermediate and deep layers). These equations were obtained using the Excel Microsoft Office program  (2007). For all the equations derived in this study, the root mean square deviation (RMSD), which is a good measure of the accuracy of the fit, the coefficient of correlation (Pearson coefficient ; r), and the number of data pairs (n) used to derive each correlation, are also mentioned in the Table  1  for each A T -S fit.
Acknowledgements This work is an essential part of the European project " Mediterranean Sea Acidification in a changing climate -MedSeA " (http://medsea-project. eu/), funded by the  EC   FP7 Cooperation program  (grant agreement  265103 ). The authors are pleased to thank the captain and the crew of the Spanish research vessel R/V Ángeles Alvariño. Authors are grateful to the  National Council for Scientific Research (CNRS) in Lebanon  for the PhD thesis scholarship granted to A. E. R. HASSOUN and E. GEMAYEL.
Monitoring and characterization of the test aerosol The oxygen concentration, relative humidity and temperature in the exposure device were measured continuously during each exposure using a calibrated device. The nominal concentration was determined for the high concentrations by weighing the generator reservoir containing the test material before and after exposure and dividing the used amount by the total air-flow volume. These data were used to monitor the performance of the generation system. During the 5-day and 90-day exposures, gravimetric determinations of the aerosol concentrations were respectively performed once and 4 to 7 times daily for high concentrations and twice and 1 to 3 times daily for the low and mid concentrations using Millipore® durapore filters, type HVLP, loaded in a 47 mm in-line stainless steel filter sampling device.
During the 90-day exposure, measurements were performed at least once per week for the high concentration and five times for the mid concentrations using a standard impactor Model 02-005 at a sampling rate of 1 L/ min, matching the air flow rate at the animal port to avoid a possible imbalance of the aerosol flow within the exposure chamber. Accordingly, impactor samples for the mid concentration of the 90-day exposure were collected over several days. No samples were collected for the low concentration of the 90-day exposure as the aerosol concentration was too low to obtain reliable results with an air flow rate of 1 L/min. The mass median aerodynamic diameter (MMAD) and the geometric standard deviation (GSD) were calculated on the basis of the results from the impactors, using Microsoft Excel® software (Microsoft Corporation, USA).
Statistical analysis The food consumption, blood pressure, grip strength, landing foot play, body temperature, body weight, food consumption, blood clinical laboratory and BALF parameters, organ weights, and sperm parameters were analyzed for statistical significance by the Dunnett-test (many to one ttest) based on a pooled variance estimate, if the variables can be assumed to follow a normal distribution for the comparison of the treated groups and the control groups for each sex. The Steel-test (many-one rank test) was applied for the locomotor activity, urinalysis, and BALF biochemical parameters instead of the Dunnett-test when the data cannot be assumed to follow a normal distribution. Fisher's exact test was applied to the ophthalmoscopy and macroscopic findings. Nonparametric Mann-Whitney test was applied to the micronucleus, comet and to cytokines test results as data did not follow a normal distribution.
Acknowledgements The authors wish to thank  Emmanuel Laux  for excellent technical assistance in performing the inhalation study,  Margrit Degert ,  Diana Hahnke ,  Nicole Mojzes  and  Mirjiam Schmid  for undertaking the histopathology work,  Regina Draheim ,  Monika Gisin  and  Conni Büschlen  for performing the BALF investigations and  Klaus Weber  for carrying out the histopathological peer review. They are also grateful to  Gwendoline Dewaele ,  Smaïl Talahari  and  Emilie Nicolas  for their technical assistance in performing the comet assay,  Maria Köditz  and  Sigrid Schneck  which did the micronucleus preparation,  Peter Kunzendorf  for performing SEM and  Sandi Murphy  for the editorial review of the manuscript.
Acknowledgement This work was performed under the shared use program of JAEA facilities. The authors are grateful to the crews of the 400-kV ion implanter at  JAEA/Takasaki  for irradiation of C 60 ions. They are also grateful to the technical staff of the accelerator facilities at  JAEA/Tokai  for the irradiation of Xe ions. This work was partly supported by  JSPS KAKENHI  Grant (Grant Numbers  24651114  and  26246025 ).
Until 2013, only glycoside hydrolases (GHs) had been shown to be implicated in N-glycan breakdown in the CAZy database (http://www. cazy. org/; Lombard et al. , 2014). Huge efforts have been made in recent years to understand exactly how this hydrolytic process takes place, particularly among gut inhabitants, as the alteration of host glycans by microbes is thought to be related to intestinal disorders, including Crohn's disease and other inflammatory ISSN 1399-0047 bowel diseases (IBDs;  Martens et al. , 2008; Sheng et al. , 2012). The aim of these studies was to identify a broad consortium of enzymes acting on different parts of the N-glycan structure, such as exo-mannosidases and endo-mannosidases or endo-Nacetyl--d-glucosaminidases produced by gut commensals and pathogens  (Roberts et al.
Currently, six GH130 enzyme structures are available in the RCSB Protein Data Bank, sharing a common five-bladed -propeller fold. The crystal structure of Bf MGP, a B. fragilis NCTC 9343 enzyme classified with 78 other sequences into the GH130_1 subfamily, was recently solved in complex with the genuine substrates 4-O--d-mannosyl-d-glucose and phosphate and the product -d-mannose-1-phosphate  (Nakae et al. , 2013; PDB entries 3wat, 3was, 3wau and 4kmi). This enzyme, which is involved in the final steps of mannan catabolism in the human gut, exhibits a very narrow specificity towards -d-Manp-1,4-d-Glc  (Senoura et al. , 2011) , like the other characterized members of the GH130_1 subfamily (RaMP1 from the ruminal bacterium R. albus 7 and the RmMGP protein from the marine bacterium Rhodothermus marinus DSM4252;  Jaito et al.
, 2014). This pioneering study on Bf MGP highlighted a probably unique reaction mechanism among known disaccharide phosphorylases, as the invariant residue Asp131, which is assumed to be the general acid/base, was not found close to the glycosidic O atom, which should be protonated in the catalytic reaction. The five other three-dimensional structures of GH130 enzymes available to date are the apo forms of (i) four proteins belonging to the GH130_NC cluster, which gathers enzymes that are not classified into the GH130_1 and GH130_2 subfamilies, namely BACOVA_03624 and BACOVA_02161 from B. ovatus ATCC 8483 (PDB entries 3qc2 and 4onz; Joint Center for Structural Genomics, unpublished work), BDI_3141 from Parabacteroides distasonis ATCC 8503 (PDB entry 3taw; Joint Center for Structural Genomics, unpublished work) and BT_4094 from B.
thetaiotaomicron VPI-5482 (PDB entry 3r67; Joint Center for Structural Genomics, unpublished work), and (ii) Tm1225 from Thermotoga maritima MSB8 (PDB entry 1vkd; Joint Center for Structural Genomics, unpublished work), which belongs to the GH130_2 subfamily. No function has yet been attributed to these five proteins, thus limiting our understanding of their structure-specificity relationships. Until now, nothing has been established regarding the molecular bases of the relaxed specificity of the enzymes classified into the GH130_2 family. In addition, no structural feature has been identified to explain the efficiency of Uhgb_MP and Bt1033 in binding and breaking down N-glycan core oligosaccharides. Here, we present the first crystal structure of an N-glycan phosphorolytic enzyme, Uhgb_MP, solved by X-ray crystallography in complex with inorganic phosphate, mannose and N-acetylglucosamine.
5-20%(w/v) polyethylene glycol 3350, 0. 175-0. 2 M ammonium chloride]. Uhgb_MP crystals grew to dimensions of 0. 2 Â 0. 08 Â 0. 02 mm in a week. They diffracted to a maximum resolution of 1. 80 A ˚, while those obtained by co-crystallization with mannose, N-acetylglucosamine or both diffracted to maximum resolutions of 1. 94, 1. 60 and 1. 76 A ˚, respectively. 2. 5. Data collection and determination of the structure X-ray experiments were carried out at 100 K. Crystals of Uhgb_MP were soaked for a few seconds in reservoir solution supplemented with 15%(v/v) glycerol (apo) or 15%(v/v) PEG 300 (complexes) prior to flash-cooling. Apo Uhgb_MP diffraction data sets were collected on beamline ID23-1 at the European Synchrotron Radiation Facility (ESRF), Grenoble, France, while those for the complexes were collected on the XALOC beamline at the ALBA Synchrotron, Cerdanyola del Valles, Spain  (Juanhuix et al.
, 2014). The diffraction intensities were integrated and scaled using XDS  (Kabsch, 2010)  and 5% of the scaled amplitudes were randomly selected and excluded from the refinement procedure. All crystals belonged to the orthorhombic space group P2 1 2 1 2 1 , with six molecules per asymmetric unit, giving Matthews coefficients of 2. 22 and 2. 11 A ˚3 Da À1 and solvent contents of 44 and 42% for the apo forms and the three complexes, respectively. The structures were solved by the molecular-replacement method using Phaser  (McCoy et al. , 2007)  from the CCP4 software suite  (Potterton et al. , 2003)  and chain A of the crystal structure of Tm1225 from T. maritima MSB8 (PDB entry 1vkd) as a search model for the apo form. The final translation-function Z-score was 42. 8 and the R and R free values of the refined structure were 0.
Samples were separated from the pushing liquid (water) by two air volumes of 6 ml each, as described previously  (David & Perez, 2009). SAXS data were collected online throughout the elution time and a total of 149 frames, each lasting 2 s, were recorded separated by a dead time of 0. 5 s between frames. The transmitted intensity was continuously measured with an accuracy of 0. 1% using a diode embedded in the beam stop. For each sample, the stability of the associated radius of gyration and the global curve shape in the frames corresponding to the main elution peak were checked, and the resulting selection of curves were averaged as described previously  (David & Perez, 2009). The recorded curves were normalized to the transmitted intensity and subsequently averaged using Foxtrot, a dedicated in-house application.
The same protocol was applied to buffer scattering. R g values were determined by a Guinier fit of the one-dimensional curves using the ATSAS package  (Petoukhov et al. , 2007). The P(r) function was calculated using the GNOM program and the corresponding ab initio envelopes were calculated using the GASBOR program. Rigid-body SAXS modelling was performed using the CORAL program. P2 1 2 1 2 1  P2 1 2 1 2 1  P2 1 2 1 2 1  P2 1 2 1 2    3. Results and discussion.
Crystallographic structure of Uhgb_MP subunits The overall structure of Uhgb_MP was determined by molecular replacement using the structure of Tm1225 from T. maritima MSB8 (PDB entry 1vkd), which shares 60% identity with Uhgb_MP, as a model. The crystal structure of  Uhgb_MP revealed a homohexameric organization. The homohexamer consisted of a trimer of dimers with D3 symmetry, with six molecules per asymmetric unit. The apo structure was refined to 1. 80 A ˚resolution, while the complexes with mannose, with N-acetylglucosamine and with the two combined were refined to 1. 94, 1. 60 and 1. 76 A ˚, respectively (Table  1 ). The electron-density maps did not enable construction of the N-terminal extremity of the polypeptide chains. The N-terminal hexahistidine tag and the following 6-8 first residues have thus been omitted from the final model.
In the apo structure, a molecule of glycerol, which was used as a cryoprotectant, occupied the À1 subsite. This glycerol molecule was hydrogen-bonded to the side-chain carboxylate moiety of Asp304 (O 1 to O 3 and O 2 to O 1 ), while its O 2 atom was hydrogen-bonded to the P i , mimicking the interactions between mannose and the surrounding amino acids that were observed in the protein-ligand complexes. Interestingly, in the Uhgb_MP structures where binding of mannose in the À1 subsite occurred (PDB entries 4udj and 4udk in Table  1 ), the mannose ring was found in a stressed B 2,5 boat conformation stabilized by hydrogen bonding to Asp304 (O 1 to the C 6 hydroxyl and O 2 to the C 4 hydroxyl); the mutation of this critical residue to asparagine abolishes 96% of the activity (Ladeveze et al.
, 2013). This unusual conformation of mannose was present in all six chains (Supplementary Fig. S1 ) and was previously observed in the Bf MGP structures (PDB entry 3was, for which in cristallo activity was observed, and PDB entry 3wat). It should be noted that this B 2,5 boat conformation is less unstable in mannose compared with other monosaccharides owing to the pseudo-equatorial position of the C 2 -OH, which is in an anti configuration to the ring O atom, thus bending the C 3 -OH towards the -glycosidic O atom, in a syn axial position. The binding of mannose in the À1 subsite induced a large conformational movement in the active site. Indeed, in the apo form, where a glycerol molecule was observed in place of mannose, the amino moiety of Asn44 interacts with the C 3 hydroxyl of glycerol through a water molecule (conformation A in Fig.
It must be noted that the B conformation of the catalytic Asp104 is probably the one that is active since it has also been observed for Bf MGP, which was demonstrated to be catalytically active in cristallo  (Nakae et al. , 2013). The A conformation of the catalytic residue Asp104 of Uhgb_MP was observed in the structure of the GH130_2 Tm1225 protein in the apo form (PDB entry 1vkd). In the Uhgb_MP structures, the B conformation was only observed when mannose was bound in the À1 subsite, and is therefore independent of the presence of N-acetylglucosamine in the +1 subsite. Indeed, the A conformation was observed in the complex with N-acetylglucosamine alone (PDB entry 4udg, with glycerol in the À1 subsite and N-acetylglucosamine in the +1 subsite), while the B conformation was observed in the complex with mannose and N-acetylglucosamine (PDB entry 4udk, with mannose in the À1 subsite and N-acetylglucosamine in the +1 subsite).
maritima MSB8 (PDB entry 1vkd) as a structural template, considering a monomeric form of the enzyme and using geometrical constraints provided by a classical inverting GH-like single-displacement mechanism. In this model, we previously hypothesized a +1 subsite formed by the Tyr103, Asp304, His174, Tyr240 and Phe283 residues, which are specifically conserved in the GH130_2 family, while the +2 subsite would be delineated by Tyr242, Pro279, Asn280 and Asp304. In this configuration, the exit of the catalytic tunnel would be orientated towards the inside of the oligomeric structure, thereby reducing access to the catalytic site. In addition, the conserved His235-Tyr240 loop from a cognate monomer would block the furrow that we have hypothesized. These new data emphasize the importance of taking into account the quaternary organization when modelling oligomeric enzymes, using SAXS data when possible to define the low-resolution envelope and avoiding restraining the possible docking modes of substrates too much to envisage original reaction mechanisms.
4b ). These interactions involve T-shaped stacking between the imidazole groups of His174 and His235 and hydrogenbond interactions between side chains between Asn40 and Tyr264 and between Ser64 and Pro263. Main-chain carbonyl and amino groups are also involved in the assembly. More precisely, the Thr63 carbonyl is in contact with Tyr264 NH, while the side chains of Asn238 and Asn280 interact with the carbonyl group of Gly276 and the amide N atom of Tyr240, respectively. Finally, the side chain of Asn238 makes contact with the Pro279 carbonyl moiety. SEC-MALLS and SAXS analysis confirmed the hexameric organization of Uhgb_MP in solution. The protein apparent molecular mass determined by SEC-MALLS was 240 kDa (n = 6. 16; Supplementary Fig. S3 ). Guinier analysis of the SAXS data revealed that in phosphate and Tris-glycerol buffers, the radius of gyration (R g ) was considerably larger than the theoretical R g , indicating protein aggregation.
Superposition of Uhgb_MP (GH130_2; red) with mannosylglucose phosphorylase (BfMGP) from B. fragilis NCTC 9343 (GH130_1; PDB entry 4kmi; blue), and BACOVA_03624 from Bacteroides ovatus ATCC 8483 (GH130_NC; PDB entry 3qc2; green), illustrating the structural differences between GH130 subfamilies. The catalytic Asp104 is shown in the B conformation. With the exception of the BfMGP loop Thr42-Met68, which does not exist in the Uhgb_MP structure, the loops are numbered with respect to the Uhgb_MP sequence. The 11-residue longer Gly121-Pro125 loop, which is specific to GH130_1, fills the entrance to the Uhgb_MP tunnel. In place of the Asp61-Arg65 loop, an extension is observed for GH130_NC, capping the catalytic site. These two loops, which are specific to GH130_1 and GH130_NC, respectively, may explain the inability of enzymes belonging to these subfamilies to phosphorolyze long substrates.
Acknowledgements This work was supported by the  French Ministry of Higher Education and Research  and by the  French National Institute for Agricultural Research (INRA , ' Meta-omics of Microbial Ecosystems ' research program). The equipment used for protein purification (ICEO facility), biophysical (DSF, SEC-MALLS) and crystallographic experiments are part of the  Integrated Screening Platform of Toulouse (PICT, IBiSA ). We thank  Dr Valerie Guillet  for technical assistance with SEC-MALLS. We also thank the  European Synchrotron Radiation Facility (ESRF), Grenoble, France , in particular the staff of beamline ID-23-1. Experiments were also performed on the XALOC beamline at the  ALBA Synchrotron (Barcelona, Spain)  with the collaboration of the  ALBA  staff ( Dr Jordi Juanhuix ). Author contributions: Uhgb_MP production and purification, SL; crystallographic studies and X-ray data collection, SL, ST, GC and LM; SAXS experiments, PR, SL and GC; DSF and SEC-MALLS experiments, SL and ST.
Data collection Data were retrospectively extracted from the medical and nurses files. Demographic data included age, sex, and body mass index. Associated comorbidity factors were defined as diabetes mellitus, congestive heart failure (using the ventricular ejection fraction measured by ultrasound, cut-off l40%), and hypertension requiring treatment. COPD status and treatment were investigated using the following data: smoking status (cumulative smoking [packs per year] and active smoker status), lung function determined by FEV (absolute value in milliliters and ratio to the predicted value expressed in percentage), previous known airways PA colonization, and chronic oral steroid treatment (5 mg/day). Results from biological tests at ICU admission were also collected: hemoglobin (g/dL), leucocytes count, serum creatinine level, serum protein level, and arterial blood gas analysis.