dataesr/scientific-paragraphs-categorization huggingface dataset:
Cell population densities, cell viability and GFP activity determinations Cell population densities, cell viability and Hsp12 promoter activity were determined by flow cytometry using a C6 cytometer (Accuri, BD Biosciences). To determine cell population densities, the cell suspension was compared to a suspension of latex beads of known concentration. For cell viability analysis, propidium iodide (PI) (Calbiochem) was added to the cell suspension (5 mL of 0. 1 mg/mL solution), and the samples mixed by gentle shaking. PI is a fluorescent nucleic acid stain (excitation 488 nm, emission 575 nm) which cannot penetrate intact cell membranes. PI flow cytometry analysis was performed 10 min after staining. Fluorescence data for cells stained by PI were collected in channel FL3. Viability was determined as the percentage of intact and fragile cells among all cells  [42].
RNAs were hybridised on 8 6 15 k array Agilent standard Yeast V2 Gene Expression Microarrays (Agilent Technologies) for 17 h in a rotating oven at 65uC following the manufacturer's recommendation. A Genepix 4000B scanner was used for array digitalization: the laser voltage was set to avoid signal saturation and data was extracted with GenePixH Pro 7 software (Molecular Devices). R. 2. 14. 21. was used for statistical analysis  [45]. The limma package  [46] [47] [48]  was used to normalise the microarray data (quantile method for normalisation between arrays). To analyse differential gene expression between experimental conditions, a modified t-test was used by filtering on confidence at p,0. 05, using the Benjamini and Hochberg false discovery rate as multiple testing corrections of the t-test p-values  [49].
Only genes with a log2 fold change greater than 1 (positive or negative) were considered. The complete data set is available through the Gene Expression Omnibus database (accession number GSE42027). For a statistical treatment of groups of genes, data were analysed using the web-based tool Funspec (http://funspec. med. utoronto. ca/; [50] ) (P-value , 0. 05 and Bonferroni correction) and genes were classified into functional categories, biological process and protein cellular localisations using the GO Database. Table  S1  Effect of nutrient imbalances on the amino acid content of S. cerevisiae EC1118 cells (mmol assimilable nitrogen/L).
4, respectively) or G-rich probes conjugated with either fluorescein isothiocyanate or Cy3. Co-denaturation was performed at 80 C for 5 min. Hybridization was carried out at room temperature for a minimum of 2 h in the dark. Slides were washed with 2Â 15 min 70% formamide, 20 mM Tris-HCl, pH 7. 4, with agitation, followed with 3Â 5 min Tris-NaCl-Tween. DNA was stained with 100 ng/ml of DAPI in Vectashield (Vector). Images were obtained with a Zeiss UV microscope equipped with appropriate excitation/emission filters. Images were captured with an HQ-Coolsnap camera (Photometrics) using the IPlab software.
Gorilla TERRA detection Total RNA was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Remaining traces of DNA were digested with DNase I (Qiagen). For northern blot experiments, 10 or 20 mg of total RNA from both gorilla and human fibroblasts (WI-38) was separated by alkaline electrophoresis in 1% agarose 1. 3% formaldehyde gel and transferred to nylon membranes. Blots were blocked with Church buffer and hybridized overnight with Cht7, Tel-C-rich or Tel-G-rich 32 P g-ATP-labeled probes. The blots were then washed 2 Â 5 min with 2Â SSC 0. 1% SDS and 5 min with 0. 2Â SSC, 0. 1% SDS, neutralized in 2Â SSC, exposed to PhosphorImager screens and visualized on a Typhoon PhosphorImager using ImageQuant software. TERRA detection by FISH was performed similarly to the FISH protocol described earlier in the text, with the exception of an RNase A digestion (10 mg/ml) for 1 h 37 C and with no denaturation step, when mentioned as well as RNase-free conditions throughout the protocol.
Among Paragonimus species, P. paishuihoensis is one of the most mysterious and poorly understood species. Metacercariae are characterized by having a unique dendritically branched excretory bladder. However, the morphology of the adult worm remains unknown. To date, metacercariae of this species have been reported only in China and Thailand. In this study, we first found P. paishuihoensis metacercariae in freshwater crabs, Potamon lipkei, in Hinheub District, Vientiane, Lao PDR, with a prevalence of 77. 7% and the average intensity of 10. 3 (range 1-28) metacercariae per crab. The molecular data based on ITS2 and CO1 markers indicated that P. paishuihoensis from Laos and Thailand were almost completely identical and were close to members of the Paragonimus bangkokensis/Paragonimus harinasutai complex.
Molecular analyses From 3 metacercariae of P. paishuihoensis (codes: MC32-MC34), we amplified and sequenced the ITS2 region using the primer pair 3S and A28  [8]  and a partial CO1 gene using the primer pair of CO1-1-forward and CO1-2-reverse  [9]. The methods for molecular study followed those described previ-ously  [10]. The obtained sequences were deposited in the Gen-Bank with accession no. AB679285-AB679290. In addition, we downloaded and used further sequences of Paragonimus spp. from GenBank, including the available sequences (ITS2: AB471886 and CO1: AB471887) of P. paishuihoensis from Thailand and 1 ITS2 sequence (AB370191), which was originally registered as Paragonimus sp. from Laos and is now reregistered as P. paishuihoensis by us. Two sequence data sets, ITS2 and CO1, were used to reconstruct the phylogenetic trees.
[1] , with P. paishuihoensis metacercariae, but no worms were established themselves in these hosts. This indicates that dogs, cats, and rats are not suitable definitive hosts for P. paishuihoensis; it might have narrow host specificity to an unknown mammalian host, or require a paratenic host. If a paratenic host is required, our results suggest that it is not the rat; no juvenile worms were found when the body of each rat was completely digested. Further studies are necessary to elucidate the life cycle of P. paishuihoensis. In molecular studies, Cui et al. [5]  reported that P. paishuihoensis obtained in Yunnan Province, China, was genetically similar to P. xiangshanensis and P. bangkokensis from China. Unfortunately, those sequence data are not registered in GenBank. To date, P. paishuihoensis from Thailand is represented in Gen-Bank by only a single ITS2 and a single CO1 sequence  [6].
In the present study, molecular phylogenetic analyses revealed that P. paishuihoensis isolates from Lao PDR and Thailand were genetically almost completely identical with each other, thus forming a moderately to well-supported group in ITS2 and CO1 trees. Consistent with the previous reports  [14, 15] , P. paishuihoensis sequences were clustered with P. harinasutai of China with a moderate bootstrap value of 76% to make a group separated from the rest of the P. bangkokensis/P. harinasutai. However, grouping with P. paishuihoensis and P. bangkokensis/P. harinasutai complex was supported by very low bootstrap values (less than 50%), especially in CO1 tree. For further investigation on taxonomic status in this group, more sampling and sequence data accumulation is necessary. Since only 1 each of ITS2 and CO1 sequence of P.
harinasutai and none of other related species (P. xiangshanensis and P. bangkokensis) from China are available in the GenBank database, more sequence data of those species from China and also from other geographical locations would be useful for better understanding of their taxonomic status and phylogenetic relationship. In conclusion, we demonstrated the presence of P. paishuihoensis metacercariae in Lao PDR, suggesting a wider distribution of this species in Indochina than previously suspected. Since the definitive hosts of P. paishuihoensis have not yet been identified, further studies are required to clarify the taxonomic status and life cycle of this species.
As such, many bacteria entering Antarctic soils from the atmosphere may be well adapted to survive in their new environment  [20]. The likelihood of colonization may be increased by the effects of climate change, as increased temperature and water availability may favor growth of foreign organisms in Antarctic soils  [6, 21]. Atmospheric processes may, therefore, have a particularly important role in shaping microbial communities in Dry Valley soils. In this study, the diversity of airborne bacteria was assessed on the floor and ridge of Miers Valley, a location with extensive landscape-scale ecological research data on the surface ecology  [18]. The objective was to set up a baseline dataset for airborne inputs of bacteria and assess how they may influence Dry Valley soils, since soil biodiversity is known to vary with elevation in this system  [16, 22].
Analysis of Sequencing Data Raw sequence data was analyzed using AmpliconNoise v1. 25 with default parameters  [24]. Chimeric sequences were removed using Perseus  [24]. Sequences were processed in Mothur v1. 24. 1  [25]. Pairwise distances were calculated using ESPRIT  [26]  and sequences grouped at 97 % identity into operational taxonomic units (OTU 0. 03 ) using average neighbour clustering. Unique sequences had to be observed a minimum of three times in order for them to be retained for further analyses. Sequences were assigned to taxonomic groups using the Classifier function of the Ribosomal Database Project (RDP) Release 10  [27]  with a confidence threshold of 80 %, and sequences were compared to those in the NCBI database using the BLASTn algorithm  [28]. Phylogenetic analyses were carried out in MEGA v5.
05  [29]. Sequences were aligned over 266 homologous positions of the 16S rRNA gene using Clustal W. A neighbour-joining tree was constructed based on the alignment using default parameters, except rates among sites were adjusted to be gamma distributed, rather than uniform. The phylogenetic tree was tested based on bootstrap analysis with 1,000 replications. In addition to the NCBI database, Miers Valley aerosol sequences were compared to those from previously published datasets using the BLASTn algorithm. The first dataset included 31 bacterial clone sequences reported in air samples over Halley Station, West Antarctica  [7]  (GenBank accession numbers FN431986-FN432029). The second dataset included all bacterial sequences observed in a Miers Valley soil sample that was used as a control site in a recent study  [17].
The third dataset included 1,320 sequences from ice-free areas of Antarctica  [16] : Anchorage Island, Coal Nunatak, Fossil Bluff, and Mars Oasis  [30]  (GenBank accession numbers EF219488-EF220012; EF220190-220371; 220735-220903), Miers Valley and Bratina Island  [31]  (GenBank accession numbers DQ062859-DQ062918), Luther Vale  [32]  (GenBank accession numbers EF464767-EF465090), Ross Island  [33]  (GenBank accession numbers AY571818-AY571845), and Marble Point and Wright Valley  [34]  (GenBank accession numbers DQ365987-DQ366018). Pyrosequencing data was also screened for possible user contamination, using commonly accepted indicators of human microflora and pathogens as previously described  [35] [36] [37] [38] [39]. The pyrosequencing datasets generated in this study are deposited in the European Nucleotide Archive, under accession number ERP002362 (http://www.
Meteorological Data and Back Trajectory Analyses Back trajectories were generated with the internet-based version of HYSPLIT, to establish the source regions of air masses advecting over Miers Valley during the sampling period  [40]. Seven-day back trajectories released at 500 m above ground level (AGL) were obtained using the GDAS database for every other day; to allow for adequate vertical mixing in the atmosphere during transport, the isentropic option for calculating the back trajectories was selected. Although the resolution of GDAS is not adequate enough to show transport within the Dry Valleys system, it should still elucidate the long-range transport source regions accurately.
6 % of the sequences observed in the Miers Floor and Miers Ridge samples, respectively (Supplementary Table  2 ). A total of 64 OTUs 0. 03 were observed only in the Miers Floor sample, and 65 OTUs 0. 03 were observed only in the Miers Ridge sample, accounting for 4. 7 % and 6. 4 % of the sequences in these libraries, respectively. We recorded only ten OTUs 0. 03 (five in both samples, one only in the Miers Floor sample, and four only in the Miers Ridge sample) in the entire dataset for both locations that displayed 91-99 % sequence similarity to human skin (Dermacoccus, Flavobacteria, Lactobacillus, Micrococcus, Propionibacteria, Staphylococcus) or fecal (Escherichia) microflora; no pathogenic taxa were detected in the libraries. These taxa indicative of human contamination comprised less than 1 % of the sequences in the two libraries, and since most were phylogenetically also very closely related to common soil bacteria, we conclude negligible human contamination to our sequence dataset.
Phylum assignments were made using the Classifier function of the Ribosomal Database Project (RDP) Release 10  [26]  with a confidence threshold of 80 %  bacteria associated with an insect host  [46]  and an uncultured bacteria associated with a mud volcano in the Mediterranean  [47] , respectively. Their closest cultured matches were with 98 % sequence identity to isolate Paenibacillus sp. C15, from Lake Vostok accretion ice and with 98 % sequence identity to Paenibacillus chinjuensis , an isolate from a soil in Korea. Few sequences in the Miers Valley aerosol libraries were also present in the Halley Station aerosols, Miers Valley soil, or Antarctic ice-free areas databases. Sequences from 5 OTUs 0. 03 observed in the Miers aerosol libraries matched 7 of the 31 clones reported in the Halley Station aerosols with >97 % 16S rRNA gene sequence identity, and these OTUs 0.
03 accounted for 3. 2 % and 0. 5 % of the Miers Floor and Miers Ridge samples, respectively. Sequences from 13 OTUs 0. 03 observed in the aerosol libraries matched sequences in the Miers soil library with >97 % 16S rRNA gene sequence identity, but these sequences made up <3 % of either aerosol library. Sequences from 34 OTUs 0. 03 were found to be present in either the Miers soil library or soils from other ice-free areas in Antarctica, and these OTUs 0. 03 accounted for 6. 6 % and 5. 3 % of the Miers Floor and Miers Ridge samples, respectively. Seven-day back trajectories indicated that the air masses influencing the sample sites came predominantly from the plateau, with few events immediately influenced by the marine environment (Fig. 3 ). An Automatic Weather Station (AWS) installed in the valley floor shows that the typical surface flow was easterly (up-valley) for December and January (data is not available between December 12 to January 18 due to equipment failure).
Carbohydrate concentrations ranging from 10 µM to 10 mM in running buffer (20 mM Hepes, pH 7. 4; 150 mM NaCl; 3 mM EDTA and 0. 005% surfactant Tween 20) were incubated for one minute on all flow cells simultaneously, at 25 °C and at a flow rate of 30 µL/min. Complete dissociation of the carbohydrates in running buffer was verified before starting a new binding cycle. All binding cycles were performed in duplicate, including a zero concentration cycle (injection of pure running buffer). All analysis was done using the BIAeval software. In each case the equilibrium resonance signal from the reference cell was subtracted from that of the various F17G flow cells (2-1, 3-1, 4-1). A Langmuir binding isotherm with a 1:1 stoichiometry was fitted to the data, from which the equilibrium dissociation constants, K d , were obtained.
Crystallization and Structure Solution F17bG was crystallized at a concentration of 12 mg/mL with 10 mM GlcNAc 1,3Gal using hanging drop vapour diffusion against 1 M Li 2 SO 4 , 0. 1 M Tris-HCl at pH 8. 5 and 10 mM NiCl 2 , as described in  [16]. Analysis of the corresponding diffraction data using the Phenix XTriage module indicated the presence of merohedral twinning. Consequently, all refinement steps were carried out using the amplitude-based twinning correction target (TWIN_LSQ_F) in the Phenix refinement program, with a twin law of h,-h-k,-l and a final refined twinning fraction of 0. 41. The ligand-free FedF structure is a further refinement of PDB entry 4B4P  [25] , from a bromide-soaked FedF crystal originally used for MAD phasing  [37].
1, exp. 2053). The same sugar is the 28th best binder for variant b (version 2, exp. 400), although caution should be excercised when interpreting the ranking because of the different versions of the arrays. The mutation in F17bG of Asn90 to Lys90 in F17aG could be at the basis of this observation, because a sulfate ion, S4, binds Asn90 in F17bG (Figure  6d ). Indeed, in the novel cocrystal structure of F17bG in complex with GlcNAc 1,3Gal, four sulfate ions could be modeled in their electron density (PDB entry 4K0O and Table  S1  for data and refinement parameters). Interestingly, the addition of 10 mM GlcNAc-6-sulfate to crystals of F17bG instantly dissolves them. The sulfate ion S4 is situated near the hydroxyl group at position 4 of galactose, where the disaccharide could be extended, towards the reducing end, into a larger oligosaccharide sequence.
FimH Has a Charged Cradle over the Edge on the other Side of Its Oligomannoside Binding Site E. coli intraspecies amino acid mutations in FimH comprise almost exclusively changes among small hydrophobic and small polar residues: only at the level of interspecies variation with Klebsiella species, charge variation comes into play (Figure  6c ). The crystal structure of FimH bound to oligomannose-3 shows the accommodation of the non-reducing 1,3-linked mannoside in a deep binding pocket on the FimH surface (PDB entry 2VCO, Figure  6f ). The minimal binding epitope is extended by interactions of the central mannose and the GlcNAc residues with the FimH tyrosine gate which protrudes from the binding pocket, resulting in a 100-fold increased binding compared to -D-mannose  [26]. Sulfate-binding residues in this crystal structure indicate a positively charged cradle on the other side of the tip of the adhesin (Figure  6f ).
Acknowledgements We are grateful to  Richard A. Alvarez , former Director of the  Protein-Glycan Interaction Core H of the Consortium for Functional Glycomics , funded by  NIGMS  grant  GM62116 , for performing the first glycan array analysis. K. M. enjoyed a doctoral fellowship under promotorship of J. B. and L. B. as postdoctoral fellows, all three granted by the  Fund for Scientific Research Flanders. We were fortunate to use EMBL beamlines  BW7A ,  BW7B ,  X11 ,  X12  and  X13  at the  DESY synchrotron in Hamburg, Germany , the  ESRF ID14-1  and  SOLEIL ProximaI beamlines in Grenoble and Saint-Aubin , respectively. We are grateful to  Martine Laitat  and  Pierre Vincent Drion  from the  Animal Breeding Centrum at the University of Liège, Belgium , for assistance with the preparation of piglet intestinal microvilli.
We applied the method on the largest neotropical herbivore, the lowland tapir (Tapirus terrestris Linnaeus, 1758). Quite recently, our knowledge on the tapir's diet has been significantly extended for both the fruit and foliar or "browse" diet  [17] ,  [18]. This provides a solid knowledge basis for comparison with metabarcoding. Field work was performed at the Nouragues Ecological Research Station, in French Guiana, where a local reference database of plant species DNA barcodes has been developed  [38]. Hibert et al. [18]  showed that it is feasible to use a classical DNA barcoding (using the plastid DNA trnH-psbA region, of 500 bp on average) of faecal material to identify items of the tapirs' diet. However, the test was conducted on a limited number of individual plant fibre samples and the molecular approach was far from providing as much information on the diet as the combination of the other classical approaches used.
All primers were modified by the addition of specific tags on the 59 end to allow the assignment of sequence reads to the relevant sample  [24]. All the PCR products were tagged identically on both ends. These tags were composed of CC on the 5' end followed by nine variable nucleotides that were specific to each sample. The nine variable nucleotides were designed using the oligoTag program (www. prabi. grenoble. fr/trac/OBITools) with at least three differences among the tags, without homopolymers longer than two, and avoiding a C on the 5' end. All the PCR products from the different samples were first titrated using capillary electrophoresis (QIAxel, QIAgen GmbH, Hilden, Germany) and then mixed together, in equimolar concentrations, before the sequencing. DNA sequencing. The sequencing was carried out on an Illumina/Solexa Genome Analyzer IIx (Illumina, San Diego, California), using the Paired-End Cluster Generation Kit V4 and the Sequencing Kit V4 (Illumina, San Diego, California), following manufacturer's instructions.
A total of 108 nucleotides were sequenced on each extremity of the DNA fragments. Sequence analysis and taxon assignation. The sequence reads were analyzed using the OBITools suite of bioinformatics routines (www. prabi. grenoble. fr/trac/OBITools). First, the forward and reverse reads corresponding to a single molecule were aligned and merged using the solexaPairEnd program, taking into account quality data during the alignment and the consensus computation. Then, primers and tags were identified using the ngsfilter program. Only sequences with perfect match on tags and a maximum of two errors on primers were taken into account. The amplified regions, excluding primers and tags, were kept for further analysis. Strictly identical sequences were clustered using the obiuniq program, keeping the information about their distribution among samples.
Sequences shorter than 10 bp for the P6 loop and 40 bp for the ITS region specific of the Sapotaceae, or containing nucleotides other than A, C, G and T, or with occurrence lower or equal to 10 were excluded using the obigrep program. Taxonomic assignation of the clusters was achieved using the ecoTag program  [28]. EcoTag relies on an exact global alignment algorithm  [44]  to find highly similar sequences in the reference databases. These databases were built by extracting the P6 loop of the trnL intron or the ITS1 fragment from the European Molecular Biology Laboratory (EMBL) nucleotide library (release 107) using the ecoPCR program  [45]. The P6 loop and the ITS1 databases contain 11,905 and 2596 unique sequences extracted from 54,239 and 5650 EMBL entries, respectively. EcoTag assigned a unique taxon to each unique sequence amplified from tapirs' faeces.
This unique taxon corresponds to the last common ancestor node in the National Center for Biotechnology Information (NCBI) taxonomic tree of all the taxids annotating the sequences of the reference database that best matched on the whole length of the query sequence. Dataset trimming. The sequencing produced 70552 unique P6 loop sequences longer than 10 bp and 15162 unique ITS sequences longer than 40 bp (Table  2 ). A number of these sequences could not be assigned to any known taxon. The P6 loop sequences that could not be identified up to the family level (41. 9%) were less frequent than those identified at a finer taxonomic resolution (Figure  1 ) and probably resulted from PCR artefacts. To eliminate the artefact sequences, we automatically removed sequences that did not correspond to any plant sequences present in the EMBL database (homology , 0.
95) except the sequences that had a perfect match with at least one of the DNA barcodes of the Nouragues databases that contain 158 species for the trnL intron and 75 species for the ITS1 region  [38]. We also removed every sequence for which there was a very similar sequence (only one base different) but always in higher occurrence, since it was assumed to be an erroneous copy of the latter. Finally, we only kept for further analysis the P6 loop and ITS sequences with a total number of occurrences higher or equal to 480 or 59, respectively. This corresponds to 1/1000 or 1/100 of the most common sequences for the P6 loop and for the ITS1, respectively.