dataesr/scientific-paragraphs-categorization huggingface dataset:
Symbiont Diversity and Phylogeny Based on 16S rRNA Gene Sequence Analysis The bacterial 16S rRNA alignment was 1459 bp long, and included 50 sequences corresponding to 9 phylotypes. A GenBank BLAST analysis revealed that phylotypes 1, 2, 3 and 4 were. 97% similar to thiotrophic symbionts of bathymodioline mussels. Among those, phylotype 1 was dominant, represented by 35 clones from all analysed specimens (i. e. independently of locality and substrate). Phylotypes 2 and 3, each represented by 2 clones, were recovered from two specimens from the Philippines. Phylotype 4, including 6 clones, was recovered from only one specimen from the Solomon Islands and one from New Caledonia. The five other phylotypes were singletons and bear no resemblance with mussel symbionts (results not shown). They most likely represent environmental bacteria, as they were.
Symbiotic Association and Insights into Nutritional Features of I. iwaotakii In previous studies  [21, 30, 67] , thioautotrophic symbionts have predictably been found in each newly examined deep-sea mussel associated with organic remains. This new dataset supports this predictability and moreover shows that, within a species, the same dominant bacterial phylotype is found, independent of geographic location (the Philippines, Vanuatu and New Caledonia), substrate type (wood versus bone) or depth (441 m to 1767 m). This dominant phylotype is closely related to a symbiont detected in another species within the Idas lineage (I. sp. C) and also in another species from a distinct lineage (G. crypta)  [30]. These two species were also collected both on wood and bone. Phylogenetic relationships among sulphur-oxidizing symbionts are however poorly resolved.
Acknowledgments New material was collected on board of M/VDA-BFAR ( PANGLAO 2005 ,  Co-PI P. Bouchet  and  L. Labe  and Aurora 2007,  Co-PI M. Manuel , and  P. Bouchet ) and on board of  R/V Alis  ( BOA1 ,  Co-PI B. Richer de Forges  and  S. Samadi ;  SANTO2006 ,  Co-PI P. Bouchet ,  O. Pascal  and  H. Le Guyader ;  Salomon2 ,  Co-PI B. Richer de Forges  and  P. Bouchet ,  Biopapua ,  Co-PI S. Samadi  and  L. Corbari ). Sincere thanks to  J. Lorion  for his keen insight and his support,  C. Djediat  for his assistance with microscopic experiments and analysis,  B. Buge  for curation of specimens and the staff of the '' Service de Systematique Moleculaire '' ( UMS2700 CNRS-MNHN ). It is part of the agreement no. 2005/67  between the Genoscope and the  Museum National d'Histoire Naturelle  on the project ' Macrophylogeny of life ' directed by  G.
This work was developed in the framework of the  European research network DiWood  ( GDRE-CNRS 225 ), in collaboration with  N. Lebris , was supported by a grant of  Fondation pour la Recherche sur la Biodiversite(BioWood   AAP-IN-2009-009 ) and by the  ANR TF-DeepEvo  ( ANR-12-ISV7-0005-01 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
II. IEEE 802. 11s ARCHITECTURE The IEEE 802. 11 Task Group S (TGs) is standardizing wireless mesh networking based on IEEE 802. 11 WLAN. The WMNs architecture is composed of three types of nodes  [4, 5] : Mesh Point (MP), Mesh Access Point (MAP) and Mesh Portal Point (MPP), as illustrated in Figure  1. A Mesh Point (MP) supports wireless mesh services and participates in the interoperable operations within a mesh network, such as path selection and data forwarding. The Mesh Portal Point (MPP) acts as a gateway connecting the internal mesh network to the exterior, where Medium Access Control Service Data Units (MSDUs) enter/exit the mesh network from/to other networks. The MPP includes the MP functionality and could be co-located with an 802. 11 portal and access point. The Mesh Access Point (MAP) is an MP playing the role of an access point: the MAP provides both mesh point and access point (AP) functionalities.
1C, F, G ). The pRNA 3WJ was coordinated by two divalent metal ions bridging four phosphates (two from helix H1 and two from helix H3) such that the contact distance between phosphates donated by adjacent helices was reduced to 4. 5 Å, with a relatively short 2. 25 Å average metalphosphate distance that was consistent with Mn 2+ /Mg 2+ binding (Fig. 1F ). Bound metal atoms were initially identified via 10-12 σ peaks in the |F o |-|F c | difference density map. Although both Mn 2+ and Ca 2+ were present in the crystallization conditions, the putative metal sites that bridge adjacent phosphate groups were confirmed as Mn 2+ by anomalous difference Fourier analysis at a wavelength where Ca 2+ has no measurable signal (Fig. 1F , inset). Therefore, the 3WJ structure deposited in the Protein Data Bank (PDB) contains Mn 2+ in the phosphate bridging metal sites.
1998; Chen et al. 2000). The availability of the structure of individual domains makes the assembly of the entire pRNA structure and the ring feasible. For model structure construction, the crystal structure of the pRNA 3WJ and the published structural data  (Hoeprich and Guo 2002; Harris and Schroeder 2010; Ding et al. 2011)  were used to build the intact 120-nt pRNA monomer as well as a hexameric pRNA ring (see Materials and Methods) (Figs. 1A, 4A ). Briefly, the entire 3WJ structure, including the two metal ions, was used as a central building block for grafting the structures of the other four domains from three PDB files (PDB codes 1L4O, 2KVN, 3R4F)  (Hoeprich and Guo 2002; Harris et al. 2010; Ding et al. 2011)  to generate an intact 120-nt pRNA (Fig. 1A ). The 3WJ served as domain 2, and all other domains were connected to the 3WJ.
6). Crystals appeared within a week and continued to grow until they reached average dimensions of 0. 03 × 0. 03 × 0. 3 mm (Supplemental Fig. S1C ). The crystals were mounted on cryoloops and directly plunged into liquid nitrogen without additional cryoprotectant prior to data collection. Native data sets were collected from single crystals cryocooled to 100 K on a MAR225 CCD detector at the SER-CAT 22BM beamline at APS. The data sets were processed with HKL2000 and scaled and merged with Scalepack  (Otwinowski and Minor 1997). The best crystals, space group I4, diffract to 3. 05 Å (Supplemental Fig. S1D ) and have unit-cell parameters a = b = 125. 01 Å and c = 26. 99 Å. Final data collection statistics are summarized in Table  1. The structure was determined by piecewise molecular replacement using three copies of a seven base-paired poly-adenine standard A-form double helix (stem) as a model.
Residues from these regions were grafted onto the 3WJ crystal structure. The left-hand loop was aligned by superposing 3WJ and PDB 3RF4 for 6 bp of region 2 leading up to the lefthand loop, followed by grafting the loop from 3RF4 onto the 3WJ core. The RNA helix containing region 1, including the ATPase interaction domain, came from PDB 1L4O, previously published 3D model for the pRNA hexamer  (Hoeprich and Guo 2002). Residues 1-20 and 100-117 were grafted from 1L4O onto the 3WJ structure after superposition of the sugar-phospate backbone for 4 bp leading up to the CCA bulge. Finally, two single-residue insertions missing from any current model in the database were built into the pRNA monomer, including a "flipped out" conformation for U35 and an in-line conformation for residue U81 of the lefthand loop.
ACKNOWLEDGMENTS We thank  Eric Westhof  for critical review on the manuscript and the crystal structure as well as assistance in refinement of the final pRNA structure model. The research was supported by  NIH  grants  EB003730  and  CA151648  to P. G. and ADA grant  7-08-CD-03  to Y. C. AFM images were obtained at Nanoimaging Core Facility supported by  NIH SIG program  and  UNMC Program of ENRI  to Y. L. P. G. is a cofounder of  Kylin Therapeutics, Inc. , and  Biomotor and Nucleic Acid Nanotechnology Development Corp. Ltd. Received October 30, 2012; accepted June 6, 2013.
Through the in vivo enzymatic quantification of PqsE variants complementing a pyocyanin-deficient P. aeruginosa pqsE 2 mutant strain, we identified residues playing key roles in the biological function of this regulatory enzyme and quantified their stability upon mutation using the PoPMuSiC software  [21]. We also present further insights on the functional importance of two structural motifs unique to this representative member of the metallo-b-lactamase fold. Because PqsE is an important drug target showing considerable promise for the design of new inhibitors directed against P. aeruginosa, mutational mapping of its active site is the first step toward exploiting functional information aimed at controlling virulence acquisition in this human pathogen.
ambifaria (32% identity), B. thailandensis (31% identity), and B. pseudomallei (31% identity) (Figure  1 ). Based on this alignment, we identified a number of highly conserved residues that are most likely involved in substrate stabilization, discrimination and/or catalysis in both PqsE and HmqE. These include a total of 16 residues delineating the immediate vicinity of the active site cavity (Figure  1 , orange residues), which will further be described below. We know from the PqsE structure  [20]  and the SCOP database  [27]  that PqsE belongs to the metallo-hydrolase/oxidoreductase superfamily, a functional enzyme clan encompassing at least 13 interspecies protein families playing various biological functions. We used T-Coffee Expresso  [28]  to perform structure-based sequence alignments of PqsE (PDB entry 2Q0I) with 21 members of 7 metallo-hydrolase/oxidoreductase subfamilies, including zinc metallo-b-lactamases, glyoxalases, ribonuclease Z, alkyl/arylsulfatases, hydroxylases, and other putative hydrolases (Figure  S1  in File S1).
Identification of two unique structural motifs in PqsE PqsE adopts a very common three-dimensional structure shared by many proteins of the metallo-b-lactamase fold  [29]. We retrieved all proteins adopting such a fold from the SCOP database  [27] , as well as members of known structure from blactamase families 2, B, B2, B3, and B4 (395 hits in the Pfam database  [30] ). The pairwise superposition of each member with PqsE was analyzed and the strong conservation among structural homologues allowed the unambiguous identification of the activesite cavity (Figure  2A ). Two structural elements that differentiate PqsE from other members of this protein fold could be identified from this pairwise superposition. First, PqsE exhibits two additional a-helices (a8 and a9) at the C-terminal end of the protein (Figure  2C ).
A previous analysis attributed a very weak phosphodiesterase activity catalyzed by PqsE on single-and double-stranded DNA and RNA substrates  [20]. This result prompted us to further analyze the structural features shared between PqsE and DNA/ RNase members of the metallo-b-lactamase fold. The pairwise structural alignment of PqsE with the TTHA0252 ribonuclease from Thermus thermophilus HB8 (PDB entry 3IE1) demonstrates that a single-stranded DNA/RNA substrate could fit in the PqsE active site tunnel, suggesting that this enzyme could be involved in RNA/ DNA metabolism in P. aeruginosa. Additionally, the structural overlay between PqsE and TTHA0252 shows a kinked helix very similar to the helix-loop-helix motif of the hnRNP K domain (KH domain) (Figure  3 ). KH domains are conserved interspecies structural motifs which are typically found in proteins associated with transcriptional and translational regulation  [32].
We also selected D130 as a mutational target because of its potential to form a salt bridge with K101. Except for the S285W variant described above, all other positions were mutated to alanine, effectively removing the side chain functionalities found in the WT context. While generally tolerant to subtle replacements, introducing mutations to a protein sequence can nevertheless cause significant changes in the native structure, which in turn may cause an important phenotypic change or loss of biological function. To evaluate undesired structural and/or stability changes, we used the PoPMuSiC software  [21]  to predict the destabilizing effects of each proposed point mutant on the PqsE structure. PoPMuSiC uses a set of 24 statistical potentials and models the volume changes caused by amino acid replacements, further expressing the folding free energy changes as a single linear combination of these terms with weighting coefficients based on solvent accessi- bility  [21].
The solvent accessible surface was computed with CAVER  [35]  and the co-crystalized benzoate moiety (BZ) is shown in green ball-and-stick representation (PDB entry 2Q0I). Residue side chains are labeled, displayed in ball-and-stick representation, and colored according to their impact on pyocyanin production upon mutation (Figure  6 ). C) The benzoate molecule is displayed from the S285 tunnel entrance in WT PqsE and shows clear solvent accessibility to the active site. D) The modeled S285W replacement shows the blocked entrance of the tunnel caused by the indole side chain of tryptophan. E) The benzoate molecule is displayed from the Q272 tunnel entrance in WT PqsE. F) The modeled Q272A replacement shows a modest yet significant tunnel enlargement. Amino acid replacements were generated using the PyMOL mutation function.
aeruginosa. Indeed, variants H69A, H159A, and D178A barely allow the in vivo synthesis of pyocyanin while H71A significantly alters production relative to WT (Figure  6 ), confirming the critical importance of maintaining Fe 1 integrity. In contrast, Fe 2 is surrounded by residues that tolerate alanine replacements relatively well, i. e. D73, H74, and to a lesser extent H221. These results suggest that Fe 1 is closely packed and more important to the catalytic mechanism of PqsE than Fe 2. All three experimentally determined WT structures of PqsE (PDB entries 2Q0I, 2Q0J, 2VW8) were co-crystallized in presence of small organic compounds in the active-site cavity (benzoate or cacodylate). Yu et al. also generated a PqsE point mutant (E182A) with an enlarged binding cavity that co-crystallized in presence of bis-p-nitrophenyl phosphate (bis-pNPP), a E182A-hydrolyzed substrate that is not turned over by WT PqsE  [20].
From structural overlays, we found that the closest non-HmqE homologue sharing a similar a-helical motif at the C-terminal end of the protein is the putative hydrolase ST1585 from the archaeon Sulfolobus tokodaii (PDB entry 3ADR)  [42]. Crystal structures of PqsE and ST1585 overlay with a RMSD of 2. 8 A ˚(Fig 2D ), raising the possibility of a function catalyzed by the enzymatic action of ST1585 in S. tokodaii. To examine this possibility, we transformed a pqsE 2 mutant of P. aeruginosa with a pUCP20-st1585 construct and quantified the resulting pyocyanin production. Expression of ST1585 in P. aeruginosa failed to complement the in vivo pyocyanin production of PqsE (not shown), suggesting that the two proteins do not act on the same regulatory system in P. aeruginosa and S. tokodaii.
HPA Genotyping by Sequence-Based Typing Method (SBT). To verify the SSP-PCR results, 20 DNA samples were selected for genotyping for HPA-1 to -6 and -15 by SBT. Sequencing primers were designed according to previously published sDNA sequences  [11]. DNA samples were amplified, followed by bidirectional sequencing of the amplicons using the ABI BigDye Terminator Cycle Sequencing kit (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's instructions. The sequencing reaction products were electrophoresed using an ABI Prism sequencer (Applied Biosystems). The sequence data were analyzed by SeqScape 2. 5 software (Applied Biosystems).
Statistical Analysis. HPA genotype frequencies were estimated by direct counting, and allele frequencies and heterozygosity were calculated by the genetic marker data analysis software (PowerMarker)  [12]. Tests for Hardy-Weinberg equilibrium in the population were performed by  2 test. Mismatch probability of different platelet alloantigens, after random platelet concentrate transfusions, was calculated  [13]  by using the formula 2(1 -), where  and  are the respective HPA gene frequencies at a diallelic focus. The probability of fetomaternal incompatibility between pregnant females and their fetuses regarding different HPA was calculated  [14]  for assessing the probability of HPA alloantibody development. Comparison between the gene frequencies of six blood centers was done with  2 test using SPSS version 14 (SPSS Inc.
We found that 0. 5% of individuals are HPA-4b positive (compared to 0% in Caucasians) and 3. 01% are HPA-5b positive; the potential for HPA-4b and HPA-5b to induce alloimmunization cannot be ignored since these alleles are known to be immunogenic  [20, 25]. They may therefore be responsible for more FNAIT cases than HPA-3a or HPA-15b. In conclusion, our data provide information on platelet antigen allele frequency in Taiwan population that can serve as a background (a) to diagnose the cause of FNAIT, PTP, and PTR and (b) to provide HPA-matched apheresis platelet for patients with HPA alloimmune disorders. Large-scale study will now be conducted to confirm these data in order to establish an apheresis donor database for the provision of HPA-matched platelets for transfusion to patients with alloimmune disorders.
Analytical, Numerical Results and Validation Numerical calculations were performed on the example of the hollow cylinder (Figures  1, 2  With the derived eigenfrequency equations, natural frequencies   = Im(] 2  ) for each pair of (, ) are calculated in the software Mathematica. and  denote the mode in axial and azimuthal (propagating clockwise around the vortex) direction, respectively. To validate the analytical results, the natural frequencies and mode shapes are also computed using Comsol Multiphysics FEM Simulation Software. The natural frequencies are computed directly from        (24)  for torsion vibration. For longitudinal vibration, (28) can be used to determine the corresponding natural frequencies. Tables  1  and 2  show the comparison of the first 18 natural frequencies and the corresponding mode shapes of viscous fluid by FEM and the present method (see  (16)  and (20)).
For example in the case of "no-slip-normal stress-free" boundary conditions, in the first 18 natural frequencies, four correspond to flexural vibration ( = 1), nine to breathing vibration ( ⩾ 2), four to torsional vibration, and one to longitudinal vibration. The very good agreement is observed between the results of the present method and those of FEM and the relative difference ((FEM-Present)/Present) is ⩽1%. This shows that the algorithm implemented in Comsol    Multiphysics  [26, 27]  software for numerical computation is highly reliable and accurate. This algorithm is based on the UMFPACK method  [28]. Is the attention to use the numerical formulation in future for more general geometries. Tables  1  and 2  and Figures  4, 5 , and 6 show that natural frequencies are very sensitive to the nature of the boundary conditions.
The B 0 -B 0 oscillation frequency ∆m d is measured by the LHCb experiment using a dataset corresponding to an integrated luminosity of 1. 0 fb -1 of protonproton collisions at √ s = 7 TeV, and is found to be ∆m d = 0. 5156 ± 0. 0051 (stat. ) ± 0. 0033 (syst. ) ps -1. The measurement is based on results from analyses of the decays and their charge conjugated modes.
Therefore, the measurement of ∆m d provides an important test of the Standard Model  [12, 13]. Furthermore, ∆m d is an input parameter in the determination of sin 2β at LHCb  [14]. This Letter presents a measurement of ∆m d , using a dataset corresponding to 1. 0 fb -1 of pp collisions at √ s = 7 TeV, using the decay channels B 0 → D -π + (D -→ K + π -π -) and B 0 → J/ψ K * 0 (J/ψ → µ + µ -, K * 0 → K + π -) and their charge conjugated modes. For a measurement of ∆m d , the flavour of the B 0 meson at production and decay must be known. The flavour at decay is determined in both decay channels from the charge of the final state kaon; contributions from suppressed B 0 → D + π -amplitudes are negligible. The determination of the flavour at production is achieved by the flavour tagging algorithms which are described in more detail in Sect.
Experimental setup and datasets The LHCb detector  [15]  is a single-arm forward spectrometer covering the pseudorapidity range 2 < η < 5, designed for the study of particles containing b or c quarks. The detector includes a high precision tracking system consisting of a silicon-strip vertex detector surrounding the pp interaction region, a large-area silicon-strip detector located upstream of a dipole magnet with a bending power of about 4 Tm, and three stations of silicon-strip detectors and straw drift-tubes placed downstream. The combined tracking system has a momentum resolution ∆p/p that varies from 0. 4 % at 5 GeV to 0. 6 % at 100 GeV, and an impact parameter (IP) resolution of 20 µm for tracks with high transverse momentum. Charged hadrons are identified using two ring-imaging Cherenkov detectors.
The decay time acceptance is evaluated in bins of t and is implemented in the fit described in Sect. 6. In the decay B 0 → D -π + there is no control dataset that can be used to measure the decay time acceptance. From an analysis of simulated events, it is determined that the decay time acceptance can be described by the empirical function acc (t|a 1 , a 2 ) = arctan(a 1 exp(a 2 t)), (4) where the parameters a 1 and a 2 are both free in the maximum likelihood fit for ∆m d described in Sect. 6.
Microarray Analysis Total cytoplasmic RNA and polysomal RNA were isolated from BRCA1-depleted MCF7 cells and control MCF7 cells as described in the ''Isolation of polysomes and total cytoplasmic RNA'' section. Microarray processing and data analysis was performed at the ProfileXpert core facility (Lyon, France). Microarray analysis was performed using a high-density oligonucleotide array (GeneChip Human Genome U133 Plus 2. 0 array, Affymetrix, Santa Clara, CA, USA). RNA (100 ng) was amplified and biotin-labeled using GeneChipH 39 IVT Express target labelling and control reagents and procedures from Affymetrix. Before amplification, spikes of synthetic mRNA at different concentrations were added to all samples; these positive controls were used to ascertain the quality of the process. Biotinylated antisense cRNA for microarray hybridization was prepared.
Data Filtering and Analysis The obtained data were normalized with Affymetrix Expression Console software using the MAS5 statistical algorithm. Normalized data were compared and filtered using Partek Genomic Suite software 6. 5 (Partek Inc. , St. Louis, MO, US). First, for each RNA type (polysomal RNA or total RNA prepared from the same cytoplasmic extract as described in the ''Isolation of polysomes and total cytoplasmic RNA'' section), samples were paired by replicate and a ratio between siBRCA1 and control sample was calculated. The ratios for the polysomal RNA (polyRNA = siBRCA1/siControl) and for total RNA (totRNA = siBRCA1/siControl) were calculated. A gene was considered only if the detected signal was above the background for at least one of the compared groups. Then, for each retained gene and for each replicate a polyRNA/totRNA Ratio (Ratio of Ratio = RR) was calculated as follows: RR i = polyRNA i /totRNA i (i = replicate).
Quantitative RT-PCR Prior to reverse transcription, the total and polysomal RNA described above from BRCA1-depleted and control cells were purified and submitted to DNase digestion with NucleoSpin RNA XS Clean-up columns (Macherey-Nagel) following the manufacturer's instructions. Reverse transcription was then performed using 500 ng of total RNA, with Bio-Rad Laboratories' iScript cDNA Synthesis Kit in a total volume of 20 ml. The reaction was incubated at 25uC for 5 min followed by incubation at 42uC for 30 min and 85uC for 5 min. Quantitative real-time PCR was performed as follows. The amount of cDNA synthesized was measured using q-PCR (SYBR Green PCR, LightCycler, Roche Diagnostics Indianapolis) following the manufacturer's recommendations. The LightCycler experimental run protocol consisted in an initial Taq activation for 8 min at 95uC, followed by a ''touch down'' program.