dataesr/scientific-paragraphs-categorization huggingface dataset:
Cross section for Higgs production We are now ready to present our precise predictions for the production of MSSM Higgs bosons at the LHC. As mentioned earlier, we rely on the code SusHi,  4  which includes all of the available NLO-QCD contributions to the gluon-fusion process, supplemented with the known SM results for the NNLO-QCD contributions in the heavy-top limit and for the EW contributions (both adapted to the MSSM by appropriately rescaling the Higgs couplings). While the results implemented in SusHi for the NNLO-QCD top contributions are strictly valid only for a Higgs mass below the top threshold, m φ < 2 m t , a comparison with the NLO results suggests that they provide a decent approximation also for larger values of the Higgs mass  [81, 82]. The NNLO-QCD contributions from stop loops are estimated following ref.
Combination of PDF and α s uncertainties The uncertainty associated to the experimental errors of the data from which the PDFs are extracted is represented by the PDF collaborations with the introduction of N R different PDF sets (replicas), all equivalent from the statistical point of view in the description of the data. Any observable has to be computed N R times with the different sets, and the spread of the results can be interpreted as the error induced by the PDF due to the data and to the fitting methodology. The replicas are determined by the PDF collaborations following the Hessian (for MSTW2008 and CT10) or the Monte Carlo (for NNPDF2. 3) approaches, and the PDF error has to be computed accordingly. In QCD the cross sections are also affected by a parametric uncertainty associated to the input value of the strong coupling constant.
Conclusions A precise prediction of the cross sections for Higgs-boson production, as well as a detailed understanding of the associated uncertainties, are of vital importance to interpret the recent discovery of a Higgs boson in the context of the MSSM. In this paper we used the public code SusHi  [53] , which computes the cross sections for gluon fusion and bottom-quark annihilation, to study the production of scalar and pseudoscalar Higgs bosons in a set of MSSM scenarios compatible with the LHC results. We showed how the cross sections can substantially differ from the SM prediction, and how their qualitative behavior over the MSSM parameter space depends mainly on the relative importance of the contributions involving top and bottom quarks. We also emphasized that, in a scenario with relatively light squarks which is not yet constrained by the LHC, the contributions to the gluon-fusion process that involve superparticles can significantly suppress the cross section for scalar production.
Acknowledgments This work was initiated in the context of the activities of the  LHC-HXSWG , and some of our preliminary findings were presented in section 14 of ref. [5]. We thank the authors of ref. [56] and the SUSY convenors of the ATLAS and CMS collaborations for helpful communication about the experimental constraints on the MSSM benchmark scenarios, and the authors of ref. [38] for helpful communication about their results. We also thank  M. Spira  for useful discussions about the uncertainties of the cross-section calculations. This work was supported in part by the  Research Executive Agency (REA)  of the  European Commission  under the Grant Agreements PITN-GA-2010-264564 (LHCPhenoNet),  PITN-GA-2012-315877  (MCnet) and PITN-GA-2012-316704 (HiggsTools), and by the  European Research Council (ERC)  under the  Advanced Grant   ERC-2012-ADG 20120216-321133  (Higgs@LHC).
The work of E. B. and P. S. at LPTHE is supported in part by  French  state funds managed by the  ANR  ( ANR-11-IDEX-0004-02 ) in the context of the  ILP LABEX  ( ANR-10-LABX-63 ). S. L. acknowledges support by the  DFG  ( SFB 676  " Particles, Strings and the Early Universe "). S. L. , H. M. and R. H. were also supported by the  DFG  grant  HA 2990/5-1. A. V. was supported in part by an  Italian   PRIN2009  grant and a  European Investment Bank   EIBURS grant.
Recently,  Descy et al. (2011)  concluded similar functioning of controlling factors on potamoplankton to those found in other large, but more regulated Europen rivers. Furthermore,  Abonyi et al. (2012)  highlighted that human impacts might be successfully indicated by the Q (r) compositional index  (Borics et al. , 2007)  along the Loire; and that besides natural processes, shifts in FGs are also related to human mediated physical and chemical impacts. The objective of this article is to compare three phytoplankton functional classifications (MBFG, MFG, FG) as potential ecological, and water quality management tools along the River Loire. The authors use the same dataset presented by  Abonyi et al. (2012) ; and apply the three functional systems independently, with the following specific questions: (i) How these classifications display river zones, reflected by the correspondent morphological, morpho-functional, and functional composition of potamoplankton? ( ii) Which relationships can be found between these river zones and basic regional differences in geography, climate and hydro-ecoregions along the River Loire? (iii) How the identified river zones (if relevant) are able to follow the main chemical characteristics in the River Loire? 2.
Geographical, chemical and hydrological data Geographical and chemical parameters were provided by the official water quality website of 'OSUR' 1  , while daily discharge values were used as monthly averages, available at 'Banque Hydro' 2. Month average of specific discharge (L km À2 s À1 ) was used to characterize hydrological differences according to catchment size at each sampling station. The distribution of essential phytoplankton nutrients was characterized using molar ratios of total nitrogen to total phosphorus; and soluble reactive silica -'SRSi' to total phosphorus (N:P and Si:P further in the text). Total nitrogen was determined by the sum of nitrate-N, nitrite-N and Kjeldahl-N; while TP and SRSi contents were directly obtained from the data set.
Statistical analyses In order to preserve both spatial and temporal variation of data, the Self Organizing Map (SOM) method was used in MATLAB TM. While conventional methods might distortion along non-linear relationships  (Giraudel and Lek, 2001) , SOM is stated to be useful for exploratory data analysis in a multidimensional scale  (Shanmuganathan et al. , 2006). The SOM method has been already used successfully in potamoplankton ecology  (Várbíró et al. , 2007; Stankovi c et al. , 2012) ; in fish zonation  (Lasne et al. , 2007) ; as well as in diatom research at large spatial scales  (Rimet et al. , 2004; Park et al. , 2006; Stenger-Kovács et al. , 2014). The data matrix contained 170 samples and 56 variables (7 MBFGs, 25 MFGs, and 24 FGs). In the first selection phase of SOM, the weights of the output layer were assigned randomly.
Acknowledgements We thank to the  Loire-Bretagne Water Authority  for the availability of environmental data, as well as for the permission to publish our results. Open access availability of this publication was supported by the  Hungarian Academy of Sciences  and the authors have no other financial support to declare. Special thanks are due to  Dr. Maria Cellamare ,  Prof. Dr. Jean-Pierre Descy , as well as to the two anonymous referees for their valuable personal comments on the manuscript. This study was presented at the 8th SEFS (Symposium for European Freshwater Sciences) conference, held 1-5 July 2013, Münster, Germany.
Two other band-gap sensors are also installed on the right and left ambiances of the box. This implementation is illustrated in Figure  4. The wall and the blocks used for the calibration were built by the same mason, using the same protocol and with a similar gravimetric water content ( = 18. 9%). Probes are placed during the manufacture and in a staggered row to prevent any electromagnetic interference between them. For technical reasons, after its manufacture, the wall is protected by a waterproof plastic film to slow its drying over 22 days. It is then placed in a box, designed in the laboratory, with 10 cm thick cork for insulation (Figure  4 ). For 130 days, one data per hour is recorded. The natural drying periods (opening of the "removable walls" of the box) are interspersed by periods of sealing tests of the boxes: from the 44th to 51st day and from the 110th to 124th day.
37%/day for the forced drying test between 90th and 98th day and 0. 33%/day for the natural drying test between 70th and 78th day). To understand this behavior, the partial differential Equation (  8 ) is solved with COMSOL Multiphysics ® using the PDE module. The simulations are made for a 1D geometry of length L=0. 5 m (x direction). It represents a lateral cross section of the tested wall. Boundary conditions of the simulations are set according to measurements within both sides of the insulated box. Thus, thermal exchanges on x = 0 and x = e are calculated by means of the following equation:  (9)  where and are temperatures of respectively the ambient air in the box and on the side of the wall; while is the heat transfer coefficient. It is assumed to be equal to 15 W•m -2 •K -1 during the drying stage and equal to 250 W•m -2 •K -1 during the forced drying stage, which are common values for resp.
Conclusion A calibration method of rammed earth and cob in-situ volumetric water content measurement with TDR sensors is presented. The main asset of this method is to allow a simple and fast calibration using only four parameters from the measurement of the evolution of the permittivity with temperature for two determined volumetric water contents. The accuracy of this methodology was tested on drying experiments of two rammed earth blocks. This calibration procedure was then used to measure the volumetric water content within a metric rammed earth wall instrumented with six TDR probes, and submitted to natural drying, forced drying and wrapped conditions with temperature variations. For a given height, the data from the probes on the left and right sides are almost identical. Knowing that the two probes operate differently and have been calibrated separately, this result confirms the robustness of the calibration protocol.
Acknowledgements Authors would like to thank,  Sté phane Cointet  and  Nicolas Meunier  for the earth supply and their technical support,  Abhilash Holur Narayanaswamy  for his review of the manuscript and  Fionn Mc Gregor  from  Bath University  for discussion about the moisture buffering of earth materials. This work is cofounded by the  French environmental agency ADEME, Lafarge  ( TEZ10-44 ), the  Ré gion Rhône-Alpes  ( 11024835 01-ENT012v   de la Direction du Climat, Environnement, Santé et Energie , and a  Fellowship CMIRA for JC Morel ) and the  French national research agency ANR  ( PRIMATERRE-ANR-12-VBDU-0001-01  Villes et Bâ timents durables).
RNA Extraction, Microarray Experiments and qRT-PCR The EDL933WT strain and its isogenic DphoB mutant were grown in Pi 2 and/or in Pi + conditions until the OD600 nm reached 0. 55 to 0. 6. Samples equal to 5 6 10 8 CFU were taken from this mid-log phase and processed for transcriptome analysis. Ten mg of RNAs were extracted and cDNAs were generated using reverse transcriptase. One mg of the fragmented and biotinylated cDNAs was hybridized onto Affymetrix GeneChip E. coli. The data were processed using FlexArray software using Robust Multichip Average (RMA) normalization procedure. The levels of transcription obtained from 3 biological replicates of each experimental condition were compared using the EB (Wright & Simon) algorithm. We then conducted comparisons between EDL933 grown in Pi 2 and in Pi + conditions and between EDL933 and EDL933DphoB strains both grown in Pi 2.
3) and blue representing downregulation (ratio of -1) on a log 2 scale. The data are represented as the means from three biological replicates. B. Expression level of LEE genes ler, sepZ, escV, tir and espB was analyzed by RT-qPCR in the wild-type, the DphoB mutant and its complement (DphoB+C) and the Dpst mutant grown in low or high Pi media as indicated. C. Western-blot using anti-EspB antibody against the supernatant of the wild-type, the DphoB mutant and its complement and the Dpst mutant grown in low or high Pi media as indicated. The DescN mutant grown in DMEM was used as a negative control. One mg/mL of Gro-El was added as a protein precipitation control. Asterisks represent the significant ANOVA p value (*,0. 05, **,0. 01, ***,0. 001). ns: Not significant. doi:10. 1371/journal. pone.
Constitutive Activation of the Pho Regulon Decreased LEE Gene Expression and Reduced Adherence of strain EDL933 to HeLa Cells To investigate the influence of the Pho regulon and PhoB on adherence, we evaluated the attachment of Dpst and DphoB mutants to HeLa cells in DMEM cell culture medium, which is a Pi-rich medium. The Dpst mutant was used because the inactivation of the Pst system results in constitutive expression of the Pho regulon. Thereby, the Dpst mutant should mimic the behavior of the wild-type strain grown in Pi-limited conditions. Accordingly, the EDL933 Dpst mutant grown in Pi-rich medium demonstrated strong Pho regulon activation as indicated by PhoA activity (350 M. U. ) (data not shown). However, expression of LEE genes in the Dpst mutant was decreased, which was in contrast to the wild-type strain in response to Pi starvation, a condition that activates the Pho regulon (Figure  2B ).
LEE3 2. 42 4. 89E-03 2. 56 9. 88E-03 operon escD LEE-encoded T3SS component 2. 17 1. 19E-02 2. 38 1. 43E-02 espF EspF / hypothetical protein. LEE4 operon 2. 02 2. 79E-02 2. 28 3. 15E-02 Unknown function. unclassified and hypothetical protein bssR Repressor of biofilm formation by indole transport regulation 18. 58 1. 35E-03 4. 86 6. 47E-03 ygaW Predicted inner membrane protein. stress-responsive 5. 98 2. 65E-04 3. 43 6. 47E-03 yfiD Autonomous glycyl radical cofactor GrcA 5. 58 1. 29E-02 3. 16 1. 42E-02 psiE P-starvation-inducible protein PsiE 20. 81 1. 59E-05 3. 10 1. 74E-03 cybC Cytochrome b562 3. 56 5. 29E-04 2. 01 1. 41E-02 microarray hybridizations and qRT-PCR demonstrated a high level of concordance between the datasets, which is represented by a correlation coefficient of 0. 87 in response to low Pi and of 0.
Introduction Hepatitis C virus (HCV) genotype identification is clinically important because it predicts the rate of sustained virological response and contributes to the determination of treatment duration. 1 In addition, HCV genotyping is a powerful tool to describe HCV epidemiology. 2 Very few data exist on HCV infection in Albania. 4] [5]  To our knowledge, HCV molecular epidemiology has been assessed only once in Albania, using a line probe genotyping assay. We determined HCV genotype prevalence in Albanian patients by sequencing.
HCV RNA was retrieved from the blood samples of 50 patients. The HCV NS3 protease gene was sequenced for 28 patients and NS5b and/or 5 0 UTR fragments were sequenced for an additional 22 patients. The predominant genotype was 1b in 25 patients (50%), followed by genotypes 2c, 4a, 3a, and 1a in 18%, 14%, 8%, and 6% of cases, respectively. Best matches for these HCV RNAs in GenBank were obtained in different countries worldwide. One NS3 protease naturally harbored an amino acid conferring minor drug resistance to newly available HCV protease inhibitors. In conclusion, HCV-1b was predominant in the present Albanian population, as in southeastern Europe. ß 2013 The Authors. Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. aligned using ClustalX v2. 0 (http://www.
clustal. org/download/ current/) with sequences from the reference set of the NCBI genotyping tool (http://www. ncbi. nlm. nih. gov/projects/genotyping/view. cgi?db=3) and the two best matches obtained through BLAST searches against the NCBI sequence database for each sequence recovered here. Pairwise nucleotide similarities were generated using BioEdit (http://www. mbio. ncsu. edu/bioedit/ page2. html). Phylogeny reconstructions were performed using MEGA v5 (http://www. megasoftware. net/).
The automorphism group sizes A(g) were calculated using the software Saucy 3. 0 (http://vlsicad. eecs. umich. edu/BK/SAUCY/, accessed in September 2013), the most scalable symmetryfinding tool available today  [40]. Saucy only deals with undirected graphs hence only directed versions of the real-world sample of networks was used to calculate the automorphism group size A(g) of each with Saucy. We made directed graphs into undirected graphs by setting an edge between two nodes i and j if in the original directed graph there was a directed edge from i to j, j to i, or both. Clearly undirected graphs are simpler than directed graphs, in general. In the case of labelled nodes, it is easy to see that the Kolmogorov complexity of a random undirected graph is typically half of a directed labelled graph, as the binary adjacency matrix for undirected graphs is symmetric.
Neighbor nets were inferred in order to detect putative recombination signatures that would result in networks rather than trees. No major splits were found. However, the pairwise homoplasy index (PHI) test predicted significant evidence for recombination events (P Ͻ 0. 001). Based on visual inspection, contiguous SNPs consisting of three or more SNPs, mirroring homologous recombination, were detected. A total of 32 independent possible recombination events involving 298 SNPs, ranging from 3 to 24 consecutive SNPs, were identified and removed (see Table  S2  in the supplemental material). A rerun of the PHI test on the pruned data set detected no traces of recombination (P ϭ 0. 142). After this preliminary stage, the phylogenetic content of the SNP data set was evaluated with likelihood mapping analyses.
aureus and is encoded on two plasmids, pUB101 and pUB102 (GenBank accession numbers NC_005127 and DQ269019, respectively). Neither of these was present in our collection. Fusidic acid has been a widely used topical agent against S. aureus-related skin and soft tissue infections in Europe, the Middle East, and North Africa since the early 1980s (Jim Frater [LEO Pharma A/S], personal communication). These three regions also define the geographical dissemination of the fusidic acid-resistant European CA-MRSA clone, and they coincide historically with our time estimate of the clonal expansion of the fusidic acid-sensitive ancestral clone into these areas around 1990. The antimicrobial resistance profiles observed in the derived clade of both MSSA and MRSA isolates exhibited striking differences compared to those in the basal MSSA clade (Table  1 ; also, see Table  S1  in the supplemental material).
). DNA microarray. A single isolate, 88-HT20060002-fa-2005, was characterized using the Alere S. aureus genotyping kit (Alere Technologies, Jena, Germany) according to the manufacturer's instructions. SNP calling. SNPs were detected by aligning Illumina reads from individual isolates against the chromosome of S. aureus 11819-97 (GenBank accession number NC_017351) (52), a complete reference genome of a Danish clinical MRSA isolate from the European CA-MRSA lineage, us-ing SHRiMP 2. 0  (85). SNPs in the conserved core genome of the strain collection were identified using Nesoni v 0. 52 (http://www. bioinformatics. net. au). Custom Perl script was used to retain only those SNPs that were supported by at least 90% of base calls in all the analyzed strains. Indications of horizontal gene transfer events were defined as calling of Ն3 unique SNPs in succession in a single isolate.
The resulting distribution of the points therefore shows whether the data are suitable for a phylogenetic reconstruction. Phylogenetic inferences. Genome-wide phylogenetic relationships were reconstructed using the maximum-likelihood approach implemented in PhyML v 3. 412  (91). The robustness of the maximumlikelihood tree topology was assessed with bootstrapping analyses of 1,000 pseudoreplicated datasets. A generalized time-reversible (GTR) substitution model  (92)  with gamma-distributed rate heterogeneity was selected based on Akaike's information criterion using jModelTest2  (93). Phylogenetic analysis determined CC1 to be the outgroup most closely related to CC80 when the CC80 sequence was compared to published genome sequences representing CC1, CC5, CC8, CC30, CC45, CC59, CC93, and CC398 (GenBank accession numbers BA000033, BA000018, CP000255, BX571856, CP006044, NC_016928, NC_017338, and AM990992, respectively) as previously described  (46).
Therefore, the phylogenies were rooted with the community-associated strain MW2 (GenBank accession number BA000033). Phylogenetic relationships for genetic elements were reconstructed using the maximum-likelihood approach implemented in CLCbio's Genomics Workbench v 6. 5 (CLCbio, Aarhus, Denmark) based on Akaike's information criterion. Coalescence-based analyses. During analysis, evolutionary rates and tree topologies were analyzed using the GTR and Hasegawa-Kishino-Yano (HKY) (94) substitution models with gamma-distributed amongsite rate variation with four rate categories (⌫4). The molecular clock was calibrated under either a strict molecular clock, which assumes the same evolutionary rates for all branches in the tree, or a relaxed clock, which allows different rates. Constant-sized, logistic, exponentially growing coalescent models were used.
We also used the Bayesian skyline plot model  (95) , based on a general, nonparametric prior that enforces no particular demographic history. We used a piecewise linear skyline model with 10 groups and then compared the marginal likelihood for each model using Bayes factors estimated in Tracer v 1. 5 (http://tree. bio. ed. ac. uk/software/ tracer/). For each analysis, two independent runs of 100 million steps were performed, and the chain was sampled every 10,000th generation. Examination of the Markov chain Monte Carlo (MCMC) samples with Tracer indicated convergence and adequate mixing of the Markov chains with effective sample sizes (ESS) for each parameter in the hundreds or thousands. The first 10% of each chain was discarded as burn-in. The MCMC samples were summarized using the maximum clade credibility topology found with TreeAnnotator v 1.
The calculations were performed with BEAST v 1. 7. 5 and Tracer. Genetic elements. Analyses of the genetic diversity of the SCCmec cassette, the PVL-encoding prophage ⌽Sa2, and the fusB plasmid were investigated by SNP diversity in conserved regions among the 97 isolates and selected references as described below. Closing of seven of the ten distinct SCCmec elements inserted in the attB site, the plasmid p11819-97, and two novel plasmids, pT45 and pT49 tet(K), was performed by de novo assembly with subsequent gap closure in silico using Genomics Workbench (CLCbio). For analysis of the SCCmec diversity, six SCCmec type IV variants were initially compared for overall similarity of content using Mauve  (98)   Plasmid p11819-97 (GenBank accession number NC_017350) resembled two other available S.
aureus plasmids from Australia, the complete plasmid pWBG753 (GenBank accession number GQ900395), from an ST8 isolate, and the draft plasmid SAP103A (GenBank accession number GQ900497)  (99) , based on BLASTN analysis against GenBank. Both were included in the SNP analysis in order to determine the diversity of p11819-97 within the CC80 collection. ⌽Sa2 diversity analysis within the CC80 strains was performed using seven lukS/F-PV-containing ⌽Sa2 prophages from five distinct community-associated S. aureus genetic lineages as part of the analysis: a CC1 isolate (MW2), two CC8 isolates (FPR3757 and TCH1516), two CC30 isolates (55_2053 and TCH60), a CC59 isolate (M013), and a CC93 isolate (JKD6159), with GenBank accession numbers NC_003923, CP000255, CP000730, CP002388, CP002110, NC_016928, and CP002114, respectively.