dataesr/scientific-paragraphs-categorization huggingface dataset:
For the  The binding area was defined here as all residues of the protein interacting with the helical peptide. proteins cavities, the same algorithm was employed using the CASTp software  [32]. Hydrophobicity and local hydrophobic density for binding pockets were determined using Fpocket  [33]. Pocket volumes were computed using CASTp  [32]. Molecular docking of terphenyl 2 was performed into the alpha-helical binding sites of calmodulin (code entry 2O5G) and troponin C (code entry 1A2X) using AutoDock 4. 2  [34]. The input files preparation and docking analysis were carried out using AutoDockTools. Grid maps were centered in the alpha-helix binding site for both structures. Grids sizes were 126 Å x 126 Å x 126 Å with a grid spacing of 0. 33 Å for calmodulin and 126 Å x 126 Å x 126 Å with a grid spacing of 0.
28 Å for troponin C. Ligand conformational searching was performed using Lamarckian genetic algorithm and all ligand torsion angles were flexible. The following docking parameters were used: 250 Lamarckian genetic algorithm runs, a population size of 250, a maximum of 2 500 000 energy evaluations and a maximum of 27000 generations. Figures were prepared using PyMol  [35]  and CHIMERA software  [36].
Genome re-sequencing A first single colony of BW4005, called BW4005. 1, was isolated after streaking the original glycerol suspension on LB plate and incubating overnight at 37°C. The BW4005. 1 clone was then inoculated into 10 ml LB and grown overnight at 37°C. This culture was used for genomic DNA extraction as described  [29]. Whole genome re-sequencing of BW4005. 1 was performed by 454 and single-end Solexa technologies  [33]. Briefly, a total of 216,058 single-end reads with an average length of 404 bps, giving a 19. 08X coverage of the genome, were generated using the GS FLX system (Roche, Welwyn Garden City, Hertfordshire, UK) and assembled to 78 contigs with 454 Newbler assembler (http://www. 454. com/products/analysis-software/). A total of 8,862,831 single-end reads with an average length of 33 bps were generated using the Solexa Genome Analyzer (Illumina, Little Chesterford, Essex), giving a 63.
9× coverage. All Solexa reads were mapped to the contigs generated from Newbler using MAQ  [52]. The order of the contigs was determined based on BLASTn alignments with the genome sequence of BW2952 as the reference (Genbank accession number NC_012759). By analyzing these data, we found a few sequencing errors in the original BW2952 genome sequence (Additional file 1: Table  S1 ). All 78 sequence gaps in BW4005 and 151 suspected SNP sites were filled or checked by sequencing PCR products with ABI 3730XL capillary sequencer (Applied Biosystems, Foster City, California, USA). In our second genome re-sequencing attempt, a second colony derived independently from the same initial glycerol stock of BW4005, and called BW4005. C6 (see below, Table  4 ), was grown as described above. (BW4005. C6 was confirmed by our molecular analyses to harbor the heterozygous duplication).
Acknowledgements We thank the  Australian Research Council  for grant support (to TF). This work was also supported by the  National Basic Research Program of China  ( 973 Program ) [2009CB522603] and the  National Natural Science Foundation of China (NSFC) Key Program [31030002 ] (to LW and LF); the  Agence Nationale de la Recherche (ANR) Program  " Blanc " ( ANR-08-BLAN-0283-01 , to DS),  Centre National de la Recherche Scientifique , and  Université Joseph Fourier  (to DS); and the  Agence Nationale de la Recherche (ANR) Program  " Génomique " ( ANR-08-GENM-023 , to DS and OT). JP thanks the  French Ministry of Research  and the  Université Joseph Fourier  for a PhD fellowship.
It includes several options allowing to choose between different collider types: proton-proton, proton-antiproton, ion-ion, between various EW parameter schemes, initial-state quark flavours, final-state lepton flavours, intermediate bosons, types of radiative corrections, weighted or unweighted events, etc. Important options are also possibilities to generate the CC DY processes with polarized W -bosons (transverse or longitudinal) in some predefined reference frames or in a user-defined ones. For QCD effects the current version of WINHAC is interfaced with the parton shower generator PYTHIA 6. 4. It generates QCD/QED ISR using parton shower algorithm, performs proton-remnant treatment, hadronisation and particle decays. Two kind of interfaces are available now: the first one is the internal interface in which the PYTHIA routines are called directly from the WINHAC code and the second one is based on the Les Houches Accord in which events from WINHAC are transmitted to PYTHIA through special LHA-format files  [20].
DATA OBTAINED WITH MICROARRAYS AND RNA-SEQUENCING ANALYSIS Four biological replicates of the microarray experiment were performed, each time with a reciprocal labeling protocol ("dyeswap"), which served both as a labeling control and technical replicate. The microarrays analysis was realized by using the AF gene chip microarrays that cover about 9600 Open Reading Frames from genome of strain ATCC_46645, sequenced by J. Craig Venter Institute (JCVI), The Institute for Genomic Research (TIGR). Scanning was performed with an Axon scanner 4000A and the resulting images were analyzed by using GenePix Pro 6. 01 software. The Bioplot software was used for statistical analysis. Quantile normalization was applied to the whole data set to account for variation between slides. Expression ratio cutoff of 2.
The Asp-hemolysin protein was down regulated in the BF. Asp-hemolysin was reported to be released into the culture supernatant by A. fumigatus during growth in presence of elastin, collagen, and keratin, where it is supposed to exhibit a hemolytic activity  (Wartenberg et al. , 2011). However, the characterization of the deletion strain asp-HS did not revealed significant hemolytic and cytotoxic activity and the impact on pathogenicity and the biological role of the Asp-HS protein is still poorly understood. All proteome data (gel images, spot information) were imported into our in-house data ware-house Omnifung http:// www. omnifung. hki-jena. de and are publicly accessible.
CONCLUSIONS In recent years, many high-throughput technologies have been developed to decipher various aspects of cellular processes, including the transcriptome, epigenome, proteome, metabolome, or interactome. The capacity to perform "omics" analyses at several different levels, such as transcriptomic, proteomic, or metabolomics, and their comparison and integration of  b Average ratios compared under biofilm and planctonic growth conditions were extracted from statistical analysis of DIGE gels by the Delta2D 4. 3 (Decodon) software program. ">2" a consistent increase of greater than twofold. "<2" a consistent decrease of more than twofold. c The transcriptional changes determined by RNA-seq are aligned. information offers an exciting potential to answer many questions asked by a biological study.
ACKNOWLEDGMENTS The research leading to these results has received funding from the  European Union 's  Seventh Framework Programme  [ FP7/2007[FP7/ -2013 ] ] under grant agreement n • HEALTH-2010-260338 (ALLFUN),  ERA-Net Pathogenomics Biomarkers  for prevention, diagnosis and response to therapy of invasive aspergillosis (AspBIOmics), and  ESF (European science Foundation) Fuminomics.
Biological Data Blood samples were drawn on admission (Median time from symptom onset to blood sampling: 16(8-30) hours). Homocysteine concentrations were determined using a chemiluminescence method on an Immulite 2000 analyzer (Diagnostic Products Corporation, Los Angeles, USA). C-reactive protein (CRP), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C) and triglyceride (TG) concentrations were measured on a Dimension analyzer (Dade Behring, Newark, NE). The level of low-density lipoprotein cholesterol (LDL-C) was calculated using the Friedewald formula  [14]. Plasma glucose concentrations (enzymatic method (glucose oxidase)) and creatinine levels were measured on a Vitros 950 analyzer (Ortho Clinical Diagnostics, Rochester, NY) and creatinine clearance was calculated with the Cockcroft formula.
Statistical Analysis All the analyses have been made on anonymous de-identified data that were available to others. Data are presented as median (interquartile range [IQR]), or proportion (n(%)). For continuous variables, normality was checked by the Kolmogorov-Smirnov test. The Student t test or Mann-Whitney test was used to test for continuous data in the two groups. Categorical variables were compared by the chi-square test or Fisher's exact test. Spearman's correlation was applied to test for associations between dimethylarginines, L-arginine and biological variables. Mann-Whitney test was used to test L-arginine and dimethylarginines concentrations in patients according to their HDL levels. In order to further investigate whether the relationship between HDL-C and ADMA was influenced by metabolic or pharmacological conditions, stratified correlation analysis was performed on subgroups of patients based on median LDL or CRP values (inframedian or supramedian), on the chronic use of statin or fibrate therapy (with or without treatment) and on levels of HDL-C (low or high HDL-C).
Factors associated with low HDL-C were studied by backward logistic regression analysis. Variables entered into the multivariate model were chosen according to their relationship (cut-off at 10%) in univariate analysis (i. e. age, BMI, diabetes, prior MI, fibrate, CRP, HbA1c, triglycerides, ADMA, SDMA, L-arginine and smoking), with an exclusion cut-off at 1%. All the analyses were performed using the SPSS 13. 0 software package (IBM Inc, USA).
Data collection and analysis Data were obtained from nine annual NTLP reports and 21 laboratory registers from the zonal and reference laboratories covering this 9-year period. Data were double-entered by two independent encoders, and validated using EpiData entry software, version 3. 1 (EpiData Association, Odense, Denmark). Discordances were resolved by cross-checking with the paper registers. Data were exported to SPSS version 17. 1 (SPSS Statistics, Chicago, IL) for analysis.
Effect of synthesis conditions XRD data indicated an improvement in pattern resolution for increasing maturation times in the precipitating a e-mail: christophe. drouet@ensiacet. fr medium. Profile-fitting analyses (JANA software) pointed out an increase in crystallite size (e. g. mean lengths varying from 9. 5 to 20. 4 nm upon maturation between 20 min and 20 days) accompanied by a decrease in crystal disorder (as derived from the Vogel and Hosemann (1970) method). TEM analyses confirmed these observations and indicated that the plate-like morphology -typical of biomimetic apatites -was conserved independently of the maturation time tested. Chemical titrations of calcium and orthophosphate ions indicated that this modification of crystallographic features was accompanied by an increase in overall Ca/P mole ratio 1.
To check which space group was responsible for the diffraction patterns many image simulations were performed using the JEMS software  28. All the ZAs were calculated for both the space groups P2 1 /n and Pmnb. The best result, obtained for the Pmnb space group with the crystal oriented along [011], is reported in Figure  4c , where the simulated electron diffraction pattern is superimposed to the experimental one. Magnetic characterization. Figure  5a  shows the temperature dependence of the magnetization (M/H vs. T curves) for the Fe-900 and Fe-650 samples in zero field cooling (ZFC) and field cooling (FC) regimes, obtained by applying a 10000 Oe magnetic field. Both the samples undergo the paramagnetic to antiferromagnetic transition, with Neel temperature T N > 20 K, typically observed for the lithium iron silicate  1, 18.
02u and counting time of 10 s per step in the angular range 15-100u/2h. Rietveld structural and profile refinement was carried out by means of TOPAS V3. 0 program  35. During the refinement, lattice parameters, isotropic thermal factors, atomic positions were allowed to vary. The weight percentage of the impurity phases was also determined. SEM measurements were performed with a Zeiss EVOH-MA10-HR microscope on Au-sputtered samples. TEM measurements were performed on a JEOL-JEM3010 microscope operating at 300 kV and having a point-to-point resolution of 1. 7A ˚. The specimens were sonicated in isopropyl alcohol, a drop was deposited on a holey carbon copper grid and let to evaporate at room temperature and then the grid was transferred into the microscope. The  7  Li MAS NMR data were acquired with a Bruker Avance III spectrometer at a field of 11.
Acknowledgments This work is performed in the frame of  Cariplo  Project  2011-0325  ''New electrolyte and electrode materials for thin-film lithium microbatteries''. A. J. P. and G. P. acknowledge financial support from the  LABEX iMUST framework  ( ANR-10-LABX-0064 ) of the  Universitede Lyon , within the  program ''Investissements d'Avenir''  ( ANR-11-IDEX-0007 ) which is operated by the  French National Research Agency (ANR). C. F. acknowledges a fellowship from the  French Ministry  for the Foreign Affairs (dossier n. 781569G).
INTRODUCTION In the genus Tetranychus Dufour the taxonomic status of the tetranychid mites known as Tetranychus urticae  Koch, 1836 complex [or Tetranychus telarius (L. , 1758)  sensu  Pritchard and Baker, 1955 ] is a long standing issue among acarologists. In the last catalogue of the spider mite family  (Bolland et al. , 1998) , 44 species names have been synonymised with T. urticae and 47 in the Spider Mites Web database  (Migeon and Dorkeld, 2006-2013). Among them, the case of the systematic status of Tetranychus cinnabarinus Boisduval, 1867 has caused a lot of ink to flow. One of the main reasons is that its original description is succinct and mainly based on the colour of the mite: "une belle couleur rouge aurore" meaning a beautiful aurora red colour. Since the second part of the last century, the validity of the taxonomical status of T.
, 2012)  or do not achieve to separate them  (Xie et al. , 2006b; Xie et al. , 2008) , a recent work wrapped up to the validity of this species  (Li et al. , 2009). While molecular studies have proved to be of high value for systematics studies of many groups including the Acari, DNA sequences information needs to be manipulated with much precaution. In particular, the reliability of the DNA data available in public sequence DNA databases, i. e. GenBank, might lack proper taxonomy. In the case of difficult taxonomic issues as T. cinnabarinus, wrongly attributed sequences to species is responsible for erroneous inferences concerning the taxonomic position of this species  (Hinomoto et al. , 2007; Ros and Breeuwer, 2007; de Mendonça et al. , 2011). Thus, rather than solving the taxonomic position of T.
cinnabarinus, molecular data have increased the confusion regarding validity of this taxon. The aim of the present paper is to review the literature used to separate or synonymize T. urticae and T. cinnabarinus. The criteria examined include: colour of mites, morphological features like the dorsal integumentary lobe pattern, aedeagus shape and female leg I chaetotaxy; biology concerning breeding, diapause and host plant adaptation and molecular approach with phylogenetical relationships between the two taxa. The ability to develop resistance to pesticides in the two colour forms was not investigated. In our opinion, data do not allow to know if the resistance development in a colour form is more due to its innate capacity to develop resistance than to variable selection pressures as a result of differences in amounts and types of pesticides applied.
New data We have performed population crosses between RF and GF (Table  6 ). We obtained respectively 110 and 87 F1 females when crossing RF Banyoles (Spain) females and GF London (Canada) males, and reciprocally. By sibmating a continuous offspring was perpetuated until we stopped after 10 generations. Colour results have been presented in colour section. GF London strain is the sequenced strain  (Grbic et al. , 2011)  and has been recognized to be T. urticae. It does not bear extra setae as the T. cinnabarinus green sensu  Zhang and Jacobson (2000). We have obtained a true compatible cross between RF and GF, strongly supporting, in accordance with the literature, the conspecific status of the green and red forms.
g. T. turkestani (Ugarov and Nikolskii, 1937), T. truncatus Ehara, 1956 and T. urticae, strongly suggesting a misidentification of mites. Hinomoto (2007)  firstly reports misidentification of COI sequences in Genbank databases which considered to likely be T. truncatus. A recent study re-examined sequences of the most studied fragment (450 nucleotides length) the COI deposited in Genebank and labelled as T. cinnabarinus, together with sequences of T. urticae and closely related species  (de Mendonça et al. , 2011). All the sequences matched 100% with at least one T. urticae Genbank entry, often to several entries at 100% -99%, and in some cases they matched with related species, T. truncatus or T. kanzawai Kishida, 1927. This work highlights the caveat of inaccuracy of species identification attached to the DNA sequences deposited in databases and in particular the confusing identification of T.
Streets and Q. Zhang (http://www. cgrer. uiowa. edu/arctas/emission. html) was used. Fire emissions were included using the Fire INventory from NCAR (FINNv1)  (Wiedinmyer et al. , 2006 (Wiedinmyer et al. , , 2011)) , with a diurnal profile as described in  Pfister et al. (2011). Fire emissions in MOZART-4 were released in the lowest model level, while in WRF-Chem an online plume rise module  (Freitas et al. , 2007)  was used to distribute the fire emissions vertically. This scheme was recently shown to perform well for the fires observed during ARCTAS  (Sessions et al. , 2011). Biogenic emissions were from Model of Emissions of Gases and Aerosols from Nature (MEGAN)  (Guenther et al. , 2006). Three WRF-Chem model runs were performed: a base run with all emissions included; a run without fire emissions (noFire run); and a run without anthropogenic emissions (noAnthro run).
Model evaluation In order to evaluate the model results, output from WRF-Chem has been compared with aircraft data collected during POLARCAT. We focus on the ARCTAS-B flights over fresh Canadian forest fires, between 29 June and 5 July 2008. These fresh fire plumes were measured downwind (typical transport time 5-7 days) between 4 July and 8 July by the French and German aircraft. Therefore, we focus on flights over southern Greenland several days after emissions were measured by the DC8 (three ATR-42 flights and three Falcon-20 flights). Because there were no specific campaign flights over the northeastern United States, the main anthropogenic source region in our study, we use MOZAIC data collected during flights in and out of Philadelphia to evaluate the model in this region. A summary of all of the flights used in the analysis is given in Table  1  and flights are shown in Fig.
Aged pollution plumes In order to evaluate the representation of aged BB and anthropogenic plumes measured over southern Greenland, we use data collected onboard the French and German aircraft, which targeted aged pollution during POLARCAT (see Table 1 for the list of flights). Vertical profiles constructed using the ATR-42 and Falcon-20 measurements and corresponding model results are shown in Fig. 6. For the ATR-42 CO (Fig. 6a ) and ozone (Fig. 6b ), the results from the base run agree well with the measurements in the mid-troposphere. In the upper troposphere, modeled CO is too low, for example at 8 km, 150 ppbv was measured compared to 120 ppbv in the model. The FireCOSens run, with additional CO emissions, is in better agreement with CO measurements in the upper troposphere. This shows that CO emissions in North America impact CO concentrations in the free troposphere downwind due to plumes that are strongly uplifted during transport.
Plume origin and aging Given that the focus of our study is ozone production in aged plumes during transport to the Arctic, we focus on selected plumes measured downwind over Greenland. In this section, we focus on one fire and one anthropogenic air mass measured by the ATR-42 over Greenland to investigate in more detail aged plume composition and origin. It is essential to look at individual plumes to understand ozone production during transport because the aircraft also measured a large number of non-polluted air masses, making it difficult to examine ozone production in plumes using campaign averages (as noted earlier). For this analysis, we use plumes sampled by the ATR-42 on 5 and 7 July. We have chosen these flights because there are pollution plumes that are correctly captured by the model and because of the availability of ozone lidar data taken onboard the aircraft.
Conclusions We have used the regional model WRF-Chem to investigate the amount of ozone produced during transport towards the Arctic from Canadian boreal forest fires and North American anthropogenic emissions in summer 2008. Modeled concentrations were first evaluated using POLARCAT aircraft observations, including ARCTAS-B measurements of fresh Canadian forest fire plumes, MOZAIC data over the northeast United States, and POLARCAT-France/GRACE measurements of aged plumes over Greenland. In general, WRF-Chem simulations correctly represent the composition of fresh and aged BB plumes with some caveats. First, CO in fire plumes is too low using the FINNv1 emissions. A run with twice the fire CO emissions is in better agreement with the DC8 measurements of fresh BB emissions, an important conclusion regarding the CO emissions in the FINNv1 emissions inventory.
Acknowledgements. We thank the POLARCAT aircraft teams especially the  NASA ARCTAS, DLR-GRACE , and  French ATR-42  teams. French ATR-42 campaigns and data analysis were part of  POLARCAT-France  funded by  French Agence Nationale de la Recherche (ANR) ,  CNES ,  CNRS-INSU-LEFE, IPEV  and EUFAR. Authors ( J. Thomas ,  K. Law  and  J. C. Raut ) acknowledge support from projects  ANR Climate Impact of Short-lived Climate Forcers and Methane in the Arctic (CLIMSLIP)  Blanc  SIMI 5-6 021 01 ,  CLIMSLIP-LEFE (CNRS-INSU ), and the  European Union Arctic Climate Change, Economy and Society (ACCESS)  project ( FP7-SCP0-2011-265863 ). J. Fast was supported by the  US Department of Energy (DOE) Office of Science (BER) Climate Change Modeling Program. We thank  D. Blake  and  E. Apel  ( NMHC measurements ) as well as  Greg Huey  (PAN measurements) and the entire ARCTAS team for the use of the measurements taken onboard the DC8.
The authors acknowledge the strong support of the  European Commission, Airbus , and the  Airlines (Lufthansa, Austrian, Air France)  who carry free of charge the MOZAIC equipment and perform the maintenance since 1994. MOZAIC is presently funded by  INSU-CNRS (France) ,  Meteo-France , and  Forschungszentrum (FZJ, Julich, Germany ). The MOZAIC database is supported by  ETHER  ( CNES  and  INSU-CNRS ). We also acknowledge valuable help from colleagues at  PNNL ,  NCAR  ( C. Wiedinmyer ,  S. Walters ) and LATMOS/IPSL ( D. Cugnet  and  T. Onishi ). The  National Center for Atmospheric Research  is operated by the  University Corporation for Atmospheric Research  with funding from the  National Science Foundation. CNRS is acknowledged for publication cost support. Edited by: P. Monks The publication of this article is financed by  CNRS-INSU.