dataesr/scientific-paragraphs-categorization huggingface dataset:
Frequency dependence We complement the power spectrum analysis of the 353 GHz map with Planck data at lower frequencies. As in the analysis in Sect. 4. 5, we compute the frequency dependence of the BB power measured by Planck at HFI frequencies in the BICEP2 field, using the patch M B2 as defined in Sect. 6. 1. We compute on M B2 the Planck D BB auto-and cross-power spectra from the three Planck HFI bands at  100, 143, 217, and 353  GHz, using the two DetSets with independent noise at each frequency, resulting in ten angular power spectra  (100 × 100, 100×143, 100×217, 100×353, 143×143, 143×217, 143×353, 217 × 217, 217 × 353, and 353 × 353) , constructed by combining the cross-spectra as presented in Sect. 3. 2. We use the same multipole binning as in Sect. 6. 3. To each of these D BB spectra, we fit the amplitude of a power law in with a fixed exponent Fig.
An upper limit on the synchrotron contribution at 150 GHz from the Planck LFI data is given in Appendix D. 4. We can see that the frequency dependence of the amplitudes of the Planck HFI D BB spectra is in very good agreement with a squared dust modified blackbody spectrum having β d = 1. 59 and T d = 19. 6 K (Planck Collaboration Int. XXII 2014). We note that this emission model was normalized only to the 353 GHz point and that no global fit has been performed. Nevertheless, the χ 2 value from the amplitudes relative to this model is 4. 56 (N dof = 7). This shows that dust dominates in the specific M B2 region defined where these cross-spectra have been computed. This result emphasizes the need for a dedicated joint Planck-BICEP2 analysis.
Acknowledgements. The development of Planck has been supported by:  ESA ;  CNES  and  CNRS/INSU-IN2P3-INP (France) ;  ASI ,  CNR , and  INAF (Italy) ;  NASA and DoE (USA) ;  STFC  and  UKSA (UK) ;  CSIC ,  MICINN , JA, and  RES (Spain) ;  Tekes, AoF , and  CSC (Finland) ;  DLR  and  MPG (Germany) ;  CSA (Canada) ;  DTU Space (Denmark) ;  SER/SSO (Switzerland) ;  RCN (Norway) ;  SFI (Ireland) ;  FCT/MCTES (Portugal) ; and  PRACE (EU). A description of the Planck Collaboration and a list of its members, including the technical or scientific activities in which they have been involved, can be found at http://www. rssd. esa. int/index. php?project=PLANCK&page= Planck_Collaboration. Some of the results in this paper have been derived using the HEALPix package. The research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013)  /  ERC  grant agreement No.
, 1995a; Schendel et al. , 2016). Another feature of xylans present in grasses is the absence of the tetra-saccharide sequence found at the reducing end of xylan in eudicots and gymnosperms. By contrast, xylose residues present at the reducing end of grass xylans have been reported to be substituted at O-2 by 4-O-methyl glucuronic acid or at O-3 by arabinofuranose residues  (Ratnayake et al. , 2014; Peña et al. , 2016). In the cell walls of grasses, ferulic acid is attached to the arabinose residues of xylans via an ester linkage. Under oxidative conditions, chains of arabinoxylan can cross-link through a ferulate bridge that forms either ferulate dehydrodimers, trimers or tetramers  (Hatfield et al. , 1999; Saulnier and Thibault, 1999; Rouau et al. , 2003; Bunzel et al. , 2004). Ferulic acids can also Abbreviations: MaizeGDB, maize genetics and genomics database; DAP, days after pollination; FAm, ferulic acid monomer; diFA, ferulic acid dehydrodimers; TriFA, ferulic acid dehydrotrimer; AIR, alcohol insoluble residue; PMT, pCA monolignol transferase; FT-IR, Fourier transform-InfraRed; RMA, robust multiarray average; pCA, p-coumaric acid; GT, glycosyltransferase; IRX, IRREGULAR XYLEM; XAT, xylan O-3 arabinosyltransferase; XAX, arabinoxylan β-1,2-xylosyltransferase; GUX, xylan glucuronyltransferase; GXMT, glucuronic acid O-methyl transferase; RWA, REDUCED WALL ACETYLATION; AXY, ALTERED XYLOGLUCAN; DUF, domain of unknown function; TBL, TRICHOME BIREFRINGENCE LIKE; PAL, phenylalanine ammonia lyase; C4H, cinnamate 4-hydroxylase; 4CL, 4-coumarate:CoA ligase; HCT, hydroxycinnamoyl transferase; C3H, pcoumarate 3-hydroxylase; OMT, O-methyl transferase, CCoAOMT, caffeoyl-CoA O-methyltransferase; CCR, cinnamoyl-CoA reductase; F5H, ferulate 5hydroxylase; COMT, caffeic acid O-methyltransferase; CAD, cinnamyl alcohol dehydrogenase; RNAi, RNA interference; ALDH, coniferaldehyde dehydrogenase; AX, arabinoxylan; CSE, caffeoyl shikimate esterase.
, 2013). One current model proposes that the feruloylCoA produced by the phenylpropanoid pathway is the active form of ferulic acid that is transferred to arabinoxylans or UDP-arabinose by members of the BAHD superfamily of acyltransferases  (Mitchell et al. , 2007; Molinari et al. , 2013). The BAHD superfamily, also referred as Pfam family PF02458  (D'Auria, 2006) , has been divided into eight clades  (Tuominen et al. , 2011) , with some clades over-represented in rice compared with Arabidopsis  (Mitchell et al. , 2007). Since feruloylated arabinoxylans are present in the cell walls of rice but are absent in Arabidopsis, these clades were proposed as candidates for feruloyltransferases acting on arabinoxylans. Feruloylated arabinoxylans are transported to cell walls by exocytosis. Oxidative coupling of ferulic acid occurs intracellularly and in the cell walls to produce dimers and oligomers, and it has been suggested that class III peroxidase is involved in the process  (Fry et al.
, 1995; Saulnier et al. , 1995b). In maize bran, the structure of xylans has been extensively documented  (Chanliaud et al. , 1995; Saulnier et al. , 1995b; Allerdings et al. , 2006; Agger et al. , 2010; Schendel et al. , 2016) , and its lignin content has been reported to be low (minimum 1%)  (Chanliaud et al. , 1995; Saulnier et al. , 1995b; Lapierre et al. , 2001). Taken together, these results facilitate the study of feruloylated arabinoxylans. Moreover, with the availability of its sequenced genome, publicly available gene expression data collected in a dedicated database (the Maize Genetics and Genomics database; MaizeGDB), mutant collections and protocols to generate genetically modified maize, the B73 maize line is a good model for functional genomics. To study grass cell walls and especially the biosynthesis of feruloylated arabinoxylans, we selected the maize grain pericarp as a model.
In this report, the feruloylated arabinoxylan content of grain tissues (pericarp and endosperm) from the maize B73 line was measured and compared with those of 18 other maize lines. We determined the stages of development where the deposition of feruloylated arabinoxylans occurs in B73 grains, and we have used published and publicly available data to monitor the expression of genes associated with feruloylated arabinoxylan and lignin  (Sekhon et al. , 2011; Courtial et al. , 2013; Barrière et al. , 2016). Our study of maize pericarp highlights the expression of cell wall genes involved in the synthesis of feruloylated arabinoxylans, and as a consequence, we propose several robust candidate genes involved in ferulate and arabinoxylan synthesis and in the feruloylation and the cross-linking of xylans.
Fourier Transform-InfraRed (FT-IR) Spectroscopy FT-IR spectra were obtained from AIRs of the maize pericarp and reference samples of maize F2 internodes (F2 line, collected at the silage stage)  (Chazal et al. , 2014) , straw of wheat (Champlein cultivar) and Brachypodium distachyon pCA monolignol transferase1 (Bdpmt1) mutant  (Petrik et al. , 2014). FT-IR spectra were recorded from KBr pellets made from 2 mg of samples mixed with 120 mg of KBr. The spectra were collected in transmission mode between 4000 and 700 cm -1 at 2 cm -1 intervals (Thermo Nicolet IS50 spectrometer). The IR spectra resulted from the co-addition of 200 interferograms. All IR spectra in the 2000-700 cm -1 region were baseline-corrected and unit vector normalized using OPUS software (version 7). Secondderivative spectral data (Norris Gap, gap size: 9) were processed to enhance spectral differences in the 875-750 cm -1 region (Unscrambler 10.
Transcriptome Analysis The expression data generated by  Sekhon et al. (2011)  for 60 maize tissues of the B73 line are publicly available via the MaizeGDB website (www. maizegdb. org) and were used in this study to investigate the expression of genes related to arabinoxylans (AX) and lignins. Robust multiarray average (RMA) normalized data were collected for the 1st internode of the maize stem at stage V7 (7 leaves with visible leaf collars) and the dissected pericarp and endosperm at the R3 stage (18 DAP/R3), together with the maximum absolute signal value. The expression data are expressed as a % of the expression potential, as in  Francoz et al. (2015) , with the expression potential defined as the maximum absolute signal value in the maize RMA normalized data. The % of the expression potential was color-coded to facilitate visualization of expression differences.
As in  Sekhon et al. (2011) , genes with expression data (RMA normalized value) <200 were considered as not being expressed in the corresponding tissue. Gene expression and co-expressed genes were checked using the same dataset analyzed by the Plant Expression Database PlexdB (www. plexdb. org) as expression profile neighbors using the data for the 60 maize tissues. The genes investigated here correspond to an updated list of maize genes established by  Courtial et al. (2013)  and  Barrière et al. (2016)  with a focus on genes potentially encoding enzymes involved in the synthesis and radical coupling of feruloylated arabinoxylans and monolignols. Maize orthologs to genes whose functions are known in other species were identified by a sequence similarity search based on protein sequences using the BlastP tool of the MaizeGDB with e-value lower than e-75  (Courtial et al.
, 2013). The list of maize genes for class III peroxidases was obtained from  Wang et al. (2015). The list of rice BAHD genes within clades A and B was found in  Molinari et al. (2013) ; their sequences were collected from the Rice Genome Annotation project database (http://rice. plantbiology. msu. edu/). Maize and Brachypodium orthologous sequences of rice BAHD genes were obtained from the Gramene database (http://www. gramene. org/).
Although no simple relationship exists between the amount of transcripts, the amount of enzymes and the amount of their product, the relative level of expression of the corresponding genes should, to some extent, reflect the relative amount of product. The expression data for 60 maize tissues of the B73 line generated by  Sekhon et al. (2011)  and publicly available via the eFP Browser of the MaizeGDB website were used to study the expression of genes related to feruloylated heteroxylans and lignins. Data were selected for the dissected pericarp and endosperm at the R3 stage (18 DAP). The deposition of feruloylated heteroxylans occurs in the B73 pericarp during this stage. It is the only stage where both pericarp and endosperm data are available in the dataset from  Sekhon et al. (2011). We also selected data for the 1st internode of the maize stem at stage V7 (7 leaves with visible leaf collars) since its cell walls contain glucuronoarabinoxylans and lignins  (Scobbie et al.
The total scattering approach contains significantly more structural information, allowing a quantitative assessment of the structure that is impossible with conventional data from such small particles. We apply PDF nanostructure analysis to Au 144 (SR) 60 clusters prepared with different ligands (Fig. 1e ): phenylethane thiol (PET), para-mercaptobenzoic acid (p-MBA), butane thiol (SC4), hexanethiol (SC6) and dodecanethiol (SC12). Sample homogeneity is characterized by electrospray ionization-mass spectrometry (ESI-MS) and electrochemical methods. The approach results in full quantitative refinements of the structure of the gold core, with a semi-quantitative assessment of the surface structure. Surprisingly, we find two distinct structural forms for this cluster's core, one based on icosahedra seen in smaller clusters, proposed earlier for this 144 gold atom cluster  [20] [21] [22]   possibility of engineering nanoparticle structure, as well as size and morphology.
2c. The homogeneity of this cluster sample was characterized by electrochemical measurements. Total scattering data were measured from samples of Au 144 (p-MBA) 60 from two different synthesis batches and as shown in Supplementary Fig. 6  the two PDFs are completely reproduced with a small difference residuum of R W ¼ 7. 8%, illustrating reproducibility of the synthesis and reliability of the measurements. We first attempt to use the Form I icosahedral structural model to establish whether this can be made to fit the different PDF by adjusting the refinement parameters. However, the model gives a very poor fit with a large difference between the calculated and measured PDF, and poor fit residuum of R W ¼ 36. 0% as shown in Fig. 3b. To further confirm that the sample does not simply contain stable clusters of a different size, for example, Au 102 (SR) 44  (ref.
22  or Lopez-Acevedo et al. 20  models fully capture the details in the PDFs, for example, in the peaks between 4 and 5 Å in Fig. 3a. Some structural details exist, which are not present in the established models. Therefore, further studies of the structure are needed, where scattering is combined with theory  54  and spectroscopy  56  , to establish the total structure. The polymorphism seen in our data suggests many new studies of gold nanoclusters. The close energies between different cluster structures may not be limited to the Au 144 (SR) 60 cluster family, but exist in a larger size range and in different materials systems. The presence of polymorphism challenges some of the characterization methods that are used for structure solution. For example, when applying single-crystal XRD, the crystallization process works as a structural sieve that will favour only one cluster polymorph over others that may be present in suspension, resulting in an incomplete picture.
Methods Synthesis and purification of Au 144 (SR) 60. Au 144 (p-MBA) 60 was synthesized as in Ackerson et al. 39  and described in Supplementary Note 7, along with the purification and characterization. Au 144 (SR) 60 , where SR ¼ PET, S4, S6 and S12, synthesis followed Qian et al. 59  , also discussed further in Supplementary Note 7. The samples were characterized by ESI-MS (Supplementary Fig. 1  and Supplementary Table  1 ) and electrochemical methods (Supplementary Fig. 14 15 16 ). X-ray total scattering experiments. Total scattering data were acquired during three different beamtimes at three different facilities. For all samples, the cluster powders were loaded in Kapton tubes with inner diameter of 1 mm. Data for both samples of the Au 144 (p-MBA) 60 cluster was obtained at ID11 at the European Synchrotron Radiation Facility with an X-ray wavelength of 0.
Acknowledgements K. M. Ø. J. acknowledges support from the  Villum Foundation. S. J. L. B and P. J. acknowledge funding from  Laboratory Directed Research and Development (LDRD)  Program  12-007  ( Complex Modeling ) at  Brookhaven National Laboratory , which is funded by the  U. S. Department of Energy, Office of Basic Energy Sciences  grant  DE-SC00112704. We acknowledge the  European Synchrotron Radiation Facility  for provision of synchrotron radiation facilities at beamline  ID11. Use of the Advanced Photon Source at Argonne National Laboratory  was supported by the  U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences , under contract number  DE-AC02-06CH11357. Use of the  National Synchrotron Light Source, Brookhaven National Laboratory , was supported by the  U.
These additional paralogs are mapped to distinct genomic loci that produce the same mature miRNA product for a given miRNA. Moreover, we identified new miRNA family members for miR-551, miR-7132 and miR-7133. Four miRNAs in miRBase, miR-722, miR-735 and miR-740 and miR-7146, were excluded from the analysis as their mapped genomic locations conflicted with miRBase annotation. Since miRNAs in bichir and axolotl are not yet represented in miRBase  [44] , we annotated known and putative novel miRNAs using miRMiner  [45]. The annotation workflow for miR-NAs is best done by aligning reads to a genome assembly, looking for characteristic stem-loop precursor structures and examining the pattern of sequence tag alignments  [46]. As bichir and axolotl don't have genome assemblies, the miRMiner software was used to compare adapter clipped and collapsed small RNA sequence reads from bichir and axolotl to mature sequences in miRBase to identify miRNAs.
To complement our analysis of known miRNAs, we also queried our dataset for 20-25-mer sequences that could represent potential novel miRNAs. We identified a total of 1,084 sequence tags that were represented in all zebrafish samples (S5-S8 Tables). Within the group, 240 sequence tags were shared with bichir and axolotl samples, of which, 232 sequence tags resembled isomiRs, mature miRNA products that differ from the canonical 5p or 3p sequences (S8 Table)  [47]. Since variation in miRNA seed sequence can control distinct target genes, we further filtered our dataset to reveal isomiRs with sequence differences within positions 2-8-nt of the mature sequence. These filtering criteria revealed 4 isomiRs: 2 variants of let-7a and 1 variant of miR-203a-1-3p and miR-143 each (Fig 4A ). The remaining 8 sequence tags shared among zebrafish, bichir and axolotl have not been previously identified, and thus, represent novel sequence tags.
Network of consistently expressed genes with functional relationships to known blastema-associated genes In order to understand the regulatory mechanisms of miRNAs during limb/appendage regeneration, we complemented our small RNA analysis with mRNA gene expression studies. Since bichir and axolotl do not have genome sequences, we generated de novo transcriptome assemblies for regenerating bichir and axolotl tissues using Trinity software pipeline  [51]. To improve these assemblies, we included RNA-Seq reads from two additional time points, 3 and 14 dpa. Together, the transcriptome assemblies contained a total of 94,273 components, transcript groups that resemble genes, for bichir and 73,787 components for axolotl (S9 Table ). From these assemblies, we predicted homologous relationships for 9,598 (56.
4%) of the 16,951 expressed zebrafish genes for both bichir and axolotl (S10-S14 Tables). We identified a set of 1,856 genes that were commonly upregulated in zebrafish, bichir and axolotl, and 1,345 that were downregulated (S15-S18 Tables). Among this filtered dataset, we identified 11 known blastema genes with differential expression patterns (S19 Table ). Nine of these genes (fgf20  [9] , hspd1  [10] , igf2  [52] , junb  [53] , mmp14  [11] , mmp9  [53] , smarca4  [53] , timp2  [54]  and ttk  [55] ) had increased expression following injury while cxcl12  [56]  and erbb2  [57] ) displayed decreased expression (Table  3 ). Real-time qRT-PCR confirmed these expression changes in all three systems (Fig  5A ). These 11 known blastema-associated genes were then used as a foundation to identify functional interactions with commonly expressed genes using STRING database  [58].
De novo transcriptome assembly and analysis Bichir and axolotl RNA-Seq reads were adapter clipped and quality trimmed using Trimmomatic  [72]  and assembled using Trinity  [51]. RNA-Seq reads from each sample were mapped to the respective assembly using RSEM  [73]  to generate read counts per transcript per sample. Read counts were analyzed using R/edgeR  [71]  to determine those that were differentially expressed. miRNA target prediction miRNA targets were predicted by analyzing annotated 3'-UTR sequences from Ensembl version 76  [74]  for zebrafish and open reading frame predictions for bichir and axolotl using miRanda  [75]. Target predictions were made using mature miRNA sequences and mature miRNA sequences that allow a nucleation bulge at positions 5-6  [76]  for the common upregulated and downregulated miRNAs (S3 File).
Data Access Zebrafish, bichir and axolotl gene expression data are accessible from NCBI Gene Expression Omnibus under accession numbers GSE74415, GSE74374 and GSE74372, respectively. Short RNA and mRNA sequence data for zebrafish, bichir and axolotl are accessible from the NCBI Short Read Archive under accession numbers SRP065355, SRP065300 and SRP065299, respectively.
This work was supported by  Institutional Development Award  ( IDeA)  from the  National Institute of General Medical Sciences of the National Institutes of Health  under grant numbers  P20 GM103423  and  P20 GM104318  to BLK and  VPY , and  US Department of Defense  grant  W81XWH-BAA-1  to VPY. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data availability All laboratory measurement data used in this study (aerosol ion concentrations and oxygen-17 excess of sulfate) are permanently archived at the University of Washington Research-Works site: https://digital. lib. washington. edu/researchworks/ handle/1773/36944  (Chen, 2016). (A9) Setting f = 0 yields Eq. (  8 ) in Sect. 5. 2. 4. f is zero when r 1 = r 2 = 0, which effectively assumes that the decreases in f mod,OH , f mod,H 2 O 2 and f mod,O 3 after adding HOX in the model could be proportional to their relative fractions in the model. r 1 will be zero if cloud pH is unchanged; i. e. , the S(IV) partitioning will remain unchanged after adding the "S(IV) + HOX" reaction. The potential magnitude of f , which is dependent on the relative magnitude of r 1 and r 2 , is discussed below.
Acknowledgements. We thank  Roland von Glasow  and  Jon Abbatt  for helpful discussions in the planning phase of this project. This  project is funded by  NSF   AGS 1343077. The sampling during the Malaspina cruise was funded by the  Spanish Ministry of Economy and Competiveness  (Circumnavigation Expedition Malaspina 2010:  Global Change and Biodiversity Exploration of the Global Ocean. CSD2008-00077 ). Z. Q. Xie acknowledges the support from  NSFC 91544103. Q. Chen  thanks  Viral Shah  for help on GEOS-Chem modeling. Edited by: E. Harris Reviewed by:  R. Sander  and  A. -L. Norman.
These reports provide additional information on people's health status. Documents on the subject are also produced by other associations and we looked at the work done by "Groupe d'Information et de Soutien aux Immigrés" (GISTI) -Group of information and support for migrants and the "Comité Médical des Exilés" (COMEDE) "Medical committee for exiled persons". Academic research on the health issues facing undocumented migrants is relatively scarce. However, we explored francophone scientific literature by entering the terms "health care" and "migrants" and synonyms into the databases CAIRN and TERRA ("Travaux Etudes et Recherches sur les Réfugiés et l' Asile" -Studies and researches on refugees and asylum). We also examined scientific literature in English, with searches in Pubmed and Academic Search Premier.
Drosophila strains and maintenance The Drosophila strains transgenic for Gal4-inducible Ciona intestinalis AOX (AOX F6 ) in the w 1118 background  [24]  and for different human Aβ variants, also in the w 1118 background  [25]  were as described previously. The X-chromosomal elav-GAL4 driver line (C155, Bloomington strain 458), as well as w 1118 and standard balancers for stock maintenance, were obtained from Bloomington stock centre. Flies were maintained at 25 °C on standard medium  [26] , except for lifespan measurements which were conducted as described  [25]  at 29 °C, in vials containing batches of $ 20 flies of a given sex and genotype. Lifespan curves were based on combined data from 4 to 8 such vials per sex and genotype, with flies tipped to fresh vials every 3 days, or on any day when dead flies were observed.