dataesr/scientific-paragraphs-categorization huggingface dataset:
e. plankton tows) may be less susceptible to this type of error and should be tested. Diversity analysis was conducted with a high-quality sequence dataset free of non-coding dubious sequences to ensure the exclusion of artefacts. A total of 344 OTUs spanning 14 different phyla were identified which further confirms the remarkable versatility of the primer set. Arthropoda, Chordata and Annelida were the most represented in terms of number of OTUs. This is in accordance with our morphological observations of prey remains, as well as with previous studies that described these three groups as the main food source of these generalist fish species  [40, [58] [59] [60]. Among all prey OTUs, 52. 5% had a direct match with a reference barcode, mostly from the Moorea BIOCODE sequence library. Although remarkable, the proportion of species-level assignments is lower than in a previous dietary study conducted in Moorea, where 94% of undigested prey found in the guts of common generalist predatory fish could be identified using DNA barcoding of individual prey items  [56].
Figure4Diversity, identity and sequence abundance of Operational Taxonomic Units (OTUs) recovered from fish gut contents. A) The number of OTUs per phylum is presented for all fish guts pooled together. OTUs were identified from BLASTn searches performed in the Moorea BIOCODE database and GENBANK. We considered a match to be at the species level when sequence similarity to a reference barcode was >98%. When sequence similarity was < 98%, we used the Bayesian assignment tool implemented in SAP to assign each OTU to a higher taxonomic group, accepting assignments at a significance level of 95% (posterior probability). B) The proportion of OTUs presented per abundance classes. Abundance corresponds to the number of sequences per OTUs.
Acknowledgements We thank  Gustav Paulay ,  Arthur Anker  and the BIOCODE teams who collected and identified marine and terrestrial specimens, the  "Centre de Recherche Insulaire et Observatoire de l'Environnement (CRIOBE) de Moorea " and the  Richard B. Gump field station in Moorea  for logistical support. We also greatly acknowledge the  Gordon and Betty Moore Foundation ,  Smithsonian Institution Fellowship Program ,  France American Cultural Exchange program  ( FACE -Partner University Fund)  and  ANR-11-JSV7-012-01 Live  and  Let Die  for financial support. Ehsan Kayal  and  Yvonne Linton  provided constructive comments on an early draft of the manuscript. We are also grateful for insightful comments provided by  Nancy Knowlton. This study was part of  M. Leray PhD  research program at  Université Pierre et Marie Curie (Paris VI)  and  Ecole Pratique des Hautes Etudes (EPHE)  under the supervision of S.
Study design and ethics This monocenter double-blind, randomized, placebo-controlled Phase I study was registered at www. clinicaltrials. gov (registration NCT01084343) and conducted at the Center for Vaccinology (CEVAC), Ghent University Hospital (Belgium). The protocol for this trial and supporting CONSORT checklist are available as supporting information; see Protocol S1 and Checklist S1 and. Trial protocol, substantial amendments, signed written subject information/Informed Consent Forms (ICFs) and subject diaries were reviewed by the Independent Ethics Committee (IEC) that gave on October 8 th 2009 the written approval for this study conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. The approbation and authorization to conduct the clinical trial was also received from the Federal Agency for Medicines and Health Products (FAGG) in Belgium.
Due to the exploratory character of the study, no formal power calculation was performed. The primary objective of the trial was to evaluate the safety and tolerability of two doses of a candidate prophylactic HIV-1 vaccine administered by the intramuscular and intranasal routes. The secondary objective of this Phase I was to verify the immunogenicity of the vaccine candidate by the quantification of P1-specific IgGs and IgAs in the serum. Ancillary studies were also conducted with vaginal and rectal secretions to assess the presence of mucosal P1-specific IgGs and IgAs and their capacity to block in vitro HIV-1 infection and transcytosis. PBMC were also isolated to measure the cellular immune responses. Double-blinding of volunteers' randomization, data management, and descriptive statistics for the analysis of safety, tolerability and immunogenicity data were conducted by Kinesis Pharma B.
2F5 IgG was used as positive control (10 mg/mL. 90% HIV-1 transcytosis inhibition, data not shown). Percentage of transcytosis inhibition was determined in three independent experiments. Samples were defined as positive when the transcytosis inhibitions were above 50% and reproduced in at least 2 experiments. The 2F5 IgG monoclonal antibody was used as positive control: Transcytosis blockade efficiency = 100 -Transcytosis efficiency (Transcytosis in presence of vaginal samples from week 25 or week 29/ Transcytosis in presence of pre-immune sample) 6100. A qualitative approach (presence of absence of antiviral activity) was used for monitoring the presence of transcytosis inhibition activity. Due to the limited number of samples and assay variability, statistical analyses according to clinical standards were not conducted.
Cellular immune responses Although the MYM-V101 vaccine formulation was primarily designed to trigger antibodies, it was estimated that it could potentially elicit also a Th1 response. Therefore PBMC were stimulated with P1 peptides and intracellular cytokine induction (IFNc, TNFa?IL-2) was analyzed by FACS. No P1-specific induction of cellular immune response in CD4 + or CD8 + T cells and NK cells could be revealed (data not shown).
Evaluation of anti-viral activities Due to limited mucosal material, not all subjects could be tested. Based on the presence of P1-specific IgG and/or IgA antibodies and the available specimen volume, selected samples were tested for in vitro antiviral activities. The genetically engineered TZM-bl cell line was tested with the clade B laboratory strain SF162 and the primary strain QHO692. 42, while the U87. CD4. CCR5 cell line was tested with the JFRL-140WT. No neutralization of HIV-1 was found for all samples tested (data not shown). Analyses on vaginal samples from the same subset of subjects were tested for their capacity to block HIV-1 transcytosis in vitro (Figure  3 ), with the mean percentage inhibition provided only as indicative value for a qualitative assessment. Vaginal samples of two out of two subjects of LD displayed 79-90% transcytosis inhibition at weeks 25 and 29.
Meanwhile, it is known that intranasal vaccination may solicit distant mucosal and systemic immune responses  [82, 89] , depending on the induction of specific sets of homing receptors during the interaction on T and B cells with mucosal dendritic cells  [90, 91]. However, activation of the mucosal responses at the vaginal and intestinal levels by the intramuscular route, using non-replicative vectors like virosomes might be more an exception than the rule. In an upcoming clinical trial, additional mucosal samples will be collected to clarify the respective contribution of the intramuscular and intranasal route for the induction of mucosal immunity. The available data allows us to conclude that MYM-V101 has successfully induced specific mucosal antibodies. At the end of the study (week 29, Tables  6  and 7 ), the mean total P1-specific antibody concentration in vaginal samples (LD: 6.
Antigen cross-presentation  [98]  leading to CTL induction is also possible with virosomes. However, the immunodominant human CTL epitopes ERYLKDQQL and CSGKLIC in the HXB2 gp41 ectodomain (HIV gp41 CTL epitope data base) are absent from our P1 peptide used for vaccination, which renders unlikely the induction of CD8 + T cell response. Meanwhile, it was important to verify this aspect and in vitro stimulation of PBMC with P1 peptide followed by intracellular cytokine staining was unable to reveal P1specific CD4 + or CD8 + Th1 response, although the threshold sensitivity of this method might be too weak for detecting low level of cell-mediated response. Both IgG or IgA antibodies may bind to their respective Fc receptor  [99]  and trigger various viral clearance mechanisms through Fc-mediated effector functions: Complement activation  [100] , antibody-mediated phagocytosis  [101, 102] , or engagement of antibodies with NK cells, neutrophils or macrophages that leads to ADCC  [103] [104] [105] [106] [107].
Acknowledgments We thank all the volunteers for their participation to the study. Special thanks to our main shareholders and  Prof. Stanley Plotkin  and  Prof. Marc Girard  for their precious long-term support and advice. We thank  Mark Spengler  and  Jan Detmers  ( Chimera Biotec GmbH ) for their strong involvement in the ImperacerH assay development. We are also grateful to  Fabienne Anjue  `re and  Selma Bekri  ( INSERM UMR 634, Facultede Medecine Pasteur, Nice, France ) who have developed and validated a B-cell ELISPOT assay which gave us important highlights on the adequate time window for mucosal sampling which would be necessary to further access gp41-derived antigen specific response in the future. We also thank the team of  Lucia Lopalco  for performance of neutralization assays, as well as  Anne-Sophie Drillet  and  Danila Tudor  from the laboratory of  Morgane Bomsel  for conducting transcytosis assays.
This work was financially supported by research grants  BB/E007295/1  and  BB/F014031/1  from the  U. K. Biotechnology and Biological Sciences Research Council (BBSRC)  (www. bbsrc. ac. uk) and by  grant-in-aid  to the  John Innes Centre  from the same source. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
C. Graph showing the fusion index of the experiment represented in (B). We measured the percentage of nuclei that were MyHC À or MyHC þ in mononucleated myotubes (<2), the % of nuclei that were inside myotubes containing between 2 and 5 nuclei (2 << 5) and the % of nuclei inside myotubes containing more than 5 nuclei (>5). Data are represented as average AE SEM, n ! 2. Statistical significance tested by one-way ANOVA, ÃÃ p < 0. 01, ÃÃÃ p < 0. 001. D. Follistatin RNAi in FAPs from ctrl mdx mice was performed by transfection of a shRNAi against follistatin (shFollistatin) and pSuper was used as ctrl. Graph shows the RNA levels of follistatin measured by qRT-PCR in FAPs upon RNAi. E. FAPs were treated (24 h) with TSA or not (ctrl) in vitro and subsequently co-cultured for 5 days in transwell, as described in B, with MuSCs isolated from mdx mice.
To stain lipids, 10% formalin fixed cells and tissues were rinsed with water and then with 60% isopropanol, stained with Oil red O in 60% isopropanol and rinsed with water. Images were acquired with a Leica confocal microscope and edited using the Photoshop software. Fields reported in the figures are representative of all examined fields. For Hematoxylin and Eosin staining, cryosections were fixed in 4% PFA, then washed in PBS-1X and then they were stained in haematoxylin for 4 min and eosin for 6 min. Then the cryosections were dried in ethanol and at the end they were fixed in xylene and mounted with EUKITT mounting (O. Kindler GmbH & CO). To stain fibrotic tissue Masson's trichrome analyses was used. Muscle cryosections were stained in Working Weigert's Iron Hematoxilin Solution for 5 min, washed in running tap water for 5 min and stained in Biebrich Scarlet-Acid Fucsin for 5 min.
Quantitative analysis The cross-sectional area (CSA) was calculated using the ImageJ software downloaded from http://rsb. info. nih. gov/ij. Fibrotic areas were measured by selecting four representative and non-adjacent sections and photographing up to three microscopic fields. The total fibrosis was calculated from sections evaluating image analysis algorithms for colour deconvolution. ImageJ was used for image processing, the original image was segmented with three clusters and the plugin assumes images generated by colour subtraction (white representing background, blue collagen, and magenta non collagen regions;  (Krajewska et al, 2009; Ruifrok & Johnston, 2001). Oil Red O areas were quantified by selecting four representative and nonadjacent sections and photographing up to three microscopic fields.
C. Graph showing the fusion index of the experiment represented in (B). We measured the percentage of nuclei that were MyHC À or MyHC þ in mononucleated myotubes (<2), the % of nuclei that were inside myotubes containing between 2 and 5 nuclei (2 << 5) and the % of nuclei inside myotubes containing more than 5 nuclei (>5). Data are represented as average AE SEM, n ! 2. Statistical significance tested by one-way ANOVA, ÃÃ p < 0. 01, ÃÃÃ p < 0. 001. D. Follistatin RNAi in FAPs from ctrl mdx mice was performed by transfection of a shRNAi against follistatin (shFollistatin) and pSuper was used as ctrl. Graphshows the RNA levels of follistatin measured by qRT-PCR in FAPs upon RNAi. E. FAPs were treated (24 h) with TSA or not (ctrl) in vitro and subsequently co-cultured for 5 days in transwell, as described in B, with MuSCs isolated from mdx mice.
Acknowledgements PLP is an Associate Investigator of  Sanford Children's Health Research Center. This work has been supported by the following grants to PLP:  R01AR056712 ,  R01AR052779  and  P30 AR061303  from the  National Institute of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) ,  MDA EPIGEN and Sanford Children Health Research  award. This work has benefited from research funding from the  European Community's Seventh Framework Programme  in the project  FP7-Health -2009 ENDOSTEM 241440  (Activation of vasculature associated stem cells and muscle stem cells for the repair and maintenance of muscle tissue). CM was supported by  AFM  fellowship. AS is supported by  MDA ,  Ellison Medical Fundation  and  NIH  grants. We acknowledge the excellent contribution of  SBMRI Animal Resources Imaging facility.
Quality of management may indeed be necessary to provide international quality and delivery standards in OECD markets. The rate of ISO 9000 varies greatly across developing countries. Following  Rauch and Watson's (2003)  methodology we find for example that in 2000, China has five times more ISO 9000 certificates per industrial workers than Morocco and 40 times more than Bangladesh while Turkey or Brazil report about 3 times more certificates than China. 3 Finally, working at the country level and using different measures of quality,  Hallak and Schott (2011)  and  Khandelwal (2010)  find substantial differences in exports quality across countries. Using a very large database of OECD imports at the 5-digit level Standard International Trade Classification (SITC) since 1963, we test the model's basic predictions by looking at the evolution of unit values during re-concentration episodes and at how the volatility of concentration indices varies across products types, taking the variation in unit values as a proxy for quality heterogeneity.
4 We find, as predicted by the model, that re-concentration, when it happens, is associated with a rise in unit values. That is, when buyers re-concentrate, they do so on higherpriced (and hence presumably higher-quality) suppliers rather than on the most price-competitive. We also find that concentration indices are more volatile, over time, for products whose quality (as proxied by unit values) is more heterogeneous across suppliers. Finally, consistent with an extension of our model, we provide evidence of an overall diversification in OECD import's sources of supplies 3 The number of ISO 9000 certificates comes from the ISO Survey of ISO 9000 and ISO 14000 certificates-Tenth cycle provided by the International Organization of Standardization. We obtain data for industrial employment combining data on share of industrial employment in total employment, share of employment in population and population from the World Development Indicators (World Bank 2011).
Concentration index and data We measure, product by product (k), the geographical concentration of OECD country i's imports in t across origin countries. Our measure is the Theil's entropy index  (Theil 1972)  given by: Theil ikt ¼ 1 n k X n k j¼1 x j ikt l ikt ln x j ikt l ikt ! where l ikt ¼ 1 n k X n k j¼1 x j ikt ; where x j ikt is imports of OECD country i from origin country j of product k at time t and n k is the total number of countries with the capability to export good k. 14 Our baseline definition of the set of potential exporters, n k , which is time-invariant, is the set of all countries having exported good k to some destination in the world (not necessarily OECD countries) at least two consecutive years in a row over the sample 13 However, supply shocks knocking out suppliers periodically could also create exogenous volatility at the extensive margin.
This definition has the advantage of being time-and importer-invariant (the latter matters for the part of our analysis where we disaggregate OECD imports by importing country). As shown in  Cadot et al. (2011) , the presence of logarithm in the Theil index is not an issue for ''zero'' trade flows as at the limit, and by L'Hopital's rule, ''zero'' trade flows do not contribute to the measure of concentration. Our index of concentration captures both actions at the extensive and intensive margin without distinction. 16 In order to explore action at the extensive margin, we also consider the simple number of exporters of good k to the OECD country i in t, Nber ikt. Our data is COMTRADE import data for OECD countries (either taken as a bloc or disaggregated by importer) at the product level. 17 Our preferred product classification is the 5-digit level SITC data (using the backwards classificationrevision 1).
The alternative, HS6, is more disaggregated (with 4,990-5,016 lines depending on the year against 1,158-1,300 for 5-digit level SITC), but the sample period is longer with SITC, which also underwent fewer revisions. In terms of country coverage, 5-digit level SITC data covers 253 countries and territories between 1962 and 2006 (44 years); HS6 coverage is nominally available starting 1988, but with only 12 countries (9 of which are OECD members) expanding gradually to 116 countries in 1995 and 140 in 2006. 18 15 In order to calculate the Theil index and capture the evolution in geographic import concentration, we need to define a potential number of source countries than is constant over time. In effect, if we let n k vary over time, (say by making it equivalent to the number of countries that export a specific product each year), we cannot disentangle concentration/diversification on actual suppliers from changes in the universe of potential suppliers.
In order to confront our main findings to the choice of disaggregation of the database, we re-run our main regression (Table  1 ) on the sub-sample of SITC codes that correspond to only one (alternatively two or less) HS6 lines. Results are similar to the ones obtain with the full SITC database and are available upon request. Proposition 1 involves unobservable quality heterogeneity. We approximate quality by unit values, of which we calculate import-weighted averages for each OECD importer, good and year. If re-concentration, when it takes place, is on the best performers, we expect positive year-on-year changes in the Theil index to correlate with positive changes in the average unit value of imports. The average unit value's rise is a composition effect, as buyers concentrate on high-quality suppliers.
However, as results on the number of exporters show, it does not occur at the extensive margin, all of the action being at the intensive margin. Considering the rising importance of OECD trade with China over the last decade, we must control for the role that China may play in that re-concentration. In column (7) of Table  3  the coefficient on time squared loses its significance when China is excluded from the sample, suggesting that China is indeed driving the observed re-concentration. Using our SITC data for China we calculated the contribution of the intensive and extensive margin to China-OECD imports growth over the 1963-2006 period. While in the early years  (1963) (1964) (1965) (1966) (1967) (1968) (1969) (1970) (1971) (1972) (1973) (1974) (1975)  the extensive margin accounted for about 35 % of China-OECD imports growth, this share shrank to almost zero in the 1993-2006 period.
Acknowledgments Research on this paper was supported by a Grant from the  World Bank. Support from France's Agence Nationale de la Recherche  under '' Investissement d'Avenir''  Grant  ANR-10-LABX-14-01  is gratefully acknowledged. Without implicating them, the authors would like to thank  Daniel Lederman ,  William Maloney ,  Marcelo Olarreaga , and an anonymous internal reviewer for useful comments. We are grateful to  Madina Kukenova  for her research assistantship on a previous version of the paper.
RNA extraction and transcriptome analysis Flowers from different plants (collected three times from 10 individuals each) and grown with and without Fe excess were ground in liquid nitrogen. RNAs were extracted using an RNeasy Mini Kit (Qiagen). For microarray analysis, 5 µg of RNA from flowers of the atfer1-3-4 mutant and the WT were processed and hybridized to Affymetrix GeneChip Arabidopsis ATH1 Genome Arrays as described in  Duy et al. (2011). For quality check and normalization, raw intensity values were processed with Robin software  (Lohse et al. , 2010)  default settings. Specifically, for background correction, the robust multiarray average normalization method  (Irizarry et al. , 2003)  was performed across all arrays (betweenarray method). Statistical analysis of differential gene expression of atfer1-3-4 versus WT flowers was carried out using the linear modelbased approach developed by  Smyth (2004).
0 software (BioRad). Missing spot volumes were estimated using a sequential K-Nearest Neighbor algorithm. Consistent spots were those present in at least 80% of the replicates from at least one class. Differentially expressed spots were defined using a Student's t-test value of P < 0. 10. Protein response ratios were defined as the abundance in a given class divided by the abundance in the control class; when ratios were <1, the inverse was taken and the sign changed. Only proteins with mean response ratios >2. 0 or below -2. 0 were considered relevant and analysed further. Partial least square (PLS) analysis was applied to the identified protein species using SPSS v. 15 (SPSS Inc. , Chicago, IL, USA).
Protein in-gel digestion and identification by nano-high performance liquid chromatography-tandem mass spectrometry Selected spots were excised, in-gel digested with trypsin, and analysed by nano-HPLC-tandem mass spectrometry as described in detail in  Rodriguez-Celma et al. (2013). Protein identification was performed by searching in the non-redundant NCBI 20120324 (17 612 906 sequences; 6 046 335 507 residues) and Plants_EST EST_111 (155 120 040 sequences; 27 373 983 152 residues) databases using the Mascot search engine (Matrix Science, London, UK). The search parameters were: monoisotopic mass accuracy, peptide mass tolerance ±0. 2 Da, fragment mass tolerance ±0. 6 Da, one allowed missed cleavage, allowed fixed modification carbamidomethylation (Cys), and variable modification oxidation (Met).