dataesr/scientific-paragraphs-categorization huggingface dataset:
SEC MALLS Purified recombinant human RIG-I was prepared as previously described  [30]  and mixed with equimolar amounts of RNA. Experiments were performed in 20 mM HEPES, pH 7. 5, 100 mM NaCl, 2. 5 mM MgCl2, 5 mM b-mercaptoethanol with an S200(10/300) column, connected to a MALLS detector (DAWN-EOS Wyatt technology) and a refractive index detector (RI2000b Schambeck). Data were analysed with the ASTRA V software  [32].
SAXS The experiments were carried out at the beamline ID14-2 of the European Synchrotron Radiation Facility (ESRF, Grenoble, France). Scattering data was collected for different protein concentrations and from the merged curves the radius of gyration (Rg) was determined from the Guinier plot. Next, the maximal distance in the size distribution function was adjusted, so the calculated Rg from the fit would be in agreement with the experimental value.
Acknowledgments The authors thank  Y. Jacob ,  D. Garcin ,  T. Fujita ,  P. Pothier ,  C. Rice ,  T. Imaizumi  and  R. Cattaneo  for providing us with useful reagents,  C. Lazert ,  L. Wouters  and  M. Ferren  for plasmid construction and  P Lawrence  for English proofreading and copiediting. We thank  T. Crepin  for the clone of influenza panhandle RNA and  P. Holenya  for help with RNA preparations, the beamline staff of ID14-2 at  ESRF, Grenoble, France , the flow cytometry ( T. Andrieu ,  S. Dussurgey ) and qPCR ( B. Blanquier ) facilities of the  SFR Biosciences Gerland-Lyon Sud  ( UMS344/US8 ).
Acknowledgements The authors would like to thank all members of the  Dumenil lab , particularly  Silke Silva  for critical reading of the manuscript. The surgery department at  Hôpital Européen Georges-Pompidou (HEGP) ,  Dr. David Maladry. Michael Hivelin  and  Dr. Patrick Bruneval ,  Pathology Department at HEGP. The animal facility at PARCC, headed by  Elizabeth Huc. This work was supported by the following grant agencies:  Marie Curie IEF  fellowship no. 273223  (KM),  ATIP-Avenir Grant from INSERM, CODDIM equipment grant  ( Ile de France Region) ,  FRM  (fondation pour la recherche médicale) equipment grant, the  IBEID Laboratory of excellence consortium, ANR (Agence Nationale pour la Recherche)  grant " Bugs-in-flow ". The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Molecular modelling The three-dimensional (3-D) crystal structure of NP monomeric form (PDB ID: 2IQH) was used as a target throughout the virtual screening in a volume centred on Y148. The NP-naproxen structure selected after the virtual screening  (Lejal et al. , 2013)  was further used to set the initial coordinates for molecular dynamics simulation. Derivatives of naproxen were designed to additionally target R152, R355, Q149 and F489. The first two residues were targeted by extending the carboxylate moiety of naproxen. The last two residues were targeted by extending the methoxy group of naproxen with short aliphatic or polar groups. The stability of naproxen derivatives in the nucleoprotein binding pocket were investigated through MD simulations of the complex. The flexible groups added to the methoxy moiety increased the entropy of the new derivatives without an enthalpic compensation, resulting in unstable interactions with the nucleoprotein.
Chemical synthesis Reagents and chemicals were purchased from Sigma-Aldrich. Solvents were freshly distilled before use. 1 H and 13 C NMR spectra were recorded on a Bruker Avance 300 using solvent residuals as internal references. Melting points (MP, uncorrected) were determined on a Büchi Melting Point B-540. TLC analysis was carried out on silica gel (Merck 60F-254) with visualization at 254 and 365 nm. Preparative flash chromatography was carried out with Merck silica gel  (Si 60,. IR spectra were recorded with a FTIR PerkinElmer Spectrum 100 spectrometer. Mass spectrometry low resolution data and high resolution data were obtained from the Centre d'Etudes Structurales et d'Analyses des Molécules Organiques (CESAMO), Université de Bordeaux.
Dynamic light scattering The measurements were performed on a Malvern Zetasizer nanoS apparatus thermostated at 20 °C. The size distribution was calibrated with latex particles of 65 and 200 nm radii. The scattering intensity data were processed using the instrumental software to obtain the hydrodynamic diameter (D h ) and the size distribution of scatters in each sample. A total of 10 scans with an overall duration of 5 min were obtained for each sample and time point. All data were analysed in triplicate. Melting curves were obtained by recording the mean size as a function of temperature in the range 20 to 70 to 80 °C, using a temperature gradient of 1 °C/ minute The Tm value was obtained from the maximum of the first derivative curve. The protein concentrations usually were in the range of 5-15 μM.
Funding This work was supported by the  French agency for research (ANR)  for funding (Flunucleovir,  ANR-2010-Blanc-1307-01  to A. S. ). This work was granted access to the HPC resources of IDRIS made by  GENCI  ( Grand Equipment National de Calcul Intensif)  under the grants  2010-99636 ,  2011-076378  and  2012-076378  attributed to A. S and B. T. We are grateful to the structural biology facility ( UMS 3033/US001 ) of the  Institut Européen de Chimie et Biologie (Pessac, France ) for access to the Biacore 3000 instrument. We thank  Nathalie Lejal  for technical assistance.
The experiments assigned 2499 HIV-negative subjects randomly to take a combination of two antiretroviral drugs, i. e. emtricitabine and tenofovir disoproxil fumarate (FTC-TDF), or placebo once a day. The subjects were observed for 3324 person-years (median, 1. 2 years; maximum, 2. 8 years). For the studied subjects 10 were revealed to have been infected with HIV at enrollment and 100 became infected with HIV during the follow-up, among which 36 and 64 were in the FTC-TDF and the placebo groups, respectively, implying a 44% reduction in the HIV incidence. Thus the experimental result concludes that oral FTC-TDF could provide protection against the acquisition of HIV infection. For a complete description of the experiment and the data see  [9]  and the Supplementary Appendix available at NEJM.
The same results are obtained if we evaluate dim g, adfg. That is omitted by the length of the calculations. But, using the software Mathematica we found that dim g, adfg = 5 for almost everywhere in R 5 +. The singularities are related to y = 0, z 1 = 0, and w = 0. As conclusions of this analysis, we have that: (i) the dynamical system ((1)-(  5 )) is accessible in the space strictly positive of R 5. (ii) However, the system cannot be linearized neither by a static nor a dynamic state feedback since H 3 is not integrable. The maximum dimension of the part that can be linearized is 2. (iii) In comparison with others models in the literature as the 3D-model in  [23]  (which can be fully linearized by state feedback as it is illustrated in  [24] ), this model is 'maximally' nonlinear, in the sense that, for any single output, the accessible system can be linearized up to order 2.
Acknowledgments The work by  H. Chang  was supported by the new faculty research program 2013 of  Kookmin University in Korea , and by the  MKE  (The  Ministry of Knowledge Economy ),  Korea , under the  ITRC  ( Information Technology Research Center) support program  ( NIPA-2013-H0301-13-2007 ) supervised by the  NIPA (National IT Industry Promotion Agency). Also H. Chang is grateful to  Prof. Hulin Wu  of the  University of Rochester  for some helpful discussions in January 2011.
Immortalized Irak2-deficient macrophage-like cells were generated by Katherine Fitzgerald (University of Massachusetts Medical School, Worcester, MA) from primary macrophages isolated from Irak2-deficient C57BL/6 mice generated by James Watson (University of Texas Southwestern, Houston, TX) and cultured as described  (13). Polymorphism Information-A list of reported SNPs in human IRAK2 (Gene ID: 4615), was obtained from NCBI, National Institutes of Health (Table  1 ). HapMap data were from the International HapMap Project  (14). Plasmids, Cloning, and Site-directed Mutagenesis-Mutations in IRAK2 were introduced into human IRAK2 (AAC50954; Imagenes IRCMP5012D0935D) using a QuikChange XL Kit (Agilent). Gateway-compatible entry clones for IRAK2 or IRAK4 full-length or DD-only or TRAF6 (gift from S.
Sequence Alignments, Structural Analysis, and Homology Modeling-Protein sequences from NCBI were aligned with ClustalX. The homology model for the IRAK2 KD was generated using the MODELLER package (16) as described (  9 ) based on the structure of the IRAK4 KD (Protein Data Bank code 2NRU)  (17). Autoimmune Disease Case-Control Study and Genotyping-The study involved 1,123 patients with systemic lupus erythematosus (SLE) fulfilling at least four of the American College of Rheumatology 1982 criteria for the classification of SLE and 1,184 ethnicity-matched healthy control subjects from a European multicenter collaboration  (18). The SNP was genotyped using a TaqMan HT7500 FAST (Invitrogen) instrument. Colorectal Cancer Cohort and Genotyping-The 613 CRC patients belonged to the population-based PopGen project in Schleswig-Holstein, Germany  (19)  and did not include hereditary non-polyposis colorectal cancer patients.
Genotyping was performed using KASPar assays on demand (KBiosciences, Hoddesdon, UK). Statistical Analysis-For functional experiments, p values were determined using an unpaired Student's t test in Figs. 1 (B,  C,  and F ), 2 (A-D), and 3D. p values are designated as follows: *, p Ͻ 0. 05; **, p Ͻ 0. 01; ***, p Ͻ 0. 001. Statistical analyses for epidemiological associations were performed with SPSS version 20. 0 (SPSS) or with SAS version 9. 2 (SAS Institute). The significance of differences was assessed in contingency tables using Pearson's 2 test and Fischer's exact test. All tests were two-sided, and p values less than 0. 05 were considered to be statistically significant. CRC analysis of prognostic significance was done by the univariate Cox proportional hazard model. Follow-up time was calculated from the date of CRC diagnosis to CRC-specific death or to the end of follow-up.
RESULTS The IRAK2 Variant R214G Is Associated with Reduced NF-B Activation-When searching public databases for reported IRAK2 variants, we identified 12 non-synonymous variants with an estimated frequency of Ͼ0. 1% in Caucasian populations (see Fig. 1A  and Table  1 ). Due to its moderately high reported frequency (9% in Caucasians), we focused here on the rs35060588 (coding arginine to glycine at position 214, R214G). To investigate its ability for downstream signaling, we measured NF-B activation in the HEK293T cell line upon overexpression of Strep-HA-tagged IRAK2 WT and R214G. It was shown earlier that IRAK2 overexpression in HEK293T cells, which do not express TLRs, drives NF-B activation and allows assessment of signaling pathways downstream of IRAK2  (20). Compared with WT IRAK2, R214G showed NF-B activation decreased (hypofunctional) by ϳ45% (Fig.
1B ), which also translated to 45% reduced IL-8 secretion from HEK293T cells (Fig. 1C ), despite comparable expression levels (Fig. 1D ). That reduced NF-B activation is not due to lower expression was confirmed by measuring NF-B activation upon expression of Renilla-tagged IRAK2 WT and R214G constructs; when NF-B-dependent firefly activity values were normalized to Renilla firefly activity (corresponding to the respective expression levels), this ratio was consistently lower for R214G (data not shown). Interestingly, Arg-214, which mapped to the IRAK2 KD coding region (Fig. 1A ), is only found in human IRAK2 (other species show a histidine at this position; see Fig. 1E ), and the change from Arg to Gly or His is expected to be tolerated in the structure according to Polyphen-2 and SIFT server predictions (not shown).
R214G Modulates Colorectal Cancer Survival-Despite its interesting functional phenotype, there is little known about the hypofunctional R214G IRAK2 variant (which occurs in 3% of African Americans and 9% of Europeans), let alone genetic associations of IRAK2 with disease in general. To test whether the functional phenotype might entail an association with certain diseases, we investigated allele frequencies in well documented collectives (see "Experimental Procedures" for details) for the autoimmune disease SLE and for CRC, in both of which TLR pathways have been implicated  (26, 27). First, IRAK2 association with SLE was analyzed in a case-control study of 1,123 patients and 1,184 controls. Interestingly, the rs35060588 GG genotype was less frequent in cases (0. 0026%) than controls (0. 0068%), but due the low frequency of homozygosity, this difference was not statistically significant (data not shown).
Acknowledgments-We thank Birgit Kaiser ,  Beate Pömmerl ,  Celine Coppard ,  Manfred Kögl ,  Lisa Waggoner ,  Kevin Dennehy ,  Stefan Wiemann ,  Stefan Pusch ,  Matthias Gstaiger ,  Tilmann Bürckstümmer , and  Hans-Peter Duerr  for technical support, helpful discussions, reagents, and statistics advice. Kate Fitzgerald  and  James Watson  kindly provided Irak2-deficient cells.
Acknowledgments. The project was supported under the  EU ITN Marie-Curie program  (CARMUSYS, Grant number  213592 ). The  CM1102 COST Action Multiglyconano  is also acknowledged. FF thanks the  Institut Universitaire de France  for financial support. A. Berzi  was supported by a fellowship of  University of Milan  and  Regione Lombardia (Programma "Dote Ricerca-Rafforzare il capitale umano", POR-Ob. 2Asse IV-FSE 2007-2013). This work has been conducted thanks to the access to the SPR and MP3 platforms of the Partnership for Structural.
Flow cytometry All reagents used for flow cytometry were purchased from BD-Biosciences (Le Pont de Claix, France). Cell suspensions were first incubated with anti-FccRIII/II (2. 4G2) monoclonal antibodies (mAbs), then stained in PBS with 0. 1% bovine serum albumin (BSA) using saturating amounts of the following mAbs: phycoerythrin-conjuguated (PE) anti-CD3 (BD-Biosciences), biotinylated anti-CD19, biotinylated anti-CD11c, biotinylated anti-CD45. 1 (eBioscience, San Diego, USA), PE-conjuguated anti-CD11b (BD-Biosciences), allophycocyanin-conjuguated MHC-II (eBioscience, San Diego, USA) and PE-cyanin 7 conjuguated streptavidin (BD-Biosciences). Dead cells were excluded using 7-actinomycine D (Sigma Chemical Co, St. , MO) staining. Cells were analyzed on a LSRII cytometer (BD-Biosciences) using Flowjo or Diva software (BD-Biosciences) or sorted on Mo-Flo cell sorter (Beckman-Coulter).
Financial support for this study was obtained from  PERSIST  ( EC FP7  large-scale integrating project  GA nu222878 ) to AG,  Fondation pour la Recherche Medicale  and the  French Ministry of Research via Ecole Doctorale   B2T ,  University Paris Diderot  to A. G and S. C. and from the  LOEWE Center for Cell and Gene Therapy Frankfurt  funded by  Hessian Ministry of Higher Education, Research and the Arts  ( III L 4-518/17. 004(2010) ) to C. J. B. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
ESCIENCE AND OPEN ACCESS TO DOCUMENTS AND RESEARCH DATA Since the 19 th century, journals have become the central vector of scientific communication  (Fredriksson 2001) , with most of the scientific work being disseminated via evaluated articles. The digital revolution deconstructed and fragmented the unity of the text, eroding the notion of a monolithic 'document' in the hypertext paradigm and disintegrating the article in several distinct elements. At the same time and partly due to fragmentation, authors and publishers growingly enrich the article with new contents and features, such as multimedia, collaborative tools and data  (Cassella & Calvi 2010). Today, more and more scientific results are disseminated as datasets in digital formats, sometimes connected to, sometimes in competition with publications 2.
Availability of datasets and online access created another world, or rather, another way of seeing the world of scientific information. After the digital revolution, does this mean the end of scientific publications? -In the age of genomic-sized datasets, the biomedical literature is increasingly archaic as a form of transmission of scientific knowledge for computers‖  (Blake & Bult 2006). Perhaps the -data deluge‖ will not substitute academic publishing, the written word remaining essential for humans, but it already transforms publications in different ways. Until now, data were part of publications as support for argumentation and hypothesis testing or for illustrative purpose. In digital scholarship, new publication formats integrate data that can be updated, enriched, extracted, shared, aggregated and manipulated  (McMahon 2010).
Data vehicle: Enhanced publications or companion versions of published articles can serve as data carrier or database for content-dependent cross-querying of literature 4. For example, enriched articles can contain ‗lively' and interactive content such as -interactive figures, semantic lenses revealing numerical data beneath graphs, popups providing excerpts from cited papers relevant to the textual citation contexts (or) re-orderable reference lists‖  (Shotton 2012). Gateway to data: Increasingly publications contain links to research data, either in the text or as part of the metadata. The reader (user) of the document can access the underlying research results but the data are not integrated into the document and bothdata and documentcan be used and reused separately. For instance, this is the case when theses and dissertations are published on an institutional repository while related spreadsheets or survey results are deposited on a data repository.
Text and data files are interconnected but they have two different metadata sets and they are archived on different servers  5. One part of these data is freely available, especially on servers that meet the criteria of open access. For example, over 8,500 social sciences datasets are aggregated in the European CESSDA-portal, 6  and in the arts and humanities, digital research data can be retrieved via the DARIAH project. 7 However, the access to many other research data is restricted or impossible. Savage & Vickers (2009)  complain that the accessibility and the potential of datasets for reuse are often neither optimal nor effective, because of failing standards, metadata, identifiers or services. As for documents, availability and openness of data is not a simple on/off concept but a continuum between more or less open and restricted solutions ranging from the simple availability on the web of data on the lower end of the scale to data dissemination in non-proprietary formats and open standards as optimal openness 8.
Shotton (2012)  discriminates between four levels in which data can be made available together with published papers. The first two levels correspond to the -data vehicle‖ mentioned above, where data are published together with a paper or as a part of it: -1 Supplementary information files available Supplementary information files are available from the journal Web site, and/or the figures and tables containing research data within the article are available for download. However, the formats for these entities are not optimised for reusefor example, figures and tables from PLoS journal articles are only available in TIFF or PNG image format.
Article data downloadable in actionable form The data contained within the figures and tables of the article, and within its supplementary information files, are available in appropriate actionable formats, for example numerical data in downloadable numerical spreadsheets or CSV files. ‖ The other two levels described by  Shotton (2012)  concern the situation where research data are published independently from a paper, i. e. where the paper has the function of a gateway to underlying datasets: -3 Underlying datasets published The full research datasets created during the research project, from which the sub-set of data included within the published article has been selected, are published in a permanent archive or repository, with a unique resolvable identifier (e. g. a URI or a DataCite DOI), with an open access data license or a CC Zero waiver and public domain dedication, and with sufficient descriptive metadata to enable their re-interpretation and reuse.
Data available to peer-reviewers In cooperation with the journal, the datasets supporting a journal article are made available to peer reviewers, to assist in evaluation of the article. This is usually achieved privately, prior to the publication of these datasets at the same time as the article. ‖ The last two options fit better with strategies in favour of open, digital science and free and unrestricted access to public research results, because they guarantee high quality standards and allow liberal reuse and exploitation of datasets.
DIGITAL PHD THESES AND RELATED RESEARCH DATA Significant part of academic -grey literature‖  (Schöpfel & Farace 2010) , produced and published by universities, PhD theses are documents submitted in support of candidature for a PhD or doctorate degree presenting an author's research and findings  (Juznic 2010). Theses and dissertations are -the most useful kinds of invisible scholarship and the most invisible kinds of useful scholarship‖  (Suber 2012). However, more and more PhD theses are available in open access through institutional repositories, i. e. open archives -serving the interests of facultyresearchers and teachers -by collecting their intellectual outputs for long-term access, preservation and management‖  (Carr et al. , 2008). In 2014, the international directory OpenDOAR listed more than 1,200 institutional repositories with electronic theses and dissertations, representing roughly half of all registered open archives.
In the new ETD infrastructures, such material is submitted and processed together with the text files or as supplementary files in various formats, depending on disciplines, research fields and methods. If disseminated via open repositories, these research results could become a rich source of research results and datasets, for reuse and other exploitation. An informal survey among 92 US academic libraries requiring ETD shows that roughly 40% allow deposit of supplemental material 9. The problem is that most of this material is not produced massively or in standard formats, sometimes structured, often semi-or unstructured, and therefore not part of the so-called -big data‖ of eScience, like those data from important equipments or projects like the Large Hadron Collider or the Human Genome Project, or shared via open and networked data repositories such as the SkyServer 10  or the Galaxy Zoo 11.
Material accompanying ETD most often is small data or -little science‖, largely hidden and unexploited, with a Janus-faced status, both publicly funded and personal production, and its large variety (but also its sometimes uncertain copyright protection) affects the accessibility, openness and reusability of this material. Searching through library catalogues, bibliographic databases and repositories (DANS, DART Europe, NDLTD, SUDOC, EThOS etc. ) but also in data repositories and with aggregators such as the DataCite metadata search engine produces anecdotic evidence on this material, in all disciplines but mostly non-indexed, in a great variety of forms and contents, e. g. maps, tables, speech samples and other sound recordings, photos, videos, reproductions of originals or manuscripts, spreadsheets, raw data about molecular modelling, non-encoded survey responses, questionnaires, worksheets, notebooks or collaborative activity, interview transcriptions, graphics, didactic sequences, statistics, glossaries and terminology, canvas and groundwork, graphical data or workflows models, evaluation checklists etc.