dataesr/scientific-paragraphs-categorization huggingface dataset:
Reads were assembled reads into contigs using a GS De Novo Assembler (Roche) with the following parameters: minimum overlap length of 35 bp, minimum identity of 98%. ORF searching was performed using Prodigal  [55] , and ORFs were blasted against the NCBI non-redundant database (BLASTP, E,1e 205 ). When possible, phylogenetic trees of the ORFs of contigs, encoding proteins that were associated to potential bacterial pathogens, were built. Regions that were homologous to the translated ORFs were searched using BLASTP against the nonredundant NCBI database. For multiple alignments of the sequences MUSCLE  [40]  was used and then curated by Gblocks  [41]. The phylogenetic tree was built using the PhyML algorithm  [42]  with a bootstrap of 100 and the protein substitution model WAG. These tasks were all performed using the pipeline www.
phylogenie. fr [44]. For the visualization of the phylogenetic trees DrawTree  [45]  was used. Principal coordinates analysis was performed using the correlated tool on the MG-RAST  [56]  metagenomic analysis server, to evaluate similarity between coprolite, soil and modern feces samples at the metabolic taxonomic level. Metabolic classifications were generated by a BLAST search against the SEED database using an E-value ,1e -05, a minimum identity cutoff of 80% and a minimum alignment length cutoff of 20 bp. The data were normalized to values between 0 and 1, distances were calculated using the Bray-Curtis method. The results of the analysis are represented in the Figure  S7  in File S1.
189-bp long fragment of the RNA polymerase C gene was generated, exhibiting 99% of sequence similarity with B. HE965807. 1), B. parapertussis (GenBank Accession No. HE965803. 1, BX640423. 1) and Achromobacter xylosoxidans (GenBank Accession No. CP002287. 1). The obtained amplicon differed in one position (T R C transition) from the B. parapertussis and B. bronchiseptica reference strains. In two positions, the amplicon differed from B. bronchiseptica MO149 strain (T R C transition) as from the reference sequence of A. xylosoxidans (T R C transition and G R C mutation) (Figure S6 in File S1) respectively.
The passage was produced by each French participant three times: (1) during the 'monitored' reading, which was supervised by the English-speaking partner and which led to (2) the 'second reading' in the course of the first recording session, and then (3) the 'final reading' performed during the second recording session 3 months later. Data analysis will allow us to address the following questions relating to the study of phonetic corrective feedback: Céline Horgues and Sylwia Scheuer -What is corrected by the native-speaking partner (henceforth NS)? Segmental or prosodic errors? Phonemic or allophonic deviations? -What is the corrective strategy adopted by the NS? Is it explicit correction, recast, or elicitation? -What is the learner's uptake after receiving feedback? We hope that our data brings a valuable and fairly unique contribution to SLA research, helping to establish which errors get corrected and how it may have implications for setting priorities in L2 pronunciation teaching.
Acknowledgments The  SITAF  project was financed thanks to a research grant obtained from the  Conseil Scientifique de l'Université Sorbonne-Nouvelle Paris 3 (Projet Innovant ,  Jeunes Chercheurs ,  2012-2014 ). Part of the orthographic transcription will be financially sponsored by two research laboratories (LPP,  Univ. Paris3  and  UMR 7110 ,  Univ. Paris7 ). We are very grateful to the SITAF team members for their invaluable help when designing the protocol, recruiting participants, monitoring the recording sessions and transcribing the data. Many thanks to the video and sound engineers at the University for their technical support (among others Charly Comino and Hervé Profit).
Background: Illuminated manuscripts are complex multi-layer and multi-material objects. To this difficulty, from the analytical point of view, is added the impossibility of removing samples from these paintings for the study of their materials and techniques. There are relatively few analytical methods that satisfy these constraints as the availability of non-invasive techniques adapted to painted manuscripts is limited and mainly focused on the characterization of inorganic compounds. In the context of a research project on the analytical study of the forty miniatures in the Marcadé collection (Treasury of the Saint-André Cathedral of Bordeaux, XIII to XVI century), the potential of two non-invasive methods, hyperspectral imaging (HSI) and spectrofluorimetry is explored. Results: The methodological development of these techniques as well as preliminary tests on miniatures recreated according to medieval recipes and materials, allowed the validation of the analytical parameters and the creation of a database of reference spectra (parchments, pigments, binders).
Fiber Optics Reflectance Spectroscopy (FORS) FORS analysis was performed with a system marketed by Ocean Optics composed of a HL2000 tungsten light source (20-watt bulb) optimized for the VIS-NIR (360-2000 nm). A FVA-UV variable attenuator is added to control the light intensity. Fiber optic reflection/backscattering probes are used for measuring specular or diffuse reflectance and fluorescence. Six illumination fibers are set around one read fiber of 200 μm diameter. The RPH-1 aluminum probe holder allows us to position the fiber with an angle of 45°or 90°. Data were carried out using R software and curves with Excel.
Spectrofluorimetry Fluorescence measurements were performed using a Jobin-Yvon Fluorolog SPEX 212 spectrofluorimeter equipped with a double monochromator on both the excitation and emission beams. The excitation lamp is a 450 W high pressure xenon lamp. A thermoelectrically cooled photomultiplier (Hamamatsu R928) is used for the signal detection, using the photon counting mode. Fluorescence signals are expressed in "counts per second" (cps). Data acquisition and data processing were computer controlled (SpectrAcq Datamax runned by the Grams/32 software). Both excitation and emission spectra (recorded with 4 nm bandwidth) were corrected for instrumental factors. The measurements are made in mode "front face". The emitted light is collected according to an angle of 22. 5°with respect to the excitation beam.
Hyperspectral imaging (HSI) The hyperspectral system is provided by LOT-Quantum Design Sarl and developed by SPECIM (Finland). The CCD camera has a 1600 × 840 pixels resolution; the entrance slit is 30 μm wide. The focal length of the lens is 23 mm. The translation system measures 1. 30 m and was controlled by IDAQ software. The hyperspectral system works horizontally or vertically. Two halogen lamps illuminate the sample. A Prophotonix Cobra slim UV line scan illuminator of 30 cm also allows excitation at 365 nm for UV fluorescence imaging. The treatment of the data cube is performed with ENVI 5. 0 + IDL software. For the study of illuminations, the experimental conditions are: working distance of 31. 5 cm, scan speed at 3 mm/s and exposure time at 25 ms.
The dark blue of the capital letter U is composed of lapis-lazuli (Figure  8 , right). The advantage of this technique is the collection of a reflectance spectrum in each pixel of the image. These spectra are used for the identification of the pigments if a database of reflectance spectra with reference pigments is constituted. To simplify, on red pigments, as we have seen before by FORS, the shape of the spectra and the inflection points of the different pigments are characteristic of  their nature. The comparison of spectra permits a mapping of the different pigments on the painting. Figure  9  is an example of assigning pigments references to the painting from the reflectance spectra. The software assigns a color code (named classification) to each pigment identified on the image (for instance, dark red is associated with cinnabar, orange with orpiment and bright red with cochineal deposited on cinnabar).
Conclusion The methodological development of these techniques as well as preliminary tests on miniatures recreated according to medieval recipes and materials, allowed the validation of the analytical parameters and the creation of a database of reference spectra (parchments, pigments, binders). Hyperspectral imaging allows the study of the entire image and offers a lot of ways to work: comparison of spectra, mapping, principal component analysis and false color images. Hyperspectral imagery was approved to its application to fragile paintings, without damage and could be applied on many Cultural Heritage objects for imagery and identification of materials. However, for a pertinent selection of the parameters to be used with the hyperspectral system, a preliminary database and study of materials under UV and visible light is needed.
Two techniques are needed for the constitution of this database: FORS to Figure  9  Mapping (classification) of the pigments based on spectra comparison: dark blue color corresponds to "azurite", turquoise blue to "lapis lazuli", dark red to "cinnabar", bright red to "cochineal on cinnabar", dark yellow to "orpiment" and pale pink to "white lead". analyze reflectance spectra under halogen light; and spectrofluorimetry under UV light. Spectrofluorimetry has proven to be an effective identification technique for the red pigments and for organic binders as regard the emission and excitation spectra. Fluorimetric analysis and reflection spectrometry are prerequisites and necessary complements to hyperspectral imaging in order to select the best wavelengths function to be used. These methods were compared with X-ray fluorescence spectrometry for the qualitative analysis and mapping of the inorganic elements in a facsimile purposely reproduced by an illumination painter who worked with original medieval recipes for the sake of developing the present study.
Acknowledgements This study is part of a project supported by the  Aquitaine region (France) ,  University of Bordeaux ,  CNRS  and the LaScArBx Cluster of excellence. We thank the cultural institutions of the  Direction Régionale des Affaires Culturelles  for their support and for providing access to the Marcadé collection of manuscripts and  Charlotte Denoël , curator at the  National Library of France. Thanks are also given to  Lydie Bourgeois  and  Alexandre Fargues  for the absorption measurements ( ICMCB, Institute for Condensed Matter Chemistry of Bordeaux ).
Current online dictionaries for learners of Spanish as a second language largely just reproduce their printed counterparts. This report summarizes the advances made in the DAELE, a prototype dictionary for learners of Spanish as a second language that has been designed solely for online publication. The purpose and main features of the macro-and microstructure of the dictionary are briefly described, as well as the methodology whereby the data are collected and the first steps taken to include the most significant collocations by applying a method based on collocational networks.
I N T R O D U C T I O N The DAELE (Diccionario de aprendizaje de español como lengua extranjera, i. e. Spanish learners' dictionary) is an ongoing project which pursues the building of an electronic monolingual dictionary for learners of Spanish as a foreign language at intermediate and advanced language levels. The InfoLex research group from the University Institute for Applied Linguistics (IULA) at the Universitat Pompeu Fabra (Barcelona) has developed the dictionary within the framework of three research projects: the first one devoted to the representation of verbs and adverbs; the second one to nouns and adjectives; [54] and finally, the third one to lexical combinatorics 1. What follows is a description of the main features of the DAELE and a brief consideration of the stage of development of this three-part project.
C O L L E C T I O N O F D A T A In the first instance, the research focused mainly on verbs and nouns, leaving adverbs and adjectives for the second stage. This decision was based on the hypothesis that understanding the behaviour of verbs and nouns and establishing the premises for representing them in a learners' dictionary would facilitate the representation of adverbs and adjectives. The DAELE is a bottom-up project, that is, it is a 100% corpus-based dictionary that builds up meaning representation from scratch, in contrast with most Spanish dictionaries. For all four categories (verbs and adverbs, nouns and adjectives), the lexicographic corpus of analysis is composed of data from the IULA50, the general-domain texts from the IULA Corpus Tècnic (CT-IULA) 2  and texts from the press, the Spanish Web Corpus included in the Sketch Engine ® 3  (SWC), Mark Davies' Corpus del Español 4  (CEsp), and the Corpus de Referencia del Español Actual 5  (CREA).
[55]  semantic roles and syntactic order;  syntactic structure;  detection of grammatical subcategories;  variety of meanings of each word;  phrases. The software used in the compilation and processing of lexicographic data is TshwaneLex ®6 (TLex), a dictionary-writing system that enables the user to export the database to any format required (MS-Word, HTML, etc. ) for its immediate publication. Thus, the website which gives access to a sample of the dictionary, showing the first project results, is easily updated every time a word class is defined. At the moment, a total of 365 verbs are available in the online version. The prototype dictionary is accessible at http://www. daele. eu.
D I C T I O N A R Y E N T R Y S T R U C T U R E The DAELE was conceived not only as a tool to help the user decode language, [57] but also as an encoding aid. Different layers of information allow various description levels. These may be displayed depending on the needs of each user. Special attention has been paid to contextual features, as well as to syntactic and pragmatic aspects, in order to facilitate the encoding process for a non-native speaker of Spanish. One of the most innovative features of the dictionary lies in the entry structure: headwords' senses are firstly organized according to semantic criteria by using signposts which specify the various senses of the headword and the semantic relations between senses  (Battaner 2010). This is bound to contribute to a better understanding of meanings on the part of the learner.
All definitions are corpus-driven in the sense that they are constructed by taking into account the different usage patterns found in the corpora. For the analysis of corpus data and in order to establish the different 'normal' usage patterns of a verb, the method of Corpus Pattern Analysis (CPA) proposed by Patrick Hanks and based on the Theory of Norms and Exploitations (TNE)  (Hanks 2004 (Hanks , 2013) )  was applied. CPA has been firstly applied to Spanish for representing specialised lexical units in general dictionaries  (Alonso 2009). It was in the framework of the DAELE project that it was fully tested and adapted to represent verbs in Spanish. In the case of the DAELE, it must be noted that CPA was originally conceived for the compilation of a Pattern Dictionary of English Verbs 7 for native speakers of English, and not as a dictionary for learners.
C O L L O C A T I O N I N T H E D A E L E Recently the project has dealt with the phenomenon of collocation, i. e. 'lexical co-occurrence of words'  (Sinclair 1991: 170). How words combine in collocations is one of the main difficulties for a learner of the language and questions arise about their use. Collocations have received minimal attention in the Spanish lexicographic tradition. Most Spanish dictionaries do not include information about collocations, or the information provided is so limited that it fails to meet the encoding needs of learners. A database of the collocates of 570 headwords belonging to four semantic fields -i. e. Family relationships, Social relationships, Information and Communication, and Verbal expression -proposed by the Instituto Cervantes 8 has been compiled and is currently under analysis in order to establish which collocates are most useful for the dictionary user.
Information and Communication 123 Verbal expression 185 TOTAL 570 Table  1 : Number of collocation nodes for each semantic field in the database. The database includes information about the collocates found for each of the 570 words in four different sources, consisting of a corpus and three dictionaries -two of them are collocation dictionaries, the third one is a dictionary focused on language use: (a) Spanish Web Corpus In order to clarify these aspects, the mechanism of collocational networks is being tested. This method was proposed by  Williams (1998)  and applied to the DicSci project for the compilation of an E-Advanced Learner's Dictionary of Verbs in Science  (Williams and Millon 2010, Alonso et al. 2011). As defined by  Williams (1998: 156).
F U T U R E W O R K The DAELE is an online corpus-driven learners' dictionary prototype whose conception derives from a practical analysis of language in use. In the previous sections, the building method of the dictionary has been presented, describing the main features and components of the dictionary. While many advances have been made on verbs in the DAELE, there are still aspects to be solved related to the other three word classes. As an ongoing project, the DAELE is not a finished work and some improvements in the interface and compilation process are planned for the near future. [70].
Childhood-Onset Schizophrenia Childhood-onset schizophrenia (COS) constitutes a rare subset of cases typically occurring before 13 y. o. (prevalence ~1/30 000). Despite its rarity, recent studies have shown that schizophrenia can be reliably diagnosed in children and that it is neurobiologically, diagnostically, and physiologically continuous with the adult disorder. 27, 28 Work with the National Institute of Mental Health (NIMH) COS cohort has accrued 2 decades of clinical rating data and a recent report has documented high rates of hallucinations across all sensory modalities. 29 Nearly all COS patients described significant auditory hallucinations. More importantly, a high rate of the cohort reported significant rates of visual hallucinations (80%) during their hospitalizations. 29 High rates for tactile (60%) and olfactory (30%) hallucinations were observed in this pediatric sample, which occurred exclusively in patients with visual hallucinations.
As Smeets et al  55  observed, the combination of hallucinations and delusions, rather than either one in isolation, may contribute to a persistence of symptoms and a deterioration in clinical outcomes. The results of Smeets and colleagues were based on data collected at 2 time points from the Early Developmental Stages of Psychopathology (EDSP) Study in a large representative general population sample of adolescents and young adults (mean ages 21. 8 and 26. 6 years, respectively). In children, associations between ToM and AVH, and the role of delusion formation, have also been examined. In a prospective longitudinal birth cohort study in Great Britain (following 2232 children), it was demonstrated that 12 y. o. children with psychotic symptoms (including AVH) exhibited impaired ToM at age 5.
Acknowledgments Parts of this review have been presented at the Durham meeting by the working group on " Hallucinations in children and adolescents " (see Waters F, Woods A, Fernyhough C. Report on the 2nd  International Consortium on Hallucination Research (ICHR) : evolving directions and top 10 'hot spots' in hallucination research. Schizophr Bull. 2014; 40: 24-27. ). Several sections of the initial multidisciplinary report (ie, organic disorders, psychometric assessment, developmental toxicology, or therapeutic strategies for early-onset hallucinations) were judged out of the scope of the present review and were not included. We would like to apologize to those whose work was not retained or cited because of space constraints. J. J. is one of the conceptors of the  HIT program  and currently runs a company that delivers HIT therapy.
In an attempt to reclaim the victims' full identities and by cross-referencing names with archives, I have been able to reconstruct a list of victims, where possible, with two complete surnames and the most probable spelling (Table  1 ). Four families were affected by the massacre: the Gil Espinosa family from Alcañiz and Barcelona (four victims), the Pardo Guirao family from Murcia (six victims), the Masachs family from Sabadell (two victims), and the Téllez family from Zaragoza and Barcelona (five victims). However, little information about these victims can be found in the police or administrative archives dating from that time. Since it was the men who were most suspect and most closely watched by the authorities of the day, most of the data refers to them. The two men who were killed in the massacre, José Serrano Robles and Juan Téllez Domínguez, were identified by the authorities as Republican refugees answerable to the 643 rd GTE.
I would like to express my gratitude to the association Ateneo Republicano du Limousin for opening their doors to me during four years of research and to Sandra Gibouin, information officer at the Center of Memory of Oradour-sur-Glane, for the valuable data and materials provided throughout my research. Many thanks go to Sara Varela Mestre and Marije Hristova for their relevant corrections and suggestions when writing this article. 2. On 9 June 1944, in the repression of Resistance fighters who had liberated the city of Tulle, SS Division Das Reich hanged 99 men and deported another 149 to Dachau, of whom 48 survived. See Soulier, 1971. 3. A mere search on Google of the names of the Spanish victims still led, in June 2013, to its website. 4. The temporary exhibition was organized in partnership with Fundación Museo de la Paz de Gernika, the Conseil Général de Haute-Vienne, the University Library for Contemporary International Documentation (BDIC) in Nanterre and Secours Populaire association.
NOTES 1. 1 I would like to express my gratitude to the association Ateneo Republicano du Limousin for opening their doors to me during four years of research and to Sandra Gibouin, information officer at the Center of Memory of Oradour-sur-Glane, for the valuable data and materials provided throughout my research. Many thanks go to Sara Varela Mestre and Marije Hristova for their relevant corrections and suggestions when writing this article. 2. On 9 June 1944, in the repression of Resistance fighters who had liberated the city of Tulle, SS Division Das Reich hanged 99 men and deported another 149 to Dachau, of whom 48 survived. See Soulier, 1971. 3. A mere search on Google of the names of the Spanish victims still led, in June 2013, to its website. 4. The temporary exhibition was organized in partnership with Fundación Museo de la Paz de Gernika, the Conseil Général de Haute-Vienne, the University Library for Contemporary International Documentation (BDIC) in Nanterre and Secours Populaire association.
As from the 1990s, the emergence of electronic publications was seen as something which would revolutionize "post-publication peer review", by allowing comments and criticisms to be added to the document itself  (Lancester 1995). Among existing journals, F1000Research (created in 2012) exemplifies the values of rapidity and open scientific discussion. Electronically submitted manuscripts are published as they arrive, accompanied by their sets of data. Putting them on line triggers an evaluation process which is rapidly performed in accordance with the principles of open review: evaluation reports come with the name and institutional affiliation of the reviewers; the authors can react and produce new versions of their manuscripts; finally, at any time during the process the reports and different versions of the article may be commented upon by readers (open commentary).