dataesr/scientific-paragraphs-categorization huggingface dataset:
Comparison with benchmark methods To assess the accuracy of our automated method, after random extraction of an analysed cell subset, three independent experimenters performed manual measures of the selected criteria as cell body area, CI and CEA. Statistical tests carried out by region showed the same trends between the control and LPS groups whatever the method considered (Additional file 7A). It is to be noted that the analysis time per cell is multiplied by 10 between the automated method and the manual method and the number of cells studied by condition is 400 times lower (Additional file 7C). We also tested whether the results of the analysis were not software specific. Using a semi-automatic analysis with the Fiji software environment on a greater number of cells than in the manual comparison, we did not find any difference in the morphological criteria between the semi-automatic and automatic methods in each region.
Cell heterogeneity by condition Although no difference was observed between the mean CI or CEA of the microglial cells in the two conditions, considering every cell of every brain in each condition, we found a high cell heterogeneity between the samples using Kruskal-Wallis test (p < 0. 0001) illustrating the biological variability across individuals (Additional file 8), whatever the morphological criteria tested. Such variability does not allow us to compare directly populations using classical statistical studies. Moreover, in order to distinguish sub-populations in our large datasets of cells, we pooled all the microglial cells from each group by region and also conducted a new statistical study using a clustering method.
It divides the data into k clusters, minimizing the squared distance between each data point to the centre of its cluster. The main interests of this algorithm are its speed and ease of interpretation, and it is particularly adapted for identifying sub-groups in a large dataset by cellular heterogeneity recognition  [53]. The principal limitations are that it requires an a priori specification of the number of cluster centres and has a strong sensitivity to outliers and noise. Together with Kongsui and colleagues  [54]  in a recent study interested in the structural alterations of the microglial cells within the prefrontal cortex in rats following LPS injection, we do not find any statistical difference in the mean values of CI or CEA. Kongsui and colleagues raise the hypothesis (i) that microglial process alteration is a later phenomenon or (ii) that a substantially larger group of cells studied associated with improved analytical approaches may reveal differences.
Funding This work was supported by the  Fondation des Gueules Cassées , the  Comité d'Interface SFAR  ( Société Française d'Anesthésie-Réanimation ),  SRLF  ( Société de Réanimation de Langue Française) ,  INSERM  and the  Fondation Pierre Deniker. Franck Verdonk  received financial support from  ANRT  ( Association Nationale de la Recherche et de la Technologie ) through an  Air Liquide-CIFRE  contract  2012/1315. The Imagopole is part of the  France BioImaging infrastructure  supported by the  French National Research Agency  ( ANR-10-INSB-04-01 , "Investments for the future") and is grateful for support from the  Conseil de la Region Ile-de-France  ( programme Sesame 2007 , project  Imagopole ,  S. L. Shorte ). SS's work was supported by the  Wellcome Trust  ( 095931/Z/11/Z ; awardee  Jason Swedlow ,  Dundee University  and SLS local partner).
We complement the data of the 2015 outburst with those collected by SPI in 2004-2005 and left unpublished so far. Results. We find a highly significant anti-correlation of the centroid energy of the fundamental CRSF and the 3-100 keV luminosity of E1 ∝ -0. 095(8)L37 keV. This trend is observed for both outbursts. We confirm the correlation between the width of the fundamental CRSF and the X-ray luminosity previously found in the JEM-X and IBIS dataset of the 2004-2005 outburst. By exploiting the RXTE/ASM and Swift/BAT monitoring data we also report on the detection of a ∼ 34 d modulation superimposed on the mean profiles and roughly consistent with the orbital period of the pulsar. We discuss possible interpretations of such variability.
2015). During this outburst, INTEGRAL carried out four observations between July 17 and October 9, covering both the rise and the decay of the outburst. In this work, we present the spectral results on the cyclotron line luminosity dependence, obtained using the SPectrometer on Integral (SPI) collected during both the source outbursts in  2004-2005 and 2015. We complemented the analysis using JEM-X and IBIS data collected during the same periods, when possible (see the next section). The observation and data analysis are described in Sect. 2. In Sect. 3, we present and discuss the results from the spectral analysis. In Sect. 4, we report the identification of a ∼ 34 d modulation superimposed on the profiles of the 2004-2005 and 2015 outbursts. Finally, in Sect. 5, we summarize our findings.
Observations and data analysis The European Space Agency's International Gamma-Ray Astronomy Laboratory (INTEGRAL), launched in October 2002, carries three co-aligned coded mask telescopes sensitive in the X-and gamma-ray bands. We analyze the data from the SPectrometer on Integral (SPI;  Vedrenne et al. 2003; Roques et al. 2003) , the Joint European X-ray Monitor (JEM-X;  Lund et al. 2003) , and the Imager on Board the INTEGRAL Satellite (IBIS;  Ubertini et al. 2003). The former operates in the 20 keV-8 MeV energy range, with a 2-8 keV energy resolution, the second is made of two independent units, JEM-X1 and JEM-X2, sensitive from 3 keV to 34 keV, with an energy resolution of 10-15%, and the latter operates in the energy range from 15 keV to 600 keV with energy resolution of 6-7%. For SPI, we performed the analysis using the SPI Data Analysis Interface (spidai) software provided by the SPI team at the IRAP Toulouse 1 and the SPI iterative Removal Of Sources (spiros) task within the Off-line Science Analysis (OSA) 10.
2 software provided by the ISDC Data Center for Astrophysics  (Skinner & Connell 2003; Courvoisier et al. 2003). The results obtained with the two softwares have been compared and found to be in good agreement. However, owing to a better response characterization below ∼ 25 keV, spidai is better suited for the specific case of V0332+53, where a broad CRSF at ∼ 27-30 keV is present. Therefore, only spectra obtained with spidai are considered in the following analysis. Spectra are obtained from a sky model fitting procedure and a background based on empty field observations (see  Jourdain & Roques 2009  for a description of the method). V0332+53 was the only bright X-ray source in the field of view, hence the contribution of any other source can be safely neglected in the sky model. Nonetheless, pointings with unusually high background activity were excluded.
2006; Tsygankov et al. 2006)  to apply the same model and definition of flux as in the rest of the present paper (see below). For the 2015 data, the current version of the software produces IBIS spectra with significant differences from the SPI ones, preventing their utilization for the present work. This is due to the aging of the instrument, which is not optimally accounted for in the software and calibration files, yet. We analyzed the public data of the TOO observations of the last two outbursts of V0332+53, corresponding to the INTEGRAL revolutions  272, 273, 274, 278, 284-288, 1565, 1570, 1596 (no   of view. The log of observations is reported in Table  1. During the spectral fitting, for the JEM-X and IBIS spectra, we considered 1% systematic errors; we ignored SPI and IBIS data below ∼ 22 keV because of uncertainties in the energy response  (Jourdain & Roques 2009) ; no systematic uncertainties are added to the SPI spectra.
1999 ) and isotropic emission. We note that the slope of the power law and the cutoff energy of revolutions 278, 1565, and 1570 are significantly different from the values obtained from the other data sets. In general, there is a strong mathematical degeneracy between these two parameters for our datasets, but we have verified using confidence contour representations that in all cases, the statistical improvement is significant. This is suggestive of a subtle difference in the spectra, which would be anyhow difficult to interpret using phenomenological models. On the other hand, the limited statistics of these datasets prevents us from using more complex, physically motivated models, which have more free parameters. The parameters describing the continuum are consistent with previous results  (Mowlavi et al.
(2006)  cannot be carried out. Cusumano et al. (2016)  studied the evolution of the fundamental CRSF during the 2015 outburst of V0332+53 using Swift data. Our measurements of E 1 are consistent with those of  Cusumano et al. (2016)  if the latter are shifted in energy by ∼ 1 keV. Such discrepancy is most likely due to calibration systematics between the two instruments. Moreover,  Cusumano et al. (2016)  found that the E 1 vs. L 37 slopes in the rise and decay phases of the outburst are significantly different, causing an increase of ∼ 1. 5 keV of the cyclotron energy E 1 from the onset to the end of the outburst. This would correspond to a drop of about 1. 7 × 10 11 G of the magnetic field in the photon emitting region. In our dataset, we have only three points, therefore our sensitivity to different trends is limited.
Summary We have reported results of the spectral properties of V0332+53 during the 2004-2005 and 2015 giant outbursts, based on SPI, JEM-X, and IBIS observations. We showed that the spectral parameters describing the continuum are consistent with previous results. The correlation of the centroid of the fundamental CRSF and the 3-100 keV luminosity is E 1 ∝ -0. 095±0. 008L 37 keV. The value of the slope lies between the slopes determined by  Cusumano et al. (2016)  for the ascending and descending phases of the 2015 outburst, while a direct comparison with the results by  Tsygankov et al. (2006)  is hampered by the different spectral model adopted by these authors. Using SPI data of the 2004-2005 outburst and left unpublished so far together with JEM-X and IBIS data, we confirmed a significant correlation between the absorption line width of the fundamental CRSF and the 3-100 keV luminosity previously found by  Mowlavi et al.
(2006)  in the JEM-X+ISGRI dataset of the same outburst. We found a modulation at ∼ 34 days superimposed on the 2004-2005 and 2015 outburst profiles in RXTE ASM and Swift/BAT lightcurves, with maxima shifted of 10-15 days after the periastron passage. Such modulation in the lightcurve of a neutron star powered by an accretion disk can be explained with an enhanced amount of matter gravitationally captured at periastron and spiraling inwards (on a timescale that depends on the dimension of the disk and its viscosity properties) until it is accreted on the surface of the neutron star.
Acknowledgements. CF thanks  G. Cusumano  for his constructive comments on our manuscript and for discussing Swift/BAT results. LD acknowledges  Jean-Pierre Roques ,  Elisabeth Jourdain , and  James Rodi  for their precious help on the use of SPIDAI. LD and MK acknowledge support by the  Bundesministerium für Wirtschaft und Technologie  and the  Deutsches Zentrum für Luft und Raumfahrt  through the grants  FKZ 50 OG 1602  and  50 OR 1207 , respectively. This paper is based on data from observations with INTEGRAL, an  ESA  project with instruments and science data centre funded by  ESA  member states (especially the PI countries:  Denmark, France, Ger-many, Italy, Spain, and Switzerland ),  Czech Republic and Poland , and with the participation of Russia and the  USA.
Verification and authentication The cell line was analysed for genome stability by G-banding and showed a normal 46XX female genotype (Fig. 4 ). SNP genotyping was carried out using the Illumina HumanCytoSNP-12 v2. 1 BeadChip and revealed a 3. 6 Mb Copy-Neutral Loss of Heterozygosity (CN-LOH) on chromosome 2 (Chromosome 2p16. 2-16. 1) as described in  Canham et al, 2015. While CN-LOH can be constitutional acquired CN-LOH can occur during oncogenic transformation however such changes are almost exclusively telomeric or greater than 25Mb when interstitial  (Kearney et al, 2011; Stephens et al, 2006). This region was cross-referenced to the Genomic Imprinting database (http://www. geneimprint. com) (Falls et al, 1999)  and was found not to reside in an imprinted region, although CCDC85A in the CN-LOH is predicted, but not validated, to be imprinted on this database.
SNP Genotyping and Analysis DNA samples were assayed using the Illumina HumanCytoSNP-12 v2. 1 BeadChip. Genotyping data was initially assessed using GenomeStudio genotyping module (v1. 94, Illumina). Karyostudio (v1. 4, Illumina)  was employed to perform automatic normalisation and to identify genomic aberrations utilising default settings of the built-in cnvPartition algorithm (3. 07, Illumina) to generate B-allele frequency and smoothened Log R ratio plots for detected regions. These parameters are designed to detect CNVs greater than 75 kb and CN-LOH regions larger than 1 MB with a confidence value greater than 35. All identified regions were first cross-matched to the Database of Genomic Variants.
Acknowledgements Research culminating in the derivation of this line was funded by a grant ( PM07321 ) from  Scottish Enterprise Economic Development Agency  to PDS, MB, and AC. Research culminating in SNP genotype analysis of the cell line was funded by a  Medical Research Council   RMRC project grant  ( MR/K017276/1 ) and  The Cure Parkinson's Trust  to TK and MAC. We thank the transgenic service core facility at the  Scottish Centre for Regenerative Medicine (Edinburgh)  for the teratoma work.
This article introduces RELPRON, a large data set of subject and object relative clauses, for the evaluation of methods in compositional distributional semantics. RELPRON targets an intermediate level of grammatical complexity between content-word pairs and full sentences. The task involves matching terms, such as "wisdom," with representative properties, such as "quality that experience teaches. " A unique feature of RELPRON is that it is built from attested properties, but without the need for them to appear in relative clause format in the source corpus. The article also presents some initial experiments on RELPRON, using a variety of composition methods including simple baselines, arithmetic operators on vectors, and finally, more complex methods in which argument-taking words are represented as tensors.
We make an analogous call here, for a wider range of compositional phenomena to be investigated in compositional distributional semantics in the near future. This article begins to answer that call by presenting RELPRON, a data set of noun phrases consisting of a noun modified by a relative clause. For example, building that hosts premieres is a noun phrase containing a subject relative clause (a relative clause with an extracted subject), and in our data set describes a theater; while person that helicopter saves contains an object relative clause, and in our data set describes a survivor. The RELPRON data set is primarily concerned with the analysis of a particular type of closed-class function word, namely, relative pronouns (that, in our examples); function words have traditionally been of greater concern than content words for formal semantics, and we address how this focus can be extended to distributional semantics.
Relative clauses, although still fairly short and therefore more manageable than full sentences, are nevertheless more grammatically complex than the short phrases in previous data sets, because of the relative pronoun and the long-distance relationship between the verb and the extracted argument-known as the head noun of the relative clause (building, person). The aim of RELPRON is to expand the variety of phrase types on which compositional distributional semantic methods can be evaluated, thus helping to build these methods up step-by-step to the full task of compositional sentence representations. RELPRON is a large (1,087 relative clauses), corpus-based, naturalistic data set, including both subject and object relative clauses that modify a variety of concrete and abstract nouns. The relative clauses are matched with terms and represent distinctive properties of those terms, such as wisdom: quality that experience teaches, and bowler: player that dominates batsman.
A unique feature of RELPRON is that it is built from attested properties of terms, but without the properties needing to appear in relative clause form in the source corpus. This article also presents some initial experiments on RELPRON, using a variety of composition methods. We find that a simple arithmetic vector operation provides a challenging baseline, in line with existing literature evaluating such methods, but we are able to match this baseline using a more sophisticated method similar to the Practical Lexical Function (PLF) model of  Paperno, Pham, and Baroni (2014). We hope that the compositional methods presented here will inspire new approaches. The remainder of the article is organized as follows. Section 2 provides some motivation for the RELPRON data set and the canonical ranking task that we imagine RELPRON being used for, as well as a description of existing data sets designed to test compositional distributional models.
Motivation for RELPRON Relative clauses have been suggested as an interesting test case for compositional distributional semantic methods by  Sadrzadeh, Clark, and Coecke (2013)  and  Baroni, Bernardi, and Zamparelli (2014). One of the main inspirations for RELPRON is the pilot experiment of  Sadrzadeh, Clark, and Coecke,  in which terms such as carnivore are matched with descriptions such as animal who eats meat. However, the data set is small and all examples are manually constructed. RELPRON aims to provide a larger, more realistic, and more challenging testing ground for relative clause composition methods. RELPRON falls into the general category of cross-level semantic similarity tasks  (Jurgens, Pilehvar, and Navigli 2014) , which involve comparing phrases of different lengths; in this case, a single word with a short phrase.
However, the definitions of Kartsaklis, Sadrzadeh, and Pulman were mined from a set of dictionaries, whereas the RELPRON relative clauses are not limited to dictionary definitions. Because there is an intuitive definition-like "flavor" to some relative clauses, we considered using dictionary definitions as a source of relative clauses for the data set. However, in practice we found that short, natural definitions in relative clause format are rare in dictionaries. For example, definitions for the word telescope from three different dictionaries, two of them learner dictionaries, are shown in Example (1). telescope a monocular optical instrument possessing magnification for observing distant objects (Wiktionary) telescope an important tool for astronomy that gathers and focuses light (Simple Wikipedia) telescope a cylinder-shaped device for making objects that are far away look nearer and larger, using lenses and curved mirrors (Cambridge Advanced Learner's Dictionary) (1) Only the Simple Wikipedia definition uses a relative clause to define the term, and would still require significant editing to shorten the phrase.
We say subject relative clause or object relative clause (or subject property or object property) to indicate which argument of the verb has been extracted. The head noun of the relative clause is the extracted noun, and is a hypernym of the term; for example, device is a hypernym of telescope. The subject or object that remains in situ in the clause we call the argument of the verb, and the general term for the subject or object role is grammatical function. The relative clauses in RELPRON are restrictive relative clauses, because they narrow down the meaning of the head noun. In contrast, a non-restrictive relative clause provides incidental situational information; for example, a device, which was in the room yesterday. Our goal was to construct a data set containing at least 1,000 properties in the form of relative clauses.
To make the ranking task more challenging, we chose groups of terms that share a head noun. For example, telescope, watch, button, and pipe are all subclasses of device, so their relative clauses will all begin device that. Because the relative clauses are not definitions, each term can be associated with multiple properties; we selected between four and ten properties per term. The construction of RELPRON also takes a novel approach to producing evaluation data sets that target a particular grammatical construction. Rather than mining examples of the construction directly from a corpus, which may be difficult because of data sparsity, the properties in RELPRON did not have to occur in relative clause format in our source corpus. Instead, the properties were obtained from subject-verb-object (SVO) triples such as astronomer uses telescope, and joined with head nouns such as device.
The head nouns are also attested in the corpus as heads of relative clauses in general, though not necessarily with these specific properties. The relative clauses in RELPRON are therefore naturalistic, plausible, and corpus-based, without having to be attested in the exact relative clause form in which they ultimately appear in the data set. The canonical task on the RELPRON data set is conceived as a ranking task. Given a term, a system must rank all properties by their similarity to the term. The ideal system will rank all properties corresponding to that term above all other properties. This is analogous to an Information Retrieval task  (Manning, Raghavan, and Sch ütze 2008) , where the term is the query and the properties are the documents, with the identifying properties for a given term as the relevant documents.
The RELPRON Data Set One challenge in targeting specific grammatical constructions for evaluation is that the more linguistically interesting constructions can be relatively rare in text corpora. The development of RELPRON takes a novel approach, using a syntactic transformation to assemble properties in relative clause form without the properties needing to appear in this syntactic form in the source corpus. The properties were obtained from SVO triples such as astronomer uses telescope, and joined with head nouns such as device, a hypernym of telescope, to create the relative clause device that astronomer uses. The source corpus used for constructing the data set was the union of a 2010 Wikipedia download and the British National Corpus (BNC)  (Burnard 2007 ). Here we describe the steps in the construction of RELPRON.
Manual Annotation of Properties The manual annotation step was the stage at which candidate head nouns, terms, and properties were filtered for the final data set. Only terms with at least four good properties, and head nouns with at least four terms, were retained after this step. Annotation was continued until the data set reached the desired size. Most of the SVO triples extracted from the corpus did not make good identifying properties for their terms. In many cases the SVO triple represented a property which, although it could be true of the term, did not distinguish it from other terms, especially from other hyponyms of the same head noun. Thus player that wins tournament is not a good property for golfer: many golfers do win tournaments, but so do other sports players. Similarly, organization that money helps is an accurate description of a charity, but does not distinguish it from other types of organizations.