dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments The authors thank the athletes and technical staff of  Emmanuel FONTAINE ,  Patrice BINELLI ,  Frédéric BARREDA , and  Cindie DECHAMBRE  for their time. We also thank  Laura BILLON ,  Carole BOIVERT ,  Pascal CHOURROUT , and the  IRBA Molecular Biology Unit  for their technical support. Finally, we thank  Keyne CHARLOT  ( Laboratoire Graphique ) for designing the figures.
Magnetization was measured using a MPMS-XL SQUID magnetometer, operating in 5 K-400 K temperature range with application of an external magnetic field reaching until 5 T. polycrystalline samples La 0. 67 Ca 0. 33-x Sr x Mn 0. 98 Fe 0. 02 O 3 for (x = 0. 15; 0. 2 and. 0. 3). From the obtained results, all the compounds have a single phase without any detectable secondary phase. The data have been refined using the standard Rietveld method using Fullprof software  [17] [18] [19]. At room temperature, we have indexed the XRD data corresponding to x = 0. 15 within a rhombohedral structure with Pnma spatial group. Inside the crystal lattice, La/Ca/Sr take 4c (x, 0. 25, z) Whycoff atomic positions, Mn/Fe are at positions 4a (0, 0, 1/2), O1 are at positions 4c(x, 0. 25, z) and O2 8d (x, y, z). For x = 0.
Study design and population This study is a planned ancillary analysis of the coVAPid cohort study. Briefly, coVAPid was a multicenter retrospective observational European cohort study. Eligibility criteria included age equal or above 18 years, the need for invasive mechanical ventilation for more than 48 h, and one of the following criteria at ICU admission:  (1)  SARS-CoV-2 pneumonia, (2) influenza (A or B) pneumonia, or (3) no viral infection. The Ethics Committee, and Institutional Review Boards approved the study protocol (Comité de Protection des Personnes Ouest VI; approved by April 14, 2020; registration number RIPH:20. 04. 09. 60039) as minimal-risk research using data collected for routine clinical practice, and waived the requirement for informed consent. The study was registered at ClinicalTrials.
Patients and bacterial isolates Five patients, who had valve replacement surgery following IE, were included. Socio-demographic and medical data were extracted from patients' files. A single surgical specimen was taken from each valvular sample, shredded and seeded onto three different chocolate agar Petri dishes (PolyViteX, Biomerieux), respectively incubated in ambient air, 5% CO 2 and anaerobic atmosphere for 48 h each. In order to catch as many diverse isolates as possible, three isolates (1 small, 1 medium and 1 large-sized) from each Petri dish were then subcultured and stored at -80°C for further analysis; i. e. a total of 9 isolates from each valvular sample. Whenever available, isolates taken from BC before surgery, as well as isolates from JF were also included and stored in the same conditions.
Sequence analysis Genomes of each isolate were assembled using shovill 1. 0. 4 (https://github. com/tseemann/shovill), with SPAdes v3. 13. 1  [8] , trimmomatic 0. 39  [9] , and Pilon 1. 23  [10]. Contamination was checked using taxonomy workflow from CheckM v1. 0. 13  [11]. Only contigs > 500 bp were retained for further analyses. We determined the Multi Locus Sequence Type (MLST) for each isolate based on PubMLST profile for E. faecalis (https://pubmlst. org/efaecalis/). The resistome, virulome, and plasmidome were analysed by means of blastN with ABRicate (https://github. com/tseemann/abricate) and Resfinder  [12] , VFDB  [13] , and PlasmidFinder  [14]  databases, respectively. Genomes were annotated on Prokka 1. 13  [15]  using standard parameters. Microdiversity was assessed by Single Nucleotide Polymorphism/Insertion/Deletion (SNP-InDels) analysis, and relied on detecting large deletions.
We observed that a large sequence of 15,600 bp encompassing ebpA, ebpB, ebpC, and srtC was deleted within the genomes of isolates #1. 1 and #1. 2 (Figures  1  and 2 ). Analysis of isolates #1. 1 and #1. 2 sequences revealed the presence of IS1216 directly upstream of the deleted sequences. This IS1216 was also observed downstream of the 15,600 bp segment in the other isolates. A deletion, totalling nearly 20,000 bp, of multiple contigs of probable plasmid origin [blastN matches with pDEF-1 (accession number: CP031028) and pSULI (accession number: CP043327. 1)], involving the fore-mentioned resistance genes (ant6-Ia, aph3 ′ -III, and ermB), was also detected in the sequence of these two isolates and of a third one (#1. 5) (Figures  2  and S1 ). As the entire contigs were deleted from the three isolates, we were not able to analyse the flanking regions.
faecalis V583 (region EF1988 to EF2043, genome accession number AE016830. 1) and replaced by an attB site (TTTGCCACTCCCCATCT-GAAATT) (Figure  4 ). Interestingly, phage pp4 carried two genes that code for PblA and PblB proteins, which promote adhesion to human platelets  [23]. The deleted 18,900 bp sequence carried genes coding for proteins involved in sugar transport, RND and MFS transporters, and other proteins (Figure  S4 ). The small deletion of 2000 bp was found in four isolates (#3. 5, #3. 6, #3. 7, and #3. 8) and corresponded to a small portion of phage pp4. This deleted sequence included two genes coding for hypothetical proteins, tRNA-Trp (EF_tRNATrp2 from E. faecalis V583), and a gene coding for a transcriptional regulator that belongs to ArpU family (EF_2024 E. faecalis V583). The BC isolate displayed the third large deletion of 35,000 bp which corresponded to another prophage, identical to the one found in E.
faecalis strain symbioflor (HF558530. 1) (Figure  S5 ). Phaster analysis revealed the proximity of this phage to Enterococcus phage vB_EfaS_IME197 (accession number: NC_028671. 2). Upon comparing all the isolates together, they differed by at least one non-synonymous mutation, except isolates #3. 1 and #3. 3 which were identical. These mutations concerned genes coding for ribosomal proteins, ADP-ribose pyrophosphatase, PTS system, ribonuclease, transcriptional regulators, and translation initiation factors. The phenotypic analysis of this case covered the isolate which missed pp4 phage sequences (#3. 4) and both isolates from BC and JF (#3. 10 and #3. 11). The closest isolate (#3. 9) was used as a control (Figure  2 ). Growth rate and early biofilm production of the three tested isolates were significantly reduced, although the BC isolate was less affected (Figure  3 ).
Cluster of orthologous groups classification analysis To obtain a more generalized insight into the microdiversity of E. faecalis, we analysed non-synonymous SNP-InDels and large deletions in terms of Cluster of Orthologous Groups (COG) classification. Given the probable phage or plasmid origin of many of the missing genes and their erroneous annotations in available databases, many genes remained unclassified or were put under unknown functions (Figure  5  and Table  S3 ). However, genes in which SNP-InDels were evidencedand to a lesser extent those missing as a result of large deletionswere more often involved in cell cycle functions (e. g. replication, recombination and repair, transcription, translation, and ribosomal structure and biogenesis), as well as in central metabolism (e. g. carbohydrate transport and metabolism).
Cohort characteristics The mean age was 31 years (range 16-60) and 71% (n = 27/38) were male. Ten patients (26%) had documented medical comorbidities. Of patients for whom data regarding smoking and body mass index (BMI) were available (n = 27/38), 7% (n = 2/27) were smokers and the mean BMI was 29. 1 kg/m 2 (range 21. 0-36. 0). All patients reported exercise-induced leg pain preoperatively. Nine patients (24%) had unilateral symptoms and 29 (76%) bilateral symptoms. Sensory disturbance was reported by 11 patients (29%), exercise-induced leg swelling by six patients (16%) and subjective weakness by one patient (3%). The mean duration of preoperative symptoms was 4. 9 years (range 0. 4-42, Table  2 ). There was not a standardised protocol for non-operative management prior to fasciotomy surgery.
The following discussion proceeds in four steps: rst, we explain the rationale behind a crosslinguistic encoding of parliamentary debates. Second, we show why the TEI is a sustainable, reproducible, highly standardized, yet equally exible annotation framework suited to capturing parliamentary interaction. Third, we describe the annotation scheme at the level of the metadata contained in the TEI header, more specically the variables associated with each speaker (each member of Parliament in our case). We also detail the annotation scheme at the level of the text, delineating why the transcription of speech vocabulary should be preferred to a more dramaoriented markup for parliamentary data. Finally, in order to invite further applications of the TEI framework, we discuss documenting and archiving the data from an open-access perspective.
Why a New It should be noted, however, that several projects involving parliamentary data have been launched in the meantime. The GermaParl R data package, a corpus that includes "all plenary protocols that were published by the German Bundestag between February 1996 and December 2016"  (Blätte and Blessing 2018, 810) , has been developed  (Blätte 2017a , Blätte 2017b). Apart from the fact that the period covered by the corpus is by no means comparable to the British House of Commons, it raises problems in terms of transcription that will be addressed below. Furthermore, as the authors acknowledge, "[a] thematically specialized corpus … may oer signicantly more detailed metadata and annotation"  (Blätte and Blessing 2018, 810). A provisory version of other annotated French parliamentary debates was also created  (Diwersy, Frontini, and Luxardo 2018)  after the rst release of the corpus in November 2016 (see sec.
We carried out the process of encoding in TEI by combining manual and automatic processing workows, with the idea of keeping both the content and the metadata of the sources. In particular, we used the GROBID software suite, 7 which provides a relatively ecient transformation process from PDFs to a decent TEI format, although not fully compliant with the target encoding scheme. Attention was given to unifying the nal format across the three languages and parliamentary settings so that the same phenomena and features would be encoded exactly in the same way for each sub-corpus.
The TEI Annotation Scheme The Text Encoding Initiative (see  Romary 2008)  has become, since its inception in 1987, the reference technical standard for the representation of textual content in the humanities. Based upon the W3C XML recommendation, it covers a wide range of genres and provides users with a vocabulary of nearly six hundred XML elements. At the core of the TEI Guidelines resides the principle that any TEI-based project should dene its own subset (or customization) where the elements which are deemed useful for the representational task at hand are selected, documented, and possibly amended. In the context of small specialized corpora, TEI annotation can be used to store the "detailed information about the speakers or writers"  (Koester 2010, 72). Linked with "the goals of the interactions or texts and the setting in which they were produced as part of the corpus database means that linguistic practices can easily be linked to specic contextual variables"  (Koester 2010, 72).
Political Speakers: The TEI Element <person> In this part, we describe the metadata attached to the TEI element <person> corresponding to each speaker. In this corpus, the TEI header contains, among others, the metadata (or variables) associated with the environment of the parliamentary debate (organization, place, and date encoded in <settingDesc>: see example 3) and with the speakers (name, sex, political party, political aliation, and position encoded in <particDesc>: see example 1). 11 An important decision was to encode speakers' related information in the header of each document and to associate such descriptions with a group of features relevant for the linguistic analysis of parliamentary discourse. In compliance with the TEI Guidelines, and more specically its Language Corpora module (TEI Consortium 2022, chap.
Both choices could probably be the most problematic ones if we were to carry out a wider dialogue with the scientic community on the standardization process and the encoding of parliamentary debates. In this section, we present the decisions pertaining to the turn level section 5. 1 as well as the intra-turn level section 5. 2. Importantly, we do not address other levels of annotation such as word-level annotation that could have been marked up in TEI as well. Indeed, for the purpose of this project, the results are based on automatic part-of-speech tagging. The open-source software TXM 21  (Heiden, Magué, and Pincemin 2010)  used in this project indeed proceeds to language-specic part-of-speech tagging when a corpus is imported. The element <u> (utterance) in the TEI Guidelines potentially covers any kind of linguistic segmentation in a transcription of a spoken sequence as long as this segment may be attributed to a single speaker.
First, we considered that beyond seeing the corpus as reusable (linguistic) content, presenting the annotation framework as an ongoing process could also play a role as a methodological point of comparison for other comparable endeavors. As a consequence, we decided to distribute all the source documents rather than limiting access through, for example, a query interface, as is the case for the EuroParl corpus. Second, although there are often fears of being plundered when data is disseminated at too early a stage in a research process, the author who compiled the corpus as part of her dissertation project took the decision to have the data online even before the actual doctoral publication was available. 23     The three corpora are available online at the following addresses: • hdl. handle.
Conclusion This paper has suggested an integrative and comprehensive approach to the linguistic annotation of parliamentary discourse that takes into account national specicities and is specically geared to proposing an annotation scheme that is both highly standardized and adaptable. The method is based on the TEI framework. We have argued that the linguistic features of parliamentary interaction call for an annotation scheme distinct from the ways theatrical plays have been accounted for within the TEI community. We have also pleaded for an easily reproducible cross-linguistic annotation framework. Specically, we have shown that including metadata such as political aliation or the distinction between majority and opposition is crucial to allowing for the comparison between several parliamentary systems.
month. day of the debate. 23 One of the points of contention could be that the dissemination through Ortolang is not fully open-source, as it would be through such a platform as GitHub. We see GitHub, which is a private platform and thus does not fulll all our criteria of a sustainable environment, as a possible front end for the further development of such a corpus as ours, while keeping an environment such as Ortolang as the nal publication setting. 24 "Parliamentary Corpora," accessed February 8, 2021, https://www. clarin. eu/resource-families/ parliamentary-corpora.
Auel, Katrin, and Tapio Raunio. 2014. "Debating the State of the Union? Comparing Parliamentary Debates on EU Issues in Finland, France, Germany and the United Kingdom. " Journal of Legislative Studies 20 (1): 13-28. Tomaž Erjavec and Andrej Pančur, Parla-CLARIN: A TEI Schema for Corpora of Parliamentary Proceedings, v. 0. 2, accessed February 8, 2021, https://clarin-eric. github. io/parla-clarin. All les are from the Compte rendu intégral (and not from the Compte rendu analytique when it exists).
Auel, Katrin, and Tapio Raunio. 2014. "Debating the State of the Union? Comparing Parliamentary Debates on EU Issues in Finland, France, Germany and the United Kingdom. " Journal of Legislative Studies 20 (1): 13-28. Tomaž Erjavec and Andrej Pančur, Parla-CLARIN: A TEI Schema for Corpora of Parliamentary Proceedings, v. 0. 2, accessed February 8, 2021, https://clarin-eric. github. io/parla-clarin. All les are from the Compte rendu intégral (and not from the Compte rendu analytique when it exists). 4 Tomaž Erjavec and Andrej Pančur, Parla-CLARIN GitHub repository, accessed February 8, 2021, https://github. com/clarin-eric/parla-clarin/. 5 Accessed February 8, 2021, https://www. clarin. eu/content/parlamint-towards-comparable- parliamentary-corpora. 6 Bayley, Paul, ed. 2004. Cross-Cultural Perspectives on Parliamentary Discourse.
Amsterdam: John Benjamins. Blätte, Andreas. 2017a. GermaParl: Corpus of Plenary Protocols of the German Bundestag. R data package, v. 1. 0. 4. http://polmine. sowi. uni-due. de/packages/src/contrib/GermaParl_1. 0. 4. tar. gz. ---. 2017b. GermaParl: Linguistically Annotated and Indexed Corpus of Plenary Protocols of the German Bundestag. CWB corpus v. 1. 0. 4. 10. 5281/zenodo. 3735141,https://doi. org/10. 5281/zenodo. 3735141. 3.
Patients and Samples Plasma samples and lung biopsies were collected as previously described  (21, 23) , from consecutive patients with advanced (not irradiable stage IIIb or stage IV) EGFR-mutated NSCLC treated by EGFR-TKIs between 08/2011 and 07/2019 at the Department of Respiratory Medicine and Thoracic Oncology (APHP-Ambroise Pare Hospital) and within the framework of the Centre León Beŕard Cancer Center LIBIL (NCT02511288)  (24, 25). All patients were included in the study after written informed consent, as approved by the two Institutional Review Boards (IRB) including the CPP IDF n°8 (ID CRB 2014-A00187-40) and the CPP Ouest 6 (ID-RCB: 2015-A00640-49). Lung biopsies (n = 14) were collected at diagnosis (diagnosis/baseline). Prospective consecutive collection of the plasma was made before the beginning of the TKI treatment, 6-8 weeks after the beginning of the TKI (first evaluation, n = 61), and at disease progression.
Patients Clinical characteristics of patients are described in Table  1. Seventy-four consecutive patients were included in the study. The median age was 67 years old (range, 35 to 90 years old). Patients were mostly females (79. 7%, n = 59) and nonsmokers (66. 2%, n = 49). The main histological type was adenocarcinoma (95. 9%, n = 71). Most patients had a stage IV disease (78. 4%, n = 58) including 29 patients with central nervous system (CNS) metastasis (39. 2%). Forty-seven (62. 2%) NSCLC were Exon 19 mutated, 22 (29. 7%) were L858R mutated patients, and 5 cases were found with another EGFR mutation type (Table  1 ). Only 61 patients with available plasma samples at diagnosis were included in correlative studies because 13 were excluded for missing data and/or no available sample at baseline (Figure  S1 ).
Shh and Gli1 Expression at Baseline To determine whether plasma levels of Shh were associated to patient outcomes, we first used the ELISA assay to analyze levels of circulating Shh in the plasma samples from NSCLC patients. Assessed in 61 samples collected before TKI initiation, the protein expression was readily found in plasma samples with a median of 466. 185 pg/ml (range: 0. 3-11,522. 6 pg/ml) (Figure  1A  and Table  S2 ). The Kolmogorov-Smirnov (KS) normality test confirmed that data were normally distributed (p < 0. 001) (Table  S2 ). We recently provided evidence that the Shh-Gli1 signaling axis is operative in NSCLC, demonstrating that primary lung biopsies from NSCLC express GLI1 transcript and Gli1 target genes including HHIP, PTCH, and JAG2 (20). Similarly, analyzing the mRNA in 14 patients' tissues, we found that NSCLC expressed HHIP, PTCH, and JAG2 transcripts (Figure  1B ), confirming that the Shh signaling is operative in NSCLC (Figure  1B ).
Correlation With Patients' Survival Then, we analyzed patients' survival. Shorter OSs were significantly related to the following parameters: the absence of del19 mutations [hazard ratio (HR) (95% CI), 0. 4A )  (29). However, preclinical data revealed that inhibition of Shh-Gli1/2 signaling is known to sensitize NSCLC to TKI treatment, supporting the fact that level of Shh-Gli1/2 signaling during TKI therapy could reflect or influence treatment outcome and patient survival  (10). Thus, we also analyzed patient survival according to Shh levels in plasma samples at the first evaluation following TKI induction. Interestingly, patients with lower Shh levels at the first evaluation underwent longer PFS (342 vs. 210 days) compared to patients with high Shh levels (HR (95% CI), 0. 578 (0. 2831-1.
Data collection and pathologic evaluation Pretreatment blood-based SII values were assessed within the 30 days prior to TURB. SII was calculated as platelet count × neutrophil/lymphocyte count. SII and demographic, pathologic, and survival outcomes data were collected and entered into a computerized database. The optimal SII cutoff value was defined by creating a time-dependent receiver operating characteristic (ROC) curve to yield the highest Youden index value. Using this score the overall population was divided into two separate SII groups (> 580 vs. ≤ 580). The specimens were reviewed at the beginning of the study at each center by expert genitourinary pathologists. They were blinded to the previous history of the patient and to the clinical development after specimen acquisition. The pathologic stage was reassigned using the 2010 American Joint Committee on Cancer TNM staging system and tumor grade according to the 1973 World Health Organization (WHO) grading system.
In these analyses, we excluded patients who received intravesical BCG therapy due to the changes of treatment strategies depending on the previous BCG therapy. All P 1 3 values were two-sided, and statistical significance was defined as P < 0. 05. Statistical analyses were performed using R version 3. 6. 3 (R Foundation for Statistical Computing, Vienna, Austria) and Stata/MP 14. 2 statistical software (Stata Corp. , College Station, TX, USA).
While we make an effort to cover all relevant aspects, which makes a certain overall length unavoidable, we deliberately organised the article in a way that allows the reader to directly skip to the (mostly self-contained) sections of interest without the need to read all preceding parts. We start by briefly introducing high-energy gamma-ray astronomy and the CTA observatory in Section 2, along with its planned observational strategy for the GC region. We then describe in more detail the expected DM signal and various astrophysical and instrumental background sources in the GC region (in Section 3), as well as the data analysis techniques adopted in our analysis (in Section 4). We present our findings concerning the projected sensitivity of CTA to a DM signal in Section 5; as this is a concise summary of our main results, many readers would typically directly want to jump there.
This implies harder and brighter gamma-ray emission in the innermost Galactic regions, explaining simultaneously the bright Galactic Ridge in the very centre and the large scale diffuse emission measured by Fermi-LAT. This model predicts a relatively bright emission also outside the ridge. • The Pass-8 Fermi IEM was derived based on the detailed analysis of 8 years Pass 8 Fermi-LAT data. 5 Special care was taken for the model to describe the high-energy (≥ 50 GeV) spectrum, and it is, therefore, more reliable regarding high energy extrapolation than previous versions. It uses different gas maps than the Gaggero et al. models and is tuned to the LAT data over the entire sky (as opposed to the Base model, which is more heavily based on theoretical expectations). 6.