dataesr/scientific-paragraphs-categorization huggingface dataset:
Additional file 1 : 1 Figure S1. Phylogenetic analysis of Anaplasma ovis msp4 sequences identified in Corsica and other regions of the world. The figure shows a maximum likelihood phylogenetic tree inferred using msp4 nucleotide sequences of A. ovis of Corsica (Corsica 1-6) and other regions of the world. GenBank accession numbers and country of origin are shown. (PDF 15 kb) Additional file 2: Figure S2. Phylogenetic analysis of Anaplasma ovis MSP4 sequences identified in Corsica and other regions of the world. The figure shows a maximum likelihood phylogenetic tree inferred using MSP4 amino acid sequences of A. ovis of Corsica (Corsica 1-6) and other regions of the world. GenBank accession numbers and country of origin are shown. (PDF 13 kb).
, 2011  for SOA formation) and with the SIze resolved Aerosol Model (SIREAM)  (Debry et al. , 2007)  for aerosol dynamics (coagulation, condensation/evaporation). SIREAM uses a sectional approach and the dry particle diameter is discretized with five sections between 0. 01 µm and 10 µm. The simulations are performed on 14 vertical levels extending from the ground to 12 km. Version 2016 of regional CTM CHIMERE is used for this work  (Menut et al. , 2013; Mailler et al. , 2017). Simulations were conducted using reduced chemical mechanism Modele Lagrangien de Chimie de l'Ozone a l'echelle Regionale 2 (MELCHIOR2), which includes 44 species and 120 reactions, and the aerosol module described in  Bessagnet et al. (2004) (nucleation, coagulation, absorption). This module is also based on a sectional representation of the size distribution.
emep. int, last access: 20 January 2019). The inventory species are disaggregated into real species using speciation coefficients  (Passant, 2002). The aggregation into model species is done following  Middleton et al. (1990). Primary particulate matter emissions are given in total mass by the EMEP emission inventory. They are speciated into dust, primary organic emissions (POA) and black carbon (BC), and distributed into five diameter bins  (Sartelet et al. , 2007). Biogenic emissions of isoprene and terpenes (α-pinene, β-pinene, limonene and humulene) are calculated using the Model of Emissions of Gases and Aerosols from Nature with the standard MEGAN LHIV database MEGAN-L for Polyphemus and MEGAN v2. 04 for CHIMERE  (Guenther et al. , 2006). Sea-salt emissions are parameterized following  Monahan (1986).
The mineral dust emissions are calculated using soil and surface databases  (Menut et al. , 2013)  and with a spatial extension of potentially emitting area in Europe as described in  Briant et al. (2017). The daily fire emissions are detailed in Sect. 2. 2. In Polyphemus, I/S/L-VOC emissions are estimated by multiplying the primary organic emissions (POA) by a factor of 1. 5, following the chamber measurements  (Robinson et al. , 2007; Zhu et al. , 2016; Kim et al. , 2016). The factor of 1. 5 is used for both anthropogenic and fire emissions to estimate the gas-phase I/S/L-VOCs that are not included in the inventories. I/S/L-VOC emissions are assigned to three surrogate species: POAlP, POAmP and POAhP (for compounds of low, medium and high volatilities, respectively), of saturation concentration C * : log 10 (C * ) = -0.
AOD level 2. 0 data (at 550 nm) and Angstrom coefficient α (derived from AOD at 500 and 870 nm) from the AERONET (AErosol RObotic NETwork) ground-based network of sun photometers  (Holben et al. , 1998)  are used. The uncertainty on AOD is estimated to less than 0. 02  (Holben et al. , 2001). AOD level 2. 0 observations are missing in Lecce University (in Italy) during the first event, and in Blida (in Algeria) during the second one. Since AOD Level 1. 5 observations at 500 nm (before filtering) are available for the latter, we have chosen to include these observations for comparison in the next sections. The considered stations are indicated in Fig. 3. AOD observations at 550 nm from the MODIS instrument on board the Terra (Equator crossing time at 10:30, ascending node) and Aqua (Equator crossing time at 13:30, ascending node) satellites are also used in order to get a more complete regional view.
This suggests the influence of local emissions that are missing in the model or limitations due to the coarse model resolutions which can not represent this station. At Bucharest, two high AOD peaks are modeled (Fig. 7 ). Compared to AERONET ground observations, the first peak is well modeled on 23 July (0. 46 against measurements 0. 5) and underestimated on 30 July (0. 51 against measurements 0. 82 but simulated 1 day after the observations, probably due to uncertainty in the MODIS fire detection). The observed values of the Ångström exponent are lower on 23 July (α ∼ 0. 57), indicating a large fraction of coarse-mode particles (probably dust transport), than on 30 July (α ∼ 1. 6, large fraction of fine-mode particles from fires). These underestimations or overestimations of the model's AOD, depending on the data set used for the evaluation (AERONET vs.
(2011)  that are used here. If fire emissions are important for the regional budget of organics, more observations are required to provide emission factors of NH 3 and concentrations of inorganics should be evaluated close to fire regions. Deposition can be considered a source of uncertainty on PM and AOD over the Euro-Mediterranean region during the summer of 2007. Roustan et al. (2010)  pointed out the importance of dry and wet deposition over Europe while studying the sensitivity of Polyphemus to input data over Europe with a focus on aerosols. They found that PM is sensitive to options influencing deposition such as wet diameter and aerosol density. They found that during both summer and winter, the uncertainties on wet diameter and aerosol density can reach 19 % and 9 %, respectively.
Acknowledgements. CEREA and LMD are members of the  Institut Pierre-Simon Laplace (IPSL). This research was partially funded by a PhD grant from  École des Ponts ParisTech , and by the  French ministry of ecology , by  CNRS-INSU (GMES-MDD program ,  NATORGA  project). This study also received financial support from MISTRALS by  ADEME ,  CEA ,  INSU , and  Meteo-France , as part of the  ChArMEx  project. We are grateful to the  EEA  for maintaining and providing the AirBase database (more particularly for the GR0039A station). We thank the principal investigators and their staff for establishing and maintaining the AERONET sites used in this study:  Brent Holben for Blida ,  Maria Rita Perrone  for  Lecce University and Doina Nicolae for Bucharest Inoe. We wish to thank the  National Aeronautics and Space Agency (NASA)  for the availability of the MODIS data.
Identification and classification of the bZIP transcription factors in the melon genome. To test whether other melon bZIP proteins could interact with CmWIP1, we performed an extensive genome-wide search using bZIP protein sequences from Arabidopsis, rice, tomato and cucumber as BLASTP queries against the melon genome database  30. A total of 63 non-redundant CmbZIP transcription factors were identified (Supplementary Table  1 ). For convenience, we assigned a unique identifier to the CmbZIPs genes, CmbZIP1 to CmbZIP63, based on their location on chromosomes 1 to 12 (Supplementary Fig. 1  and Supplementary Table  1 ). Three CmbZIPs mapped to unanchored scaffolds and were numbered CmbZIP61, CmbZIP62 and CmbZIP63 (Supplementary Fig. 1  and Table  1 ). The CmbZIP proteins range from 129 to 721 aa with an average size of 318 aa and with a range of molecular weights from 15.
Fluorescent images of interactions or absence of fluorescence in tobacco leaf cells were captured using the ZEN software. Bioinformatic and phylogenetic analysis. Multiple sequence alignment of the S2 bZIP protein sequences of melon and Arabidopsis was performed using the ClustalW (http://www. ebi. ac. uk/Tools/clustalw)  2. Phylogenetic trees were constructed using the Neighbor-Joining method by MEGA 7. 0 (http://www. megasoftware. net/index. html). b-d ) Quantitative RT-PCR of CmACS-7, CmWIP1 and CmbZIP48 in carpel and stamen primordia of female, hermaphrodite and male flowers of gynoecious, hermaphrodite and androecious melons, respectively. Shown are the mean + -SD of three biological replicates. GC: gynoecious carpel primordia, GS: gynoecious stamen primordia, HC: hermaphrodite carpel primordia, HS: hermaphrodite stamen primordia, AC: androecious carpel primordia, AS: androecious stamen primordia.
Identification of bZIP proteins in melon. To identify candidate bZIP proteins from melon, the melon database (http://www. melonomics. net/) was searched first using the keywords 'bZIP'. In addition, Arabidopsis, rice, tomato and cucumber bZIP protein sequences were downloaded from The Arabidopsis Information Resource (http://www. arabidopsis. org/), the Rice Genome Annotation Project (http://rice. plantbiology. msu. edu/), the Sol Genomics Network (http://solgenomics. net/) and the Cucurbit Genomics Database (http://cucurbitgenomics. org/), respectively. These sequences were used to identify homologous peptides from melon by performing a BLASTP search at melon genome v3. 5 database (http://www. melonomics. net/)  30. The BLAST E-value was set to 1e -3. The retrieved sequences were searched using SMART (http://smart.
embl-heidelberg. de/), and Pfam (http://pfam. sanger. ac. uk/) databases for the presence of the conserved bZIP domain. Finally, repeated and incomplete sequences were removed manually and the non-redundant CmbZIP sequences were subjected to further analyses. Chromosomal distribution and gene structure. The CmbZIP genes were mapped onto the corresponding chromosomes by BLASTP against the melon genome v3. 5 database (http://www. melonomics. net/) using default settings. The CmbZIP genes were plotted onto the melon chromosomes according to their ascending physical position (bp). Tandem duplications were characterized as adjacent genes of same sub-family located within 10 predicted genes apart or within 30 kbp of each other. The exon-intron structure of the CmbZIP genes was determined using the Gene-Structure Display Server (gsds.
Preparation of cDNA libraries. 2 ng of total RNA was used for each cDNA library preparation using the SMARTer Ultra Low RNA Kit for Illumina Sequencing from Clontech according to manufacturer's instructions (16 cycles of PCR were used for cDNA amplification). cDNA were used to assessed the expression of the S2 bZIP and CmWIP1 genes by qPCR experiments. Reverse transcription polymerase chain reaction (RT-PCR) and qPCR. Total RNA was extracted from frozen flowers with the Trizol reagent (Invitrogen). Contaminating DNA was removed by DNaseI treatment (Invitrogen). First strand cDNA was synthesized from 2 μg of total RNA with the Superscript ® III reverse transcriptase (Invitrogen). Primer design was performed with the Primer3 software (http://frodo. wi. mit. edu/ cgi-bin/primer3/primer3_www. cgi).
Primers sequences are listed in Supplementary Table 2. To check specificity of the designed primers, all amplicons were sequenced and blasted against NCBI database. Polymerase chain reactions were performed in an optical 384-well plate with the Bio-Rad CFX96 Real-time PCR apparatus, with qPCR MasterMix Plus for SYBR ® Green I w/o ROX (Eurogentec) and according to manufacturer's instructions. PCR amplification specificity was verified by a dissociation curve (55 °C to 95 °C). A negative control without cDNA, technical replicates on three independent synthesis of cDNA (derived from the same RNA sample), and three independent biological experiments were performed in all cases. To compare data from different PCR runs and cDNA samples, CT values for CmbZIP49, CmbZIP14, CmbZIP52, CmbZIP42, CmbZIP48 and CmWIP1 were normalized to the CT value of CmActin2 (primers shown in Supplementary Table  2 ).
Acknowledgements We thank  P. Audigier  and  F. Vion  for plant handling, the cell biology imaging platform and research facilities provided by the  Institute of Plant-Science Paris-Saclay  ( IPS2 ). This work was supported by the  Plant Biology and Breeding department in INRA , the grants Program  LabEx Saclay Plant Sciences-SPS  ( ANR-10-LABX-40-SPS ),  EPISEX  ( ANR-17-CE20-00019 ) and the  European Research Council  ( ERC-SEXYPARTH ).
Patients and methods: Women referred for endometrial cancer at the tertiary oncological referral center of Tours (France) were prospectively entered into a multidisciplinary team meeting register between October 1975 and June 2014. With the authorization of the institutional review board we retrospectively reviewed this prospective database. Inclusion criteria were: women with EC managed between October 1975 and June 2014 with available histological data. Exclusion criteria were: women with uterine sarcoma (leiomyosarcoma, endometrial stromal sarcoma or adenosarcoma). Individual records of all patients were reviewed and analysed from the medical records held by our institution on a computerized database. Variables included patient demographics, histological and survival data. Patients with known Body Mass Index (BMI) were categorized as: underweight (BMI < 18,5 kg/m 2 ), normal (18,5 ≤ BMI ≤ 24,9 kg/m 2 ), overweight (25 ≤ BMI ≤ 29,9 kg/m 2 ) and obese (BMI ≥ 30 kg/m 2 ).
In the first part of "results" section, patient's age, BMI, were treated as continuous variables. Survival data were extracted from medical files when available, if not, the birthplace (city hall) of each patient was contacted to consult survival data of the birth registry. The date of death was noted on the marginal notes on the birth certificate. In the absence of a marginal mention of death, the patient was considered alive. In the absence of a mentioned birthplace, the residence city hall or departmental archives made it possible to find survival data. Overall survival (OS) was calculated. As stated in the introduction, ECs are classified into two major types based upon clinicopathologic features. Bokhman in 1983,  (31)  was the first who hypothesized that there are two types of ECs driven by different metabolic and endocrine signals: type I being more common, consisting of endometrioid, low grade, diploid, hormone-receptor positive tumors that are moderately-or well-differentiated and more common in obese women.
Type II ECs are more common in non-obese women, of non-endometrioid histology, high grade, aneuploidy, poorly differentiated, hormone receptor negative and associated with higher risk of metastasis and poor prognosis. This historical system has been useful but overlap between type 1 and 2 is now well recognized. For numeric data, results are reported as mean and median values ± standard deviation (SD). The Fischer exact and χ² chi-square tests were used to compare categorical values. Characteristics of women and tumors were analyzed using Chi-square statistics or Fisher's exact test for categorical variables and t-test or analysis of variance (ANOVA) for continuous variables. Values of P<0. 05 were considered to denote significant differences. Data were managed with an Excel database (Microsoft, Redmond, WA, USA) and analyzed using the R 3.
There was no real evolution of the gynaecological surgery team or neither in the modalities of patient's recruitments nor in the administrative region The comparison with literature data is more delicate because of adjunction of grade 3 endometrioid EC to type II EC during the study period, because they are considered as having similar prognosis  (35) (36). When performing our analyses, grade 3 endometrioid EC was included in type II ECs as reported in the latest recommendations. Despite emergence of more aggressive histological subtypes, overall survival remained stable whatever the decade of management. Boll et al found a significant rise in 5-year overall survival for type I EC from 83 % in 1990 to 85 % in 2007 (p<0. 001) (8) , and in parallel a diminution in 5-year overall survival from 15 to 18 % for type II EC  (29).
150 patients extracted from the SEER database (Surveillance, Epidemiology, and End Results) between 1988 and 2001, found a proportion of 83. 7% of type I EC. Rates of type II ECs progressed over time with 14. 7 % in the 1990s to 17. 3 % in the 2000s (p<0. 001). Serous histological subtype increased from 5. 8 % to 6. 7 %(35).
Methods This study was conducted in accordance with the Declaration of Helsinki, and approved by the EBMT Autoimmune Disease Working Party and Severe Aplastic Anaemia Working Party. All EBMT centres performing allogeneic HSCT for aAA were invited to participate in the study. Centres agreeing to participate provided data on all consecutive paediatric and adult patients with aAA treated between January 2002 and December 2012 with first allogeneic HSCT. Centres confirmed whether AIC was diagnosed post-HSCT. Patients diagnosed with AIC at any time point prior to HSCT were excluded. Data for all patients were extracted from the EBMT registry, and centres identifying cases of AIC provided additional data on diagnostic criteria and investigations undertaken, therapies administered and patient outcome.
Conclusions In conclusion, the incidence of AIC post allogeneic HSCT for aAA is similar to that reported among recipients of HSCT for other primary diseases. Autoimmunity should be considered in the differential diagnosis of cytopenias occurring in both the early and late post HSCT period. Our study highlights heterogeneity in the approach to investigation and management of AIC between EBMT centres. As such standardization of diagnostic and therapeutic approaches, along with data registration (via the EBMT and other databases), is warranted to inform harmonized recommendations for investigation and management of suspected AIC. Response rates in this cohort are similar to previous data and OS in the AIC group was not shorter than in the overall cohort. In multivariable analysis we identified an increased risk of AIC following PBSC and RIC HSCT in this cohort, which may contribute further to the evidence that BM is the preferred stem cell source for transplant of patients with aAA.
Acknowledgements PDEM, JAS, CD, RPDL, SI, RFD, PB, DF, JR and JAM designed and performed the research study, contributed to the acquisition, analysis and interpretation of data, critically revised the paper and approved the final version. SI designed the research study, critically revised the paper and approved the final version. D-JE analysed and contributed to interpretation of data, critically revised the paper and approved the final version. JCWM, CR, MK, FF, SCJF and CK contributed to the acquisition of data, critically revised the paper and approved the final version. JAS declares honoraria for speaking from  Sanofi  and  Jazz. Compliance with ethical standards.
Study design and treatment regimens ERT-naïve male pediatric patients with Fabry disease without clinically evident kidney, heart, or brain involvement were enrolled in this randomized, open-label, parallel-group, phase 3b study (clinicaltrials. govNCT00701415) and received 1 of 2 low-dose agalsidase beta regimens (0. 5 mg/kg 2-weekly [0. 5q2w] or 1. 0 mg/kg 4weekly  [1. 0q4w] ) for 5 years. The inclusion and exclusion criteria are described in the study protocol (Appendix) and elsewhere  [11]. Briefly, males were aged 5-18 years and had a confirmed diagnosis of Fabry disease with evidence of GL-3 accumulation in plasma or increased levels in urine. Exclusion criteria included prior ERT or use of an investigational drug for treating Fabry disease; urine albumin-to-creatinine ratio (UACR) > 30 mg/g; glomerular filtration rate (iohexol plasma disappearance, iGFR) < 90 mL/min/1.
Statistical analyses No formal statistical sample size calculation was performed. The number of potential study participants was determined on medical grounds as a compromise between the need to assess efficacy and safety in the pediatric Fabry patient population, and the limitations for recruitment in a rare disorder. The study was not intended to formally compare the 2 treatment regimens; any comparison may only be considered as exploratory. All data prior to a subject's dose increase (n = 2) are included in the analyses. Descriptive statistics were presented for continuous variables. Statistical tests included a Wilcoxon Signed-Rank test (change from baseline), a Wilcoxon-Mann-Whitney test (comparing ADA data from the treatment groups), a Spearman rank correlation test (correlation coefficients, r s ), and a Fisher's exact test (comparing SSCE GL-3 scores).
However, normalization of plasma GL-3 levels and substantial reduction in lyso-GL-3 levels were maintained, and samples were not tested for inhibitory activity of ADAs. The low-dose agalsidase beta regimens had acceptable safety profiles which were not different from the profile of the approved dose  [8] , and there were no new safety observations compared with another study of agalsidase beta in pediatric Fabry patients  [15]. Of the 10 patients who were initially considered to meet pre-defined criteria for increase in agalsidase dose (for 2 patients at the 5-year time point), 2 had their dose increased, whereas 6 continued with the lower dose regimens throughout the remainder of the study, based on the clinical judgment of the treating physicians. Our study has several limitations. No age-matched controls were included in the study and data from such controls have not been reported, preventing direct comparison of our findings with observations in normal children, and untreated and pediatric, classic patients treated with the approved dose of ERT followed by a similar protocol.
Moreover, published data on the natural progression of Fabry disease and outcomes of ERT in pediatric and adolescent, classic patients is scarce. Optional research kidney biopsy samples were obtained only at a few study sites. One patient who had met the study inclusion criteria had a p. Asn215Ser mutation. At the time of development of the final Study Protocol (January 2008), p. Asn215Ser phenotype data were Fig. 2. Plasma GL-3 and lyso-GL-3 (A), and urine GL-3 (B). Note: Comparisons between baseline and follow-up visit, for the combined group. For plasma GL-3 and plasma lyso-GL-3 *P <. 0001, and for urine GL-3 **P =. 0010 at 5 years. scarce. Recent efforts have confirmed that this mutation is associated with a non-classic, later-onset cardiac Fabry phenotype generally without the early symptoms observed in classic male patients and generally without clinically relevant extracardiac organ impairment  [14, 35].
Acknowledgements The authors would like to thank the patients who agreed to participate in the study and their families, as well as all physicians and other hospital personnel involved in the conduct of this study. In addition, the authors would like to acknowledge all individuals who have been involved in skin and kidney biopsy reviews, production of biopsy slides, selection of the appropriate slides for review and scoring, iohexol measurement, retinal imaging reviews, and glycolipid assessments. The patient recruitment sites are described elsewhere [11].
S1  in the ESM). A very instructive representation of the PED-based twist data is presented in the form of animations where each frame include the real space measurement position, the PED pattern and the inverse pole figure of the crystal orientation (Videos ESM1 and ESM2). These animations compare data for well-oriented and disoriented NWs. From the orientation maps it is also possible to estimate the NW diameter, allowing the theoretical twist rate for the Burgers vector length |B| = |c|. Using annular dark field (ADF) scanning TEM images, the value obtained was RADF = (16 ± 1) nm (see Fig. S2  in the ESM). The actual NW crystal size can also be estimated from PED data using individual diffraction patterns and PED fit quality factors. Considering this additional information, our best estimate of the wire radius becomes RNW = (15 ± 1) nm (see Fig.