dataesr/scientific-paragraphs-categorization huggingface dataset:
(EPS) Figure S13 EZL1 retention score for DCL2/3 and DCL5 retained IESs. Boxplots show the distribution of EZL1 retention scores for EZL1-retained IESs (green), DCL2/3-retained IESs (yellow) and DCL5-retained IESs (blue), showing that the significantly retained IESs in the DCL2/3 and the DCL5 datasets are among the most retained IESs in the EZL1 dataset. Significant differences are designated by asterisks (p,2. 2 10-16) and were determined using a Mann-Whitney test. (EPS).
SET domain proteins identified in the somatic MAC genome of P. tetraurelia. Accession numbers (see ParameciumDB, http://paramecium. cgm. cnrs-gif. fr/),names and conserved domains are indicated. (DOCX)Table S2 Sequencing and mapping statistics. Read statistics are provided for the samples sequenced for this study, with the exception of the PGM and DCL5 silencing samples, which were previously published [2,6]; European Nucleotide Archive Acc No. ERA137444 (PGM); GenBank Sequence Read Archive Acc No. SRX387766 (DCL5). (DOCX).
Acknowledgments We thank  Sophie Malinsky ,  Raphae ¨l Margueron ,  Eric Meyer  and  Augustin de Vanssay  for critical reading of the manuscript. We thank Frederic Guerin and  Haifa Touzi  for technical support,  Olivier Arnaiz ,  Laurent Duret  and  Franck Picard  for advice on sequencing data analysis and  Sophie Malinsky  for the PiggyMac silencing and PiggyMac GFP constructs.
This work was supported by the  ANR-2010-BLAN-1603  ''GENOMAC'', the  ANR-12-BSV6-0017  ''INFERNO'', a  CNRS ATIP-Plus  grant to SD. MLA, AF, CDW were supported by  Ph. D. fellowships from the  Ministere de l'Enseignement Superieur et de la Recherche , and MLA was recipient of a fellowship from the  Fondation de la Recherche Medicale. We acknowledge the  ImagoSeine facility , member of the  France BioImaging infrastructure supported  by the  ANR-10-INSB-04. The sequencing benefited from the facilities and expertise of the high-throughput sequencing platform of  IMAGIF (Centre de Recherche de Gif  -www. imagif. cnrs. fr). This study was carried out in the context of the CNRS-supported  European Research Group ''Paramecium Genome Dynamics and Evolution'' , the  European COST Action BM1102  and the  LABEX ''Who am I?''  supported by the  ANR-11-LABX-0071_WHOAMI  and the  ANR-11-IDEX-0005-02.
MDA-MB-231 paclitaxel-treated cells were also highly sensitive to Bcl-xL depletion (Figure  3c ), as were MCF-7 (Supplementary Figure  3A ) or Cal-51 (data not shown) cells. Of note, the pan-caspase inhibitor Q-VD-OPh potently prevented cell death onset in these settings (Figures  3b  and c ). We then performed a series of single-cell analysis by videomicoscopy using cells expressing a red fluorescent protein (RFP)-tagged histone-2B (H2B) as a marker of chromatin morphology (i. e. , chromosome condensation or nuclear fragmentation) and a green fluorescent proteintagged shRNA construct targeting Bcl-xL to follow cell cycle progression and define kinetic cell response (i. e. , mitotic arrest, mitotic slippage, cell death upon paclitaxel treatment) under these conditions. We first observed that in control cells, Bcl-xL depletion triggered a partial cell death response that mostly happened during interphase (Figure  3d ).
The lentivector coding for Histone-2B-RFP was kindly provided by Jan Van Deursen, Mayo Clinic, Rochester, MN, USA. FACS-based cell death assays. For the detection of apoptosis, floating and adherent cells were harvested and analysed by flow cytometry using the Annexin-V-binding assay (Beckman Coulter, Villepinte, France), according to the manufacturer's instructions. Flow-cytometry analysis was performed on a FACSCalibur by using the CellQuestPro software in the Flow Cytometry Facility, CytoCell, SFR Bonamy, INSERM, Nantes, France. For RNA interference, cells were first transfected with siRNA-targeting Cdc-20, Bcl-2, Bcl-xL, Mcl-1, Bax or Bak; 24 h later, cells were treated or not for 24 h with ABT-737 (1 mM), paclitaxel (70 nM) and/or Q-VD-Oph (10 mM added 1 h prior further treatment), depending on experiments.
MDA-MB-231, MCF-7-eYFP and MCF-7-eYFP-Bcl-xL cells were infected with H2B-RFP lentivectors (MOI ¼ 3), washed 6 h later and grown during 48 h. Cells were then harvested and seeded in 24-well plates at 3 Â 10 4 cells per well. A double thymidine block (0. 626 M) of 24 h separated by a 16-h release was applied before analysis. When applicable, shCt or shBcl-xL lentivectors were added for 48 h before the double block thymidine was made. Finally, cells were released 1 h before addition of drugs and analysis. Imaging was performed using a Leica DMI 4000 Bioimager (Leica, Nanterre, France) with the Metamorph in the MicroPIcell imaging facility (SFR Bonamy, FED4203/Inserm UMS 016/CNRS 3556, Nantes, France). Images were collected every 10 min using a Â 10 objective. Image sequences were viewed using NIH ImageJ software, and cell behavior was analysed manually.
For dose-response effect of ABT-737, %BRET is calculated using the following formula: (BRET meas -BRET min ) Â 100/(BRET max -BRET min ), where BRET meas is the BRET ratio obtained for every ABT737 concentration, BRET min is the BRET ratio measured at the highest ABT concentration and BRET max is measured for untreated condition. All data were analysed using the commercial programme GraphPad PRISM 6. 0 (GraphPad Software, La Jolla, CA, USA). Immunofluorescence imaging. MCF-7 cells were plated onto glass coverslips and grown for 24 h before transfection with peYFP-Bcl-xL, pS62A-eYFP-Bcl-xL or pS62D-eYFP-Bcl-xL plasmids. Forty-eight hours after transfection, cells were stained with the cell-permeant MitoTracker probe (MitoTracker Red CMXRos, Invitrogen) as described by the manufacturer. Slides were then counterstained with DAPI and images were viewed on a Zeiss Axiovert 200 M microscope (MicroPIcell imaging facility).
Acknowledgements. We thank  Philippe Hulin  for his technical support in Cellular and  Tissular Imaging Core Facility of Nantes University (MicroPICell). We also thank the  Cytometry Facilty Cytocell from Nantes  for expert technical assistance. We thank  Claude Prigent  and  Franc¸ois Paris  for fruitful discussions. We thank  Sophie de Carne  ´for providing us the MCF-7-YFP and MCF-7-YFP-Bcl-xL cell lines. N Bah  was supported by  la Ligue contre le Cancer de Loire-Atlantique. We thank la  Ligue Regionale contre le Cancer Grand-Ouest  and the  French Society of Cancer  for their financial support.
RNA EXTRACTION AND MICROARRAY Total RNA was extracted from granuloma cells using the RNeasy Mini kit (Qiagen) and DNAse treatment. The granuloma cell gene expression was analyzed using 45,000 probes microarray chips (4 × 44K whole human genome G4112F, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis kit, as previously described  (Ben Amara et al. , 2010). Three samples per experimental conditions were included in the analysis. Following array scans, image analysis and correction of intra-array signals were performed with Feature Extraction Software A. 10. 5. 1. 1 (Agilent Technologies) using default parameters. Minimum Information About a Microarray Experiment-compliant data are provided in the Gene Expression Omnibus (GEO)  (Moal et al. , 2013)  at the National Center for Biotechnology Information (http://www.
MICROARRAY ANALYSIS Raw signal data were normalized with a False Discovery Rate below 0. 1 and an absolute fold change (FC) value of 3. 0. All analyses were performed using R software (version 3) with the bioconductor libraries  (Gentleman et al. , 2004). Functional annotation was performed using ClueGO plug-in  (Bindea et al. , 2009)  and selecting terms belonging to GO Biological  (Moal et al. , 2013)  in Cytoscape software  (Smoot et al. , 2011 ). An enrichment/depletion test, along with the Benjamin-Hochberg correction method, was performed for statistic analysis. GO terms from levels 6 to 8 in GO tree were selected, with a kappa score above 0. 44, to create functional annotation network. Each node represents a GO term and contains at least 3 genes. The leading group term of a functional group was defined as the group containing the largest number of genes.
REAL-TIME QUANTITATIVE RT-PCR (qRT-PCR) Reverse transcription of 100 ng of total RNA was performed as previously described  (Ben Amara et al. , 2010). Primers were designs using Primer3  (Moal et al. , 2013)  and their sequences were listed in Table  1. Quantitative PCR was performed with Light Cycler Fast Start DNA master PLUS SYBR Green I (Roche applied Science). The results were normalized with the housekeeping gene β-actin. The FC of target genes relative to β-actin was computed using the formula FC = 2 -Ct , where Ct = [(Ct Target -Ct Actin ) stimulated -(Ct Target -Ct Actin ) unstimulated ]  (Moal et al. , 2013). The agreement between qRT-PCR and microarray data was assessed by Pearson correlation coefficient.
1) CLIMATIC DATA The analyses of the local climate 1  and its evolution are based on local daily rainfall and temperatures from the Spanish Meteorological State Agency database [Agencia Estatal de Meteorolog ıa (AEMET)] (Fig. 3 ; see the appendix; Table  A1 ). The description of the current climate is based on 29 rainfall gauges and 12 temperature stations (Fig. 3 ), with datasets that cover a rather short time period  (1988 -2008; H. Garcin 2010, unpublished manuscript). The analysis of climate variability has been carried out using a smaller number of stations (Fig. 3  and Fig. 4 ), but with longer time series (from 1955 to 2009 for 15 rainfall gauge stations and from 1974 to 2009 for 7 and 8 stations measuring maximum and minimum temperature, respectively). All the stations are geolocated and integrated in a GIS system, using Arcgis 10.
DATA From 1999 to 2009, areal extent, olive production, and yield data of rainfed and irrigated olive groves are available for the province of Ja en, at the annual time scale, on the Agriculture, Food, and Environment Department website (MAGRAMA; http://www. magrama. gob. es). We copied older data (period 1955-99) from MAGRAMA's provincial registers in Ja en. Olive harvesting runs from November (year Y 2 1) to January-February (year Y), and the MAGRAMA database attributes the corresponding yield to year Y. The MAGRAMA data Sistema de Informaci on Geogr afica de Parcelas Agr ıcolas (SIGPAC) (common agricultural policy GIS; MAGRAMA 2006) provide information about land use, and the Guadalquivir Basin Authority data (CHG 2010) provide information about irrigation. An aerial photography of the region is available online (www.
Our companion paper (Part II) discusses the paradoxical relationships between climate predictions, their consequences for water resources, and olive yields and farmers' doubts about climate change. (French Institute for Research and Development, IRD, and the Laboratory of Oceanography and Climate, Locean) coordinated this program and incentivized our participation. The UMR Ladyss and the University Paris Diderot (Erasmus Program) have also provided financial support. We would also like to thank the DPO Sierra M agina, Larva and Bedmar's city hall, AEMET, MAGRAMA, and the Agriculture Secretary of Ja en for the data provision and the farmers' generous contribution. Thanks also to the researchers, Alia Gana, Philippe Boudes, Catherine Darrot (UMR Ladyss), Benjamin Sultan (UMR Locean), Vincente Jos e Gallego-Simon (Universidad Internacional de Andaluc ıa), Jos e Domingo Sanchez-Martinez (Universidad de Ja en), and Pascal Oettli (Locean), and the master students who contributed to this work: Joelle Salam e (University of Paris Diderot, 2010) and Imanol Sinde  (Agro-ParisTech, 2012).
Assignment and statistical analysis Given that numbers of fall and late-fall migrants substantially exceed those from winter and spring runs in most scenarios in the lower reaches of the Sacramento River or the NW Pacific Ocean, simulations performed to test for precision and accuracy were designed to approximate these relative abundance differences. This was achieved through utilizing the 'realistic fishery' option within the statistical package ONCOR  (Kalinowski 2008 ; www. montana. edu/ kalinowski/Software/ONCOR. htm). Note that this technique utilizes a cross-validation over a gene copies method demonstrated to be less prone to providing over-optimistic estimates of assignment power than earlier methods  (Anderson et al. 2008; Anderson 2010). For HMSC baselines, parameters were set to construct 1000 hypothetical mixtures of size 100 individuals each, using a 0.
Acknowledgments We are grateful to:  Pat Brandes  who provided valuable comments on an earlier draft manuscript;  Renee Bellinger  and  Nick Sard  for help with figures; the  California Department of Fish and Game  and the  US Fish and Wildlife Service  for samples provided; and  Environmental Services ,  California Department of Water Resources  and  California Bay-Delta Authority (now Delta Stewardship Council)  for funding this research. Findings and conclusions in this article are those of the authors and do not necessarily represent the views of the universities, agencies, or departments with which they are associated.
Pellets from a single sample were pooled, resuspended in 25 ml PBS and again centrifuged at 100,000 g for 70 min. Finally, the exosome pellet was resuspended in 100 μl PBS. Exosomal proteins were quantified using a Bradford protein assay. A NanoSight (Malvern Instruments, Orsay, France) was employed to measure the size of particles  [16]. The number of particles and their movement were recorded for 1×60 s and analysed using the NS500 software. Exosomes were visualised by transmission electron microscopy as previously described  [15]  (ESM Fig. 2 ). Production of C2C12 exosomes containing green fluorescent protein Non-replicative adenoviruses expressing the green fluorescent protein (adeno-GFP) were generated as previously described  [17]. Differentiated C2C12 cells were infected with adeno-GFP for 24 h in differentiation medium.
Twenty-four hours later all myotubes had green fluorescence in the cytoplasm indicating that all cells had been infected. Myotubes were washed with PBS to remove both non-integrated adenovirus and exosomes from FBS and then were incubated for another 48 h in exosome-depleted DMEM. GFP-containing exosomes accumulated in CM for 48 h were extracted. Differentiated C2C12 myotubes were incubated with 2 μg GFP-containing exosomes depleted of viral particles (EXO-GFP) per ml of medium  [14, 15]. Forty-eight hours later cells were visualised with a Zeiss Axiovert 200 M Fluorescence/Live cell Imaging microscope equipped with Axiovision software (Carl Zeiss, Marly le Roi, France). Microarray data analysis C2C12 RNA profiling was performed using the Mouse GE 4*44K v2 Microarray kit (Agilent Technologies, Les Ulis, France).
Briefly, 100 ng of RNA was labelled with Cy-3 using the Low Input Quick Amp Labeling kit (Agilent Technologies) and microarrays were hybridised and scanned following the manufacturer's instructions. Microarray analyses were performed with R environment using Agi4x44PreProcess and Limma packages from BioConductor  [18]. The dataset is available from the GEO database GSE52048 (www. ncbi. nlm. nih. gov/gds/). Quantitative real-time PCR Quantitative real-time PCR (qRT-PCR) was performed using ABsolute QPCR SYBR Green ROX Mix (Abgene, Courtaboeuf, France) with a Rotor-Gene 6000 system (Corbett Life Science, Qiagen, France). Results were normalised with a reference gene encoding TBP (TATA box binding protein)  [19]. PCR primers are listed in ESM Table  1. Western blotting Cells were lysed in RIPA lysis buffer (PBS, 0.
D. Block PARALIND/CONFAC models In some applications, the data tensor X ∈ C I1×•••×IN is written as a sum of P sub-tensors X (p) , each sub-tensor admitting a tensor model with a possibly different structure. So, we can define a block-PARALIND/CONFAC model as X = P p=1 X (p) , (45) X (p) = G (p) × N n=1 A (p,n) , (46) G (p) = I N,R (p) × N n=1 Φ (p,n) , where A (p,n) ∈ C In×R (p,n) , Φ (p,n) ∈ C R (p,n) ×R (p) , and N ) are the mode-n factor matrix, the mode-n constraint/allocation matrix, and the core tensor of the PARALIND/CONFAC model of the p th sub-tensor, respectively. The matrix representation (44) then becomes G (p) ∈ C R (p,1) ×•••×R (p, X S1;S2 = P p=1 ⊗ n∈S1 A (p,n) ⋄ n∈S1 Φ (p,n) ⋄ n∈S2 Φ (p,n) T ⊗ n∈S2 A (p,n) T. ( 47 ) Defining the following block partitioned matrices A (n) = A (1,n) • • • A (P,n) ∈ C In×R (n) (48) where R (n) = P p=1 R (p,n) , Eq.
The considered constrained tensor models allow to take constraints into account either independently on each matrix factor of a PARAFAC decomposition, in the case of PARALIND/CONFAC models, or between factors, in the case of PARATUCK models. A perspective of this work is to consider constraints into tensor networks which decompose high order tensors into lower-order tensors for big data processing  [97]. In this case, the constraints could act either separately on each tensor component to facilitate their physical interpretability, or between tensor components to explicit their interactions.
EARSS-Net database. http://ecdc. europa. eu) [5] , the USA, South America and Asia. Prevalence of MRSA infections decreased in the last few years in many European countries, and this can be considered as a very positive and promising result. Vancomycin-resistant enterococci (VRE) are also very frequent, with large differences between countries. In the European point prevalence study organized by ECDC [6], VRE prevalence was going from 1% to more than 50%. The prevalence of Escherichia coli and Klebsiella pneumoniae harboring extended-spectrum beta lactamases (ESBL) is increasing regularly worldwide  [7]  reaching 50 to 70% for Escherichia coli in some European or Asian countries  [5, 7]. In the European point prevalence study, prevalence of Klebsiella pneumoniae with carbapenemases was going from 1% to more than 50%  [6].
Even more, as in the present case, the mode decomposition formalism makes it possible to compare structures with different symmetry since the primary modes are essentially equivalent in both phases. In spite of these advantages, the mode decomposition formalism has not been commonly used because it requires a deep knowledge of group theory and complex calculations must be performed for every particular case to obtain the mode decomposition. However, the development of new free computational tools with an adequate crystallographic parameterization of the mode decomposition [ISODISPLACE  (Campbell et al. , 2006)  and AMPLIMODES  (Orobengoa et al. , 2009) ] has significantly reduced the time and effort needed to apply this approach. The symmetry-adapted modes formalism is nowadays fully implemented in some software used for structure refinement  (Rodrı ´guez-Carvajal, 1993) , providing deep and detailed descriptions of structures and phase transitions of complex materials  (Iturbe-Zabalo et al.
Also, a bender curves the second crystal sagittally in order to focus the beam at the sample position  (Rubio-Zuazo et al. , 2013). The sample was finely ground and loaded into a 0. 4 mm-diameter capillary mounted in a spinning goniometer. Room-temperature data were collected in a continuous 2 scan mode from 7 to 48 using an incident wavelength of 0. 62100 (6) A ˚[calibrated with NIST SRM 640c silicon powder; a = 5. 431195 (9) A ˚]. The counts from the different channels were re-binned to produce an equivalent normalized step scan of 0. 01 step intervals, with a count time of 1 s per step. NPD experiments at room temperature were performed on the high-resolution diffractometer D2B at the Institut Laue-Langevin. A monochromatic beam of wavelength 1. 5940 A ẘas selected with a Ge monochromator from the primary beam, the divergence of which was defined by an additional 10 0 collimator to increase the instrumental resolution.
The structural refinements were carried out by the Rietveld method by the simultaneous fitting of SR-HRPD and NPD data, using the AMPLIMODES formalism  (Perez-Mato et al. , 2010 , Orobengoa et al. , 2009)  implemented in the FullProf program  (Rodrı ´guez-Carvajal, 1993). The neutron scattering amplitudes used in the refinement were 0. 824, 0. 702, 0. 249, À0. 344 and 0. 581 (10 À12 cm) for La, Sr, Co, Ti and O, respectively. Selected area electron diffraction and HREM were performed using a JEOL 3000 field emission gun electron microscope, fitted with a double tilting goniometer stage (AE25 , AE25 ). Simulated HREM images were calculated by the multislice method using the MacTempas software package (R. Kilaas, Total Resolution, Berkeley, CA, USA).
Epidemiology Robust epidemiologic data on AOSD are lacking. The disease occurs worldwide and affects usually young adults (the median age at diagnosis is circa 36 years  [4, 5] ) though onsets were described up to 83 years  [6, 7]. Its incidence has been estimated at 0. 16 (per 100,000 persons) in France  [8] , 0. 22 in Japan  [9] , and 0. 4 in Norway  [10]. In the Japanese and the European populations, the reported prevalence rates range from 1 to 34 cases per 1 million persons. In rheumatologic case series, women seem to be more often affected than men; they represent up to 70% of the patients  [5, 11, 12] ; however, in internal medicine case series, women represent only 45 to 53% of the patients  [4, 13]. The hormonal influences are poorly understood; nevertheless, the second trimester of pregnancy and the postpartum period would increase the risk of disease recurrence  [14].
Recently, Chen et al. have shown that circulating Th17 cells are significantly higher in patients with active untreated AOSD than in healthy controls  [77]. The levels of Th17 correlated with the disease activity, with ferritin levels, and with remission after treatment. However, it is still unknown whether Th17 cells are part of the pathogenic mechanism or only markers of AOSD progression. Indeed, Th17 polarization could occur downstream of other more complex mechanisms. For example, some missense mutations of the NLRP3 gene may cause inflammasome hyperactivation, overproduction ofIL-1β, and a subsequent increase in Th17 differentiation  [78]. Nevertheless, some data propose Th17 cells as possible targets for therapy  [78, 79]. Finally but not surprisingly, it has been shown that circulating CD4+ CD25 high regulatory T cells (Treg) and transforming growth factor (TGF)-β are inversely correlated with AOSD activity scores.
The mean Disease Activity Score (DAS) 28 dropped from 5. 61 to 2. 91 at the 6-month follow-up visit. The systemic symptoms resolved in six out of seven patients and corticosteroid dose was reduced by 56%  [240]. In 2013, Cipriani et al. reported on 11 patients with refractory AOSD treated with 8 mg/kg tocilizumab monthly during 12 months  [241]. The patients responded rapidly and experienced a sustained clinical remission over time during the treatment. The median DAS 28 decreased from 5. 62 at baseline to 1. 61. Remissions of fever and improvements of systemic symptoms were observed in the eight patients with such symptoms. The beneficial effect of tocilizumab seemed preserved after 6 months of treatment cessation. Very recent results on 15 Israeli tocilizumab-treated refractory AOSD patients seem to confirm these data  [242] ; at the end of a 16-month mean follow-up, only two patients suffered from persistent arthralgia whereas a single patient had to be switched to canakinumab to control a RHL.
Acknowledgements: The work conducted by the  U. S. Department of Energy Joint Genome Institute  is supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC02-05CH11231. This research was funded by the  National Science Foundation  ( DBI 0822258 ),  USDA-NIFA 2006-35300-17266  to SAJ, and  USDA-CSREES  ( 2009-01860 ) and ( 2009-01929 ) to SAJ and PM, respectively.