dataesr/scientific-paragraphs-categorization huggingface dataset:
Antigenic profile analysis Cells detached with TrypLE-Express (12605-010, Invitrogen) were counted and then incubated in blocking solution (PBS containing 0. 5% BSA (Sigma)) at 4uC for 30 min. Cell distributions were determined with FITC-CD44 G44-26 (BD Pharmingen), and PE-CD24 ML5 (BD Pharmingen) monoclonal antibodies and the FACScan Calibur (Becton Dickinson) and analyzed with the FlowJo software.
Annexin/PI analysis Cells collected by centrifugation were counted and then incubated with annexin V-FITC in binding buffer 1X (10 mM Hepes/NaOH pH 7, 140 mM NaCl, 2. 5 mM CaCl 2 ) for 10 min in the dark according to the manufacturer's protocol (Abcyss). DNA staining was then performed with propidium iodide (0. 6 mg/ ml) for 10 min. For each condition, 10 4 events were recorded by FACS (FACScan Calibur, Beckman Dickinson) and results were analyzed with the FlowJo software. Immunofluorescence 10 4 cells were seeded onto an 8-well Lab-TekII chamber slide, fixed in 3. 7% formaldehyde solution (Sigma), and permeabilized in 0. 1% Triton 100X (Sigma), PBS buffer at room temperature for 10 min. The cells were then washed 3 times with PBS and incubated for 1 h with 10% horse serum in PBS blocking solution.
Acknowledgments We are thankful to the  Centre de Ressources Biologiques of the Centre Leon Berard  for providing the cohort of human breast tumor samples, to  Martin Eilers  ( Wu ¨rzburg University, Germany ) for providing the c-MYC expression vector. We are thankful to  Julie Pourchet ,  Guillaume Collin ,  Fabienne Barbet ,  Marjorie Carrere ,  Delphine Demangel ,  Audrey Pierrot ,  Mojgan Devouassoux-Shisheboran ,  Jeremy Bastid and Claire Ciancia  for their technical help, and  Dr Kathleen Broman  and  Louise Hill  for critical reading of the manuscript.
This work was financially supported by the  Association pour la Recherche contre le Cancer  and was performed within the framework of the  LABEX DEVweCAN  ( ANR-10-LABX-0061  of  Lyon University , within the  program ''Investissements d'Avenir  ( ANR-11-IDEX 0007 ) operated by the  French National Agency (ANR). BG received support from the  Ministere de la Recherche  and the  Fondation des Treilles. LJ is a recipient of fellowships from the  Ligue Nationale Contre le Cancer. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
METHODS Patients who underwent a first allogeneic HSCT in our center from December 2006 to August 2010 and were regularly followed in our center were eligible to be included in this study. Clinical and biological data were extracted from our local database completed by chart review. During the study period (December 2006 to June 2011), patients with respiratory symptoms possibly related to a respiratory virus had nasopharyngeal aspirates for PCR multiplex viral analysis  [4]  designed to detect RSV types A and B; AdV; HRV; human MPV; HCoV 229E, OC43, and NL63; PIV-1 to -4; influenza virus types A and B; and 4 different bacteria (Chlamydophila pneumoniae, Mycoplasma pneumoniae, Legionella pneumophila, Bordetella pertussis). Bacterial and fungal infections were documented by usual methods including bronchoalveolar lavage in patients with a suspicion of pneumonia.
Real-time quantitative PCR (RT-qPCR) analysis Total RNAs were extracted from adult flies using Absolutely RNA Miniprep kit from Stratagene. For real-time PCR analysis, cDNAs were synthesized with AffinityScript QPCR cDNA Synthesis Kit (Stratagene). An amount of cDNA equivalent to 0. 01 μg of total RNA was subjected to 40 cycles of PCR amplification consisting of a 10s incubation at 95°C and 30s at 60°C. Output was monitored using SYBR Green core reagents and the Mx3000P instrument (Stratagene). All the results were normalized to the rpl32 RNA level. The primer sequences were designed using PrimerQuest (http://eu. idtdna. com/Scitools/Applications/ Primerquest/).
Immunoprecipitation and immunoblotting Co-immunoprecipitation were performed following standard procedures in S2 cotransfected cells with 10 μg of Myc tagged full length USP2 construct in pAc/HisB vector (Invitrogen) (USP2-Myc) and 10 μg of V5-tagged Imd full length or truncated constructs. Pull Down assays were performed in S2 cells transfected with full length Imd-V5 construct and lysed after 48 h. The lysate was employed in a GST-USP2 N-ter domain [AA 1 to 531] or C-ter domain [AA 475 to 856] pull down assays. Pull downs were blotted with antibody against V5 to detect bound Imd-V5. Proteomic analysis (supporting data deposited in a database) Protein digestion and nano-liquid chromatography (LC)-MS/MS analyses were performed as described in  [50]. Only proteins identified specifically in the USP2 sample and not in the control one, with a minimum of 6 peptides and specific spectral counts above 6, were retained (indicated in green in Additional file 3: Table  S2 ).
Acknowledgments We thank  Dr Daniel Finley  and  Dr Gilles Courtois  for powerful discussion,  Dr Jean-Marc Reichhart  for sending anti-Imd antibody,  Dr Jean-Luc Imler  for AttA-luciferase reporter construct. We are grateful to  Nicole Assard ,  Dr Jacques Baudier ,  Dr Maxim Balakirev  for scientific advices,  Claire Bama  and  Christine Magnin  for fly food and laboratory maintenance. The fly stocks were obtained from  NIG-Fly Stock Center ,  Bloomington Drosophila Stock Center  and  VDRC. The cDNA clones were obtained from  DGRC. This work was supported by the  Fondation pour la Recherche contre le cancer  ( ARC n°SFI20111204045  to MOF), the  CEA -including CEA-Irtelis doctoral grants  (to EE and PV)-and the  Agence Nationale pour la Recherche  ( ANR   Investissement d'Avenir Infrastructures ,  ProFi  project  ANR-10-INBS-08-01  to YC).
Context. In 2009, the Sun and the Earth passed through the equatorial plane of Jupiter and therefore the orbital planes of its main satellites. It was the equinox on Jupiter. This occurrence made mutual occultations and eclipses between the satellites possible. Experience has shown that the observations of such events provide accurate astrometric data able to bring new information on the dynamics of the Galilean satellites. Observations are made under the form of photometric measurements, but need to be made through the organization of a worldwide observation campaign maximizing the number and the quality of the data obtained. Aims. This work focuses on processing the complete database of photometric observations of the mutual occultations and eclipses of the Galilean satellites of Jupiter made during the international campaign in 2009.
These files are provided by the observers but it is not these files which are provided in our database rather the files described in Sect. 6. 1  1. Figures  1 to 5  show examples of lightcurves. We note that the determination of the light flux on each image may be made either through a Gaussian fit of the object or an aperture photometry integrating all the light in a specific area with the careful elimination of the light from the sky background.
(  2 )), and third, the light flux modelled after the fit of the parameters on the observation as explained above (the value S (X th (t i ) + D x , Y th (t i ) + D y ) in Eq. (  2 )). The catalogue also contains a file of relative astrometric positions of the two satellites involved in each mutual event (one line per event) as described in the Sect. 6. 2 and in Tables  5  and 6. The lightcurves and the astrometric results are available for anyone interested from the electronic database of the Natural Satellite Data Center (NSDC) server 2.
Conclusions We reduced the entire database of photometric observations of the mutual occultations and eclipses of the Galilean satellites of Jupiter made during the international campaign in 2009 to determine the topocentric or heliocentric angular differences for satellite pairs at 457 time instants on the time interval from April 17, 2009 to December 24, 2009. The standard errors of the relative satellite coordinates due to the random errors of the photometry are equal to 18. 4 mas and 15. 6 mas in right ascension and declination, respectively. For successful observations, the r. m. s. of O-C residuals with respect to the theory by  Lainey et al. (2009)  are equal to 45. 8 mas and 81. 1 mas in right ascension and declination, respectively, and the mean O-C residuals are equal to -2 mas and -9 mas in right ascension and declination, respectively, for mutual occultations and -6 mas and +1 mas in right ascension and declination, respectively, for mutual eclipses.
Acknowledgements. This work was supported by the  Russian Foundation for Basic Research  (project no. 12-02-00294 ), by The  European contract ESPaCE  ( FP7-grant  agreement  263466 ), by the  Scientific Council of Paris Observatory , by the  CNRS PICS 3840 France-Russia , by the  Programme National de Planétologie  (CNES and CNRS) and by the  National Science Foundation of China  (Grant No  11273014 ) and the  Fundamental Research Funds for the Central Universities.
We found 20 genes whose overexpression altered strain abundance in the multi-strain biofilm. Only one gene (ORF19. 2781) was common to both planktonic and biofilm data, suggesting that the remaining 19 genes were not linked to a growth defect (Table  1 , Fig. 3  and S3 Table ). Overexpression of 16 out of these 20 genes resulted in increased strain abundance within the multi-strain biofilm (Table  1 ). A gene ontology (GO) term enrichment analysis was performed using the GO Term Finder at the Candida Genome Database  [38] [39] [40]  and the 531 gene set as a reference. Strikingly, among the 20 identified genes we found a significant enrichment of the GO term ''cell wall'' (P = 1. 4610 25 ) including 10 genes encoding (or predicted to encode) proteins involved in cell wall biogenesis and integrity (IHD1/PGA36, PGA15, PGA19, PGA22, PGA32, PGA37, PGA42, PGA59, PHR2 and TOS1, Table  2 ).
Labeled DNA was resuspended in 50 mL DigEasy Hyb solution (Roche), incubated at 95uC for 5 min, snap-cooled on ice and directly deposited on a barcode microarray (Agilent Technologies, GEO platform # GPL17420) containing: i) ,12 on-chip replicates of both sense and antisense DNA sequences complementary to 657 tags (representing 531 strain tags +126 unused tags) and ii) different negative control spots (Agilent reference). Hybridization was performed overnight at 25uC, followed by washing and scanning of the arrays using GenePix 4200 AL scanner (Molecular Devices). This experiment was repeated twice independently. Microarray data were analyzed using two distinct data processing softwares: GeneSpring GX 11 (Agilent Technologies) and ArrayPipe v2. 0  [69]. Z-score (i. e. number of standard deviations from the population mean) calculations were performed using ArrayPipe v2.
0. The thresholds for GeneSpring were kept at Fold Change values equal or superior to 2 and p-values equal or inferior to 0. 05, while thresholds for ArrayPipe v2. 0 were absolute Z-score values equal or above 1. 5 and p-values equal or below 0. 05. Only strains that met both algorithm thresholds for both sense and antisense barcode fluorescence signals were kept as altering planktonic growth. Microarray data have been deposited at GEO under accession number GSE48647 and Z-score and fold-change data are available in S2 Table.
Confirmation of the microarray fitness data by liquid growth assay Strains were individually grown three-times independently in 96-well plates at a starting optical density (OD 600 ) of 0. 1 in 100 mL of YPD supplemented with or without 50 mg. mL 21 doxycycline. The OD 600 was measured every 5 min using a Tecan Infinite 200 reader. Tecan OD 600 readings were converted into ''flask OD 600 '' reading using the following formula: OD Flask = OD Tecan 6 12. 2716-1. 0543 [70]  and doubling times were calculated within the exponential growth interval as previously described  [71].
The flow of GHAUM medium is controlled by a recirculation pump (Ismatec) set at 0. 6 mL. min 21 and pushed by pressured air supplied at 10 5 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37uC and biofilms (8 independent biological replicates) were grown for 40 h followed by genomic DNA extraction, barcode amplification and differential labeling (Doxtreated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays as described above. We performed two independent analyses of our microarray data using the Arraypipe  [69]  or GeneSpring softwares. Arraypipe analyses identified 29 genes with absolute Z-score values above or equal to 1. 5, fold change above or equal to 2, and p value below or equal to 0.
Cells were immobilized in the PDMS stamps as described elsewhere  [72] , and immersed in the same acetate buffer. To get statistical significance of the AFM data, about 10-15 cells have been analyzed from three independent experiments for each strain. AFM experiments were conducted on a Nanowizard III from JPK Instruments (Berlin, Germany). We used MLCT probes from Bruker probes with a spring constant of 0. 02 N. m 21 +/2 10% measured before each experiment by the thermal noise method. Adhesion force maps were recorded in force volume mode (32632 or 64664 force curves). The maximum applied force has been set to 2 nN, the Z displacement to 2 mm and the retract time to 50 ms (with a loading rate of 800,000 pN. s 21 ). Force curves were analyzed using JPK data processing software to extract the maximum adhesion force on each force curve.
Confocal microscopy fluorescence images and quantification Mixed biofilms with two strains expressing either the BFP or the GFP genes under the control of the P TDH3 promoter were grown for 40 h as described above. Confocal microscopy was then performed on the recovered plastic substrates, using a Zeiss LSM 700 laser scanning confocal microscope on an upright Axio Imager Z2 stand, using a Zeiss W-nACHROPLAN 40X/0. 75 working distance 2. 1 mm objective; z-stacks of the biofilms were obtained using the blue and green lasers, for the whole biofilm thickness. Z-stacks were then analyzed using Volocity software to acquire the volume occupied by the cells in the green channel (overexpression mutant, expressing GFP) and by the cells in the blue channel (control strain, expressing BFP).
Images were subsequently analyzed with the GenePix Pro 6. 1. 0. 2 software (Molecular Devices, Downington, PA). GenePix Results (GPR) files were imported into the Arraypipe 2. 0 for spot filtering, background subtraction (limma normexp BG correction) and Lowess global normalization of signal intensities  [73]. Replicate arrays (n = 3) were combined and fold-change and P-values (standard Student's t-test) were calculated. For RT-qPCR analyses, the strain CEC3785 (S4 Table) was grown exactly as described above and used as a negative control for doxycycline treatment. Total RNA from both the PGA22 overexpression-and control strains was extracted using the hot phenol method  [36]  and reverse transcription (RT) was performed using the SuperScript III first-strand synthesis system using 5 mg of total RNA (Invitrogen, catalog # 18080-051) in a total reaction volume of 20 mL.
The qPCR reaction was made of 1 mL from the RT reaction mixture combined with 4 mL of primer mix at 10 pmol. mL 21 each (forward and reverse primers of the selected genes, S6 Table ), 10 mL of 2X Takyon Rox SYBR MasterMix dTTP Blue (Eurogentec) and 5 mL of H 2 O (total volume = 20 mL). Q-PCRs were performed in a MicroAmp Optical 96-Well Reaction Plate (Applied Biosystems) using an Eppendorf realplex 4 Mastercycler real-time PCR instrument (Eppendorf) with 1 cycle at 50uC for 2 min, 1 cycle at 95uC for 10 min and 50 cycles at 95uC for 15 sec and 58uC for 1 min. Data analysis was performed using the realplex software version 2. 2 (Eppendorf). For each experiment, threshold cycle (C T ) values were determined using the realplex software. The levels of relative gene expression (n-fold) for the doxycycline-treated samples as compared to the untreated controls of PGA22, ORF19.
Supporting Information the Assembly 21 version of the Candida albicans genome at the Candida Genome Database (CGD, www. candidagenome. org); Gene name, gene name according to CGD; Category, functional category of the overexpressed open reading frame (ORF); Recipient strain, Lab identifier of the strain background carrying the corresponding ORF; Barcode, barcode sequence matching the corresponding ORF; Forward primer, forward primer used for polymerase chain reaction (PCR)-amplification of the corresponding ORF; Reverse primer, reverse primer used for PCR-amplification of the corresponding ORF. (XLSX) S2 Table Complete fitness profiling data of planktoniccell growth. Headers: Probe ID, Microarray probe identifier; ORF19 #, orf19 nomenclature from the Assembly 21 version of the Candida albicans genome at the CGD; Gene name, gene name according to CGD; Description, gene description according to CGD; fold change, fold-change abundance of the strain carrying the corresponding ORF treated with doxycycline as compared to untreated control; Z-score, Z-score value of the strain carrying the corresponding ORF; p-student, p-value of the corresponding fold-change value using a Student's t-test (within group).
Acknowledgments We are grateful to  Cosmin Saveanu ,  Antonia Doyen , and  Laurence Decourty  for valuable advice on competitive screens; members of  Institut Pasteur Transcriptome and Epigenome platform  for help with microarray processing;  Anne Neville  for critical reading of the manuscript and other members of the  UniteBiologie et PathogeniciteFongiques  for their constant support and numerous insights during the course of this project. We thank  Gillian Milne  from the  University of Aberdeen  for help with EM. We are grateful to  C. Gouyette  for oligonucleotide synthesis and  C. Bouchier ,  L. Ma  and  S. Cre  ´no for sequencing of the plasmid clones. Confocal imaging was performed at the  Plateforme d'Imagerie Dynamique, Institut Pasteur.
This work has been supported by the  European Commission  (EURESFUN, LSHM-CT-2005-518199; Galar Fungail 2, MRTN-CT-2003-504148; FINSysB,  PITN-GA-2008-214004 ) and  Agence Nationale de la Recherche  ( KANJI ,  ANR-08-MIE-033-01 ) to CE and the  Wellcome Trust  (The  Candida albicans ORFeome project ,  WT088858MA ) to CM and  Cd. Oligonucleotide  synthesis and plasmid sequencing were supported by  Pasteur-Genopole-Ile-de-France. VC was the recipient of a PhD fellowship of the  European Commission (FINSysB ,  PITN-GA-2008-214004 ). SZ was the recipient from post-doctoral fellowships of the  European Commission (FINSysB ,  PITN-GA-2008-214004 ) and  Agence Nationale de la Recherche  ( KANJI ,  ANR-08-MIE-033-01 ). ML was the recipient of a post-doctoral fellowship of  Institut Pasteur (Bourse Roux ).
TR was the recipient of a post-doctoral fellowship from the  European Commission  (EURESFUN,  LSHM-CT-2005-518199 ). CM acknowledges financial support from a  Medical Research Council   New Investigator Award  ( G0400284 ). ED acknowledges financial support of a young scientist program of  Agence Nationale de la Recherche  ( AFMYST  project  ANR-11-JSV5-001-01 nu SD 30024331 ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
5 ORF19. 6102 RCA1 bZIP domain-containing transcription factor of the ATF/CREB family involved in regulation of carbonic 1. 5* anhydrases; controls CO 2 sensing ORF19. 7277 Predicted ORF in retrotransposon Zorro2 with similarity to zinc finger-containing retroviral nucleocapsid proteins 1. 5 a orf19 nomenclature as described in Assembly 21 of the Candida albicans genome (see the Candida genome database at www. candidagenome. org) b Gene name according to CGD (www. candidagenome. org).
Positive and negative controls (using either a known infected sample from another bird species or 1 lL H 2 O, respectively) were included in all PCR reactions and on the agarose plates. Each sample was run twice to ensure the detection of infected birds and reduce false negatives. When there was inconsistency between two runs, a third screening was run to ensure the correct assignment of infection status. Only individuals that gave positive results in two runs were counted as being infected. All positive PCR products were sequenced on an ABI 3730 XL sequencer. Sequences were aligned using BioEdit  (Hall 1999)  and ClustalW  (Thompson et al. 1994). We compared the sequences to homologous sequences deposited in the National Centre for Biotechnology Information (NCBI) GenBank  (Benson et al. 2005)  and MalAvi  (Bensch et al.
2009)  databases to identify already known lineages. Exact matches with already published sequences were labelled according to the name of the known strain. When a sequence was already referred to by different names, we chose to keep the first published name. Sequences that differed by 1 bp or more were assigned a new name following the guidelines suggested by  Bensch et al. (2009) : the abbreviated scientific name of the host species (here CRECRE) followed by a number. The phylogenetic relationships between lineages is given in Figure  S1 , following the protocol described in Appendix S1.
2010 ): the standardized heterozygosity stH  (Coltman et al. 1999 ), the internal relatedness Ir  (Amos et al. 2001)  and the homozygosity by locus Hl index  (Aparicio et al. 2006 ). We also estimated population-level heterozygosity and genetic diversity using the following measures, computed with 'HIERFSTAT' R package  (Goudet 2005 ): observed heterozygosity Ho, gene diversity or expected heterozygosity He, rarefied allelic richness Ar and the inbreeding coefficient F IS. The effective population size (N e ) was calculated for each sampling site using an approximate Bayesian computation (ABC)  (Beaumont et al. 2002)  approach. We used simulations already computed to investigate the demographic history of corncrake across Europe (Y. Fourcade, D. S. Richardson, O. Kei ss, M. Budka, R. E. Green, S.
Statistical analyses We assessed the effect of individual measures of genetic diversity on infection probability using binomial regressions. We computed generalized linear mixed models (GLMMs) with population identity as random effect using the 'lme4' R package  (Bates et al. 2014). We used linear regressions to test the relationships between haemosporidian prevalence and the three measures of population-level genetic diversity: Ho, Ar and F IS. We then investigated the effect of three main categories of ecological factors on the variation of malaria prevalence: 1 Climate: We obtained climatic variables from the WorldClim project  (Hijmans et al. 2005 ), downloaded at a 2. 5-arc-min resolution (www. worldclim. org). The original database contained 19 variables but, as some of them were highly redundant, we selected the subset of eight predictors that described the spatio-temporal variations of temperature and rainfall across the study area: the annual mean temperature (Bio1), the maximum temperature of the warmest month (Bio5), the minimum temperature of the coldest month (Bio6), the temperature annual range (Bio7), the annual precipitation (Bio12), the precipitation of the wettest month (Bio13), the precipitation of the driest month (Bio14) and the precipitation seasonality (Bio15).
One bird was found to be infected by both a Leucocytozoon strain and a Plasmodium strain. Another four Polish birds showed evidence of mixed infection with both the Plasmodium strain SW2 and a previously undescribed haplotype that was 1 bp different (CRECRE1; GenBank accession number KJ783457). This new lineage was confirmed by the repeated amplification and sequencing of the original DNA sample. Among the ten haemosporidian strains detected, one Plasmodium lineage (SW2) occurred in 71% (25/36) of infected corncrakes (Table  1 ). This haplotype was restricted to the six easternmost populations (Poland, Latvia, Belarus and Russia) with an average prevalence of 11. 6% across these locations. SW5 was found only in Russia, infecting two birds. Regarding the western populations, France was characterized by a single lineage found only at this site: ACCTAC01.