dataesr/scientific-paragraphs-categorization huggingface dataset:
aureus cultures (OD 600 ¼ Z1) were centrifuged, washed once in 0. 9% NaCl containing 0. 02% Triton X-100, then washed twice in 0. 9% NaCl. Cell pellets were treated with 0. 5 ml of 1 N sodium methoxide. Heptane (200 ml) was then added, together with methyl-10-undecenoate (Sigma-Aldrich) as internal standard, vortexed for 1 min, and centrifuged. Fatty acid methyl esters were recovered in the heptane phase. Analyses were performed in a split-splitless injection mode on an AutoSystem XL Gas Chromatograph (Perkin-Elmer) equipped with a ZB-Wax capillary column (30 m Â 0. 25 mm Â 0. 25 mm; Phenomenex, France). Data were recorded and analysed by TotalChrom Workstation (Perkin-Elmer). S. aureus fatty acid peaks were detected between 12 and 30 min of elution. DNA sequencing. The fabI, accABCD and fabD genes of selected S.
The 2 Â 250 base pair reads were aligned and sequence variations were analysed using CLC Genomics Workbench 5. 5. 2 software (CLC Bio). SNPs were found when comparing our control Newman strain to that in the Newman reference sequence (GenBank Nucleotide accession code NC_009641). Only differences between our laboratory Newman strain and FA-T R mutants were considered in genome comparisons. Cloning of fabD and acpP. The fabD gene (locus NWMN_1140) and the fabD G196R variant gene were PCR-amplified from chromosomal DNA prepared from the Newman strain using the forward primer fabD-tail-F (5 0 -ATAAGC CGGGGGATCCACTAATGAGTAAAACAGCAATTATTTTTCCGGG -3 0 ) and reverse primer fabD-tail-R (5 0 -GCGCGCAATTAACCCTCACTAAAGGGTTA GTCATTTTCATTC CATCCTTTCACATC-3 0 ). Amplified DNA was cloned by Gibson assembly  63.
The presented data are pooled from animal studies performed as two independent experiments. Statistical analyses. The Mann-Whitney U-test was used to evaluate whether differences in CFUs in mice infected by Newman or mutant derivatives were statistically significant. Differences were compared for day 2 or day 6 between Newman and mutant derivatives. Analyses were performed with GraphPad Prism Software Version 6. 00 (GraphPad Software, USA). Statistical significance was given as P values. Growth capacity of fabD clinical variants and mutants on FA-triclosan. Precultures of Newman, M0251, M1532, SA957, SA40, CondT R -4, and CondT R -17 strains were prepared in BHI medium, and used to inoculate BHI or BHI-FA-T medium at an initial OD 600 ¼ 0. 01. Cell density was determined as OD 600 measurements after 16 h growth.
Acknowledgements This work was supported by  Agence Nationale de la Recherche (ANR)  funding of the  FattyBact  project  ANR-132101. C. M. was awarded a stipend from the  French Ministry. We are grateful to  Friedrich Go  ¨tz and  Regine Stemmler  ( Tu ¨bingen University ), and  Mary Delauney  and  Michael Calderwood (Bingham and Women's Hospital, Boston, USA)  for providing S. aureus strains and information on their characteristics. We thank  Philippe Bouloc  ( I2BC, Orsay, France), Melanie Guillemet and MicrobAdapt team colleagues  for stimulating discussions, and  Anne Six  and  Asma Tazi  for excellent technical help and advice.
Data availability. Genome sequence data for DepT R -5, DepT R -72, DepT R -45, CondT R -17, and our parental Newman strain have been deposited in the European Nucleotide Archive and can be accessed at http://www. ebi. ac. uk/ena/data/view/ PRJEB11476. The authors declare that all other data supporting the findings of this study are available within the article and its Supplementary Information files, or from the corresponding author upon request.
This study presents results from the European Centre for Medium-Range Weather Forecasts (ECMWF) carbon dioxide (CO 2 ) analysis system where the atmospheric CO 2 is controlled through the assimilation of columnaveraged dry-air mole fractions of CO 2 (XCO 2 ) from the Greenhouse gases Observing Satellite (GOSAT). The analysis is compared to a free-run simulation (without assimilation of XCO 2 ), and they are both evaluated against XCO 2 data from the Total Carbon Column Observing Network (TC-CON). We show that the assimilation of the GOSAT XCO 2 product from the Bremen Optimal Estimation Differential Optical Absorption Spectroscopy (BESD) algorithm during the year 2013 provides XCO 2 fields with an improved mean absolute error of 0. 6 parts per million (ppm) and an improved station-to-station bias deviation of 0.
7 ppm compared to the free run (1. 1 and 1. 4 ppm, respectively) and an improved estimated precision of 1 ppm compared to the GOSAT BESD data (3. 3 ppm). We also show that the analysis has skill for synoptic situations in the vicinity of frontal systems, where the GOSAT retrievals are sparse due to cloud contamination. We finally computed the 10-day forecast from each analysis at 00:00 UTC, and we demonstrate that the CO 2 forecast shows synoptic skill for the largest-scale weather patterns (of the order of 1000 km) even up to day 5 compared to its own analysis.
The accumulation of surface fluxes errors then leads to biases in the atmospheric CO 2. On the other hand, the strength of the CO 2 forecast model is its ability to provide a realistic CO 2 synoptic variability. The first objective of this study is to determine the quality of the XCO 2 fields resulting from the assimilation of GOSAT XCO 2 data with a CO 2 forecast model where the CO 2 surface fluxes are not constrained. The atmospheric CO 2 synoptic variability on a regional scale is related to the passage of frontal systems  (Wang et al. , 2007). These events are difficult to capture with the GOSAT measurements as the availability of the data is limited due to cloud contamination. Therefore, the second objective of this study is to document whether the assimilation helps improve the simulation of atmospheric CO 2 for synoptic events despite the lack of measurements nearby frontal systems.
Within CAMS, ECMWF is providing a CO 2 analysis based on the assimilation of GOSAT XCO 2 data with a delay of 5 days behind real time. A 10-day forecast is then issued from the analysis in order to provide the atmospheric CO 2 field in real time and for the next few days. The last objective of this study is to assess the quality of this forecast. The forecast quality as a function of the lead time and the season is evaluated against the analysis. This paper is structured as follows. Section 2 introduces the data sets used in this study. Section 3 describes our atmospheric CO 2 simulations with and without assimilation of the GOSAT XCO 2 data, and how we compared them with independent measurements. Sections 4 to 6 present the global evaluation of our simulations, a case study and the evaluation of the CO 2 forecast based on the analysis.
Data sets In this study, we used two sets of data. The first one is the measurements from the GOSAT's Fourier transform spectrometer and the XCO 2 product retrieved from these measurements by the University of Bremen (UoB) and is described in Sect. 2. 1. The second one is the collection of measurements provided by the Total Carbon Column Observing Network (TCCON) and is described in Sect. 2. 2.
We used an inhomogeneous GOSAT BESD XCO 2 data set in this study as the GOSAT BESD algorithm was still under development. This intermediate version of the GOSAT BESD XCO 2 data is referred to as MACC GOSAT BESD XCO 2 (MACC standing for Monitoring Atmospheric Composition and Climate, the precursor of CAMS). Nevertheless, from the beginning of 2014 onwards, we have been assimilating the current version of the  GOSAT BESD data (v01. 00. 02; Heymann et al. , 2015)  in near-real time. The TANSO-FTS detector has a circular field of view of 10. 5 km when projected on the Earth's surface (at exact nadir). In 2013, it measured in a mode with three measurements across track, and the footprints were separated by ∼ 263 km across track and ∼ 283 km along track. GOSAT can also operate in target mode, resulting in a finer sampling distance.
For these specific situations, we further thinned the observations on a 1 • × 1 • grid by removing all the observations but one chosen at random. This procedure avoids having several measurements in the same model grid cell during the assimilation. This thinning, plus the characteristics of the instrument (measurement only during sunlit periods) and the processing of the level-2 data procedure (retrievals for clear-sky conditions and only over land), reduces the number of GOSAT XCO 2 data to about 100 per day. The assimilation window of 12 h means that about 50 GOSAT XCO 2 data points are assimilated during each time window. The geographic distribution of these data is dependent on the season and the atmospheric conditions as illustrated by Fig. 1. For example, in July 2013, GOSAT BESD data are available up to 75 • N, and in October 2013 they are available only up to 60 • N.
The reason for this is the solar geometry and the filtering of measurements under high solar zenith angle (SZA) conditions, where XCO 2 is more challenging to retrieve as the impact of atmospheric scattering becomes larger compared to low-SZA conditions. Other data gaps are due to the strict cloud filtering and other types of filtering, like those based on the quality of the spectral fits, on scattering parameters, on the meteorological state, and on the measurement geometry. The MACC GOSAT BESD XCO 2 data sets have been bias-corrected using the TCCON data. As this data set is delivered in near-real time and the TCCON data are delivered with a delay of few months, it was not possible to directly compare the two data sets. Instead, the TCCON data from the previous year were used and they were corrected assuming a 2 parts per million (ppm) global atmospheric growth of CO 2.
A global offset was then computed and applied to the MACC GOSAT BESD XCO 2 based on the comparison between this data set and the corrected TCCON data set of the previous year. Moreover, with this procedure the TCCON data used in this study (same year as for the MACC GOSAT BESD XCO 2 data set) can be considered as independent data. For the assimilation, the observation error covariances have to be specified. In this study, we assumed that the observation errors are not correlated in space and time. For the standard deviation of the observation error, we used the uncertainty of the BESD XCO 2 product provided together with the data. The BESD XCO 2 uncertainty product accounts for the various sources of uncertainty of the retrieval process. It varies in time and space around an average value of 2 ppm.
Analysis vs. free run To assess the impact of the assimilation of the MACC GOSAT BESD XCO 2 , we compared the evolution of XCO 2 from the analysis with XCO 2 from the free simulation. Figure  5  presents the Hovmöller diagram (time vs. latitude) of this difference. It shows that the first region where the analysis impacts XCO 2 is the tropics. There, compared to the free run, the analysis continuously decreases XCO 2 by up to 1 ppm in June and by more than 2 ppm from September to December. The assimilation of the GOSAT data consequently causes an improvement as the free run has a positive bias in this region in autumn compared to the TCCON data. The analysis also decreases XCO 2 over the southern extra tropics (region between 23 and 66 • S) when compared to the free run (Fig. 5 ). The decrease extends to the southern high latitudes (≥ 66 • S) even when no GOSAT data were assimilated in this region.
This decrease results mainly from the transport of CO 2 from the equatorial region and southern mid-latitudes towards southern high latitudes. Unfortunately, there are no independent XCO 2 data available at southern high latitudes to assess the merits of the analysis there. Despite the fact that some GOSAT data are assimilated in the northern mid-latitudes during the first months of the simulation, the analysis only starts to differ significantly from the free run from March onwards. In this region, north of 30 • N, the analysis has higher values of XCO 2 than the free run, with a difference of more than 2 ppm during the northern summer. Again, the assimilation of the GOSAT data improves the simulated XCO 2 as the free run shows a strong negative bias there. Similar to the behaviour discussed for the southern high latitudes, the change in the CO 2 concentration at northern mid-latitudes is transported northward to higher latitudes.
Acknowledgements. This study was funded by the  European Commission  under the European Union's  Horizon 2020 programme. The development of the GOSAT BESD algorithm received funding from the  European Space Agency (ESA) Greenhouse Gases Climate Change Initiative (GHG-CCI ). TCCON data were obtained from the  TCCON Data Archive , hosted by the  Carbon Dioxide Information Analysis Center (CDIAC)  -http://tccon. ornl. gov/. Garmisch work was funded in part via the  ESA GHG-CCI  project. Four Corners TCCON was funded by  LANL 's  LDRD programme. Darwin and Wollongong TCCON  measurements are funded by  NASA  grants  NAG5-12247  and  NNG05-GD07G  and the  Australian Research Council  grants  DP140101552 ,  DP110103118 ,  DP0879468 ,  LE0668470  and  LP0562346. We are grateful to the  DOE ARM programme  for technical support in Darwin, and  Clare Murphy ,  Nicholas Jones  and others for support in Wollongong.
Microscopic fluorescence resonance energy transfer measurements and data evaluation Dynamics of arrestin-receptor interaction were performed on an inverted fluorescence microscope (IX71, Olympus, Hamburg, Germany). Single cells plated on poly-D-lysine-coated glass coverslips were observed using a ×100 oil-immersion objective (UPlanSApo 100×/1. 40 oil, Olympus). YFP was excited with a laser at 491 nm; CFP was excited at 405 nm. An optosplit II (Cairn Research, Faversham, UK) was used to split YFP and CFP (T495lpxr, Chroma, Olching, Germany). To minimize photobleaching, the illumination frequency was set to 0. 2 Hz. For CFP detection, an ET470/40× filter and, for YFP detection, an ET535/30 filter (Chroma) were used. The signal was amplified by a charge-coupled device (CCD) camera (ImagEM, Hamamatsu, Herrsching, Germany).
Data analysis Concentration-response relationships were analyzed by three-parameter non-linear regression using GraphPad Prism 5. 0 software (San Diego, CA, USA). For statistical tests, where only two datasets were being compared, unpaired Student's t-test (two-tailed) was used, where P < 0. 05 was deemed statistically significant. Where more than two datasets were compared, one-or two-way analysis of variance (ANOVA) tests were used with P < 0. 05 being accepted as significantly different. ANOVA tests were followed by Bonferroni's post hoc test, Dunnett's multiple comparison test or Dunn's multiple comparison test. All statistical analyses were performed using GraphPad Prism 5. 0 or GraphPad 4. 0 software. For BRET titration-binding experiments, a one-site binding equation was fitted.
Funding This work was supported by the  Deutsche Forschungsgemeinschaft  as part of the project  A13  of the SFB593 'Mechanisms of cellular compartmentalisation and the relevance for disease', awarded to M. B. D. Z. was the recipient of a  DAAD PROMOS Travel Grant  and is supported by  Labex EPIGENMED  and the  University of Montpellier, France. ERK1/2  and cAMP functional experiments were performed using the  Arpège Pharmacology Screening Interactome platform facility  at the  Institut de Génomique Fonctionnelle (Montpellier, France). A. J. B. and A. B. T. are funded by a  MRC  programme leader grant through the  MRC Toxicology Unit.
On a total of 20313 genes spotted on the human cDNA arrays there were between 116 (0. 6%) and 399 (2. 0%) genes differentially expressed depending on the RCCPDX model (data not shown). No specific molecular features could be deduced from the analysis of these differentially expressed genes. Analysis of the combined data showed that 33 differentially expressed genes were common among all RCCPX models tested 32 were downregulated and 1 was up-regulated. However, no specific molecular features could be deduced from this restricted list (Table  4 ). Importantly, there was no change in gene expression among passages (Figure  4 ). The expression data files have been deposited in GEO, accession number GSE83820 (http://ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE83820). We further investigated whether genetic alterations were similar between the primary and subsequent grafted tumors through STR fingerprinting (Table  5 ) and VHL gene   6 ).
Metastasis analysis Primary tumors and metastasis were monitored during one month following implantation (Figure  6 ). No signal was observable before IR780 injection. In the model shown, RCCPDX20, primary tumor and lung metastasis were observed 3 weeks post-implantation; 4 weeks post-implantation, we also observed brain metastasis. These data indicate that during passages in mice, tumor tissues conserved their ability to invade, and at classical metastatic localizations.
Transcriptome analysis Total RNA from patients' primary tumors and from corresponding tumors at passage ranging from P1 to P8 was obtained using Qiagen columns according to manufacturer's protocol. The concentration and integrity/purity of each RNA sample were measured using RNA 6000 LabChip kit (Agilent) and the Agilent 2100 bioanalyzer. U133 Plus 2. 0 array containing 54,624 probe sets excluding the AFFY quality control probe sets representing 20313 human genes (Affymetrix, Santa Clara, CA, USA). The Transcriptome analysis was performed by Firalis SAS (Huningue, France), a biotech specialized in biomarkers identification on 100 ng of total RNA that were amplified and labeled according to the Affymetrix protocol. The RMA data were reported as log2-transformed intensities. Descriptive statistics antilog intensities across all tumors were used.
Short tandem repeat analysis DNA from patients' primary tumors and from corresponding tumors at passage ranging from P1 to P4 was obtained by phenol/chloroform extraction A nanodrop ND-1000 spectrophotometer (Thermo scientific, Illkirch, France) was used to determine DNA concentration and purity. DNA samples were subjected to short tandem repeat (STR) DNA fingerprinting using the AuthentiFiler PCR amplification Kit (Life technologies, Saint Aubin, France) that amplifies 9 unique STR loci (8 that comprise tetranucleotide repeat units and one locus trinucleotide) and the Amelogenin gender-determining marker, according to manufacturer instructions. PCR products were separated by capillary electrophoresis on a genetic analyzer ABI PRISM 3100 and results analyzed using the GeneMapper software.
ACKNOWLEDGMENTS We thank the team of  Pr Seiamak Bahram ,  Molecular Immuno Rhumatology ,  INSERM U1109 ,  Strasbourg, France , for access to the  ABI   PRISM 3100  and the team of  Dr David Brasse ,  Institut Pluridisciplinaire Hubert Curien (IPHC), Imabio group ,  CNRS UMR 7178 ,  Strasbourg Cronenbourg, France , for small animal imagery. We also thank the competitivity pole  Alsace Biovalley, Illkirch-Graffenstaden, France  for advices and labelization. Finally, we also thank  Alsace Satt Conectus ,  Illkirch-Graffenstaden, France , for technologies transfer and advices. We thank  BPI France , the  Region Alsace , the  European Funds for Regional Development , the  Strasbourg Urban Community, INSERM  and the  University of Strasbourg  for financial supports. We also thank the  Alsace incubator SEMIA, Strasbourg, France , for financial supports and advices.
Immunostainings Cells plated in 12-well plates used for immunofluorescence were cultured under the same conditions as cells on MEAs. Briefly, after fixation in 4% paraformaldehyde cells were permeabilized and blocked before being stained with primary and secondary antibodies. Examination was performed by Leica SPE confocal laser scanning and Leica Application Suite Advanced Fluorescence software (Leica Microsystems, Buffalo Grove, IL, http://www. leica-microsystems. com). Immunofluorescence images were analyzed using ImageJ software, version 1. 50i (National Institutes of Health, Bethesda, MD, https://imagej. nih. gov/ij).
Statistical Analysis Continuous and normally distributed variables are presented as mean 6 SD (unless otherwise mentioned) and were compared by using an independent t test. For more than two groups, a one-way analysis of variance was performed with the Bonferroni correction as a post hoc analysis. In case of a skewed distribution, data are presented as median with the interquartile range and tested with the Mann-Whitney test; in case of more than two groups, a Kruskal-Wallis analysis was performed with post hoc analysis using the Dunn test. A p value of ,. 05 was considered to indicate statistically significant differences. All graphs were made by using GraphPad Prism software, version 5 (GraphPad Software, La Jolla, CA, http://www. graphpad. com/).
Thus, measurement of OSP-specific antibodies may provide further information regarding isotype-specific (especially class-switched) responses to vaccine. Here, we present results from an immunogenicity study conducted within a population at high risk for cholera in Juba, South Sudan. We enrolled a subset of vaccinees (n = 205) from a 2015 OCV campaign in a camp of internally displaced persons to measure their immune responses to the vaccine. We use this data to estimate the proportion of vaccinees seroconverting after each dose, and explore different aspects of the participants' baseline and post-vaccination immunologic markers of cholera exposure. In particular, we compare seroconversion proportions between children and adults, and compare the responses after one and two doses of OCV.
Ethics Statement. All study staff, most of whom were recruited from the community, received theoretical and practical training about the study methodology and human subjects research ethics. The study protocol was reviewed and approved by the ethical review committee of the South Sudan Ministry of Health and the institutional review boards of Johns Hopkins Bloomberg School for Public Health and the University of Utah and carried out in accordance with relevant guidelines and regulations. Given that this study was embedded in a large public health campaign, and was not an intervention study, it was not registered in a WHO primary clinical trial registry. Data Availability. All data used in this manuscript are available at https://github. com/scottyaz/ juba-ocv-immuno. Additional protocol details and raw data files are available from the corresponding author on reasonable request.
A significant proportion of individuals had a self-reported history of receiving an OCV in a vaccination campaign about one year earlier  (90/205; 44%)  23. Young children were evaluated further for their physical and nutritional status (Supplementary Table  1 ). Baseline log 2 vibriocidal titers to O1 Inaba and Ogawa ranged from 5 to 1280 in study participants. Geometric mean titers (GMT) in study participants to O1 Inaba were 21. 6 (95% CI 17. 1-27. 4) and that to Ogawa were 28. 5 (95% CI 22. 4-36. 2). Over one in five participants had baseline titers > 80 to Inaba (21%) and Ogawa (29%). Baseline vibriocidal GMTs to both O1 serotypes generally increased with age, with older children having 2-to 3-fold higher baseline titers than younger children (Fig. 2 ). Since our sample was not representative of the age-distribution of the population, we used data on the PoC age-distribution from the month of the campaign to estimate the age-standardized baseline GMTs to O1 Inaba and Ogawa.
Acknowledgements The authors would like to thank the study staff, participants, community leaders in the  UN House PoC , staff at the  WHO Juba Country Office, IMC Staff  ( Dr Meroni Abraham ,  Alejandro Guzman ,  Kourtney Rusow ,  Emebet Dlasso ),  MSF-Switzerland  for help with logistics,  Paul Kovac  and  Peng Xu  at  NIDDK  for the gift of OSP:BSA. This work was sponsored by The  National Institute of Health  ( K08 AI100923  grants to D. T. L,  R01 AI106878  to E. T. R. ), The  Bill and Melinda Gates Foundation  ( OPP1089243  to J. L. , A. S. A,  Delivering Oral Vaccine Effectively (DOVE)  Project,  OPP153556  to D. A. S. , F. J. L. , A. S. A. , and  OPP 1089248  to WHO) and  Margaret A Cargill Foundation  grants to the  WHO.