dataesr/scientific-paragraphs-categorization huggingface dataset:
We registered the estimated dose at the centre of the cancer from the isodose curves in the central slice covered by the cancer position, and documented this as the point dose. We also registered the range of dose between the maximum and minimum possible dose at the breast cancer site taking into account the cancer size, location and an uncertainty margin in 3 dimensions and called this the dose uncertainty range. As a measure of inter-observer variation, a random sub-set of 22 cases were assessed again independently by a second radiation oncologist (BA). The breast cancer location according to ICD-10 definition  [17]  was recorded for the UK and Dutch patients groups and according to laterality. For 47 cases included in an earlier study we had data available to compare the inter-method variation in dose estimation with the CT phantom-based method to that obtained with the radiographbased method  [10].
In the WECARE study of asynchronous contra-lateral breast cancer  [15]  most second breast cancers were detected early as the patients were under regular screening following their first breast cancer diagnosis. However, 99/708 were excluded from the analysis due to multiple tumours in different locations, or single tumours that spanned multiple locations, or lack of information on location. In our study we included these tumour types by choosing the first largest tumour as the index tumour, and utilizing clinical and pathology  reports if no mammography was available. This makes our dataset more complete as we did not exclude the larger tumours.
Acknowledgements We thank all colleagues, patients, hospitals and registries who contributed. We thank  Annemieke Opstal-van Winden  for valuable discussions. Funding: this study was supported by the  Dutch Cancer Society  (grant no NKI  2004-3068  and  NKI 2010-4720 ) and  Euratom Programme  (grant number  012926 FI6R ), and in the UK by  Breast Cancer Now.
Statistical analysis The variables introduced in the analysis were checked for normality by examining histograms and considering values for kurtosis and skewness. Descriptive statistics were used to summarise these data and Pearson's Product Moment Correlation Coefficients were used to explore associations between the various domains of interest. Path analysis was used to estimate the strength of the direct and indirect relationships between the variables of interest. Chi-squared, the Root Mean Square Error of Approximation (RMSEA) and the Comparative Fit Index (CFI) statistics were used as measures of fit. SPSS Version 21 for Windows was used to undertake the descriptive and correlational analyses and AMOS 20. 0 structural equation modeling software for the path analyses. We imputed missing data using a multiple imputation method based on a Monte-Carlo Markov Chain algorithm  [36].
In the experiment, each combination of streptavidin with different fluorescent labels is specifically associated with one type of DNA strand/loop structure to distinguish them using fluorescence confocal microscopy. From fluorescence spectroscopy measurements, we estimate surface coverage of streptavidin on droplets is ~1000 μm -2 (Supplementary Methods and Supplementary Fig. 3 ). Confocal imaging and data analysis. After DNA functionalization, the droplets are mixed together at a number ratio of A:B:C: D:E = 1:2:2:2:2, and loaded into a homemade sample chamber (Supplementary Methods). The droplets cream to the top surface forming a monolayer, and diffuse thermally. The chamber was placed on a leveled surface in an incubator at 12 °C. The sample is imaged using fluorescence confocal microscopy (Leica TCS SP5 II) at different time points.
Acknowledgements This research has been primarily supported by  DOE   DE-SC0007991  to P. M. C. , N. C. S. , R. S. , and X. H. for initiation, design, analysis, and imaging. We acknowledge partial support from the  Gordon and Betty Moore Foundation  to P. M. C. , N. C. S. , R. S. , and X. H. for DNA sequence design, preparation, and characterization; grants  EFRI-1332411  and  CCF-1526650  from the  NSF ,  MURI W911NF-11-1-0024  from  ARO  and  N000141110729  from  ONR  to N. C. S. and R. S. for data analysis. Y. Z. acknowledges support from  DOE CBES  for sample preparation, confocal microscopy, and data analysis. A. M. , L. -L. P. , X. H. , and J. B. acknowledge partial support from the  MRSEC program of the National Science Foundation  under Award Number  DMR-1420073  for synthesis and characterization of the emulsion droplets.
Acknowledgments: The authors want to thank  Kate Grieve  for her expertise on cornea and retina experiments, and for revising the manuscript. We acknowledge the important help from  Thu Mai Nguyen  on tissue biomechanics, and passive elastography. We thank  Peng Xiao  for his help to understand adaptive optics FF-OCT and the role of incoherent illumination for FF-OCT. We are also grateful for the help of  Jena Sternberg  and  Claire Wyart  for discussion and preparation of the live zebrafish larvae experiments. We thank  Ralitza Stavena  for preparations and discussions about tumorous intestine samples. We finally express our gratitude to the team of  Diana Zala , for fresh tissue preparation, and the numerous discussions. This work was supported by grants from the  European Research Council   SYNERGY Grant scheme (HELMHOLTZ, ERC Grant  Agreement #  610110 ;  European Research Council, Europe)  and  LABEX WIFI (Laboratory of Excellence   ANR-10-LABX-24 ) as part of the  French Program 'Investments for the Future'  under reference  ANR-10-IDEX-0001-02 PSL.
Understanding person-centered reproductive health care: definitions and measures While PCC has received increased attention in developed settings, there is no consensus on how to measure it for reproductive health outcomes. Thus, in order to define PCRHC and identify unifying measures for it, we assessed separate bodies of work that discuss overlapping issues related to PCC, identified from PubMed and other databases as part of a forthcoming systematic review on measures of maternal health person-centered care (unpublished study, Nicholas Rubashkin, Nadia Diamond-Smith, Ruby Warnock; UCSF). This includes literature from health system responsiveness  [17] [18] [19]  , perceived quality of care  20, 21  , mistreatment of women during childbirth  6, 22, 23  , and the general literature on quality of care for maternal health  [24] [25] [26] [27] [28]  and family planning  29, 30.
The detectors were calibrated monthly by inserting a source of thoriated wires close to the outer vessel of the cryostat. The data acquired between two consecutive calibration measurements are referred to as dataset. Using the known energy of gamma lines between 511 keV and 2615 keV we were able to evaluate the calibration curve for each bolometer and for each dataset. We used the strongest line in calibration data (2615 keV from 208 Tl) to evaluate the detector response to a monoenergetic deposit near the ROI, for each bolometer and dataset. The physics-exposure-weighted mean of the resolution values for all of the bolometers is 4. 9 keV (FWHM), with a corresponding RMS of 2. 9 keV. This demonstrates that the CUORE goal of 5 keV energy resolution is feasible. We evaluated the background in the alpha-dominated region (between 2700 keV and 3900 keV) as 0.
The background in the ROI is 0. 058 + 0. 004 (stat) + 0. 002 (syst) counts/keV/kg/y. With these data, we set a 90% C. L. lower bound on the 0 decay half-life of 2. 7x10 24 yr. Combining this result with the 19. 75 kg-y exposure of 130 Te from the Cuoricino experiment, we obtain a limit of t1/2 > 4. 0x10 24 yr (90% C. L. ), which is the most stringent limit to date on the 130 Te 0 half-life  [9]. We also used the CUORE-0 data for an extended and comprehensive study of the background sources that contribute to the count rate in the region of interest. We built a Geant4-based Monte Carlo (MC) simulation to study the contribution of the particle interaction in the entire CUORE-0 setup (including the detector components, the cryostat and the shielding). We used, as input to the simulation, the values of the material contaminations obtained from screening measurements (i.
Acknowledgements The CUORE Collaboration thanks the directors and staff of the  Laboratori Nazionali del Gran Sasso  and the technical staff of our laboratories. This work was supported by the  Istituto Nazionale di Fisica Nucleare (INFN) , the  National Science Foundation , the  Alfred P. Sloan Foundation , the  University of Wisconsin Foundation , and  Yale University. This material is also based upon work supported by the  US Department of Energy (DOE) Office of Science, Office of Nuclear Physics. This research used resources of the  National Energy Research Scientific Computing Center (NERSC).
2 , bottom). We therefore examined our images from the swarming community with respect to the percentage of cells where GFP-DnaA was dispersed and clear foci were absent. Close to the edge of the mother colony, where most of the cells are in a long-chain form, 80% of cells belonged to this category. This percentage was 70% at the base of the monolayer and decreased progressively toward the tip of a dendrite, where only 17% of cells showed a diffuse DnaA distribution, while 75% had easily detectable foci (Fig. 2 ; see also Fig. S1b  in the supplemental material). The DnaA localization data thus clearly suggested that the swarmer cells are the most actively replicating cells within the community and that DNA replication in most of the stem cells of the dendrite is largely arrested or at least severely reduced.
Both microscopes were equipped with an AxioCam MRm camera (Zeiss). GFP fluorescent images with the Lumar instrument were taken using filter set 38 HE eGFP (Zeiss), and filter set 10 (Zeiss) was used with the Axio Imager M1. Highmagnification in situ images were obtained with a 63ϫ air or a 100ϫ oil objective. For the latter, we gently placed a coverslip over regions of dendrites to be observed. This ensured minimal disturbance of the sample with the displacement of, at most, a few cells from the edge of a dendrite. Image acquisition was done with AxioVision software (release 4. 6. 3). Semiquantitative analysis of fluorescence intensity along an entire dendrite was carried out on false-colored images in order to visualize the relative levels. Calculation and formatting of the fluorescence intensities were carried out using ImageJ software  (53).
Quantitative analysis of fluorescence signals (dispersed or in foci) was done on high-resolution false-colored images using the AutoMeasure module associated with the AxioVision software. When measuring the intensity of foci, local background fluorescence was measured within the individual bacteria and subtracted. The fluorescence distribution within a given population was analyzed as described previously  (18). For the visualization of cells from exponentially growing and stationary-phase cultures, overnight cultures in B medium were diluted to an OD 570 of ~0. 1 and grown at 37°C in fresh B medium for at least three generations (exponential phase) and to T4 (4 h after the transition from exponential growth) for stationary phase. Cells were mounted on 1% (wt/vol) agarose pads, and images acquired by an AxioCam MRm camera (Zeiss) using a 1.
3 numeric aperture (NA) 100ϫ oil objective on a phase-contrast/ fluorescence microscope (Zeiss Axio Imager M1). For the examination of fluorescence intensity of DnaA foci, cells were scraped from different regions of the dendrites (edge of mother colony, base, dendrite body, and tip) and dispersed in B medium. One microliter of the cell suspension was spotted on 1% (wt/vol) agarose pads and gently covered by a new coverslip. Cells were imaged using a phase-contrast/fluorescence microscope (Zeiss AxioImager M1) with a 1. 3 NA 100ϫ oil objective. Quantitative single-cell analysis of the fluorescence intensity of DnaA foci was performed using ImageJ software. The fluorescence intensity of GFP-DnaA foci was analyzed along at least 40 dendrites from three independent experiments, totaling 1,008 cells from the base, 1,246 cells from the body, and 1,213 cells from the tip of the dendrites to be analyzed.
Measurement of population density. Population densities were measured in situ in entirely monolayered 1-to 1. 5-cm dendrites. Images were captured using a 40ϫ Neofluar objective mounted on an AxioImager M1 microscope (Zeiss). Images were processed using ImageJ software. The calculated population densities were confirmed manually by counting at least 2,000 cells in three adjacent fields. Cells containing a clear septum were counted as two cells. In order to obtain sharp images of hypermobile cells in the tip region, swarms were placed under the microscope at room temperature without a coverslip for 5 min to reduce mobility. Fluorescent D-amino acid staining of the peptidoglycan. Staining with 7-hydroxy-coumarinamino-D-alanine (HADA) was used to track regions of active peptidoglycan synthesis  (43).
ACKNOWLEDGMENTS We are grateful to  Yves Brun  for useful discussions and for providing the fluorescent D-amino acids. CNRS and  University Paris Diderot ,  Sorbonne Paris Cité  provided funding to the  Research Unit UMR8261. The " Initiative d'Excellence" program  from the  French State  (grant  DYNAMO ,  ANR-11-LABX-0011 ) provided funding to H. P. and S. L. The  Lebanese Council for Scientific Research (CNRS-L)  awarded a doctoral fellowship to L. H. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Acknowledgements The authors thank  Simon Greenstreet ,  Cristina Herbon ,  Simon Jennings ,  Tiziana Luisetti ,  Lucille Paltriguera , and  Christian Wilson  for comments on previous versions of this paper. This work has resulted from the  DEVOTES (DEVelopment Of innovative Tools for understanding marine biodiversity and assessing Good Environmental Status ) project funded by the  EU  under the 7th  Framework Programme, 'The Ocean of Tomorrow' Theme  (No. 308392 ), www. devotes-project. eu. Further, A. G. R. was partially funded by the  Natural Environment Research Council  and the  UK Department for Food, Environment and Rural Affairs (Defra)  within the  Marine Ecosystems Research Program  (MERP), C. P. L. by  Defra  ( M1228 ), A. Z. by  BIO   C3  within the  joint Baltic Sea Research and Development Programme  ( EU 7th  and  Research Council of Lithuania ,  BONUS-1/2014 ), and M.
Methods LASV infection data. The experimental data have been described previously in ref. 7. In brief, chimeric Ifnar -/-B6 C57BL/6 mice were infected intraperitoneally (i. p. ) with 1000 focus-forming units (FFU) of LASV Ba366. Signs of disease, body weight, and body temperature, as well as levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and infectious virus particles were measured in the blood every 3-7 days over a period of 21 days  7. Viral load was quantified in immunofocus assay as FFU, with a limit of detection of 2 log 10 FFU/ml. Mice were separated into groups treated with different doses of ribavirin and/or favipiravir. Doses used comprise treatment with 80 mg/kg (n = 5) or 160 mg/kg (n = 5) of ribavirin administered daily by the i. p. route; favipiravir at 75 (n = 5), 150 (n = 5), or 300 (n = 5) mg/kg administered twice daily per os using a stomach probe; and for control, placebo-treated mice (n = 12) received twice daily PBS (Fig.
Data In this paper, we used two consecutive years of 1-min data collected at two sites that exhibit completely different sky conditions. The first site (Le Tampon) is located on La Réunion Island and experiences variable sky conditions, while the second one is situated in the continental U. S. and experiences an arid climate (Desert Rock). Table  1  lists the characteristics of the two sites. For this study, we computed 1-h averages of global horizontal solar irradiance (GHI) directly from the raw 1 min-data. The first year (2012) constitutes the training dataset used to build the forecasting models. The second year (2013) was used to evaluate the probabilistic forecasts (testing or evaluation dataset). Solar irradiance is characterized by deterministic diurnal and seasonal variations. Such a component can be removed from the analysis by working with the clear sky index (kt * ) instead of the original GHI time series, where kt * is defined as: kt * (t) = I(t) I clr (t) (1) This quantity corresponds to the ratio of the measured GHI I(t) to the theoretical GHI observed under clear sky I clr (t).
This preprocessing technique separates the geometric and the deterministic component of GHI from the stochastic component that is related to the cloud cover. The target variable for the forecasting model is then the stochastic component. Here, we used the clear sky data provided by the McClear model  [14]  publicly available on the Solar radiation Data (SoDa) website  [15]. This model uses aerosol optical depth, water vapor and ozone data from the MACC (Monitoring Atmospheric Composition and Climate) project  [16]. Finally, data points corresponding to nighttime and low solar elevations (solar zenith angle θ Z greater than 85 • ) were discarded from the dataset. This filtering removes less than 1% of the total annual sum of solar energy and discards measurements with large uncertainty (uncertainties associated with pyranometers are typically much higher than 3.
Site Analysis Figure  1  plots the clear sky index distribution of each location. As shown by Figure  1 , the continental station of Desert Rock experiences weather dominated by clear skies, evidenced by the high frequency of kt * near one. For the insular location Le Tampon, the occurrence of clear skies is much lower. In Figure  1 , one can notice a significant number of occurrences of the clear sky index above one. These events result from a phenomenon known as the cloud edge effect and can be observed anywhere in the world  [17, 18]. Table  1  (last row) lists the solar variability of each site. This quantity is calculated as the the standard deviation of step changes in the clear sky index σ(∆kt * ∆T )  [19]. This metric was computed for hourly kt * values (∆T = 1 h) for the whole dataset (two years).
ECMWF Day-Ahead Forecasts Besides ground data, the last model developed below also requires NWP forecasted data. As mentioned above, we used in this work data retrieved from the IFS model maintained and ran by ECMWF. Although NWP models outperform forecasts based on satellite data or ground measurements (only) for horizons longer than 5 h  [20] , they provide useful information as exogenous inputs. IFS provides hourly GHI data with a spatial resolution of 0. 125 • × 0. 125 • (approximately 14 km × 14 km; see Figure  2 ). For the purpose of this work, we retrieve IFS data (GHI and total cloud cover (TCC)) generated at 12 h 00 UTC (16 h 00 for Réunion Island).
Acknowledgments:  Philippe Lauret  has received support for his research work from  Région Réunion  under the  European Regional Development Fund (ERDF)-Programmes Opérationnels Européens FEDER   2014-2020-Fiche action 1. 07. The authors would like also to thank the  European Center for Medium-Range Weather Forecasts (ECMWF)  for providing forecast data and the meteorological network SURFRAD for providing ground measurements.
Finally, bacteria with intact cell membranes were fluorescently stained green whereas bacteria with damaged membranes were fluorescently stained red. After the staining, samples were placed in a saline buffer solution and analyzed with a confocal laser scanning microscope. The imaging software Fluorview V 4. 2 was used to process the CSLM images. The 3D images were first deconvoluted with Auto-quant × 3 (Media Cybernetics, Bethesda, MD) using an adaptive point spread function. Finally, 3Dreconstruction of the biofilm was created as volume rendered data sets using Imaris (Bitplane Scientific Software, Zurich, Switzerland).
Acknowledgements This work was supported by the research project No. N N518 291940  (Polish National Science Center). CLSM was purchased in the project " BIOFARMA Silesia. Centre for Biotechnology, Bioengineering and Bioinformatics " (co-financed by ERDF OP IG, 2007-2013). The authors gratefully acknowledge the consultations and supervision of  Prof. Wojciech Simka  ( Silesian University of Technology, Gliwice, Poland ) in terms of the alloys samples preparation and the surface treatment.
RNA isolation from mice and real-time RT-PCR A SMA mouse model (SMN2 +/+ , SMN 7 +/+ , Smn -/-) reproducing the phenotype of a SMA type II pathology (Jackson's laboratory, #5025) was used for this study and called SMN 7  (54). Ten-day-old SMN 7 mice (n = 3) and age-matched wild-type (WT) controls (n = 3) were anesthetized and sacrificed as described in  (51). Brain and spinal cord total RNAs were extracted. After DNase treatment, RNAs were reverse transcribed using M-MLV (Promega). Levels of mRNAs were measured by quantitative RT-PCR (qRT-PCR). Reactions were carried out on a LightCycler (Roche) using the Maxima SYBR Green PCR kit (Fermentas). Oligonucleotides used for qRT-PCR are listed in Supplementary Table  S2. Data were calculated according to the CT method. Results were expressed as mean ± standard error of an average of three measurements.
ACKNOWLEDGEMENTS We thank  A. Besse  for RNA extracts preparation,  R. Lührmann  and  L. Pellizzoni  for the gift of HeLa cell extracts and antibodies;  L. Schaeffer ,  A. Schweigert  and  S. Baudrey  for technical assistance. We are grateful to  A. Krol  for providing lab space and for critical reading of the manuscript. We thank  G. Eriani  for helpful discussions, constant support and critical reading of the manuscript. We thank  R. Smyth  for critical reading of the manuscript. Author contributions: AS. GB, M. L. , S. M. , V. C. and C. A. designed research. AS. GB, M. L. , L. W. , A. H. , F. S. , N. T. C. , V. C. , S. M. , M. B. and C. A. performed research. AS. GB, M. L. , V. C. , J. C. , S. M. and C. A. analyzed data. C. A. wrote the paper.
FUNDING French  Centre National de la Recherche CNRS ;  Agence Nationale de la Recherche  [ ANR-2011-svse8 02501 ];  French Infrastructure for Integrated Structural Biology (FRISBI)  [ ANR-10-INSB-05-01 ,  ANR-10-LABX-0030-INRT ,  ANR-10-IDEX-0002-02  to N. T. C. , V. C. , J. C. , IGBMC];  La Ligue Nationale Contre le Cancer , the  Région Lorraine , the  Université de Lorraine  (to A. H. , F. S. , S. M. );  French Ministry of Research and the National Research Fund, Luxembourg  (to L. W. );  University of Strasbourg Doctoralship  (to AS. GB. ); La Ligue Nationale Contre le Cancer  (to AS. GB. ); Région Lorraine Pre-doctoral Fellowship  (to A. H. );  Université de Lorraine  (to A. H. );  Fondation pour la Recherche Médicale  (to A. H. ). Funding for open access charge: CNRS.
Typical polysome profiles were obtained for non-treated and treated HCT-116 cells using both real-time absorbance detection and RNA visualization on agarose gel. The total quantity of 40S, 60S subunits, 80S monosomes and polysomes for a given amount of cytosolic extract was decreased in 5-FU treated cells. In particular, the 60S subunits and the monosomes 80S were drastically decreased. Using 32 P pulse labeling, we confirmed that levels of ribosome decreased in 5-FU-treated cells compared to non-treated ones, and that 60S and 80S are more prone to reduction than 40S (data not shown). This decrease in ribosomes quantity is concordant with the reduction of ribosome production previously described in response to 5-FU  [15, 18, 21]. Reduction in ribosome production in response to 5-FU was probably partly responsible for the decrease of global protein synthesis (Figures  2A-2B ).