dataesr/scientific-paragraphs-categorization huggingface dataset:
Estimation of Ya The accuracy of estimating Yg is determined by the weakest link, which perhaps in many cases may be the actual yields (Ya). Accurate geospatial distribution of current crop yields and their spatial-temporal variability are needed, preferably more granular than the FAO data or global datasets based on FAO data (such as  Monfreda et al. , 2008; You et al. , 2009) , that use national or sometimes provincial or state-wide averages. More detailed information on actual farmers' yields for specific locations can be based on farmers' surveys and data from wholesale buyers. Some projects are currently underway to achieve this greater spatial granularity, such as Global Futures (http://globalfuturesproject. com/) and a number of household panel survey datasets in progress at several international agricultural research centers.
Data and upscaling The minimum data to estimate Yp and Yw include data on weather (daily time-step Tmax, Tmin, precipitation, solar radiation, relative humidity and possibly windspeed), soil (in particular root zone water holding capacity and runoff as determined by soil texture, soil depth and slope) and cropping systems (actual and optimal sowing and harvesting dates, cultivar maturity, and optimum plant population density). We propose to use local agronomic information obtained from literature, surveys, government agencies, international institutions, or experts. Increasingly global databases with sowing and harvesting dates are becoming available (e. g. ,  Bondeau et al. , 2007; Waha et al. , 2012) , and these can eventually be used as a substitute, but only if local, observed data are not available.
Assuming the choice for a point or polygon-based approach and observed data (as opposed to generated or interpolated data), we recommend use of spatial maps of crop areas (e. g. , the MIRCA dataset of  Portmann et al. , 2010 , the SPAM dataset of You et al. , 2009  or more refined national maps) as a reference to identify important points or polygons for which Yg must be estimated for up-scaling to larger geographical units. To account for variation in climate, an agro-climatic zonation (ACZ-  Van Wart et al. , 2013b)  is proposed as the extrapolation domain for upscaling point estimates of Yp, Yw, Yg to regional and national scales. An ACZ is relatively homogenous in three parameters that are sensitive in defining growth potential for both individual crops and cropping systems: growing degree days, temperature seasonality, and aridity index  (Van Wart et al.
, 2013b). Within an ACZ a limited number of points (defined by their weather data availability) in key cropping areas are used to represent its variation in climate, soils, cropping systems and management (i. e. , sowing dates, cultivar maturity, plant population, etc. ). Yp or Yw are estimated for the dominant soils, cropping systems and management in a defined area (perhaps a circle of 50or 100-km radius) around the point for which the weather observations are estimated to be representative. Van Wart et al. (2013a)  have shown that a fairly robust estimation of Yp or Yw at a country level is achieved if ca. 50% of the total harvested area of a crop in that country is covered in this way. This focuses the yield gap assessment on the most important ACZs and specific locations within these ACZs, e.
Acknowledgements We thank  Justin van Wart  ( University of Nebraska-Lincoln, US ) and  Lenny van Bussel  ( Wageningen University, The Netherlands ) for their stimulating contributions in defining a protocol for yield gap analysis. We gratefully acknowledge  Delphine Deryng  ( School of Environmental Sciences, University of East Anglia, UK ),  Rachel Licker  ( University of Wisconsin-Madison, Madison, US ),  Christoph Müller  ( Potsdam Institute for Climate Impact Research, Potsdam, Germany ),  Kathleen Neumann  ( Netherlands Environmental Assessment Agency (PBL) & Wageningen University , The Netherlands) and  Elke Stehfest  ( Netherlands Environmental Assessment Agency (PBL), Bilthoven, The Netherlands ) for kindly sharing data from their global studies (Section 3. 4).
Aim of the project The project aims at providing a scientifically sound concept for an extended sewage and rainwater treatment in densely populated river catchment areas in view to reduce micropollutants and sanitarily relevant pathogens (including antibiotic-resistant bacteria) in surface waters. By a combination of chemical and microbiological analyses and effect-oriented biological studies which reflect consequences of the applied technologies for biota in the rivers from the molecular to the community level, the effectiveness of the applied technologies will be assessed. In addition, the optimization of assays that characterize exposure and biological effect is envisaged. Extrapolation of data on micropollutant and pathogen reduction to the entire catchment area of the river Schussen will result in scenarios whose potential for implementation will be critically assessed by a comprehensive cost-benefit analyses.
Acknowledgements The project SchussenAktivplus is funded by the  Federal Ministry for Education and Research (BMBF)  and cofounded by the  Ministry of Environment Baden-Württemberg. In addition,  Jedele & Partner GmbH ,  Ökonsult GbR , the city of Ravensburg, the  AZV Mariatal  and the  AV Unteres Schussental financially contribute  to the project. SchussenAktivplus is connected to the  BMBF action plan "Sustainable water management (NaWaM) " and is integrated in the  BMBF frame programme "Research for sustainable development FONA ". It is part of the the funding measure " Risk Management of Emerging Compounds and Pathogens in the Water Cycle (RiSKWa) " introduced to the public by  Huckele & Track  [44]. Contract period:  1/ 2012  to  12/2014 , Funding number:  02WRS1281A-L.
Marine phytoplankton, exempt of lignin, was assumed to display a Δ 14 C OC signature following the Δ 14 C DIC values (~ 100 -120‰) of the Mediterranean Sea surface waters  (Yechieli et al. , 2001)  and δ 13 C OC signatures were taken from  Harmelin-Vivien et al. (2008). The parameters for the two contemporary and kerogen-BC terrestrial end-members were taken from both our isotopic measurements and values from the literature. Based on these end-members, we show that sediment of the continental shelf would need a contribution of 30%, 40% and 30% of fresh terrestrial material from the Rhône River, kerogen-BC and fresh marine OM respectively (Fig. 9 ). The mixing model clearly indicates a gradient of increasing contributions of marine OM and kerogen-BC mixture along the dispersal axis. Immediately after the transition zone, the model-based contribution of kerogen-BC to OC increases from 10% in the prodelta to ~40% all over the continental shelf (station C and E): this is in good agreement with our BC data (Fig.
ACKNOWLEDGMENTS: We thank the captains and crews of the R. V. Tethys II for their help during the two scientific cruises of this project. We would like to thank  B. Bombled ,  E. Kaltnecker ,  C. Hatte , G. Gontier for their work and technical support during the cruises and laboratory analyses. We thank  F. Eyrolle  for providing us SPM samples collected in the Rhône River during the flood of June 2008. We thank  Robert C. Aller  and  Miguel Goñi  for proofreading our article and improving the quality of this manuscript from its early stage to its more final version. This work was supported by the  French National Research Agency , programme " Vulnérabilités: Milieux et Climat ", under the grant no. ANR-06-VULN-001  to the  CHACCRA  project, the  French INSU-EC2CO program  RiOMar. fr, the  MISTRALS/Mermex  programme and the  CEA.
05 eV. H(z)/[D A (z)b(z)] 2 P g (k ref , µ, z) k ref (h/ We fit the mock and Euclid-like spectra using the MCMC code MontePython  [27]. MontePython uses the Metropolis-Hastings algorithm like CosmoMC  [28] , but is interfaced with class  [29, 30]  instead of camb  [31] , is written in python, and has extra functionality; it will soon be released publicly, including the Euclid-like likelihood codes used in this work. Technical details of the assumed likelihood and our analysis are presented in Appendix A. Let us summarize here the essential points. As in most of the recent Fishermatrix-based forecasts, we assume that the reduced data is described by a set of observable power spectra P obs (k ref , µ, z), related to the familiar non-linear matter power spectrum P N L (k, z) in a non-trivial way in order to take into account redshift space distortions, linear light-to-mass bias, spectroscopic redshift errors and the Alcock-Paczynsky effect (see A.
These edges are directly given by ±α. We see in this figure that our assumption for α leads to an error of 1% at k = 0. 1hMpc -1 and 2. 5% at k = 0. 6hMpc -1 for the first redshift bin centered on z = 0. 5. For the last redshift bin in the galaxy survey, centered on z = 2, non-linear corrections appear on smaller scales, and the error is only 1% at k = 0. 6hMpc We performed several forecasts for a combination of Planck data and a Euclid-like galaxy redshift survey data. It should be stressed that the characteristics of Euclid are not yet finalized. Our choice for V survey and n g (z), detailed in A. 3, should be taken as indicative only. For Planck, we follow the method presented in  [22]  and do not include lensing extraction. For the experimental Planck sensitivity, we use the numbers presented in the Planck Bluebook 7.
Acknowledgements We would like to thank  Henk Hoekstra ,  Tom Kitching  and  Valeria Pettorino  for their comments on this manuscript. This project is supported by a research grant from the  Swiss National Science Foundation. MV acknowledges support from grants:  INFN/PD51 ,  ASI/AAE, PRIN MIUR ,  PRIN INAF 2009  and from the  ERC   Starting Grant  "cosmoIGM". BA and JL acknowledge support from the  Swiss National Fundation. SB is supported by  NSF  grant  AST-0907969.
Acknowledgements We thank the  CNRS  and the  ANR  (program  BLAN07-1_190839 ) for funding and the  Ministère de  l'enseignement supérieur et de la recherche (A. L. and  D. G. Ph. D. grants). We are grateful to  Christophe Chendo  and  Dr. Valérie Monnier  for mass spectrometry analyses and  Dr. Michel Giorgi  for X-ray determination (Spectropole,  Fédération des Sciences Chimiques de Marseille). We also thank  Dr. Nicolas Vanthuyne  for chiral HPLC separation.
Cells were let to recover for 1 hour before observation using Nikon automated microscope (ECLIPSE Ti, Nikon INTENSILIGHT C-HGFIE, 100x objective) and the Metamorph software (Molecular Devices, Roper Scientific), at 37°C. Phase contrast and fluorescence images (25% lamp energy, 1 second illumination LF movies and 600 milliseconds for HF movies) were sampled at two different time-scales. For low-frequency (LF) movies, images were taken every 3 seconds for a total of 5 minutes, while for high-frequency (HF) movies, fluorescence images were taken about very 0. 60 seconds for a total of 2 min (and phase contrast images were sampled about every 7 fluorescence images). Fluorescence excitation light energy level used here is 5-fold higher than previously described  [7]  to allow proportional decrease of exposure time, enabling a higher temporal resolution.
Image analysis and aggregate tracking. Phase contrast images were analyzed by customized software "Cellst"  [58]  for cell segmentation and single cell lineage reconstruction. Phase contrast images were denoised using the flatten background filter of Metamorph software for long movies or a mixed denoising algorithm  [58]  for fast movies. The mixed denoising algorithm combines two famous image denoising methods: NL-means denoising  [59] , which is patch-based and Total Variation denoising  [60, 61] , which is used as regularization. The Cellst software was used to automatically segment the cells on most of the images, albeit when necessary, manual corrections were applied. At the end of the whole segmentation and tracking process, Cellst also calculates the lineage of every cell in the movie.
This was achieved by computing a weighted average of the coordinates of the pixels in a circular neighborhood of the detected spot. The weights were given by the intensity values of the pixels to which the local background is subtracted. The local background was then computed as the median value of the pixel intensity in the neighborhood. Only pixels having intensity bigger than the median value were considered in the weighted average. This algorithm has been tested on both synthetic and real image and it shown a precision of 1/10 of a pixel on very poor contrasted spots. After detection and localization, the movements of the fluorescent aggregates were tracked and quantified by a third customized software named "aggtracker" based on the cell lineage and the detected spots. The algorithm uses the lineage and cell information to ensure that an aggregate is consistently tracked through points with points that are inside the same cell.
Background: Vaccine-serotype (VT) invasive pneumococcal disease (IPD) rates declined substantially following introduction of 7-valent pneumococcal conjugate vaccine (PCV7) into national immunization programs. Increases in non-vaccineserotype (NVT) IPD rates occurred in some sites, presumably representing serotype replacement. We used a standardized approach to describe serotype-specific IPD changes among multiple sites after PCV7 introduction. Methods and Findings: Of 32 IPD surveillance datasets received, we identified 21 eligible databases with rate data $2 years before and $1 year after PCV7 introduction. Expected annual rates of IPD absent PCV7 introduction were estimated by extrapolation using either Poisson regression modeling of pre-PCV7 rates or averaging pre-PCV7 rates. To estimate whether changes in rates had occurred following PCV7 introduction, we calculated site specific rate ratios by dividing observed by expected IPD rates for each post-PCV7 year.
Search Strategy We identified datasets from IPD surveillance systems that report rates through two approaches. First, we identified datasets gathered from a comprehensive systematic literature review on PCV dosing schedules  [11]. In that systematic literature review, a search for English language publications on the immunogenicity, and direct and indirect effects of various PCV schedules on nasopharyngeal (NP) carriage, IPD, and pneumonia among children was performed using 14 databases (i. e. , African Index Medicus; BioAbst/Reports, Reviews, Meetings; Biological Abstracts; Cochrane Library; EMBASE; Global Health; Index Medicus for Eastern Med. Region; Index Medicus for South-East Asia Region; IndiaMed; Latin America and Caribbean Health Sciences Information; Pan-American Health Organization; Pascal Biomed; PubMed; and Western Region Index Medicus) as well as meeting abstracts of the International Symposium on Pneumococci and Pneumococcal Disease (ISPPD) and the Interscience Conference on Antimicrobial Agents and Chemotherapy (ICAAC).
The search included studies published between 1994 and 2010. The complete list of database-specific and Medical Subject Headings (MeSH) search terms used in the literature search is detailed by the authors. We reviewed those publications with IPD as an outcome; these publications needed to include at least one ''narrow vaccine'' search term as well as an IPD related search term, i. e. , (''Invasive disease'' [all fields]), (''invasive pneumococcal disease'' [all fields]), and/or (''invasive bacterial disease'' [all fields]). Second, we solicited potential datasets from experts in pneumococcal disease, WHO headquarters and regional offices, and by reviewing references from publications.
Data Collection We solicited datasets from investigators using a standardized format, requesting IPD case counts for up to 5 years before and 10 years after PCV7 introduction, stratified by age groups (0-1, 2-4, 5-17, 18-49, 50-64, and $65 years old), clinical syndrome (overall IPD and meningitis specifically), hospitalization status, and serotype (Text S1). Meningitis was defined as isolation of pneumococcus from cerebrospinal fluid by culture. We requested age-and year-specific catchment population denominators to estimate rates, and we solicited descriptions of the PCV7 vaccination program, IPD surveillance system, changes to surveillance methodology or clinical practices, and potential IPD outbreaks.
Data Analysis The inclusion criteria of the datasets for collection and analysis are given in Figure  1. In datasets where serotypes 6A and 6C were not differentiated, we distributed these serotypes according to the known distribution of 6A and 6C in the same geographic region or globally in the pre-and post-PCV7 periods  [12]. First, we calculated the percentage of 6A isolates out of all 6A and 6C isolates, using datasets where 6A and 6C isolates were distinguished. The percentage of true 6A isolates was calculated for all datasets, as well as by region for datasets from Europe and North America. Estimates of the percentage of true 6A isolates were weighted by the size of the site and calculated in four different time periods: pre-PCV introduction; 1-2 years post-; 3-4 years post-; and 5+ years post-PCV introduction.
In sites that did not differentiate 6A and 6C serotypes, 6A/6C isolates were then redistributed according to the estimated regional (for North America and Europe datasets) or using all datasets' (for datasets from sites outside of Europe or North America) distribution of differentiated 6A and 6C isolates. After redistributing serotype 6A with VT (serotypes 4, 6B, 9V, 14, 18C, 19F, and 23F) and 6C with NVT (all other serotypes), remaining isolates with unknown serotype were redistributed. Specifically, isolates with known serotype were classified into four groups: VT serotypes (PCV7 serotypes and 6A); serotypes 1 and 5; serotypes 3, 7F, and 19A; and all other NVT serotypes. Serotypes 1 and 5 were grouped together to allow for modeling expected rates absent the potential influence of outbreaks of these two serotypes.
Because the impact of PCV7 was expected to be heterogeneous across sites, we used random effects meta-analysis to pool the sitespecific RRs  [20]. Meta-analysis was performed for each age and serotype group for each of the 7 years after PCV7 introduction, generating a summary RR with 95% confidence intervals. Metaanalysis of RRs was performed both including all datasets available for each year post-PCV7, as well as including only those datasets with at least 7 years of post-PCV7 data, which was the last year with enough datasets for robust meta-analysis (i. e. , five datasets). The same analysis comparing observed and expected rates was performed limited to meningitis cases. We performed several sensitivity analyses for IPD. First, we used a continuity correction of 0?1. Second, we performed an analysis completely excluding serotypes 1 and 5 from both pre-and post-PCV7 IPD rates.
To compare the contribution of these two NVT categories to the overall IPD incidence post-PCV7 introduction, we performed a separate analysis restricted to the post-PCV7 period where we  Proportion of children receiving the full infant dose by 12 months. N/P (not provided), meaning that immunization coverage not provided for year 1 and/or last year of surveillance data provided, although all included datasets were from sites that indicated they reached $70% coverage in the post-PCV period. c Active (A), proactive effort to identify all cases in an area; passive (P), reporting of cases by clinicians or laboratories without a systematic approach to capture cases not reported. defined the RR as the observed rate of IPD due to the NVT included in the higher valency vaccines over the observed rate of all other NVT not included in those vaccines.
Description of Sites We identified 72 potentially eligible datasets and requested information from the investigators (Figure  1 ). Of 32 datasets received, 21 from four geographic regions (six North America, 11 Europe, three Australasia, one South America) met the inclusion criteria for analysis (Figure  1 ). For children, 19 datasets were included in the IPD and meningitis analyses, although two sites were included only for IPD and two different sites were included only for meningitis. For adults, 15 and 11 datasets were included in the analyses of IPD and meningitis, respectively. At least 19 datasets included in the analysis have previously published IPD surveillance data, though not necessarily including the same data used for this analysis (i. e. , age group, case population, syndrome, and years of surveillance)  [3, 4, 16, [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36].
Specific reasons for exclusion from analysis for 11 datasets received were the following: no denominator provided (one); serogroup 19 not serotyped (one), ,70% coverage of the primary PCV7 series by 12 months of age (four)  [37] ; ,2 years of pre-PCV7 data (three); inability to define a proper denominator population (one); and substantial changes over time in case ascertainment of the surveillance system (one). The average annual number of IPD cases pre-PCV7 introduction for the 11 datasets excluded (six Europe, three North America, one Africa, and one Western Pacific) ranged from 8-1,490. Furthermore, among datasets included, two and six site-age group strata were excluded from the IPD and meningitis analyses, respectively, because ,50% of isolates in those strata were serotyped (Table  1 ).
The rate of NVT IPD increased significantly by 2 years after introduction (summary RR 1?34, 95% CI 1?02-1?77) and increased through 5 years, with little change thereafter through year 7 (summary RR 2?81, 95% CI 2?12-3?71) (Figure  3 ; Table  3 ). Most sites (seven statistically significant) showed an increase in NVT IPD rate in at least one post-introduction year (Figure  6 ). To account for the possible confounder of varying numbers of datasets included by year after PCV introduction, we repeated the meta-analysis including only the five sites with 7 years of post-PCV7 data. For VT, NVT, and all serotypes, the summary RRs were similar to those when all sites were included (Tables  3  and S2 ). The results were also similar when using a continuity correction of 0?1 instead of 0?5 (Table  S3 ) and when excluding serotypes 1 and 5 (Table  S4 ).
Adults For adults, the annual number of IPD isolates at baseline ranged from 3 to 4,929 with a median IPD baseline rate of 14?2 cases per 100,000 (range 0?6-101?7) (Figure  2 ; Table  2 ). The summary RR point estimates from the meta-analysis showed reductions in overall IPD for most years, though not statistically significant in years 1-6 post-introduction (Figures  3, 8 , 11, and 14; Table  3 ). Among the five sites with data 7 years post-introduction, statistically significant reductions were seen in year 7 for persons 18-49 years (summary RR 0?52, 95% CI 0?29-0?91), for persons 50-64 years old (summary RR 0?84, 95% CI 0?77-0?93), and for persons $65 years old (summary RR 0?74, 95% CI 0?58-0?95) (Figures 8, 11, and 14; Table  S2 ). VT IPD decreased significantly for all adult age groups by the second year after PCV7 introduction (Figures  3, 9 , 12, and 15; Table  3 ).
Discussion This study was unique in being able to collect, restrict, adjust, and analyze multiple IPD surveillance datasets in a standardized and systematic way, allowing summary estimates and cross-site comparisons of PCV7 impact on IPD rates that are not possible from individual site-specific publications  [4, 14, 38]. The most important public health implication of our analysis was that decreases in overall IPD rates in children-the group targeted for PCV7 vaccination-occurred quickly and were sustained after vaccine introduction despite increases in NVT rates. The summary reduction in the rate of overall IPD in children was 50%-60% compared with pre-introduction rates through 7 years after PCV7 introduction. We found similar overall rate reductions for pneumococcal meningitis as for overall IPD; meningitis might be less susceptible to changes over time in clinical practice and reporting compared to bacteremia.