dataesr/scientific-paragraphs-categorization huggingface dataset:
e. , for all of the geometric primitives that made up the canopy. The only exceptions to this were related to the anisotropy of the backgrounds in the two winter scenes. Here, the BRDF of the snow-covered backgrounds were mimicked with the semi-empirical RPV model  (Rahman, Pinty, & Verstraete, 1993; Rahman, Verstraete, & Pinty, 1993)  using parameter values obtained from fitting the RPV model with the procedure of  Lavergne, Kaminski, Pinty, Taberner, Gobron, Verstraete, et al. (2007)  to a directional reflectance dataset acquired with a portable goniometer  (Sandmeier, 2000). For the summer scenarios, the prescribed background albedos were based on in situ measurements at the respective test sites (and ignored any spatial variability). In addition, while actual reflectance measurements of species-specific wood and foliage spectra were available for most of the tree species, this was not always the case for transmission data.
Whenever reflectance or transmission data were missing, spectra from similar species was used to fill in the gaps (again using the Lambertian scattering assumption). For the various forest stands, only a single illumination scenario was defined (see rightmost column in Table  2 ). However, due to a lack of information about the directional distribution of the incident radiation (and thus across all relevant spectral bands in the visible and near-infrared), only the spectrally varying ratio of (isotropic) diffuse to total incident radiation was reported on the RAMI website. These data were based on measurements acquired either directly at the site  (Kuusk et al. , 2013)  or using the nearest AERONET  (Holben, Eck, Slutsker, Tanré, Buis, & Setzer, 1998)  station to the test sites. For the actual canopy scenes with regular planting patterns, 5 different sun positions (parallel and perpendicular to the plant rows) were provided.
More specifically the uncollided transmission component should be a spectral constant. However only DART, rayspread and pbrt provided this information in all 19 bands. While the data for the last two was spectrally flat, the DART simulations for the Järvselja pine stand were slowly increasing from 0. 19 in B01 to about 0. 21 in B05 and with a spurious dip (down to 0. 18) occurring at B17. On the basis of the RT quantities prescribed for RAMI-IV, it was possible to assess the energy conservation of simulation methods in a given spectral band. Ignoring the impact of non-zero horizontal radiation fluxes  (Widlowski, Lavergne, Pinty, Verstraete, & Gobron, 2006 ) the deviation from energy conservation can be written as: ΔF ¼ 1A þ f dir Á R dir þ f iso Á R iso ½ -1-α ð ÞÁ f dir Á T dir þ f iso Á T iso ½ ð1Þ where the fractions of incident direct and isotropic diffuse radiation are related as f dir = 1f iso and A is the total absorption of the canopy.
7  documents how the compliance rate of the RT simulation methods, i. e. , P(|ε| ≤ Δ) changes as a function of the width of the tolerance interval (Δ). For ease of representation, the latter is defined as a percentage of the reference value, i. e. , Δ = (f/100) • R and varied from f = 1% to f = 50% of the reference (R). Due to the substantial spread between the contributing RT simulation results (see Fig. 3 ), as well as the lack of an obvious cluster of methods providing closely agreeing simulation results for all of the actual canopy scenarios of RAMI-IV, it was decided to define a qualified reference dataset on the basis of all submitted simulation results. This is in accordance with the procedure defined in ISO-13528 for cases where neither an absolute reference value is available nor a trustworthy participant can be identified.
However, rather than working with a simply ensemble average, the robust mean algorithm proposed in annex C of  ISO-13528 (2005)  was used instead. The visual adequacy of this algorithm as well as the angular smoothness of the resulting reference BRF data can, for example, be seen in Fig. 7  of  Widlowski et al. (2013). Each panel in Fig. 7  relates to a different radiative quantity. Simulation results from all of the RAMI-IV actual canopy scenarios are included, with N max indicating the maximum number of simulation results that could be submitted for a given RT quantity. In the case of flux quantities pertaining to isotropic illumination conditions, N max corresponds to a mere 76 data points whereas for BRF simulations along an azimuthal ring, N max was of the order of 48000. As a consequence the curves of the BRF quantities are smoother than those of the flux quantities.
These model verifications can nowadays be carried out autonomously and in quasi-real time with the RAMI Online Model Checker (ROMC) facility that contains a reference dataset from six credible Monte Carlo RT models developed in the wake of the third phase of RAMI (see http:// romc. jrc. ec. europa. eu/). The ROMC is continually expanded, among others with a reference dataset (of flux quantities in the visible and near-infrared) that was used to evaluate the quality of RT formulations embedded in the land surface schemes of soil-vegetation-atmosphere transfer (SVAT), numerical weather prediction (NWP), and global circulation models  (Widlowsk Pinty, Clerici, Dai, De Kauwe, de Ridder, et al. , 2011. ). -C| b Δ -k•u ε , where k is a coverage factor, u ε is the combined standard uncertainty of the reference (R) and candidate (C) methods, and Δ is the tolerance interval (expressed as a percentage of the reference, i.
Concluding remarks In this phase of RAMI, RT simulation methods were executed on some of the most complex 3D canopy reconstructions currently available. These virtual plant environmentswhile based on field inventory data from actual test sitesdo not constitute identical copies of their real world originals, however. This is because even the most intensive field measurement campaigns are not yet in a position to deliver descriptions of the spectro-directional and architectural properties for every element along the vertical and horizontal in the target canopy volume. A large number of data gaps thus had to be filled in order to arrive at comprehensive descriptions of the RAMI-IV virtual plant environments capable of meeting the input data requirements of the most versatile of RT simulation models.
Outside of the scope of RAMI, these virtual plant environments can be used, for example, to assess the quality of quantitative retrieval algorithms on the basis of simulated satellite and in situ measurements, to improve spatial sampling techniques of radiative quantities in virtual field campaigns, or, to perform closure experiments that aim at matching actual remote sensing observations within their inherent uncertainty ranges. The latter process in particular, may identify potential gaps in our abilities to characterise complex forest sites in the field, as well as, in the manner in which in situ information is used in RT models. As better field measurement techniques become available (e. g. , terrestrial and/or airborne laser scanning, as well as UAV-borne radiometers and/or portable leaf goniometers), and the necessary parameterisation schemes are developed to transfer these data into RT model relevant formats, then the gap between simulated sensor responses and actual remote sensing measurements over real test sites should gradually diminish.
In addition, there were rarely any obvious clusters of simulation results that might help to guide the analysis. One exception was the HET14 Wellington Citrus Orchard scene where both rayspread and pbrt showed quasi-identical results across several thousand BRF simulations. In all other cases, a weighted ensemble averaging technique (robust mean) was used to establish a reference dataset for the subsequent performance analysis. Possible causes for the substantial dispersion among the simulation results could be 1) operator choices when transferring the prescribed test site properties to the needs and capabilities of a given RT model (e. g. , representing the realistic-looking trees from the RAMI website by cylindrical trunks and ellipsoidal hulls filled with scatterers), 2) operator errors during this scene creation process, and/or during the setup of the actual model run, and/or any eventual post-processing steps (e.
A rerun of the various actual canopy scenes should help in clarifying these questions (as it did for the RAMI phases 1 to 3). The dispersion among the various BRF, flux and THP simulations was already foretelling the outcome of any subsequent performance analysis. As such, the emphasis was not so much placed on a detailed analysis of model quality, but rather on presenting methods to test conformity with respect to permissible deviations from a reference. This topic is increasingly relevant due to the recurring need to demonstrate the fitness-for-purpose of quantitative data (e. g. , whether obtained from field measurements, model simulations, retrieval algorithms, processing chains) in application-specific contexts. More specifically, both the shared and guarded risk approaches were introduced to highlight the role of uncertainties associated with both the reference and candidate methods.
Truly, a dataset can only be eligible to act as reference solution in compliance testing if its associated uncertainty is but a small fraction of the width of the tolerance interval within which the candidate method must fall. Thus, whenever the width of the permissible tolerance interval is changed, one must evaluate the suitability of the reference solution anew. The examples provided in this study can be used to place confidence on compliance declarations (as well as on the rejection) of items. Crucial to the outcome of any conformity testing, however, are the choices made a priori for the width of the permissible tolerance interval, the minimum required compliancy rate (or alternatively the maximum permissible non-compliance rate), as well as the confidence level required for making (non-)conformity declarations.
Once these items have been defined, the uncertainty of potential reference datasets must be established in order to assess the eligibility of that dataset to act as reference in a subsequent conformity testing effort. Assessing the uncertainty of in situ measurement efforts for the validation of medium spatial resolution satellite products, for example, is not only costly, but also rather difficult. However, given the ability to simulate the radiative signatures of increasingly realistic terrestrial environments at both the local and domain-level scales, state-of-the-art three-dimensional RT models may be used to assess the magnitude of many of the contributing uncertainty components of current in situ efforts. This is then where intercomparison activities like RAMI come in again: To make sure that the quality of these simulation tools is well characterised and suitable for the requirements of the task at hand.
Acknowledgements This study would not have been possible without the continuing support of  A. Belward , head of the Land Resources Monitoring unit, at the  Institute for Environment and Sustainability of the European Commission's Joint Research Centre in Ispra, Italy. A special thank you must also go to  M. Buzica  and  M. Gerboles  who clarified the first authors' understanding of both equivalence and compliance testing in the context of European ambient air quality directives. The technical support of  M. Robustelli , as well as the contributions of  J. Písek  and  T. Lükk  for the test site characterizations, are also greatly appreciated. The field work at Järvselja was funded by the  Estonian Ministry of Education and Research  (target financing) as well as by  Estonian Science Foundation  grants.
Western blot analysis BMDMs and mouse joint tissues were disrupted in lysis buffer (PhosphoSafe™, Novagen, Gibbstown, NJ) containing a protease inhibitor cocktail. Proteins were separated by SDS-PAGE and transferred to a nitrocellulose membrane. Blots were probed with antibodies against phospho-AMPKα (Thr172), total AMPKα, phospho-p65 (Ser536), total p65, phospho-p38 (Thr180/Tyr182), total p38, phospho-ERK (Thr202/Tyr204), total ERK, phospho-ACC (Ser79) and total ACC (Cell Signaling Technology, Denvers, MA). Horseradish peroxidaseconjugated anti-IgG (Cell Signaling Technology, Danvers, MA) was used as secondary antibody. Membranes were developed using a chemiluminescence system (ECL detection reagent: Amersham Life Science, Aylesbury, UK). Densitometry analysis was done using Quantity One 1-D analysis software (Bio-Rad).
The amount of mobilized iron (AMI) was calculated as follows and expressed as grams  [9] : [Removed blood volume (L) Ã Hb at baseline (g/L) Ã 0. 0034]-[duration of phlebotomy treatment (days) Ã 0. 002]-[(Hb at baseline (g/L)-Hb at the end of therapy (g/L)) Ã 0. 0034]. Results are expressed as median and interquartile range [IQR] for continuous variables and as proportions for categorical variables. The normality of variables was evaluated by the Shapiro-Wilk test. Statistical comparisons between the 2 groups were performed using matched ttest or chi-square test as appropriate. Correlations were performed using Spearman's test. For all analyses p < 0. 05 was considered significant. Statistical analysis was conducted on SAS 9. 3 (Cary, NC, USA).
Transcriptomic tools such as the "Aedes detox chip"  [12]  are useful to identify detoxification gene regulation in insecticide resistant populations. However, while some of these genes are related to insecticide resistance, others are a response to environmental and evolutionary factors. The study of several mosquito populations could identify a common pattern of genes associated with pyrethroid resistance and eliminate those associated with environmental factors. Therefore, the objective of this work is to obtain and compare data on pyrethroid resistance and the underlying resistance mechanisms in three Ae. aegypti populations collected in geographically distinct French overseas territories.
DNA was isolated and suspended in 100 μl of PureLink Genomic Elution Buffer (from the kit) and stored at -20°C. The TaqMan reaction contained 12. Relationships between phenotypes and putative resistant genotypes were tested using a Fisher's test for each population with the MASS package in R 3. 2. 1 (R Development Core Team, Vienna, Austria). Linkage disequilibrium was tested with GENEPOP v4. 2  [19, 20].
Microarrays experiment RNA extraction and purification. Total RNA was extracted from 3-day-old female mosquito samples using the RNeasy Mini Kit from Qiagen, according to manufacturer's instructions. RNA quality and integrity was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA Integrity Number (RIN) was obtained for each sample, and samples with acceptable RINs were employed for the microarray experiments. RNA was also quantified using a spectrophotometer (NanoDrop 1000 Thermo Scientific). Experiment design and microarray hybridization. The array used was an updated version of LSTM Ae. aegypti detox chip (A. -MEXP-623). The 'Ae. aegypti detox chip plus' (A-MTAB-574, http://www. ebi. ac. uk/arrayexpress)(8x15K Agilent Technologies) housed two 60-mer unique probes with a 3'bias for 1089 genes associated with responses to insecticide and xenobiotics identified from previous studies using including all cytochrome P450s, GST and COEs  [12].
It also contained one probe for 2435 transporter genes and a unique probes for 222 'miscellaneous' genes (associated with immunity, heat shock proteins and housekeeping). A one-color microarray experiment was performed. Three sample groups corresponding to the three populations investigated (GUY, GUA and CAL) were all compared against the susceptible population from New Orleans (NO, reference strain). We used four biological replicates for each sample. In total, 16 one-color hybridizations were performed in this study. Experimental data are available under the accession number E-MTAB-4022. The cDNA synthesis, labeling, hybridization and subsequent washing steps were performed using Agilent's One-Color Microarray Gene Expression Analysis (Low input Labelling), according to the manufacturer's instructions.
Labeled cRNAs were hybridized to "Ae. aegypti Detox Chip Plus" to compare transcription levels of Ae. aegypti detoxification genes of the different populations against the susceptible New Orleans strain. Arrays were scanned by the Agilent microarrays scanner G2565BA, using the default settings for all parameters. Raw data were collected using the Agilent Feature Extraction Software (Agilent Technologies, version 10. 7). Quality and statistical analysis of the microarray data. The quality of each hybridization was analyzed with Agilent Feature Extraction software using the information provided by the statistics and the spikes (known mixtures of RNAs used as positive controls in Agilent platforms). Statistical analyses were performed with the Expression Analysis Software GeneSpring GX 12 (Agilent Technologies).
Arrays were normalized by applying LOWESS normalization. To directly compare arrays, a median baseline transformation was performed. In addition, probes were filtered according to the following criteria: positive and uniform, not saturated and above the background signal. Unpaired T-tests were performed to compare the differential expression of genes from each of the three populations of interest (GUA, GUY and CAL) separately, against the reference population (NO) using a Benjamini-Hochberg multiple testing correction, and a threshold of significance of 0. 001. Real time PCR data validation. Four mosquito samples, two used in microarrays and two new batches, were used to validate, by real-time PCR, some of the over-expressed and repressed genes in the GUA, GUY and CAL populations compared to the NO population.
5%) were in the three resistant populations: 12. 2% were up regulated and 2. 4% were down-regulated. In addition, 23 (18. 7%) were common to GUY and GUA strains, 4 (3. 3%) were common to GUY and CAL strains, 5 (4. 1%) were common to GUA and CAL strains. Almost 16% of the differentially expressed genes are not annotated as 'conserved hypothetical proteins' or are specified as 'metadata non available' in Vectorbase (S3 Table ). The expression data from these microarray experiments can be accessed at Vectorbase (E-MTAB-4022, http://www. vectorbase. org).
This work was funded by the  Institut Pasteur funds  through the  ACIP-A-03-2010  (www. pasteur. fr). This work has benefited from an " Investissement d'Avenir " grant managed by  Agence Nationale de la Recherche  (CEBA, ref. ANR-10-LABX-25-01 )(www. agence-nationale-recherche. fr). This study received a European commission "REGPOT-CT-2011-285837-STRonGer"Grant within such differences.
This survey gets two summary scores, physical and mental score, that are normalized with values taken from population norms, and 50 (a standard deviation of 10) is the general population mean. Any values over or below 50 should be interpreted as better or worse values, respectively, than the reference population used. The physical and mental summary components, calculated with specific Spanish weightings, are valid and reliable, and the reference norms for these summaries facilitate the interpretation of the quality of life results evaluated with SF surveys in studies conducted in Spain  [10]. The statistical analysis was done with the SPSS. 19 software, and expressed the qualitative variables in frequencies and percentages, the qualitative variable in means ± standard deviation, and also calculated the 95%CI in the variables of interest.
Acknowledgements This work was also partially supported by the  Research Commission of the Integrated Care Manegement, in Albacete (Spain). Many thanks any  Merry Chritsmas. Dra Mª Pilar Orgaz. The Research Comission Integrated Care, in Albacete" since this organization was the one which paid the bill of the article, and we wish to avoid ethical problems with it. We hope you can help us.
pneumoniae serotype 19F. 14 A phase I trial in adults 18-50 years of age showed that a aluminum phosphate-adjuvanted PhtD vaccine candidate was well tolerated, immunogenic, and could be boosted by a second vaccine dose. 15 During development of an enzyme-linked immunosorbent assay (ELISA) to measure antibody responses in the phase I trial, we found that individual and pooled serum from unimmunized healthy adults contained substantial PhtD-binding antibody (data not shown). To further investigate the immune response elicited by a PhtDbased pneumococcal vaccine, we developed a murine passive protection sepsis model for assessing the functional activity of human anti-PhtD antibodies. Naturally occurring human PhtD-binding antibody was purified from a commercial pooled serum (obtained from approximately 200 healthy individuals; Sigma, St.
Louis, MO). The concentration of anti-PhtD antibody was determined by ELISA, and its purity and specificity were confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Western blotting, and competition with recombinant PhtD (data not shown). The purified PhtD-binding antibodies were passively transferred by intraperitoneal injection (200 ml) to 6-to 8-week-old female CBA/CaHN-Btk xid /J (CBA/N) mice (Jackson Laboratories, Bar Harbor, ME). After 1 h, the mice were challenged by intravenous injection with a lethal dose (50 colony forming units [cfu] in 200 ml) of S. pneumoniae strain A66. 1 (serotype 3) (obtained from D. Briles, University of Alabama-Birmingham). The proportion of mice surviving at 14 days post-challenge increased with the concentration of anti-PhtD antibody (Fig.
pneumoniae strain A66. 1 (serotype 3), and survival was monitored for 14 days. Data were analyzed using logistic regression with probit link under PROC GLIMMIX in SAS version 8. 2 to determine the ED50. In each plot, circles indicate survival data for individual samples, and the best fit regression is shown as a green line, with the upper and lower limits of the 95% confidence interval shown as yellow and red lines, respectively. The horizontal line indicates a median response of 50% survival. In (A), mice were injected with 2. 8-27. 5 EU (1-10 mg) of purified anti-PhtD antibody or PBS. Survival data were from 4 passive protection experiments, which included 13 survival points. In five of the 13 cases (206, 275, 687, 1375, 2063, and 2750 EU/ml), the passive protection experiment was performed twice, and for 2 of these (275 and 2750 EU/ml), the points overlap and appear as a single data point.
Protection experiments for 3 cases (43, 435, and 2178 EU/ml) were not repeated and were included to provide a more appropriate range of antibody concentrations. In (B), mice were injected with 1:20 to 1:60 postimmune sera. To account for the baseline levels of protection seen in the pre-immune sera, the analysis was corrected for over-dispersion using PROC GENMOD with the SCALE D option in SAS version 9. 13 and based on survival data from mice that received pre-and post-immune sera. survival at day 14 compared to the pre-immune sera, and sera from subject nos. 37 and 43 were selected because the postimmune sera increased survival at day 14 and delayed death compared to the pre-immune serum. We also selected sera from subject no. 21 because the post-immune serum had weak or no functional activity, as indicated by a non-significant delay to death (P D 0.
Paired pre-immune and post-immune sera from these subjects were tested in the passive protection assay, and survival after 14 days is shown. Delay to death was assessed by survival distribution functions using the product-limit approach and compared between groups of mice by log-rank test using PROC LIFETEST in SAS version 9. 13. Differences in protection were compared by one-sided Fisher's exact test using PROC FREQ with the exact option in SAS version 9. 13. vaccine increases functional activity, at least in part, by increasing the antibody concentration. Whether vaccination also improves antibody quality is less clear. Our preliminary epitope mapping studies and experiments measuring serum binding to bacterial surfaces suggest that vaccination can also expand the epitope repertoire of anti-PhtD antibodies (data not shown).