dataesr/scientific-paragraphs-categorization huggingface dataset:
26 for the second half of the run (0. 18 for the full run). Although naively one might expect log(R HK ) to be a good predictor of plage filling factor, and hence of the convective RV component, there are several physical factors that might reasonably be expected to degrade the correlation over short time scales (our dataset spans 2-3 solar rotations). Foreshortening and limb darkening affect the Ca II HK emission cores and the brightness-weighted line-of-sight granular velocities in different ways. Near the limb, the Ca II emission in plages originates in higher, hotter regions of the chromosphere and remains bright. The limb darkening of facular pixels is less than that of quiet-sun pixels, but near the limb the line-of-sight component of the radial motion of bright granule cores is reduced by foreshortening.
In fact,  Lanza et al. (2016)  find a much weaker correlation between the mean total magnetic flux measured by the SOLIS VSM instrument and RV (Spearman correlation coefficient of 0. 131) over their 8-year dataset, which spans both active and less active phases of the solar cycle. When compared against correlations with the traditional spectroscopic activity indicators (the FWHM, BIS and log(R HK )), we see that the disc-averaged magnetic flux | Bobs | is a much more effective predictor of activity-induced RV variations, over the timescale of a few rotation periods. The averaged magnetic flux may therefore be a useful proxy for activity-driven RV variations as it should map onto areas of strong magnetic fields, which suppress the Sun's convective blueshift. The line-of-sight magnetic flux density and filling factor on the visible hemisphere of a star can be measured from the Zeeman broadening of magnetically-sensitive lines  (Robinson 1980; Reiners et al.
ACKNOWLEDGMENTS We wish to thank the referee for their thoughtful comments, which have greatly helped improve the analysis presented in this paper. RDH gratefully acknowledges  STFC  studentship grant number  ST/J500744/1 , and a grant from the  John Templeton Foundation. The opinions expressed in this publication are those of the authors and do not necessarily reflect the views of the  John Templeton Foundation. ACC and RF acknowledge support from  STFC  consolidated grants numbers  ST/J001651/1  and  ST/M001296/1. JL acknowledges support from  NASA  Origins of the Solar System grant No. NNX13AH79G  and from  STFC  grant  ST/M001296/1. The Solar Dynamics Observatory was launched by  NASA  on 2011, February 11, as part of the  Living With A Star program. This research has made use of  NASA's Astrophysics Data System Bibliographic Services.
1b ). This was in line with increased toxin levels in supernatants from PUNE08 as compared to M37 (Supplementary Table  1 ). The higher toxin production was also evident as judged by the larger hemolysis zones around PUNE08 colonies on sheep blood agar as compared to M37 (Fig. 1c  and Supplementary Fig. 1e ). The two reference strains showed hemolysis and cytotoxic patterns resembling that of PUNE08, i. e. larger hemolysis zones and greater cytotoxicity as compared to M37 (Fig. 1a-c ). To identify the genetic factor responsible for this phenotypic diversity the whole genome of PUNE08 and M37 was determined (sequences are deposited in DNA data bank of Japan (DDBJ) and the accession numbers are M37: BCLL01000001-BCLL01000060 and PUNE08: BCLM01000001-BCLM01000056). Sequence analyses revealed a single nucleotide mutation at position 667 of the agrC gene in strain M37 compared to PUNE08 leading to an amino acid substitution from tyrosine (Y) to cysteine (C) at position 223 (Fig.
4b ). Gene expression analyses of the infected skin tissue model (Fig. 4c, d ) revealed a similar differential virulence gene expression profile as noted in stationary phase bacterial cultures (Fig. 3a, b ). In addition, IL-1β , TNF, CXCL8 and IL-6 were assessed at mRNA and protein levels in infected skin models. This revealed that the cytotoxic PUNE08 wt and M37 agrC-C223Y strains induced higher IL-1β , CXCL8, and IL-6 as compared to the colonizing M37 wt and PUNE08 agrC-Y223C (Fig. 4e-h ), whereas the reverse was true for TNF (Fig. 4f ). Thus the data are in agreement with the noted activated caspase-1 versus upregulated TNF-R1 expression in infected keratinocytes. Colonizing strains harboring cysteine in position 223 of AgrC show a persistence phenotype in a human 3D skin model. To further investigate the noted difference in adherence and internalization between the strains, imaging studies were performed in infected keratinocytes and organotypic skin tissue.
Two reference tips, one with the ligand and the other with highest concentration of analyte were used. These experiments were performed in a buffer containing 20 mM HEPES, pH 7. 6, 200 mM KCl, 2% glycerol. Both AgrC Y223C and AgrC wt were incubated separately with 5 μ M of DTT and H 2 O 2 respectively in these experiments. The binding kinetics were analyzed using the Octet Data Analysis Software v 8. 0. Whole genome sequencing and analyses. Whole genome sequencing of S. aureus M37 and PUNE08 isolates was performed using massively parallel high throughput sequencer Illumina Hiseq-1000. The raw-reads for both isolates were filtered for quality and more than, 8 million reads were obtained with at-least 100X coverage for the 2. 8 Mb S. aureus genome. The raw reads were assembled into contigs using VELVET version 1.
25  47  and gene predictions were made using GLIMMER 3. 02  48. The protein sequences were derived from the above gene sequences using EMBOSS transeq  49  the relative arrangement of the contigs was determined by BLASTP and TBLASTN  50. The sequences are deposited in the DNA data bank of Japan (DDBJ) and the accession numbers are M37 wt: BCLL01000001-BCLL01000060 and PUNE08 wt: BCLM01000001-BCLM01000056. In total, 14 genes (spa, hla, hld, hlg, pvl, psmα and β, sarA, rot, sigB, agrA, B, C and D) associated with virulence or regulation of virulence factor expression were analyzed. After the BLASTP/BLASTN prediction of the genes, 1 kb upstream/downstream region sequences (to include the promoter region also) were extracted from the contig sequences using PERL script. The extracted sequences were aligned using online CLUSTAL W tool.
1. 1). In short, images were threshold, smoothed and segmented based on the respective channels for S. aureus and LC3AB or LAMP. Based on the segmented area, the fraction of S. aureus inside the LC3AB or LAMP positive areas (% colocalization) was calculated. The mean fluorescence intensity (MFI) in 10-15 fields/tissue sections was determined using the image analysis software CellProfiler (version 2. 1. 1).
Statistical analysis. No statistical methods were used to predetermine sample size. Data are presented as mean ± s. d. for the indicated number of experiments. The data were analyzed with use of the Graphpad Prism v. 5 software (GraphPad, San Diego, CA). Due to small sample size no normality test was performed and non-parametric two-tailed Mann-Whitney U-test was applied for all comparisons between PUNE08 and M37 or between wild-type strains and their respective mutant, p values less than 0. 05 were considered significant.
Acknowledgements The study was supported by grants from the  Karolinska Institutet  (ANT),  Swedish Research Council (ANT) ,  The Stockholm County Council (ANT) , The  European Union   Seventh Framework Program  ( FP7/2007-2013 ) under the grant agreement  305340  and  Swedish International Development Agency grants (GA). HAR22 strain was kindly provided by  Dr. Hermínia de Lencastre ,  ITQB-UNL , and The  Rockefeller University. We Thank  Dr. Tim Stinear  and  Dr. Benjamin Howden ,  Doherty Institute, University of Melbourne  for providing reagents required for creating allelic exchange of agrC in S. aureus strains. Genomic DNA sequencing was performed by the  Next-Generation Genomics Laboratory facility at the Centre for Cellular and Molecular Platforms at National centre for Biological Sciences, Bangalore.
We thus excluded the 143 previously unringed immigrant females out of 327 observations, i. e. 44. 8 %. As in many species, dispersal was more frequent in yearlings than in older females (respectively 75 and 26 %; χ 2 1 = 26. 5, P > 0. 001; see Additional file 1: Table  S2 ). Our final dataset included 97 females in 2012 and 87 females in 2013, among which 26 females were caught in both years.
For ROMs concentration and plasma antioxidant capacity, adult body mass during nestling feeding (continuous) was included as a covariate, and for body mass and body composition, tarsus length (continuous) was included as a covariate. To account for the non-independence of data for individuals measured in both years and for individuals breeding in the same plot, individual and plot were included as random effects in linear mixed models. The plate was also added as a random effect when modelling ROMs concentration and antioxidant capacity. The effect of female age (yearling vs. older adult) and its interaction with dispersal status were included in preliminary analyses of oxidative balance markers, body composition, body mass and reproductive success to account for potential differences between natal and breeding dispersal, which are under different selective pressures  [1].
For nestling body mass, weighing time (continuous) was also included as a covariate. In a second step, we directly tested the effect of female oxidative balance on reproductive output. The foster mother antioxidant capacity and ROMs concentration as well as their interaction with dispersal status, wing load manipulation, and plot density were included to the final models of nestling body mass and fledging success obtained in the first step. Fixed effects were selected by stepwise elimination, starting with interactions. Selection criteria were the p-values of type-III F-tests for LMM, with denominator degrees of freedom calculated using Satterthwaite's approximation (R package 'lmerTest' , function anova  [78] ) and the p-values of type-III Wald chi-square tests for GLMM (R package 'car' , function Anova  [79] ).
ASSOCIATED CONTENT * S Supporting Information The Supporting Information is available free of charge on the ACS Publications website at DOI: 10. 1021/acs. nanolett. 6b01240. Supporting Information provides refractive indices (n and k) used for FDTD calculations, additional data from measurements and numerical calculations, detailed numerical analysis of the diffraction efficiencies and angular photon distribution, derivation of the analytical model for the light trapping of diffracted waves and the expression of the optical path enhancement factor F, and measurement results of every patterned solar cells from the same sample. (PDF).
Materials and Methods All experimental and analytical procedures are described in the supplementary method file, Supplementary Material online. This study was approved by the Research Ethics Commission of the Eijkman Institute for Molecular Biology (Jakarta, Indonesia). accommodating the sampling program. The authors wish to acknowledge support from the GenoToul bioinformatics facility of the Genopole Toulouse Midi Pyrenees, France. They also thank Harilanto Razafindrazaka for her useful comments on the manuscript. This research was supported by French ANR grant number ANR-14-CE31-0013-01 (grant OceoAdapto to F. -X. R. ), the French Ministry of Foreign and European Affairs (French Archaeological Mission in Borneo (MAFBO) to F. -X. R. ), and the French Embassy in Indonesia through its Cultural and Cooperation Services Genetic Ancestry of the Malagasy in Southeast Borneo.
The mean values are separated by latitude bands, along with estimates of their uncertainties. The asymmetric isotopomer shows a mean enrichment of ∼ 8 %, with a vertical profile that increases up to 33 km and decreases at higher altitudes. This decrease with altitude is a robust result that does not depend on retrieval settings, and it has not been reported clearly in previously published datasets. The symmetric isotopomer is considerably less enriched, with mean values around 3 % and with a large spread. In individual retrievals the uncertainty of the enrichment is dominated by the measurement noise (2-4 %), which can be reduced by averaging multiple retrievals; systematic uncertainties linked to the retrieval are generally small at ∼ 0. 5 %, but this is likely underestimated because the uncertainties in key spectroscopic parameters are unknown.
(1) Since the isotope effects for O 3 are very large, they are often reported in percent (%) rather than parts per thousand (‰), and this convention is followed in the present paper. The primary international reference ratio R( In this paper, satellite retrievals of δ(a-50 O 3 ) and δ(s-50 O 3 ) derived from the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) instrument on Envisat are presented. The purpose is to investigate whether and how the MIPAS observations can be used to provide independent data on ozone enrichment in the middle and upper stratosphere, and to detect and quantify possible temporal and geographical variations. For validation, these enrichments are compared to previously published results from the balloon-based thermal emission Fourier transform infrared (FTIR) spectra of  Johnson et al.
In this work, the retrieval processor developed by KIT-IMK (Karlsruhe) and IAA/CSIC (Granada) is used. A detailed description is given in von  Clarmann et al. (2003) ; its performance on ozone retrievals was studied in detail by  Glatthor et al. (2006). Validation studies performed by  Steck et al. (2007)  and  Laeng et al. (2014)  showed that MIPAS ozone retrievals have realistic error estimates, and suffer from only small biases of 5-20 % (depending on altitude and reference instrument). MIPAS data have been used to retrieve the ozone isotopologues 49 O 3 and 50 O 3 by  Piccolo et al. (2009). There was generally a good agreement between the MIPAS Envisatderived enrichments and those obtained from  FIRS-2 (Johnson et al. , 2000)  and  MIPAS-B (Friedl-Vallon et al. , 2004)  for a-50 O 3 and s-50 O 3 ; the enrichments for 49 O 3 were higher than expected from either theory or FIRS-2 observations.
Tikhonov, 1963; Steck, 2002). This term maps the shape (but not the values) of the a priori O 3 profile to the heavy O 3 profile when the measurement does not resolve the full structure of the latter. D is a diagonal matrix, which is usually zero everywhere except for the elements referring to the topmost altitudes of 100 and 120 km; it forces the ozone Table  1. Microwindows used in this study. The first two are in the A band (685-970 cm -1 ), the remaining six in the AB band (1020-1170 cm -1 ). VMRs at these altitudes to be close to zero. The a priori values x a come from MIPAS IMK/IAA V5H ozone profiles. For 48 O 3 these exact profiles are used, while for 50 O 3 they are scaled according to δ( 50 O 3 ) = 0 with respect to the standard used in the HITRAN database; in terms of the standard adopted in the present paper, this is a prior enrichment of -3.
By excluding the AB band both a-50 O 3 and s-50 O 3 are limited to 3 degrees of freedom (defined as the trace of the averaging kernel; see  Rodgers, 2000) , while including the AB band increases this number to 6. The precision of the retrievals also suffers when the AB band data are disregarded, with standard deviations that are a factor of 4 larger. Thus, the gain in isotopic information by including the spectral lines in the MIPAS AB band outweighs the problem of a possible bias between the A and AB bands. Conversely, the A band includes many s-50 O 3 lines, so this band cannot be ignored without a significant loss of information. From the resulting VMRs of 48 O 3 , a-50 O 3 , and s-50 O 3 , the isotopic enrichments δ(a-50 O 3 ) and δ(s-50 O 3 ) are calculated. The total enrichment, used for comparison with mass spectrometer data, is then given by δ( 50 O 3 ) = 2δ(a-50 O 3 ) + δ(s-50 O 3 ) /3.
Error analysis With the retrieval set-up in place, the uncertainties in the profiles of the VMRs and their covariances are calculated. The following sources of uncertainties in the retrievals are considered: measurement noise, based on instrumental parameters; uncertainties in the temperature profile, and in horizontal temperature gradients; the temperature is a retrieved quantity, and the uncertainty in the retrieval is used here; for the horizontal gradient, a fixed value is assumed (see Table  2 ); - uncertainties in the spectroscopic data in the HITRAN database; it should be noted that for a-50 O 3 and s-50 O 3 several critical parameters, such as line position and intensity, have no uncertainties given in the HI-TRAN database at the frequencies considered here; this component of the systematic uncertainty is therefore underestimated in the calculations; uncertainties in the instrumental parameters: line of sight, residual spectral shift, gain calibration, and instrumental line shape; the assumed values for these uncertainties are given in Table  2.
The total random uncertainty, and thus overall precision, is around 4 %, dependent on latitude and altitude. The systematic errors caused by uncertainties in the spectroscopic parameters and the instrumental line shape are generally small at 0. 5 %. However, it should be noted that, in the microwindows considered here, the magnitudes of the uncertainties in the spectroscopic data for 50 O 3 are not given in the HITRAN database for several key parameters, such as line position and intensity. This is likely caused by the difficulty in distinguishing between the symmetric and asymmetric isotopomers, noted by  Janssen (2005). Therefore, this uncertainty is underestimated here. The uncertainties all increase sharply in all latitude bands at altitudes above 50 km. While the uncertainty due to measurement noise can be reduced by averaging over a large number of profiles, the uncertainties in retrieval parameters, particularly instrumental parameters, will typically remain.
Datasets The isotopic composition of stratospheric O 3 has been studied extensively since its discovery. The most comprehensive datasets, used here for validation of the MIPAS data, are the space-based solar absorption spectra by the ATMOS Fourier transform infrared spectrometer  (Irion et al. , 1996) ; the balloon-borne thermal emission spectra by the FIRS-2 Fourier transform spectrometer  (Johnson et al. , 2000) ; the balloon-borne solar absorption spectra by the MkIV FTIR spectrometer  (Haverd et al. , 2005) ; the mass spectrometer data of  Krankowsky et al. (2007) ; and the space-borne emission spectra by the SMILES submillimetre sounder  (Sato et al. , 2014). The ATMOS dataset consists of observations from the Spacelab-3 mission in July 1973 and the Atlas-1, Atlas-2, and Atlas-3 missions in  March 1992 , April 1993 , and November 1994.
It shows global average enrichments of 12 ± 6 % for a-50 O 3 and 7% ± 7 for s-50 O 3 (using the isotopic standard adopted in this paper), with no discernible variations with latitude or altitude. The uncertainties indicate the standard deviation in the measurements. The FIRS-2 dataset uses data of seven balloon flights between 1989 and 1997, launched from Fort Sumner, Daggett, and Fort Wainwright. The mean enrichments between 25 and 35 km of altitude are 12. 2±1. 0 % for a-50 O 3 and 6. 1±1. 8 % for s-50 O 3. Note that the uncertainties given here are the standard error of the mean as opposed to the standard deviation, which is typically larger. No significant variation with altitude is found. The FTIR dataset uses data of seven balloon flights between 1997 and 2003, launched from Fort Wainwright, Esrange, and Fort Sumner.
Mean enrichments of 13. 8 ± 2. 9 % and 7. 0±2. 6 % are reported for a-50 O 3 and s-50 O 3 , respectively; it was not specified in the original publication whether these uncertainties denote standard deviations or standard errors. The absolute precision of the enrichments due to uncertainties in the retrieval parameters (temperature, pressure broadening coefficients, zero offset, and slant column integration) is estimated to be around 2 %. A pronounced vertical trend is attributed to photolytic enrichment. For two balloon flights, anomalously low enrichments are associated with a high stratospheric aerosol content due to the eruption of Mount Pinatubo. The mass spectrometer data were collected from 11 balloon flights from Kiruna, Aire-sur-l'Adour, and Teresina between 1998 and 2005. These measurements show the highest precision of the datasets considered here; at high altitudes an absolute precision of 0.
4 % in the enrichment is reported. The use of mass spectrometry makes it impossible to distinguish a-50 O 3 and s-50 O 3 , however. The measurements at midlatitude and equatorial latitudes show vertical trends that cannot be explained by the temperature effect in the formation re-action alone, and are ascribed to photolytic enrichment. The polar data show a seasonal trend that is consistent with the temperature. The SMILES dataset was gathered at the International Space Station in February and March 2010. Only latitudes between 20 and 40 • N were considered. It only contains enrichments for the a-50 O 3 isotopomer, but it covers higher altitudes (up to 52 km) than the other datasets. The absolute systematic error in the enrichment varies between 4 and 6 % at altitudes between 25 and 45 km.
By latitude band In the Northern Hemisphere there is generally good agreement between the MIPAS-derived enrichments and previously published data (see Fig. 3 ). In the polar latitude band there is a slight discrepancy between MIPAS and the mass spectrometer data of  Krankowsky et al. (2007) , but this is within the uncertainty limits of both datasets. Interestingly, the MIPAS data show a decrease at high altitudes (> 35 km) that is not seen in other datasets. In order to exclude that this decrease is due to an artefact of the retrieval procedure, several tests were performed. -The vertical extent of the microwindows was expanded in order to increase the altitude range in which information is gathered. In particular, the A-band microwindows were extended up to 47 km in altitude. This did not result in a better agreement of the retrievals with previous independent data, and increased the number of retrievals with convergence problems.
Global At altitudes below 33 km the global mean total enrichments of MIPAS are in good agreement with previous observations (cf. Fig. 4 ), particularly with the mass spectrometer data of  Krankowsky et al. (2007). The disagreement with other datasets that is visible in the tropical and Northern Hemisphere latitude bands persists in the global average. The global mean enrichments of a-50 O 3 derived by MI-PAS are generally in good agreement with previous observations. As is the case for total 50 O 3 in the tropical and northern latitude bands, discussed above, the MIPAS global mean δ(a-50 O 3 ) shows a decrease above 33 km; other datasets also show a decrease with altitude, starting at 40 km for the FTIR dataset of  Haverd et al. (2005)  and the SMILES dataset of  Sato et al. (2014) , or at 30 km for the FIRS-2 dataset of  Johnson et al.
(2000). The ATMOS dataset of  Irion et al. (1996)  shows a steady increase up until the maximum retrieval altitude of 40 km. Furthermore, a decreasing enrichment above 35 km is also predicted by photochemical models, caused by the large fractionation in the long-wavelength tail of the Hartley band  (Liang et al. , 2006; Ndengué et al. , 2014). These models predict maxima at 35 km with amplitudes of 3 % for a-50 O 3 and 6 % for s-50 O 3. The symmetric isotopomer profiles show large standard deviations below 30 km and above 45 km, making comparison with other datasets problematic at those altitudes. Between 30 and 45 km, the MIPAS enrichments are lower than those of the FTIR and ATMOS datasets; where the latter show the enrichments increasing with altitude, the former is steady or shows a slight decrease.