dataesr/scientific-paragraphs-categorization huggingface dataset:
AMTD Acknowledgements. The optical parameters of sulphate aerosols layers used in this work are obtained with the  IDL Mie  scattering routines developed by the Earth Observation Data Group of the  Department of Physics of Oxford University , and available via the following website: http: //eodg. atm. ox. ac. uk/MIE/. NOVELTIS is gratefully acknowledged for the support with the 4A/OP model. Alain Chédin ,  Virginie Capelle  and  Cyril Crevoisier  are gratefully acknowledged for the help with 4A/OP, TIGR and the GEISA database. Hervé Herbin  is gratefully acknowledge for the stimulating discussion during the last few years. This project has been partially supported by the  EU   7th Framework Program  under the grant  603557  (StratoClim).
in Sect. 2. As done for Sects. 3. 3 and 3. 4, we restrict our attention to H 2 SO 4 mixing ratios of 60, 64, 70 and 75 % and temperature of the droplets of 213-215 K, within the set of tabulated values. As demonstrated in Sect. 3. 2, the extinction properties of the H 2 SO 4 /H 2 O droplets layers are very weakly dependent on the temperature. The chosen parameters are intended to mimic a realistic tropical UTLS situation, given the constrains of our dataset. The altitude of the sulphate aerosol layer has been fixed at about 150 hPa. A typical tropical atmosphere (temperature, humidity and gas concentration profiles) is selected from those available in 4A/OP. Then we conduct 256 simulations by varying the four H 2 SO 4 mixing ratio/temperature combinations and all the available effective number concentrations and effective radii (see Tables Figures Back Close Full Screen / Esc Printer-friendly Version Interactive Discussion Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper |.
In this paper we have presented sensitivity analyses on the optical properties and BT signatures of secondary sulphate aerosols in the UTLS, based on TIR IASI pseudoobservations obtained with the 4A/OP radiative transfer model. We have modelled the sulphate aerosols as layers of H 2 O/H 2 SO 4 binary solution droplets with varying temperatures, mixing ratios and size distributions. The optical properties of these layers are obtained with a Mie code, taking as inputs the complex refractive indexes of H 2 O/H 2 SO 4 bynary solution with different temperatures and H 2 SO 4 mixing ratios from laboratory measurements and archived in the GEISA database, and size distribution with different effective radii and effective number concentrations. 6 Conclusions Discussion Paper | Discussion Paper | Discussion Paper | Discussion Paper | Figures Close Full Screen / Esc Back Printer-friendly Version Interactive Discussion.
g. ,  Engel et al. 2010; Alonso-Herrero et al. 2012; Wild et al. 2014). Some merging objects have been included in large ob-Fig. 1. Example of the evolutionary scheme for interacting and merging galaxies described in Sec. 2. 1. Top: SDSS r-band images of galaxies included in the CALIFA survey, from left to right: pre-merger stage, well-defined separation between the galaxies, no evident interaction signatures (IC 0944 and KUG 1349+143); merger stage: two defined nuclei with evident interaction features (NGC 169 and NGC 169A); post-merger stage, single extended nucleus in optical with prominent tidal features (NGC 2623); merger remnant stage, possible tidal debris (NGC 5739). Middle: stellar velocity fields. Bottom: Hα+[NII] velocity field for each galaxy example. Contours represent the continuum obtained from the data cubes.
We note that for these objects the velocity field distributions are extracted from a single IFU data cube, except for the pairs of galaxies in the pre-merger stage, where each galaxy has its own IFU data cube. The size of each box is 2 arcmin. Top is north and left is east. servational samples devoted to studying specific science cases for local galaxies. For instance the stellar kinematics in early type galaxies, (e. g. , NGC 5953 included in the SAURON project Falcón-  Barroso et al. 2006)  or ionized gas kinematics for spiral or irregular galaxies  (GHASP, Epinat et al. 2008). More recently, a significant number of studies focus on the characterization of the ionized gas velocity fields of (Ultra)-Luminous IR Galaxies ([U]LIRGs) with morphological tidal features or merging remnants (e. g.
We applied the same methods to characterize the velocity fields in both samples. The layout of this article is as follows. In Section 2 we describe the classification of our interacting sample. We also present a comparison of this sample with the CALIFA mother and control samples as well as the extraction of the velocity fields from IFU data and the methodology used to determine kinematic properties directly from the velocities distributions. In Section 3 we compare the different kinematic parameters derived from the interacting galaxies with those from the control sample, and we study these properties at different interaction stages. In Section 4 we discuss our results, while in Section 5 we summarize our results and present the conclusions from this study. In Appendix A we present the tables with the kinematic properties, and in Appendix B we present the kinematic velocity distributions for the ionized gas and the stars.
Is J. K. Barrera-Ballesteros and G. van de Ven). For this study we include 13 additional companions observed and reduced with the same procedure as the CALIFA galaxies (see Sec. 2. 4). In total there are 19 additional objects. The final number of objects between the pre-merger and merger stages is 85 (see Table  1 ). We note that despite our efforts to observe both companions of the binary system, some of them only have IFU data available for one galaxy in the system. Top: Morphological type distribution against SDSS r-band absolute magnitude distribution of the interacting sample. The number in each bin represents the sources included in it. Bottom: Color magnitude diagram for the CALIFA MS, control and interacting samples. Morphologies and absolute magnitudes are taken from  Walcher et al.
CALIFA observations and velocity fields extraction Observations were carried out using the PPAK instrument at Calar Alto Observatory  (Roth et al. 2005). Its main component consists of 331 fibers of 2. 7 diameter each, concentrated in a single hexagon bundle covering a FoV of 74 × 64 , with a filling factor of ∼60 %. Three dithering pointings are taken for each object to reach a filling factor of 100% across the entire FoV (see details in  Husemann et al. 2013). The final data cube consists of more than 4000 spectra at a sampling of 1 × 1 per spaxel  (details in Husemann et al. 2013). The median spatial resolution of the survey is 2. 5  (García-Benito et al. 2015). The CALIFA survey has two spectral setups, V500 and V1200, low and intermediate resolution, respectively. Objects included in this work have been observed in the V500 setup.
It has a nominal resolution of λ/∆λ ∼ 850 at ∼5000Å and its nominal wavelength range is 3745-7300Å. However, the final data cube has a homogenized spectral resolution (FWHM) over the entire wavelength range of 6. 0Å and the wavelength sampling per spaxel is 2. 0Å. The total exposure time per pointing is fixed for all the observed objects to 45 min. The data reduction is performed by a pipeline designed specifically for the CALIFA survey. The reduction process is explained in detail by  Sánchez et al. (2012)  and improvements on this pipeline are presented by  Husemann et al. (2013). For consistency we follow the same kinematic extraction used in the control sample (see details in Paper I). For the stellar kinematic extraction we selected spaxels with continuum S/N > 3. To achieve a minimum S/N of 20, we used a Voronoibinning scheme for optical IFU data implemented by  Cappellari & Copin (2003).
Second, as we note in Sec. 2. 1 our ability to determine whether a galaxy is a merger remnant is based only on the observation of low-surface brightness tidal features. These features could be the result of a recent minor merger or a new supply of gas  (Davis et al. 2011; Lagos et al. 2015)  leading to the observed strong difference between the kinematic orientation of the stars and the ionized gas in these galaxies. The wealth of data allows us to compile the different kinematic parameters presented in this study to quantify the impact of interactions and mergers on the galactic kinematics. We find that 63% (65/103) of the interacting sample has a kinematic misalignment larger than 90% of the control sample in at least one of the parameters for any component. We also estimate the fraction of interacting galaxies with differences in at least two kinematic indicators larger than 90% of the control sample in each component.
We should point out however, that the alignment in the kinematic parameters presented in this study do not always represent rotational support. For instance,  (Engel et al. 2010)  found that even though circular-kinematic signatures are present in the velocity distributions of the binary system NGC 6240, the interacting galaxies are not necessarily dynamically supported by rotation. In a future work we will explore the dynamical support of our interaction sample through better spectral resolution data from CALIFA (V1200 configuration, Husemann et al. 2013).
The CALIFA survey allows us to characterize the spatially resolved properties of galaxies at different stages of interaction. In particular, this study provides a nearby Universe benchmark for kinematic comparisons with high-redshift galaxies. Further studies with simulated high-redshift observations using the current spatially resolved data will allow us to quantify the fraction of rotating disks and compare it with the fraction observed at high redshift. Such simulations for the ionized gas in CALIFA galaxies have been already carried out  (Mast et al. 2014). Our findings encourage the comparison of observational velocity fields with those obtained from numerical simulations. Exploring different configurations of the merging galaxies with different properties of the progenitors will give significant insight and will reveal which parameters yield the variety of observed velocity fields in merging galaxies.
thanks the CAHA staff for the dedication to this project. J. B-B. and B. G-L acknowledge support from the Plan Nacional de I+D+i (PNAYA) funding programs (AYA2012-39408-C02-02-1 and AYA2013-41656-P) of Spanish Ministry of Economy and Competitiveness (MINECO). J. F. B. acknowledges support from the Plan Nacional de I+D+i (PNAYA) funding programs from MINECO (AYA2013-48226-03-1-P, RAVET) A. M. -I. acknowledges support from Agence Nationale de la Recherche through the STILISM project (ANR-12-BS05-0016-02) and from BMBF through the Erasmus-F project (grant number 05 A12BA1). I. M. acknowledges financial support by MINECO grant AYA 2010-15169, Junta de Andalucía TIC114 and Proyecto de Excelencia de la Junta de Andalucía P08-TIC-03531. J. M. A. and V. W. acknowledge support from the European Research Council Starting Grant (SEDmorph; P.
I. V. Wild) J. I. P. acknowledges financial support from the Spanish MINECO under grant AYA2013-47742-C04-1 and from Junta de Andalucía Excellence Project PEX2011-FQM7058. R. A. M is funded by the Spanish program of International Campus of Excellence Moncloa (CEI). L. V. M. acknowledges support from the grant AYA2011-30491-C02-01 co-financed by MICINN and FEDER funds, and the Junta de Andalucia (Spain) grants P08-FQM-4205 and TIC-114. 163. 9 ± 0. 7 158. 0 ± 3. 4 7. 7 ± 1. 9 157. 3 ± 4. 9 12. 5 ± 2. 5 6. 0 ± 3. 5 6. 6 ± 5. 0 0. 6 ± 6. 0 796 5584 ± 7 15 2. 0 ± 0. 6 170. 7 ± 3. 3 9. 5 ± 2. 7 179. 6 ± 3. 0 9. 0 ± 3. 9 11. 3 ± 3. 4 2. 4 ± 3. 0 8. 9 ± 4. 5 797 5577 ± 2 15 121. 4 ± 0. 4 130. 6 ± 3. 7 11. 5 ± 2. 9 125. 9 ± 6. 9 19. 2 ± 4. 5 9. 2 ± 3. 7 4. 5 ± 6. 9 4. 21. 1 ± 6. 5 2. 8 ± 3. 9 6. 3 ± 6.
Acknowledgments The authors thank the referee for her/his useful comments and suggestions. This study makes use of the data provided by the  Calar Alto Legacy Field Area (CALIFA)  survey (http://www. califa. caha. es). Based on observations collected at the  Centro Astronómico Hispano Alemán (CAHA) at Calar Alto , operated jointly by the  Max-Planck-Institut für Astronomie  and the  Instituto de Astrofísica de Andalucia (CSIC). CALIFA is the first legacy survey performed at the  Calar Alto. The CALIFA collaboration would like to thank the  IAA-CSIC  and  MPIA-MPG  as major partners of the observatory, and CAHA itself, for the unique access to the telescope time and support in manpower and infrastructures. The CALIFA collaboration also.
2] [3] [4]  Two randomized, double-blind, phase 3 studies, Determination of the Efficacy and Safety of Oral Fumarate in Relapsing-Remitting Multiple Sclerosis (DEFINE) and Comparator and an Oral Fumarate in Relapsing-Remitting Multiple Sclerosis (CONFIRM), were conducted among patients with relapsing-remitting MS (RRMS). 5, 6 In both studies, DMF treatment produced significant clinical and neuroradiologic benefits over 2 years, including reductions in relapses, new lesion counts, and lesion volumes assessed by MRI, with an acceptable safety profile. DMF is approved in the United States for the treatment of relapsing forms of MS. 7  Here, we report the effects of DMF on MRI brain lesions observed in CONFIRM. 10] METHODS Standard protocol approvals, registrations, and patient consents. The CONFIRM study (ClinicalTrials.
gov identifier NCT00451451) was approved by central and local ethics committees and performed in accordance with The International Conference on Harmonisation Guidelines on Good Clinical Practice  11  and the ethical principles outlined in the Declaration of Helsinki. 12 Written informed consent was obtained from all patients before evaluations were performed to determine eligibility. Study design. CONFIRM was a 2-year, phase 3, randomized, international, multicenter, parallel-group, placebo-controlled study, with active reference comparator, that evaluated the safety and efficacy of DMF in patients with RRMS, as reported previously. 6 atients from 200 sites in 28 countries were randomized 1:1:1:1 to receive PO placebo, PO DMF 240 mg twice daily (BID), PO DMF 240 mg 3 times daily (TID), or glatiramer acetate (GA) 20 mg once daily by subcutaneous injection for 96 weeks.
MTR has not been explored previously in a large phase 3 study and, therefore, investigation of MTR in the present study and companion phase 3 study, DEFINE, represents a novel approach to obtain exploratory information and guide future study design. Brain atrophy data were also collected for tertiary analysis. Statistically significant treatment effects of DMF on MTR outcomes (both doses) and brain atrophy (BID only) were observed in DEFINE. 27, 28 However, MTR outcomes and brain atrophy results with DMF did not reach statistical significance in CONFIRM. The rate of atrophy in the placebo arm during the CONFIRM study was lower in comparison with the placebo arms of other phase 3 studies of oral MS therapies. 22, 24 In addition, there was no increase in brain volume loss with DMF during the first 24 weeks, indicating no significant pseudoatrophy effect due to a decrease in inflammatory tissue and edema.
Acknowledgments This paper is based on a synthesis of presentations and discussions from the workshop ' Incorporating climate and ocean impacts into an Ecosystem Approach to Fisheries Management ', held on 6-9th March 2012 in Bohol, the  Philippines. We are grateful to the  United States Agency for International Development (USAID)  and the  U. S. National Oceanic and Atmospheric Administration (NOAA)  for funding this work. We thank  Amanda Dillon  and  Amanda Toperoff  for creating Figs. 2 and3. The contents in this manuscript are solely the opinions of the authors and do not constitute a statement of policy, decision, or position on behalf of NOAA or the  U. S. Government.
K. Advanced Cell Technology 11/08/2011 dystrophy pigmented epithelial cells NCT01344993 Advanced dry age-related hESC-derived retinal I/II USA Advanced Cell Technology 4/28/2011 macular degeneration pigmented epithelial cells NCT01345006 Stargardt's macular hESC-derived retinal I/II USA Advanced Cell Technology 4/28/2011 dystrophy pigmented epithelial cells Abbreviations: hESC, human embryonic stem cell; ICTRP, International Clinical Trial Registry Platform.
Methods: We did a large-scale, cross-sectional genomic epidemiological study of shigellosis cases collected from 29 countries between December, 1995, and June 8, 2014. Focusing on an ongoing epidemic in the UK, we collected and whole-genome sequenced clinical isolates of Shigella flexneri serotype 3a from high-risk and low-risk regions, including cases associated with travel and sex between men. We examined relationships between geographical, demographic, and clinical patient data with the isolate antimicrobial susceptibility, genetic data, and inferred evolutionary relationships.
Study design and isolate collection In this cross-sectional study, we representatively sampled all (both travel and domestically acquired) isolates of S flexneri serotype 3a isolated in the UK in 2004-13, including during an outbreak that began in 2009. To contextualise this outbreak, we included smaller (although still representative) numbers of isolates from the French reference laboratory and three highrisk areas (Africa, Asia, and Latin America). To determine whether the outbreak was connected to other international outbreaks in MSM, we also included isolates from MSMassociated outbreaks in Canada and Australia. Correlating the genomic analyses of these isolates with clinical data from patients provided novel insights into the infection and transmission of antimicrobial resistance and diarrhoeal pathogens in MSM.
Sequencing data and quality control Sequencing data was generated by study authors from genomic DNA at three collaborating sites for this study with Illumina platforms (San Diego, CA, USA; appendix). All sequence data is available at the European Nucleotide Archive (appendix). Sequencing data was de novo assembled and verified by in-silico multilocus sequence typing, as previously described. 17 Phred (>50) and mapping (>30) quality filters were applied in downstream processing. The annotated contiguous sequence of the multidrug resistance plasmid (pKSR100) from sample SF7955 is available at the European Nucleotide Archive under accession number LN624486.
Bioinformatic analyses To construct the phylogenetic tree of the full collection, we mapped isolate sequence data against S flexneri serotype 2a strain 301 (NCBI accession number NC_004337. 2), generated pseudosequences incorporating single-nucleotide polymorphisms (SNPs), and removed mobile elements and pathogenicity islands as previously described. 17 The resulting alignment was stripped of suspected sites of recombination, and we used the remaining 19 940 SNP sites to construct a phylogenetic tree using RAxML version 7. 8. 6 as previously described. 17 We constructed the pKSR100 phylogeny similarly from plasmid-containing (≥96% coverage) isolates and compared it with the genome tree. The multiple sequence alignment for the dated phylogeny of the MSM-outbreak associated lineage isolates was constructed similarly, mapping against a representative draft genome assembly (sample ERS369461).
This generated a final alignment with 1243 SNPs, which underwent Bayesian evolutionary analysis by sampling trees (BEAST)  18  with a strict molecular clock and both constant and exponential population growth models (congruous results), accounting for invariant sites. In all cases, isolate sequencing data covered at least 96% of the reference. For genetic analyses, we annotated isolate assemblies and detected antimicrobial resistance genes (ARGs) as previously described. 17 Further ARGs were identified by BLAST, and nonsynonymous changes in GyrA and ParC protein sequences, and integron insertion into plasmid pKSR100 were identified manually.
RESULTS Here we representatively sampled all (both travel and domestically acquired) isolates of Shigella flexneri serotype 3a isolated in the United Kingdom while a novel sexually transmitted lineage emerged and became endemic. To contextualise the outbreak, we included smaller (though still representative) numbers of isolates from the French reference laboratory and high-risk regions. To determine whether the outbreak was connected to other international MSM-outbreaks, we also included isolates from MSM-associated outbreaks in Canada and Australia. Correlating the genomic analyses of these isolates with clinical data from patients provided previously unachievable insights into the infection and transmission of antimicrobial resistance and diarrhoeal pathogens in MSM.
Research in context Evidence before the study In addition to an existing library of articles on shigellae evolution and bacteriology, the following literature searches were used in PubMed and Scopus: Added value of this study Using clinical data and whole genome sequencing of pathogens, this study characterised an emergent strain of Shigella flexneri 3a causing a UK-wide outbreak that was detected epidemiologically, and included features of atypical infection. Combining the UK samples with those from many other countries, we unequivocally distinguished this sexually transmitted outbreak from travel-acquired cases, and demonstrated that this pathogen had transmitted intercontinentally in men-who-have-sex-with-men. Using phylogenetic inference, we demonstrate that this antibiotic-resistant enteric infection has spread to all inhabited continents traditionally considered low-risk for shigellosis in less than 20 years.
Contributors KSB designed study, performed data collection, curation and analysis, and wrote manuscript. NRT designed study, contributed to data analysis and wrote manuscript. SRH and JP contributed to data analysis and wrote manuscript. FXW contributed to sample collection, culture, antibiotic sensitivity testing, contributed to the analysis of mechanisms of resistance and reviewed, critiqued and offered comments on the text. BH performed resistance analysis, sequencing data and contributed to manuscript preparation. TT performed genome sequencing of isolates. MV characterised isolates and performed resistance testing. JDB contributed to the collection of data. AMS was responsible for strains, DNA and data collection for Shigella isolated in South Africa, interrogating the database and deciding on which strains would be selected, organizing extraction and shipment of genomic DNA and edited the manuscript.
Acknowledgements. The authors are grateful to staff at the  Wellcome Trust Sanger Institute (WTSI) , including  David Harris ,  Theresa Feltwell ,  Derek Pickard , and core members of the sequencing and informatics teams, as well as  Alison Mather  for bioinformatics training. The authors also thank the anonymous reviewers and  Dr. Estee Torok  for helpful comments on the manuscript. Wellcome Trust grant number  098051  funded authors from the WTSI. We thank  Isabelle Carle ,  Monique Lejay-Collin ,  Corinne Ruckly  from the  Pasteur Institute  for their excellent technical assistance. The IP authors are funded by the  Institut Pasteur , the  Institut de Veille Sanitaire , and by the  French Government "Investissement d'Avenir" program  ( Integrative Biology of Emerging Infectious Diseases" Laboratory of Excellence , grant no.
ANR-10-LABX-62-IBEID ). VS was supported by the  National Health and Medical Research Council's Career Development Award (Australia). We acknowledge the expert technical assistance of  Alex Kuzevski  for isolate characterisation at  The University of Melbourne , which is funded by the  Department of Health, Victoria, Australia. SB is a Sir Henry Dale Fellow, jointly funded by the  Wellcome Trust  and the  Royal Society  ( 100087/Z/12/Z ). BPH is supported by a Fellowship from the  National Health and Medical Research Council, Australia  ( APP1023526 ).