dataesr/scientific-paragraphs-categorization huggingface dataset:
Data analysis for the FTS spectra For these three FTSs, a similar retrieval technique has been applied to estimate the total column amounts from the recorded solar absorption spectra. This retrieval method is based on an optimal estimation method (OEM)  (Rodgers, 1976 (Rodgers, , 2000)) , where a calculated spectrum is fitted to the observed one by adjusting the target trace gas profile. Multiple microwindows, typically each with a width between 0. 3 and 1. 0 cm -1 , are employed simultaneously in the retrieval process. This analysis has been applied to the observed spectra from the three FTSs described above using the SFIT2 v3. 94c retrieval package  (Pougatchev et al. , 1995 (Pougatchev et al. , , 1996) )  and the HITRAN 2008 spectroscopic database  (Rothman et al. , 2009). Total column amounts were calculated from the retrieved volume mixing ratio (VMR) profiles by integrating the atmospheric density and the trace gas VMR throughout the altitude range (from the ground to 100 km).
AEROCAN/AERONET The ground-based AOD measurements were obtained by AEROCAN, a Canadian subnetwork of the AErosol RObotic NETwork (AERONET)  (Holben et al. , 1998). Data across the network are acquired by a CIMEL Electronique 318A sun photometer. Direct sunlight measurements are taken across eight narrow spectral bands in the ultraviolet, visible and near-infrared spectral region. The typical time interval be-tween measurements is 3 min for AEROCAN measurements under favourable weather conditions. The fine-(sub-micron) and coarse-(super-micron) mode AOD are obtained from these measurements using a spectral deconvolution algorithm developed by  O'Neill et al. (2003) , which is applied to a five-wavelength subset of the CIMEL bands  (380, 440, 500, 675 and 870 nm). The enhancement of fine-mode AOD is a signature indicator of smoke events, which makes it possible to study the enhancement of aerosols associated with the boreal fire plumes, while excluding AOD enhancements due to super-micron aerosols and clouds (identified by an enhancement of coarse-mode AOD).
Origin of the enhanced trace gas columns The FLAMBE inventory  (Reid et al. , 2009)  was used to estimate the location and the total carbon emissions from boreal fires during the BORTAS-B campaign in 2011. This inventory provides hourly estimates of carbon and aerosol emissions based on observations from the Geostationary Operational Environmental Satellite (GOES) platforms and the two Moderate Resolution Imaging Spectrometers (MODIS) on the NASA EOS Terra and Aqua satellites. Figure  4  shows the daily carbon emissions obtained from the combined GOES and MODIS dataset between 7 July and 31 July 2011 from boreal fire regions (≥ 50 • N). The majority of boreal fire emissions from 17 to 20 July originated from fires in eastern Siberia and Canada, where emissions from northwestern Ontario essentially dominate the total Canadian emissions.
The groundbased FTS measurements and GEOS-Chem agree well in the magnitude of the CO total columns. However, there are differences in the timing of the enhancement, where the model simulation shows CO enhancements approximately 6 h after the measured total columns CO enhancements on 20 July 2011. Supplementary material related to this article is available online at http://www. atmos-chem-phys. net/13/ 10227/2013/acp-13-10227-2013-supplement. zip. Acknowledgements. Funding for this work has been provided by a grant from the Natural Sciences and Engineering Research Council of Canada (NSERC). Funding for the DGS measurements has been provided by NSERC, the Canadian Space Agency (CSA) and Environment Canada (EC). The BORTAS project is funded by the Natural Environment Research Council under grant NE/F017391/1.
For more information visit: www. geolsoc. org. uk/LyellCollection The Lyell Collection Foundation Sponsors © Fugro NPA Satellite Mapping Limited For more information visit: www. lyellcollection. org Geofacets is a web-based research tool developed for geoscientists working in upstream exploration. Elsevier and the Geological Society of London joined together to provide access to an extensive database of over 190 000 geological maps from Elsevier's Earth science journals and the GSL's Lyell Collection. Its unique interface delivers relevant and high quality content for geoscientists working in the early stages of upstream exploration to assess a region's or basin's geological characteristics. • Intuitive map-based search features • Over 115 000 maps downloadable as georeferenced files • Seamless integration with GIS and other software Geofacets recently won the award for best Education/Industry Partnership at the 2012 Getenergy awards ceremony.
For For more information visit: www. geolsoc. org. uk/LyellCollection The Lyell Collection Foundation Sponsors © Fugro NPA Satellite Mapping Limited For more information visit: www. lyellcollection. org Geofacets is a web-based research tool developed for geoscientists working in upstream exploration. Elsevier and the Geological Society of London joined together to provide access to an extensive database of over 190 000 geological maps from Elsevier's Earth science journals and the GSL's Lyell Collection. Its unique interface delivers relevant and high quality content for geoscientists working in the early stages of upstream exploration to assess a region's or basin's geological characteristics. • Intuitive map-based search features • Over 115 000 maps downloadable as georeferenced files • Seamless integration with GIS and other software Geofacets recently won the award for best Education/Industry Partnership at the 2012 Getenergy awards ceremony.
Dengue 1 genome sequencing Eighteen PCR amplification systems (Table  S1 ), distributed along the complete dengue 1 (DENV-1) genome (from bases 17 to 10,737), were designed from the alignment of complete genome sequences of 36 DENV-1 strains isolated worldwide (GenBank accession numbers in supporting material Text S1). They were used to produce overlapping PCRs along the viral genome from random hexamer RT reactions. The PCRs were performed using 3 ml of RT with 1. 25 unit of AmpliTaq Gold DNA polymerase (Applied Biosystems), 2 mM of MgCl 2 , 200 mM of dNTPs and 400 nM of each primer. The 39 end fragment of the genome was amplified using the QuantiTect SYBR Green RT-PCR Kit (Qiagen) directly from 5 ml of RNA extract. The corresponding PCR products were sequenced by Macrogen Inc. Nearly full-length DENV-1 genome sequences were produced directly from the sera of 7 patients: two patients from Latsavang, 2 patients from Northern Laos (Luang Namtha, October 2008 and September 2009), 2 patients from Southern Laos (Salavan, September and October 2008) and one patient from Vientiane (December 2008).
Phylogenetic and recombination analyses All 2,160 DENV-1 envelope sequences available in the Hemorrhagic Fever Viruses (HFV) database (http://hfv. lanl. gov) were downloaded and aligned, using ClustalX2. 1  [20] , with the 39 Lao DENV-1 envelope sequences obtained in this study. A Neighbour-Joining tree was constructed using Mega 5. 05 software with Kimura-2 model  [21]. Reliability of nodes was assessed by bootstrap resampling with 500 replicates. Another tree using the Maximun Likelihood method was constructed using the same alignment. In addition to this 'exhaustive' reconstruction, another Neighbour-Joining tree was constructed from the alignment of the 39 Lao envelope sequences with the 1,318 complete or nearly complete DENV-1 genomic sequences (10,000 bases or more) available in HFVdb, to produce a tree with a robust phylogenetic backbone.
The 1,318 complete (or nearly complete) DENV-1 genomic sequences were aligned, using ClustalX2. 1, to the 7 Lao DENV-1 genome sequences obtained in this study. Indication for the presence of molecular recombinations was investigated using the Recombination Detection Program (RDP) version 3 software  [22]. RDP, GENCONV and MAXCHI methods were used for primary screening and the BOOTSCAN and SISCAN methods for automatic checking of the recombination signals  [23, 24, 25, 26, 27]. For optimal recombination detection, we selected the RDP3 automask procedure that allows automatic masking of all sequences except one within groups of similar sequences. This means that within each group of similar sequences, only one sequence was examined during the exploratory search for recombination signals. When the program finds a recombination signal in an unmasked sequence it then examines all masked sequences from the same group (RDP user manual, http://darwin.
Analysis of dengue sequences from the outbreak and elsewhere in Laos The 18 overlapping DENV-1 PCRs yielded an almost full sequence of the genome of the DENV-1 virus infecting two patients from the outbreak, XB998 (10,629 bases) and XB1011 (9,823 bases), in addition to two patients from Luang Namtha, Northern Lao PDR, (9,823 bases each), two patients from Salavan, Southern Lao PDR, (9,823 and 10,648 bases respectively) and one patient from Vientiane (10,641 bases) (GenBank accession numbers in Table  S2 ). All sequences were obtained from direct processing of patients' sera and shared a high level of identity at the nucleotide level (. 97%, Table  S3 ). The tree constructed with 2,199 DENV-1 envelope sequences, including 2 sequences from the Latsavang outbreak, 5 from Luang Namtha, 13 from Salavan and 19 from Vientiane between 2007 and 2010 (GenBank accession number in Table  S2 ), shows (Figure  2 ) that all Lao strains belong to genotype I.
Two subtrees, including only genotype I strains, were extracted from the tree constructed with 2,199 DENV-1 envelope sequences and from the tree constructed with the 39 Lao envelope sequences aligned with 1,318 complete sequences. The two subtrees are presented in Supporting Material Figure  S1  and Figure  3 , respectively. Seven clusters supported by high bootstrap value (. 90) can be distinguished in Figure  3. The sequences from the Latsavang outbreak group with a strain from Vientiane of the same period (cluster 4), whereas most of the other Lao strains belong to six other defined clusters. Similar topologies were obtained with the Maximum Likelihood method (complete tree and genotype 1 subtree are presented in Supporting Material Figures  S2  and S3 ). An alignment of 1,325 DENV-1 sequences of 9,756 nucleotides (starting at ORF position 21) was submitted to RDP3 software.
It is likely that infections may exacerbate thiamin deficiency and it is possible that dengue infection could precipitate fatal thiamin-deficiency heart failure  [35]. However no biological confirmation could be provided to support this hypothesis. Dengue was not suspected to be the responsible pathogen during the outbreak, as in Laos dengue is regarded as an urban disease and incidence is low during the cooler months of November and December. Latsavang is a river bank village of 1,526 inhabitants living in 298 households among maize and paddy fields and surrounded by tropical forest, 120 km as the crow flies from the nearest large town (Xayabury), that has inhabitants. During the outbreak there were no reports of high dengue incidence in adjacent parts of Laos or Thailand. Daily rainfall data collected in Xayabury town does not show significantly higher rainfall or temperature in November or December 2008 in comparison to the same months in 2009.
This study provided the opportunity to perform the first analyses of the molecular epidemiology of dengue in Laos. Despite endemic dengue infection in Laos, only four partial genomic sequences of dengue virus were available in public databases prior to the current study (including one DENV-1 from 1996). Here, (nearly) complete genomic sequences were established for two patients from the 2008 Latsavang outbreak, but also for two patients from Luang Namtha  (2008) (2009) , two patients from Salavan (2008), and one patient from Vientiane (2008). In addition, complete envelope sequences were produced for a number of Lao DENV-1 positive sera sampled between 2007 and 2010 (Luang Namtha: 3; Salavan: 11; Vientiane: 18). The tree constructed with 2,199 DENV-1 envelope sequences, shows (Figure  2 ) the five DENV-1 genotypes previously described  [36].
Groups of sequences supported by a high bootstrap value (. 90) that contain at least one of Lao sequence are designated as cluster (1 to 7). doi:10. 1371/journal. pntd. 0002360. g003 strains  (1998) (1999) (2000) (2001) (2002) , and the only Lao strain (1996) available in GenBank before those sequenced for this study. (iv) the 'Asia 4' clade includes Chinese strains  (1997) (1998) (1999). Molecular characterisation of Latsavang DENV-1 outbreak strain shows that it belongs to the 'Asia 3' clade of Genotype I, with a genomic sequence very similar to other strains that have caused human infections in the region. Therefore, although the outbreak was in a forested area, it was not caused by a genotypically 'sylvatic' dengue virus in the conventional use of the term. Sylvatic dengue strains have been considered to be ecologically and genetically distinct from endemic strains  [38, 4] , circulating in the forest between non-human primates and arboreal Aedes mosquitoes, in contrast to strains responsible for human infections by domestic Aedes aegypti and peridomestic Aedes albopictus mosquitoes  [39, 40].
Sequences from 2007 are in yellow, the ones from 2008 (except those from Latsavang) are in purple, the ones from 2009 in blue and the ones from 2010 in green. For the other sequences only the country, using ISO3166 code, and the year of origin are indicated. Groups of sequences supported by a high bootstrap value (91 for cluster 1, 100 for cluster 2, 3 and 4, 97 for cluster 5, 84 for cluster 6, 97 for cluster 7) that contain at least one of Lao sequence are designated as cluster (1 to 7). (TIF) Figure  S4  Neighbour-Joining trees performed for recombination events analyses. The trees were made using Mega 5. 05 with Kimura 2 model from the alignment of the 570 sequences selected by RDP software. Bootstrap values (in percentage) were generated by using 500 replicates. Trees A, C, E, G were done by selecting the sequences inside the breakpoints for the recombinants 2, 3, 10 and 13 respectively.
Trees B, D, F, H were done by selecting the sequences outside the breakpoints for the recombinants 2, 3, 10 and 13 respectively. In each tree the recombinant strain is indicated by a blue dot, the major parent by a green dot and the minor parent by a red dot. (TIF) Table  S1  Primers used for the amplification of the DENV-1 genome. Primers DENV1_F2, DENV1_R2, DENV1_F3, DENV1_R3, DENV1_F4, and DENV1_R4, were used for the amplification of the DENV-1 envelope gene. (DOC) Table  S2  GenBank accession number of the DENV-1 sequences produced in this study.
Acknowledgments We are very grateful to all patients who participated in this study, to  Dr Koukeo Phommasone  for drawing Figure 1, to  Antoine Nougairede  for helping with the Maximum Likelihood tree production, and to the staff of  NCLE, WHO-Vientiane and the Microbiology Laboratory, Mahosot Hospital. We are very grateful to the  Directors of Mahosot Hospital ,  Prof. Sommone Phounsavath , the Director of Curative Medicine Department, and  Dr. Ponmek Dalaloy ,  Minister of Health, Lao PDR  for their very kind help and support.
skin relief Skin relief (fine lines and wrinkles) was evaluated using a Visioscan ® VC 98 device (Courage and Khazaka, Cologne, Germany, Figure  3 ). 13, 14 The Visioscan VC 98 features a blackand-white high-performance digital camera that takes pictures of the skin surface under standardized homogenous ring-shaped ultraviolet A illumination (340-400 nm, peak 375 nm). Each 640 × 480 pixel picture was analyzed using dedicated software Rz, or circular roughness, is the arithmetic average of five measurements of the distance between the highest and lowest value, referred to as reference length 1, on a selected line. conducted (three values per zone per volunteer) and mean values were calculated. The data were analyzed by proprietary software (Skinexigence, Besançon, France). The thickness was calculated from a region of interest determined directly on the image.
Statistical analysis The statistical analysis was conducted using Statistica ® version 6. 0 (Statsoft, Tulsa, OK, USA) and Instat GraphPad ® version 3. 0 (Graphpad Software Inc, San Diego, CA, USA) software. The analyses were based on the intention-to-treat population that comprised all subjects included in the study. Statistical significance was set at 5% (double-sided) and at 5%-10% for trends. Descriptive statistics were reported for each parameter, ie, mean standard deviation, minimum, maximum, and median, quartiles for quantitative data, and percentages for qualitative data. Quantitative variables were tested by analysis of variance (if normal distribution was ensured, or Friedman test if not normally distributed). The effect of time (at T0, T4, and T5. 5) was investigated using these tests.
Conclusion The results of this study indicate that the skin is prone to being affected by seasonal changes, particularly in exposed areas. Our data also confirm that oral supplementation with specific nutrients is safe and may prevent or even eliminate the negative effects of the winter months on skin. Among the instruments used in this trial, Visioscan and high-frequency ultrasound were considered to be more sensitive because they recorded even small changes. The Reviscometer could be a very sensitive instrument if skin surface hydration is considered adequate. During winter time, the most important and also statistically significant changes has been observed in the exposed area as the most prone zone to seasonal changes.
Animals Semi-quantitative and Real-time PCR analysis. RNA was isolated using Trizol (Invitrogen) and digested with DNase I to prevent amplification of genomic DNA. Reversed transcription was performed using M-MLV reverse transcriptase and gene expression analyzed using SybrGreen in an ABI Biosystems Real-Time PCR machine. β-actin was used as a reference gene. Immunohistochemistry. To localize protein expression, eyes were enucleated from mice and fixed in 4% paraformaldehyde at room temperature for 4h and incubated in 30% sucrose overnight and then frozen in OCT compound. We then embedded the whole eye in optimal cutting temperature compound at -20˚C and performed 12um serial sections. We carried out immunohistochemistry experiments and visualized the sections with an epifluorescent microscope (Zeiss AxioImager) or confocal microscope (Olympus confocal FV1000) and 3D rendering performed using Volocity software.
Migrated cells were coloured using Hema-Stain and counted. Bone marrow chimera. For the generation of chimeric mice, bone marrow cells were obtained by flushing both tibias, femurs and iliac crests of wt C57/B6 CD45. 1 or CD45. 2 or SUCNR1 -/-donor mice. 4 week old C57/B6 CD45. 2 or SUCNR1 -/-recipient mice were irradiated with 8 Gy from a 6MV linear particle accelerator (Elekta) and injected intravenously with 1x10 7 bone marrow cells. Chimeric mice were sacrificed 20 weeks later. Flow cytometry. Blood leukocytes populations were analyzed using a BD LSRII flow cytometer and postanalysis was done using the FlowJo 7. 6 software. Compensation was done using single-stained cells. Leukocyte were stained with antibodies (all from BioLegend) against CD11b-FITC (clone M1/70), CD11c-PE (clone N418), Gr-1-PerCP (clone RB6-8C5) and F4-80-Pacific Blue (clone CI:A3-1).
Cells were first gated for CD11b+/CD11c-population. Then, Gr-1 low or intermediate and F4-80+ cells were counted as macrophages. For calculation of bone-marrow transfer efficiencies, cells were also stained with CD45. In brief, three independent cohorts from the University of Michigan in Ann Arbor, the University of Pennsylvania in Philadelphia, and the Mayo Clinic in Rochester, Minnesota contributed data to this genome-wide association study. Our analytic sample contained respectively 329, 110, and 95 people with GA or GA+NV AMD from the University of Michigan, University of Pennsylvania, and The Mayo Clinic. There were 508, 194, and 308 AMD-free people, aged > 65 years from these respective sites.
1-APC (clone A20) or CD45. 2-PE-Cy7 (clone 104) antibodies. Statistical analyses. Data are presented as mean ± s. e. m. We used Student's T-test to compare the different groups; a P ˂ 0. 05 was considered statistically different. Human genetic analysis. Data used for genetic analyses in this report were obtained from the NEI Age-Related Eye Disease Database (NEI-AREDS) Database and the NEI Study of Age-Related Macular Degeneration (NEI-AMD) Database at the U. S. National Center for Biotechnology Information (NCBI) database of Genotypes and Phenotypes (dbGaP). Details are presented in the Supplementary Information. NEI-AMD is a collaborative of researchers from the University of Michigan, Mayo Clinic, University of Pennsylvania, and the AREDS group including National Eye Institute intramural investigators.
PS holds a Canada Research Chair in Retinal Cell Biology and the  Alcon Research Institute New Investigator Award. This work was supported by grants from the  Canadian Institutes of Health Research  ( 221478 ), the  Canadian Diabetes Association  ( OG-3-11-3329-PS ), the  Natural Sciences and Engineering Research Council of Canada  ( 418637 ) and  The Foundation Fighting Blindness Canada. Support was also provided by the  Reseau de Recherche en Santé de la Vision du Québec. FB holds a  Fonds de la Recherche en Santé du Quebec (FRSQ) fellowship. Additional funding was provided by the  Maisonneuve-Rosemont Hospital Foundation. We would like to thank  Johanne Ouellette  and  Dr. Ribeiro-Da-Silva  for electron microscopy. We thank  Dr. Emily Chew  for comments on the manuscript.
Moreover, most of rodent species being abundant and non-protected (when not pest organisms), they are relatively easy to sample, thus facilitating the gathering of datasets that are appropriate for phylogeographic/population studies. This may explain why all African species investigated so far led to strong phylogeographic signals, as well as remarkable congruence between sometimes highly divergent taxa. Indeed, data are now available for rodent species inhabiting arid zones (Jaculus jaculus:  [12] ), steppes, shrub and tree savannahs (Lemniscomys striatus:  [13] ; Praomys daltoni:  [14] ; Mastomys erythroleucus:  [15, 16] ; Mastomys natalensis:  [17] ), rocky habitats (Acomys chudeaui:  [18] ), humid areas (Mastomys huberti:  [19] ), forest-savannah mosaics [Mus (Nannomys) minutoides:  [20]  and forests (Praomys rostratus and P.
In addition, 54 cytb sequences were downloaded from GenBank, among which 34 A. niloticus representatives (one from Egypt, one from Senegal, two from Niger, seven from Cameroon and 23 from Sudan), nine representatives of other Arvicanthis species as well as 11 representatives of other genera (Aethomys, Desmomys, Golunda, Mylomys, Otomys, Pelomys, and Rhabdomys). For the fib7 dataset we also used a sequence from a specimen of Mastomys erythroleucus that was trapped in Mali. Finally, one Lemniscomys cytb sequence was kindly provided by V. Nicolas (Museum National d'Histoire Naturelle, Paris, France). The rationale here (see also the Phylogenetic and dating analyses section for details) was: (i) to have a dense sampling of Arvicanthis species in order to properly enforce the corresponding fossil constraint; (ii) include species used in previous studies within Arvicanthini and Murinae  [41, 42]  in order to perform secondary calibrations.