dataesr/scientific-paragraphs-categorization huggingface dataset:
For comparison to the satellite data, we archive GEOS-Chem daily output at the local satellite overpass time and regrid it vertically to the instrument retrieval levels. Since GEOS-Chem has little predictive capability in the stratosphere due to the use of climatological chemical rates, we replace the simulated profiles above the tropopause with the observed profiles as in  Zhang et al. (2006). The simulated ozone and CO profiles are then smoothed with the instrument averaging kernels to account for the measurement sensitivity. The ozone-CO statistics from GEOS-Chem are calculated using the same methodology as the satellite data described above. Random noise in individual ozone and CO profile retrievals degrades the ozone-CO correlations but this can be greatly reduced by averaging (central limit theorem).
The high density of OMI and AIRS observations is of considerable advantage for this purpose. After data filtering, there are typically 10-30 OMI and AIRS profiles binned daily in each 2 • × 2. 5 • grid square where data are available, with more profiles at lower latitudes. Tests applying random retrieval error to the GEOS-Chem profiles, as in  Zhang et al. (2006) , indicate little effect of retrieval noise on the simulated ozone-CO correlations from OMI and AIRS. This is in contrast to the TES results of  Zhang et al. (2006)  and  Voulgarakis et al. (2010)  where the correlations were found to be significantly degraded by that noise.
Evaluation with MOZAIC aircraft data We evaluate the ozone-CO correlations and regression slopes derived from OMI/AIRS with in situ aircraft profiles over commercial airports in 2006 and 2008 from the MOZAIC program  (Marenco et al. , 1998 and www. iagos. fr). MOZAIC ascent/descent profiles extend up to a permanent 12 km limit. The profiles are vertically interpolated to the satellite retrieval grids and smoothed with the mean instrument averaging kernel matrix for the corresponding day and 2 • × 2. 5 • horizontal grid square. The 700-400 hPa ozone and CO mixing ratios are then calculated for MOZAIC in the exact same manner as for the OMI/AIRS data described in Sect. 2. 4. We require at least 10 MOZAIC vertical profiles with coincident satellite data at a site in a given season to derive ozone-CO correlations.
Conclusions Ozone-CO correlations provide a valuable constraint to test models of tropospheric ozone but have hitherto been limited to in situ measurements and sparse satellite observations. By using satellite instruments with near-daily global coverage of the same scenes, OMI for ozone and AIRS for CO, we constructed a global data set of ozone-CO correlations in the free troposphere on a 2 • × 2. 5 • grid with seasonal resolution and for individual years. The high data density avoids the degradation of the correlations by instrument noise that was a problem in previous satellite studies. The correlation coefficients r are highly significant, showing strong positive values in continental outflow in the northern extratropics. The tropics and Southern Hemisphere show seasonally varying patterns of positive and negative correlations.
The well-known tropical ozone maximum over the South Atlantic features a strongly negative dO 3 /dCO, consistent for different years and meteorological data sets. GEOS-Chem reproduces this observation and attributes it to lightning. Previous model studies had reached a range of conclusions as to the origin of the South Atlantic ozone maximum, but the independent information from the ozone-CO correlations provides evidence of a dominant lightning source. The northeastern Pacific is a region of particular interest for transpacific ozone pollution. Here we find that GEOS-Chem fails to reproduce the observed ozone-CO correlation in summer-fall, yielding negative dO 3 /dCO values when the observations show positive values. Remarkably, all ozone sources in the model yield negative d O 3 /dCO values in that region.
This reflects the remote subsiding environment, where ozone is produced while CO is oxidized as air masses subside slowly around the Pacific High. Further analysis combined with independent evidence suggests that correcting this model bias would require both a reduction in the lightning source at northern midlatitudes and an increase in CO emissions in East Asia. We have shown in this paper that the combination of OMI ozone and AIRS CO provides a robust global data set of ozone-CO correlations in the free troposphere, and that these correlations provide a powerful tool for testing ozone sources in global models. In future work we will exploit this data set further to examine interannual variability in ozone-CO correlations and the implications for our understanding of ozone sources. Supplementary material related to this article is available online at http://www.
Acknowledgements. This work was funded by the  NASA   Aura Program  and in part by the  Department of Energy Office of Science Graduate Fellowship Program  ( DOE SCGF ), made possible in part by the  American Recovery  and Reinvestment Act of 2009, administered by  ORISE-ORAU  under contract no. DE-AC05-06OR23100. The authors acknowledge the support of the MOZAIC program by the  European Commission, EADS, Airbus , and the airlines (Lufthansa, Austrian,  Air France , and  Air Namibia ) who carry the MOZAIC equipment free of charge and who have performed the maintenance since 1994. The MOZAIC database is supported by  ETHER  ( CNES  and  INSU-CNRS ). Edited by:  J. Ma.
Acknowledgments Mosquito collections in Mayotte were carried out by agents from the  "Service de Lutte anti-vectorielle" of the "Agence régionale de  santé" headed by  J. Thiria :  I. Anassi ,  N. Bérou ,  L. Hassani Ali ,  H. Inoussa ,  O. Ousseni ,  M. Said ,  M. Saindou  and  C. Toty. We would like to thank partners of the project AnimalRisk-OI:  A. Faharoudine ,  S. Girard ,  M. Halifa ,  MR. Jaumally ,  JM. Héraud ,  BA. Lalaonirina ,  S. Laurette ,  L. Lasnes ,  S. Licciardi ,  M. Maquart ,  D. Meenowa ,  J. Melanie ,  MM. Olive ,  R. Rakotondravao ,  J. Ravaomanana  and  M. Roger. We are indebted to ML Tantely,  L. Andrianaivolambo , and all inhabitants of the different sites of study in Madagascar. We are also thankful to the partners of the project RIFT-OI:  Dr. David  and  Dr H. Rasamoelina.
Sequence analyses Sequences were compared with sequences available in GenBank using BLAST  [25]. Phylogenetic trees were constructed for each gene including the best BLAST hits and reference sequences. Because GenBank contains data obtained prior to the new taxonomic revision of Vesicomyidae, we renamed unidentified or misidentified specimens of sequences retrieved from GenBank according to their identification in the most recent taxonomic revisions by expert taxonomists  [5, 9, 26, 27]. Consequently, some species belong to undetermined genera (e. g. 'Undetermined genus' cordata formerly Vesicomya cordata). Alignments of nucleotide sequences were conducted using Geneious Pro 4. 6  [28] , and checked by eye to maximize positional homology. The Akaike's information criterion (AIC)  [29]  implemented in Modeltest v.
Estimation of symbiont densities by 3D-FISH For each specimen (three specimens per species per site), symbiont densities were estimated using 3D FISH as the percentage of gill volume occupied by the bacteria strain. On 48 gill sections, a total of 720 square subsections of 1006100 mm and 10 mm thickness (12 specimens64 sections per specimen615 squares per section) were sampled randomly and the fraction of total volume occupied by bacteria was computed using the SYMBIONTJ application  [19]  (http://www. snv. jussieu. fr/ %7Ewboudier/softs/symbiontj. html) implemented in ImageJ  [33]. Percentages of volume occupied by bacteria were analyzed using R software  [34]  after an arcsine transformation, and compared between species and sites with a non-parametric test (Kruskal-Wallis test if n. 2 and Wilcoxon-Mann Whitney test if n = 2).
To test this, presence and abundance of non-specific symbionts need to be investigated in the reproductive tissues, gametes and larvae of Vesicomyidae, and their likelihood of being transmitted needs to be estimated. No evidence for recombination or lineage sorting due to competition between dominant and minority symbionts was observed in our dataset, suggesting that incidental leakage has little consequence. However, even if rare, events of symbiont displacement may have occurred over longer evolutionary times. They could be detected as incongruencies between host and symbiont phylogenies, emphasizing the importance of including as many species as available in future host-symbiont phylogenetic studies. Overall, physical proximity (or co-occurrence in a single bed) of Vesicomyidae hosts may be a driving force for the evolution of their symbionts either toward displacement or emergence of new mosaic lineages through recombination.
Acknowledgments We are grateful to the chief scientist of the Guineco (MARUM) cruise ( A. Boetius , MARUM); to the captain and crew of the  R/V Meteor  for leg  M76/3b  and the crew of the ROV Quest 4000 (MARUM). We thank  Anne Godfroy  and  Marie-Anne Cambon  ( Laboratoire Microbiologie des Environnements Extremes ) for the access to the Apotome and the  Developpement et Evolution des Vertebres team  ( Station Biologique de Roscoff ) for the access to the microtome. We thank  Felix Muller  for his help in processing samples onboard for FISH. We thank  Cyrielle Jan  and  Mathieu Guri  for their help with FISH image acquisition and  Marie Roumagnac  for her technical help. The manuscript was professionally edited for English usage by  Carolyn Engel-Gautier. We are grateful to the three anonymous reviewers and to  Dr.
Some examples of improvements which have been done are given in the following paragraphs. Concerning the static dilution different types of syringes were tested and the individual syringe volume was determined by an independent method based on the weight of masses. The preparation procedure was automated and the timing was defined for each step to improve the repeatability. The data acquisition system such as the temperature logging of all relevant system parts (vessel, housing, syringes, laboratory) and the pressure logging (vessel, laboratory) was improved. For the dynamic dilution of high concentration gas mixtures the measurement of the flows (dilution flow and gas flow) was studied by comparing different flow measurement techniques to seek the method that leads to the lowest uncertainty for the dynamic gas mixtures at low concentration such as mass-flow controller, critical orifices and laminar flow element: this study showed that mass-flow controller and laminar flow element led to the lowest uncertainties.
Emissions from the combustion of fossil fuels and cement production Carbon dioxide emission statistics were taken from the CDIAC database of consumption of fossil fuels and cement production  (Boden et al. , 2011). CO 2 emissions were derived from energy statistics published by the United Nations (2010) and processed according to methods described in  Marland and Rotty (1984). CO 2 emissions from the production of cement were based on data from the US Department of Interior's Geological Survey (USGS, 2010), and emissions from gas flaring were derived from data provided by the UN, US Department of Energy's Energy Information  Administration (1994), and Rotty (1974).
Fire emissions Fire emissions for the region were obtained from the Global Fire Emissions Database version 3. 1 (GFEDv3. 1). GFED is based on a combination of satellite information on fire activity and vegetation productivity (van der  Werf et al. , 2006 Werf et al. , , 2010)). The former is based on burned area, active fires, and fAPAR from various satellite sensors, and the latter is estimated with the satellite-driven Carnegie Ames Stanford Approach (CASA) model.
Transport of riverine carbon To estimate the land to ocean carbon flux, we used the six ocean coastline segments with their corresponding river catchments for South Asia, as described by the COSCAT database  (Meybeck et al. , 2006). The lateral transport of carbon to the coast was estimated at the river basin scale using the Global Nutrient Export from WaterSheds (NEWS) model framework  (Mayorga et al. , 2010) , including NEWS basin areas. The carbon species models are hybrid empirically and conceptually based models that include single and multiple linear regressions developed by the NEWS effort and  Hartmann et al. (2009) , and single-regression relationships assembled from the literature. Modeled dissolved and particulate organic carbon (DOC and POC) loads used here (from  Mayorga et al.
, 2010)  were generated largely using drivers corresponding to the year 2000, including observed hydroclimatological forcings, though some parameters and the ob-served loads are based on data spanning the previous two decades. Total suspended sediment (TSS) exports were also estimated by NEWS. Dissolved inorganic carbon (DIC) estimates correspond to weathering-derived bicarbonate exports and do not include CO 2 supersaturation; the statistical relationships developed by  Hartmann et al. (2009)  were adjusted in highly weathered tropical soils (ferralsols) to 25 % of the modeled values found in  Hartmann et al. (2009)  to account for overestimates relative to observed river exports (J. Hartmann and N. Moosdorf, unpublished data); adjusted gridcell scale exports were aggregated to the basin scale using NEWS basin definitions  (Mayorga et al.
The historical changes in atmospheric CO 2 concentration for the period of 1901-2009 were derived from ice core records and atmospheric observations from the Scripps Institution of Oceanography  (Keeling et al. , 2001). For the climate forcing datasets, monthly climate data for the period of 1901-2009 from CRU-NCEP datasets with a spatial resolution 0. 5 • × 0. 5 • (http://dods. extra. cea. fr/data/p529viov/cruncep/) were used. Information on land-use change was derived from HYDE 3. 1 land cover dataset  (Goldewijk, 2001, ftp. pbl. nl; path: /hyde/hyde31 final). These models do not include lateral fluxes of C exported away from ecosystems (from soils to rivers, biomass harvested products) nor fluxes resulting from forest and agricultural management. We performed correlation analyses between detrended net carbon flux and two climate drivers, annual temperature and annual precipitation, in order to diagnose the modeled interannual response of net carbon fluxes to these drivers (positive for carbon source, negative for carbon sink).
Atmospheric inverse models The biospheric (non-fossil CO 2 ) CO 2 fluxes are available from state-of-the art atmospheric inversion models from the TransCom database at IPSL/LSCE (http://transcom. lsce. ipsl. fr; Peylin et al. , 2012). Estimated fluxes from the following models are included in this analysis: C13 CCAM, C13 CCAM, Carbontracker EU, Jena s96 v3. 2, JMA 2010, LSCE an v2. 1, LSCE var v1. 0, NICAM MRI, RIGC TDI64, TransCom-L3 mean. We also obtained regional specific inversion results for South Asia using the CARIBIC  (Schuck et al. , 2010)  data in the upper troposphere over India and Pakistan, which is subsequently validated using the CONTRAIL  (Machida et al. , 2008)  data of vertical profiles over Delhi and upper troposphere over Asia  (Patra et al. , 2011a). CONTRAIL observations are also used for inversion, with CARIBIC data for validation  (Niwa et al.
Emissions from fires South Asia is not a large source of CO 2 emission due to biomass burning as per the GFED3. 1 (Global Fire Emission Database, version 3. 1; van der  Werf et al. , 2006 Werf et al. , , 2010)). Out of about 2,013 ± 384 Tg C yr -1 of global total emissions due to open fires as detected by the various satellites sensors, only 47 ± 30 Tg C yr -1 (2. 3 % of the total) are emitted in the South Asian countries. The average and 1σ standard deviations are calculated from the annual mean emissions in the period 1997-2009. The total emission is reduced to 44 ± 13 Tg C yr -1 if the period of 2000-2009 is considered. The total fire emissions can be attributed to agriculture waste burning (14 ± 4 Tg C yr -1 ), deforestation fires (21 ± 11 Tg C yr -1 ), forest fires (2. 6 ± 1. 5 Tg C yr -1 ), savanna burning (4.
Modeled long-term mean ecosystem fluxes from inversions Top-down estimates of land-atmosphere CO 2 biospheric fluxes (i. e. without fossil fuel emissions, and inclusive of LUC flux and riverine export) are estimated by using atmospheric CO 2 concentrations and chemistry-transport models. Results are available from 11 atmospheric inverse models participating in the TransCom intercomparison project with varying time periods between  1988 -2008 (Peylin et al. , 2012)). The inversions were run without any observational data over the South Asian region for most part of the 2000s. Therefore, we place a very low confidence in the TransCom inversion results, and a medium confidence in the results of two additional regional inversions using aircraft measurements over the region. The estimated net land-atmosphere CO 2 biospheric fluxes from the two regional inversions are -317 and -88.
Acknowledgements. This work is a contribution to the  REgional Carbon Cycle Assessment and Processes (RECCAP) , an activity of the Global Carbon Project. The work is partly supported by  JSPS/MEXT (Japan) KAKENHI-A  (grant# 22241008 ) and  Asia Pacific Network  (grant# ARCP2011-11NMY-Patra/Canadell ). Canadell is supported by the  Australian Climate Change Science Program of CSIRO-BOM-DCCEE. The inverse model results of atmospheric CO 2 and terrestrial ecosystem model results are provided under TransCom (http://transcom. lsce. ipsl. fr)and TRENDY (http://www-lscedods. cea. fr/invsat/RECCAP)projects, respectively, and we appreciate all the modelers' contribution by providing access to their databases. Edited by:  C. Sabine.
H alomonas sp. strain A3H3, a slightly halophilic bacterium (0. 5 to 9% NaCl)  (1) , was isolated from the harbor sediments of l'Estaque in the south of France. These sediments are highly contaminated with various metals, metalloids, and organic compounds, particularly with arsenic (653 g/liter in sediment interstitial water and 165 mg/kg in solid phase)  (2, 3). A 16S rRNA-based phylogenetic analysis revealed close similarity to Halomonas neptuniae strain Eplume1 (GenBank accession number NR_027218. 1). The genome of Halomonas sp. A3H3 was sequenced from one paired-end and one 500-bp mate-paired library of 5-kb inserts. The resulting reads were assembled into 131 contigs using SOAPdenovo and GapCloser assemblers, achieving 150-fold coverage. The sequence assembly completed by optical mapping (4) resulted in two scaffolds representing a total of 5,646,978 bp.
The bacterium oxidizes 100 mg/liter arsenite under aerobic conditions or under anaerobic conditions in the presence of nitrate used as an alternative final electron acceptor, as supported by the presence on the chromosome of the narGHJI operon  (15). Halomonas sp. A3H3 is motile by means of peritrichous flagella, the genes of which are clustered in a large chromosomal region. The motility of the bacterium increases with arsenite, as shown by swarming assays, which further supports the use of arsenite oxidation in the energy metabolism of Halomonas sp. A3H3. Further studies will provide insights into the strategies evolved by Halomonas sp. A3H3 to deal with the toxic compounds present in marine anaerobic harbor sediments. Nucleotide sequence accession numbers. The whole-genome sequence has been deposited at DDBL/EMBL/Genbank under the following accession numbers: contigs, CBRE010000001 through CBRE010000131; scaffolds, HG423310 through HG423342; and chromosomes, HG423343 and HG423344.
ACKNOWLEDGMENTS This work was supported by the  French National Research Agency , under the reference number " 2008 CESA-003. " Sequencing was performed by the IGBMC microarray and sequencing platform, a member of the  France Génomique program. We thank  Genoscope (Évry, France)  for the use of MicroScope, the  Microbial Genome Annotation & Analysis Platform  (http://www. genoscope. cns. fr/agc/microscope).
Pattern recognition In the context of coral measurement, the implemented system is based on the use of the coded targets. This approach has certain advantages; mainly it is easy to use, gives a semantic link between what is seen and the knowledge base of the system through a coded pattern and the calculation of the camera pose is performed in real-time and with high accuracy. The principle of the coded target method is based on the deployment of a number of special graphics whose geometry is known. Instead of trying to directly recognize the objects in the real world, it is only necessary to recognize the targets that are linked to them. As coded targets' geometry is known, it is possible to optimize the image processing used to recognize them. There are many visual tagging systems. We can cite the CyberCode system which was formally proposed by Rekimoto  (Rekimoto, 1998) and called Matrix before being renamed CyberCode in  (Rekimoto & Ayatsuka, 2000).
This approach has been implemented in many applications including mobile telephones  (Rohs & Gfeller, 2004). Figure  3. ARToolkit and InterSence. The ARToolkit system  (Kato et alii, 2000)  is a library that can be used to create augmented reality applications. In particular, it contains a system of square targets with a black border and an internal pattern. The process to extract and identify the code is similar to the process of the previous system. The code is recognized by calculating the correlation coefficient between the standardized image and the standardized reference database. In order to increase the recognition rate of targets, some variations have been brought. These variations are based on the calculation of the correlation rate between the extracted pattern and the reference patterns that are learned by the system  (Owen et alii, 2002).
The use of underwater photogrammetry was proven very valuable, but a new avenue of applications for the study of such complex communities is already available with the development of affordable geo-referenced mosaic techniques. These mosaics will offer marine biologists new data sets of spatial related information which was just unachievable few years ago. Based on almost ten years of collaboration we will use these data, collected during these years, to study the evolution of coral during this time even if the methodology, implemented algorithms and photograph technology has changed.
A temporally and spatially resolved estimate of the global surface-ocean CO 2 partial pressure field and the sea-air CO 2 flux is presented, obtained by fitting a simple data-driven diagnostic model of ocean mixed-layer biogeochemistry to surface-ocean CO 2 partial pressure data from the SOCAT v1. 5 database. Results include seasonal, interannual, and short-term (daily) variations. In most regions, estimated seasonality is well constrained from the data, and compares well to the widely used monthly climatology by  Takahashi et al. (2009). Comparison to independent data tentatively supports the slightly higher seasonal variations in our estimates in some areas. We also fitted the diagnostic model to atmospheric CO 2 data. The results of this are less robust, but in those areas where atmospheric signals are not strongly influenced by land flux variability, their seasonality is nevertheless consistent with the results based on surface-ocean data.
Currently, two data streams are used to estimate the variability of sea-air CO 2 fluxes: -Based on measurements of the CO 2 partial pressure (p CO 2 ) of surface water, the sea-air CO 2 flux is calculated through a gas exchange parameterization. As p CO 2 measurements only exist at discrete locations and ship tracks, spatial and temporal interpolation is needed. The following interpolation methods have been Published by Copernicus Publications on behalf of the European Geosciences Union. proposed: (1) statistical interpolation combined with an advection-diffusion equation  (Takahashi et al. , 2009) ; (2) purely statistical interpolation with error quantification  (Jones et al. , 2012b) ; (3) multi-linear regressions between p CO 2 and ocean state variables (e. g. Park et al. , 2010; Chen et al.