dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2012). The repeatability of automatic procedures is another interesting research issue. In the author's experience, different and not consistent results can be obtained using the same image dataset but importing images in a different sequence order. Since photogrammetry was born, network design has been a key topic when accurate and reliable measurements have to be performed. The reliability is the ability of a camera network to resist systematic and gross errors in the observations i. e. how undetectable and unmodelled systematic errors affects the accuracy of final results. Camera network with high redundancy and intersection angles close to 90 degrees are more reliable if compared to image sequences as usually seen in SfM procedures  (Alsadik et al. , 2013). In this paper some qualitative and quantitative analyses using different UAV and terrestrial camera network configurations are reported in the case of the digital documentation of a complex archaeological structurethe roman theatre in Ventimiglia, Italy.
3D surveying network and GNS S survey The surveying data were processed in a free network solution, providing an accuracy of  XY of 4 mm and  Z of 3 mm. The poorest planimetric accuracy was very likely due to faulty centring of the prism pole over the key points, mainly caused by reflector and circular bubble centring errors. Indeed, for the employed prism pole, a theoretical accuracy of the circular bubble of 10' is reported, that corresponds to a planimetric error of about 4 mm for a pole height of 1. 5 m. The GNSS data processing provided a sub-centimetre accuracy. The coordinates of the stations, obtained in WGS84, were used to compute the datum transformation to provide the products in the UTM /WGS84 reference system.
ACKNOWLEDGMENTS The project of the Roman theatre in Ventimglia was founded by  ARCUS SPA  and supported by  Direzione Regionale per i Beni Culurali e Paesaggistici della Ligura  (M iBAC) and  Soprintendenza per i Beni Archeologici della Liguria. The authors would like to thank  Francesco Zucca  and  Davide Zizioli  ( University of Pavia ) for providing the GNSS receivers employed during field work. A special thanks also to  Belen Jimenez Fernandez-Palacios  (FBK),  Alessandro Rizzi  ( Smart3K ) and  Nicolas Nony (CNRS)  for their valuable support during the survey operations and to  Sara Gonizzi Barsanti  (Politecnico of M ilano),  M atteo Rapanà  and  Giorgio Baratti  ( University of M ilano ) for the digitization work and production of CAD drawings.
After diversion of the main wastewater discharge at the beginning of the 1980s, TP winter concentrations gradually dropped to 17 µg L -1 in 2009 (INRA long-term lake observatory). Moreover, Lake Bourget has been experiencing significant climatic changes over the last decades. Previous analysis of the HISTALP (historical instrumental climatological surface time series of the greater alpine region) datasets (http://www. zamg. ac. at/histalp) has shown that annual and seasonal air temperatures exhibited a common and significant increasing trend beginning in the late 1980s  (Auer et al. , 2007 ). Between 1986 and 2009, mean  annual air temperature at Lake Bourget increased by more than 1 • C  (Alric, 2012).
To determine the first phylogenetic affiliation, each OTU was compared with sequences available in databases using the alignment search tool (BLASTN) from the National Centre for Biotechnology Information and the Ribosomal Database Project  (Altschul et al. , 1990). We retrieved the closest sequences identified in this way to include them in an alignment containing sequences from the closest cultivated members and some representative sequences of the major taxa. Sequences were re-aligned, and the resulting multiple alignment was checked and corrected manually. A phylogenetic tree was then constructed by the maximum likelihood (ML) method using MEGA5 software  (Tamura et al. , 2011). The ML analyses were carried out using the optimum model of sequence evolution selected according to the Akaike information criterion (AIC); as a result, the GTR+G+I model of nucleotide substitution was used.
, 2001)  and the non-parametric richness estimators Chao1  (Chao, 1984)  and ACE  (Chao and Lee, 1992) , which are the most appropriate for microbial clone libraries  (Kemp and Aller, 2004). The sequences reported in this paper have been deposited into GenBank (accession numbers: JX456478-JX456528). ITS1 analysis. The ITS1 sequences were analysed to assess the homogeneity of ITS1 sequences within the same OTU. The ITS sequences were analysed by similarity searches using the BLAST program and then aligned on the basis of conserved domains  (Iteman et al. , 2000)  using the BioEdit aligner. The ITS sequences were grouped into "ITS types", which are groups of sequences that can be meaningfully aligned  (Wilmotte, 1994 , from Fernandez-Carazo et al. , 2011)  sharing at least 80 % pairwise identities.
OTUb20 (represented by 24 sequences) showed high similarity (99. 4 %) to a strain isolated from Lake Champlain (Vermont, USA; accession number: HQ687069). Two strains from the Thonon culture collection (TCC 222 and TCC 218 isolated in 2005 from lakes Annecy and Bourget, respectively) were also affiliated with the same group, together with sequences originating from various freshwater systems (i. e. Rimov reservoir, Czech Republic and Lake 124, UK). The bootstrap value is 90 % for this cosmopolitan group that we propose to name Group N (similarities between pairs of the sequences in group N varied from 99. 2 to 100 %). The rare OTUb4 (9 sequences found in layers  1987-1988 and 1972-1973)  clustered with a novel group composed of  environmental sequences from a mesotrophic Masurian lake in Poland (strains MA0607, for which the phylogenetic position was not resolved;  Jasser et al.
, 2011) , a shallow eutrophic lake in Finland (sequence AM259252 from Lake Tuusulanjarvi), together with nine sequences retrieved from Lake Bourget sediment, formed a well-defined group (here named Group I; bootstrap 91 %; Fig. 3 ). The similarities between pairs of 16SrRNA gene sequences within this group varied between 99. 4 and 99. 7 %. Group I and Group N were confirmed by two different phylogenetic analyses (maximum likelihood and neighbour joining). It is notable that two sequences (OTUb3) fall within Group M, previously proposed as a new "Masurian clade" because it was composed of sequences from the Masurian lakes  (Jasser et al. , 2011). Some rare OTUs (number of sequences lower than 3), such as OTUb14, perfectly matched reference sequences from the NCBI database. OTUb14, retrieved during two distinct periods  (1991-1993 and 1972-1973)  in the sediments, showed 99.
5 % pairwise similarity to a sequence from Lake Kanui (New Zealand; accession number: EF638720), and a 100 % bootstrap associated these sequences with Group O. Of the 23 OTUs, the precise phylogenetic position of 9 rare OTUs (representing about 20 sequences in total) could not be resolved (Fig. 3 ), and BLAST searches failed to identify any closely related sequences in GenBank. Some of these OTUs Table  3. Total number of OTUs and richness estimators (SChao and SAce) obtained for each period (i. e. for each of the 8 sediment layers selected between 1951 and 2009) from 16S rRNA gene sequences (∼ 1100 bp alignment) presented in phylogenetic tree (Fig. 4 ). 2008-2009 2000-2001 1991-1993 1987-1988 1981-1983 1972-1973 1956-1960 1951   (i. e. OTUs 5, 6, 16, 17, 18) might be considered with caution since they occur as single sequence types in just one sediment layer and are not unambiguously associated to another reference.
, 2005). Other identified limitations Fig. 4b. The left part present the ML phylogenetic tree obtained from partial 16S rRNA gene sequences (1100 bp alignment). Sequences from sediments (black diamond), sequences from Synechococcus strains in Thonon Culture Collection (TCC; white diamond) and sequences from GenBank database (no specific sign) were used in this phylogenetic analysis. One representative clone was selected for each of the 23 OTUs identified from the sediment samples. A phylogenetic tree was constructed with the maximum likelihood method. ML phylogenetic trees were calculated using MEGA5  (Tamura et al. , 2011). The ML analyses were carried out using the optimum model of sequence evolution selected according to the Akaike information criterion (as a result the GTR+G+I model of nucleotide substitution was used).
, 2001)  was previously described as being specific to a certain geographical region (lakes in Japan). However, our results showed that this lineage was well represented in the PC assemblage of Lake Bourget consistently during the past century (OTUs b7 and 8 (Fig. 4 ) are affiliated with this group). These data demonstrate that greater care should be taken before inferring conclusions about the geographic restriction of novel PC clades, as recently noted by  Felföldi et al. (2011). To our knowledge, the Subalpine clusters I and II (four OTUs from our dataset, Fig. 4 ) remain specific for a geographical region. The rest of the dominant OTUs (based on 16S rRNA phylogeny) identified in this study should be considered cosmopolitan taxa because they clustered with strains isolated from various geographic places.
SSU rDNA and ITS sequences represent a useful resource for determining the phylogenetic relationships of se-quences within closely related strains derived from natural environmental samples (a large amount of sequence data is now available in GenBank), but conserved genetic markers such as SSU rRNA may not provide the best molecular resolution to identify ecotypes adapted to distinct ecological niches. For this specific purpose, other marker genes have to be developed and validated. Recently, multi-locus sequence analysis was employed by  Mazard et al. (2011)  to provide the taxonomical resolution of marine Synechococcus isolates showing that the recent availability of full genome sequences for several Synechococcus strains  (Dufresne et al. 2003; Rocap et al. 2003; Palenik et al. 2003 Palenik et al.
This chronological marker implied an average sedimentation rate of 4. 4 mm yr -1 for Lake Bourget between 1986 and 2005. The well-resolved peak of 137 Cs, visible at 17. 5 cm, coinciding with a peak of 241 Am confirmed that sediment at these depths were deposited at the period of max-imum artificial radionuclide fallout due to nuclear weapon tests in 1963. Age-depth relationships corresponded to an average sediment rate of 4. 2 mm yr -1 between 1963 and 2005. The good agreement between average sedimentation rates deduced from 210 Pb exc , 137 Cs and 241 Am profiles allowed the extrapolation of the regular sedimentation rate of 4. 2 mm yr -1 giving 183 yr of sedimentation. (Wunsam and Schmidt, 1995). The calibration dataset covered a large trophic gradient, with mean annual TP ranging from 2-266 µgP L -1.
Several models were tested: weighted averaging with classical deshrinking WA cla regression, weighted averaging with inverse deshrinking WA inv regression  (Ter Braak and Van Dame, 1989) , weighted averaging partial least squares regression  (WAPLS -Ter Braak and Juggins, 1993) , Modern Analogue Technique (MAT) with squared chord distance  (Overpeck et al. , 1985) ; and their relative performances were estimated using the r 2 and the root mean square error of prediction (RMSEP) calculated after a cross validation method (bootstrapping, 500 permutations) on the calibration dataset. The selected model was then applied to a diatom biostratigraphy of Lake Bourget from  Millet et al. (2010). DI-TP reconstructions were performed using program C2  (version 1. 7. 2, Juggins, 2007). [TP]  in Lake Bourget water column had been measured sporadically in the 1970s and then monitored from 2004.
These monitoring data could hence be used to confirm the models relevancy (Database SOERE-INRA of Thonon-les-Bains -France). Compared to WA and WAPLS models, MAT models had the lowest performance. There were no relevant differences between WA and WAPLS models performances. Statistical results for DI-TP showed a relatively good predictive ability of the WA model with classical deshrinking (r 2 jackknife = 0. 604, RMSEP = 0. 34 log unit). Of all the samples from Lake Bourget, 91 % of the fossil assemblage was comparative to the training set of the DI-TP. The bootstrapped average bias was low (0. 92 %) Generally, DI-TP changes were consistent with expected dynamics. Values and timing of DI-TP maxima matched measured TP (Fig. B1 ), and DI-TP for current time periods were in close agreement with the monitored chemical data.
There is f land = À NEP in equation (  1 ). [17] The integration time step is 20 min for the photosynthesis of vegetation, 24 h for the biomass accumulation and phenological variation as well as soil carbon decomposition processes. The vegetated surfaces are divided into 15 plant functional types (PFTs) including natural vegetation and crop as the present situation. In BCC_AVIM1. 0, a grid cell contains up to four PFTs which is similar to CLM3. The composition and abundance of PFTs within a grid cell are time-invariant and prescribed from 1 km satellite data  [Bonan et al. , 2002]. [18] In this study, only the land use-associated CO 2 emissions are involved in terms of E landuse in equation (1). The actual land-cover changes as boundary conditions of the BCC_AVIM1. 0 are not involved. Fractional land use patterns are fixed in BCC-CSM1.
Experiments [24] The preindustrial climate state of BCC_CSM1. 1 is obtained from a 300 year control simulation following the requirement of CMIP5. At first, the initial state of each component of BCC_CSM1. 1 is obtained through individual "spinup" runs. The atmospheric model is integrated for 50 years forced by fixed preindustrial forcing of the year 1850, including global reconstructed SST and sea ice concentration. The land model BCC_AVIM1. 0 is forced with a fixed atmospheric CO 2 concentration of 285 ppmv in 1850 and the atmospheric forcing of 1950-2000 NCEP reanalyses data in an offline way to yield a first estimate of equilibrium states for the land carbon pools. The ocean component is integrated alone for 200 years using the surface forcings from the above mentioned 50 year atmospheric integration with an atmospheric CO 2 content fixed at the value in 1850 for the OCMIP module of MOM4-L40.
Herbaceous biomass was harvested at the end of July 2010 during the first year after turf transplantation, and served as an estimate of annual AGB production. At each plot, the vegetation within a fixed area of 35 cm × 35 cm was cut down to ca. 1 cm above the soil surface, determined to species level, dried at 70ºC for 48 h, and weighed. Climate parameters were monitored continuously throughout the experiment by means of one automated weather station (Sensor Scope Sàrl, Switzerland) per experimental site, which measured at a one-minute interval air temperature and humidity 2 m above the ground surface, as well as rain precipitation. ECH 2 O EC-TM sensor probes coupled to Em50 data-loggers (Decagon Devices, Inc. , USA) recorded soil temperature and volumetric water content at topsoil horizon (0 to -3 cm) every minute, and data were averaged over onehour intervals.
Statistical analysis of experimental data The experimental design allowed for the explanation of annual variation in herbaceous biomass during the first year after transplantation by four factors: two categorical ones-initial pasture type and altitude of the transplantation site, and two continuous physical ones-soil temperature and soil moisture. Each of the two edaphic variables was averaged per plot over the growing season (between respective soil thaw and day of harvest), thus integrating the microclimate conditions experienced by the plants. An ANCOVA model was fit through the raw data to test the significance of single factors and their two-way interactions. Assumptions of normality and homoscedasticity of the residuals were verified visually using diagnostic plots. In order to extrapolate from experimental plot data, obtained under a distinct set of environmental conditions, to continuous site gradients in real landscapes, we built a linear regression model to predict the seasonal AGB production from the two continuous variables-tree cover percentage and degrees of temperature change.
Acknowledgments: This work was supported by the  CCES (Competence Center Environment and Sustainability of the ETH Domain, Switzerland)  as part of the  Mountland  project, and by the  State Secretariat for Education and Research  ( SER C07. 0112 ) in the framework of the  COST Action FP0603. We thank  Arboretum National d'Aubonne, Commune of St-George (VD) ,  Parc Jurassien Vaudois ,  Fondation Les Bois Chamblard  for their logistics and infrastructure support. Special thanks go also to  Dr. Silvana Siehoff  who provided us with constructive comments on the manuscript and to various people from the  ECOS laboratory  who gave a precious hand during fieldwork.
The launch of the French/US mission Topex/Poseidon (T/P) (CNES/NASA) in August 1992 was the start of a revolution in oceanography. For the first time, a very precise altimeter system optimized for largescale sea level and ocean circulation observations was flying. T/P alone could not observe the mesoscale circulation. In the 1990s, the ESA satellites ERS-1/2 were flying simultaneously with T/P. Together with my CLS colleagues, we demonstrated that we could use T/P as a reference mission for ERS-1/2 and bring the ERS-1/2 data to an accuracy level comparable to T/P. Near-real-time high-resolution global sea level anomaly maps were then derived. These maps have been operationally produced as part of the SSALTO/DUACS system for the last 15 yr. They are now widely used by the oceanographic community and have contributed to a much better understanding and recognition of the role and importance of mesoscale dynamics.
In the end of the 90s, a major international initiative was launched to develop Argo, the global array of profiling floats, as an initial joint venture between CLIVAR and the Global Ocean Data Assimilation Experiment (GODAE). Argo has been an outstanding success. The unique capability of satellite altimetry to observe the global ocean in near-real-time at high resolution and the development of Argo were essential to the development of global operational oceanography. GODAE (1998 GODAE ( -2008) )  was phased with the T/P and ERS-1/2 successors (Jason-1 and ENVISAT) and was instrumental in the Published by Copernicus Publications on behalf of the European Geosciences Union. P. Y. Le Traon: From satellite altimetry to Argo and operational oceanography development of global ocean analysis and forecasting capabilities.
Geostrophic velocity (slightly) underestimates (overestimates) velocity in anticyclonic (cyclonic) eddies. Differences in EKE are thus highly correlated with sea level variability skewness  (Thompson and Demirov, 2006). This is an interesting result that highlights the importance of a better understanding of observed signals. Note that altimeter data have recently been used to diagnose errors in global drifter array velocities due to drogue loss  (Rio et al. , 2011; Grodsky et al. , 2011). Merged T/P and ERS data sets have also allowed a better investigation of EKE seasonal variations. A very nice illustration is given in the Qiu and Chen (  2004 ) study. They detected high EKE bands in the South Pacific with well-defined annual cycles along the eastward-flowing surface currents of the South Tropical Countercurrent (STCC) and the South Equatorial Countercurrent (SECC).
Final step: the operational SSALTO/DUACS products In 2002, DUACS was integrated in the CNES multi-satellite ground segment (SSALTO) processing facility. This final step allowed DUACS to move from a project to a sustained operational system SSALTO/DUACS. The system was then regularly improved through different R&D or operational projects (e. g. ENACT, MERSEA, MyOcean). Thanks to SSALTO/DUACS, we now have a long time series (20 yr) of high-resolution mesoscale altimeter products based on a homogenous two satellite configuration (T/P and ERS-1/2 and Jason-1/2 and ENVISAT). These products have been used for a wide range of science and operational applications (see previous section): mesoscale variability and global characterization of eddies, monitoring fronts in the Antarctic Circumpolar Current, multiple migrating quasi zonal jets, eddies and Rossby waves, ocean-atmosphere coupling at the mesoscale, model validation, testing turbulence theories, coupling physics and biology, coastal dynamics, Argo and altimetry, data assimilation, operational oceanography and applications.
SSALTO/DUACS is now the main multi-mission altimeter data center used by the scientific community and by operational oceanography and climate centers. It provides directly usable, high quality near-real-time and delayed-mode global and regional altimeter products. Main processing steps include product homogenization, data editing, orbit error correction, reduction of long wavelength errors, and production of along-track and mapped sea level anomalies. A mean dynamic topography (MDT) is also used to obtain absolute dynamic topographies. Several versions of MDTs were derived and the most recent ones benefit from GRACE and GOCE observations (e. g. Rio et al. , 2011). The SSALTO/DUACS weekly production moved to a daily production in 2007 to improve timeliness of data sets and products. A new real-time product was also developed for specific real-time mesoscale applications.
To improve further our understanding of mesoscale variability, one must observe it at higher space and time resolution. From October 2002 to September 2005, sampling of the ocean has been exceptional with four altimeter missions flying simultaneously (Jason-1, ENVISAT, T/P interleaved with Jason-1 and Geosat Follow-On). These data sets were merged to improve the estimation of mesoscale surface circulation in the Mediterranean Sea and in the global ocean by  Pascual et al. (2006 Pascual et al. ( , 2007)). These studies demonstrated that, at least three, but preferably four, altimeter missions are needed for monitoring the mesoscale circulation. The effect is much larger for real-time applications. Pascual et al. (2009)  showed that four altimeters are needed in real time to get a similar quality performance as two altimeters in delayed mode.
GODAE development and achievements GODAE has been a major breakthrough in oceanography. The GODAE demonstration (2002 -2008)  was phased with the Jason-1 and ENVISAT altimeter missions. GODAE has had a major impact on the development of global operational oceanography capabilities  (Bell et al. , 2009). It was instrumental in the development of Argo and GHRSST (GO-DAE High Resolution Sea Surface Temperature) (GODAE pilot projects), altimetry and in situ data processing systems (e. g. SSALTO/DUACS and Coriolis). Global modelling and data assimilation systems were progressively developed, implemented and inter-compared. In situ and remote sensing data have been routinely assimilated in global and regional ocean models to provide an integrated description of the ocean state. Products and services were developed for a wide range of applications: marine environment monitoring, weather forecasting, seasonal and climate prediction, ocean research, maritime safety and pollution forecasting, national security, the oil and gas industry, fisheries management and coastal and shelf-sea forecasting (see GODAE Oceanography Magazine Special Issue -  Bell et al.
5. 3). This was initially anticipated (e. g. Le Traon et al. , 2001b)  and was demonstrated as part of GODAE. The capability of Argo to complement altimeter observations to constrain both large-scale and mesoscale ocean fields through data assimilation is a major asset and explains why these two observing systems now provide the backbone of the global observations for operational oceanography. A review of the role of altimeter and Argo observation data to constrain global ocean models is given by  Oke et al. (2009). A continuous assessment of the impact of Argo and altimeter observations is now organized at international level through GODAE OceanView.