dataesr/scientific-paragraphs-categorization huggingface dataset:
CityGML for Ordnance Survey Feedback has shown that customers see Ordnance Survey as a prime candidate for promoting the use of 3D data through internationally recognised standards. CityGML fits this bill very neatly. The OGC standard CityGML is one of the few (if not only) internationally recognised standards for 3D geoinformation. It has a rich semantic description of terms and allows for the modelling of most of the objects found within a city. Its semantic interoperability aligned to the formal description of 3D features is one of its key advantages. Ordnance Survey already supplies its detailed 2D data products in GML format, and so CityGML would seem to be a logical extension of this. There are several ways in which OSGB could use CityGML. These include: • As a basis for a 3D database model • As a transfer format between internal systems e.
g. from data capture to database environment. • As a transfer format for data supply to our customers While there are many advantages to using CityGML, OSGB also perceive some challenges, in particular: • The need to define an accepted national profile for CityGML that is • Fully supported by software vendors in order to exploit the richness of the information Both of these carry the risk of resistance to the take-up of CityGML across all involved parties. Therefore the wide support of CityGML by data providers, software vendors as wells as users needs to be addressed.
In addition, TOP10NL is less detailed than IMGeo and therefore better suitable for fully automatic 3D object reconstruction since fewer details are present (therefore less special cases). We assume that the resulting dataset is sufficient for a nationwide dataset (i. e. acceptable performance for nationwide applications), and that it can be further refined (for example with 3D IMGeo data) when applied in future projects. Some tests on generating 3D TOP10NL fully automatically, have been done in the past years, see Figure  8  (Oude  Elberink et al, 2012). Currently, the research results will be made further ready for practice. The developments of 3D TOP10NL builds on the insights obtained by the pilots on 3D IMGeo, since the techniques to obtain LOD0 and LOD1 representations from a combination of 2D data and high-resolution height points are similar.
3D MAPPING IN SWITZERLAND The Swiss Federal Office of Topography (swisstopo) offers a wide range of products ranging from traditional paper maps to digital multimedia products. Since 2008 swisstopo has been developing and updating the Topographic Landscape Model (TLM). TLM is the basis landscape model for Switzerland. It is a seamless GIS containing 3D primary geometry without generalisation with an accuracy of better than 1meter in x, y & z. TLM consists of 10 themes, which in turn contain several independent datasets previously maintained separately such as boundaries, names and terrain (see Figure  9 ). It also has a revised extended data model to meet the needs of reference partners such as road and water authorities. The TLM describes around 10 million natural and artificial landscape features, complete with their position and shape, the corresponding landscape feature type and many other attributes: The content of the TLM and the landscape feature definitions were developed in cooperation with various professional institutions from both the federal government and the cantons.
Geometries and a wide range of attributes are provided for all landscape features. All objects have x, y and z coordinates which also means that objects in TLM maintain consistency with DTM-TLM, for example 3D roads should lie on the DTM. TLM is not a product, but rather will be the basis for a wide variety of products including the derived 1:25k cartographic base maps. It serves also the bases for Switzerland's National Spatial Data Infrastructure (NSDI).
Production and updating The ever-increasing demand for better, more up-to-date diverse digital data has meant that the rapid updating of swisstopo products has taken on a high importance. With the new established production process for TLM an updating infrastructure for a central data set from which all products could be then produced was established. Reference partners (such as the cadastre, road and rail authorities among others) deliver their up-to-date data for rapid insertion into the TLM in order to maintain top up-to-dateness. The updating process itself is performed in a modern database based system comprising of hardware and software for the capture, editing, management, storage and distribution of the TLM. The associated Digital Terrain Model will also be edited using this infrastructure.
Natural and artificial landscape features Compared with the formerly existing geodata (VECTOR25, SwissNames, etc. ) the TLM offers higher geometric accuracy, but is also more extensive and up-to-date. The existing data was migrated into the TLM as a basis, mainly due to the rich information in attributes and topology maintained over the years. The data is then updated based on an update cycle of 6 years and improvements and additions are made to the geometries and attributes. Parallel to the six-year update process, an annual update is carried out through the integration of data from so-called reference partners for selected topics. Initially, this annual update is implemented mainly for the administrative boundaries, buildings and road links. The official cadastral survey plays an important role as a reference partner in this process.
3D Products Various 3D data sets extracted from the TLM are available since autumn 2010. They comprise the entire territory in reduced form -measured according to the final requirements of the TLM. To be more precise, the number of landscape features on offer is reduced compared with the TLM landscape feature catalogue and the geometric accuracy in the areas where the systematic improvement has not yet been made corresponds to that of data set VECTOR25. This is an initial version (1. 0) of the products extracted from the TLM. The systematic improvement of the data will mean that a Version 2. 0 of the various products can be made available alongside Version 1. 0. Version 2. 0 will be made available sector by sector in accordance with the update blocks. It will contain significantly more landscape features, offer a higher geometric accuracy for all data and will therefore fulfil the requirements with regard to TLM quality.
Pending issues as for true 3D data models As mentioned above, automated processes are good at creating the bulk of a city model, but failures are costly to identify, and corrective editing can be painstakingly long. Further work on automated identification of failures, and on assisted editing tools are therefore underway, to provide better quality models at an affordable cost. Compression of textures is another issue, since texture atlases can represent a too heavy load when loading a CityGML dataset, this may be linked with both limitation of the chosen encoding, and of available tools on the user side. Last but not least, comes the issue of 3D data model maintenance: How to appropriately update such data sets at an affordable cost? There is a whole range of R&D matters to consider, from aerial coverage options (including UAVs or ultralight aviation) to exploiting images captured from the ground by light cameras (e.
CityGML and IGN-F 3D data products Insofar CityGML has proved to be up to the task, robust enough to provide a good basis for 3D data exchanges. Only ongoing research suggests that further developments are needed. This being said, many users still require data to be provided in a different data model, because of limited support on the side of software vendors. IGN-F will keep supporting this standard, and contributing to its evolution, in the context of the anticipated development of LOD2 (or higher) data production at the national level.
Conclusions From the approaches described in this paper, several conclusions can be drawn. Firstly, 3D data is more and more available but still suffers from a low level of usage (mainly visualisation). In addition standards and formats based on CityGML have been stabilised although software support is still in the early stage. We also observe low level of European harmonisation. A cross-European profile for CityGML would be beneficial for several reasons. It would raise the level of adoption of CityGML 3D data, and hence raise usage level; it would push software developers to provide better support for the standard; it would be an important step towards European-wide harmonized data and finally, a better support of the standard would lower the costs needed for data conversion. Another conclusions that can be drawn from the approaches described in this paper, is that for 3D mapping at the national level, two approaches can be distinguished.
For the digitising of maps resulting in 2D databases, the benefits were clear: initially production lines were improved and later the digitised point, lines and areas could be upgraded to 2D information needed in spatial analyses. In contrast, 3D does not contribute to the improvement of an existing process. Instead 3D makes new applications possible and therefore it is much easier to identify the costs to acquire 3D than the benefits of having 3D information available. Many benefits will only become clear after having the 3D information available for large areas. Finally, a reluctance to make the step towards 3D mapping can be explained by the lack of a widely adopted 3D standard. While CityGML is a good candidate, software support is limited. In addition, more agreements need to be made at international level on how to implement the standard in specific applications or domains.
Further work Now 3D techniques have matured and OGC has established a standard for 3D data which is well stabilised, in many countries it is no longer a question if countrywide 3D mapping should be realised, but "when" and "how". From the findings in this paper several issues can be identified that require further (research) attention to progress in the domain of 3D (no ranking): For most mapping authorities 3D geo-information originates from their legacy datasets in 2D. In using this as a basis many associated issues emerge. • Maintenance and incremental updating of sustainable 3D datasets (sustainability vs. visualization) requires further attention. • The need of national and European policies on spatial information to stimulate the use of available 3D technologies. For CityGML, the following recommendations can be formulated for future directions.
Firstly, CityGML needs further support in software systems. This includes implementation of standard products and development of open source tools to support operations. In addition, as a generic standard CityGML needs further agreements defined in profiles. Therefore European CityGML profiles (as the INSPIRE Building profile) need to be defined to harmonise 3D needs and standardise 3D implementations at international level. Relationships with INSPIRE portfolio beyond buildings need to be investigated. Finally, interfaces with other standards are needed to exchange 3D data with other domains. For example the link with BIM-IFC (at least in practical uses) needs to be further investigated.
• More insights in real customer needs of 3D data sets are required (i. e. what topics are relevant and to what extent). These needs should be formulated in terms of what problems 3D can solve. This will stimulate other use of 3D data than visualisation. • More research is needed on how to fuse data, combining existing data into 3D databases can create problems, i. e. integrating existing non-3D datasets (addresses, boundaries, etc. ) with 3D datasets. • Consistency between 2D and 3D needs further attention.
miRNAs regulate gene expression at the posttranscriptional level  (1, 2). To date, $1500 human miRNAs have been documented in the database of miRNAs, miRbase  (23). miRNAs are believed to regulate the expression of upwards of 30% of human genes by enabling RISC to recognize complementary sequences in target messenger RNAs. Many miRNAs have oncogene-or tumor-suppressor-like behaviour  (24). Mis-expression or mutation of miRNAs can have considerable cellular consequences  (25). For example, miR-155 has been implicated in lung and breast cancer as well as different leukaemias and lymphomas  (24). Mutations in the proteins involved in the processing or regulation of miRNA biogenesis have also been linked to different cancers. For example, certain frame-shift mutations implicated in colorectal or endometrial cancers result in truncated forms of TRBP that lack dsRBDs 2 and 3  (26).
Sedimentation velocity analytical ultracentrifugation Sedimentation velocity experiments were performed with a Beckmann Coulter XLI analytical ultracentrifuge at 50 000 rpm (185 000g), 25 C with an An-50Ti rotor. Samples or reference (NMR buffer) were loaded into sapphire-windowed cells with 12-mm optical paths, which had previously been treated with RNase ZAP (Sigma-Aldrich). Acquisition was performed at 260 nm and 280 nm, and using interference optics. The molar masses for the polymers were calculated from their composition. A partial specific volume ( " v) of 0. 74 ml/g was estimated for TRBP-D12 using the software SEDNTERP version 2  (40). The " v used for pre-miR-155 (0. 508 ml/g) was taken from a study of a viral RNA in dilute aqueous KCl solutions  (41). The data were analysed in SEDFIT [Version 12.
52; (42)] using the c(s) analysis and non-interacting species models. The latter was used to estimate buoyant molar masses, M b , using the equation, M b = M Â [1 À (r Â " v)], where M is the molar mass and r the solvent density. Hybrid models and multiwavelength analysis were performed in the program SEDPHAT  (43). Results in terms of buoyant mass and multi-wavelength analysis are given for the more concentrated sample, which yielded higher signal-to-noise ratios. The mass density (1. 005 g/ml) and viscosity (0. 898 cP) of the buffer were calculated using SEDNTERP (v20120328 beta, www. jphilo. mailway. com). The " v for possible protein/RNA complexes was estimated by summing the individual " v values of each component weighted by their fractional mass in the complex (Supplementary Table  S1 ).
Isothermal titration calorimetry All isothermal titration calorimetry (ITC) experiments were conducted using a MicroCal ITC-200 at 25 C. ITC experiments were performed in two ways: either with the 'ligand', in this case the protein, in the cell, or with 'ligand' in the syringe. Protein concentrations varied between 30 and 60 mM in the sample cell and 250 and 500 mM in the syringe. RNA concentrations varied between 25 and 40 mM in the sample cell and 150 and 300 mM in the syringe. The heat evolved after each injection of protein or RNA was obtained from the integral of the baseline-corrected calorimetric signal. The equations used to analyse ITC data of TRBP-D12 were derived from the classical sequential binding equation using activity coefficients of 1. Previous assumptions of independency or co-operativity were not made.
The resulting binding isotherms were fitted to maximize the likelihood of the data assuming a Gaussian noise distribution. The titration data were globally fitted for each pair of experiments using previously described protocols  (44). The standard deviation of the estimation of each binding parameter was determined by computing 100 Monte Carlo simulations of each experiment performed assuming a Gaussian noise of 70 nanocals (estimated from our data) followed by a global fitting of the data. The stoichiometry for each protein/RNA pair was estimated by comparing the fits of sequential models for 1:1 and 1:2 protein/RNA complexes (see Supplementary Material).
Taken together, these data suggest that the RNA-binding region of TRBP is composed of two independent dsRBDs connected by a flexible linker and, therefore, that it is similar to the tandem dsRBDs that form the dsRNA-interacting region of PKR  (45). Both dsRBDs of the RNA-binding region of TRBP interact with pre-miR-155 Large, site-specific changes in ( 1 H, 15 N) chemical shifts are observed when unlabelled pre-miR-155 is added to constructs of TRBP (Figure  2a ). Backbone resonance assignments were obtained of TRBP-D12 in the presence of an excess of pre-miR-155. Using these sequence-specific assignments, it was possible to evaluate which regions of each dsRBD were involved in the formation of protein/ RNA complexes. A comparison of the amide chemical shifts of apo-and RNA-bound TRBP-D12 revealed large RMSD values between the two data sets (0.
Furthermore, the macroscopic binding enthalpy obtained for TRBP-D12 is approximately equal to the sum of that of TRBP-D1 and TRBP-D2, which indicates that the polar interactions formed by each single domain and pre-miR-155 are unaffected in the context of the full-length protein. Thus, these ITC data support the conclusions derived from NMR analysis that each dsRBD interacts independently with pre-miR-155. The formation of a complex between TRBP-D12 and pre-miR-155 in solution was evaluated by sedimentation velocity analytical ultracentrifugation (svAUC). A series of samples were prepared to characterize the behaviour of the free protein, free RNA and the protein/RNA complex under different conditions. SEC-MALLS (Figure  1b ) strongly suggests that TRBP-D12 is monomeric in solution. This observation was supported by svAUC data at 10 and 20 mM, which revealed an experimental sedimentation coefficient, s exp , of 2.
35. Non-interacting species analysis gives a molecular mass of 18. 5 kDa, which is again close to the theoretical value of 19. 4 kDa. An additional minor contribution at 7. 2 S (6% of the main peak) was also detected. This peak is likely to result from a small fraction of dimerized pre-miR-155. This species was also observed by SEC-MALLS (data not shown). SvAUC analysis of the TRBP-D12/pre-miR-155 complex was performed using three samples, each with a different excess of protein. In the resulting sedimentation profiles, the RNA contribution at 4. 4 S has disappeared and a new faster contribution is visible, which sediments at 5. 9 S (Figure  4c ). The composition of the 5. 9 S peak was estimated using the data obtained from the three different optical signals. The ratios of these signals as well as theoretical values calculated for TRBP-D12/pre-miR-155 complexes with different stoichiometries are given in Supplementary Table  S1.
ACKNOWLEDGEMENTS The authors thank  Drs. A. Favier  and  E. Condamine  for help with the acquisition of NMR data;  Drs. R. Rasia ,  B. Bersch ,  C. Petosa  and  A. Leech  for critical reading of the manuscript; and the  Grenoble Partnership for Structural Biology (PSB)  for access to integrated structural biology platforms, including: A. le  Roy  from the  IBS/PSB AUC  platform for help in the acquisition and analysis of AUC data;  Dr. M. Noirclerc-Savoye , from the  IBS/PSB RoBioMol platform , for the generation of the constructs used in this study; and the  IBS/PSB  high-field NMR spectroscopy platform; and IBS/PSB cell free expression platform.
Acknowledgements. This work was undertaken under the  MI-AVITA  project, financed by the  European Commission  under the 7th  Framework Programme for Research and Technological Development, Area "Environment", Activity 6. 1  " Climate Change, Pollution and Risks ". The authors would like to thank  A. Vagner ,  J. Douglas ,  P. Gehl ,  J. Loiseau  and  E. Vanoudheusden  for useful comments that led to the improvement of the proposed method. Very special thanks go to PHIVOLCS and particularly V. Antonia Bornas ,  M. Martinez -Villegas M. and  E. Bariso  for the invaluable support during fieldwork, and highly useful discussions on the geology of Kanlaon. S. Conway has improved the English language. We thank  Dmitri Rouwet  and two anonymous reviewers for their constructive comments that greatly improved the paper.
Another study identified a universal set of residues, I,V,Y,W,R,E,L (IVYWREL measure), enriched in thermophiles  [19]. More complex discrimination functions have also been proposed, such as the function employed by THERMORANK  [20]. This method uses a linear combination of 10 sequence-based features to rank a set of input sequences by relative thermostability. Another method, the Tm-Index tool, uses dipeptide composition to predict a melting point index for a single protein sequence  [21]. These measures have not yet been systematically tested on the Alvinella proteome. Recently, a large A. pompejana cDNA resource, prepared from three different tissues and whole animals was published  [5]. Analysis of this dataset in comparison with various metazoan homologs showed that A. pompejana protein sequences have the highest proportion of charged amino acids.
This bias was interpreted as a sign of protein thermostability  [5]. Another EST resource, generated by the Joint Genome Institute (JGI, http:// www. jgi. doe. gov/), is also publicly available. These A. pompejana EST resources could form the basis for reconstituting and determining structures of metazoan proteins and multiprotein complexes. However, in order for structural biologists to identify all components of large multiprotein complexes, where the lack of a single component will impede reconstitution, more extensive sequence coverage is essential. To increase the available dataset, we first carried out deep sequencing of the A. pompejana transcriptome. Using this resource and the published sequences, we established a large orthologous dataset with a taxon sampling that included other annelids, as well as the thermostable fungus, Chaetomium thermophilum  [8].
Deep sequencing of the A. pompejana transcriptome To gain insights into the mechanisms of thermoadaptation of A. pompejana, we first performed deep sequencing of its transcriptome. We used a combination of the Sanger, Roche/454 and Illumina technologies. With the 454 technology we obtained 2,717,445 reads of an average length of 220 bp. Using Illumina paired-end sequencing (~300 bp fragments) we obtained 87 million reads of an average length of 76 bp. These resources, and an additional 10,063 novel Sanger ESTs we generated, were assembled into a reference transcriptome dataset. Large-scale EST sequencing projects have also been carried out by the Joint Genome Institute (JGI) and Genoscope  [5] , yielding a total of 218,458 publicly available ESTs (as of Feb 2011). We also assembled these sequences with our resource, creating a combined MPI + JGI + Genoscope dataset.
To estimate the number of novel sequences in our resource (MPI dataset, Additional file 1) we compared it with the already available ESTs (JGI + Genoscope dataset, Additional file 2), as well as the combined dataset (MPI + JGI + Genoscope dataset, Additional file 3). First, we compared the length distribution of contigs and singletons in the three assemblies (Figure  1A ). The final combined assembly nearly doubled the available transcriptome resources for A. pompejana, with 60,475 contigs longer than 500 bp, compared to 34,860 in the JGI + Genoscope dataset. Due to the small size of the 454 and Illumina reads, the MPI and the MPI + JGI + Genoscope datasets were dominated by short contigs (Figure  1A ). However, they also contained a larger number of long contigs (>1,500 bp) than the JGI + Genoscope dataset  (7, 269   many novel full-length and partial sequences (Figure  1B  and Table  1 ), and also extended the length of already known partial proteins.