dataesr/scientific-paragraphs-categorization huggingface dataset:
Optimisation of uranyl binding Existing literature datasets on uranyl binding to HFO were collated from the literature (Table  S3 ). A single parameter fit was made to all datasets. Where only % UO2 adsorption data were available, rather than direct measurements of dissolved uranyl, points representing less than 20% or greater than 80% adsorption were removed, to avoid errors in deriving dissolved urnayl concentrations. The total number of data points found was 289, of which 165 points were suitable for fitting. Fitting was done by minimising the sum of squares error in the log dissolved uranyl concentrations. Following  Lofts and Tipping (1998) , we initially postulated that the binding species comprised the uranyl free ion (UO2 2+ ) and its first hydrolysis product (UO2 2+ ). Initial fitting suggested a need to include additional carbonate binding species, e.
We present the R package Chemically Aware Model Builder (camb)  [5] , which is able to perform the above mentioned modelling tasks. camb is an open source platform for the generation of Structure-Activity and Structure-Property models. The functionalities of camb include: (i) standardisation of chemical structure representation, (ii) calculation of 905 one-dimensional descriptors and 14 fingerprints for small molecules, (iii) 8 types of amino acid descriptors, (iv) 13 whole protein sequence descriptors, and (iv) training, validation and visualization of predictive models.
However, for general parametric formalisms such as Parametric Timed Automata, the existence of a parameter value such that some state is reachable is undecidable and there is currently no algorithm that solves the synthesis problem of parameter values except for severely restricted subclasses, whose practical usability is unclear. This work was partially funded by the ANR national research programs ImpRo (ANR-2010-BLAN-0317) and PACS (ANR-2014). A preliminary version of this work appeared in  [20]. It is then a challenging issue to define a subclass of parametric timed automata, which retains enough of its expressive power and such that, for both reachability and unavoidability properties, the existence of parameter values is decidable and for which there exist efficient symbolic synthesis algorithms.
A. The tool We have implemented the synthesis of integer parameter valuations in our tool ROM ÉO  [25]. The formal timed model: With its textual input language, ROM ÉO 1  handles a model called Clock Transition Systems (CTS)  [19]  with timed intervals, which are particularly well-suited for the modeling of real-time systems. This model encompasses classical models with implicit clocks such as Time Petri Nets (TPNs)  [26]  or Duration Kripke structures  [23] , and models with explicit clocks such as Product Interval Automata  [13] ,  [14] , which are networks of particular kind of Timed Automata with a single clock which must be reset along every transition. Though best presented in the more well-known framework of parametric timed automata, the method we have proposed in this paper can be naturally adapted to the model of Clock Transition Systems with parametric timed intervals, on which operates ROM ÉO.
with simulated data, we focus on a real data set. We thus consider the three days ACM Hypertext conference held in Turin, June 29th -July 1st 2009. Proximity interactions between attendees during the first day are modelled and an interesting clustering of the daily hours is finally obtained, with times of social gathering (e. g. coffee breaks) recovered by the approach. Applications to large networks are limited due to the computational complexity of the greedy search which is dominated by the number K max and D max of clusters used in the initialization. Therefore, advanced clustering tools are considered to reduce the number of clusters expected in the data, making the greedy search applicable to large networks.
Real Data The dataset we used was collected during the ACM Hypertext conference held in Turin, June 29th -July 1st, 2009. Conference attendees volunteered to to wear radio badges that monitored their face-to-face proximity. The dataset represents the dynamical network of face-to-face proximity of 113 conference attendees over about 2. 5 days  4. Further details can be found in Isella, Stehlé, Barrat, Cattuto, Pinton, Van den Broeck  [7]. We focused on the first conference day, namely the twenty four hours going from 8am of June 29th to 7. 59am of June 30th. The day was partitioned in small time intervals of 20 seconds in the original data frame. We considered 15 minutes time aggregations, thus leading to a partition of the day made of 96 consecutive quarter-hours (U = 96 with previous notation).
High resolution images were taken from the ground level, using two off-the-shelf reflex cameras, equipped with a 35 mm, a 100 mm and a 200 mm focal length lens according to the needs. The MicMac software was used for the bundle adjustment, the georeferencing and the dense correlation procedures, including orthoimage calculation. Added to plane-based orthoimages, cylinder-based orthoimages were generated for the 2D representation of the outer walls of the château de Chambord including façades and towers. Fitting the 2D projection to the mean characteristics of the geometry has a promising documentation potential for GIS applications in heritage studies. This contribution has been peer-reviewed.
Image orientation The goal of this phase is to compute the position and orientation of the 1595 cameras during the image survey in the reference coordinate system, as well as the camera geometry itself (principal points, principal distance and distortion law). At first, tie points between all images were extracted within the MicMac software, in a specific module based on the SIFT algorithm  [Lowe, 2004] , followed by a multiple matching phase. To accelerate the computation, this phase was made in two steps: first, tie points between all the short focal length lens images were computed; then, for each façade or tower, tie points between the long and the short focal length images were added. More than 10 million tie points were extracted from the short focal length images, and more than 35 million in total.
Then, a bundle adjustment of all 35 mm focal length images was calculated, leading to an average image residual of 0. 4 pixels. This computation optionally includes an autocalibration of the camera. The principle is to start the first iterations of the bundle adjustment with an approximate camera, derived from the Exif data and a given camera model. After some iterations, the camera parameters are added to the system of equations and adjusted in a way that the average image residual is minimized. Since the focusing parameters change the geometry of the camera, the autocalibration procedure should determine different cameras when they change. It is unfortunately not done automatically, since they are not part of the Exif data. Hence, a specific recording was made in the field: as far as possible, whole sets of images were taken with the same parameters (same aperture and fixed manual focus), and anytime the focusing distance had to be modified, an image of the sky was made, so that the images could be properly sorted taking the different cameras into account.
It is then possible within the MicMac software to ask for a separate camera for a specific pattern of images. At the end, 15 different cameras were calibrated for the short focal length lens images. Two types of ground control points were then measured on the 35 mm focal length images: reliable and accurate GCPs specifically designed for these images, and other GCPs designed to georeference already existing laser data (only natural points could be used for the laser georeferencing). Both types of points were weighted differently in the final bundle adjustment. At the end, 59 well-spread GCPs were measured on 341 images. The final global compensation in the MicMac software led to rather good results (average image residual around 0. 4 pixels on the tie points, 0. 8 pixels on the GCPs, average ground control point residual around 1 cm in X,Y,Z).
3D reconstruction and orthoimage production 4. 2. 1 Image matching from the "image" space or from the "object" space MicMac software can be used to calculate the depth map in several geometries: "image" geometry, specified by a master image, with a dynamic in 1/Z, or "cartographic" geometry, well adapted to classical aerial surveys (see Figure  7 ). Image matching from the image space using epipolar geometry "Cartographic" 3D reconstruction geometry Image matching from the object space The second approach (cartographic geometry) requires the projection plane to be defined by drawing polygons considered to belong to the main façade plane on the input images. The projection plane is then computed as the best plane passing through the tie points contained in these polygons. This reconstruction geometry makes it direct and easy to compute orthoimages.
Case of high walls: orthocylindric geometry However, since ground resolution within the images of the façade may vary considerably, especially for high walls viewed without perspective, it is not recommended to compute a depth map at a constant spatial resolution as is done when using cartographic reconstruction geometry. MicMac software also makes it possible to compute a depth map at a constant angular resolution, through a mere temporary change of coordinates to avoid computing Z as a function of (X,Y). New coordinates, U,V,L may indeed be defined, so that U=D. atan(X/Z) ; V=Y ; L=Z (see Figure  8 ). The problem is thus turned into computing L=f(U,V).
Fully automated computation mode A new computation mode has been recently proposed in the MicMac software. This method, based on image geometry reconstruction (see 4. 2. 1), is designed for non-expert users, since it does not demand any parametric setting; in fact, only a few user interactions are needed. One is required to define the working area by drawing a box in the 3D tie point cloud, computed right after the image orientation (see example of such a point cloud in Figure  6 ). Then, a depth map is computed in "image" geometry for some images, which view the working area. The master images are automatically defined by the software, and, for each of them, the best set of secondary images is defined using different criteria: efficiency in terms of occlusion management, number of images to be used, incidence angles and space coverage.
Shapes, dimensions and absolute positionning The comparison of the photogrammetric 3D point clouds with the laser data previously acquired by the PRISME laboratory makes it possible to check for any deformation, which may happen in case of inadequate determination of the camera or an insufficient number of ground control points. The CloudCompare tool  [CloudCompare, 2015]  was used to compare laser and photogrammetric data. The comparison was first made on FSE (see Figure  5 ) which is the longest wall, thus the most likely to be distorted by photogrammetric processes. The difference between the two datasets is around 1 cm. No systematic error was observed, except for some strong discontinuities like the windows, which are not well reconstructed on the photogrammetric dataset, probably because of the image survey geometry (camera axes roughly perpendicular to the walls) and the cartographic 3D reconstruction geometry.
Efficiency of the tools Image acquisition in the field is relatively fast and efficient; however, some rules need to be strictly respected: keep a fixed focus for a whole set of images, document any change in focus, and take both short and long focal length images. MicMac software is highly promising because on the one hand, it makes it possible to check intermediate results at any stage of the process and, on the other hand, it deals with a great number of cases (flat walls, high walls, cylindrical towers, image acquisition with almost any kind of camera). More tests remain to be made to improve the choice criteria of one or the other computation mode. However, the way MicMac was used for the Chambord project needs to be improved, mainly insofar as computational time is concerned, whatever stage of the process (tie point computation, bundle adjustment, dense image matching).
From the users' point of view The digital model made by the ENSG can be directly used in classical CAD or GIS software. Moreover, the selected digital assets do not require additional workflows to deal with annotation. The produced orthoimages provide a metric support with sharp details of stone features and a relevant radiometric quality. These criteria are currently nearly impossible to meet with any other acquisition method. On the one hand, with 3D scanners (used by PRISME laboratory for other applications), geometric correctness could be better than MicMac processing, but color information would need additional photographic processing. Other photogrammetric software solutions favor ease of use over parametric settings at the expense of metric and radiometric quality. Moreover, as far as we know, none of these can handle cylindric geometry or orthocylindric geometry, which is critical in our case.
A current project on lapidary signs already takes advantage of this documentation. The aim of this archaeological study is to cross-reference various data collected during in situ surveys (architectural elements, dating, nature and origin of stones)  [Janvier-Badosa et al. , 2012]  with anthropic marks engraved by stonecutters. These archaeological and historical studies were, until now, mainly carried out without computer tools. Our approach on a free software stack based on GIS plugged into a spatial database, makes it possible to run spatial queries added to systematic and automatic spatial distribution calculations of these lapidary signs (see Figure  17 ). Finally, this will help provide new information about the chronology of the building process of the château de Chambord in the 16 th century.
PERSPECTIVES This work, whose data was with a MicMac pipeline, is totally based on open format that will ensure the completion of this work by further studies. Moreover, the digital assets provided by MicMac are totally transposable into the future 2D/3D hybrid annotation framework developed in the MONUMENTUM ANR project  [Manuel et al. , 2014]. As it was already written, several reconstruction methods were used to reconstruct the outer walls of the castle in 3D (fully automated way using the image reconstruction geometry for the cylindrical towers, and cartographic orthocylindric geometry for all the other walls). Since the software was being developed and improved during the production, it was hard to run all the necessary experiments to properly assign one type of computation to one type of architectural structure.
Results Results are presented in two sections. First, we present the performance observed on the rule falsification task (RFT) before the learning stage, and second, the performances observed on the Wason selection task (WST), which measured the transfer effect from the pre-test to the post-test. For each task we computed the participant's responses in terms of matching (total or partial) or logical responses. To capture the fine-grained transfer effect on the WST for the two learning groups (EL and CL), we computed the selection (1) or the non-selection (0) of each card (A, D, 3 and 7). We used non-parametrical and parametrical statistical tests to test the effects of the Test (pre vs. post) and the type of Learning (executive vs. logical) factors. Raw values are presented in (see S1 Dataset).
New Caledonia experiences a decrease in surface solar irradiation since 2004. It is of order of 4 % of the mean yearly irradiation over the 10 years period: 2004-2013, and amounts to -9 W m -2. The preeminent roles of the changes in cloud cover and to a lesser extent, those in aerosol optical depth on the decrease in yearly irradiation are evidenced. The study highlights the role of data sets offering a worldwide coverage in understanding changes in solar radiation and planning large solar energy plants such as the ICOADS (International Comprehensive Ocean-Atmosphere Data Set) of the NOAA and MACC (Monitoring Atmosphere Composition and Climate) data sets combined with the McClear model.
Data Measurements of global SSI and DNI were collected from Meteo-France for the stations of Koumac and Noumea (Fig. 1 ). Global SSI and DNI are measured at Koumac while Noumea provides global SSI only. The values delivered by Meteo-France are monthly irradiation, from 1998 to 2013. The clearness index K T , also called atmospheric transmissivity or transmittance, is computed by dividing the observed monthly irradiation by the monthly irradiation received by a horizontal plane located at the top of atmosphere. K T allows to disentangling the seasonal variations of the atmosphere transparency from those due to the orbit of the Earth around the Sun. Published by Copernicus Publications. Re-analyses are another means to assess the SSI. They offer worldwide and multi-decadal coverage. Several authors (see a review in  Boilley and Wald, 2015)  have compared SSI estimated by re-analyses to coincident ground measurements.
They found a tendency of a majority of reanalyses to overestimate the SSI. Reanalyses often predict clear sky conditions while actual conditions are cloudy. This overestimation of occurrence of clear sky conditions leads to an overestimation of the SSI. The opposite is also true though less pronounced: actual clear sky conditions are predicted as cloudy. For these reasons, reanalyses are not used in this study. Proper processing of satellite images is another means to assess the SSI. Several databases offer daily irradiation over the area under study, such as the NASA SSE data set available at http://eosweb. larc. nasa. gov/sse/. However, none of these data sets can be used here because they are not appropriate for this study like NASA SSE which is limited to the period 1983-2005, or they are not available freely such as the data sets from the 3Tier or GeoModel Solar companies.
The European-funded projects MACC (Monitoring Atmosphere Composition and Climate) have created a set of global aerosol properties together with physically consistent total column content in water vapour and ozone  (Kaiser et al. , 2012). These data are available on a grid of approximately 100 km every 3 h. Once collected from the MACC web site (http://www. gmes-atmosphere. eu), these data were interpolated in space and aggregated to yield monthly means of aerosol optical depth at 550 nm, and total column contents in water vapour and ozone for Koumac and Noumea, from 2004 to 2013. The McClear model  (Lefèvre et al. , 2013)  uses the MACC data sets as inputs and provide monthly irradiation of global SSI and DNI that should be observed if the sky were clear i. e. cloud-free, from 2004 to 2013.
These quantities are called clear-sky SSI and DNI. As discussed above, cloud coverage from meteorological analyses is not very accurate. Since New Caledonia is an island of limited extension, it was thought that cloud coverage may be provided by the International Comprehensive Ocean-Atmosphere Data Set (ICOADS). ICOADS is a global ocean marine meteorological and surface ocean dataset formed by merging many national and international data sources that contain measurements and visual observations from ships (merchant, navy, research), moored and drifting buoys, coastal stations, and other marine platforms. Cloud coverage is available in okta on a grid of 2 • in size. The KNMI Climate Explorer (climexp. knmi. nl) offers access to these data and processing capabilities. Cloud coverage has been collected from this site as monthly values averaged over the oceanic region in the vicinity of New Caledonia defined by latitude ranging from -22 to -18 • , and longitude from 156 to 164 •.
Conclusions This study demonstrates that New Caledonia experiences a decrease in surface solar irradiation since 2004. The decrease over the 10 years period: 2004-2013, is of order of 4 % of the mean yearly irradiation for this period. This change amounts to -9 W m -2 and is very large with respect to climatic changes as reported by  Wild (2012). The available data set for the study is limited and hence our conclusions are fairly questionable. The study has demonstrated the preeminent role of the cloud cover on the decrease of the yearly SSI and has found that it cannot be the sole cause of the changes in solar radiation. Changes in aerosol optical depth play a role in changes in SSI though more moderate. This study highlights the role of data sets offering a worldwide coverage in understanding changes in solar radiation and planning large solar energy plants.
Two independent manuscripts by Berger and by Kavitha discuss an algorithm (implemented by Python-NetworkX) the theoretical basis of which was first described by Paton in 1969  [14]. 2. Persistent homology is a more involved topological measure of networks  [3, 10, 15]  an abstract n-simplex {v 0 , ⋯, v n } of a set of n + 1 called vertices. Persistent homology can be geometrically represented as the convex hull of these n + 1 vertices in an n-dimensional Euclidian space. Simplices are generalizations in any dimension of convex polytopes such as points (0-simplices), segments (1-simplices), triangles (2-simplices) and tetrahedra  (3-simplices). The faces of an n-simplex σ are all the (n-1)-simplices, which are subsets of σ. For example, a 3-simplex (tetrahedron) contains four 2-faces. A simplicial complex K.
The abstraction of the network into Betti numbers facilitates an analysis of the correlation between Betti numbers and percent survival. The mapping the Betti numbers space onto the survival curves using a computational algorithm, indirectly maps the PPI-space onto survival space. This indirect mapping is of central Fig. 2  Mapping of Betti numbers onto survival data from Surveillance Epidemiology and End Results (SEER) database. Nominal Betti numbers were calculated on the Kyoto Encyclopedia of Genes and Genomes (KEGG) and correlated with Surveillance, Epidemiology and End Results Database (SEER). Nominal Betti, a measure of network complexity, was inversely correlated with percent 5-year survival (R = -0. 551, p = 0. 0789), suggesting an inverse relationship between network complexity and cancer survival interest because we are abstracting a large amount of network information into a single number, and this abstraction is associated with a particular amount of uncertainty.
Thus, the uncertainty of mapping Betti number-space to percent survival-space leads to a significant increase in uncertainty. Because many networks can give rise to the same Betti number (surjective mapping), Betti number mapping to survival must be done with this caveat in mind. The actual mapping of Betti numbers onto the Surveillance Epidemiology and End Results (SEER) database (Fig. 2 ) revealed an inverse linear correlation (R = -0. 551, p-value 0. 079) between Betti number (a dimension of persistent homology from filtration index one to two) and percent 5-year survival for a variety of cancers. The inverse correlation implies that the higher the Betti number, the lower the probability of five-year survival. Our interest in this approach lies not simply in describing this mapping, but rather in using such a mapping for developing tools for evaluation of therapeutic targets and designing personalized therapies.