dataesr/scientific-paragraphs-categorization huggingface dataset:
4. 2) and setting them as initial values when defining the co-simulation graph (compare lines 15 and 19 in Figure  5 ). However, IntegrCiTy's DAL and the Simulation Package also allow to persistently store associations with attributes of 3DCityDB objects and generic parameters. This is demonstrated in the following pseudo code snippet, which basically extends the setup shown in Figure  5   Please note that in above example the resulting co-simulation graph object sim would not be valid to deploy an actual cosimulation (because parameter c is not associated to a scalar or vector). However, when writing the setup to the database, the association of parameter c with the corresponding table attribute is stored persistently. Furthermore, when reading this stored cosimulation setup from the database (using class DBReader), the association is automatically resolved.
CONCLUSION AND OUTLOOK This paper has presents initial work carried out to link semantic 3D city modelling and multi-domain co-simulation for urban energy modelling at urban scale. Starting from the CityGML data model (and the derived 3DCityDB as database schema implementation), a Simulation Package extension for the 3DCityDB has been conceived and implemented. The Simulation Package is meant to model and store in an integrated way additional meta-information which is required to execute an actual simulation or co-simulation. In the latter case, not only configurations are required for each individual simulator, but also specific information regarding the coupling and orchestration of several simulator instances. In the context of project IntegrCiTy, the Simulation Package has been adopted in order to build on top of it a Python-based data access layer allowing for linkage with an OBNL-based co-simulation tool.
It lays the foundation for a two-way connection between a detailed city-scale data model and simulation models of centralised and distributed complex energy systems, and it tries to answer the lack of extensible and adaptable cross-domain ontologies. Work carried out within the IntegrCiTy project is a first step towards linking semantic 3D city modelling and multi-domain cosimulation for urban energy modelling at urban scale. Although at a rather initial state of development, the assumption is that the developed tools are generic and flexible enough to be used also in other contexts. The wish is that the availability of a common, shared data model and the accompanying data access layer will contribute and foster adoption and further improvement of the Simulation Package in a sort of virtuous circle.
with the Simulation Package: The DAL also implements the mapping of the Simulation Package scheme to IntegrCiTy's concepts for representing co-simulation graphs (as defined in Section 3. 2), providing basically a persistence layer for co-simulation setups. For storing co-simulation setups to the extended 3DCityDB, the DAL provides class DBWriter. Upon connecting to the database (line 1), a co-simulation setup can be assigned a name and written to the database with the help of a single command. Lines 3-5 show how this is done for the example from Section 3. 4. 1. The parameters in line 4 indicate that a co-simulation setup already defining meta-model MetaBase and model BaseModel has been previously written to the same database (otherwise the corresponding parameters should be omitted).
ACKNOWLEDGEMENTS Research and implementation work presented in this paper has been carried out within the project  IntegrCiTy (IntegrCiTy Project Team, 2018) (ERA-NET Cofund Smart Cities and Communities call ). In Switzerland, it is funded by the  Swiss Federal Office of Energy  (contract  SI/501404-2 ), as well as by the industrial and institutional partners of the project. In Austria , it is funded by the  Austrian Federal Ministry for Transport, Innovation and Technology  within the framework of the  ENERGIE DER ZUKUNFT/JPI Urban , with support from the  European Union 's  Horizon 2020 research and innovation programme. Please visit the project website for a full list of project consortium partners.
Obviously, as any non-trivial type system, our type system is not complete and rejects certain programs that would not produce unbounded numerical errors. Our type system has been implemented in a prototype language Numl and we show that, in practice, our type system is expressive enough to type implementations of usual simple numerical algorithms  [2]  such as the ones of Section 6. Let us also mention that our type system represents a new application of dependent type theory motivated by applicative needs. Indeed, dependent types arise naturally in our context since accuracy depends on values. This article is organized as follows. Section 2 introduces informally our type system and shows how it is used in our implementation of a ML-like programming language, Numl. The formal definition of the types and of the inference rules are given in Section 3.
This issue is important if we want to advance in our understanding on this topic and extract general conclusions from past and future studies. We had four main aims in our study: First, we used meta-replicated field data to test if leucism is associated with urban habitats. Second, we investigated whether there are sex differences in leucism. Third, we analyze the progressive graying hypothesis by testing for an association between leucism and age. Finally, we compared the results obtained from leucism estimates derived from three different methods (bird captures, transects and citizen science data). We used all three methodological procedures to quantify the presence of leucism in urban and non-urban adult blackbirds. We used the common blackbird Turdus merula as our model species since it has a wide geographical distribution  (Collar 2005)  and can inhabit both urban and nonurban areas  (Evans et al.
Citizen science data We collected pictures available on the internet by using a web application called Morphic, developed and tested as a tool to study geographic color patterns in animals  (Leighton et al. 2016). This application allows users to search for photographs from Google Images employing specific keywords ('Turdus merula', 'common blackbird' and 'Eurasian blackbird' in our case) and ensures no duplicates are retrieved. The image search was conducted on the 14 May 2017 and provided 1200 pictures. For each photographed blackbird we collected the following variables: age, sex, presence/absence of leucism, locality and habitat type. Only those pictures providing information from all variables were used in our analyses (186 pictures from three different continents; Fig. 1 ). Sex and age was determined as in the previous methodologies.
Statistical analysis We first performed a GLMM (generalized linear mixed model, binomial distribution and logit link function) with all collected data (637 individuals; Supplementary material Appendix 1 Table  A1 ) to investigate the effects of sex, habitat and the different methodological approximations on the presence of leucism in an individual. Leucism (presence/absence) was tested as the response variable, with several fixed factors (type of the methodology, habitat and sex) included. We also included the interactions between methodology and sex or habitat to explore potential biases associated with the different methods. We included locality as a random factor to account for samples from the same geographic site. Second, to analyze the specific effect of age on the probability of leucism, we fitted a binomial GLMM (logit link function) including only the captures and citizen science data (only data with age information available; 437 individuals).
The model was the same as described above but adding age as an additional fixed factor and their interaction with methodology. We also added the interaction between age and habitat because of the known effect of urbanization on the age structure of blackbirds  (Evans et al. 2009 , Ibáñez-Álamo et al. 2018). Finally, we run two sensitivity analyses to explore whether the different geographic scales of each methodology could explain our results. We did so by running the previously described models using only the data from Europe (i. e. we restricted the data obtained using the citizen science methodology to European blackbirds). All models were run using the 'lme4' package (ver. 1. 1-13;  Bates et al. 2015). We followed a stepwise model selection procedure to obtain a minimum model from the initial starting model.
The factor with the highest p-value according to a likelihood ratio tests (LRT) for nested models was removed subsequently until all included terms were significant. We used the 'lmtest' package for the LRT (ver. 0. 9-35;  Zeileis and Hothorn 2002). The main effects were tested with Wald tests using the 'car' package (ver. 2. 1-5; Fox and Weisberg 2011). Tukey post hoc analysis was performed with the 'phia' package (ver. 0. 2-1; De Rosario-Martinez 2015). All analyzes were performed with the R software (ver. 3. 4. 1, R Core Team).
This step will allow treating the energy and water budgets with the same level of detail, which is critical to the impact assessment of NBSs on a citywide scale. In the first step presented herein, the model concept will be described. Attention will be placed on the model's hydrological component and recent model developments, since the energy and radiation components of the model have not changed, performed by  Masson (2000)  and  Lemonsu et al. (2012a). The experimental sites and observational data will then be presented. Afterwards, the model evaluation will be provided in Sect. 4 by means of analysing the simulations run by the new model version. 2 Description of the TEB-Hydro hydrological model TEB-Hydro is an evolved version of TEB-Veg, using surface externalisée (SURFEX) v7. 3  (Lemonsu et al.
Rezé catchment The Rezé experimental site is located in the southern part of the city of Nantes, close to the Atlantic coast (Fig. 2 ). This site was instrumented (for measurements of precipitation, rainwater network discharge and soil water) from 1993 to 1998, and a complete continuous database is available for that period. The climate is oceanic with an average annual rainfall of approximately 830 mm over this period; the year 1994 was the wettest. The 4. 7 ha basin is entirely residential, comprising single-family homes with private gardens. The separate sewer network is divided into wastewater and stormwater sewers, with lengths of 803 and 480 m, respectively. The impervious surface area of the catchment accounts for 45 % of its total area, of which 84 % is connected to the stormwater system.
A detailed site description can be found in  Berthier et al. (1999)  and  Dupont et al. (2006)  (Table 1). The Rezé catchment and its database have been the subject of several studies  (Rodriguez et al. , 2003; Berthier et al. , 2004; Dupont et al. , 2006; Lemonsu et al. , 2007; Rodriguez et al. , 2008). Berthier (1999)  modelled the role of soil in generating urban runoff on the Rezé catchment. He studied both the hydrological aspects and site observations. Among other achievements, he examined the discharge observed in the wastewater sewer during the winter periods between 1993 and 1997, before estimating the discharge due to soil water infiltration; this value was then compared to the simulated base flow in the sewer network.
Meteorological forcing Forcing the model with observations requires atmospheric data, such as precipitation, temperature, specific humidity, atmospheric pressure, wind speed and direction, and incoming shortwave and longwave radiation. For both experimental sites, the precipitation rates (with no snowfall for all simulation periods) were collected on-site by means of rain gauges. All other forcing data were generated from records at the nearby Météo-France weather station (Nantes Airport), including incoming solar radiation, cloudiness, pressure, air temperature and humidity at 2 m above ground and wind speed at 10 m above ground. To avoid the direct influence of the urban canopy, the forcing level height for temperature, humidity and wind speed had to be set above the roughness sublayer top; hence, the atmospheric data had to be adjusted accordingly  (Lemonsu et al.
(2007). The simulation period for the Pin Sec catchment is 2. 5 years, i. e. between May 2010 and September 2012. The morphological site data, radiative and thermal properties of materials (TEB), and soil and vegetation properties (ISBA) were determined on the basis of several sources (FluxSAP database, Furusho, 2012; Nantes metropolitan urban databank and Ecoclimap I,  Faroux et al. , 2013). Due to inconsistencies between previous studies (Le  Delliou et al. , 2009; Seveno et al. , 2014) , the Pin Sec catchment area has been delimited again using a Geographic Information System (GIS) (Fig. 2b ). Lemonsu et al. , 2007; d Ramier et al. , 2011; e Furusho et al. , 2013; f Allard, 2015).
0). For all further information or access to real-time code modifications, please follow the procedure in order to open the SVN account provided via the previous link. The routines modified with respect to the TEB-Hydro model SURFEX v7. 3, as well as the run directories of the model experiments described above, may be retrieved via https://doi. org/10. 5281/zenodo. 1218016  (Stavropulos-Laffaille et al. , 2018). The Rezé and Pin Sec catchment databases are available upon request submitted to the authors of the Water and Environment Laboratory at the French Institute of Science and Technology for Transport, Development and Networks (IFSTTAR). principal effect of a parameter called A (-) e (AB) effect of the interaction between two different parameters A and B (-) y * + mean response of all combinations where the parameter or interaction of two parameters is at its high level (+1) (-) y * - mean response of all combinations where the parameter or interaction of two parameters is at its low level (-1) (-) Q tot town total stormwater sewer discharge (m 3 h -1 ) derived from total urban runoff (R town ) (m 3 h -1 ) Q sew sewer discharge due to soil water infiltration (m 3 h -1 ) derived from sewer runoff (R sew ) (m 3 h.
Near Surface Temperatures Screen level (2m) air temperatures (T 2m ) from ARP-AMIP simulation are compared to those of the ERA-Interim driven MAR simulation in winter (JJA) and summer (DJF) for the reference period 1981-2010. Differences are shown in Fig. 4. On the same figure, circles represent T 2m differences between ARP-AMIP and weather stations from the READER data base. In this analysis, weather stations where less than 80% of valid observations were recorded for the reference period were not used for the computation of climatological mean. Altitude differences between corresponding ARPEGE grid point and weather stations have been taken into account by correcting modelled temperatures with a 9. 5 K km -1 vertical gradient. Errors on T 2m in ARP-AMIP simulation for each weather station and each season are presented in Tab.
3. A map showing the location of these stations can be seen in the supplementary material (Fig. B1 ). The  West Antarctic Ice Sheet (WAIS) in summer. Except for some coastal stations of East Antarctica, T 2m error in the ARP-AMIP simulation are very similar in the comparisons with MAR-ERA-I and READER data base. Considering errors on surface temperatures of the Antarctic Plateau as large as 3 to 6K for ERA-I reanalysis in all seasons  (Fréville et al. , 2014) , the magnitude of the errors in this region in ARP-AMIP simulation is encouraging. The error for Amundsen Scott station is even insignificant at p=0. 05 level in all seasons but autumn (MAM). The warm bias on the large ice-shelves is due to the fact that ice-shelves are not considered as land in the ARPEGE version used. In order to correct this weakness, we prescribed an SIC of 100% and a thickness of 40 m in grid points corresponding to ice-shelves.
Acknowledgements. This study was funded by the  Agence Nationale de la Recherche  through contract  ANR-14-CE01-0001-01  ( ASUMA ) and  ANR-15-CE01-0003  ( APRES3 ). We acknowledge the  World Climate Research Programme 's Working Group on Coupled Modelling, which is responsible for CMIP, and we thank the climate modeling groups participating to CMIP5 for producing and making available their model output. For CMIP the  U. S. Department of Energy's Program for Climate Model Diagnosis and Intercomparison  provides coordinating support and led development of software infrastructure in partnership with the  Global Organization for Earth System Science Portals. The  Centre National de Recherches M'et'eorologique (M' et'e-France, CNRS) and associated colleagues are warm-fully thanks for providing resources and help to run ARPEGE model.
DISCUSSION In contrast to other sensory modalities, the vestibular pathway has long remained inaccessible to functional investigations using calcium imaging. The here-introduced compact, rotating light-sheet microscope enables for the first time whole-brain recordings in a vertebrate submitted to physiological vestibular (G) Visualization of the average density map of N = 8 paralyzed fish with eyes. 3D visualization is in Video S5, part III. Color intensity scales linearly with density. Outlines of the indicated brain regions from rostral to caudal: habenula, torus longitudinalis, tegmentum, optic tectum, nMLF, oculomotor nucleus nIII, trochlear motor nucleus nIV, cerebellum, and inferior olive. (H) Average density map of N = 11 bi-enucleated fish. All data were recorded in Tg(elavl3:H2B-GCaMP6s) fish.
In addition, other laser lines could be coupled with the same optical light guide to extend the range of fluorescent probes that could be used. A tailtracking unit and/or a screen under the fish associated with a miniature video projector may also be easily mounted on the rotating platform in order to provide additional visual stimulation  [23]  and motor readout. A Novel Graphical Tool to Visualize, Inspect, and Analyze 4D Whole-Brain Functional Data Light-sheet imaging of the zebrafish brain produces massive datasets. Visualization and analysis of such data are challenging, yet essential, to providing researchers with flexible means of access, inspection, and interaction. For this purpose, we have developed an efficient graphical software tool, the Fishualizer. The Fishualizer allows one to display large 4D datasets such as calcium or spiking traces of neurons of the entire brain along with the corresponding stimulus and/or behavioral responses, and with the possibility to freely rotate, zoom, or pan across the data.
Although various species can be visualized, the present implementation includes several specific options for calcium imaging in zebrafish, e. g. , the visualization of Z-Brain regions  [22]  and spike inference from calcium-imaging data  [25]. Visualizations in Figures  5E, 5G , and 5H and Video S5 were generated with the Fishualizer (see STAR Methods for details). The Fishualizer is provided freely under the General Public License (GPL) license (https://bitbucket. org/benglitz/fishualizer_public/).
The Fishualizer The Fishualizer is built on a range of core techniques to display large datasets in 3D without noticeable loading times or memory constraints. Specifically, OpenGL is used for rapid visualization via pyqtgraph (http://www. pyqtgraph. org), datasets are memorymapped from HDF5 (via h5py, i. e. , datasets can be displayed even on computers with little working memory), and a user-friendly, crossplatform interface is provided (via QT5, PyQt5). Fishualizer provides a feature-rich, easily accessible interface, including the possibility to: d show dynamic data, e. g. , calcium or spiking data d show static datasets, e. g. , regression clusters as the output from data analysis d show stimulus or behavior alongside activity d compute basic analysis functions online for data exploration (e.
g. , correlating against a time-series, such as the stimulus or the behavior) d deconvolve spike-times from calcium data (via built-in OASIS  [18] ) d select subsets of neurons by anatomical region (using the zBrain atlas  [22] ) d visually select and display single neuron activity d flexibly limit set of displayed neurons in X, Y, and Z directions d freely rotate, zoom, or pan across data d adapt color-mapping and transparency of visualization d export videos and screenshots for inclusion in presentations and publications The code is released alongside this publication, and is available open source. Fishualizer is written in Python 3. 6 and was tested on Linux, Windows and Macintosh operating systems on regular desktop and laptop computers. Further instructions for installation and usage are provided alongside the code repository.
ACKNOWLEDGMENTS We would like to thank the IBPS fish facility staff, and in particular  Alex Bois  and  St ephane Tronche , for their invaluable help. We are also grateful to  Carounagarane Dore  for his important contribution to the realization of the mechanical parts of the light-sheet microscope. We thank  Misha Ahrens  for providing the GCaMP6 lines,  Elim Hong  for the HUC-Gal4:UAS-RFP line, and  Filippo Del Bene  and  Christoph Gebhardt  for the protocol and help with the enucleation procedure. This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  grant agreement number  715980  and by the  ATIP-Avenir program  from  CNRS and INSERM. Further funding sources were the  ANR program  ( ANR-16-CE16-0017 ) and  Human Frontier Science Program  ( RGP0060/2017 ).
G. M. was funded by a PhD fellowship from the  Doctoral School in Physics, Ile de France  (EDPIF). T. L. v. d. P. had an  Erasmus+ fellowship  ( European Union ). H. T. had a PhD fellowship from  Ile de France  ( ARDoC 17012950 ). B. E. was supported by  NWO  grants (ALWOP. 346and ALW VIDI:  016. vidi. 189. 052 ). R. P. was supported by the  Simons Foundation Autism Research Initiative   Pilot Award  ( 402454 ).
The suitable representation of this information in a manner that can be efficiently stored, envisioned and queried is important for obtaining a mechanistic understanding of disease. What is the most appropriate way to represent diseaserelated information in a computable format that can be useful for hypothesis generation and for obtaining mechanistic insight? To some extent, this depends on what questions are being asked of the data. Here, we describe three approaches to representation of contextual information, namely, pathwaycentric approaches, molecular network centric approaches and information graphs (Figure  1 ). We contend that data integration is a key component of all three approaches. Network and graph-based representations are prodigiously effective representations for integration, query, exchange and visualization of numerous possible relationships and interactions between biological entities.
Owing to well-studied formal mathematics of graphs, they also often serve as a key data structure for algorithmic, machine learning and statistical approaches for analysis of these data. Construction of biological networks from high-throughput experimental data is an essential first step that enables many types of analysis discussed below. While we recognize importance of this research, in this review, our focus will be primarily on downstream applications of biological and knowledge networks for molecular signature contextualization, but for completeness, we would like to recommend the following works, which cover this closely related topic in detail  [7] [8] [9] [10]. For convenience of readers, we have included a list of abbreviations used throughout the article in Table  2. To provide a practical illustration of how different types of contextualization approaches can be used, we have included examples based on a severe asthma differential expression gene signature and a manually curated core asthma gene signature acquired from DisGeNET database  [11].