dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements We thank  Ludivine Molina  and  Charlotte Pariente  from the  UMR190-Emergence des Pathologies Virales (Marseille, France)  for their technical contribution. We thank  Ernest A Gould  from the  UMR190-Emergence des Pathologies Virales (Marseille, France ) for his valuable review of the manuscript. This work was supported by the  Zikalliance  project ( European Union  - Horizon 2020 programme  under grant agreement no. 734548 ), the  French "Agence Nationale de la Recherche"  (grant agreement no. ANR-14-CE14-0001 ), the  PREDEMICS programme (European Union Seventh Framework programme  under grant agreement no. 278433 ) and the  European Virus Archive goes global project  ( EVAg ;  European Union  - Horizon 2020 programme  under grant agreement no. 653316 ; http://www. european-virus-archive.
Agent-based model overview All models were coded and simulation experiments performed in the ABM programming environment Netlogo 5. 1  [26]. Model data were analysed and plotted in the statistical programming environment R v. 3. 1. 2 [27]. Below, we describe our model using the overview, design and details format as is now widely adopted for ABMs  [28] [29] [30]. All Netlogo code can be found in the electronic supplementary material, S2 'Netlogo Code'.
Process overview and scheduling On each iteration of the ABM, the following three processes occur (detailed below, and in figure  2a ): (i) 'Find Food', where those individuals not located on a food find one; (ii) 'Eat', where individuals located on a food eat some of it (i. e. move their NS through the environment); and (iii) 'Leave Food', where individuals may decide to leave a food on which they are feeding to seek an alternative. A new generation begins after 500 iterations. Data on the evolution of K soc are recorded after 1000 generations.
Acknowledgements Gabrielle C. Ciquier ,  MSc. , MBPsS , translated the manuscript from French to English. Our research laboratory remunerated her for services as a professional translator. the authors also acknowledge the help of  Tatsiana Leclair , a doctorate student and member of our laboratory, who participated in the transcription of the interviews. She was remunerated with our own funds. Finally, the authors thank their research team members for their support and the parents they interviewed, whose collaboration made this study possible.
The reaction mixture was loaded on a native 5% polyacrylamide gel (19:1, acrylamide:bisacrylamide (w/w); TBE) and then electrophoresed for 1 h. After staining and quantification of band intensity, the fraction of DNA bound to protein for each retarded band was calculated according to the following equation: fraction minicircle bound = [protein-minicircle complex/total minicircle]. NF-B binding data obtained with minicircle containing a single B binding site were fitted to a square hyperbola using non-linear least squares analysis with the origin 9. 0 software (Microcal). When the minicircle contained two B binding sites, the binding curves corresponding to unbound, singly bound and doubly bound forms were fitted as previously described  (20)  where the dissociation constant for each binding site was assumed to be identical since these two binding sites are identical.
The cooperativity parameter was determined by measuring the maximum value of the singly bound form using equation numbered 16  (20). For the gel-based methodology, gel staining was carried out by using SYBR Green before exposition to a Typhoon phosphorimager to determine bands intensity using Image-Quant 5. 1 software. The DNA was visualized by fluorescence and thus the molar ratio of the starting linear duplex over oligomers was calculated by taking into account the fact that band intensity is increased as a function of the oligomer length.
34 nm. The longest diameters measurement was performed from analysis of 32 imaged minicircles using Image J software. The histogram shown in Figure  2D  was obtained by splitting the range of diameter values into 5 equal-sized classes as derived from Scott's normal reference rule. The distribution was fitted with a Gaussian function using the origin 9. 0 software (Microcal) providing a mean value of the diameter as indicated further. It was also verified whether the diameter values measured in the sample were normally distributed by using the Shapiro-Wilks normality test. As we failed to reject the null hypothesis with a P-value of 0. 35, the diameter values were normally distributed. We then performed a parametric test to determine whether the mean value of diameters was statistically different from the diameter value calculated for a perfect round-shaped minicircle.
6 nM that is similar to that reported with specific linear DNA substrates  (39). Our data indicate that the pre-bent B sequence did not substantially modulate NF-B DNA binding activity that suggests that DNA bending is involved in indirect readout of B sites by NF-B. Our observation is in line with the fact that several linear B sequences adopt a pre-bent conformation  (40). In order to test the capacity for a minicircle to attract specifically more than one NF-B p50/p50 protein, we therefore prepared a 95 bp minicircle containing two B sites (Figure  4D ). The binding activity of NF-B with this minicircle was carried out as described above. As shown in Figure  4E , two retarded bands are now present on the EMSA gel upon addition of the NF-B protein, indicating the binding of two proteins per minicircle.
The gaze data protocol Eye trackers measure a person's visual attention on a stimulus. In our experiment the stimuli consist of ski map which is the result from assembling a plurality of graphic-geographic objects: ski trails and colored slopes tracing, vegetation, peaks, rocks, shadows and light, buildings, etc. Ski map was reproduced in real dimension as that of a display panel that can be found at ski tracks departures. Visual attention is measured by recording eye movements on the stimulus and, in our case study, the recording was set up with wearable eye-tracking because the subject was standing up face to stimulus and he/she was free to make natural and spontaneous motions. The basic recordings of eye movements are called gazes. It is generally assumed that perception takes place only if gaze remains almost still for a minimum amount of time.
Gaze data analysis. Gaze data were processed by Tobii Analyzer software with Custom I-VT filter. This filter refers to the Velocity-Threshold Identification (I-VT) fixation classification algorithm that is a velocity based classification algorithm  (Salvucci and Goldberg, 2000). The general idea behind an I-VT filter is to classify eye movements based on the velocity of the directional shifts of the eye. The velocity is most commonly given in visual degrees per second (°/s). If it is above a certain threshold the sample for which the velocity is calculated is classified as a saccade sample and below it is seen as part of a fixation  (Olsen and Matos, 2012). Filter: The Tobii Custom I-VT filter we applied had the main following settings: -I-VT fixation classifier: 100 degrees/second; -Minimum fixation duration: 100 ms.
Techniques: Gaze data were analyzed with classical techniques: a) Heatmaps: a heatmap uses different colors to illustrate the number of fixations participants made within certain areas of the snapshot 1 or for how long they fixated within that area. Red usually indicates the highest number of fixations or the longest time, and green the least, with varying levels in between. Tobii Heat Map calculates the distribution of color values around a fixation point by using an approximation to the Gaussian curve (cspline). The radius of this function is set by default at 50 pixels. Heat maps were rendered with absolute count and absolute duration of fixations. b) Areas of interest (AOI): an AOI is a polygonal area in the stimulus the researcher considers relevant for the research question at hand. If a fixation occurs in an AOI, it is generally assumed that the participant perceived the object surrounded by the AOI  (Kiefer et al.
Users' trend to focus their attention on the main (linear) structuring elements on the map is also highlighted by the recent work from Ooms (2015) about complex map designs. The author indicates that in order to be able to create more effective maps it is essential to visualize data in a structured way. Linear geographic objects, as rivers and road network, also are the preferred information suggested by users in the survey carried out by  Petrovic and Masera (2005)  about 3D map content. Information related to the landscape seems very poorly exploited. This leads us to discuss the second research question. The most interesting output relies on the relevance of the panorama view which has impacted the ski maps representation for decades and has led to the representation of local distortions of the mountain.
manufacturing history. Moving from macroscale to microstructure, atomic and electronic structure require a multidisciplinary approach involving physics, chemistry, materials science and engineering. In the specific case of materials under extreme environments, the rational design of phase distribution vs. different external parameters (temperature, pressure, radiation. ) requires generating and managing materials databases for specific technological and industrial applications. An example is the NIMS Materials Database [16] and Genome Materials [17] existing at International Centre for Critical Raw Materials including and improving nuclear materials and molten salts properties. The SUPERMAT Consortium will be focused on developing modelling methods related to structural alloys and coatings to predict the final properties based on processing-structure and structure-properties relationships.
Fig. 1. Modelling approach for structural alloys properties for extreme conditions As an example, partially stabilized zirconia doped with different rare earth and transitional oxides (Y, Ce, Mn, Gd, Yb…. ) for abrasion resistance sintered parts and high temperature functionally graded materials have been obtained by this processes. Thermodynamic prediction using HSC 8 software (allowing chemical reactions and equilibrium calculations based on extensive scientific thermodynamic database) was primary used to evaluate the influence of temperature, pH and metal activity coefficient on the final composition. As shown in Fig. 2 , the use of hydrothermal solutions highly enlarge the pH stability domain of doped ZrO2. At normal temperatures T ≤ 100 0 C) the crystalline ZrO2 is expected to be formed in the pH range 6.
Acknowledgement: All authors acknowledge the Grant Agreement 692216 SUPERMAT receiving funding from the  European Union 's  Horizon 2020 research and innovation programme. Prof. Yi Qin  and  Dr. Radu-R. Piticescu  acknowledge also the Grant Agreement 608720 MicroFAST, receiving funding from the  European Union 's  Framework 7 Programme. Dr. Radu-R. Piticescu ,  Dr. Antonio Rinaldi  and  Dr. Santiago Cuesta Lopez  acknowledge also  COST Action CA 15102 Solutions for Critical Raw Materials under Extreme Conditions.
The sub-model of farmers uses an agent-based BDI formalism  (Rao and Georgeff, 1991)  to describe their decision-making process. This sub-model is then coupled with other sub-models, each of them built using a suitable formalism for carrying out a realistic description of the context they represent. As a matter of fact, the dynamics present in these sub-models obey to different logical processes, operate at different scales and rely on different datasets, so they need to be designed with specific modeling techniques. In its most stable form, the one discussed in this paper, the integrated model makes use of a GIS-based model of parcels, soils, and rivers; a cellular automaton is then used to account for the evolution of land-cover changes and the diffusion of salinity; an aggregated mathematical model represents the fluctuation of prices on the regional and national markets; and, finally, a graph-based social network is used to represent familial networks of influence.
, 2008)  remains restricted to highlands and mountainous areas in Vietnam. • Lack of flexibility: finally, with the notable exception of Aporia (which partially supports the change of sub-models), most of the existing hybrid LUCC models are designed as a static composition of carefully chosen (or written) sub-models. This does not allow to consider sub-models as possible parameters of experiments, something that can be necessary to explore different configurations or scenarios. In our case, given the variety of factors identified, explaining LUCC in the Mekong Delta with an integrated model requires that we explore several causes, some of them represented not only by parameters, but by entire sub-models or specific combinations of them. The underlying software architecture need then to provide a high degree of modularity and flexibility, in order to easily add, remove or change sub-models, but also to change their way of interacting, exchanging information and contributing to the overall outcome.
An interesting example of weak coupling is the work of  Nicolai et al. (2011) , who have coupled UrbanSim with MATSim in order to produce an integrated model of urban mobility. UrbanSim contains information on residential locations, workplaces and urban development, while MATSim provides access to large-scale models of land-use, transportation network and economic dynamics. The two models are synchronized through the exchange of specific data (mobility needs from UrbanSim to MATSim, accessibility indicators in the reverse way). The literature provides other examples, like  Yez et al. (2008) , with an integrated model of a marine environment composed of local ecosystems of pelagic species, which adds an explicit translation between models at different scales, or  Steiner et al. (2009) , which couples a community land model with the regional climate model of the West African monsoon, and of course others.
Presentation In H2 (see Section 3. 1), we make the hypothesis that economic factors like regional market prices and costs of production strongly influence the decision of farmers regarding the landuse to adopt. To verify this, we then designed a simple economic model to represent the evolution of these two factors. The data concerning market prices has been collected from 2005 to 2010 (averaged every year) from regional sources. However, the costs of production within the corresponding period could not be obtained so easily; we then used the costs in 2010 (evaluated in  Nguyen et al. , 2014)  and extrapolated them from 2005 to 2010 using the regression equations depicted in Figure 9  (Judge et al. , 1988). Two main assumptions are made in this sub-model: (1) the investment cost and selling price of each agricultural product are the same for all farmers; (2) external incentives (such as the opening of new markets) and perturbations (such as economic crises) are not taken into account.
This approach to models coupling is still experimental for the moment, and it needs to be validated especially in its advanced uses, for example dynamically coupling/uncoupling models during simulations. What is interesting, however, is that it supports modelers in designing flexible experiments, with the possibility to add, remove or change micro-models at runtime. In our case, this possibility will be extensively used for testing, individually and collectively, the different hypotheses. As specified in Section 2. 2, current land-use change integrated models are not flexible enough when it comes to switch between different micro-models. By considering a model as an agent, and an integrated model as a multi-agent system, our approach tries to bring this flexibility to modelers. In addition, GAMA offers several software design capabilities that support very powerful features: because models are agents, they can inherit from other agent definitions, even abstract ones that only define interfaces for getting and setting parameters or manipulating the model.
This allows to define abstract integrated models (like frameworks use to be defined in an object-oriented approach) in which micromodels, which only need to respect the interfaces, are instantiated at runtime, whatever their actual contents or definition. Thanks to its multi-formalism approach, GAMA also allows these models to be written in whatever formalism is available as a plug-in to the platform. Finally, because of the possibility to call external programs or libraries during simulations, a model in GAMA can perfectly be a simple wrapper around a legacy model written in another language or on another platform, provided this model can be launched and monitored during execution by an external process. In Figure  6  we present the conceptual diagram that describes the wrapping and the coupling of the models listed above: M_F, M_E, M_P, M_S, M_N respectively represent the models of farmers, parcels, environment, economy and social relationships.
Implementation Using GAMA/GAML The integrated co-model is implemented in the GAML language  (Grignard et al. , 2013). Its workflow is presented on Figure  12. The micro-models are first imported as "wrapping" agents, which need to be instantiated and initialized like any other agent. Each step of the co-model simulation corresponds to 1 year, during which micro-models are executed depending on their temporal scale (from 1 month to 1 year), their inputs and outputs being taken in charge by the co-model in a completely transparent way. The full GAML code used to implement the co-model can be found in the Annex. In the following, we highlight some of its parts, mainly to show that manipulating micro-models is not different than manipulating agents. The life cycle of the comodel begins with the importation of the micro-models, which are provided with an alias identifier: i m p o r t < m o d e l _ f i l e.
All of them, for the sake of the article, have been programmed in the GAML language (which natively offers the support of multiple formalisms), but reusing legacy models just involves wrapping their invocation in the definition of an agent behavior. There are three main perspectives of this research that we plan to explore in the near future. The first one will consist in refining the current integrated model, by progressively completing it with more micro-models targeting the other factors identified in land-use change (e. g. , an institutional model, local climatic models, models of urban growth) or enhancing the realism of the existing micro-models (by conducting more focused surveys and fieldwork with farmers). The second one will consist in expanding the case study so as to address the problem of landuse change in non-coastal regions of the Mekong Delta, where the environmental conditions are quite different.
ACKNOWLEDGMENTS The authors would like to thank  Prof. Patrick Taillandier  ( IDEES, France ),  Prof. Benoit Gaudou  ( IRIT, France ),  Prof. Jean-Daniel Zucker  ( IRD, France ),  Prof. Philippe Caillou  ( LRI, France ),  Prof. Huynh Xuan Hiep  ( CICT, Vietnam ),  Prof. Nguyen Hieu Trung  ( CENRES, Vietnam ), and  Prof. Vo Quang Minh  ( CENRES, Vietnam ) for their contributions to the various stages of this research.
She applied the mixture to a clean wig of human hair (Snab Cap, Pivot Point Stockholm, Sweden) using a hair bleaching brush. The thermal manikin was used to imitate any effect that heat convection from a human being may have on the exposure of the hairdresser. The treated hair was successively covered by a commercial folio for hair-bleaching. After 20 min, another scoop (45 g) of powder was mixed. The mass of bleaching powder and hydrogen peroxide used was measured and the amounts did not differ significantly between the two groups. According to the Safety Data Sheets, the ingredients in RP were dipotassium peroxodisulphate (40-60%), disodium metasilicate (5-< 10%), peroxydisulfuric acid, disodium salt (1-< 10%), kieselguhr, soda ash flux-calcined (1-<5%), cocosfattyacidmonoethanolamide (5-< 10%), sodium dodecyl sulphate (1-< 5%), and magnesium peroxide (1-< 10%).
Statistics Changes in parameters within the groups were evaluated by Wilcoxon Signed Ranks Test. For comparisons between groups (regular vs. dust-free and high vs. low exposure groups for ammonia and persulfate ) , Mann-Whitney's U-test was employed. Statistical significance refers to p values < 0. 05 (two-tailed). The statistical tests were performed in IBM SPSS statistic, version 22 for Windows (SPSS Inc. , Chicago, Il, USA).
Δ7 and Δ1b were fused in frame to the 5' end of the GFP gene in pCS2+ expression plasmids (pCMV promoter) as previously described  [12]. Segment Δ1b (= Δ1 without the 5'ITR-UTR region) or the full length MOS1 ORF were used as controls. the NeoR marker. In addition, complementary experiments demonstrated that an intragenic Δ7 DNA segment in frame with a marker gene had a silencer effect on its expression since Δ7-GFP and MOS1-GFP fusions expression is similar and significantly lower (~5-fold) than the GFP control (Fig  1F ). These data support that Δ7-MOS1 segment has a silencer effect when it is fused in frame within a gene and that the silencer effect could be operating with the pCMV promoter. These results were confirmed by RT-qPCR using total RNA extracted from transiently transfected cells and GFP specific primers.
These results were consistent with the sequence binding site prediction analysis, showing that there was one YY1 binding site within Δ81 and Δ83, two in Δ84, and none in Δ82 and Δ85. This last result suggested that the motif located in 3' was unable to be bound by YY1 under our experimental conditions. However, this was likely an artefact due to its location at the 5' end of the Δ85 probe. Indeed, when both YY1 sites are located in the middle of the Δ84 probe, two shifted bands were observed (Fig 6D, lane 12), suggesting that both sites could be bound. Taken together, these data supported the conclusion that the silencer activity of the Δ8 segments was possibly mediated by one or several YY1 silencing pathways. Other TFs binding to the mariner silencer element: The case of NRSF Since the definition of PREs in vertebrate genomes is an issue that has yet to be fully elucidated  [31, 32] , we searched for motifs conserved for both sequence and location using the MEME software suite with the DNA sequences of 34 mariner Δ7 segments (S6 Fig).
Epigenetic status of MLEs in the human genome Since there is no available animal model with active MLEs for which high throughput chromatin data are available in public databases, we have investigated the chromatin status of two human MLEs, Hsmar1 and Hsmar2, that appeared in the human genome approximately 50 and at least 80 million years ago respectively  [48, 49]. Currently these elements have lost their ability to transpose due to the accumulation of nucleotide mutations in the ORF coding for their transposase. The advantage of the human model is that it has the richest set of ChIP-Seq data for TFs and histone modifications. Because the recruitment of TFs bound to DNA at the moment of the establishment of histone modifications is not subsequently required for their maintenance and transmission over cell divisions  [50] [51] [52] [53] , we have focussed our investigations on histone modifications.
Novel approaches will also be necessary to investigate the possible role of Hsmar1 and Hsmar2 silencers and whether they were also exapted during human evolution. As noted above, MLEs have co-evolved with their animal hosts and it is therefore not a surprise to observe that they use certain housekeeping proteins to control their activity. Even if our results do not elucidate the involvement of NRSF in the functioning of the mariner silencers and its possible links with Alx1 and NFAT-5, we found information in various databases and in the literature indicating that part of the genes containing a mariner silencer might be related to the functioning of neuron and the central nervous system. Unfortunately, these preliminary data were not statistically confirmed using facilities of the GREAT platform  [88].