dataesr/scientific-paragraphs-categorization huggingface dataset:
Atmospheric analysis data from the European Center for Medium-Range Weather Forecasts (ECMWF) have been acquired and are used to characterize the meteorological situation in Maroua, Cameroon (10. 614 • N, 14. 361 • E) at 12:00 UTC. These are then used to simulate downward global solar radiation (DGSR) with the moderate-resolution transmittance (MODTRAN) radiative transfer code (RTC). In comparison with meteorological data measured during the year 2014 in Maroua, ECMWF atmospheric quantities at ground level, in general, showed good correlation coefficients and slight differences. It is shown that ECMWF atmospheric profiles can thus be used to complete the scarce atmospheric data and to study the atmosphere state and dynamics, such as the African monsoon phenomenon detected in this region, which regulates the rainy season.
Introduction The acquisition of atmospheric profiles and solar radiation data is a great challenge for developing countries such as Cameroon. These parameters play an important role in climate monitoring, environmental control and human activities  [1, 2] , and they can be obtained through measurement, remotesensing or simulation  [3]. In Maroua (10. 614 • N, 14. 361 • E), a locality situated in the far-north region of Cameroon, the meteorological situation is not well known. There is no recent and continuing measurement, neither of diffuse, direct or global solar radiation, nor of atmospheric parameter and constituent profiles. Not only are meteorological dataset profiles hardly accessible, but the existing sunshine databases also present substantial disparities and contain some gaps  [4].
Given that meteorological data in Maroua are most often measured only at ground level, efforts have to be made to acquire more atmospheric profiles and solar radiation data, in order to complete rare existing in situ measurements. For the year 1984, aerosol thickness, cloud fraction profiles and water content were deduced from ground-level diffuse and global solar radiation measurements  [12, 13]. Unfortunately, this method could not be applied after 1984, as a result of the suspension of regular and reliable measurements, leading to an absence of a local recent database of diffuse and global solar radiation  [4]. Nowadays, given that the atmosphere sounding with weather balloons is no longer available in Maroua, endowment with appropriate meteorological equipment is considered, but a certain time will be necessary to constitute good database series.
Thus, currently, the easiest way to obtain access to atmospheric data may be by consulting global atmospheric databases such as standard atmospheric profiles, and real-or near-real-time atmospheric data. These certainly have some limitations, but their usage may make the computation of solar data more realistic and even more accurate  [14, 15]. Dedicated centers, such as the European Center for Medium-Range Weather Forecasting (ECMWF), the National Aeronautics and Space Administration (NASA), and the National Oceanic and Atmospheric Administration (NOAA), collect and provide data for climate studies, weather forecasting or other purposes. Some, such as ECMWF, have Maroua in their observational data coverage, but as far as we know, no study on the validation of these data has been carried out in zone.
We chose to use ECMWF databases that have been tried and tested elsewhere  [16] [17] [18] [19]. Maroua is located in an area of high solar potential, which can be exploited to overcome the local energetic and economic needs  [20, 21]. However, the control and exploitation of this solar energy require good updated knowledge of site's sunshine  [22] [23] [24]. The Heliosat_2 method is used to derive global solar radiation from Meteosat satellite images  [25]. It has been exploited to retrieve global daily solar irradiation in Cameroon but was established to be appropriate in Maroua only for monthly variations  [26]. This method is under improvement to take into consideration surface albedo and vertical profiles and also to provide direct and diffuse irradiation as well as their spectral distribution  [27, 28].
This task must be reproducible over time in order to continuously provide meteorological observations and analyses as required for environmental purposes. Therefore, the present work shows the advantages of using relative recent measurements and accessible databases to fill the measurements gaps in Maroua. This study presents a method for permanent access to atmospheric parameters through the extraction of ECMWF vertical atmospheric profiles and their analysis. It also describes the simulation of solar radiation components with the MODTRAN RTC in the standard atmosphere. The impact of the insertion of ECMWF vertical profiles in simulations is finally evaluated by comparing simulated downward global solar radiation (DGSR), in clear-sky and various aerosol conditions, with in situ measurements.
ECMWF Atmospheric Profiles of 12:00 UTC ECMWF routinely produces global analyses for the four main synoptic times 00, 06, 12 and 18 UTC and global 10 day forecasts on the basis of 12:00 UTC data  [37, 38]. We are interested in the ECMWF analysis database made up of observations that can roughly be divided into conventional (in situ) and non-conventional (remotesensing) observations. The ICARE Data and Services Center of the University of Lille 1 Science and Technology (http://www. icare. univ-lille1. fr) provided a set of ECMWF analysis data of 12:00 UTC over Cameroon for the year 2014. These data are given on a 0. 5 • × 0. 5 • grid and include the following: -At the surface level: surface pressure (Sp), total column water vapor (TCWV), total column ozone (TCO) and total cloud cover (TCC).
Measured Meteorological Data In 2014, ground-level meteorological data were measured daily in Maroua (10. 614 • N, 14. 361 • E; 398 m)  [4]. The Integrated Sensor Suite (ISS), the UV sensor and the solar radiation sensor of the Davis Vantage Pro2Plus weather station  [39]  were used in that experiment. Data collected during the campaign were the wind speed and direction, the atmospheric pressure, the temperature, humidity, and global UV radiation in the spectral range (290-390 nm), and the global solar radiation in the spectral range (300-1100 nm). These were archived with three temporal resolutions: 30 min from January to August, 5 min for September and 1 min from October to December. We note that the DGSR values are averaged on each archive interval. Referring to the available 12:00 UTC ECMWF atmospheric profiles, 12:00 UTC meteorological data of this campaign were extracted to constitute an annual meteorological measurement database that will be used for further comparison.
MODTRAN Radiance Simulation with Standard and ECMWF Atmospheric Profiles This subsection is a brief presentation of some features of the RTC MODTRAN4 Version 1 Revision 1 used for the simulations. One can refer to the user manual  [40]  or MODTRAN report  [41]  for more explicit explanations. MODTRAN code is one of the state-of-art radiative transfer computer codes. It integrates over the radiance contribution of a finite number of homogeneous layers in order to obtain the transmittance or radiance for a specified atmosphere. The band model parameters are generated from the high-resolution transmission molecular absorption database HITRAN96  [42, 43] , and the code has a set of standard atmospheric profiles. The inputs of each MODTRAN simulation stand on one single input file (file_name. tp5) constituted of at least five CARDs.
Thus, it is not surprising that ECMWF data are greater than measurements, but the substantial biases observed and the way measured wind data appear, as shown in Figure  2c , bring us to suspect a problem with the anemometer used. These differences between ECMWF and measured winds at the surface led us to be very cautious with the results obtained for IHAZE = 10, as the wind surface is used to characterize desert dust uploading and visibility. Consequently, a comparison with other wind databases such as MERRA (https://gmao. gsfc. nasa. gov/reanalysis/MERRA/) or CFS (https://rda. ucar. edu/datasets/ds094. 0/) is required to conclude on the accuracy of each source. Apart from the wind speed, the ECMWF meteorological parameters at ground level are comparable to measurements, given the close annual averages, good correlation coefficients, and slight RMSE and MBE (Table  2 ).
Total Column Quantities To characterize atmospheric conditions at the Maroua site, the surface pressure and total column quantities for water vapor, ozone and cloud cover were extracted from the 2014 ECMWF database. The annual variations of these quantities are illustrated in Figure  3 , where horizontal segments represent monthly averages. The TCC is particularly analyzed in Section 3. 2. 2. Surface pressure is closely related to the atmospheric circulation described previously. During the first dry period, the surface pressure decreased from 967. 2 mbar in January to the minimum value, about 964. 0 mbar in April, when the monsoon flux takes place. Next, the pressure increased to reach a stable level around the maximum (968. 2 mbar) between June and September in the wet period. Afterward, a slight decrease occurred during October and November, when the monsoon flux withdraws.
In the mid-and upper-troposphere, during the dry season, the subtropical westerly jet (STJ) blew. With the arrival of the monsoon flux during the wet season, it was shifted northward (negative anomaly of U wind) and was replaced in the mid-troposphere by the AEJ between May and October, as noticed in Niamey in 2006  [11]. These phenomena, previously detected in Niamey in 2006 and largely explained in  [9] , presented in Maroua a temporal shift of about 2 weeks. This delay could be due to the 12 year difference between the two databases used. However, further investigations are necessary, knowing that the determination of the effective start of the rainy season is capital for sowing in such regions. The analysis of the ECMWF atmospheric profiles shows that the Maroua atmosphere state and dynamics present many similarities with what was reported in some studies in West Africa, a neighboring zone  [9, 11, 47, 48].
These measured data were thus directly compared to 12:00 UTC simulations. All the simulated DGSR curves have practically the same shape, mainly following the seasonal variations of the global solar radiation measured during the year. The DGSR curves simulated are very smooth, with standard profiles. Indeed, no specific information on daily atmospheric parameter variations is inserted, and the databases used here comprised only parameter values averaged over long time periods. Maroua ECMWF atmospheric profiles completed with standard values for missing data were used to refine the simulations. To evaluate the impact of the use of these profiles, we computed the clear-sky DGSR in this case with the six previous aerosol models and compared these again with the same in situ measurements (Figure  6b ).
Summary and Perspectives In this work, ECMWF atmospheric profiles have been used to characterize ground-level and vertical atmospheric profiles in the site of Maroua, where in situ measurements are very scarce. A set of 12:00 UTC daily atmospheric data of this site was extracted for the year 2014 and was used to simulate DGSR. Over the same period, a campaign was carried out to measure the pressure, temperature, humidity, wind speed and global solar radiation at ground level. A comparison of ECMWF atmospheric parameters with surface measurements has shown good correlation coefficients and slight errors for pressure, temperature and humidity, whereas some discrepancies have been observed for wind speed, making the ECMWF wind speed for this site to be used with caution. For upper atmospheric levels, there was unfortunately no in situ measurement to compare with the ECMWF data acquired to improve the characterization of the site atmosphere.
-Wind data biases have to be investigated further in order to determine any source of inaccuracy. A three-party comparison between ECMWF, measured, and MERRA or CFS wind data is considered. -Surface albedo variations, aerosol optical properties and cloud microphysics parameters could be assessed with the use of satellite data retrievals (ECMWF, MACC, MERRA,. models) and could thus better characterize the atmosphere. -Another issue relates mainly to solar radiation simulation, which may gain accuracy with the insertion of aerosol properties and surface albedo variations, and which could be more reliable with the consideration of cloud parameters to simulate DGSR under any atmospheric conditions. Validations may be performed by comparing these to CERES or ECMWF surface radiative flux products.
Acknowledgments: The authors would like to thank the ICARE agency, which furnished ECMWF data;  A. Vermeulen  and  J. Descloitres , who extracted the data over Cameroon; and  F. Parol  and the  Atmospheric Optical Laboratory of Lille 1 University team , who provided computing facilities. They are also grateful to the anonymous reviewers whose thoughtful comments and constructive suggestions improved the quality of this manuscript.
Measured Variables As mentioned before, verbal feedbacks were collected at the end of the use of each modality. They were used to understand how the users felt about each interaction modality and the adequacy with each of the menus. At first they were free to give their feedback and then they were encouraged to give more information. A form allowed collecting qualitative data about perceived characteristics, namely the intuitiveness, the perceived speed, the reliability and the effort needed to interact. The users were asked to grade each characteristic on a 7 -ank Likert scale (the 7rank choice was made accordingly to Symonds' work  (Symonds, 1924) ) where 1 meant, for example, not intuitive at all and 7 meant very intuitive. Then the users marked the modalities on 20. The data are presented as mean ± SD.
Activation Speed and Perceived Speed Pairwise Wilcoxon signed rank tests show no impact of the menu type on the perceived speed by the user (all p > 0. 05). Thus no interaction modality felt faster on a menu type than on the other. The impact of modalities was analyzed by merging data from both kinds of menus. Friedman test shows a significant effect of interaction modalities on perceived speed (p < 0. 001). Post hoc analysis shows that only the Relocated DwellTime modality is significantly different from each of the others modalities. It is particularly striking in comparison with the Instant or Button modalities (p < 0. 001) while it is less obvious against DwellTime (p = 0. 02). Relocated DwellTime scores 1. 2 point less on average than Instant and Button (0. 8 less than DwellTime). Users say that having to stay focused on fixating a point seems long; they feel they are waiting for the interface to respond.
Reliability Contrary to other variables, the Wilcoxon test shows a significant effect of the menu on the perceived reliability of DwellTime (p < 0. 01) and for DwellTime only (other p-values > 0. 05). An explanation was quickly highlighted: this is due to the fact that the sub-menu superimposes the main menu for the circular design (cf. Figure  4 ). This implies that the waiting time of one of the sub-menu items hiding the main menu starts just as the menu opens, even before the user processes this opening. This has no impact on other modalities as they either need the user to press a button or to look further to activate any item. So this result is probably more due to a design difference than to a real impact of menu type. Because of that, the others statistical tests were performed considering only DwellTime data coming from linear menus.
In gametocytes, these loci showed strong interaction with the subtelomeric regions, while these contacts were not observed in the IDC. To quantify this observation, we assessed the number of significant contacts between invasion gene loci and virulence clusters in each life cycle stage. A larger number of significant contacts were observed between invasion genes and virulence clusters in the transmission stages than in IDC stages (p-value < 2. 2e-16, sign test; Fig. 2e  and Supplementary Fig. 9C ). The lack of interactions between invasion gene GLURP on chromosome 10 (PF3D7_1035300) and var gene PF3D7_0800300 during the IDC was confirmed by DNA-FISH (Supplementary Fig. 8B ). As mentioned earlier, DNA-FISH experiments were unfortunately not successful for the gametocyte stage. Collectively, our data indicate that, similar to the pfap2 gene family, the expression of invasion genes during the life cycle is correlated with association with or dissociation from repressive heterochromatin.
Pastis uses a maximum likelihood approach based on modeling contacts using a negative binomial model to account for the observed overdispersion. This method generates more accurate and robust structures when compared to the optimization-based approach we used previously  16. To identify significant contacts, we modeled the effect of genomic distance on contact count probability with a spline using fit-hic  19. Because of the possibility of differing statistical power between datasets, we report both the number of significant contacts above a given threshold, as well as the percent of significant contacts meeting a criterion (e. g. , between pfap2 gene loci and virulence clusters) out of all significant contacts. Significant co-localization of gene sets was assessed using previously developed tests (refs.
Contact count matrices were subsampled to account for differences in interaction counts measured at the various stages and only intrachromosomal contacts for which the sum of the contacts was above the 80% percentile were tested. The resulting fold-change values were filtered after FDR estimation to only include loci that show a two-fold or larger difference in contacts, after normalizing for the effect of genomic distance, with a false discovery rate of less than 1% (Supplementary Data 3). For details of the model and implementation, see Supplementary Information.
Acknowledgements We thank  Till Voss  ( Swiss Tropical and Public Health Institute ) for preparation of the PfHP1 transgenic strain samples,  Clay Clark ,  John Weger , and  Glenn Hicks  ( Institute for Integrative Genome Biology, University of California Riverside ) for their assistance in Illumina sequencing, Xueqing ( Maggie) Lu  for help with ChIP-seq analysis, and  Justin Moroney  and  Paolo Casali  for their assistance with Southern blotting. We are grateful to the  Insectary and Parasitology Core Facilities  at the  Johns Hopkins Malaria Research Institute  and in particular would like to thank  Abai Tripathi ,  Godfree Mlambo  and  Chris Kizito  for their outstanding work and  The Bloomberg Family Foundation  for supporting these facilities. SMRU is part of the  Mahidol-Oxford University Research Unit , supported by the  Wellcome Trust.
The following reagents were obtained through the  MR4  as part of the  BEI Resources Repository, NIAID, NIH :  NF54 (MRA-1000 ) deposited by  Megan Dowler ,  Walter Reed Army Institute of Research. This study was financially supported by the  National Institutes of Health  (grants  R01 AI85077-01A1  to K. G. L. R. ,  R01 AI06775-01  to W. S. N. and K. G. L. R. , and  R01 AI056840  to P. S. ), the  University of California, Riverside  ( NIFA-Hatch-225935  to K. G. L. R. ), the  European Research Council  (grant  ERC-SMAC-280032  to N. V. and J. P. V. ), the  French National Research Agency  (grant  ABS4NGS ANR-11-BINF-0001  to N. V. and J. P. V. ), the  Miller Institute for Basic Research in Science  (J. P. V. ), the  Fulbright Foundation  (J. P. V. ), the  Bill & Melinda Gates Foundation  ( OPP1040938  to D.
Code availability. Python scripts for mapping, binning, and normalization are described in the Supplementary Information and source code is available from Bitbucket (https://bitbucket. org/noblelab/plasmo-hic-2018/). ICE normalization was done using iced (https://github. com/hiclib/iced). The source code for ACCOST is available at https://github. com/cookkate/ACCOST. Data availability. The Hi-C and ChIP-seq sequencing data that support the findings of this study have been deposited in the NCBI Sequence Read Archive with accession numbers SRP091967 and SRP091939, respectively. Fold-change heatmaps can be accessed at http://noble. gs. washington. edu/proj/ plasmo3d_sexualstages/.
In this paper, we address the problem of vehicle localization in urban environments. We rely on visual odometry, calculating the incremental motion, to track the position of the vehicle and on place recognition to correct the accumulated drift of visual odometry, whenever a location is recognized. The algorithm used as a place recognition module is SeqSLAM, addressing challenging environments and achieving quite remarkable results. Specifically, we perform the long-term navigation of a vehicle based on the fusion of visual odometry and SeqSLAM. The template library for this latter is created online using navigation information from the visual odometry module. That is, when a location is recognized, the corresponding information is used as an observation of the filter. The fusion is done using the EKF and the UKF, the well-known nonlinear state estimation methods, to assess the superior alternative.
The algorithm is evaluated using the KITTI dataset and the results show the reduction of the navigation errors by loop-closure detection. The overall position error of visual odometery with SeqSLAM is 0. 22% of the trajectory, which is much smaller than the navigation errors of visual odometery alone 0. 45%. In addition, despite the superiority of the UKF in a variety of estimation problems, our results indicate that the UKF performs as efficiently as the EKF at the expense of an additional computational overhead. This leads to the conclusion that the EKF is a better choice for fusing visual odometry and SeqSlam in a long-term navigation context.
Vision-based localization techniques fall into several broad categories including real-time Structure from motion (SfM) or Visual Odometry (VO) and Place Recognition. While VO methods calculate the egomotion by incrementally estimating the rotation and translation undergone by the vehicle using only the input of a single or multiple cameras, Place Recognition methods are based on learning a database of images (the map) and the vehicle consecutively tries to find matchings between this database and the actual visual input (query image(s)). Within the place recognition paradigm, numerous research papers have addressed visual appearance-based place recognition by ground vehicles especially in varying environments  [1] [2] [3] [4] [5]. A leading method is SeqSLAM aiming at matching image sequences under strong seasonal and illumination changes through the computation of image-by-image dissimilarity scores between all query and database images.
Despite its performance under strong changes, SeqSLAM tends to fail in correctly matching images when dealing with changes in viewpoint that can be found between them  [6]. Hence, our motivation is to create a vision-driven localization method in urban environments that uses cues from SeqSLAM and VO. Our method is able to localize vehicles in the global reference system if a georeferenced database of images has been learned beforehand. However, in this paper, we address the problem of long-term navigation where loop closures, referring to when the vehicle has returned to a past location after having discovered new terrain for a while, are used to reduce the drift caused by VO. Such detection makes it possible to increase the precision of the actual pose estimate. To this end, we present the integration of the robust sequence-based recognition capabilities of the SeqSLAM system with the accurate 3D metric properties of monocular VO in a probabilistic framework through the use of the Extended Kalman Filter (EKF), the efficient recursive estimator  [7]  and the unscented Kalman filter (UKF).