dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2016; Denjean et al. , 2016). Data gathered during ChArMEx-ADRIMED campaign give us an excellent opportunity to evaluate the recently developed algorithms for retrieving aerosol microphysical and optical profiles. In that framework, the main objective of this study is to evaluate the aerosol optical and microphysical proper-ties obtained with GRASP during the ChArMEx-ADRIMED field campaign in Granada, Spain. The GRASP configuration evaluated in this study here is the one that combines lidar signals and sun-sky radiance measurements. The paper is structured as follows: Sect. 2 gives a brief description of the experimental site and the instrumentation employed in this study. GRASP and LIRIC codes are described in detail in Sect. 3. The results are discussed in Sect. 4 and, finally, the main conclusions are summarized in Sect.
The uncertainty of the AERONET inversion products is described by  Dubovik et al. (2000). Briefly, the uncertainty in the retrieval of SSA is ±0. 03 for high aerosol load (AOD 440 > 0. 4) and solar zenith angle > 50 •. For measurements with low aerosol load (AOD 440 < 0. 2), the retrieval accuracy of SSA (λ) drops down to 0. 02-0. 07 (Dubovik et al. , 2000). For high aerosol load and solar zenith angle > 50 • , errors are about 30-50 % for the imaginary part of the RI. For particles in the size range 0. 1 < r < 7 µm, errors in PSD retrievals are around 10-35 %, while for sizes lower than 1 µm and higher than 7 µm retrieval errors rise up to 80-100%. In this work, the AERONET Version 2 Level 2. 0 data obtained at Granada and Cerro Poyos during ChArMEx-ADRIMED 2013 are used. However, due to the strong limitations imposed by the AERONET inversion algorithm (AOD 440 > 0.
4 and solar zenith angle > 50 • ), there was no SSA and RI AERONET Level 2. 0 retrievals during the campaign. Thus, for comparing AERONET SSA values with GRASP retrievals, the AERONET Level 1. 5 cloud screened data corresponding to AOD > 0. 2 and solar zenith angle > 50 • are used in this study. The multiwavelength Raman lidar MULHACEN, based on a customized version of LR331D400 (Raymetrics S. A. ), is used for obtaining vertical profiles of the atmospheric aerosol properties. This system, located at Granada, was incorporated to EARLINET in April 2005 and at present a contributing station to ACTRIS research infrastructure (Aerosols, Clouds, and Trace gases Research InfraStructure Network; http://actris2. nilu. no/). The system has a monostatic biaxial configuration alignment, pointing vertically to the zenith and uses a pulsed Nd:YAG laser with secondand third-harmonic generators, that emits simultaneously pulses at 1064, 532 and 355 nm.
(2016). Besides the VC, the algorithm retrieves additional datasets, including profiles of particle α and β coefficients, and LR, among others. AERONET column-integrated products used as input are not modified by LIRIC during the retrieval process. The GRASP inversion code  (Dubovik et al. , 2011; Lopatin et al. , 2013)  was developed at Laboratoire d'Optique Atmospherique (LOA) of the University of Lille. GRASP is based on a similar philosophy than LIRIC code but goes a step further since it simultaneously inverts both the coincident lidar and sun-sky photometer measurement, retrieving vertical, but also column, aerosol optical and microphysical properties for both fine and coarse modes. The simultaneous inversion of lidar and sun-sky photometer measurements is expected to improve the retrievals since the lidar data complement the sky photometer measurement at scattering angles of 180 • and the photometer data provide the information (e.
6. Data are analysed only for those layers with total VC above 20 µm 3 cm -3 to avoid undesirable outliers for low aerosol loads. Hence for 16 June we analyse the layer between 1. 2 and 4. 5 km a. s. l. , and for 17 June the analysed layer is from 2. 6 to 5. 0 km a. s. l. There is a slight contribution of the fine mode in the dust layers on both days, with values between 3 µm 3 cm -3 for the airborne data and 5. 3 µm 3 cm -3 for LIRIC. In general, it is observed that the coarse mode contributes the most to the total VC, which is expected due to the predominance of mineral dust. Coarse mode concentration values range between 28 ± 4 and 46 ± 4 µm 3 cm -3 on 16 June and 35 ± 5 and 42 ± 11 µm 3 cm -3 on 17 June, depending on the dataset considered. GRASP and LIRIC retrievals both overestimate the airborne data for the fine mode while they overestimate the total mode on 16 June and underestimate the total mode on 17 June using sun-photometer data at both Granada and Cerro Poyos stations.
Volume concentration (µm 3 cm ment for the coarse mode is high with differences lower than 6 µm 3 cm -3 (25 %), except for the LIRIC inversion from Cerro Poyos on 16 June, where the difference is 19 µm 3 cm -3 (around 80 %). Both algorithms show the largest differences for the retrievals from Cerro Poyos on 16 June, whereas the differences for the retrievals from Granada for total and coarse mode are around 15 and 25 % using GRASP and LIRIC, respectively. On 17 June for Granada retrieval, the differences between both algorithms and airborne data below 2 km a. s. l. could be explained because the flight was not exactly over Granada, as shown in Fig. 1 , and differences are expected in the lower 2 km of the atmosphere because of the influence of the city. In the dust layer on 17 June, the differences are around 20 % for coarse and total VC by both algorithms for Granada and Cerro Poyos stations.
However, the presented analysis is representative of Saharan dust transport to southern Europe, and still it is necessary to test a more complete dataset that includes different aerosol loads and types. In future studies, we could try to combine one lidar with two sun-sky photometers at different heights to try improving the retrievals in the cases with different aerosol layers. In addition, in order to validate the presented GRASP scheme, in the future we plan to use a database from global aerosol models (e. g. GEOS-5) following an approach similar to  Whiteman et al. (2018).
Acknowledgements. This work was supported by the  Andalusia Regional Government  through project  P12-RNM-2409 , by the  Spanish Ministry of Economy and Competitiveness  through project  CGL2013-45410-R  and  CGL2016-81092-R  and through grant  FPI  ( BES-2014-068893 ), by the " Juan de la Cierva-Formación" program  ( FJCI-2014-22052 ) and the  Marie Skłodowska-Curie Individual Fellowships (IF) ACE_GFAT  (grant agreement no. 659398 ), and by the  University of Granada  through " Plan Propio. Programa 9 Convocatoria 2013 ". The financial support for EARLINET in the ACTRIS Research Infrastructure Project by the  European Union 's  Horizon 2020 research and innovation programme  through project  ACTRIS-2  (grant agreement no. 654109 ). The authors thankfully acknowledge the  FEDER program  for the instrumentation used in this work and the  Sierra Nevada National Park , for its support for the operation of Cerro Poyos station.
Data availability. The data from lidar system of the Granada station can be accessed through the EARLINET database (see http: //access. earlinet. org/EARLINET/SearchPage. aspx). The data corresponding to column-integrated properties at Granada and Cerro Poyos can be obtained from the AERONET database (see https: //aeronet. gsfc. nasa. gov/). The aircraft data are available on the ChArMEx database (http://mistrals. sedoo. fr/ChArMEx/). GRASP inversion algorithm software used in this work is free and publicly available at http://www. grasp-open. com.
Literature Data Collection Data on specific associations of I. ricinus and its hosts are the backbone of this study. Data on pairs of associations among ticks, vertebrates, and pathogens were compiled from a literature review focused on the Western Palearctic. A "record" is a pairwise combination of "pathogen and tick, " "tick and vertebrate" or "pathogen and vertebrate" at one site. The pathogen can be associated to either the vertebrate or to the tick, while the tick is only associated with the vertebrate. The literature review was based on journals searchable in Thomson Reuters, Scopus, and PubMed. We performed a deliberately relaxed query, including only the name "I. ricinus, " to manually select the papers reporting ecological information after a critical evaluation of the abstract. The obtained papers were included in the dataset only if adequate information about the host, tick and/or pathogen was available.
The difference with Authority is that the importance of the neighbor nodes is considered. Both indexes, Authority and PageRank are complementary. Weighted Clustering Coefficient: Evidence suggests that in most networks, nodes tend to create tight groups characterized by a relatively high density of ties, which is greater than the average probability of a tie randomly established between two nodes. The Weighted Clustering Coefficient measures the degree to which nodes in a graph tend to cluster together. The meaning in our application is that nodes with a high value of centrality will have a tendency to tightly cluster with others, meaning for an ecological interaction that is higher than with other nodes of the network. and each host species in the environmental niche. We used a previously developed global dataset of environmental variables  (Estrada-Peña et al.
, 2014)  based on the transformation by harmonic regression of monthly data derived from the MODIS series of satellites at a nominal resolution of 0. 05 •. The dataset includes day temperature (LSTD) and the Normalized Difference Vegetation Index (NDVI), an index of vegetation vigor, which were obtained for the period 2001-2015. We retained three variables for LSTD (LSTD1-LSTD3) and three for NDVI (NDVI1-NDVI3) that explain the annual average and the slope (seasonality) in spring and autumn, respectively. The ability of the dataset to capture the environmental niche of organisms has been already demonstrated  (Estrada-Peña et al. , 2014). We obtained pairs of coordinates of every species of host for the tick querying the Global Biological Information Facility (GBIF)  (Garcia-Rosello et al.
, 2014). Approximately 11 million records were obtained for 203 unique species. We retained a set of 142 hosts for which phylogenetic information and reliable distribution data (at least 100 geo-referenced records) were simultaneously available. We independently trained environmental suitability models of each species of host using the niche modeling program MaxEnt  (Phillips et al. , 2006). MaxEnt was chosen because it demonstrated robust model performance compared to other modeling algorithms when presence-only data is available. We used the lineal and quadratic features with a maximum number of 10,000 background points and 70% of points for training purposes, using cross-validation to compare the resulting models. The regularization multiplier was set to 1. Each model was replicated 100 times using the cross-validation function in MaxEnt to partition the data into replicate folds, with each fold being used in turn to test the model.
Building the Network of Hosts of I. ricinus and Transmitted Pathogens The analyses before produced an estimation of the niche overlap between I. ricinus and its hosts as well as the correlation between the phylogenetic tree and the environmental variables. The last step of our framework aims to evaluate the impact of each host on the circulation of the pathogens. We used a dataset on reported relationships between ticks, hosts, and pathogens to develop a network of biotic connections (Estrada-Peña and de La Fuente, 2016) in terms of "who is a parasite of whom" and then obtain conclusions on the effects of that structure on the circulation of pathogens. In host-parasite networks (see Box 1), nodes represent "cargos" that are linked to "carriers. " Thus, the network is directed: each edge links a pathogen "to" a vertebrate or a tick, or a tick to a vertebrate.
DISCUSSION This study captured the structural details of a community of pathogens transmitted by a tick and circulating through different clades of vertebrates. It is the development of a proof-of-concept  (Estrada-Peña et al. , 2015)  intended to accommodate the structure of a network to the biotic relationships between parasites and hosts, and combines techniques from phylogenetics and niche modeling. The different parts of this study were derived from distinct disciplines with their own intrinsic assumptions, limitations, and requirements. Therefore, integration is critical for the success of this methodological approach. Significant challenges are apparent because these datasets are commonly affected by bias due to the abundance of common hosts or interest in a given pathogen. Therefore, the dataset must be weighted adequately to not reflect bias affecting the structure of relationships.
Statistical Methods The data were collected from computerized medical records: the emergency medical record (DMUnet) or the global medical record (Cora). The epidemiological characteristics of the 2 groups were compared using a χ 2 test for qualitative variables, a Student test for the normally distributed quantitative variables, or a nonparametric Mann-Whitney U test for the other continuous variables. Differences were considered significant if the P value was <. 05. An analyses were performed with Stata software, version 12. 0. A map was developed with MapInfo 12. 0 software, to illustrate the distribution between districts and their socioeconomic level. declared to the Commission National Informatique et des Libertés (CNIL N°TFN1490159N) following French legal requirements.
Experimental Overview This work demonstrates a low-cost open source automatic measurement system for sheet resistance. The developed system aims to perform automated measurement of sheet resistance of several points within a sample. Various existing open source hardware and software were utilized to make equipment development faster and more reliable. The system consists of a modified open source RepRap 3-D printer, a custom-designed measurement circuit, and graphical user interface (GUI) for a computer. A user enters data on the GUI about the geometry of the sample, points on the sample to be measured, current value, and center coordinate of the sample on the 3-D printer coordinate system. The precise center coordinate is not important as it is not possible to precisely position the sample (with 100 micron accuracy) on the print bed.
The 100 micron accuracy discussed here is the distance between two points of measurement. Thus it should be pointed out that the uniformity of the conductivity values is in relation to the distance between two or more points on the sample, which are highly accurate rather than an absolute position on the sample. The GUI software then sends ASCII G-Code to the modified RepRap directly, as it has been pointed out previously that a RepRap 3-D printers can be used as 3-D motion control equipment for scientific experiments  [26]. The RepRap, with a four-point probe head in place of a hot-end, is able to move the probe automatically to several points on the sample with positional accuracy of 100 microns. The GUI software controls the measurement circuit to perform the measurements automatically and saves the results to the computer as a CSV file.
The second part is a carriage part which slides around the x-axis smooth rods of the printer and is attached to the toothed belt (Figure  3b ). The design of the carriage makes it possible for the printer to move the probe assembly around the x-axis smooth rods using linear bearings tied with cable ties underneath the holder. The GUI is able to control the printer directly by sending ASCII G-Code over a USB connection, configured as an emulated serial port. Care must be taken to ensure that there is no z-wobble (change in x-y coordinate when z coordinate is changed) on the printer as this will possibly damage the sample when lowering the probe to the sample. A pair of specimen clips was also 3-D printed to hold the sample in place on the bed so that the sample will not move around and get scratched by the needles of the probe.
The bed itself was fixed using springs so that precise z-positioning of the probe is not needed (Figure  4 ). This way the printer will lower the probe head all the way until minimum z-coordinate, and the force of the springs will ensure that the sample will touch the plastic pad on the probe. The sample must touch the plastic pad for proper operation of the probe as recommended by Jandel  [66]. The GUI is able to control the printer directly by sending ASCII G-Code over a USB connection, configured as an emulated serial port. Care must be taken to ensure that there is no z-wobble (change in x-y coordinate when z coordinate is changed) on the printer as this will possibly damage the sample when lowering the probe to the sample. A pair of specimen clips was also 3-D printed to hold the sample in place on the bed so that the sample will not move around and get scratched by the needles of the probe.
Firmware A custom firmware was written using the Arduino Integrated Development Environment (IDE) and open source libraries for rapid development. The firmware was designed to receive and reply to commands over a USB connection via GUI software running on a PC. Several features of the firmware include: detecting whether samples are connected to the probes, disabling and enabling the current source, automatically detecting suitable current levels for the connected sample, automatic gain setting for instrumentation amplifier, switching forward or reverse current configuration, and also include a digital low pass filter to reduce noise from the measurement results. The auto current feature will select among these current values: 10 nA, 100 nA, 1 µA, 10 µA, 100 µA, 1 mA, 10 mA, that will generate sufficient voltage between the two inner needles when the sample is touching the probe.
Software and Graphical User Interface (GUI) The Java swing toolkit, included in the Java Development Kit  [80] , is used to develop the GUI because they are platform independent and the GUI could be rapidly generated using tools such as WindowBuilder  [81]. The GUI could be designed easily using drag and drop methods, and uses a "what you see is what you get" (WYSIWYG) interface of this open source tool. The finished user interface is shown in Figure  9.
The measurement settings are straightforward to use, with numbered steps to follow. Users can enter which point on the sample to measure manually or it could be generated automatically. The measurement process and result can be seen in the text display. The software will automatically turn off the current source before lowering the probe head, and then turn it on again after touching the sample. This is done to prevent arcing between the needles and the sample. The software will control the printer to move the probe head through all programmed points. The coordinate of each point, current and voltage measured is stored as a CSV file as the measurement process is ongoing and can be exported after the characterization process is complete. The GUI is released under GNU FDL and can be downloaded from  [78, 79].
The use of the self-replicating rapid prototyper (RepRap) printer, together with a custom measurement circuit, have been investigated to provide a low-cost, open source alternative to expensive automated sheet resistance measurement equipment. A four-point probe head has been installed in place of a 3-D printer head and controlled with software. A custom-designed measurement circuit together with graphical user interface (GUI) software were developed to measure sheet resistance of ultra-thin indium tin oxide (ITO) film samples. The validation shows that the circuit could measure sheet resistances smaller than 1 MΩ with less than 1% error. The results indicate that all measured values are within the same order of magnitude when compared to two proprietary measurement systems. This compares favorably with proprietary commercial systems.
A R Y The Western Alps, although being intensively investigated, remains elusive whenit comes to determining its lithospheric structure. New inferences on the latter are important for the understanding of processes and mechanisms of orogeny needed to unravel the dynamic evolution of the Alps. This situation led to the deployment of the CIFALPS temporary experiment, conducted to address the lack of seismological data amenable to high-resolution seismic imaging of the crust and the upper mantle. We perform a 3-D isotropic full-waveform inversion (FWI) of nine teleseismic events recorded by the CIFALPS experiment to infer 3-D models of both density and P-and S-wave velocities of the Alpine lithosphere. Here, by FWI is meant the inversion of the full seismograms including phase and amplitude effects within a time window following the first arrival up to a frequency of 0.
They notably underlined the extent of a high P-wave velocity anomaly (from 7. 4 to 7. 7 km s -1 ) up to 10 km depth interpreted as the Ivrea body and pointed out its Adriatic mantle origin. Nonetheless, the limited aperture of the available seismic arrays restricted the resolution of these tomographic images to the upper crust. More recent LET studies made use of wider seismic arrays  (Diehl et al. 2009; Potin et al. 2015)  with a larger number of data allowing the inference of crustal structures down to the lower crust. The tomographic model of  Diehl et al. (2009)  shows an upper to middle crust dominated by the high velocity anomaly associated with the Ivrea body that can be traced down to 45 km depth. In the upper crust, this Ivrea body is surrounded by low velocity anomalies attributed to the Molasse and Po sedimentary basins that are also well-visible on ambient-noise tomography  (Stehly et al.
2013). A first exploitation of the CIFALPS data by common conversion point migration of the teleseismic P-wave receiver functions has provided the first conclusive seismic image of a subducting continental crust in the Western Alps  (Zhao et al. 2015). The aim of this study is a second attempt to develop new P-and S-wave velocity and density models of the lithosphere of the western Alps from the CIFALPS data with a resolution of the order of the wavelength. We present an application of full-waveform inversion (FWI) on the CIFALPS data to derive 3-D high-resolution P-and S-wave velocity and density models of the lithosphere of the Western Alps and compare them with the migrated image of  Zhao et al. (2015). Beyond receiver function migration, waveform inversion methods are expected to provide quantitative broad-band lithospheric models with a resolution close to the wavelength.
The reliability of FWI for teleseismic application was further demonstrated with an application to real data collected in the framework of the Pyrope experiment across the Pyrénées range  (Wang et al. 2016). FWI of five events recorded by 29 stations provided tomographic P-and S-wave velocity models of the Pyrenean lithospheric structure with an unprecedented resolution. Moreover,  Wang et al. (2016)  showed the consistency between the P-and S-wave velocity models developed by FWI and migrated images inferred from receiver functions. In this study, we present an application of FWI on the CIFALPS data set following an approach similar to that of  Monteiller et al. (2015). A key difference is that we update the density parameter (ρ) in addition to the P-and S-wave velocity parameters (V p and V s ).