dataesr/scientific-paragraphs-categorization huggingface dataset:
Annotation of Infinium 450K and EPIC probes in Macaca mulatta and Chlorocebus sabaeus To annotate probes, the annotations files for Macaca mulatta and Chlorocebus sabaeus were retrieved from Ensembl (Version 84), containing respectively 44,725 and 28,078 transcripts for 30,246 and 27,985 genes (coding, non-coding and pseudogenes). In accordance with the annotation file provided by Illumina for the arrays we divided transcripts into 6 different categories: promoter region ranging from 1 bp to 200 bp upstream of the TSS (TSS200), promoter region ranging from 201 bp to 1,500 bp upstream of the TSS (TSS1500), 5' untranslated region (5'UTR), first exons (1stExon), 3' untranslated region (3'UTR) and gene bodies, excluding the 5' and 3' UTRs and first exons (Body). Similarly, CpG islands prediction files were downloaded from the UCSC genome browser (containing respectively 24,226 and 26,663 CpG islands for Macaca mulatta and Chlorocebus sabaeus) for the annotation relative to CpG islands following again the annotation criteria used by Illumina for the human genome.
10 µl of PCR product were rendered single-stranded as previously described  [41]  and 4 pmol of the respective sequencing primer were used for analysis. Quantitative DNA methylation analysis was carried out on a PSQ 96MD system with the PyroGold SQA Reagent Kit (Qiagen) and results were analyzed using the PyroMark CpG software (V. 1. 0. 11. 14, Qiagen).
It is important to point out the different annotation levels between these distinct species, which impacts the number of identified/predicted genes and transcripts in each species. Indeed, human GRCh37 annotation (version 75 from Ensembl) contains 57,952 genes and pseudogenes for 196,501 transcripts plus thousands of alternate sequences, whereas 30. 246 genes are annotated in Macaca mulatta for 44. 725 transcripts and 27,985 genes are annotated in Chlorocebus sabaeus for only 28,078 transcripts  [55, 56]. CpG island feature annotations, in counterpart, are directly predicted from reference sequence. This might explain the observed differences between the species depending on the genomic region. It is indeed important to keep in mind that simian annotations generally are still less precise and documented than human annotation and this lack of information may contribute to the observed differences.
Statistical methods The statistical analysis was conducted with STATISTICA 12 software (Statsoft, Poland). The absolute numbers (n) and percentages (%) were estimated for the categorical variables. Arithmetic mean (M) and standard deviation (SD) were estimated for continuous variables. The following statistical tests were used: • one sample t test against a value of 5. 5 to check whether readiness to promote health is neutral or statistically significantly positive or significantly negative, • two paired samples t test to compare readiness to promote health between at workplace and in local community, • two unpaired samples t test to compare readiness to promote health between men and women, • F-test analysis of variance to compare readiness to promote health between 3 levels of education, 4 intervals of job seniority, 3 intervals of number of employees, 4 locations of pharmacies, 3 intervals of average number of customers daily, • Pearson's correlation coefficient r to correlate readiness to promote health with age of pharmacy staff.
Monitoring of the drainage-imbibition experiments with dielectric permittivity Dielectric permittivities were monitored using TDR probes (Decagon Devices 5TE 40567) with a 70 MHz frequency. Data acquisition frequency was 2 signals per minute. In addition to permittivity (-), these probes monitor volumetric water content-VWC (m 3. m -  ), temperature (°C), and bulk electrical conductivity-EC (dS. m -1 ). They were connected to a Campbell Scientific CR1000 (4M) data logger to acquire temperature and permittivity data. The permittivity values were corrected relative to the reference values measured in air and water using the following equation (Eq. 3) [Kargas and Soulis (2012)]: = ε !" # $%& -ε ! ε -ε ! + ε ! !" Eq. 3 where εw-theoretical (-) is the relative effective permittivity of pure water (εw-theoretical = 80 at 20 °C), εmeasured (-) is the relative effective permittivity of the medium measured with the TDR probe during the experiments, εair (-) is the relative effective permittivity of air measured at the beginning of the experiment, εw (-) is the relative effective permittivity of tap water measured at the beginning of the experiment, and εair-theoretical (-) is the relative effective permittivity of pure air (εair-theoretical = 1).
Monitoring of the drainage-imbibition experiments with electrical resistivity Electrical resistivity was monitored using unpolarizable potential electrodes for voltage measurement, metallic current electrodes for current injection, a resistivity meter and data acquisition software. To limit electrode polarization phenomena, which can add noise to the measurements, potential electrodes must be unpolarizable  [Dahlin (2000) ]. Cu/CuSO4 electrodes were used and the method developed by  Noel [Noel (2014) ]. These electrodes were made by mixing milli-Q water 72. 2%, CuSO4 26% and Gelatin 1. 7% and heated the mixture to ≈80 °C for 45 minutes using a shaking heating plate. The resulting electrodes are unpolarizable, i. e. , they do not polarize the ground and therefore the electrode action on the potential measured can be considered negligible.
The metallic current electrodes were made of nickel-cobalt alloy (MP35N). The resistivity meter was SIP LAB IV and data acquisition software was SIP LAB IV. Resistivity was measured between 0. 1 to 20 000 Hz but analysed at 1. 4 Hz. This frequency was chosen because it is close to that used in the field  [Chambers et al. (2004) ; Constable and Srnka (  2007  The values measured were resistance values, R , which were transformed into apparent electrical resistivity values, ρ , using the geometric coefficient, Kg (Eq. 4 and Eq. 5)  [Reynolds (2011) ] : * + = R , - Eq. 4. = -* + Eq. 5 where Kg (m) is the geometric coefficient, and R , (Ω. m) is the initial estimated resistance value. The conductivity of the tap water, measured at the beginning of each experiment, made it possible to determine Ro and to calculate Kg (using Eq.
Drainage-imbibition experiments without enhancement The Pc-Sw curves for 0. 5 and 0. 1 mm GB are compared in Figure  2a. Table  1  shows the results of these experiments and the van Genuchten-Mualem (VGM) fitting parameters. The experimental data were fit to the VGM capillary pressure-saturation function (Eq. 1 and Eq. 2) using sum of squared errors (SSE) minimization. The SSE were low (SSE<0. 0014), which demonstrated that the VGM model can be used to describe the experimental results. The experimental results are mainly focused on residual DNAPL saturation and irreducible water saturation. It is clear from the graph that the parameters differed slightly for each size of glass bead. For 0. 5 mm GB, Srn was approximately 10. 9% vs. 12. 7% for 0. 1 mm GB. According to the results, Srw was around 24.
Drainage-imbibition experiments without enhancement Calibration curves (ρc = f(Sw)) were plotted for 0. 5 and 0. 1 mm GB (Figure  6 ). Experiments with DNAPL alone in GB were performed to determine the experimental values corresponding to Sw = 0% and Sw = 100%. Resistivity data were found to be more dispersed than permittivity data. Resistivity can be correlated to water saturation via a power relationship. The correlation factor, considering all the measured data, was satisfactory for 0. 5 mm GB: R 2 = 0. 81. The results were more dispersed with the 0. 1 mm GB than with the 0. 5 mm GB. Resistivity was related to Sw via a power law for 0. 1 mm GB; with a correlation factor R 2 = 0. 74. The results were different for 0. 5 and 0. 1 mm GB: the features of the trend curves are similar but are shifted.
Acknowledgments This research was carried out as part of the  SILPHES  project cofunded by  ADEME (French Environment and Energy Management Agency)  in the framework of the  Future Investments ("Investissements d'Avenir ") funding scheme and the  BRGM   MULTISCALEXPER  project. The authors acknowledge ADEME and the  BRGM/DEPA division  for its financial support. The authors.
Microarray Analysis RNA isolation following immunoprecipitation with anti-BRCA1 antibody and control antibody (NR) was performed in triplicate as described in the "RNA-binding protein immunoprecipitation (RIP)" section. Microarray processing and data analysis was performed at the ProfileXpert core facility (Lyon, France). Details are provided in Supplementary Material and Method. The complete set of raw and normalized data is available at the GEO database under accession number GSE119886 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE119886). For each replicate, the probe intensities issued from the BRCA1 and NR immunoprecipitations were obtained. The obtained data were normalized with Affymetrix Expression Console software using the RMA statistical algorithm. Control expression values (NR) were subtracted from their respective sample counterparts on a probe set basis; the 3 replicates were then averaged.
Only genes showing an immunoprecipitation (IP) ratio IP BRCA1/IP NR (Fc) greater than 1. 5 and a p-value lower than 0. 05 were retained. The retained genes of interest were listed and classified according to their biological process (BP), cellular compartment (CC), and molecular function (MF) using DAVID (Database for Annotation, Visualization and Integrated Discovery) on 10th of March 2017  [22]  (https://david. ncifcrf. gov/summary. jsp). 2. 11. Quantitative RT-PCR 2. 11. 1. RIP Analysis Three additional replicates of RIP, including inputs, were dedicated to RT-qPCR. RNA extracted from RIP (IP BRCA1 and IP NR) and RNA extracted from the corresponding inputs, was reverse-transcribed and pre-amplified with the Nugen Ovation WTA System (TECAN, Redwood City, USA). Quantitative real-time PCR (qPCR) was carried out using the light cycler 480 II real-time PCR thermocycler (Roche, Meylan, France).
Only genes showing a Te greater than 1. 4 or lower than -1. 4 in the three replicates were retained. Primers were designed using the Primer-Blast software (National Centre for Biotechnology Information/NCBI, Bethesda, USA; http://www. ncbi. nlm. nih. gov/tools/primer-blast) and purchased from Eurofins Genomics (Ebersberg, Germany). For each gene, primers were designed within exons that displayed high exon probe intensities on arrays. Genes tested for polysomal profiling and RIP, and primers, are listed in the Table  S1.
Funding: This research was funded by the  "Ligue Contre le Cancer, comité départemental du Rhône" , the  Conseil de Radioprotection Electricité de France (EDF) , the translational program CRCL-CLB, with  AJORA (Association des Jeunes Oncologues de Rhône-Alpes) , the  Spanish Ministry of Economy and Competitiveness  under Grant [ BIO2015-64752 ] to L. R. P. J. J. D. laboratory is supported by  Inserm ,  CNRS ,  Université Claude Bernard Lyon 1, Centre Léon Bérard ,  Agence Nationale pour la Recherche  ( RIBOMETH ANR-13-BSV8-0012-01 ),  Programmes d'Actions Intégrées de Recherche (PAIR Sein, RiboTEM ,  ARC_INCa_LNCC_7625 ),  SIRIC LYriCAN  ( INCa-DGOS-Inserm_12563 ),  Ligue Nationale contre le Cancer, Ligue contre le Cancer comité départemental  ( Drôme, Rhône, Isère, Puy-de-Dôme, Allier ) and  Fondation ARC pour la Recherche sur le Cancer  ( 2016120486 ).
The results are obtained with the ALICE detector. The data are compared, in terms of the m ee and p T,ee distributions, to the sum of the expected sources of e + e -pairs from known hadron decays, the so-called hadronic cocktail. The spectra are shown after the application of fiducial requirements on single electrons (|η e | < 0. 8 and 0. 2 < p T,e < 10 GeV/c) without an extrapolation to the full phase space. In addition, for the first time at LHC energies, a direct comparison between the dielectron cross section obtained in pp and p-Pb collisions is possible since both data sets were recorded at the same √ s NN. In particular, the analysis of the pp data resolves the model dependence on the expected m ee and p T,ee distributions of correlated e + e -pairs from open heavy-flavor hadron decays in pp collisions, used as reference for the p-Pb study.
About half of the pp and p-Pb data samples were recorded without the silicon drift detector information to reach maximal data acquisition rates. For this reason, even when available, the information from this detector is not used to have uniform detector conditions over the entire data sets. The main detector for particle identification (PID) and tracking is the TPC. This 500 cm long cylindrical detector, with an outer radius of 247 cm, is located around the ITS. The TPC readout is based on multi-wire proportional chambers and provides up to 159 three-dimensional space points as well as the specific energy loss of the particle. The outermost detector used in this analysis is the TOF. It provides a time-of-flight measurement for particles from the interaction point to its active volume, at a radius of 370 cm.
Additional selections are applied to the recorded events. The background from beam-gas interactions and pileup events are rejected by using the correlations between the V0 detector and ITS signals. Only events with at least one track segment reconstructed in the ITS contribut- ing to the vertex reconstruction with the SPD are used. To assure a uniform detector coverage at midrapidity, the vertex position along the beam direction is restricted to ±10 cm with respect to the nominal interaction point. A summary of the number of events N ev passing the event selection criteria and the corresponding integrated luminosity L int is given in Table  I. These requirements are fulfilled by 77% (75%) of the recorded events for the pp (p-Pb) data samples. The L int is calculated as L int = N MB /σ MB , with the number of analyzed events after the vertex reconstruction efficiency correction N MB , and the minimum bias trigger cross section σ MB measured via a van der Meer scan in the corresponding collision system  [59, 60].
5 GeV/c 2. The resulting cross sections are listed in Table  III. The systematic uncertainties originating from the data were determined by repeating the fit after moving the data points coherently up-and downward by their systematic uncertainties. Additional uncertainties on the effective beauty-and charm-to-electron branching ratios, arising from the semileptonic decay branching ratios of open heavy-flavor hadrons and the fragmentation functions of charm (beauty) quarks, amounting to 22% and 6% for the charm and beauty cross sections, respectively, are also listed in the table. All uncertainties are fully correlated between the two generators, which differ only in the implementation of the heavy-quark production mechanisms. In both calculations, the hadronization of the c-and b-quarks, and the decays of the open heavy-flavor hadrons, are performed using PYTHIA 6.
We present the latest version of the ISBA-CTRIP land surface system, focusing on the representation of the land carbon cycle. We review the main improvements since the year 2012, mainly added modules for wild fires, carbon leaching through soil and transport of dissolved organic carbon to the ocean, and land cover changes but also improved representation of photosynthesis, respiration, and plant functional types. This version of ISBA-CTRIP is fully described in terms of land carbon pools, fluxes, and their interactions. Results are compared with the previous version in an off-line mode forced by observed climate during the historical time period. The two simulations are presented to demonstrate the model performance compared to an ensemble of observed and observation-derived data sets for gross and net primary productivity, heterotrophic and autotrophic respiration, above and below ground biomass, litter, and soil carbon pools.
New developments specific to the new version such as burned area, fire emissions, carbon leaching, and land cover are also validated against observations. The results show clearly that the latest version of ISBA-CTRIP outperforms the former version and reproduces generally well the observed mean spatial patterns in carbon pools and fluxes, as well as the seasonal cycle of leaf area index. The trends of the global fluxes over the last 50 years agree with other global models and with available estimates. This comparison gives us confidence that the model represents the main processes involved in the terrestrial carbon cycle and can be used to explore future global change projections. Plain Language Summary The land surface exchanges energy, water, and carbon with the atmosphere and partly controls the atmospheric CO 2 concentration.
It is therefore crucial to represent correctly the carbon cycle on land in models designed to be used in Earth System Models. We present here the improvements made to the representation of the land carbon cycle by the land surface system ISBA-CTRIP. We improved the representation of several processes using published data, and we added processes that were not represented. The new version of the model performs better than the previous one at representing the carbon fluxes and pools, when compared to a series of observation data sets. This evaluation suggests that we can use ISBA-CTRIP to explore the changing climate and carbon cycle.
, 2017)  but also their direct role on the physical climate through changes in land surface properties, notably albedo (see for instance  Rocha et al. , 2012 Bonan, 2008 , or Randerson et al. , 2006). These shortcomings prompted a thorough update of the biogeochemical module of ISBA-CTRIP. In parallel, the land surface physics was also thoroughly upgraded (14 layer-discretized solution of the energy and water balance in soils, 12-layer snow model, etc. ; see  Decharme et al. , 2019). The resulting model serves as the land surface component of CNRM-ESM 2-1  (Séférian et al. , 2019) , the Earth system of second generation developed by CNRM-CERFACS for the sixth Coupled Model Intercomparison Project (CMIP6;  Eyring et al. , 2016). The first goal of this study is to present the new version of ISBA-CTRIP, focusing on the changes that concern the land carbon cycle: mainly the added modules for wild fires, carbon leaching through soil and transport of dissolved organic carbon (DOC) to the ocean, and land cover changes, but also improved representation of photosynthesis, respiration, and plant functional types (PFTs).
The energy and water balances are influenced by soil texture, soil albedo, and soil carbon content. Evapotranspiration results from the direct evaporation of canopy-intercepted rainfall, from bare soil evaporation and from vegetation transpiration controlled by stomatal conductance (see below). In contrast 10. 1029/2019MS001886 Journal of Advances in Modeling Earth Systems to most land surface models, ISBA with its river routing module CTRIP includes a representation of aquifers  (Vergnes & Decharme, 2012 ) that feed back on soil moisture content. It also represents inundation from rivers in floodplains. A detailed description of the snow module is given in  Decharme et al. (2016). A detailed study of the land surface physics and hydrology, including the effects of aquifers and inundation on the surface energy and water budgets, is presented in  Decharme et al.
Processes ISBA_bgc5 ISBA_bgc6  Farquhar et al. (1980)  and  Collatz et al. (1992). Goudriaan's approach was originally chosen by  Calvet et al. (1998)  because it uses conductances instead of enzyme kinetics and was conceptually closer to what was used at the time in the land surface modeling community. Goudriaan's approach has the advantage of being fairly simple, but its parameters are rarely measured by the ecophysiology community. Here, we show how we recently related Goudriaan's main parameters to Farquhar's model to be able to use the ecophysiology body of science and the TRY database in particular  (Kattge et al. , 2011). The model uses an empirical light response function of net assimilation An to combine the effects of light and CO 2 as limiting factors: An ¼ Am þ Rd ð Þ 1 -exp À ϵIa Am þ Rd -Rd: (1) Am is the asymptotic value of the light response curve of photosynthesis, Rd is the dark respiration, ϵ is the initial light use efficiency, and Ia is the absorbed photosynthetically active radiation (aPAR).
Plant Functional Types ISBA_bgc5 used nine PFTs (three tree types, three grass types, and three crop types) and three land covers (bare soil, rock, and permanent snow and ice) derived from the ECOCLIMAP vegetation and soil database  (Masson et al. , 2003). The tree types (broadleaf deciduous, needleleaf evergreen, and tropical broadleaf evergreen) did not allow for a correct representation of plant types covering large or important areas like the deciduous needleleaf forests of Eastern Siberia, the tropical deciduous broadleaf forests of subtropical Africa, or the dry broadleaf evergreen forests in Mediterranean climates. We therefore added five tree types distinguishing boreal and temperate types and one deciduous shrub type using the updated ECOCLIMAPII database  (Faroux et al. , 2013). Similarly, we added an arctic grass PFT.
The geographical distribution of boreal, temperate, and tropical tree types is based on LPJ bioclimatic limits (Table  2  in  Sitch et al. , 2003). Arctic grasses were defined using information present in the original ECOCLIMAP database. Shrubs were defined as deciduous trees less than 2 m high. The resulting PFT distribution for year 2000 is given in Figure  2  with the dominant vegetation type. The wetland and irrigated crop vegetation types are currently treated by the model as simply grass and crops. Vegetation height and vegetation and soil albedos are prescribed for all the surface types subgrid patches based on a mean annual cycle at a 10-day time step. Vegetation and bare soil albedos in ECOCLIMAP are derived from satellite observations  (Carrer et al. , 2014). The rooting depth is specified for each vegetation type according to  Canadell et al.
Fire The fire carbon module implemented in ISBA derives from GlobFIRM  (Thonicke et al. , 2001). It represents natural wildfires over forest and grassland areas. The GlobFIRM fire fraction calculation is adapted to a daily time step using the same methodology as  Krinner et al. (2005). It has been recalibrated using Météo-France fire occurrence measurements over the 2000s. It is set to zero when the carbon content of the surface litter is below 200 gC/m 2 and when soil temperature is lower than 0°C or when the soil is frozen. It is also set to zero when more than 20% of the grid cell is covered by croplands. Agricultural fires are not negligible (8-11% of all fire occurrences in 2001-2003 according to  Koronzi et al. (2006) ) but are largely related to human practice (see for instance  Lin et al.
The CRU-NCEP product has a 0. 5°spatial resolution and a 6-hr temporal resolution. ISBA uses a 900-s time step and interpolates in time the climate forcing. To limit computing time, we degraded the original spatial resolution to 1°. To focus our comparison on the representation of the carbon cycle, we used the new physics of the model described in  Decharme et al. (2019)  in both versions of the model. The soil textural properties and the soil carbon content affecting the physical soil properties  (Decharme et al. , 2016)  are given by the Harmonized World Soil Database (HWSD; http://www. fao. org/soils-portal/ soil-survey/soil-maps-and-databases/harmonized-world-soil-database-v12/en). The topographic information comes from the 30-arcsecond resolution GTOPO30 data.