dataesr/scientific-paragraphs-categorization huggingface dataset:
ECHAM/MESSy Atmospheric Chemistry (EMAC) model EMAC is a 3D general circulation model that includes a variety of sub-models to describe numerous processes in the troposphere, their interaction with oceans and land surfaces and incorporates anthropogenic influences. Here we use the second development cycle of the Modular Earth Submodel System (MESSy2)  (Jöckel et al. , 2010)   The sum of peroxy radicals was estimated as the sum of all radicals R i O 2 with less than 4 carbon atoms. Net ozone production based on data retrieved from EMAC was estimated as NOPR = [NO] • (𝑘 NO+HO 2 [HO 2 ] + ∑ 𝑘 NO+R i O 2 [R i O 2 ] 𝑖 ) -[O 3 ] • (α • 𝑗(O1D) + 𝑘 OH+O 3 [OH] + 𝑘 HO 2 +O 3 [HO 2 ]). (8) A list of all included peroxy radicals R i O 2 for the reaction with NO is given in the supplementary Table  ST9.
Net ozone production rates around the Arabian Peninsula In the following, net ozone production rates (at noon) are calculated based on Eq. 7 for the different regions. These noontime values are then scaled to diurnal production rates (Fig. 8 ) based the integrated actinic flux as photochemical net ozone production is in good approximation linear with actinic flux. Due to contamination by the ship exhaust and due to the availability of OH and HO 2 data only from July 18 th 2017 onwards, we have limited the analysis to the period from July 22 nd   Over the Mediterranean and the Southern Red Sea, NOPR values do not significantly deviate from zero (production equals loss) within the atmospheric variability (the uncertainty of the regional NOPR is 40 % which has been estimated by error propagation).
Acknowledgements We acknowledge the collaborations with  King Abdullah University of Science and Technology (KAUST) ,  The Cyprus Institute (CyI)  and the  Kuwait Institute for Scientific Research (KISR). We would like to thank  Marcel Dorf  and  Claus Koeppel  for the organization of the campaign. We would like to thank  Hays Ships Ltd. and the ship crew for caring about the physical well-being of the scientific participants and for an unforgettable time on board Kommandor Iona. Last but not least we would like to thank the whole  AQABA community  for a successful campaign. https://doi. org/10. 5194/acp-2019-1031Preprint. Discussion started: 3 December 2019 c Author(s)  2019. CC BY 4. 0 License.
Samples with low fluorescence were manually reanalysed with a minimum fluorescence of 100 RFU. For the Madang 2005 and Wosera 2006 P. falciparum data, previously published cleaned and rounded microsatellite allele repeat numbers for P. falciparum single clone infections  (Schultz et al. , 2010)  were converted back to allele sizes using the known number of nucleotides/repeat, whereas for P. vivax the raw data (allele calls) was available  (Jennison et al. , 2015). These data were combined with the newly generated MS data from the other studies before binning the alleles using the TANDEM software  (Matschiner & Salzburger, 2009). Allele frequencies of the entire dataset (incl. previously genotyped datasets) were investigated and outlying alleles (most likely caused by PCR artefacts) were removed.
Author Manuscript This article is protected by copyright. All rights reserved (60%) or more MS loci were excluded from further analysis. We attempted to calibrate the P. falciparum data from pre-LLIN Madang 2006 and Wosera (ESP1 2005) by converting rounded repeat numbers back to allele sizes, binning together with the newly generated data and removing outliers. However, there was strong population structure when compared to the new dataset, indicating experimental differences despite the use of the same protocols. Thus, we excluded direct comparisons between old and new datasets for P. falciparum. To conduct the population genetic analyses, allele frequencies and input files for the various population genetics programs were created using CONVERT version 1. 31  (Glaubitz)  and PGD Spider version 2.
1. 0. 1  (Lischer & Excoffier, 2012). Genetic diversity was measured by calculating the number of alleles (A), Nei's gene diversity (expected heterozygosity (He)  (Nei, 1987) ) and allelic richness (Rs)  (Hurlbert, 1971 ) that corrects for sample size, using FSTAT version 2. 9. 3. 2  (Goudet, 1995). Pairwise genetic differentiation was measured by calculating pairwise Jost's D  (Jost, 2008)  and Weir and Cockerhams F ST  (Weir & Cockerham, 1984)  values and 95% confidence intervals were estimated with 1000 bootstraps using the diveRsity package in R  (Keenan, McGinnity, Cross, Crozier, & Prodöhl, 2013). In contrast to some earlier studies  (Schultz et al. , 2010) , where haploid genotypes were coded as diploid genotypes, but homozygote at each locus, the data in this study was analysed using haploid datasets (as in Jennison et al.
Author Manuscript This article is protected by copyright. All rights reserved Evanno et al. (Evanno, Regnaut, & Goudet, 2005)  to determine the most likely K (most likely number of populations). CLUMPP version 1. 1. 2 (Jakobsson & Rosenberg, 2007)  was used to facilitate the interpretation of population genetic results using files generated with STRUCTURE HARVESTER Web v0. 6. 94  (Earl & vonHoldt, 2011)  and Distruct 1. 1  (Rosenberg, 2004)  was used to visualize the structure plots with the data generated with CLUMPP. Statistical analysis of molecular epidemiological and population genetic parameters was done using non-parametric methods as indicated in the results-section using STATA v12. 1 (StataCorp, USA). QGIS 2. 18. 24 (OpenSource Geospatial Foundation) was used to map the villages and households and maps were constructed with spatial layers from DIVA-GIS ("Diva GIS country level data,").
falciparum, matching haplotypes (allowing missing loci) were seen in all post-LLIN datasets and the pre-LLIN ESP2 2005 dataset. However, for P. vivax, matching haplotypes (allowing missing loci) were rarely seen and only in post-LLIN data sets. Among the 332 complete P. falciparum multilocus haplotypes (9-loci successfully genotyped) from all study sites, 16 repeated haplotypes were found, with 11 haplotypes represented two times, three represented three times, and two represented four times. Clonal haplotypes were always found within the same year and province, and in all cases except one in the same catchment.
, 2015; Wahlund, 1928)  (Table  S4 ). In post-LLIN Madang, the observed mLD for P. falciparum is not the result of subpopulation structure, as significant mLD remained in the subpopulations (Table  S4 ). In the Mugil area in 2014, significant mLD for P. falciparum remains due to the circulation of a few very closely related haplotypes in the Megiar village (Table  S4 , Dataset 1). Population Bottleneck for P. falciparum but not P. vivax post-LLIN Bottleneck analysis was performed using a two-phase mutational model (TPM) and testing for heterozygosity excess with a 2-tailed Wilcoxon sign rank test (see Materials and Methods). Significant heterozygosity excess was observed for P. falciparum in ESPII 2005 (but not in ESPI 2005), MAD 2006 and 2010 populations (p=0. 020, p=0. 049 and p= 0. 010, respectively).
All other analyses were conducted using mean values across markers or allele frequencies and thus limit the impact of such errors. Moreover, the dataset included a large proportion of single infection haplotypes in all populations, and the detected clones included dominant haplotypes suggesting that allele calling was reliable. Finally, the highly polymorphic and rapidly evolving nature of microsatellite markers  (Ellegren, 2004)  may limit the resolution of the population genetic parameters such as population level diversity and population structure in high transmission areas  (Branch et al. , 2011). This may both lead to false assignment of unrelated parasites (e. g. from different provinces) as related and reduce the detection of truly related parasites.
| Vineyard management We collected data on pesticide use (i. e. , fungicide, insecticide and herbicide), soil tillage and field age by interviewing the 38 involved vine-growers. The intensity of pesticide application was calculated using the Treatment Frequency Index ("TFI") which is the sum of all the ratios between the applied and the recommended dose for each pesticide application  (OECD, 2001). Tillage intensity was evaluated by calculating the "tillage intensity index" which summarizes the number of tilling operations per year weighted by the area involved each time  (Muneret et al. , 2019). We also measured vine trunk density and crop productivity. To calculate the crop productivity, we multiplied the average number of bunches per vine stock by the average bunch weights and the vine stock density per vineyard (Mg/ ha, see  Muneret, Thiéry, et al.
| Data analyses As the above-ground community and the foliage community represent two guilds, we analyzed the response of each community to environmental conditions separately. For each community, we calculated total abundance, species richness, and evenness (Pielou index) over the year. At each sampling date, approximately 10% of the vineyards were not sampled because of pitfall trap destruction (N = 4 for the first until the fourth sampling dates and N = 5 for the fifth date). Species richness was rarefied to take into account differences in terms of detectability within fields  (Gotelli & Colwell, 2001). For the foliage community, we calculated the abundance of ants, spiders, earwigs, and lacewings and the richness of ants and spiders. For the above-ground community, we calculated both the abundance and the richness of ants, spiders, ground beetles, and rove beetles.
Finally, we calculated the total abundance of harvestmen (those from both the foliage and the ground). All these metrics represented 21 descriptors of natural enemy communities which were then used as response variables in our models and data were log-transformed for further analyses when it was necessary. Linear mixed models were used to investigate the effects of local management intensity, farming systems and landscape composition on each response variable. Because of some trap destructions, we corrected the abundance of the communities for each vineyard having an uncompleted sampling. Therefore, separately for the foliage and the above-ground community, we calculated the relative contribution of each sampling date to the total abundance of the community and we divided the total number of individuals collected by the sum of the relative contribution of the sampling dates that were sampled for the given vineyard.
Co-cultivation of M. bovis With Bovine Lung Cells and Crystal Violet Cell Cytotoxicity Assay M. bovis and EBL cells were co-cultivated in DMEM-based medium, as previously described  (Baranowski et al. , 2010). Briefly, EBL cells were seeded in 24-well plates (Falcon) at a density of 5 × 10 3 cells/cm 2 and inoculated with M. bovis at multiplicity of infection (MOI) of 2. Since SP4 medium (up to 0. 1%) has no apparent toxic effect on EBL cells (data not shown), M. bovis inoculums were prepared by direct dilution of mycoplasma stock cultures with predefined titers in DMEMbased medium. At different time post-inoculation, mycoplasma titers were determined by CFU titration following one freezethaw cycle. Mycoplasma cytotoxicity was determined by staining cell monolayers with crystal violet. Cell monolayers were washed with Dulbecco's phosphate-buffered saline (DPBS, Gibco) and stained for 60 min with 0.
Illumina Whole-Genome Sequencing, Bioinformatic Analyses The genome of M. bovis RM16 was sequenced using HiseqIllumina technology (paired-end, 2 × 150 bp, with an average of 3,000 X for coverage depth; Illumina, San Diego, CA) at the GATC Biotech facility (Konstanz, Germany). Bioinformatics analyses were conducted using the GenoToul Bioinformatics facility, Toulouse, France. Quality of the sequencing reads was controlled with FASTQC tool. 1  De novo assembly was done using Abyss v2. 1. 5 (Simpson et al. , 2009)  and resulted in 61 contigs. The RM16 genome was annotated using the RAST pipeline  (Overbeek et al. , 2014). Co-linear analysis of the RM16 sequence with the genome of PG45 and HB0801 strain was performed using MUMmer 3. 0 or ACT 13. 0. 0 software  (Kurtz et al. , 2004; Carver et al.
M. bovis Proliferation in Cell Culture Transtracheal aspirates from animals showing signs of bronchopneumonia were used to isolate M. bovis RM16 (Table  1 ). This field isolate, whose draft genome sequence was determined by illumina sequencing, was used as a low-passage strain to investigate the influence of eDNA on M. bovis proliferation upon co-cultivation with embryonic bovine lung (EBL) cells. RM16 and EBL cells were seeded in DMEM-based medium at a MOI of 2, and mycoplasma growth was monitored by enumerating CFUs over a period of 72 h (Figure  1A ). Data showed that EBL cells were required for RM16 proliferation, and DMEMbased medium alone was unable to sustain mycoplasma growth. However, EBL cells had only a limited effect on RM16 growth and maximum mycoplasma titers were about 10 3 -fold lower than those yielded in SP4, a medium commonly used for the propagation of mycoplasmas under axenic conditions.
101 (Table  2 ) were consistent with our previous studies that identified apt and the sufS-sufU locus as essential for the proliferation of Mycoplasma agalactiae in cell culture  (Baranowski et al. , 2010; Skapski et al. , 2011). These three mutants were not further characterized since their non-cytopathic phenotype was associated with a severe growth deficiency in cell culture (data not shown). The non-cytopathic mutants, whose proliferation in cell culture produced CFU titers similar to RM16 (Figure  2A ), were characterized by a transposon inserted within six CDS located at three distant chromosomal regions (Figure  3 ). Remarkably,  a The position of the mTn insertion was defined based on the PG45 published sequence in GenBank database (CP002188. 1). The orientation of the mTn is given in parenthesis using the gentamicin-resistance marker as a reference.
The mTn in T11. 15 and T11. 48 was inserted at the same chromosomal position. b Mutants were designated according to transformation and clone numbers (e. g. , T03. 179 designates clone 179 isolated from transformation T03). c The CDS found disrupted in M. bovis are indicated by their mnemonic codification in GenBank. d For each CDS, the relative position and orientation of the mTn are indicated. several CDS found disrupted in these distant regions were homologous to components of the pyruvate dehydrogenase (PDH) complex or were located in close proximity to this gene cluster (Figure  3  and Table  2 ). These included (1) a pdhD homolog (mutant T6. 185), (2) a CDS sharing similarity with the N-terminus of pdhC, which is located upstream of the lactate dehydrogenase homolog in RM16 (mutant T07.
bovis available in databases. Another particular feature of RM16 is that cytotoxicity was not dependent on close contact between bacteria and EBL cells since the amount of H 2 O 2 released by RM16 in the cell culture medium can induce cytotoxicity. This was shown by using gentamicin-treated cell culture supernatants collected after 72 h of co-incubation with RM16 (Supplementary Figure  S1C ). Indeed, these bacteria-free supernatants were found cytotoxic for EBL cells. Catalase (60 U/ml) was shown to abolish the cytotoxicity of the supernatants discarding any possible cytotoxic effect due to the depletion of nutrients. These results clearly identified H 2 O 2 as responsible for the cytotoxicity of RM16 and further suggest that this toxic metabolic compound may be a common virulence factor in ruminant mycoplasma species, although several different metabolic pathways may be involved.
The recent release of M. bovis draft genome sequences in databases led us to further examine the influence of IS-elements on H 2 O 2 production. The alignment of PG45 with the draft genome sequence of 1067 revealed several contigs ending at positions corresponding to IS-elements in PG45 suggesting a conserved organization at genomic regions associated with H 2 O 2 production in these two strains that were found unable to produce detectable levels of this metabolic compound. In contrast, no IS-element was identified in the atypical strain 8790 suggesting that additional genomic regions may modulate H 2 O 2 production in this distant phylogenic species. The cytotoxicity of M. bovis for EBL cells raised questions regarding the role of eDNA and H 2 O 2 production on its virulence upon replication in the natural host.
, 2008). Remarkably, no GlpO homolog has been identified in M. bovis genome sequences available in databases, suggesting that this species has evolved glycerolindependent mechanisms of virulence  (Bürki et al. , 2015). Recently, the hydrogen sulfide producing cysteine desulfurase/ desulfhydrase HapE of M. pneumoniae was found to promote erythrocyte lysis and to alter the cytokine profile and growth of bronchial epithelial cells  (Großhennig et al. , 2016; Li et al. , 2019b). Previously annotated as a cysteine desulfurase NifS/ SufS, HapE is highly conserved across Mollicutes together with the iron-sulfur cluster assembly scaffold protein (SufU). Whether other pathogenic species are producing hydrogen sulfide is unknown, but the sufS-sufU locus in the ruminant pathogen M. agalactiae was found essential for survival in cell culture and colonization of the animal host  (Baranowski et al.
FUNDING This work was supported by financial supports from  INRA  and  ENVT , and grants from the  National Nature Science Foundation of China (NSFC)  ( 31772745 ),  Wuhan International Science and Technology Cooperation Program  ( 2017030209020258 ),  Special Fund for Chinese Agricultural Research System (Beef/yaks)  ( CARS-37 ), the  Special Fund for National Distinguished Scholars in Agricultural Research and Technical Innovative Team  and the  Fundamental Research Funds for the Central Universities  ( 2013QC001 ).
1/CP007590. 1, respectively. Draft genome sequences of strains 1067 and 8790 are available as whole-genome shotgun projects with accession numbers LAUT01 and LAUS01, respectively. RM16, SA1, SA2, SA5, SA7 are colony- purified isolates originating from the French department number 15 (Cantal; RM16), 44 (Loire-Atlantique; SA1, SA2, SA7), and 85 (Vendée; SA5). SA1 and SA2 were isolated from the same animal (SA1, transtracheal aspirate; SA2, lung sample). These isolates were originaly named as 415 MAE 04 (SA1 and SA2), 413 MAE 05 (SA5), and 453 MAE 06 (SA7).
The high-Alpine ice-core drilling site Colle Gnifetti (CG), Monte Rosa, Swiss/Italian Alps, provides climate records over the last millennium and beyond. However, the full exploitation of the oldest part of the existing ice cores requires complementary knowledge of the intricate glaciometeorological settings, including glacier dynamics. Here, we present new ice-flow modeling studies of CG, focused on characterizing the flow at two neighboring drill sites in the eastern part of the glacier. The3-D full Stokes ice-flow model is thermo-mechanically coupled and includes firn rheology, firn densification and enthalpy transport, and is implemented using the finite element software Elmer/Ice. Measurements of surface velocities, accumulation, borehole inclination, density and englacial temperatures are used to validate the model output.
We calculate backward trajectories and map the catchment areas. This constrains, for the first time at this site, the so-called upstream effects for the stable water isotope time series of the two ice cores drilled in 2005 and 2013. The model also provides a 3-D age field of the glacier and independent ice-core chronologies for five ice-core sites. Model results are a valuable addition to the existing glaciological and ice-core datasets. This especially concerns the quantitative estimate of upstream conditions affecting the interpretation of the deep ice-core layers.
As an alternative approach,  Konrad and others (2013)  used the parallel slab approximation (2D), but with an additional parameter accounting for transversal ice fluxes and constraints from various glaciological and geophysical datasets. Notably, ice-flow modeling studies require adequate knowledge of the glacier geometry. To provide this essential boundary condition, geophysical investigations were extensively conducted at CG since the 1980s  (Haeberli and others, 1988) , providing information on bedrock topography, internal structure (e. g. reflections of isochronic origin) and accumulation distribution  (Eisen and others, 2003; Böhlert, 2005; Bohleber, 2011; Konrad and others, 2013). In this work, we present a new full Stokes ice-flow model of the CG glacier saddle using Elmer/Ice  (Gagliardini and others, 2013).
admin. ch/en/maps-data-online/calculation-services/navref. html). Areal imagery from https://map. geo. admin. ch (here and in the next figures). for enthalpy (here 200 K) and it is assumed that the yearly-averaged surface temperature (T s + T dev ) does not reach the pressure melting-point temperature. Air temperature anomalies T dev (t) are based on instrumental data recorded at weather stations located at the Regina Margherita Hut (4560 m a. s. l. , operated by Arpa Piemonte, http://www. arpa. piemonte. gov. it), Gornergrat and Zermatt (respectively 3129 and 1638 m a. s. l. , both operated by MeteoSchweiz, http://www. meteoschweiz. ch). Instrumental temperature data further back in time (until the year 1901) are taken from the Monte Rosa grid cell of the HISTALP database (5 × 5 arcmin 2 grid;  Auer and others, 2007).
Temperature anomalies are arbitrarily calculated with respect to the mean temperatures recorded after 1982 and the correlation between the different datasets is high. The T dev time series used as input for the model is obtained averaging over all available datasets (see  Fig. 5. 8 in Licciulli, 2018). The data show an increase of atmospheric temperatures at CG of ∼2°C since 1901. The yearly-averaged amount of released latent heat Q lat (t) is estimated by applying a variation of the degree-day model used in  Gilbert and others (2014b)  and previously introduced by Hock (1999): Q lat (t) = aT + (t), (7) where T + (t) is the positive yearly-averaged daily-maximum air temperature and α the melt factor. We are interested in yearly-averaged quantities, since the simulations run with 1-year time steps.
Numerical implementation The ice-flow model is implemented using the open-source FE software Elmer/Ice  (Gagliardini and others, 2013). Among other applications, this software is widely used to investigate small-scale glaciers (e. g. Gagliardini and others, 2011; Gilbert and others, 2015). The mesh used to approximate the model geometry consists of 3088 nodes and 2505 trilinear hexahedrons. The 3-D mesh is extruded from a 2-D mesh of the footprint of the glacier, which has an horizontal resolution of 50 m. We use 16 extrusion layers, which are gradually more closely together approaching the glacier surface. The evolution of the density field is calculated selecting the bubbles stabilization method  (Arnold and others, 1984; Brezzi and others, 1992; Baiocchi and others, 1993). This method was preferred to the discontinuous Galerkin method  (Brezzi and others, 2004) , to avoid density oscillations, especially close to the model boundaries.
Borehole inclination measurements We measured borehole inclination angles at KCC and KCI in September 2016, i. e. 3 and 11 years after drilling, respectively (low accumulation and successive casing guaranteed access to the boreholes for several years). The measurements were performed using the DIgital BOrehole Sensor System (DIBOSS)  (Ryser, 2014; Ryser and others, 2014). Results of the survey are presented in Figs  4a, b. Inclination angles are measured downward, letting the probe down from the top to the bottom of the borehole (blue squares), and upward (red squares). The positioning of the inclinometer probe inside the borehole should be parallel to the borehole walls. Although equipped with centralizers, some of the recorded data show evidence of mispositioning (nonparallel) of the probe and are excluded from the dataset (transparent squares in Fig.