dataesr/scientific-paragraphs-categorization huggingface dataset:
1A ). However, after 7 dpi, the levels of these two proteins were not different to that of uninfected cells, but then the enzyme NADH-cytochrome B5 reductase (ISCW021232) was underrepresented in infected cells (Fig. 1A ). The absence of correlation between the changes in mRNA and protein levels is a well-known phenomenon described in many other systems  [37] [38] [39] [40] [41] [42] [43] [44]. In the context of A. phagocytophilum infection, this mismatch could be due, among other reasons, to delay between transcription and translation and/or the role for post-transcriptional and post-translational modifications in tick cells  [16] [17] [18] 36. The datasets used in this analysis on the tick transcriptomics (i. e. midguts, salivary glands and ISE6 cells) and proteomics (i. e. midguts and salivary glands) response to A.
ESI ionization was done using a Nano-bore emitter Stainless Steel ID 30 μm (Proxeon) interface. Peptides were detected in survey scans from 400 to 1600 amu (1 μscan) with Orbitrap resolution set at 30. 000, followed by twenty data dependent MS/ MS scans (Top 20), using an isolation width of 2 u (in mass-to-charge ratio units), normalized collision energy of 35%, and dynamic exclusion applied during 30 s periods. The MS/MS raw files were searched against a compiled database containing all sequences from Ixodes scapularis proteome and Anaplasma phagocytophilum taxonomy (20,473 and 21,920 Uniprot entries, respectively, in March 2019) (http://www. uniprot. org) using the SEQUEST algorithm (Proteome Discoverer 1. 4, Thermo Fisher Scientific, Waltham, MA, USA). For database searching, parameters were select as follows: trypsin digestion with 2 maximum missed cleavages, tolerances of 800 ppm for precursor ions and 0.
8 Da for fragment ions, and variable modifications of Met oxidation and Cys carbamidomethylation. Searches were also performed against a decoy database in an integrated decoy approach. A false discovery rate (FDR) < 0. 05 was considered as condition for successful peptide assignments and at least two peptides per protein in at least one of the samples analyzed were the necessary condition for protein identification (Table  S2 ). Two biological replicates were used for each uninfected and infected tick cells and two technical replicated were run per sample. For the quantitative analysis of tick proteins, after discarding Anaplasma proteins in infected cells, the total number of peptide-spectrum matches (PSMs) for each tick protein was normalized against the total number of PSMs in tick cells and compared between uninfected and infected cells by Chi2-test (P < 0.
05). The mass spectrometry proteomics data have been deposited at the PeptideAtlas repository (http://www. peptideatlas. org/) with the dataset identifier PASS01351. characterization of the I. scapularis mRnA and protein levels in response to A. phagocytophilum infection. The quantitative transcriptomics data for uninfected and A. phagocytophilum-infected I. scapularis female midguts and salivary glands and ISE6 cells were obtained from previously published results  33, 36. Quantitative proteomics data for uninfected and A. phagocytophilum-infected I. scapularis female midguts and salivary glands was obtained from previously published results  33. Data deposited at the Dryad repository database, NCBI's Gene Expression Omnibus database and ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002181 and doi: 10.
6019/PXD002181. The genes identified in the tick ROS metabolic pathways were searched against the transcriptomics and proteomics data to characterize their mRNA and protein levels in response to A. phagocytophilum infection. Transfection of ISE6 and differentiated HL-60 cells. Before transfection, HL-60 cells were differentiated to a neutrophil phenotype by culturing the cells in medium supplemented with 1. 3% DMSO for 5 days  60, 61. The human isolate of A. phagocytophilum (strain NY-18) was used to infect human and tick cells as described previously  33, 57, 59. On the day of transfection, approximately 1 × 10 5 cells per well were plated out in 0. 5 ml of complete media. For each well to be transfected, 500 ng of pLPCX-roGFP2-Orp1 plasmid DNA  62  were diluted in 100 µl of Opti-MEM ® (Gibco, Waltham, MA, USA) without serum.
Images were saved as 16-bit tif files and processed by ImageJ software. Background was substracted using the rolling ball procedure set to 50 pixels. Pictures were then converted to 32-bit format. A ratio image was created by dividing the 405 nm image by the 488 nm image pixel by pixel and displayed in false colors using the lookup table "Fire" as previously described  65. Pharmacological studies in ISE6 tick cells. ISE6 tick cells uninfected and infected with A. phagocytophilum were left untreated or treated for 2 and/or 7 days with 2 μM Antimycin A (AA; Sigma-Aldrich, St. Louis, MO, USA) to inhibit Ubiquinol/cytochrome c oxidoreductase  53  , 100 μM 4-Hydroxy-2-nonenal (4-HNE; Invitrogen, Carlsbad, CA, USA) to inhibit Thioredoxin-reductase  52  , and 10 μM N-acetyl cysteine (NAC; Sigma-Aldrich), a free radical scavenger antioxidant agent that reacts with ROS such as H 2 O 2 and OH-  [45] [46] [47].
All samples were analyzed on a FAC-Scalibur flow cytometer equipped with CellQuest Pro software (BD Bio-Sciences, Madrid, Spain). The viable cell population was gated according to forward-scatter and side-scatter parameters. The level of ROS in the viable cells was determined as the median fluorescence intensity (MFI). Results were compared between groups by Student's t-test with unequal variance (P < 0. 05; N = 4 biological replicates). For immunofluorescence microscopy, mt from uninfected and infected tick ISE6 and human HL-60 cells were stained with Mitotracker Red (Thermo Scientific, Waltham, MA, USA) and then fixed with 4% paraformaldehyde in PBS for 20 min at room temperature (RT). After washes in PBS, cell smears were prepared using a cytocentrifuge, then mounted in ProLong Antifade with DAPI reagent (Molecular Probes, Eugene, OR, USA) and examined using a Zeiss LSM 800 laser scanning confocal microscope (Carl Zeiss, Oberkochen, Germany) with x60 oil immersion objectives.
Acknowledgements MV was supported by  Research Plan of UCLM. PA was supported by the  Junta de Comunidades of Castilla-La Mancha (JCCM, Spain). We thank  Ulrike Munderloh  ( University of Minnesota, USA ) for providing the I. scapularis embryo-derived tick cell line ISE6, and  Katherine M. Kocan  and  Edmour F. Blouin  ( Oklahoma State University, USA ) for technical assistance and fruitful discussions.
Data Availability Quantitative transcriptomics and proteomics data for uninfected and A. phagocytophilum-infected I. scapularis female midguts and salivary glands, and ISE6 tick cells are available at the Dryad repository database, NCBI's Gene Expression Omnibus database and ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD002181 and doi: 10. 6019/PXD002181.
One project about the relationships between biodiversity and infectious diseases has been funded FRB in this context, and it was led by Jean-François Guegan (France) working with 11 other scientists from France, the USA, Italy and Mexico. Bringing together ecologists, public health scientists, veterinarians, modelers and parasitologists working in four different regions of the world, this project addressed three major issues: (1) which life-history characteristics may confer to hosts a better capacity to be 'good vessels', (2) how do we quantify the parasites' capacity to cross species boundaries; and (3) what is the role of biodiversity in transmission of infectious diseases on different spatial scales. Deliverables were databases, disease modelling, reviews and exploratory articles, actionable public health policy information shared with health-protection agencies and the media; and training of young scientists in this new research.
Data and methodology During RV Meteor cruise M111 wide-angle refraction seismic data were acquired simultaneously with multi-channel seismic reflection seismic (MCS) data. Profile DY-05 is 131 km long and crosses the IAP from SW to NE (red line in Fig. 1 ). The location of the line was chosen to cover the area of the IAP that is neither affected by the emplacement of volcanic structures (Medina seamounts in the south) nor by the advancing thick accretionary prisms of deforming sediment in the north and east in order to gain an "unobstructed view" into the deep IAP crust and lithosphere. The central part of the profile was covered by eight sea-floor stations (OBH501-OBS508) with a spacing of 7. 4 km. Shooting (946 shots) was extended for ∼ 40 km beyond the first and last instrument, respectively, in order to record long offsets from shots travelling through the subsurface.
An airgun array consisting of six G-gun clusters with a total volume of 84 L (5440 cu in) at 210 bar was fired at a 60 s shot interval. Data quality was very good and arrivals were recorded over the entire profile length. Mantle phases, PmP reflections, and Pn phases were recorded on all stations. A mini-streamer with four channels spread over an active length of 65 m was towed at a depth of 8 m between the airguns. For each channel, six hydrophones with a distance of 0. 5 m were grouped together. The streamer served two purposes: it was used to control the correct functioning of the airguns and to provide information on the uppermost sedimentary structures in regions where sea-floor roughness does not cause aliasing. A medium gun delay of 78 ms could be identified, with one gun firing out of sequence, as recognized on the streamer data near trace 800 in Fig.
Methodology and modelling strategy By developing a velocity model for profile DY-05 we targeted the structure of the sedimentary strata, the crust, and the uppermost mantle. This was achieved by forward modelling of the observed travel times using the ray-tracing software RAYINVR  (Zelt and Smith, 1992; Zelt and Forsyth, 1994). It runs on the graphical user interface MODELING  (Fujie et al. , 2008). Travel times were picked using the software PASTEUP  (Fujie et al. , 2008). Attempts to apply tomographic inversion approaches failed due to the presence of a thick low-velocity zone. The final forward model (Fig. 4 ) was developed starting with the water layer and progressing starting at the basement and extracted from the final velocity model every 10 km according to the coloured sections. Observed velocities are compared to oceanic crust (red grey ensemble)  (Grevemeyer et al.
6 ). A finite-difference scheme for the solution of the elastic isotropic wave equation from  Hestholm et al. (1994)  was used to calculate the synthetic data for a 2-D structure. The input velocity model had a grid cell size of 50 m. The seismogram was computed with a P -wave source frequency up to 30 Hz, while a 2 ms time step was chosen. No random noise was added. 4 Interpretation and results.
During RV Meteor M111 cruise, wideangle refraction seismic data (DY-01) were acquired along CROP M3  (Dellong et al. , 2018). In this study the deeper crustal structures along the profile could be better resolved and the authors proved that oceanic crust has been subducted into the CA. -  De Voogd et al. (1992)  analysed the ESP5 data from a two-ship experiment in the vicinity of OBS502. We find similar results for the shallow part of the models (Fig. 7b ), while the deeper portions vary regarding the depth of the layers. The crustal thickness at ESP5 is about 8 km versus 6 km at OBS502 along profile DY-05. The lower crust has a similar thickness for both experiments. We observe a seismic mantle velocity of 7. 8 km s -1 at the crust-mantle boundary that is increasing with depth in at least the upper 2 km below the Moho, while the studies of the ESP5 experiment (de Voogd et al.
Acknowledgements. The cruise M111 of RV Meteor was funded by the  Deutsche Forschungsgemeinschaft (DFG)  with additional support from  GEOMAR. Our special thanks go to the captain and crew of RV Meteor for their excellent support at sea. We thank  Alina Polonia  and  Eline Le Breton  for their detailed and helpful reviews to improve the paper. The article processing charges for this open-access publication were covered by a  Research Centre of the Helmholtz Association.
Research Evidence About the Effectiveness of the Proposed Pedagogies There is an emergence of literature that uses formative analytics to support SRL and to understand how students are setting goals and solve computer-based tasks  (Azevedo et al. , 2013; Winne, 2017). For example, using the software tool nStudy  (Winne, 2017)  recently showed that trace data from students in forms of notes, bookmarks, or quotes can be used to understand the cycles of self-regulation. In a study of 285 students learning French in a business context, using log-file data  (Gelan et al. , 2018)  found that engaged and self-regulated students outperformed students who were "behind" in their study. In an introductory mathematics course amongst 922 students,  Tempelaar et al. (2015)  showed that a combination of self-reported learning dispositions from students in conjunction with log-data of actual engagement in mathematics tasks provide effective formative analytics feedback to students.
An animation is provided online as supporting information (ms01. mp4) that depicts the horizontal scales resolved at the OSMOSIS mooring site and contrasts these with mesoscale motions, as seen by satellite altimetry. Additionally, the central mooring housed an acoustic instrument capable of measuring dissipative turbulence at approximately 50-m depth and that remained within the OSBL from December 2012 to April 2013. These data are complemented by reanalyses of winds, waves, and heat and precipitation fluxes, or hereafter buoyancy fluxes. Here, we use these data in concert with existing and in some cases new turbulence parameterizations to help understand the relative contributions of submesoscale processes to energy dissipation in the open-ocean environment. The study is outlined as follows.
Data Sets 2. 1. 1. OSMOSIS Observations The OSMOSIS moored array consisted of nine moorings: four inner, four outer, and a single central mooring. Inner moorings were spaced approximately 2 km apart, while outer moorings were spaced approximately 14 km apart (Figure  2b ). Additionally, inner moorings were more heavily instrumented, with paired conductivity-temperature-depth (CTD) sensors and acoustic current meters located every 50-100 m, starting at approximately 50-m depth. Finally, a 600-kHz acoustic Doppler current profiler (ADCP) mounted on the central mooring enabled us to estimate dissipative (i. e. , meter-scale) turbulence for an entire year. This approach assumes a functional form for the structure function of velocities measured by the instrument and inverts a regression of the data to this functional form to obtain dissipation rate (supporting information)  (Lucas et al.
Ocean-Atmosphere Reanalysis: ERA5 While meteorological observations exist for a portion of this year-long deployment period, we have limited knowledge of the marine boundary layer except from that given by atmospheric and wave reanalysis. Here, we have opted to supplement ocean observations with reanalyses from the European Centre for Medium-Range Weather Forecasts referred to as ERA5 (https://www. ecmwf. int/en/ forecasts/datasets/archive-datasets/reanalysis-datasets/era5). These data are expected to provide improvements over existing reanalysis data  (Dee et al. , 2011)  (https://www. ecmwf. int/en/newsletter/150/news/ era5-aids-forecast-performance-monitoring). The atmospheric products consist of hourly winds, waves, and ocean-atmosphere buoyancy fluxes (i. e. , heat and precipitation fluxes) from which surface and Ekman buoyancy fluxes, B o and B e respectively, were estimated  (Cronin & Sprintall, 2001; Stull, 1988; Thomas & Lee, 2005).
Forryan, personal communication, May 2015) but which were unfortunately unavailable for the presently examined period. (Data accessible from the Porcupine Abyssal Plain website, a EuroSITES observatory [http://projects. noc. ac. uk/pap/]) Finally, we also obtained historical reanalysis of wave forecasts from ERA5. These data are at coarser horizontal resolution but were used to parameterize dissipation due to both breaking waves and Langmuir turbulence.
, 2017)  (also https://www. mercator-ocean. fr/en/science-publications/glorys/). Boundary conditions at the ocean-atmosphere interface use the Drakkar Forcing Set DFS5. 2 (https://sextant. ifremer. fr/record/c837b2f8-4152-41fd-8592-d4cd887d0b51/), which is based on ERA-interim reanalysis  (Dee et al. , 2011). The version of NATL60 used in our study is not forced by tides. In our study, we seek to better understand dissipation rates in the open ocean resulting from surface and submesoscale processes. We obtained 1 year of high-resolution model output from the NATL60. Using ERA5 reanalysis, we computed the same forcing terms as from the observations. For example, we used the ERA5 data to provide winds, waves, and surface fluxes. From these, we calculated the dissipation due to winds, waves, and buoyancy-forced convection.
Spatial Resolving Capability of OSMOSIS and NATL60 Data Sets The spacing of OSMOSIS moorings was specifically designed to resolve submesoscale fronts and eddies within the OSBL while simultaneously preventing entanglement of moorings over the year-long deployment. Similarly, as stated above, the model was designed to resolve submesoscale dynamics in anticipation for the SWOT satellite altimeter mission. While not the focus of this study, it is worth considering the resolving capability of these data sets to determine to what extent the observation and model data can resolve the relevant horizontal scale. The relevant horizontal scale is here argued to be the ML deformation radius. Submesoscale fronts and eddies have been shown to be characterized by horizontal e-folding scales consistent with the ML baroclinic Rossby deformation radius.
Given a grid spacing of 1 km at the site location, we therefore expect that the effective resolution of NATL60 is about 8 km (wavelength). However, rationalizing one can resolve two eddies of opposite polarity (e. g. , sea surface temperature or sea surface height anomaly) within a single wavelength, we estimate that NATL60 model resolves eddy-like structures with diameters near 4 km. This is slightly larger than the diameter of submesoscale eddies observed during winter. Thus, relative to the OSMOSIS moorings, we expect NATL60 resolves scales larger than those resolved by the inner moorings but smaller than those resolved by the outer moorings. This is consistent with statistical comparisons of lateral buoyancy and velocity gradients at the OSMOSIS mooring site. The aforementioned discussion concerns the horizontal resolving capability of these data sets.
We focused on histone modifications associated with active promoters (H3K4me3, H3K9ac, H4ac, and H3K27ac) and active enhancers (H3K4me1 and H3K27ac) as well as repressive Polycomb-dependent marks (H3K27me3 and H2AK119Ub). All nChIP-seq datasets were sequenced to a depth of at least 40 million reads and showed a high signal-to-noise ratio (Figures  S1B  and S1E ). The reads were split according to content of allele-specific SNPs (B6, mapping to Xi; Cast, mapping to active X); this allelic information was then analyzed in detail to define XCI-specific changes. Histone Deacetylation Is One of the Earliest Events during Initiation of XCI Upon Xist coating, the Xi becomes rapidly depleted of active histone modifications. Although this global loss of euchromatin occurs in a similar time window as the changes in X-linked transcriptional activity  (Chaumeil et al.
, 2002) , the precise chronology and possible mechanistic relationship of these two events have remained unclear. To address this, we first analyzed nChIP-seq datasets for a panel of active histone modifications  (H3K27ac, H3K4me1, H3K4me3, H3K9ac, and H4ac; Figure S1E). This revealed progressive depletion of B6-specific reads (originating from Xi) upon Xist induction, with different marks showing different kinetics of loss (Figure  S1D ). To analyze this in detail, we performed peak calling on all the reads (STAR Methods). For each peak with at least 50 allele-specific reads, we calculated its d-score (reads B6 /[reads Cast + reads B6 ]). This parameter of allelic skewing uses the active X chromosome as a powerful internal control, rendering the analysis less sensitive to variability in nChIP-seq quality and, thus, more stable between replicates.
Histone Deacetylation Is Tightly Linked to Transcriptional Silencing To gain insight into the relationship between loss of active chromatin marks and transcriptional silencing of X-linked genes, we compared our nChIP-seq dataset with transient transcriptome sequencing (TT-seq;  Schwalb et al. , 2016). This allows a direct measure of newly synthesized RNA and, thus, enabled us to measure transcriptional activity as the X chromosome becomes inactivated. Comparison of the IC35 for TT-seq and individual histone modifications at associated promoters revealed that transcriptional silencing dynamics are most tightly linked to promoter deacetylation at H3K27 and, to a lesser extent, to loss of H4ac, H3K9ac, and H3K4me3 (Figures  2A  and 2B ; Figure  S2A ). A similar pattern of gene silencing and promoter deacetylation dynamics further exemplifies this correlation (Figure  2C ).
PRC1-Dependent H2AK119Ub Accumulation Precedes H3K27me3 Deposition Repressive chromatin modifications are also known to appear shortly after Xist RNA coating, in particular H2AK119Ub (PRC1-dependent) and H3K27me3 (PRC2-dependent). However, the early dynamics of this process, as well as the relative timing of H3K27me3 and H2AK119Ub deposition, have remained largely unexplored. To address this question, we have performed nChIP-seq for both PcG-dependent marks. These datasets showed a reproducible and stable pattern of enrichment on autosomes, both between time points and biological replicates (Figure  S6A ). In contrast, the X chromosome showed a bias in H2AK119Ub enrichment toward the B6 allele (Xi) after 4 hr of DOX induction and after 8 hr in the case of H3K27me3 (Figure  S6B ). First, we analyzed relative B6-read enrichment within 10-kb windows across the whole X chromosome normalized to t = 0 hr and observed rapid deposition of H2AK119Ub (A) IF/RNA FISH on TX1072 (Hdac3 +/+ ) and two Hdac3 À/À ESC clones induced with DOX for 24 hr.
We also investigated genes that normally escape from XCI (constitutive) or escape more variably and in specific tissues (facultative escapees)  (Disteche and Berletch, 2015). We examined a highly expressed constitutive escapee (Kdm6a; Figures  6F  and 6G ) and found no PcG-dependent mark accumulation at its promoter or gene body in our dataset. In line with this, both constitutive and facultative escapees show no or lower accumulation of H2AK119Ub and H3K27me3 at their gene bodies (Figures  S6J  and S6K ). This is consistent with significantly delayed H3K27ac loss at their promoters (Figure  S6L ). Thus, genes escaping transcriptional silencing do not undergo promoter deacetylation and do not accumulate PcG-associated marks. All in all, our analysis reveals the hierarchy of PcG marks during XCI, with H2AK119Ub accumulating significantly prior to H3K27me3.
65) with options [REMOVE_DUPLICATES = true] (https://broadinstitute. github. io/picard/) and reads mapped on blacklisted regions from Encode Consortium were discarded. SNPSplit (0. 3. 2)  (Krueger and Andrews, 2016)  was then used to generate allele-specific BAM files by separating the alignment into two distinct alleles (CAST and B6) based on SNPs information downloaded from Sanger. Bigwig files were created with bedtools genomeCoverageBed (2. 25. 0) (Quinlan and Hall, 2010) , using a scale factor calculated on the total library (10. 000. 000/total reads) for both allele specific bigwigs, and loaded on UCSC genome browser. Analysis of active histone marks (H3K27ac, H4ac, H3K9ac, H3K4me3, H3K4me1) Peak identification Peak calling was done with MACS2 (2. 0. 10)  (Zhang et al. , 2008)  with options [--broad -B -f BAMPE --broad-cutoff 0.