dataesr/scientific-paragraphs-categorization huggingface dataset:
Analysis of GFP::SPT-2 tissue expression For the analysis of the tissue expression of GFP::SPT-2, L4 animals were mounted in M9 buffer with 0. 25mM levamisole on 2% agarose pads. Imaging was performed at 20°C using a microscope equipped with a 63X 1. 25 NA oil lens (Imager M2; Carl Zeiss, Inc. ) and a charge-coupled device camera (Axiocam 503 mono). Nomarski and GFP Z-stacks (2μm/slice) were sequentially acquired using the Zeiss acquisition software (ZEN 3. 1 blue edition). The same LED intensity and acquisition time was used for all images (Nomarski (50%, 20ms), GFP (50%, 100ms)).
Processing of sequencing data ATAC-seq and ChIP-seq reads were pre-processed using trim-galore (version 0. 6. 7; available at https://github. com/FelixKrueger/TrimGalore) and mapped on the C. elegans genome (wormbase release WS285) using bwa-mem (version 0. 7. 17) 72. Reads with mapping quality (MAPQ) higher than 10 were extracted using Samtools 73. ATAC-seq peaks were called by first generating read depth-normalized coverage tracks with MACS2 74 (version 2. 7. 1; settings: --nomodel -extsize 150 -shift -75 --keep-dup all -SPMR -nolambda) and then running YAPC 71 (version 0. 1) using bigwig tracks from both replicates for each condition as input. CeSPT-2 ChIP-seq peaks were called using MACS2 (settings: --SPMR --gsize ce --keep-dup all --nomodel --broad) using the GFP ChIP-seq samples from wild type animals as controls.
The final SPT-2 peak set was defined by the strict intersection of the broad peaks called on each replicate. RNA-seq data were aligned on annotated transcripts (Wormbase release WS285; gene types included: protein coding, lincRNAs and pseudogenes) using kallisto 75 (version 0. 45. 0) to estimate gene expression (in TPM). Coverage profiles were obtained by aligning reads to the genome using STAR 76 (version 2. 7. 1a).
Annotation of CeSPT-2 bound genes A gene was considered a CeSPT-2 target if more than 50% of the length of its longest annotated transcript was covered by a CeSPT-2 peak. The average CeSPT-2 coverage over CeSPT-2 targets was calculated using coverageBed from the BEDTools suite 77 (v. 2. 30. 0). Coverage plots over gene models were produced using the DeepTools suite 78 (version 3. 5. 1).
Analysis of differentially accessible genes (ATAC-seq) We used DiffBind 79 (version 3. 8. 0) to identify genes showing differential accessibility in the spt-2 KO-A and the spt-2 HBM strains compared to the wild type. For this analysis, we had to redefine gene coordinates to avoid overlaps, which would be otherwise merged in DiffBind. The boundaries of the longest transcript for each gene were trimmed to remove overlaps with neighbouring transcripts; if more than 50% of the length of the transcript was trimmed, the whole gene locus was removed from the analysis. Genes were defined as differentially accessible if the |LFC| > 0 and FDR < 0. 05, and their enrichment evaluated at non-CeSPT-2 targets and at CeSPT-2 targets divided in 4 equally-sized groups based on their CeSPT-2 levels.
Differential gene expression We used DESeq2 80 (version 1. 34. 0) to identify genes differentially expressed in the spt-2 KO and the spt-2 HBM strains compared to the wild type. Genes were defined as differentially expressed if the |LFC| > 0 and p. adj < 0. 001. Volcano plots were generated using the EnhancedVolcano R package (available at https://github. com/kevinblighe/EnhancedVolcano). GO-enrichment analysis of differentially expressed genes was performed using clusterProfiler 81. The overlap between genes upregulated in spt-2 and hira-1 mutant 36 was tested using an hypergeometric test.
Fluorescence analysis of human GFP-SPT2 To analyse GFP-SPT2 intensity on chromatin, U-2-OS Flp-In cells grown in 96-well plates (Greiner) were treated with 1μg/ml tetracycline for 24 hours to induce expression of GFPtagged SPT2. Cells were then either directly fixed with 4% paraformaldehyde (10 minutes at room temperature), or pre-extracted for 5 minutes on ice with CSK/0. 5% Triton buffer (supplemented with Roche Complete Protease inhibitor and PhosSTOP Phosphatase inhibitors) to remove soluble proteins, prior to fixation for 10 minutes with 4% paraformaldehyde at room temperature. DNA was stained with DAPI, and images were acquired using a Perkin Elmer Operetta high-content automated microscope (equipped with a 20X dry objective) and analysed using the Perkin Elmer Columbus software.
Statistical analysis The difference of variance between two populations was measured using Prism 9 software, and a Welch's correction was applied when the variances were not equal. p values are provided and defined in the legend of the figure. The multiple comparisons in Fig. 5d  and e  were performed with One-way ANOVA test with Bonferroni's correction. The overlap between genes upregulate in spt-2 and hira-1 mutant worms (Fig. 5g ) was performed using a hypergeometric test.
Acknowledgments We are grateful to members of the  Labib lab  for invaluable advice on recombinant protein purification and C. elegans techniques, and to members of the  Rouse lab  for fruitful discussion. We thank  Constance Alabert  and  Karim Labib  for helpful comments on the manuscript;  Ramasubramanian Sundaramoorthy  and  Tom Owen-Hughes  for the gift of recombinant Xenopus histones;  Bettina Meier  and  Federico Pelisch  for their help with C.
b, Structural homology model for the putative HBD of C. elegans T05A12. 3 (blue). This was generated using the crystal structure of the H. sapiens SPT2 HBD (yellow) in complex with the H3-H4 tetramer (shaded white) as a search template (PDB code 5BS7 25 ). The positions of the aC1 and aC2 helices and the connecting loop are shown. c, Same as d, except that only the CeSPT-2 HBD is shown, colour-coded according to the degree of amino acid conservation. d, Coomassie gel staining of recombinant full-length HsSPT2 and CeSPT-2 produced in bacteria. e, Pull-down of full-length recombinant CeSPT-2 or human HsSPT2 with beads covalently coupled to histone H3-H4 in the presence of 500mM NaCl. One representative experiment of two is shown. f, H3-H4 pull-down with recombinant CeSPT-2 HBD (wild type (WT) or histone binding mutant (M627A)), or HsSPT-2 HBD (wild type (WT) or histone binding mutant (M641A)).
, 2018)  which use more detailed Chinese data. This difference in China has been reduced when CEDS was used to derive future SSP scenarios in CMIP6 simulations (published on ESGF on 28 June 2018 on https://esgf-node. llnl. gov/search/cmip6), and has been included in a post-CMIP6 version of CEDS  (McDuffie et al. , 2020). Of the fourteen models, all output the MMRs of OA, BC, sulfate, dust and sea salt, five output ammonium, and four output nitrate (Table  S1 ). Seven models output the MMRs of total PM2. 5, as the sum over all components with suitable particle sizes. The MMRs are converted to mass concentrations (μg m -3 ) based on air density in each model. In evaluating PM2. 5 components (Sect. 2. 3), modeled OA is converted to organic carbon (OC) to be comparable with the observational dataset.
Satellite-based total PM2. 5 We take satellite-based near-surface total PM2. 5 concentrations from the V4. CH. 03 product of the Washington University Atmospheric Composition Analysis Group  (Hammer et al. , 2020). The dataset is constructed by combining multiple satellite products of AOD with simulations from a chemical transport model (GEOS-Chem) to predict PM2. 5, and then constraining these estimates by ground-level PM2. 5 monitoring. It provides the annual average PM2. 5 concentrations during 2000-2014 with a high spatial resolution of 0. 01° × 0. 01° (~1 × 1 km 2 ). Detailed data descriptions are provided elsewhere  (van Donkelaar et al. , 2019; van Donkelaar et al. , 2016). At a given site, the records are not continuous in time. These records cover varying sampling periods ranging from a few days to several years, although most are monthly data.
5 and its five components over China during 2000-2014, and discuss the likely causes for model errors, and their climate implications. Our assessment helps to understand the capability of the current-generation models in the simulation of aerosols and aerosol-climate interactions, towards further improvement of climate predictions and projections. Our findings are summarized as follows: (1) Twelve of the 14 CMIP6 models tend to underestimate the total PM2. 5 concentrations over China (NMB = -65. 5% to -1. 1%) and the other two models overestimate them (NMB = 17. 0%-39. 2%), as compared to a satellite-based dataset. The seven models that output total PM2. 5 concentrations exhibit underestimation between -47. 9% and -3. 3% over the eastern regions, although four of them capture the observed spatial pattern (R > 0.
Data availability CMIP6 data are available on the Earth System Grid Federation (ESGF) and can be freely downloaded via the website interface https://esgf-data. dkrz. de/search/cmip6-dkrz/ (last access: 8 September 2020, WCRP, 2020). Satellite-derived surface PM2. 5 concentration products can be accessed from the Washington University Atmospheric Composition Analysis Group website as version V4. CH. 03 at https://sites. wustl. edu/acag/datasets/surface-pm2-5/. Observational data used in this paper are provided in the SI, with raw data available upon request to the corresponding author Jintai Lin (linjt@pku. edu. cn).
3 Ground-based PM2. 5 components data https://doi. org/10. 5194/egusphere-2023-2370 Preprint. Discussion started: 16 November 2023 c Author(s) 2023. CC BY 4. 0 License. Since national-scale continuous measurements of near-surface PM2. 5 components are unavailable in China, we collect observational PM2. 5 component data from the literature. Our collected dataset includes 2469 component records of OC, BC, sulfate, nitrate, and ammonium nationwide (627, 66, 645, and 1131 records in western regions, Northeast China, North China, and Central and South China, respectively), as shown in Figure 1. Here a record represents one measured PM2. 5 component at the specific sample site and period. These records cover 30 provinces (including provinces and provincial-level municipalities) and multiple land use types (urban, rural, near the road, and industrial park, etc.
). The dataset does not cover Ningxia, Guizhou, Heilongjiang, and Taiwan. A total of 472, 459, 518, 519, and 501 records are available for OC, BC, sulfate, nitrate, and ammonium over China, respectively. The site locations, sampling periods, data sources, and other information are summarized in the Supplement. Here the satellite-based total PM2. 5 data are re-gridded to 1° × 1° for model evaluation purposes. 2.
Although the spatiotemporal oscillations of the Greenland Ice Sheet (GrIS) during the last millennia have played a prominent role in global environmental changes, its glacial response to the natural variability still needs to be better constrained. Here, we focused on the reconstruction of the glacial behavior and deglaciation process along the Tyroler Valley (74 N, 22 E), within the Northeast Greenland National Park. This NW-SE valley connects with the GrIS via the Pasterze Glacier and divides two ice caps (A. P. Olsen Land and Payer Land), this last one feeding two piedmont glaciers (Copeland and Kløft glaciers). For this study, we combined the interpretation of the spatial pattern of geomorphological features and the chronological framework defined by a new dataset of 15 10 Be cosmic-ray exposure (CRE) ages from glacially polished bedrock surfaces and moraine boulders together with one optically stimulated luminescence (OSL) age of a glaciolacustrine deposit.
| Sample collection Considering the geomorphological map and field observations, we collected 18 samples for 10 Be CRE dating from two types of glacial features (Figure  2 ): moraine boulders (11 samples) and polished bedrock surfaces (7 samples). For each sample, we took approximately 1 kg of the rock's most surficial layer (≤5 cm thick) using a hammer and chisel and recorded the main field data: geomorphological unit, geographical coordinates, elevation, and the measurements for the subsequent geometric correction of the topographic shielding by the surrounding relief. Field data and sample attributes are listed in Table  1. In addition, we also collected two samples for OSL dating from an alluvial fan deposit upstream of the Copeland Glacier front (Figure  3 ). Samples were collected from the upper, middle, and lower parts of this 20-m thick sedimentary deposit composed of fine gravels and coarse sands.
ACKNOWLEDGMENTS This study was funded by the  NEOGREEN  ( PID2020-113798GB-C31 ) and  PALEOGREEN  ( CTM2017-87976-P ) projects of the  Spanish Ministerio de Economía y Competitividad. Field research was also supported by the research group  ANTALP (Antarctic, Arctic, Alpine Environments ;  2017-SGR-1102 ) funded by the  Agència de Gesti o d'Ajuts Universitaris i de Recerca of the Government of Catalonia. Julia Garcia-Oteyza  was supported by an  FPI fellowship  from the  Spanish Ministry of Science, Innovation and Universities , and  Marcelo Fernandes  by a PhD fellowship of the  Fundação para a Ciência e Tecnologia of Portugal  ( UIDB/00295/2020 ). The 10 Be measurements were performed at the  ASTER AMS national facility  (CEREGE,  Aix-en-Provence ), which is supported by the  INSU/CNRS  and the  ANR  through the " Projets thématiques d'excellence" programme for the "Equipements d'excellence "  ASTER-CEREGE  action and IRD.
F I G U R E 6 Probability distribution functions of 10 Be ages with (with external uncertainties) for all the samples of our final accepted age dataset (TYR-09 and TYR-17 were not considered). [Colour figure can be viewed at wileyonlinelibrary. com] the most considerable change is found in the Kløft Glacier, which reached the bottom of the valley in 1937 CE, forming a terminal lobe surrounded by the outermost moraine (Figure 8). Indeed, Google Earth Pro satellite images ranging from 1984 until 2015 (Google Earth Pro 7. 3. 4. 8642 (1984-2015), 74 37 0 31. 99"N, 22 10 0 03. 48 00 , elevation 70 m, LANDSAT/COPERNICUS, [Online]. Available at https://www. google. com/earth/) show that the front of the Kløft Glacier still formed a lobe in the valley floor inside the inner moraines until ca. 2010, when it began to recede upslope.
F I G U R E 9 (a) δ 18 O record of the NGRIP ice core smoothed with 15 interval moving average (GICC05modelext, 5-point running mean; Rasmussen et al. (2006). (b) δ 18 O record of the ice core from Renland Ice Cap in eastern Greenland with 10 interval moving average (GICC05 timescale) (Vinther et al. 2008). (c) NGRIP ice core reconstructed temperature from argon and nitrogen isotopes ( 15 N -40 Ar), with 2σ error bands (gray shading)and 150 interval moving average (Kobashi et al. 2017). (d) Probability distribution functions of our final dataset of exposure ages. [Colour figure can be viewed at wileyonlinelibrary. com].
Acknowledgements This work was supported by the  LabEx PALM  ( ANR-10-LABX-0039-PALM ) as part of  France 2030  programme  ANR-11-IDEX-0003. The authors acknowledge  Cyril Bachelet  and  Jérôme Bourçois  for the proton irradiations using the ARAMIS accelerator at IJClab in Orsay.
ricinus datasets (Figure  2 (b)). The PCoA revealed a significant difference between the viral communities infecting I. ricinus sampled in different biotopes. In Alsace region, the most predominant families were represented by Flaviviridae and Luteoviridae while, in Ardennes region, the most abundant viral families were Nairoviridae and Rhabdoviridae. In Tulcea region, most viral sequences belonged to unclassified Bunyavirales and Hepeviridae families while the Phenuiviridae family was dominant in Iasi. These results may suggest that the collection site is a major factor influencing the composition of tick virome. Among the core virome, apart from sequences belonging to the Phenuiviridae or Nairoviridae families (see below), sequences related to the Peribunyaviridae family mapped onto six novel strains of Bronnoya-like virus (BroBV-like) which were present in all tick pools  [22].
, 2012; Smith et al. , 2014). To circumvent this problem, we expressed BRI1-mCit and BRI1 Q -mCit under the control of the heat shock-inducible promoter (pHS) in the Col-0 background and studied the protein internalization during the recovery phase after a heat treatment at 37ºC for 1 h, which did not affect the endocytic rates of FM4-64 in wild type seedling (Supplemental Figure  S6 ). Firstly, we selected transgenic lines expressing pHS::BRI1mCit and pHS::BRI1 Q -mCit with similar expression levels following the heat induction (37ºC) for 1 h (Supplemental Figure  S2C ). Taking advantage of a vertical confocal microscope setup equipped with the TipTracker software (von Wangenheim et al. , 2017) that allows the monitoring of growing root tips over time, we observed that BRI1 Q -mCit reached the PM a little later than the BRI1-mCit (Figure  3, E  and F ).
Xylem was imaged with Leica SP8X confocal microscope equipped with a HC PL APO CS2 63x/1. 20 n. a. water-corrected immersion objective. The excitation/emission wavelengths used were of 561 nm/600-650 nm for Basic Fuchsin staining with WLL laser intensity of 70 % and gain 180. The BRI1 heat shock lines were analyzed under a vertical ZEISS LSM900 microscope equipped with a Plan-Apochromat M27 20x/ 0. 8 n. a. objective. The excitation/emission wavelengths were 514 nm/530-600 nm for BRI1-mCit with laser intensity of 10 % and gain 660. The root tip was tracked over time with the TipTracker software  (von Wangenheim et al. , 2017). Quantification was obtained by measuring the PM signal of the same cell over time and normalized by the time point with the highest PM signal. Because the heat shock promoter generated a patchy expression pattern, for quantification cells with similar fluorescence intensity were selected.
Right-angle light scattering (RALS) BRI1 ectodomains (residues 1-788 with a C-terminal Avi-tag as well as a TEV protease cleavable TwinStrep -9x His tag) were expressed and purified as described previously  (Hohmann et al 2018b)  and analyzed by size-exclusion chromatography (SEC) paired with a RALS and a refractive index (RI) detector, using an OMNISEC RESOLVE / REVEAL system. The calibration of the instrument was carried out with a BSA standard (Thermo Scientific). In a 50 µl volume, 100 µg of protein was separated on a Superdex 200 increase column (GE Healthcare) in 20 mM sodium citrate, pH 5. 0, 250 mM NaCl at a column temperature of 35°C and a 0. 7 ml/min. Data were analyzed using the OMNISEC software (v10. 41).
Homology modeling and structure visualization BRI Q ectodomain structure was modeled using the Modeller 9. 18 program  (Šali and Blundell, 1993)  with the BRI1 ectodomain (PDB ID 3RJ0) as a template. The structures of wild type BRI1 and BRI1 Q ectodomains (Figure  1 ) were visualized by UCSF Chimera  (Pettersen et al. , 2021). Multiple sequence alignment was prepared using the Jalview program  (Waterhouse et al. , 2009).
ACKNOWLEDGMENTS We thank  Yanhai Yin  ( Iowa State University, Ames, USA ),  Gregory Vert  ( CNRS/Université de Toulouse, France ),  Cyril Zipfel  ( University of Zurich, Switzerland ) and  Yasin Dagdas  ( Gregor Mendel Institute, Austria ) for providing the anti-BES1 antibody, the pBRI1::  BRI1-mCit/bri1  Arabidopsis transgenic line, pDONRP4P1r-pBRI1, pDONRP1P2-BRI1 and pDONRP2rP3-mCit.
Methods: We performed a single-center, retrospective study based on a prospectively collected database in a tertiary cardiac surgery center. Using logistic regression, we assessed risk factors of PFO finding around surgery and subsequent clinical complications. Results: Between January and July , patients who underwent cardiac surgery in our center were included. A total of patients (. %) presented a finding of PFO including per-operative disclosures and post-operative finding for hypoxemia. In the whole cohort, the mean age was. ±. years including. % of men. Post-operative PFO finding was associated with more ischemic strokes compared with per-operative finding and control group [ (. %) vs. (. %) vs. (. ), respectively; p =. ]. Moreover, patients with post-operative PFO reopening experienced a higher rate of pneumonia, reintubation, and longer length of stay in the ICU.
Methods We conducted a single-center retrospective cohort study, from a prospectively collected database. We included all patients aged more than 18 years who underwent cardiac surgery with cardiopulmonary bypass, from June 2007 to July 2019. Patients who died during surgery were not included in the analysis, considering that the main goal was to explore postoperative outcomes. All data are part of the Registry for the Improvement of Post-operative OutcomeS in Cardiac and Thoracic Surgery (RIPOSTE) database (https://clinicaltrials. gov/ ct2/show/NCT03209674)  (21) (22) (23) (24). Abbreviations: PASP, Pulmonary arterial systolic pressure; PFO, Patent foramen ovale; ICU, Intensive care unit. This registry systematically collected pre-operative variables of patients, allowing them to compute risk scores, and also collected surgical procedure information (including the type of procedure and circulatory bypass information) and post-operative clinical outcomes with a follow-up extended until discharge from the hospital.
Statistical analysis Continuous variable distribution was assessed using the Shapiro-Wilk test. They were expressed as mean ± standard deviation when satisfying normal distribution, and median [interquartile range] otherwise. Categorical variables were expressed as numbers (percentages). The Chi-2 or Fisher exact tests were used to compare categorical variables. Comparisons of continuous variables were performed by two-way ANOVA for repeated measurements followed by paired Student ttests with Bonferroni correction if needed, or by Friedman test followed by Wilcoxon tests if needed, according to data distribution. To assess the association between PFO reopening and ischemic strokes, we used multivariable logistic regression models constructed with a stepwise mixed method with a pvalue entry threshold of 0.
Yet, Krasuki et al. reported data from a large database with systematic research of PFO and with a high rate of peroperative closure (28%). Our study design differs because we reported here only the outcomes of patients with the decision of per-operative closure or with the post-operative finding of PFO but not the incidence and outcomes of pre-operative PFO disclosure. Patent foramen ovale has already been described as an important risk factor for stroke  (7, 8) ; with a correlation among the size of the PFO, the number of microbubbles during the bubble test (and therefore the importance of the shunt), and the risk of embolism  (29). Stroke is a frequent event after cardiac surgery affecting ∼1-5% of patients, leading to disability and higher post-operative mortality  (30) (31) (32). In our study, the post-operative stroke rate was 2.
Moreover, despite systematic pre-operative echocardiography, there was no standardized pre-and post-operative screening protocol for PFO, and the presence of pre-operative PFO was not reported in the database, so the incidence of PFO was probably underestimated. Therefore, we only reported PFO found and closed during surgery, as well as PFO revealed in the post-operative setting. Moreover, the screening of PFO mainly in patients with hypoxemic post-operative may have overestimated the association with other causes of hypoxemia (pneumonia and reintubation). Third, another major issue is that we are unaware of what medications our patients were taking before or after surgery. We did not report the use and the effects of stopping or starting treatment as anticoagulation and anti-platelet therapy on the risk of stroke.