dataesr/scientific-paragraphs-categorization huggingface dataset:
3 with an optical resolution of 176 nm). Alexa 594 and NucBlue were imaged using UV, argon 488 nm and 561 nm lasers. Images were processed with Zen software and analyzed with Icy software. BODIPY 493/503 staining Cells seeded on coverslips were fixed in 4% paraformaldehyde for 10 min at 4 °C and incubated with BODIPY 493/503 (Molecular Probes) at 200 ng/ml and NucBlue ® for 20 min at room temperature. Cells were mounted in fluorescent mounting medium (GBl Laboratory). Acquisitions were performed using an inverted confocal microscope (LSM 710, Zeiss) with an airyscan detector and 340 oil-immersion lens (NA 1. 3 with an optical resolution of 176 nm) and 1. 83 digital zoom. BOD-IPY and NucBlue fluorescence were imaged using argon 488 nm and UV lasers, respectively. Images were processed with Zen and analyzed with Icy programs respectively.
The white-clawed crayfish (Austropotamobius pallipes) is an endangered species in Europe with limited genomic information. Despite its conservation status there is no transcriptomic data available for A. pallipes in public databases. The data here represents the first transcriptome profile of the white-clawed crayfish generated using Illumina stranded RNA sequencing. Pair-end reads were assembled de novo with three separate transcriptome assemblers (Trinity, RNABloom, and RNASpades) followed by transcript assembly reduction and gene reconstruction using the EvidentialGene pipeline. The transcriptome was functionally annotated using Inter-ProScan and genes coding for carbohydrate-active enzymes were identified through the dbCAN2 server.
Data description Stranded RNA sequencing was performed to generate the first de novo transcriptome assembly from the endangered white-clawed crayfish (Austropotamobius pallipes). Sequencing on the HiSeq 2500 generated a total of 58. 88 million raw paired-end 150-bp reads. After Illumina adapter and quality trimming, 54. 77 million paired-end reads longer than 50 bp were retained and subsequently used for de novo assembly. The final non-redundant and contaminant-filtered assembly consists of 79,886 contigs and exhibits a BUSCO transcriptome completeness of 88. 1% (Table  1 ). A total of 18,026 and 11,809 transcripts coded for proteins containing InterProScan protein signatures and Gene Ontology (GO) terms, respectively. A majority of the functionally annotated transcripts with high abundance were associated with muscle function (Table  2 ).
Crayfish, tissue sampling and RNA extraction An adult white-clawed crayfish was collected from a wild population. Approximately 30 mg of abdominal tissue was aseptically dissected and immediately lysed in Buffer RLT provided in the RNeasy mini kit (Qiagen). Total RNA extraction was carried out as per the manufacturer's instructions. Value of the Data First transcriptome dataset for the endangered white-clawed crayfish. High transcriptome completeness will enable its use in phylotranscriptomic studies of decapod crustaceans. The data will facilitate genetic management for the conservation of remaining white-clawed crayfish populations. The data adds to the limited genomic available for this and related species [1,2].
de novo assembly and transcriptome completeness assessment Sequencing quality and yield before and after trimming was assessed using FASTQC v0. 10. 1  [3]. Data were filtered using fastp v0. 20. 0  [4]  that performed adapter sequence and quality trimming. Only reads longer than 50 bp after trimming were used for assembly and transcript abundance quantification. The trimmed paired-end reads were assembled separately with Trinity v2. 8. 5  [5] , RNABloom v1. 1. 0 [6] and rnaSPAdes v3. 13. 0  [7]  using the default setting. These primary assemblies were merged and used as the input for EvidentialGene v2013. 03. 11 (default setting) that performed transcript assembly reduction with coding-sequence classifier  [8]. The reduced assembly was submitted to NCBI Transcriptome shotgun assembly portal to screen for any residual adapter sequence contamination as well as humanderived contigs.
Transcript annotation and abundance quantification The translated coding sequences produced from EvidentialGene were functionally annotated using InterProScan v5. 35e74. 0 [10]. These sequences were also uploaded to the dbCAN2 meta server for automated carbohydrate-active enzyme annotation based on the dbCAN HMMdb v8. 0 database (E-Value < 1e-15, coverage > 0. 35)  [11]. For the quantification of transcript abundance, the final version of the transcriptome assembly was first indexed with Kallisto v0. 46. 0  [12]  followed by pseudoalignment of the trimmed paired-end reads with the "dbias" option activated to correct for sequence-specific, fragment-GC and positional biases.
Total RNA extraction was performed using QIAgen RNeasy mini kit (Qiagen) followed by rRNA removal using the Ribo-Zero rRNA depletion kit (Illumina). The rRNA-depleted RNA sample was subsequently processed with the Illumina TruSeq Stranded Total RNA kit (Illumina) following the manufacturer's instructions. Paired-end sequencing of the constructed library was performed on a HiSeq 2500(2 Â 150 bp run configuration). Data source location 0 23 0 35. 7691 00 E; 46 56 0 10. 6771 00 N Data accessibility Raw data and final assembled contigs were deposited in the NCBI database under the Bioproject PRJNA592270. Additional files such as BUSCO analysis output, Interproscan annotation, transcript abundance estimation and the initial transcriptome assemblies from three separate transcriptome assemblers are available in the Zenodo database (http://doi.
org/10. 5281/zenodo. 3581499) Specifications Table Subject Biology Specific subject area Transcriptomics Type of data Sequencing raw reads, assembly, Table, Figure, How data were Illumina HiSeq 2500 acquired Data format Raw Reads (fastq), Assembly (fasta) Parameters for data rRNA-depleted RNA from the abdominal muscle tissue of an adult specimen was used for library collection preparation and sequencing. Description of data collection.
Human Samples Human blood samples, from five smokers before smoking cessation and five non-smokers, were obtained from Tabacology Unit at CHU UCL Namur asbl, Belgium. Ethical approval for the study was obtained from the ethical committee of CHU UCL Namur Godinne (NUB: B039201316167). Venous blood was collected in a BD Vacutainer ® spray-coated K2EDTA tube. Immediately after collection, the tubes were placed and then stored at -80˚ C until the DNA was extracted using Macherey-Nagel kit (Macherey-Nagel, Nucleobond ® CB 100). Along with the blood samples, four tobacco smoking-related markers were collected as follows: number of cigarettes/day, delay of the last cigarette smoked, measurement of CO level in exhaled air by electrochemistry (Smokerlyser Micro+, SineFuma, Breda, The Netherlands), and urinary cotinine concentration measured by UHPLC with a photodiode array detector (Waters Acquity UPLC H-Class system, Waters Association) and a data acquisition and processing module (Empower 2 Software, Waters Association, Milford, MA, USA).
Analysis of ctDNA treated with single aldehyde UHPLC-MS/MS analysis of untreated ctDNA revealed the presence of a basal level of adducts induced by Acro, AA, FA and HNE. Therefore, levels of AcrodG, HNEdG, as well as both reduced AAdG and FAdG, could only be measured starting at incubation concentrations of 0. 05 mM. Whereas, for the other aldehydes (Croto, MDA, Gx and MG), the increase in the level of induced adducts was noticed from the incubation concentration of 0. 005 mM. In vitro treatment of ctDNA with different concentrations of aldehydes (0. 005 to 1 mM) for 24h in phosphate buffer maintained at 37 °C gave rise to linear dose-response curves for the formation of their stable adducts (Supplementary Data figures 1-9). The concentrations were chosen taking into account the physiological concentrations already reported in humans.
Acknowledgments The authors would like to thank the  Tabacology Unit at CHU UCL Namur asbl, Belgium  for its generosity. Also, the authors express their sincere thanks to  Leila Morcos  for reviewing English language. The authors declare that there is no conflict of interest. direct mutagen formed in model lipid peroxidation reactions as dGuo adducts. Chemical Research in Toxicology, 2006, vol. 19, no. 1, pp. 130-138. MATSUDA T. , TAO H. , GOTO M. , YAMADA H. , SUZUKI M. , WU Y. , XIAO N. , HE Q. , GUO W. , CAI Z. , KURABE N. , ISHINO K. , MATSUSHIMA Y. , SHINMURA K. , KONNO H. , MAEKAWA M. , WANG Y. and SUGIMURA H. Lipid peroxidation-induced DNA adducts in human gastric mucosa. Carcinogenesis, 2013, vol. 34, no. 1, pp. 121-127. MEDEIROS M. H. G. Exocyclic DNA  adducts as biomarkers of lipid oxidation and predictors of disease.
Rather than dividing TG by a fixed factor of 5, the Martin-Hopkins equation requires the use of a 180-cell table to match each patient's TG and non-HDLC with 1 of 180 different factors ranging from 3. 1 to 9. 5, to give a more personalized estimation of VLDLC in mg/dL  [46]. These personalized TG/VLDLC ratios were determined by direct comparison of TG to VLDLC concentrations directly measured after lipoprotein separation by ultracentrifugation in > 10 6 US individuals from the Very Large Database of Lipids Study  [46]. In this database, TG and non-HDLC are the two variables that explained most of the variance in TG/VLDLC  [46]. The novel Martin-Hopkins formula improves the accuracy of cLDLC at various conditions including very low LDLC < 1. 8 mmol/L and in nonfasting samples  [47, 48]. We recommend to use it preferably in the range of TG concentrations 2.
Reference intervals in children and adolescents are available from recent populationbased cohort studies and databases  [92] [93] [94]. Countries are encouraged to establish reference intervals in their local populations, to account for differences in lifestyle and risk factors in different European regions. Ideally, these reference intervals should be regularly updated because significant changes in population lipid concentrations occur mainly related to the substantial increase in unhealthy lifestyle and obesity and changes of analytical methods over time  [95] [96] [97]. In the adoption of published reference concentrations with known biological or analytical sources of variation, the clinical laboratory should verify the reference interval with its own analytical method on 20 samples drawn from its local population under similar pre-analytical conditions  [96, 97].
Financial support Supported by unrestricted educational grants to EAS and EFLM from Merck, Roche Diagnostics, and Denka Seiken. These companies were not present at the Joint Consensus Panel meetings, had no role in the Nonfasting TG, TC, and HDLC were measured by automated assays (Thermo Scientific Konelab, Vantaa, Finland). LDLC was calculated by the Friedewald equation when TG were < 4 mmol/L and was measured directly (Konelab) when TG were ≥4 mmol/L  [3]. Population percentages of men and women are subdivided according to LDLC values above 5 mmol/L (roughly the 95th percentile above which FH should be considered), between 3 and 5 mmol/L, and below 3 mmol/L (the guideline-recommended threshold). Flagging based on reference intervals instead of threshold values should be avoided, as use of reference limits would not flag a majority of LDLC test results (~60%) associated with increased ASCVD risk.
Regulation involving these mechanisms might be complex  24  , and their effects may be invisible to polyadenylated mRNA-based RNA-seq differential expression analyses, such as the present study. Gene ontology (GO) and pathway analyses were performed with 102 orthologous human genes among the 122 S. pistillata nonredundant differentially expressed genes (DEGs), determined by identifying the best BLAST hits against the UniProtKB/Swiss-Prot database. GO terms related to lipid metabolism and small-molecule transport were overrepresented among downregulated genes (i. e. , more present in night samples; Fig. 1d ), and those associated with circadian rhythms, cellular responses to stimuli, and stress and protein stability were overrepresented among upregulated genes (i. e. , more present in day samples; Fig.
Methods Detailed methods for coral total RNA extraction, cDNA synthesis, transcriptomic data processing and spFOXO purification and antibody development are available in Supplementary data. Coral culture. Experiments were conducted with the tropical symbiotic scleractinian species Stylophora pistillata which is kept in long-term culture at the Centre Scientifique de Monaco. Colonies were supplied with water from the Mediterranean Sea (exchange rate 2% per hour) under controlled conditions, including a semiopen circuit, a temperature of 25 °C, salinity of 38, irradiance of 175 µmol photons m -2 s -1 on a 12:12 photoperiod. Corals were fed daily with frozen rotifers and twice a week with artemia nauplii. Microcolonies were propagated by cutting terminal portions of branches (6-10 mm in length) from three syngenic parent colonies, hung by nylon thread with a specific label in a dedicated aquarium under similar conditions, and left for 10 days for recovery prior to experiments.
Acknowledgements We acknowledge the coral culture coral facility at the  CSM  and  Dominique Desgre  for assistance. We are extremely grateful to the IRCAN's facilities: the  Molecular and Cellular Core Imaging (PICMI) and Genomics Core Facility  (supported by le  Cancéropole PACA , la Région PACA, le  Conseil Départementale 06 , l'INSERM,  ARC ,  IBiSA , and the  Conseil Départemental 06 de la Région PACA). We thank  Ryan Mc Minds  for critical reading and English language improvement of the manuscript. This work was supported by  Laboratoires CLARINS.
#3595). Once plated, cells were seeded at 3,000 cells per well. Plates were then imaged once per hour for 100hrs using a 20X objective using an Incucyte Zoom v2016 (Essen BioSciences) kept in standard cell incubation chamber conditions. Raw data Images were collected and analyzed using Incucyte. Graphs were assembled and exported using Graphpad/Prism (version 8).
Acknowledgements We thank the  University of Vermont College of Medicine Microscopy Imaging Center , specifically  D. Taatjes  and  N. Bouffard  for their help using the Asylum Research MFP-3 D BIO atomic force microscope. The microscope was purchased with support from  NIH  award number  S10RR025498  from the  National Center for Research Resources  (to DT). We thank  Alan Howe ,  Robert Bauer  and  Albert van der Vliet  ( University of Vermont ) for their help with AFM data collection and suggestions on Myosin Light Chain detection and  Steven Huth  ( Christian-Albrechts University of Keil ) for his help implementing AFM Hertz fit analysis to our data. We thank  Jan Lammerding  ( Cornell University ) for his generosity with reagents and use of equipment and  Adam Martin  ( MIT ) for his helpful discussions and reviewing the manuscript.
The dataset was supplemented with closely related sequences from GenBank and worldwide reference sequences from De  Crop et al. (2017)  (Table  1 ). Sequences were aligned online in the multiple sequence alignment program MAFFT v. 7  (Katoh & Toh 2008) , using the E-INS-I strategy. Trailing ends were trimmed and the alignment was manually edited where needed in Mega 6  (Tamura et al. 2013 ). The alignment is deposited in TreeBASE (Submission ID 24693). First, the ITS+LSU alignment was partitioned into partial 18S, ITS1, 5. 8S, ITS2 and partial 28S. Both RPB1 and RPB2 alignments were partitioned into the intron(s) and the first, second and third codon positions of the exon. PartitionFinder was used to find the appropriate partitioning scheme  (Lanfear et al. 2017). Maximum likelihood (ML) analyses, using RAxML v.
Acknowledgements The first author was funded by a doctoral scholarship of the  Special Research Fund (BOF , grant  BOF-DOC-2015-007001 ). E. De Crop  is supported by the  'Special Research Fund Ghent University' (BOF , grant  BOF-PDO-2017-001201 ). The collecting trips to the Lesser Antilles (2006 -2015) were financially supported by various organizations and structures such as ONF (French Forestry Office), DIREN, DEAL (Regional counterparts of the  French Ministry for Ecology in Guadeloupe and Martinique ), Regional administrations (Martinique in 2015) and  Regional Parks  ( PNRM -Parc naturel régional de Martinique ). We thank the  Environmental Ministry of Panama (MiAmbiente)  for issuing collection and export permits ( SE/PH-4-18 ,  SEX/H-2-18 ). O. Cáceres,  M. Cuevas  and  J. Rodríguez  are thanked for logistic support during fieldwork in Panama.
Part of the molecular work was funded by the  Laboratoire d' Excellence CEBA  ( ANR-10-LABX-25-01 ) and the  Bibliothèque  du vivant sequencing project. The authors thank  L. Martinez-Suz  and  B. Dentinger  for the DNA extractions of the dried collections from Kew herbarium. The authors would also like to thank  P. -A. Moreau , for his collections and the picture of L. venezuelanus. A. Verbeken wants to thank  J. Perez Moreno  for organizing the fieldtrip in Mexico at the occasion of IWEMM9.
Current-Voltage Recording and Analysis Patch pipettes (5-10) were pulled from Kimax-51 glass capillaries (Kimble 34500; Kimble, Owens-Illinois) using a two-stage puller (Narishige PP-83, Japan). Experiments were performed at room temperature (20 to 22 • C) using standard whole-cell patch clamp techniques, with an Axopatch 200B integrating patch clamp amplifier (Axon Instruments, Inc. , Union City, CA, USA). Voltage commands and simultaneous signal recordings and analyses were assessed by a microcomputer connected to the amplifier via a multipurpose input-output device (Digidata 1320A) using pClamp software (versions 8. 0 and 10; Axon Instruments, Inc. ). After giga ohm seals were formed, the whole-cell configuration was then achieved by gentle suction and the membrane was immediately clamped to a holding voltage (h v ) of -36 mV.
Identification of Candidate Mg 2+ -Dependent Cation Channels in Arabidopsis thaliana Given the data from the physiological experiments, we undertook a search for candidate Mg 2+ -dependent cation channels in plants (Figure  8 ). The residues of the pore and linker regions are underlined in green and yellow, respectively. (B) Structural model of AtCNGC8 based on human HCN1 (PDB accession number 5u6o; for the sequence: see Figure  S2A ). Top panel: side view, with the transmembrane region colored in green, the linker region in yellow, and the cytoplasmic cAMP binding domain in grey. The diacidic motifs (residues E437 and E438 in AtCNGC8) are highlighted as red sphere models. Bottom panel: view from the cytoplasm into the channel (90˚ rotation with respect to top panel). (C) Electrostatic surface representation (color-ramped from negatively charged in red to positively charged in blue) of homology models of AtCNGCs containing the diacidic motif (AtCNGC8 and 6) and of AtCNGC2 (model) and human HCN1 (PDB 5u6o) lacking this motif.
) Alignment of the Arabidopsis thaliana CNGC8 pore region and the Kir2. 2 (PDB accession number 5u6o_341_471). (B) Mechanism of inward rectification by magnesium ions. Tao et al. (Science 2009, 326, 1668-1674) have shown that inward rectification through Mg 2+ can be explained by the ion binding to negatively charged regions in the pore (formed by D173) and in the cytoplasmic regulatory domains (D256 and E300/E225). The crystal structure of the inward rectifying potassium channel Kir2. 2 (Tao, 2009; PDB entry3JYC) is shown in ribbon presentation. The four subunits are color-coded. Potassium ions in the channel are shown as magenta spheres. Negatively charged residues that bind the Mg 2+ mimic Sr 2+ in the crystal structure are shown in pink on their molecular surfaces. (C) Sequences of pore-forming transmembrane helix (TM) from AtCNGCs.
Treatment of hormone-depleted control T47D cells with 17β-estradiol (E2) induced proliferation at 24-72 h, which was blunted by 4OH-Tamoxifen (TMX). By contrast, neoGATA3-expressing cells showed a significantly lower response to E2 (P = 0. 025) (Fig. 5c, d ). WtGATA3-overexpressing cells showed an intermediate phenotype (Fig. 5c, d ). Similar, although less prominent, findings were made using ZR75-1 cells (Supplementary Fig. 8a, b ). This observation was at odds with the enrichment of the two "Estrogen response" Hallmarks genes sets among overexpressed genes in the neoGATA3 tumors from patients. However, the Hallmarks gene sets do not discriminate between up-or down-regulated genes, therefore we performed GSEA on the METABRIC gene expression dataset, using an ad-hoc subset of estradiol-and TMXrelated signatures selected from the MSigDb, with separate up-and down-regulated genes.
However, we did not find evidence for this using multiple methods of analysis. The tumor immune milieu is indeed altered in neoGATA3 tumors, but the exact contribution of the immune infiltrates to their phenotype and whether/how neoGATA3 directly or indirectly influences the tumor microenvironment remains to be understood. Our analyses of patient-derived datasets highlighted the ER-dependent transcriptome as highly altered in neo-GATA3 tumors, in line with the known function of GATA3 as a crucial ER co-factor  [11]. Indeed neoGATA3 expression reduced, but did not fully abrogate, the response to estrogen in two ER + BC cell lines. In particular, we observed a significant reduction of the chromatin-bound ER. In addition, ChIP-Seq revealed that the loss of ER binding was especially pronounced on regions far from the TSS, possibly enhancers.
Acknowledgements We want to thank  G. Timelthaler ,  M. A. Quintela , and  F. Reyal  for valuable contributions,  J. Valcárcel ,  J. Muñoz-Pérez , and  O. Domínguez  for discussions. Funding Work in the lab of PM was supported by the  Institute of Cancer Research of the Medical University Vienna  and by the grant  P27361-B23  from the  Austrian Science Grant (FWF) , FXR was supported by  SAF2011-29530  and  SAF2015-70553-R  grants from  Ministerio de Economía y Competitividad (Madrid, Spain)  (co-funded by the  ERDF-EU) ,  Fundación Científica de la Asociación Española Contra el Cáncer. CNIO is supported by  Ministerio de Ciencia, Innovación y Universidades  as a  Centro de Excelencia Severo Ochoa   SEV-2015-0510. Work in the lab of JSC and CC was supported by  Cancer Research UK. Work in the lab of SRM was supported by the  Spanish Ministry of Science, Innovation and Universities  ( BFU2016-80570-R; AEI/FEDER ,  UE ).
Finally, the study of the biology of rbPSCs makes it possible to understand the maintenance of pluripotency in a model species other than rodents and primates, rabbits being suitable for this purpose due to the accessibility of their early embryonic development. INGESTEM, and the Laboratoires d'Excellence Revive (ANR-10-LABX-73), and by a PhD grant from MEDEZE Foundation (Thailand; for W. S. ).
Real-Time RT-PCR. Quantitative values were obtained from the cycle number (Ct value) at which the increase in the fluorescence signal associated with exponential growth of PCR products started to be detected by the laser detector of the ABI Prism 7900 sequence detection system (Perkin-Elmer Applied Biosystems, Foster City, CA), using PE Biosystems analysis software according to the manufacturer's 2 Analytical Cellular Pathology manuals. The precise amount of total RNA added to each reaction mix (based on optical density) and its quality (i. e. , lack of extensive degradation) are both difficult to assess. Therefore, transcripts of the TBP gene (GenBank accession NM_003194) encoding the TATA box-binding protein (a component of the DNA-binding protein complex TFIID) were also quantified as an endogenous RNA control.
Acknowledgments The results of this manuscript were obtained from the samples used in  Dr. Didier Meseure 's thesis. This work was supported by the  Comité départemental des Hauts-de-Seine de la Ligue Nationale Contre le Cancer  and the  Association pour la recherche en cancérologie de Saint-Cloud (ARCS). We also thank the staff of  Curie Institute-Rene Huguenin Hospital  for their assistance in specimen collection and patient care.