dataesr/scientific-paragraphs-categorization huggingface dataset:
GWA mapping Analogous to previous successful GWAS studies using 200-300 diverse Arabidopsis accessions  [52] [53] [54] [55] [56]  , 231 diverse natural accessions (12 plants/accession were planted) were grown on 1× MS agar plates containing 300 μM Ferrozine under long day conditions (16 h light) at 21 °C. Plant images were acquired by EPSON flatbed scanners (Perfection V600 Photo, Seiko Epson CO. , Nagano, Japan) every 24 h for 5 days (2 DAG-6 DAG). Root image analyses and trait quantification were performed using the BRAT software  57. Median root growth rate (n ≥ 3) values between 4 to 5 days were used for GWA study. For more accuracy, the roots not detected or not germinated were not included in the analyses. Population structure corrected GWA mapping was conducted using AMM with the 250 K SNP dataset (by using the GWAS pipeline implemented on https://gwas.
gmi. oeaw. ac. at/)  58. For population structure control, this webservice uses an identity by state (IBS) genetic relatedness matrix, first a priori for the full genotype dataset and then by removing the contributions of SNPs of accessions that are not contained in the GWAS trait dataset. SNPs with minor allele counts equal or greater to 10 were taken into account. To control for false positives, we used a 5% FDR threshold calculated by the Benjamini-Hochberg-Yekutieli method to correct for multiple testing  59. The GWAS peak in proximity of SRF3 (Fig. 1a ) contained 4 significant SNPs. By analyzing the unique combinations of these 4 SNPs in the 231 accessions, four groups of haplotypes were defined as Group A, Group B, Group C, and Group D.
SRF3 transcript expression by RT-PCR Total mRNA was extracted from wild type, and three insertions each of: pUBQ10::SRF3-mCITRINE, pUBQ10::SRF3 KD -mCITRINE, and pUB-Q10::SRF3 ΔExtraC -mCITRINE using Sigma-Aldrich Spectrum Plant Total RNA Kit. cDNA was produced using Applied Biosystems (by Thermo Fisher Scientific) High-Capacity cDNA Reverse Transcription Kit. The expression of SRF3 and the ubiquitous TCTP transcripts was tested by PCR using primers starting with "RT" in Data S6.
FRAP experiment Fluorescence in a rectangle ROI (50 μm 2 , 15 μm long), in the plasma membrane region, was bleached in the root optical section by four successive scans at full laser power (150 W) using the FRAP module available on the Zeiss LSM 880 Airyscan 2. Fluorescence recovery was subsequently analyzed in the bleached ROIs and in controlled ROIs (rectangle with the same dimension in unbleached area). FRAP was recorded continuously during 90 s with a delay of 0. 3 s between frames. Fluorescence intensity data were normalized using the equation: I n = [(I t -I min )/(I max -I min )] × 100 where I n is the normalized intensity, I t is the intensity at any time t, I min is the minimum intensity postphotobleaching, and I max is the mean intensity before photobleaching. For visualization, kymographs were obtained using kymograph function in Fiji.
Acknowledgements We thank  Y. Belkhadir ,  B. Lacombe ,  I. Helariutta , and all the  Busch lab members  for critical discussions. Y. Jaillais  for sharing cloning materials,  F. Berger  for providing H2B in PDONR P1P2,  J. B. D. Long  for providing SV40,  Y. Benitez-Alfonso  for providing 35s:PdBG1-mCITRINE line,  I. Helariutta  for providing feedback on the manuscript and sharing 35s: GFP-CALS3 , cals3-3d, and cals3-6 as well as  R. Stadler  for providing 35s:DRONPA-s line. J. Y. Lee  for providing 35s::PDLP5-GFP line. E. Bayer  for providing pPDLP3::PDLP3-YFP and pSUC2::GFP lines. pCYP72A::GUS line was kindly provided by  Y. Belkhadir. We thank,  T. Zhang  and the  Salk Biophotonics core team  for microscopy advance and assistance in quantification. We thank the Salk peptide synthesis core especially  Jill Meisenhelder  and finally  Br.
Moussu  for thoughtful discussion. We would like to thank  N. Gibbs  and  C. N. Miller  for their careful reading of the manuscript. This study was funded by the  National Institute of General Medical Sciences  of the  National Institutes of Health  (grant number  R01GM127759  to  W. Busch ), a grant from the  Austrian Science Fund  ( FWF I2377-B25  to  W. Busch ), funds from the  Austrian Academy of Sciences  through the  Gregor Mendel Institute (W. Busch) , and start-up funds from the  Salk Institute for Biological Studies  ( W. Busch ). M. P. Platre was supported by a long-term postdoctoral fellowship ( LT000340/2019  L) by the  Human Frontier Science Program Organization. R. A. and J. E. P. were supported by The  Max-Planck Society and Germany's Excellence Strategy CEPLAS  ( EXC-2048/1 , Project  390686111 ).
The reaction volume was adjusted to 25 μL with PCR grade water. Triplicate PCR products were pooled and purified using the Geneclean Turbo kit (MP Biomedicals). Partial adapters were added by ligation at the sequencing facility (Genewiz) and llumina MiSeq 2 × 300 paired end sequenced. Demultiplexed paired-end sequences were dereplicated, denoised, assembled and chimeras discarded using the DADA2 pipeline  [34]. 10,923 to 34,844 reads were obtained per sample (23,361 reads/ sample on average). In total, >1. 8 millions of high quality nifH sequences were obtained resulting in 1566 ASVs (Amplicon Sequence Variants). ASVs were annotated down to the genus level using a DADA2 formatted nifH gene database (https://github. com/moyn413/nifHdada2). ASVs accounting for 1% or more of the reads for at least one of the samples were grouped into 14 genera according to the database (Table  S1 ), and those sequences not identified to the genus level were grouped as "rare", although they represented 37 phylogenetic groups (clustered at 95% of nucleotide identity).
Filters were then rinsed twice in 0. 2 µm filtered in seawater (15 min), rinsed in osmium (30 min), and rinsed thrice with filtered seawater to eliminate excess osmium. Filters were then passed through a series of ethanol drying solutions (50, 70, 95 and 100%, 10 min each), and a series of HDMS solutions (30, 50, 80 and 100%, 10 min each), before being air-dried, and stored at room temperature until visualized onshore using a Phenom-Pro benchtop scanning electron microscope at 10 kV. Tara Oceans sampling and read recruitments in metagenomes 23 metagenomes, collected from five stations along the Tara Oceans expedition transect and corresponding to a subset of the data presented in  Karlusich et al. , (2021)   [37] , were selected for this study since these stations were the only ones for which: i) metagenomic reads belonging to nifH gene sequences from distinct cyanobacterial diazotrophs were detected in surface waters and ii) metagenomes samples from both surface (5 m) and mesopelagic waters (200-1000 m) were collected and sequenced (Table  S3 ).
Briefly, the plankton were separated into discrete organismal size fractions using a serial filtration system  [40]  corresponding to picoplankton size (0. 2-3 µm), nanoplankton (0. 8-3 µm or 0. 8-5 µm) and a 'bulk' size fraction corresponding to the fraction >0. 8 µm or >3 µm. Metagenomes were sequenced as Illumina overlapping paired reads of 100-108 bp, which were merged and trimmed based on quality, resulting in 100-215 bp fragments  [41]. Metagenomic reads were recruited against a database of 9 representative genomes of cyanobacterial diazotrophs (Table  S3 ) using BLASTN (v2. 9. 0;  (Altschul et al. , 1990 [42] ) with default parameters but limiting the results to one target sequence (--max_tar-get_seqs 1) and keeping only results with an E-value below 1e-30 (-evalue 1e-30) and with a query coverage of, at least, 90% of the read length (-qcov_hsp_perc 90).
B Abundance of metagenomic reads recruited against different diazotrophic cyanobacteria genomes in surface and mesopelagic samples. See Table  S3  for the complete dataset. Note that to better visualize the data, read abundance was expressed as number of reads per 100,000 total reads for surface samples (left axis) and per 1,000,000 total reads for mesopelagic samples (right axis). and N composition remains unknown. Thus, our assessment may actually underestimate the contribution of diazotrophs to overall PON export in this study. More than 90% of the organic matter sinking below the euphotic zone is respired before it reaches a depth of 1000 m  [9]. Fast-sinking particles will therefore theoretically make a greater contribution to the deep ocean flux than slow sinking particles since the latter will be rapidly recycled at shallow depths.
ACKNOWLEDGEMENTS This research is a contribution of the  TONGA  project (Shallow hydroThermal sOurces of trace elemeNts: potential impacts on biological productivity and the bioloGicAl carbon pump; TONGA cruise https://doi. org/10. 17600/18000884 )funded by the  Agence Nationale de la Recherche  (grant TONGA  ANR-18-CE01-0016  and grant  CINNAMON ANR-17-CE2-0014-01 ), the  LEFE-CyBER program  ( CNRS-INSU) , the  A-Midex foundation , the  Institut de Recherche pour le Développement (IRD). FMCC and LG acknowledge funding from the  European Union 's  Horizon 2020 research programme  under the  Marie Sklodowska-Curie  grant agreement No. 749380  ( UCYN2PLAST ). FMCC has also received the support of a fellowship (grant no. 105090 ) from "la Caixa" Foundation  ( ID 100010434 ) and from the  European Union 's  Horizon 2020 research and innovation programme  under the  Marie Skłodowska-Curie  grant agreement No  847648 ", and acknowledges funding from the  Spanish government through the 'Severo Ochoa Centre of Excellence ' accreditation ( CEX2019-000928-S ).
Principle We begin by assuming that a liquid water reservoir is emplaced in Europa's ice shell. Whether emplaced by melting or by fracturing and ascent of oceanic water, it acts as a heat source that warms and decreases the viscosity of the surrounding ice, promoting viscoelastic behavior (further details are given in Section 2. 3). For this reason, we use the approach of  Dragoni & Magnanensi (1989) , which is summarized in Figure  1. We define R 1 to be the reservoir radius and R 2 the viscoelastic shell radius (see Figure  1 ). Each of the physical parameters used below are summarized in Table  1. The Cryoreservoir Freezing-Induced Eruption Simulation (CryoFRIES) code developed and used in this study is available at https://github. com/ElodieLesage/ CryoFRIES. git.
Portions of this research were carried out at the  Jet Propulsion Laboratory, California Institute of Technology , under contract with the  National Aeronautics and Space Administration (NASA). This work was partially supported by  Scientific Exploration Subsurface Access Mechanism for Europa (SESAME)  grant No. 80NSSC19K0614. The code developed and used in this study is available at https://github. com /ElodieLesage/CryoFRIES. :/ /orcid. org/.
The complete mitochondrial genome of Calanus simillimus is 27,876 bp in length (GenBank accession OK500294) and containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 transfer RNA genes. The gene order is novel compared to other Calanus species and copepods with sequenced mitogenomes. Phylogenetic analysis suggests that C. simillimus represent a fourth group within Calanus genus in addition to C. hyperboreus, C. finmarchicus and C. helgolandicus groups. The complete mitochondrial genome of C. simillimus will be useful for species identification, population genetics, phylogenetic and evolutionary studies among copepods.
2017). Therefore, the complete mitochondrial genome of C. simillimus will be useful for species identification, population genetics and phylogenetic studies in Calanus genus and Copepoda, as well as evolutionary studies on appearance and role of long non-coding elements in mitogenomes. Zooplankton samples were collect during cruise MOBYDICK south of The Kerguelen Islands (lat: 50. 62S; long 72. 00E) in March 2018 by WP2 net and preserved right away in ethanol. Individuals of C. simillimus were morphologically identified using the reported literature  (Razouls 1994). DNA was extracted from a single individual using DNeasy Blood and Tissue kit (Qiagen) and 300 ng were used as library input. Remaining DNA and voucher specimens were deposited at Faculty of Biosciences and Aquaculture, Nord university (DNA accession number: Csim_4, collection code M2-WP2-13.
03. 18, contact Irina Smolina, irina. smolina@nord. no). Genomic DNA was sonicated to 350 bp fragment length peak using a Covaris S220 (Covaris) and further prepared using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) and consequently sequenced using Illumina NextSeq 500 platform (Illumina, USA). Resulting 52 millions pair-end raw reads were used for de novo assembly using SPAdes v3. 13. 0  (Bankevich et al. 2012)  with K-mer auto. The longest obtained contig was blasted against nucleotide database at NCBI data base and resulted in significant hits to mitochondrial genes of calanoid copepods. The contig was inspected for terminal repeats to evaluate its circularity and completeness leading to conclusion that obtained mitochondrial contig is complete and circular. Further, the contig was annotated using web server MITOS2 with RefSeq 63 Metazoa database and invertebrate genetic code  (Donath et al.
2019 ). Gene rearrangements were explored using CREx  (Bernt et al. 2007 ). The complete mitogenome of C. simillimus (GenBank accession OK500294) is 27,876 bp in length and includes a standard set of 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and three large (over 1,5 Kb) non-coding regions. Order of mitochondrial genes in C. simillimus is novel compared to other Calanus species and copepods. In relation to the pan-crustacean basal pattern  (Kim et al. 2013 ) the gene rearrangements in C. simillimus include several gene reversals, transpositions and a tandem duplication random loss event. The frequency of nucleotides is A: 35. 3%, T: 34. 3%, G: 15. 0% and C: 15. 4% with a GC content of 30. 4%. The 13 identified PCGs vary in length from 162 (ATP8) to 1,713 bp (NAD5).
1. 3 (Biomatters). A Maximum-likelihood tree was constructed using PhyML online server (http://www. atgc-montpellier. fr/phyml/, Guindon et al. 2010) , using GTR þ I þ G substitution model with 1000 bootstrap replicates. The analysis showed that C. simillimus was grouped within Calanus genus with high bootstrap values and the five Calanus species form a monophyletic group (Figure  1 ). Given the ecological importance of C. simillimus in the Antarctic ecosystem and limited previous genetic information, the complete mitogenome of C. simillimus together with raw shotgun genomic sequences will be a useful resource for species identification and population genetics, as well as for phylogenetic and comparative genomics studies in Calanus and copepods. under the accession no. OK500294. The associated BioProject, BioSample, and SRA numbers are PRJNA769242, SAMN22106487, and SRR16229808 respectively.
| Station selection based on heuristic search The database of EUROCONTROL September 2018 is used to provide the position information of DME/TACAN stations in Europe. There are 521 DME stations and 96 TACAN stations in Europe. These stations can be en route or approach stations. All of them are considered as the stations that contribute to multi-DME for A-PNT. The distribution of the DME stations over Europe is shown in Figure  1  as red dots. The numbers of visible DME stations at each location of Europe at FL 290, are also shown in Figure  1. Some regions are covered by more than 10 stations, which exceed the tracking capability of DME receivers and increase the computation burden. A station selection should be proposed to get a reduced but still performing subset of stations for multi-DME.
The regions benefitting from more than seven visible DME stations are shown in Figure  2. 4D-trajectories of the demand data repository 2 (DDR2) provided by EUROCONTROL is used. Each SO6 file stores a description for 4D-trajectories of flights in the European airspace. Each trajectory entry describes a phase of a flight in the network, which includes latitude, longitude, flight level and additional information. The phases of flights can be identified by the name of segments. We choose the data of 28 August 2015. This day having 2,529,401 segments is the busiest day of 2015. From the segments of DDR2, the average velocity of each segment is calculated. Then, the position information for each second can be obtained. Three different one-hour time periods are simulated. They are 8:00-9:00, 12:00-13:00 and 23:00-24:00, which represent the distribution of flights in the morning, noon and evening of the day.
3D Printing of Structures 3D models were prepared using SolidWorks (Dassault Systèmes SE, Vélizy-Villacoublay, France) computer-aided design (CAD) software. Prior to 3D printing, the models were imported into the computer-aided manufacturing (CAM) software, Repetier (Hot-World GmbH & Co. KG, Willich in North Rhine-Westphalia, Germany), for slicing into discrete layers. The resulting toolpath control code (gcode) was modified using custom MATLAB (MathWorks, Natick, MA, USA) scripts to redefine the position axis such that the extrusion head would move downward on the Z-axis, and along the Y-axis for horizontal prints for each layer. Structures were subsequently printed through a 0. 58 mm diameter nozzle onto glass substrates at a printing speed of 10 mm s À1 and extrusion pressure of 75 kPa.
Acknowledgements C. D. A. and L. Y. contributed equally to this work. H. J. Q. acknowledges the support of  AFOSR  grants ( FA9550-19-1-0151  and  FA9550-20-1-0306 ;  Dr. B. -L. "Les" Lee ,  Program Manager ). H. J. Q. also acknowledges the gift funds from  HP, Inc. and  Northrop Grumman Corporation. C. D. A. acknowledges the support from  Paper Science & Engineering Fellowship.
Statistical Analyses OS, defined as the time between the date of randomization and the date of death due to any cause, was compared between treatment arms using a two-sided log-rank test Downloaded from https://academic. oup. com/neuro-oncology/advance-article/doi/10. 1093/neuonc/noac099/6568419 by Frankfurt Univesity Library user on 08 November 2022 stratified by extent of surgical resection (complete or partial). The final OS analysis was planned after follow-up of ≥ 23 months or when ≥ 390 deaths were reported, providing ≈ 90% power with an overall type I error of 0. 05. At the time of the database lock, some patients had < 24 months of follow-up. However, given the number of events at the time of the database lock, it was considered that the number of patients with follow-up of < 24 months at the time of the current analysis would not have affected the data maturity or interpretability of the results.
27, 28 PD-L1 expression in this study (≈ 41% of all patients expressed PD-L1 ≥ 1%) was similar to that observed in other GBM studies. 18 However, it did not predict survival benefit with NIVO, suggesting that other factors may hinder successful immune responses in this tumor type. Notably, recent results from the CheckMate 548 study (NCT02667587) in newly diagnosed GBM with methylated MGMT have also shown the addition of NIVO to TMZ + RT does not prolong PFS or OS compared with TMZ + RT alone. 29 Taken together, these results clearly highlight.
Supplementary Material Supplementary material is available at Neuro-Oncology online. a Data are based on a March 21, 2019, database lock. The safety analysis included all patients who received ≥ 1 dose of study drug. Some patients had > 1 adverse event. Includes events reported between first dose and 30 days after last dose of study therapy. Three treatment-related deaths were reported in the nivolumab arm due to vasogenic cerebral edema, sudden death, and respiratory failure (1 each); no treatment-related deaths were reported in the temozolomide arm. b These treatment-related adverse events were reported in ≥ 5% of the patients in either study arm. The full-length treatment-related adverse events table is included in Supplement Table  S5. Downloaded from https://academic. oup. com/neuro-oncology/advance-article/doi/10.
Acknowledgments We thank the patients and their families who made this study possible;  Corina Taitt  for her contribution to study development and design; investigators and research staff at all study sites;  ONO Pharmaceutical Company Ltd. (Osaka, Japan ); and the staff of Dako, an  Agilent Technologies, Inc. , company, for collaborative development of the PD-L1 IHC 28-8 pharmDx assay. Editorial assistance was provided by  Bridget Sackey-Aboagye, PhD ,  Judith Matray-Devoti, PhD , and  Larra Yuelling, PhD , of  SciMentum, Inc , a Nucleus Holding Ltd company, and was funded by  Bristol Myers Squibb.
Regulation of BMAL1 Activity in Obesity and Liver Diseases in Humans. To study the impact of obesity and NAFLD pathogenesis on the expression of circadian clock genes, we analyzed RNA sequencing (RNA-seq) data from human liver biopsies collected from healthy volunteers as well as from obese volunteers and from patients with a spectrum of NAFLD, including simple steatosis (nonalcoholic fatty liver [NAFL]), and NASH  (16). As shown in Fig. 1A , most of the genes encoding the core clock repressors (PER2, PER3, and CRY2), the ROR/REV-ERB loop (NR1D2 and RORA), and clock-regulated PARbZip transcription factors (TEF) showed reduced expression, mainly in patients with NAFL and NASH (Dataset S1). The genes encoding the core clock activators BMAL1, as well as its heterodimerization partners CLOCK and NPAS2, appeared marginally affected (SI Appendix, Fig.
S1A ). This decreased expression correlated with the level of fibrosis and inflammation as indicated by increased expression of related marker genes (SI Appendix, Fig. S1B ). Because no information about the time of tissue collection was available for this dataset, we next performed a similar analysis in a cohort with recorded time of liver biopsy (tissues collected between 8:20 AM and 3:10 PM). Liver gene expression was analyzed in liver tissue from patients with various liver disease etiologies (chronic Hepatitis C virus infection, NASH, and alcohol-related liver disease) at different stages of liver fibrosis  (17). While the expression of the genes encoding the circadian clock activators did not significantly change (SI Appendix, Fig. S1C ), the expression of the genes encoding the circadian clock repressors (PER2, PER3, and CRY2), the ROR/ REV-ERB loop (NR1D1 and RORC), and PARbZip transcription factors was significantly decreased, correlating with the increased expression of genes linked to fibrosis and inflammation (Fig.
1B , SI Appendix, Fig. S1D , and Dataset S1). BMAL1, as a heterodimer with CLOCK and NPAS2, is the key regulator of circadian clock genes  (6). To characterize a potential modification of BMAL1 activity that can explain these changes in gene expression, we predicted the activity of BMAL1 based on RNA-seq data from patients with liver fibrosis. This analysis confirmed a decreased activity of BMAL1 with the level of fibrosis (SI Appendix, Fig. S1E ). These results are consistent with the hypothesis that liver disease-associated inflammation can interfere with the DNA-binding activity of BMAL1 and the organization of the circadian clock  (18, 19)  and suggest a link between BMAL1 activity and the progression of liver diseases.
To this end, we compared the lipidomic profiles of the livers from the four genotypes. We performed a differential analysis and grouped detected lipid species into statistical models to predict differential mean levels between the four genetic backgrounds (SI Appendix, Fig. S4A  and Dataset S2). Unsurprisingly, liver lipid composition was strongly altered in WT-Ob mice at both quantitative and qualitative levels (Fig. 4  A and B and SI Appendix, Fig. S4 B-D ). However, KO-Ob mice showed lower levels of glycerol esters (TAG and diacylglycerols [DAG]) compared to WT-Ob mice but also decreased Ceramides (Cer) and most phospholipids. Because DAG and Cer accumulations play a key role in hepatic inflammation and insulin resistance  (34) , their low levels in of KO-Ob mice livers likely contribute to the insulin sensitivity of these animals.