dataesr/scientific-paragraphs-categorization huggingface dataset:
The data set including colon adenoma  30  clearly showed that hypermethylation of SEPT9_v2 first exon is induced in early development of colon tumors, and at a specific locus matching the hypermethylated amplicon 5 described independently by Wasserkort et al. 25  (Fig. 1b ). This preliminary examination of published datasets suggested that hypermethylation of SEPT9_v2 first exon is a sensitive epigenetic marker of tumorigenesis, not only in colon, but also in breast cancer.
S2 ). Pan-Sept9 and Sept9_i1 antibodies generated   24  , SEPT9_v1, _ v2,_v3,_v5,_v6 and_v7, coding for Sept9_i1,_i2,_i3,_i4,_i4 and_i5 isoforms, respectively. Middle panel displays the position of CpG islands (dark green > 300 bases; 200< light green < 300 bases), hypo-methylated regions (dark blue bars on top of corresponding genome) and methylated CpGs (golden brown vertical lines whose height is proportional to CpG methylation level). Four groups of human methylome datasets are presented: first set, HMEC (Human Mammary Epithelial Cells, primary cell line) vs HCC1954 (grade 3, ductal carcinoma cell line)  28  ; second set, normal colon and colon cancer derived primary epithelial cell lines  29  ; third set, normal colon, colon adenoma and tumor biopsies  30  ; fourth set, normal colon and colon cancer biopsies  31.
Bottom panel is the zoomed region delineated by a dashed red frame including the large CpG island 138 and the first exon of SEPT9_v2; the location of the differentially methylated amplicon identified by Wasserkort et al. 25  in microdissected colon cancer cells is represented by a black bar on top of CpG 138 island (dark green bar). Public bisulfite-seq datasets were extracted from the MethBase methylome database using the UCSC Genome Browser on Human Feb. 2009 (GRCh37/hg19) assembly and the MethPipe software package (smithlabresearg. org). strong cytoplasmic labeling in MCF7, which was abrogated upon Sept9_i1 knockdown (Supplementary Fig. S2 ); moreover the pan-Sept9 antibody showed a strong positive signal in Sept_i2 and Sept9_i3 expressing cells, while the Sept9_i1 antibody did not, illustrating the specificity of the antibodies.
Human breast tissues. All samples of human origin and associated data were obtained from the IPC/ CRCM Tumour Bank that operates under authorization # AC-2007-33 granted by the French Ministry of Research for tumor sample. Before scientific use of samples and data, patients were appropriately informed and asked to consent in writing, in compliance with French and European regulations. The project was approved by the IPC Institutional Review Board. Antibodies. The pan Sept9 polyclonal antibody against Sept9 C-terminus was a kind gift from Pascale Cossart (Institut Pasteur, Paris, France). We produced rat monoclonal antibodies against Sept9_i1, i2 or i3 specific N-termini (Supplementary Fig. S1 ) using the rat medial iliac lymph node method as described previously  54. The following commercial antibodies were used for Western blotting (WB) and/or immunofluorescence (IF): polyclonal anti-Sept2 from Sigma (IF, Prestige Antibodies), polyclonal anti-Sept2 from Millipore (WB), polyclonal anti-Sept7 and anti-Sept11 (WB, Sigma), monoclonal anti-α-tubulin (DM1A, WB/IF, Sigma), monoclonal anti-acetylated tubulin (6-11B1, IF, Sigma), monoclonal anti-actin (AC-15, WB, Sigma).
Boyden chamber assay. Heregulin-induced SKBr3 cell migration was performed in 8-μ m pore membrane Transwell chambers (Corning Costar), as described previously  55  , except that nuclei of migrated cells were labeled with 5 μ g/ml Hoechst 33342 (Sigma) in water. For MCF7 cell lines, the same protocol was followed except that 10% FBS was used as chemoattractant. The entire bottom face of the Transwell insert membrane was imaged and cell counted with the cell counter function of Image J software on ten squares of 93625 pixel 2 each. GFP pull-down and analysis by mass spectrometry. GFP-Sept9 expressing MCF7 cell lines were lysed and GFP pulldowns performed as described previously  53  using GFP-Trap agarose beads (Chromotek, Planegg-Martinsried, Germany). Control pull-downs were obtained from lysates of parental MCF7.
Primary antibodies were validated for IHC with expression controls (Supplementary Fig. S6 ) that were included in all IHC run as internal experimental standards. Slides were entirely scanned on a Nanozoomer 2. 0HT scanner (Hamamatsu Photonics, Massy, France) and images were produced using the CaloPix 3. 0. 0 software (Tribvn, Chatillon, France). Histological examination and staining scoring of each slide was performed independently by two certified pathologists. An independent semi-quantitative analysis of each image using the RVB sampling tool of Adobe Photoshop software (RVB average on 12 sampling spots per image) was performed and led to very similar scoring results.
Four groups of human methylome datasets are presented: first set, HMEC (Human Mammary Epithelial Cells, primary cell line) vs HCC1954 (grade 3, ductal carcinoma cell line) 28  ; second set, normal colon and colon cancer derived primary epithelial cell lines 29  ; third set, normal colon, colon adenoma and tumor biopsies 30  ; fourth set, normal colon and colon cancer biopsies 31. Bottom panel is the zoomed region delineated by a dashed red frame including the large CpG island 138 and the first exon of SEPT9_v2; the location of the differentially methylated amplicon identified by Wasserkort et al. 25  in microdissected colon cancer cells is represented by a black bar on top of CpG 138 island (dark green bar). Public bisulfite-seq datasets were extracted from the MethBase methylome database using the UCSC Genome Browser on Human Feb.
Acknowledgements The authors are grateful to  Estelle Duprez  for advice and  Manos Mavrakis  for critical review of the manuscript, to  Luc Camoin  and  Emilie Baudelet  for protein handling and mass spectrometry data analysis, to  Sailaja Naga Imjeti  for help with HUVEC culture setting, to  Pascale Cossart  for providing a purified rabbit polyclonal antibody against septin 9, and to  Cristina Montagna  for providing GFP-septin 9 isoform constructs and MCF7. GFP-septin 9 stable cell lines. This work was supported by  SIRIC  (grant  INCa -DGOS-Inserm 6038 ) and  GEFLUC Marseille-Provence. Marseille Proteomic (MaP, IBiSA)  and  IPC/CRCM Experimental Pathology (ICEP)  platforms are supported by  Institut Paoli-Calmettes (IPC)  and  Canceropole PACA.
Acknowledgements Research in the Aspergillus Unit was supported by the  Association Vaincre La Mucoviscidose  ( RF20140501052/1/ 1/141 ). We thank  V Aimanianda  ( Aspergillus Unit, Institut Pasteur, Paris, France ) for language editing. We thank  A Mallet  ( Ultrapole, Institut Pasteur, Paris, France ) for her help in scanning electron microscopy.
V. CONCLUSION We have briefly illustrated the genericity of the algorithm recently introduced in  [3]  for the analysis of networks in life sciences with various bioimaging problems and for various informational tasks (segmentation, denoising, simulation). Other tasks may benefit from this technically simple approach (registration for instance) where some prior on the structural topology of the underlying network helps in the image processing step. Each bioimaging problem presented would also, beyond the proof of feasibility given here, deserve more attention by benchmark with alternative methods (based on graph or not) on larger datasets.
ACKNOWLEDGMENT Authors thank  Frédéric COINTAULT  for image on root systems and  Bénédicte CHAZAUD  for image on muscles. This work was supported by the  LABEX PRIMES  ( ANR-11-LABX-0063 ) of  Université de Lyon , within the  program Investissements dAvenir  ( ANR-11-IDEX-0007 ) and in the framework of the program " Investissements d'Avenir"  under reference  ANR-11-BTBR-0007  ( AKER program ) both operated by the  French National Research Agency (ANR).
Using complementary approaches, we found that the F. cylindrus genome assembly consists of 15. 1 Mb of loci with highly divergent alleles that were assigned to different scaffolds. The remaining 46 Mb of sequence consists of alleles similar enough to be assembled onto the same scaffold (Supplementary Information 2-5). The haplotype assembly size of the genome (61. 1 Mb; Extended Data Table  1 ) was confirmed by quantitative PCR with reverse-transcription (qRT-PCR) (57. 9 Mb). The genome completeness according to the Core Eukaryotic Genes Mapping Approach 15 is 95. 6% and the nuclear scaffold N50/L50 is 16/1. 3 Mb, corresponding to assembly size (Extended Data Table  1 ). The haplotype-resolved genome contains 21,066 predicted protein-coding genes (Extended Data Table  1 ) with 6,071 genes (29%) being represented by diverged alleles (Allele sets 1 and 2, Supplementary Data 1).
than that between paralogous genes (Extended Data Fig. 1  and Supplementary Information 4, 5). We compared the F. cylindrus genome with those of Thalassiosira pseudonana  16  and Phaeodactylum tricornutum  17  (Extended Data Table  1 ), both of which live in temperate and neritic marine environments  18, 19  characterized by higher water temperatures, turbidity and concentrations of dissolved iron. The haploid gene content of F. cylindrus is enriched for two conserved metal-binding protein families (structural classification of proteins (SCOP) fold families; Supplementary Information 6). When accounting for its genome size, it is enriched for copper-binding but not iron-binding proteins (Fig. 1c ), and it contains a disproportionate abundance of domains belonging to the plastocyanin/azurin-like family fold (SCOP ID 49504).
The presence of lineage-specific protein families might indicate specific adaptations to the extreme conditions in the Southern Ocean. Some of these protein families appear to have been acquired through horizontal gene transfer from bacteria (Supplementary Information 8). Those proteins include groups of ice-binding proteins  23  and protonpumping proteorhodopsins 24 (Supplementary Information 9, 10). There is also an unusually large number of genes for chlorophyll a/c light-harvesting complex (LHC) proteins, including 11 members of the Lhcx clade, which is involved in stress response (Extended Data Fig. 2  and Supplementary information 11). Gene Ontology analysis show significant enrichment of genes in the categories 'catalytic activity' , 'transporter activity' , 'metabolic process' , 'transport' and 'integral to membrane' in the group of diverged alleles compared to the non-diverged alleles (Fisher's exact test, adjusted P < 0.
2b ). The broadest transcriptome response (approximately 60% of total genes, including divergent alleles) was observed under prolonged darkness, characteristic of polar winters (Supplementary Information 14 and Supplementary Data 5). Placing F. cylindrus in darkness for seven days downregulated genes involved in photosynthesis, light harvesting and photoprotection relative to their expression under continuous light. By contrast, genes involved in starch, sucrose and lipid metabolism were strongly upregulated in the dark (Extended Data Fig. 3 ), indicating the utilization of chrysolaminarin and fatty acid storage products. Notably, under prolonged darkness, the percentage of RNA-seq reads that did not map to predicted genes (30%) was higher than under any other tested growth condition. In allele-specific analyses of transcriptomes, approximately 66% (4,030) of diverged alleles showed greater than fourfold significant differential expression (likelihood ratio test, P < 0.
37 Gb of raw data. Additionally, a 4-kb insert size library was sequenced using four SMRT cells with a yield of 3. 85 Gb of raw data. Sanger assembly. A total of 671,171 sequence reads (7. 25× final sequence coverage) were assembled using Arachne v. 20071016 (ref. 30). The final genome assembly was produced by passing the initial assembly through the Rebuilder module to merge adjacent haplotypes, followed by another complete Arachne assembly process. We obtained 4,622 contigs that were linked into 286 scaffolds, including 105 scaffolds larger than 100 kb. To exclude organelle sequences and contaminating scaffolds from the nuclear genome assembly, each scaffold was screened against bacterial proteins and organelle sequences in the NCBI GenBank database and a set of known microbial proteins using megaBLAST and blastp searches  31.
Finally, under the assumption that gene duplicates are more divergent than alleles, we compared the sequence similarity between predicted diverged alleles and duplicates. We independently validated the sequence similarity for the alleles by Sanger sequencing of diverged F. cylindrus alleles from a natural sea ice population (see 'Evolutionary genetic analysis' below). PacBio assembly. PacBio data from seven SMRT cells were used, and after filtering the shortest reads, we obtained 1,971,632 reads and 3. 8 Gb of data which gave 63× coverage. We used the diploid aware PacBio assembler FALCON 0. 3. 0 (ref. 32), which has recently been used to successfully assemble highly heterozygous genomes  33  , to assemble the F. cylindrus genome. The cut off for long reads was 2,000 bp. The FALCON assembly consisted of 745 primary contigs with a total length of 59.
The assembly was masked for repeats using RepeatMasker  35  and the RepBase library  36  , and the most frequent (> 150 times) repeats were recognized by RepeatScout  37. Protein-coding gene models were predicted using three levels of evidence: ab initio Fgenesh 38 ; homology-based Fgenesh+  38  and Genewise  39  seeded by BLASTx alignments against the NCBI NR database; and transcriptome-based Fgenesh. For each genomic locus, automated filtering selected the best model based on homology and transcriptome support. tRNAs were predicted using tRNAscan-SE  40. All predicted proteins were functionally annotated using SignalP  41  for signal sequences, TMHMM  42  for transmembrane domains, interProScan  43  for integrated collection of functional and structural protein domains, and protein alignments to NCBI NR, SwissProt  44  , KEGG  45  for metabolic pathways, and KOG  46  for eukaryotic clusters of orthologues.
InterPro and SwissProt hits were used to map Gene Ontology terms  47. Additionally, custom analyses were performed on selected protein families. Analysis of metal-binding protein families. Metal-binding protein families were annotated using the Structural Classification of Proteins (SCOP) database v1. 75 (ref. 48), which provides a classification of protein domains published in the Protein Data Bank 49 into a hierarchy including classes, folds, fold superfamilies, fold families, and domains. Metal annotations of the SCOP database were built upon those in refs 50, 51. New fold families and fold superfamilies were manually curated according to metal binding and compared to automated annotation of metal binding by SCOP fold families from the PROCOGNATE database  52. We used hidden Markov models (HMMs) from the Superfamily database  53, 54  to annotate protein sequences according to structural composition.
Using the Superfamily HMMs and HMMER3 we analysed the F. cylindrus genome in comparison to other phytoplankton and Phytophthora genomes from the PHYTAX database. To perform an evolutionary genetic analysis of zinc-binding MYND protein domains, nucleotide sequences were aligned using Muscle within MEGA5 (ref. 55); DNAsp v5 (ref. 56) was used to obtain measures of nucleotide diversity. We then used BEAST 1. 6. 2 (ref. 57) to infer tree topology and relative divergence times between sequence clusters using a HKY+ G nucleotide substitution model  58  under a relaxed molecular clock  59  and a Yule tree prior  60. The assembly and annotation were released as a public web portal available at http://genome. jgi-psf. org/Fracy1/Fracy1. home. html. Identification and analysis of diverged alleles. To produce a non-redundant single haplotype gene set with only one allele of each gene, we aligned the genomic assembly against itself using BLAT 61 with thresholds of 95% nucleotide identity and ≥ 50% alignment coverage for the smaller scaffold.
We obtained alignments of 210 smaller scaffolds against larger scaffolds, with a total length of 15. 9 Mb and an alignment coverage over the entire length of the smaller scaffold for 74. 3% of the alignments. Syntenic scaffolds that were homologous over the entire length were analysed using Mauve genome alignment software  62. Gene models of the aligned smaller scaffolds, which formed the best bi-directional blastn hit pairs with corresponding genes on larger scaffolds and > 90% nucleotide identity were removed to produce a final non-redundant protein-coding gene model set. We also defined the set of diverged alleles for allele-specific downstream analyses. Diverged alleles on the larger scaffolds were referred to as allele 1 set and alleles on the smaller scaffolds as allele 2 set. Additionally, the assembly based on PacBio sequencing was used to validate the allelic divergence observed in the assembly based on Sanger sequencing.
Promoter analysis of diverged alleles. Putative promoter nucleotide sequences were collected by extracting good quality sequences from different regions relative to the transcription start site (TSS). The collected sequences were divided into promoters (before TSS) and transcripts (after TSS) and ClustalW  64  alignments of both sets were parsed with custom scripts using Bioperl  65. We calculated the average identity of the alignments and the average percentage identity in 10-bp intervals using a sliding window approach.
Letter reSeArCH Environmental metatranscriptome signature of F. cylindrus. Sequences from a Southern Ocean, eukaryote-targeted metatranscriptome were quality filtered, clustered and taxonomically classified using PhymmBL 66 with a custom reference database  6. To identify F. cylindrus-like transcripts a BLASTx search (E value ≤ 1 × 10 -10 ) of sequences classified as Bacillariophyta (PhymmBL confidence score ≥ 0. 9) was performed against all predicted gene models in the genome assembly, including gene models for diverged alleles on scaffolds that could not be collapsed into a single haplotype. The total number of hits was then calculated for all genes, including genes present as diverged alleles. We used a functional Gene Ontology analysis to assess the abundance of metatranscriptome reads associated to diverged alleles and investigate the environmental significance of bi-allelic transcript abundance for diverged alleles.
A total of 68,832,506 RNA-seq reads were aligned to the F. cylindrus genome assembly using GSNAP  70  , and HTSeq 71 was used to count unique fragments mapping in each genomic feature. Differential expression analysis. Data were analysed using edgeR  72  for differential expression and goseq  73  for functional Gene Ontology analysis. Results were visualized using REViGO  67  and graphical packages of R statistical software  74. Statistical testing for genes that were differentially expressed between an experimental treatment and optimal growth reference condition was performed using the generalized linear model (glm) functionality implemented in edgeR. After estimating genewise (tagwise) dispersions and fitting negative binomial models, the glm likelihood ratio test  75  was applied to test for differentially expressed genes and P values adjusted  63.
Acknowledgements We thank  A. Stecher  and  K. Schmidt  for extracting and providing environmental DNA samples and the  Natural Environment Research Council UK (NERC) Biomolecular Analysis Facility  ( NBAF ) for conducting transcriptome sequencing and providing bioinformatics support. C. B. acknowledges funding from the  ERC  Advanced Grant ERC-2011-ADG (Diatomite). The work conducted by the  U. S. Department of Energy Joint Genome Institute , a  DOE Office of Science User Facility , was supported by the  Office of Science of the U. S. Department of Energy  under Contract No. DE-AC02-05CH11231. PacBio sequencing and library construction was delivered via the  BBSRC National Capability in Genomics  ( BB/J010375/1 ) at the  Earlham Institute (formerly The Genome Analysis Centre, Norwich ), by members of the  Platforms and Pipelines Group, PacBio assembly  and sequence analysis was strategically funded by the  BBSRC ,  Institute Strategic Programme Grant  ( BB/ J004669/1 ).
Data Availability. The Sanger genome assembly and annotations used in this study are available via the JGI genome portal at http://genome. jgi. doe. gov/ Fragilariopsis_cylindrus and the Whole Genome Shotgun Project has been deposited to DDBJ/EMBL/GenBank under accession number LFJG00000000 (BioProject PRJNA32761). ESTs have been deposited to DDBJ/EMBL/GenBank under accession number GW070125. The PacBio genome assembly has been deposited at DDBJ/EMBL/GenBank under accession number PRJEB15040. F. cylindrus RNA-seq data are available in the ArrayExpress database (http:// www. ebi. ac. uk/arrayexpress) under accession number E-MTAB-5024. Metatranscriptome sequences have been deposited at the Sequence Read Archive under accession number SRR1752079. P. multistriata RNA-sequencing data has been deposited at DDBJ/EMBL/GenBank under accession number PRJNA80045 and is available at http://www.
Furthermore, patient participants were selected at the discretion of haematologists which may have introduced selection bias. Nevertheless, descriptive studies using qualitative interviews have an important role to play in highlighting patient needs as well as family and carers' perspectives. Data obtained using VRS support the findings of the qualitative interviews in showing that many people living with MM perceive greater psychological, physical, financial, and logistical burdens associated with relapse or disease progression. Insights from this study also highlight physicians' workload and the need for additional support beyond the prescriber (counselling nurses, oncology psychologists, 'carers-for-the-carer' etc. ). There is a need for modification of existing patient-reported outcome (PRO) tools or development of new PRO questionnaires reflective of patients' day-to-day experiences to help tailor treatment plans  [30].
Adipocyte size determination Epididymal WAT was collected and fixed in 70% ethanol. The tissue was processed on the STP 120 Spin Tissue Processor by ethanol dehydration (increasing bath from 70% to 100%), xylene substitution and paraffin infiltration. 5-lm paraffin sections were obtained using a Microtome Microm HM 340E and stained by haematoxylin/ eosin. Stained sections were imaged on a Zeiss PALM MicroBeam system with Plan-Neofluar 10× (0. 3 NA) air objectives and AxioCam MRm black and white camera. Images were analysed using MotionTracking software  (Collinet et al, 2010)  following a pipeline developed by Dr Giovanni Marsico. First, the centre of the adipocytes was manually located. Then, adipocyte border was automatically segmented by a region growing algorithm based on the watershed transform.
Metabolomic analysis Plasma samples (100 ll, out of a pool of n = 6 mice per group) were diluted with 600 ll of deuterium oxide (D 2 O) and centrifuged at 5,000 g for 10 min before they were placed in 5-mm NMR tubes. 1 H NMR spectra were obtained on a Bruker DRX-600 Avance NMR spectrometer operating at 600. 13 MHz for 1 H resonance frequency using an inverse detection 5 mm 1 H-13 C-15 N cryoprobe attached to a CryoPlatform (the preamplifier cooling unit). The 1 H NMR spectra were acquired at 300 K using the Carr-Purcell-Meiboom_Gill (CPMG) spin-echo pulse sequence with pre-saturation, with a total spin-echo delay (2 nt) of 64 ms to attenuate broad signals from proteins and lipoproteins. A total of 128 transients were collected into 32 k data points using a spectral width of 12 ppm, a relaxation delay of 5 s and an acquisition time of 2.