dataesr/scientific-paragraphs-categorization huggingface dataset:
Data analysis Unassembled sequence reads in sff format where subjected to further quality checking using mothur v. 1. 29. 2  [30]. Briefly, after demultiplexing of the reads and trimming them to 720 flows, sequences where subjected to denoising (PyroNoise implemented in mothur). After removal of reads shorter than 200nt or with more than seven homopolymers, sequences were aligned against the Silva v102 compatible SSU reference alignment. For further reduction of sequencing errors preclustering was applied which clusters sequences only differing in up to two nucleotides. Chimera check against the Silva database was conducted applying Chimera UCHIME, as implemented using the "chimera. uchime" command in mothur and chimeric sequences were dismissed. To account for possible contamination bias, OTUs were first clustered on 99% identity and all sequencing reads from OTUs that had a significant (P<0.
05) and negative spearman correlation with amplicon concentration in one of the three library amplification runs were removed for further analysis as previously described  [31]. The remaining sequencing reads were subjected to a second run of the mothur software by clustering OTUs at an identity cutoff of 95%. Subsequent classification of OTUs was performed using the RDP trainset applying a bootstrap cutoff of 80%. For all OTUs that were unclassified on genus level but classified on family level representative sequence reads were retrieved, automatically aligned using SINA  [32]  and imported in ARB  [33]. Maximum Likelihood Treeing algorithm PhyML, embedded in ARB, was used to reconstruct phylogenetic trees of partial 16S rRNA gene sequences of selected OTUs derived from this study and of reference organisms.
For the estimation of diversity in terms of species evenness and richness, we applied Pielou's evenness  [35]  and the Chao richness index  [48]. In addition, rarefaction curves and PERMANOVA were computed using the R package vegan (S2 Fig)  [49]. To test for differences in abundances between binary metavariables, two-sided Wilcoxon-Mann-Whitney tests were applied. P-values of individual genera and PERMANOVA analyses were adjusted for multiple testing using Benjamini-Hochberg's method  [36]. Such P-values will be referred to as P adj throughout the manuscript. To construct interaction networks of genera, we used the CCREPE method  [37]  with pairwise Spearman's rank correlation coefficients for relative abundances of all genera larger than zero in at least 5 samples. To obtain P-values we used 1000 random permutations and set an edge, if P<0.
In the study of Glassing et al. [70]  more than 80 genera with far more than 100 tentative species have been detected as contaminants of different kits, most of them in low abundance. Moreover, the study of Segal et al. [72]  described reads with similarity to Streptococcus thermophilus as contaminants, whereas Streptococcus mitis affiliated reads were detected as part of the microbial community harbored in supraglottic and lung samples. Thus, extracting all contaminating genera present in contaminant databases is no option, as contamination is very specific to the kits used as well as species or even strain specific. To account for this problem, we tested our sequencing reads according to the method described by Jervis-Bardy et al. [31]. These authors could show that relative abundance of OTUs identified as potential reagent contamination showed a strong inverse correlation with amplicon concentration allowing for objective removal.
Likely enough, the higher LogP of BP2 (3. 16, based on the American Chemical Society, 2007, calculated properties) compared to BPS (1. 65 based on US EPA Estimation Program Interface (EPI) Suite; 1. 9 based on XLogP3 from PubChem), could explain the easier uptake and bioavailability of BP2. In adult zebrafish as well, marked qualitative differences were noticed between BPS and BP2 despite their chemical similarities. The ratio between the respective quantities of radioactivity in water and fish (apparent bioconcentration factor) was 1. 7 ± 0. 4 for BP2, and 0. 6 ± 0. 1 for BPS. For BP2, these results are consistent with the bio-concentration factor reported in a previous work in fathead minnows (Pimephales promelas) exposed to BP2 (0. 4 µM) in a 15-day study (1. 1 ± 1. 0;  [12]. Glucuronidation was the major pathway for BPS, with more than 78.
Western blot analysis showed that the sepa-1 mutant caused the accumulation of PGL granules. Immunostaining assay revealed the co-localization of SEPA-1 with both PGL granules and LGG-1 dots, which indicated that the SEPA-1 protein may be a bridge molecule in mediating P granule selective autophagy. Then, the co-immunoprecipitation confirmed the interaction of SEPA-1 with PGL granules and LGG-1. These data demonstrated that SEPA-1 is a receptor for selective autophagy in P granules degradation. Several tools have been generated to allow the analysis of aggrephagy in the embryo. P granules can be analyzed by EM, immunofluorescence or Western blot on embryo extract, and transgenic worms expressing GFP::PGL-3 or GFP::PGL-1 in germline allow in vivo observation. In wild-type embryos, GFP::PGL-1 granules are detected only in germ cell precursors, while in autophagy mutant embryos (lgg-1, atg-3, atg-4.
Acknowledgments: The authors would like to thank their colleagues for helpful discussion and particularly  Céline Jenzer  and  Céline Largeau  for providing pictures. We are grateful to  Nektarios Tavernarakis  for sending the mitoRosella and the DsRed::LGG-1; mtGFP strains. We are also grateful to the C. elegans autophagy community for sharing informations and reagents and apologize if some data could not be mentioned in this review due to size limitations. The Legouis' group is supported by the  Agence National de la Recherche  (project  EAT ,  ANR-12-BSV2-018 ) and the  Association pour la Recherche contre le Cancer  ( SFI20111203826 ). Y. C. is a recipient of a fellowship from the  China Scholarship Council  and VS received a fellowship from of the  Ligue Nationale contre le Cancer.
001) and that their mature miRNAs are detected during limb regeneration (21 and 45 reads per million, respectively) (Fig. 2e ; Supplementary Fig. 4 , Supplementary Table  9  and Supplementary Data 4). In addition, we found that five orthology groups containing Myb or Harbi domains were upregulated at 3 days post amputation (p < 0. 001) (Supplementary Table  9 ) similar to mir-93b and mir-427 primary transcripts (Fig. 2e ). On the contrary, the two vertebrate Harbinger derivative genes Naif1 and Harbi1 were expressed at low levels in all our datasets and showed no regulation during regeneration (Supplementary Table  10 ). Four Gypsy orthology groups were also upregulated 3 days post amputation (p < 0. 01), however, their expression levels were an order of magnitude lower than the Harbingers (Supplementary Table  9 ).
Lampbrush chromosome analyses. Ovarian biopsies were performed on adult females of P. waltl that were anesthetized in 0. 15% MS222 (Amino-benzoic Acid Ethyl, Fluka). Stage IV-VI oocytes were selected and maintained in MBS buffer (Modified Barth's solution) at 18 °C. Germinal vesicles were manually isolated from the oocytes and dissected in 75 mmol L -1 KCl, 25 mmol L -1 NaCl, 0. 01 mmol L -1 MgCl2 and 0. 01 mmol L -1 CaCl 2 , pH7. 2, and LBCs were prepared as previously described  51. Nuclear spread preparations were centrifuged at 300 × g for 10 min, and at 3000 × g for 30 min at 4 °C. Standard transmitted light were performed at the ImagoSeine core facility (member of the IBiSA and the France-BioImaging (ANR-10-INBS-04) infrastructure) using a wide field Leica microscope with phase contrast plan Apo oil objectives: ×40 (NA = 1.
3), ×63, ×100 (NA = 1. 4). Images were captured using a CoolSnap HQ, Photometrics camera driven by the software Metamorph6 (Universal imaging). Series of 11 confocal Z-planes (0. 7 µm distance) were collected. Pixel size of the images were 0. 1625 μm, 0. 103 μm, and 0. 065 μm for the ×40, ×63, and ×100 objectives, respectively. Genome size calculation. Nuclear content was measured using Vicia faba nuclei as reference (2C DNA content = 26. 9 pg)  52  (Supplementary Fig. 1 ). All samples were prepared according to  52  and stained with 4ʹ,6-diamidino-2-phenylindole (DAPI) and measured using a BD Influx™ by Becton Dickinson flow cytometer. The lasers used for detection and excitation were 488 nm and 355 nm, respectively. From the mean peak positions of P. waltl (20,255) and V. faba (13,746) the 2 C DNA content was calculated as 39.
6 pg using the equation: P. waltl 2 C value = V. faba 2 C value (reference) × ((P. waltl 2 C mean peak position)/(V. faba 2 C mean peak position)) Based on the equation: haploid genome size = (0. 978 × 2 C value)/2, the haploid P. waltl genome size was calculated to be 19. 38 Gb (Supplementary Fig. 1 ). Our estimates agree with Licht and Lowcock (2 C value = 42. 7 pg)  53  , Morescalchi and Olmo (2 C value = 39 pg)  54  and are lower than Lizana and collegues (2 C value = 48. 25 pg)  55. Short read genome sequencing. Libraries for Illumina sequencing were generated and sequenced at SciLifeLabs (Stockholm). Two Illumina TruSeq PCR-free libraries (insert size 180 bp) were prepared and paired-end 2 × 125 bp sequencing was done on HiSeq2500 (HiSeq Control Software 2. 2. 58/RTA 1. 18. 64) with a setup in High Output mode (Supplementary Table  2 ).
Since our small-RNA dataset was intended for discovery, not differential expression analysis we did not have replicates for each source. To mitigate the lack of replicates in pursuit of miRNAs associated with regeneration, we divided the miRNA expression data into three groups: adult tissue (brain, eyes, heart, liver, lung), regenerating limb (limb 3 dpa, limb 7 dpa); and embryo (larvae, late embryo). Then we tested whether there was significant miRNA up or downregulation between these groups based on a Gauss-Laplace distribution, as implemented in moose2  65  (http:// grabherr. github. io/moose2/). The top 10 miRNAs upregulated in the regenerating group compared to the adult group (ranked by Bonferroni-corrected e-value) were also the top 10 upregulated in the embryonic group compared to the adult group.
Acknowledgements We thank  Elly Tanaka  and colleagues for sharing the axolotl genome assembly prior to publication. We acknowledge continuous support from members of the  Frisén Lab (KI/ CMB) ,  Science for Life Laboratory , the  National Genomics Infrastructure (NGI ) the  Swedish National Infrastructure for Computing (SNIC)  and  Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX)  for providing assistance in massive parallel sequencing and computational infrastructure (projects b2015079, b2015188, b2016417,  SNIC 2016/1-20  and  SNIC 2016/1-251 ). We thank  Agustin Gonzalez  and his lab ( UCM, Madrid ) for facilitating the embryos from which our initial colony was established. Mihaela Martis  ( BILS -SciLifeLab ) is acknowledged for assistance concerning transcriptome assembly,  Sarantis Giatrellis  ( CMB -KI ) for assistance measuring nuclear DNA content and  Karen Echeverri  for facilitating miRNA in situ.
Acknowledgements This work has been supported by grants  AIRC  ( IG-2013-14455 ),  Italian Health Office 'Tevere project' and MIUR 'Epigen' Epigenomics Flagship Project  (EPIGEN; sub-project 7. 6) to GB; by an  AIRC  and  Marie Curie Actions-People-COFUND  fellowship to MC and by the  ArceloMittal Dofasco Company  to PM.
We first focused on GAL1, a gene locus reported to relocalize to the periphery when activated by galactose. GAL1 relocalization was readily observed in the genemap shown in Figure  2A. We also confirmed the augmentation of  by 20% in galactose vs. glucose for loci with a central localization (red vs. blue datasets in Fig. 2A ). Notably the dynamics of peripheral loci in galactose was intermediate between the response in glucose and galactose for central localization (Supplementary Fig. S3 ). Because the entire chromosome bearing GAL1 genes is reorganized upon transcription activation  (33) , increased dynamics can be the consequence of local transcription activity as well as global genome reorganization. We next explored the behavior of the GAL2 locus, which is strongly transcribed in galactose.
After half-nucleus photobleaching of the probe TetR-GFP, we monitored fluorescence redistribution kinetics in WT and TS cells at 25°C or 37°C (supplementary Fig. S4 ). Similar kinetics detected in these four conditions imply that the variation of Tet-GFP diffusion coefficient, associated to transcription arrest, which is proportional to the nucleoplasmic viscosity  (39) , was marginal. Therefore, the onset in chromatin dynamics after transcription shut-down suggests that transcription arrest per se modulates the internal properties of chromatin. , and the red one shows experimental 3C data  (40). The blue dataset corresponds to simulations in absence of contacts. In the right, the two datasets present the MSD vs. time deduced from the simulation with or without contacts (black and blue datasets, respectively).
As a first step, we ran the simulations with no interaction in order to fit chromatin fluctuations in vitro and to define the simulation time step of ~3. 0 10 -4 s (blue dataset in the right panel of Fig. 3C ). Then we focused on the kinetic parameters of the loop formation reaction using the average contact probability vs. genomic distance plot obtained by 3C  (40)  and the MSD data in living cells as inputs (left and right panels of Fig. 3C , respectively). The fitting of 3C data was first carried out by adjusting the k b /k u ratio of ~0. 40 +/-0. 03 (left panel in Fig. 3C ). We could then fit the amplitude of chromosome fluctuations of Γ~0. 01 μm 2 /s 1/2 by setting the dissociation constant k u to ~0. 5 +/-0. 15 s -1 (right panel in Fig. 3C ). Notably, the prediction of the model for contact probability vs.
genomic distance was inconsistent if the contact formation reaction was neglected (blue dataset in the left panel of Fig. 3C ). Consequently the RIF model allowed us to probe the dynamics of chromatin contacts in vivo, which appeared to be transient, as characterized by a lifetime of only ~2 s. Furthermore we could determine the Gibbs free energy of the contact formation reaction of ~1 k B T given the ratio k u /k b. This value, which is far less than the energy associated to ATP hydrolysis of ~20 k B T, but comparable to nucleosome-nucleosome interaction energy of 0. 3 k B T (49), is compatible with a scenario where populations of contacts of various lengths are formed dynamically, as speculated in 3C studies  (44).
Microscopy and image processing Genemaps were acquired using an Andor Revolution Nipkow-disk confocal system installed on an Olympus IX-81, featuring a CSU22 confocal spinning disk unit (Yokogawa) and an EMCCD camera (DU 888, Andor). The system was controlled with Andor Revolution IQ2 software (Andor). Images were acquired with an Olympus 100 x objective (Plan APO, 1. 4 NA, oil immersion). The single laser lines used for excitation were diode-pumped solidstate lasers (DPSSL), exciting GFP fluorescence at 488 nm (50 mW, Coherent) and mCherry fluorescence at 561 nm (50 mW, CoboltJive); a Semrock bi-bandpass emission filter (Em01-R488/568-15) was used to collect green and red fluorescence. Pixel size was 65 nm. For 3D analysis, Z-stacks of 41 images with a 250-nm Z-step were used. An exposure time of 200 ms was applied.
For the extraction of genemaps, confocal stacks were processed with the Matlab script Nucloc, available at http://www. nucloc. org/ (MathWorks). Chromosome loci tracking was performed with a Nikon TI-E/B inverted microscope equipped with an EM-CCD IxonULTRA DU897 (Andor) camera and a 488nm laser illumination (Sapphire 488, Coherent). The system was controlled by NIS Element software and equipped with SPT-PALM rapid acquisition unit drive by a dedicated plugging. Microscope Images were acquired with a Nikon CFI Plan fluor X100 SH (Iris), Oil, (NA=0. 5-1. 3) objective and a Semrock filter set (Ex: 482BP35, DM: 506, Em: 536BP40). Pixel size was 106. 7 nm. A heating system (PE94, Linkam) was used to monitor the temperature at 37°C, whenever necessary. Acquisitions were performed with inter-frame intervals of 50 to 200 ms for a total frame number of 300-1000 depending on the strains.
The trajectories were subsequently extracted using the TrackMate Plugin  (53). Note that we only considered "long" trajectories with more than ~100 consecutive tracked positions. Coordinates were then processed in Matlab to extract the MSD. We focused on time intervals lower than 30% of the total duration of the trajectory to keep a sufficiently high level of averaging  (54). For each condition, we averaged the MSD over 30-40 cells. FRAP experiments were carried out on a LSM 710 NLO-Meta confocal laser-scanning microscope controlled by Zen software, equipped with a 40x/1. 2 water immersion objective (Zeiss, Germany). The pixel size was 208 nm, and the typical size of ROI was 14x18 pixel 2. The 488 nm laser was set to 1% during acquisitions, and we checked that photobleaching was marginal with this dose of illumination in the time course of our experiments (not shown).
The inter-frame time was ~50 ms. Typical experiments consisted of 5 scans before bleaching, followed by 10 scans with the 488 nm laser set to 100% for bleaching half of the nucleus (Supplementary Fig. S3 ). We then recorded the signal during 40 scans with the laser power restored to 1%. After background intensity subtraction, we monitored fluorescence intensity in the bleached region (white rectangle in Figure  S3A ) over time normalized to the intensity in the same region before FRAP, as shown in Figure  S3B  with the datasets collected in 16 cells pooled together. In order to focus on the relaxation dynamics, we normalized the data in Figure  S3B  to the steady concentration level after 1. 4 s (Supplementary Fig. S3C ). The temporal evolution of the MSD for the Rouse model is given in equation (  2 ).
2 and 0. 5 s -1, and the red one shows experimental 3C data (40). The blue dataset corresponds to simulations in absence of contacts. In the right, the two datasets present the MSD vs. time deduced from the simulation with or without contacts (black and blue datasets, respectively). The red solid or dashed lines correspond to trend lines with anomalous diffusion parameters (,) of (0. 03 µm 2 /s 0. 5 , 0. 5) or (0. 01 µm 2 /s 0. 5 , 0. 5), as in the in vitro assay or in living yeast, respectively.
Acknowledgements: The authors thank the  French CNRS network GDR ADN  for stimulating workshops,  Serge Mazère  for help in the FRAP experiments, as well as Vincent Dion,  Julien Mozziconacci , and  Romain Koszul  for critical reading of the manuscript. RW thank the  CSC  for PhD fellowship. KB, OG, and DJ acknowledge the grant programs  ANR-13-BSV5-0010 -ANDY ,  IDEX ATS NudGene ,  ANR-15-CE12-0006  EpiDevoMath, and  Fondation pour la Recherche Médicale  ( DEI20151234396 ), respectively. DJ acknowledges the CIMENT infrastructure (supported by the  Rhône-Alpes region , Grant  CPER07_13 CIRA ) for computing resources.
2 )Figure S1 : 2S1 Figure S1: Zimm model for DNA fluctuations. The green dataset represents the average MSD over time for DNA loci dispersed in a weakly crowded solution composed of 2% PVP 40 kDa. The solution's viscosity is 2. 3 mPa. s. The green and black solid lines show the predictions of the Zimm and Rouse models, respectively (see analytical expression in supplementary material).
Structural comparative analysis of iSpinach and Spinach aptamers The overall structure of iSpinach/DFHBI complex is very similar to that reported for Spinach 1 and 2 aptamers, suggesting that the beneficial mutations contained in iSpinach may have subtle yet important effects. To shed light on the contribution of these mutations, we compared the structure obtained in the present study with those previously reported with different RNA constructs  (Huang et al. 2014; Warner et al. 2014). To this end, we selected from each study the structure of the aptamer in complex with DFHBI having the highest resolution (i. e. , PDB code 4KZD. pdb [Huang et al. 2014 ] and 4TS0. pdb [Warner et al. 2014] ). Hereafter, these structures will be called, respectively, Spinach-P and Spinach-FdA for ease of reading (Supplemental Fig.
Data collection and processing Data were collected at the X06DA beamline at the SLS using a PILATUS 2M detector. The wavelength was set to 1. 8 Å. Several data sets were collected for "lentils/ball shape" crystals for iSpinach-D5 and iSpinach-D5-G30-A32 constructs as well as for iSpinach-D5-G30-A32 with "laminar" crystal shape. Whereas most of the crystals had very poor (or no) diffraction (Supplemental Table  S2 ), the "laminar" crystal obtained with iSpinach-D5-G30-A32 allowed the structure of the complex to be solved. All data sets collected from the "laminar" crystal were processed and scaled independently with XDSGUI  (Kabsch 2010). All of them showed the same space group and cell dimension, therefore all were merged together in one data set for the refinement process with XDSGUI software.
For phase determination, one of the Spinach structures solved previously (PDB code: 4Q9R. pdb, Huang et al. 2014)  was used as a search model for molecular replacement using PHASER (PHENIX)  (Adams et al. 2010 ). The final structure was obtained after alternative cycles of refinement with PHENIX and manual refinement with COOT (Supplemental Table  S3 ;  Emsley and Cowtan 2004). The final refined model was deposited on the PDB under the reference 5OB3.
2016). The collected emulsions were then loaded into the same capillary as those used with crystals. Fluorescence intensity decay was monitored by placing the loaded capillaries onto the platform of an epi-fluorescence microscope (TiE, Nikon) and exposing it to a constant illumination at 475 nm at the maximum intensity of the light source (Lumencor). An Orca Flash 4 camera using a proper filter set was used to collect the light emitted at 490-530 nm and the fluorescence was quantified using custommade analysis software written in MatLab.
ACKNOWLEDGMENTS We thank  Redmond Smyth  for his help in manuscript proofreading and  Guillaume Bec  for his assistance in using the Mosquito liquid handling robot. This work has been published under the framework of the  LABEXs :  ANR-10-LABX-0036_NETRNA  and  ANR-11-LABX-0057_MITOC   ROSS , and benefits from funding by the state-managed  French National Research Agency  as part of the  Investments for the Future program. We also received the financial support of the  Agence Nationale de la Recherche  (project  BacNet :  ANR-10-BINF-02-01 ), the  Université de Strasbourg , and the  Centre National de la Recherche Scientifique. Received July 16, 2017; accepted September 5, 2017.
2a ) was located within the ABO gene. This SNP was in complete linkage disequilibrium (pairwise linkage disequilibrium (LD) r 2 = 1. 00) with rs651007, already associated with variation of sE-Selectin levels in two large Caucasian cohorts  30. We also observed a nominally significant eQTL association within the same region of the ABO gene (Supplementary Fig. 2b ) at baseline (eQTL association signal for rs630510, p = 3. 0 × 10 -4 in moderate LD r 2 = 0. 27 with rs495828 pQTL SNP). Based on the GTEx database, sE-Selectin trans-pQTL SNP rs495828 was associated with the expression of ABO gene in visceral and subcutaneous adipose tissues. Among others, an interesting trans-pQTL is for calpastatin on chromosome 10. Calpastatin is an endogenous calpain inhibitor and is involved in inflammatory processes  31.