dataesr/scientific-paragraphs-categorization huggingface dataset:
Statistical analysis Results are presented as the mean ± SEM with significance calculated by two-tailed Student's t or Chisquare tests with standard software (GraphPad Prism, GraphPad Software, La Jolla, CA, USA). Significance was assigned for a P-value < 0. 05. *, P < 0. 05; **, P < 0. 01; ***, P < 0. 001.
ACKNOWLEDGMENTS We wish to thank  Dr. N. Foray  ( CRCL, Lyon, France ) for providing the GST-tagged BRCA1 constructs,  Dr. J. H. Chung  ( NHLBI, NIH, Bethesda, USA ) for the HA-tagged wtBRCA1 vector,  Dr J. M. Stark  ( Beckman Research Institute, Duarte, CA, USA ) for the HEK/DR-GFP cell line and  Dr N. Puget  ( LBCMCP, Toulouse, France ) for the myc-tagged I-SceI plasmid. We also thank  Emilie Gross  and  Gregory Ségala  for early technical assistance.
Femtosecond transient absorption measurements Transient absorption measurements on the femtosecond time scale were performed at RT essentially as described earlier  (Gibasiewicz et al. 2009)  using the 1 kHz femtosecond laser system (Ti:sapphire, Spectra Physics) and a grating polychromator (Spectra Pro 150, Acton Research Corp. ) with a thermoelectrically cooled CCD camera (Back Illumin. , Princeton Instruments) described in detail previously  (Maciejewski et al. 2000). The data were collected over a 2 ns temporal window and over a *330-700 nm spectral window using *300 fs excitation at 800 nm. RConly membranes were diluted in either 15 mM Tris-HCl (pH 8. 2) containing 0. 025 % LDAO and 1 mM EDTA, or 50 mM glycine-NaOH (pH 10. 5) containing 0. 025 % b-DM. In order to keep the RCs in the open state (all electron transfer cofactors in their neutral state), fresh 10 mM sodium ascorbate was added to the sample before each experiment.
This way, the experiments took less time that was essential for maintaining RCs in fully closed state all the time during the measurements. The temporal evolution of the transient absorption spectra was subjected to global and target analysis  (Holzwarth 1996; van Stokkum et al. 2004 ) using the software package Asufit developed at Arizona State University (available at http://www. public. asu. edu/*laserweb/asufit/ asufit. html) as well as Glotaran software  (Snellenburg et al. 2012). This evolution was fitted using sum of typically four exponential lifetimes convoluted with an instrumental response function modeled by a Gaussian of *400 fs width.
Femtosecond transient absorption measurements from 400 to 700 nm In order to verify the above considerations on the different sizes of the initial free energy gap between P ? B A -and the unrelaxed (P ? H A -) 1 state, RT femtosecond transient absorption measurements were performed over 2 ns and in a wide 400-700 nm spectral window allowing more precise identification of RC states and transitions between these states than is possible from single wavelength measurements. In addition, the better temporal resolution of femtosecond measurements enabled a more exact estimation of the fastest, subnanosecond phase of charge recombination  (Gibasiewicz et al. 2009; Wang et al. 2012). Figure  5  compares the results of global fits of RT femtosecond data for the WT and mutant RCs in the form of decay-associated difference spectra (DADS)  (Holzwarth 1996; van Stokkum et al.
In brief, assuming that the 20 ns SADS is contributed to exclusively by relaxed state (P ? H A -) 2 (with the band at *545 nm assigned to H A -and the band at *600 nm assigned to P ? ), the ''excess'' of the photobleaching signal of the *600 nm band in the fast charge recombination SADS (0. 49-1. 6 ns) relative to the 20 ns SADS in each dataset (except for GML RCs) is a measure of the population of P ? B A -that is in equilibrium with (P ? H A -) 1. Assuming further similar differential extinction coefficients of the photobleaching signals, De, for P ? /P and B A -/B A at *600 nm(0. 5De(P ? -P) \ De(B A -B A ) \ 2De(P ? -P))-B A ) \ 2De(P ? -P)) and testing somewhat different ways of estimation of the photobleaching bands' areas at *545 and *600 nm (one of them is illustrated in Fig. 7 ; in another, we limited the integration of the band to the region of the band minimum (*545 or *600 nm) ± 20 nm), a set DG 1 of ranges was obtained (Table  2 ).
Acknowledgements K. G. acknowledges financial support from the  National Science Center, Poland  (project entitled '' Bio-semiconductor hybrids for photovoltaic cells '' No. 2012/07/B/NZ1/02639. MRJ acknowledges funding from the  Biotechnology and Biological Sciences Research Council of the UK  (Project  BB/I022570/1 ). Open Access This article is distributed under the terms of the Creative Commons Attribution 4. 0 International License (http://crea tivecommons. org/licenses/by/4. 0/),which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
30) reports: r. m. s. d. between C␣ atoms of MotA and similar PBP structures are Ͼ2. 2 Å with sequence identity around 17-29%. The closest structure (r. m. s. d. of 1. 8 Å Ͼ301 C␣ atoms and 32% sequence identity) is that of A. tumefaciens Atu4243 in complex with GABA (PDB code 4EUO)  (28). The two x-ray structures of the mature monomeric SocA liganded with DFG were obtained at 1. 93 and 1. 5 Å and that with glucopine at 1. 84 Å (Table  1 ). Although SocA with DFG crystallizes in two different cell parameters from the same space group (one monomer versus two monomers in the asymmetric unit), the three SocA-DFG complexes are very similar, displaying an average r. m. s. d. of 0. 4 Å for all C␣ atoms. Moreover, all liganded forms adopt a similar closed conformation (average r. m. s. d. for all C␣ atoms of 0.
46 Å). SocA belongs to cluster F (29) and resembles several PBPs from the same cluster, which mainly bind amino acids or derivatives of amino acids such as ArtI from Caldanaerobacter subterraneus and STM4351 from Salmonella enterica, both in complex with arginine (PDB codes 4YMX and 2Y7I with r. m. s. d. of 1. 14 Å and 1. 2 Å Ͼ207 and 211 C␣ atoms, respectively)  (31, 32). The PBP NocT from A. tumefaciens in complex with nopaline (PDB code 4POX) (11) displays with SocA a r. m. s. d. of 1. 68 Å Ͼ214 C␣ atoms, corresponding to a sequence identity of 31%. MotA Recognizes Mannopine, DFG, and the Synthetic Glucopine: the Mannopine/DFG Binding Signature-Mannopine, DFG, and glucopine bound between the two closed lobes of MotA are surrounded by Ser-37, Trp-41, Gln-67, Gln-87, Gly-89, Asp-92, Ser-128, Tyr-130, Trp-235, Arg-238, Asp-261, and Thr-297 residues.
SocA Is Present in Numerous Bacteria-SocA relatives search in the bacterial kingdom (protein database at NCBI), and subsequent phylogenetic analysis reveals Ͼ240 PBPs with conserved DFG binding signature. To refine this analysis, we reconstructed a phylogeny with the SocA relatives extracted from the complete genome NCBI database only (Fig. 7 ). The SocA-clade delineated with a solid bootstrap value (100%) encompasses PBPs from ␣-proteobacteria such as Rhizobiales (Agrobacterium, Aureimonas, Rhizobium, and Sinorhizobium), ␥-Proteobacteria such as Enterobacteriales (Klebsiella, Pantoea, Erwinia), and Actinobacteria (Arthrobacter) that all possess the DFG binding signature. Outside the SocA-cluster, the DFG signature degenerates, but modeling indicates that only the Glu-201/Asp-201 side chain variation in the Micromonospora sub-branch may affect the DFG binding.
Crystals were transferred to a cryo-protectant solution (paraffin oil or 22% (w/v) PEG 400) and flash-frozen in liquid nitrogen. Diffraction data were collected at 100 K on the PROX-IMA I and II beamlines at SOLEIL synchrotron (Saint-Aubin, France). Data collection and processing statistics are given in Table  1. All structure determinations were performed by molecular replacement (MR) with PHASER  (36). The coordinates of the N-terminal (residues 31-128 and 260 -310) and the C-terminal (residues 131-258 and 324 -352) domains of a model from @TOME-2meta-server (37) was used for MotAmannopine structure. Structures of the other liganded forms and the unliganded form of MotA were determined using MotA-mannopine coordinates. Structure determination of both SocA-DFG complexes and the SocA-glucopine complex was performed using the coordinates of the N-terminal (residues 43-133 and 227-270) and the C-terminal (residues 138 -222) domains of a SocA model from @TOME-2 (37).
Each ligand had no emission signal at 335 nm. The data were analyzed using Origin 7 software (ORIGIN) and fitted to the equation f ϭ ⌬Fluorescence max ϫ abs(x)/(KD ϩ abs(x)), where KD indicates the dissociation constant, abs indicates absolute value, and x indicates ligand concentration. Isothermal titration microcalorimetry experiments were performed with an ITC200 isothermal titration calorimeter from MicroCal Llc (Northampton, MA). The experiments were out at 20 °C in 50 mM Tris-HCl, pH 8, and 150 mM NaCl (same buffer as fluorescence titration). Protein concentration in the microcalorimeter cell (0. 2 ml) was 50 M. 19 injections of 2 l of the ligand solution at 500 M were performed at 180-s intervals while stirring at 1000 rpm. The experimental data were fitted to theoretical titration curves with the software supplied by MicroCal (ORIGIN).
This software uses the relationship between the heat generated by each injection and ⌬H (enthalpy change in Kcal⅐mol Ϫ1 ), K a (the association binding constant in M Ϫ1 ), n (the number of binding sites), total protein concentration, and free and total ligand concentrations. Phylogenetic Analysis-Sequences were analyzed using blastP from NCBI (blast. ncbi. nlm. nih. gov). Alignments of MotA/SocA and related sequences were conducted using the ClustalW software. A relationship tree was built using the MEGA software, Version 5. The phylogeny was inferred using the neighbor-joining method. The bootstrap consensus tree inferred from 1000 replicates was taken to represent the evolutionary history of the taxa analyzed. The evolutionary distances are in units of the number of amino acid substitutions per site.
9 31. 5 50. 6 Protein Crystallization conditions PDB code Space group Cell parameters (Å,°) R sym (%) Completeness (%) I/ CC 1/2 R cryst (%) R free (%) ) Average B (Å 2 Protein Ligand Solvent Values for the highest resolution shell are in parentheses. CC 1/2 , percentage of correlation between intensities from random half-dataset (41). r. m. s. d. bond (Å) r. m. s. d. angle (°) sponding to Phe-96, Arg-121, Ala-114, and Asp-201 in SocA.
Background In the 1970s, Ohno  [1]  proposed that gene duplication was an important mechanism to produce evolutionary novelties. Later on, it was effectively shown that two rounds (2R) of whole genome duplications (WGDs) occurred early during vertebrate evolution  [2] [3] [4]. Although this idea was initially very controversially discussed, the existence of these two WGDs is now well accepted, and this is mainly due to the unique datasets provided by the sequencing of the complete genomes of various chordate species  [3, [5] [6] [7]. Evidence for these ancient duplication events can be found in vertebrate genomes, even if only some duplicated genes (called 'ohnologues') organized in 'paralogons' have been retained in extant vertebrate species  [8]. In contrast, the timing of the two rounds of WGD in vertebrates relative to the main phylogenetic events, that is the emergence of the different vertebrate groups, has been difficult to determine.
Sequence analysis The accession numbers of the RAR proteins used to compile the sequence alignment are as follows: human RARα (P10276. 2), RARβ (P10826. 2) and RARγ (P13631. 1); spotted gar (Lepisosteus oculatus) RARα (BAH03351. 1), RARβ (BAH03352. 1) and RARγ (BAH03353. 1); small-spotted catshark (Scyliorhinus canicula) RARα (BAH03356. 1), RARβ (BAH03357. 1) and RARγ (SSC-transcript-ctg66621 from SkateBase. org); Japanese lamprey (L. japonicum) RAR1 (BAH03333. 1), RAR2 (BAH03334. 1) and RAR3 (BAH03335. 1); inshore hagfish (E. burgeri) RAR1 (BAH03345. 1), RAR2 (BAH03346. 1) and RAR3 (BAH03347. 1). The protein sequences were aligned with MAFFT  [45]  and visualized with either JALVIEW  [46]  or SEAVIEW  [47].
Probabilistic orthology assessment We prepared datasets consisting of five operational taxonomic units (OTUs; electronic supplementary material, table  S1 ): (i) only one cyclostome RAR gene; (ii) gnathostome RARα genes; (iii) gnathostome RARβ genes; (iv) gnathostome RARγ genes; and (v) the outgroup (electronic supplementary material, figure  S1 ). By inputting each sequence dataset, including one selected cyclostome gene, we computed likelihood with TREE-PUZZLE v. 5. 2 for individual tree topologies specified in the user-defined trees mode  [48]. We subsequently prepared the tree topology files using two different approaches: (i) all possible tree topologies using the five OTUs or (ii) focusing on only nine tree topologies that are compatible with the 1-2-4 duplication pattern predicted by the 2R WGDs in vertebrates (electronic supplementary material, table  S2 ).
Output files of TREE-PUZZLE were processed with the program CONSEL v. 0. 20 to obtain bootstrap probabilities based on resampling of estimated log-likelihood (RELL BP)  [49]. With and without the assumption of the fourth paralogue generated in 2R WGDs, we added up the RELL BPs of tree topologies supporting the one-to-one orthologies of cyclostome RAR1, RAR2 and RAR3 to four (RARα, RARβ, RARγ and RARδ) or three (RARα, RARβ and RARγ) gnathostome RAR subtypes, respectively (electronic supplementary material, table  S3 ).
Three-dimensional modelling of retinoic acid receptor ligand-binding domains Three-dimensional models of the lamprey and hagfish RAR LBDs were constructed using the modelling meta-server @TOME 2  [56]  and the crystal structures of the LBDs of human RARα (PDB code 3KMR)  [57]  or human RARβ (PDB code 4JYI)  [58]  as templates.
We also detected a weak activation with the highest dose of BMS641 (the RARβ-selective compound), but no activation with BMS961 (the RARγ-selective compound). These results suggest that LjRAR3 displays a RARα-type transactivation profile [33,  [40] [41] [42]. Ligand binding assessed by limited proteolysis assays confirmed this conclusion. We observed that in the presence of ATRA, of BMS753 and, to a lesser extent, of BMS641 the receptor was protected from proteolysis (figure  3b ). Together, these data indicate that LjRAR3 binds to RARα-and RARβ-selective synthetic retinoids, but is only efficiently activated by BMS753, the RARα-selective compound [33,  [40] [41] [42]. Similar results were   obtained with EbRAR3. This receptor was hence activated by ATRA, BMS753 and BMS641 (figure  3g ), but protected from proteolysis only in the presence of ATRA and BMS753 (figure  3h ).
Structural modelling of the ligand-binding pockets of cyclostome retinoic acid receptors We next used structural modelling approaches to reconstruct the LBDs of the six cyclostome RARs based on the previously characterized X-ray three-dimensional structures of the human RARs. Given the overall sequence conservation within the LBP (figure  2 ), we used the structures of human RARα and RARβ as templates for our modelling work: while the structure of human RARα in complex with the RARα-selective agonist AM580 (PDB code 1KMR)  [57]  was used to model the lamprey and hagfish RAR1 and RAR3 proteins, the cyclostome RAR2s were rebuilt with the structure of human RARβ bound to the RARβ-selective ligand BMS641 (PDB code 4JYI)  [58]. The resulting cyclostome RAR structure models were subsequently superimposed on the corresponding human RAR structures (i.
Acknowledgements. We thank  Jeramiah J. Smith ,  Chris T. Amemiya  and  Masatoshi Matsunami  for their help in identifying open reading frames of genes encoding retinoic acid receptors (RARs) in the genomes of the lampreys Petromyzon marinus and Lethenteron japonicum. We are further indebted to  Guillaume Holzer  for exploring the feasibility of RAR synteny analyses.
Funding. This study was supported by the  CNRS , the  ENS de Lyon , the  UPMC (Université Paris   06 ), the  Agence Nationale de la Recherche  (grants  ANR-2010-BLAN-1234-01  to V. L. and  ANR-11-JSV2-002-01  to M. S. ),  MINECO  ( SAF2013-48397-R, FEDER ) and  Xunta de Galicia (Consolidación, INBIOMED-FEDER 'Unha maneira de facer Galicia')  to A. R. dL. and the  European Union  ( FP7 ,  BIOCAPS 316265/REGPOT-2012-2013. 1 ) to S. A.
Timothy O'Brien. 28 he plasmid pCMV-GFP containing the GFP reporter gene under the cytomegalovirus (CMV) promoter was produced by PlasmidFactory (Bielefeld, Germany). All the other plasmids were purified from Escherichia coli-transformed cells using NucleoBond PC2000 EF kit (Macherey-Nagel, Hoerdt, France) and then diluted in endotoxin-free water. Light absorption at 260 nm was used to determine DNA concentration and the quality of the plasmid was assessed by calculating the ratios of light absorption at 260/280 nm and 260/230 nm. Control experiments using dialyzed preparations of plasmids showed no effects on survival or on transfection efficiency of the possible remaining salts (data not shown). Electrotransfer. Cells were detached with TrypLE Express, centrifuged at 300 × g for 10 minutes, and then resuspended at 10 7 cells per milliliter in minimum essential medium, modified for suspension cultures, without calcium and without glutamine (S-MEM, ref.
The cuvette was washed twice with culture medium to collect all the cells. Flow cytometry analysis and measurement of viability. At different time points after the electrotransfer, the culture media was removed (with all the floating dead cells). Living cells were then detached with TrypLE Express and analyzed by flow cytometry on a BD Accuri C6 flow cytometer (BD Biosciences, Erembodegem, Belgium) to evaluate the levels of GFP expression and the number of living cells using the BD Accuri CFlow Plus software. The percentage of surviving cells was determined 24 hours after treatment and expressed as a percentage of the number of cells counted in the control. Unless otherwise specified, the percentage of GFP-positive cells presented in the figures corresponds to the percentage of surviving cells expressing GFP.
The counting accuracy of the BD Accuri C6 was assessed by comparing with manual counting (hemocytometer) and no significant difference was found. Statistical analysis. All data are presented as mean plus SD. Kendall's rank correlation was used to measure the association between the variable measured and the parameters tested. One-way analysis of variance with Holm-Šídák (to compare the mean of every group with each other's) or Dunnett's (to compare the mean of every group with the mean of a reference group) multiple comparison test was used for statistical analysis for multiple comparisons among the groups. P <0. 05 was considered to be statistically significant. Statistics were performed using GraphPad Prism 4 and R Statistical Software.
Acknowledgments We thank  Bassim Alsaker  for providing the biological samples for AT-MSC isolation. We also thank  Laurence MICHEL  ( INSERM U976 ) for kindly providing the human We acknowledge the funding support from the  ITMO Cancer  in the frame of the Plan Cancer 2015-2019 (project  PC201517 ), as well as the  ANR  through the projects  IPSIOAT  ( ANR-11-BS09-031-02 ),  INTCELL  ( ANR-10-BLAN-916 ) and  MEMOVE  ( ANR-11-BS01-006-01 ). This research was conducted in the scope of the  EBAM European Associated Laboratory (LEA). The authors declare no conflict of interest.
Consistent with the hypothesis of common pathways between genders, 16 common genes can be identified within heifer and bull QTL regions: ARL2, CAPN1, CDC42EP2, DPF2, FRMD8, MRPL49, PARPBP, POLA2, SAC3D1, Slc22a20, SNX15, SPDYC, TIGD3 , TM7SF2 , VPS51, ZFPL1. Figure  5. Only a few genes known to be associated with puberty onset in human are also located within cattle QTL regions. Cattle QTL regions were identified using the Animal QTLdb, taking into account "Age at first calving" for females and "Scrotal circumference" for males. Regions associated with "Age at puberty" were spread over female or male according to the experiment. QTL regions were defined as the critical mapping interval for linkage studies or a 500kb interval centered on the most significant marker for GWAS studies. Ensembl database was used to list genes located within these intervals and OMIM was used to establish a list of genes associated with puberty in Human.
Microscopy. Live cells were imaged on a LSM 710 (Zeiss) confocal microscope, using a 405 nm laser diode exciting Hoechst 33342, a 488 nm argon laser line exciting GFP and a 561 nm diode laser line exciting Nile Red. Emission was detected between 410 and 480 nm for Hoechst 33342, 495-530 nm for GFP and 565-max nm for Nile Red. Live imaging studies were made at 37 °C in self-conditionned medium. Acquisition was made in channel-separated mode and with a line-scanning mode, with a line average of 2 and an 8-bit dynamic range. Images were analyzed using the softwares Fiji/Image J  43  and Mathworks Matlab softwares.
1B ). The average diameter of the droplets was chosen to be slightly larger than the smallest dimension of the channels, so drops with a diameter bigger that 8 μ m are squeezed horizontally and hence remain immobilized into the device. 3D reconstructions of Nile Red-stained droplets into the channels (Fig. 1C ) show that droplets with a diameter larger than the channel width are pancake-shaped, the top and bottom interfaces being flat thanks to pressure exerted by the PDMS walls in the z dimension (Figure  S2 ). We confirmed the shape of the droplets in this size range by numerical simulations (Figure  S1B ) made with the software Surface Evolver  48. HL-60 migration in the microdevice. Cells of the immune system, such as HL-60, represent a simple model system to study cell migration without the need to derive cells from primary tissue  49.
Acknowledgements We thank  Guillaume Charras  ( LCN ) for having provided the Actin-GFP HL-60 cell lines;  Ana-Maria Lenon-Dumesnil  ( Curie Institute ) for having provided primary murine dendritic cells,  J. Bibette  ( ESPCI ) for lending us the Couette emulsifier;  Nicolas Bremond  ( ESPCI ) and  Patrick Perrin (ESPCI)  for their help regarding interfacial tension measurements;  Thomas Boudier  ( UPMC, NSU ) for his help on image segmentation;  Zoher Gueroui  ( ENS ) for the helpful discussions. This work has received support of " Institut Pierre-Gilles de Gennes" (Laboratoire d' excellence:  ANR-10-LABX-31 , " Investissements d'avenir ":  ANR-10-IDEX-0001-02 PSL  and Equipement d' excellence:  ANR-10-EQPX-34 ).
As a first step, we established the limits of online biomass detection by scattered light as well as the online detection of lipid concentration by Bodipy fluorescence (see ''Methods'' section). Strain JMY3675, which expresses an optimized invertase expression cassette, was used to evaluate these parameters. This expression cassette contains the Saccharomyces cerevisiae SUC2 gene under the control of the strong promoter pTEF, and has been shown to confer efficient growth both in sucrose and in cost-effective industrial sucrose-based substrates like molasses  [18, 27, 32, 33]. Moreover, in Y5P10D15 (C/N = 3. 5) medium, strain JMY3675 did not differ significantly from the W29 wild-type strain in growth or lipid accumulation (data not shown), showing that it was a suitable candidate for the calibration of the BioLector.
Impact of the carbon concentration at a constant carbon-to-nitrogen ratio The source and concentration of carbon are important parameters for the growth of a strain and its accumulation of intracellular lipids, as shown in Fig. 2. To evaluate the influence of carbon concentration, the growth of Y. lipolytica JMY3675 was monitored at different glycerol concentrations with a constant C/N ratio of 35. Under these conditions, biomass and specific growth rate were maximal at a carbon concentration of 1 M (30. 6 g L -1 of glycerol) and quickly decreased with higher concentrations (i. e. 3 and 6 M) (Fig. 4a ). The same effect was observed with regard to lipid accumulation and total lipid production (Fig. 4a, b ). Similar effects were observed when glucose or sucrose was used as a carbon source (data not shown).