dataesr/scientific-paragraphs-categorization huggingface dataset:
9 KCl, 1. 2 MgCl 2 , 10 HEPES, 10 glucose and 2. 1 CaCl 2 ; 290 mOsm, adjusted to pH 7. 7-7. 8 with NaOH)  38. Ventral nerve root activity was recorded with B10 mm tip diameter pipettes filled with ACSF. Data was recorded in current clamp mode using a MultiClamp 700 A amplifier (Molecular Devices-Axon Instruments, USA), a Digidata series 1322 A digitizer (Axon Instruments, USA) and pClamp 8. 2 software (Axon instruments, USA). 10 ms water jet at 8-15 psi delivered through a pipette located in the vicinity of the otic vesicle induced reliable escapes. Experiments on tail-free larvae: larvae were embedded dorsally and the tail was freed so that B1/3 remained fixed in the agar. An 890 nm LED was used to illuminate the fish from the side and behavior was recorded at 675 Hz from the bottom through a 5x microscope objective and imaged on the camera with a 50 mm camera objective.
Probe deflections were driven with a mechanotransducer device controlled through LabView software. Tail bend was induced by probe deflection and repeated 10 times. Calcium imaging data analysis. Regions of interest around CSF-cN cell bodies expressing both GCaMP and tagRFP were manually defined in the software ImageJ. To extract raw fluorescence from the image time series in moving samples (either due to passive mechanical stimulation or active tail movement), the ROIs were shifted with the moving cell using a custom-made tracking algorithm based on cross correlation. In frames where the normalized correlation coefficient fell underneath a given threshold due to the movement artifact, data were omitted for that given frame. This threshold was manually adjusted to minimize tracking errors for each imaging time series.
During motion of the tail, cells can usually not be imaged so between (DR/R) pre and (DR/R) post there is a gap of 4 frames (external pressure experiment) or 1 frame (tail free experiment). Behavior setup and analysis. To assess fish behavior, a video recording chamber was constructed. 6 dpf larvae from Tg(pkd2l1 icm02/ þ ,-pkd2l1:GCaMP5G) or Tg(pkd2l1:Gal4, UAS:BoTxBLC-GFP) incrosses were placed in circular swim arenas (Bioptech) atop a plexiglass plate. An Arduino Due software circuit (Arduino) was used to trigger one second-long recordings on a high speed camera (Vieworks) operating at 650 fps. To trigger escape behaviours, a 500 Hz, 10 ms sine wave stimulus was played through a 20 W amplifier (Adafruit) over two speakers (Monacor) at maximum volume 200 ms into the recording. Larvae were allowed to acclimate to the chamber for 5 min prior to the experiment and were allowed to rest 2 min between each stimulus.
Each larva was subjected to five trials, the properties of which were averaged within subjects. Larvae were genotyped after data acquisition. Sample sizes were selected by performing a Lehr analysis on preliminary data sets with a threshold of 5% difference in means. Two software packages were used to extract kinematic parameters from high-speed videos of fish during escapes. The first executable, developed in collaboration with R&D Vision, fits a series of eleven points to the fish body-two for each of the eyes, one for the swim bladder, and the remaining eight to the tail. The program identifies these 11 points for each of the 650 frames of video. The second executable consists of a series of MATLAB scripts that derives kinetic parameters from these points. First, the tail angle a was calculated by identifying the midpoint of the two eye points, then calculating a head direction vector based on this point and the center of the swim bladder.
A tail direction vector based on the last point on the tail minus the swim bladder was then calculated, and a was calculated as the inverse cosine of these two vector lengths. To remove noise due to tracking error, the raw trace of a was median-filtered, linearly interpolated, and finally smoothed using a smoothing spline method in MATLAB's Curve Fitting Toolbox. Simultaneously, the unprocessed tail angle trace was differentiated to estimate angular velocity, which was smoothed as above. The angular velocity trace was used to define frames of movement-any frame with angular velocity 41°/ frame is defined as 'in motion'. These frames were then connected into movement bouts using morphological closing with a block size of 10 frames. Detected bouts were then assigned priority weights by their distance from stimulus onset to identify the escape.
Mean tail beat frequency was calculated as the inverse of two times the mean hemicycle of sequential peaks. MATLAB package is available on request; the tail-tracking algorithm is property of R&D Vision. Zebrafish dissociated cell cultures. Dissociated cells from 4 dpf Tg(pkd2l1:GCaMP5G) and Tg(pkd2l1:tagRFP) larvae were plated acutely in zebrafish ACSF (see Ca 2 þ imaging section) on plastic petri dishes based on a published protocol  39. Dissociated CSF-cNs were identified based on their GCaMP5G/tagRFP fluorescence and imaged three hours after platting. Statistical analysis. All values are mean ± s. e. m. unless otherwise noted. To account for the fact that all our data are intrinsically nested (multiple measurements of cells and/or repetition of trials within the same fish), we used linear mixed models for all our hypothesis testing  40.
Acknowledgements We thank  Natalia Maties  and  Bogdan Buzurin  from  Animalliance  for expert fish care. We thank  D. Delpeuch  for help with culture,  D. Langui  for EM imaging, RD Vision for high-speed data acquisition and tracking. We thank  Dr Kilborn  for customization of 2-photon setup,  Vincent Guillemot  and  Ivan Moszer  from the  ICM Biostatistics/ Bioinformatics core facility  for advices on statistics and the imaging facility PICPS from  ICM  supported by ' Investissements d'avenir'   ANR-10-IAIHU-06. This work received support from the  E ´cole des Neurosciences de Paris Ile-de-France  ( ENP, Chaire d' excellence for CW and doctoral fellowship for UB), the  Fondation pour la Recherche Medicale (FRM) , the  Bettencourt-Schueller Foundation  with the  ATIP/Avenir program  organized by  INSERM  and  CNRS , the  ERC  starting grant 'Optoloco' #  311673 , the  HFSP  research grant #  RGP0063/2014 , the  ANR-II-INSB-0014 , the  ANR-10-IAIHU-06  and a  Research-in-Paris fellowship  with an  EMBO  fellowship #  ALTF 549-2013  for AP.
Here we report generation of a transcriptome dataset and identification of a surprisingly rich Wnt repertoire (ten genes, in contrast to only three present in the genome of Amphimedon). Two of these genes are expressed in nested domains in the posterior half of the larvae, and six along the adult body axis, with two specific to the osculum. Moreover, Wnt expression is elevated in the region undergoing regeneration, suggesting conservation of the Wnt role in axial patterning and restoration of lost body parts across the animal kingdom.
Transcriptome assembly The transcriptome was assembled de-novo from the two RNA-Seq libraries. The assembly was performed with Trinity 2. 1. 1  [37]  including reads' pre-processing with Trimmomatic  [38]. We have modified Trinity's final step called Butterfly to use read pairing information: The fasta sequence files prepared for Butterfly runs were supplemented to include both ends for all the fragments (missing-pair reads were added) and option 'run_as_paired' was added to all Butterfly commands. Assembled transcriptome was screened to exclude eukaryotic contaminations by aligning reads from the clean juvenile gDNA library. The alignments were done using bowtie with default parameters. Transcriptome contigs not aligned to any of the clean read were removed from the assembly. Assembly was screened for sequencing vectors using blastn against UniVec database.
Ten Wnt genes are present in Halisarca dujardini We have generated transcriptome dataset for Halisarca dujardini representing genes expressed in adult specimens and free-swimming larvae (see Methods for details). Using a variety of sponge, cnidarian and bilaterian sequences we have BLAST-searched this dataset for Wnt genes and recovered ten complete coding protein sequences (Additional file 1). This stands in contrast with only three Wnt genes present in another demosponge, Amphimedon queenslandica, and also differs from the number of 21 genes identified in Sycon ciliatum (Calcarea, Calcaronea)  [16, 18]. For comparison, at least eight Wnt genes are present in Homoscleromorph sponges, e. g. Oscarella sp. [18]. We next wanted to know whether the ten newly identified Halisarca Wnts are orthologous to other sponge (or other metazoan) Wnt genes.
We have thus carried out Bayesian analysis adding these new sequences to the previously constructed comprehensive Wnt sequence dataset  [18]. Surprisingly, only one Halisarca sequence appeared to be in orthologous relationship with previously described Wnt genes, namely the Amphimedon WntC sequence, while no AmqWntA or AmqWntB orthologues could be identified in Halisarca (Fig. 1  and Additional file 2). We have named this gene HduWntC, and the remaining nine sequences HduWntD-WntL according to the order in which they were identified. Of these, six clustered together in our analysis with high support, suggesting they are likely a result of independent subfamily expansion in the Halisarca lineage (Fig. 1 ). Another pair of Halisarca Wnts was associated with Sycon ciliatum WntS, although with very weak support, and the last one showed no particular affinity to any of previously identified Wnt genes (Fig.
Availability of data and materials The datasets supporting the conclusions of this article are available in the ENA-SRA and ENA-TSA repositories. Reads were deposited in under study ERP013253, biosamples: SAMEA3672117 for RNA-Seq from larvae, SAMEA3672118 for the RNA-Seq from the adult specimen and SAMEA3672119 for gDNA from larvae. Final transcriptome was deposited in ENA-TSA database under accession numbers HADA01000001 -HADA01138992 http://www. ebi. ac. uk/ena/data/view/ HADA01000001-HADA01138992.
Acknowledgments We thank  Sven Leininger  for providing adult Halisarca RNA. We thank the "Molecular and cell technologies" research resource center of  Saint-Petersburg State University  for technical support. The authors are grateful to  Dr. A. A. Sukhotin , the director of the  White Sea Biological Station of the Zoological Institute of the Russian Academy of Sciences , and  The Sven Lovén Centre for Marine Sciences  for providing facilities for field research.
Funding We acknowledge funding from the  Sars International Centre for Marine Molecular Biology  to  M. Adamska  and grants from the  Russian Foundation for Basic Research  ( n°13-04-01084  and  16-04-00084 ), research grant № 1. 38. 209. 2014awarded by  Saint-Petersburg State University and European Community  grant  ASSEMBLE , agreement no. 227799. I. Borisenko  was supported by funds from the  Master student research training program  at the Sars Centre in 2010 and 2011, and a fellowship of  French Government  for master students in 2013.
D. Acquisition and post-processing In each experiment, acquisition of the 3D velocity vectors is carried out in multiple x y slices allowing for the volumetric reconstruction. For phase-averaged measurements, the SPIV (Stereoscopic Particle Image Velocimetry) system is triggered with the square signal used for the burst modulation. Image processing indicates peak values of high correlation, ensuring a good estimation of instantaneous velocities in the region of interest. No special filtering of the raw vector fields is undertaken. The Reuse of AIP Publishing content is subject to the terms at: https://publishing. aip. org/authors/rights-and-permissions. Downloaded to IP: 157. 92. 4. 4 On: Fri, 15 Jul 2016 13:43:46 parameters used for vector calculation of the SPIV data are set as follows: no image pre-processing, cross-correlation, multi-step with a size decrease of the interrogation window from 32 × 32 (2 passes) to 16 × 16 (2 passes), overlap of 50%, and post-processing with median filter.
Immediately after injection (t=0. 5 hours) and at t=3. 5 hours, t=24 hours, and t=48 hours, mice were imaged using the Nano-SPECT/CT scanner (Bioscan, Washington, D. C. , USA). CT scans were performed at the beginning of each SPECT acquisition. SPECT images were obtained in 24 projections over 40-60 minutes using a four-head scanner with 1. 4 mm pinhole collimators. All images were reconstructed with MEDISO software (Medical Imaging Systems, Budapest, Hungary). Fusion of SPECT and CT images was carried out using the PMOD software (PMOD Technologies, Zurich, Switzerland). For quantitative assessment of tissue distribution of [ 111 In]DTPA-S-CNHs or [ 111 In]DTPA-L-CNHs, mice were injected via the tail vein with 250 µL containing 50 µg of [ 111 In]DTPA-S-CNHs or [ 111 In]DTPA-L-CNHs labeled with approximately 0.
Acknowledgments The authors thank  Dr Kasuya  and  Dr Azami  for synthesis of CNHs. MZ thanks  Grants-in-Aid for Scientific Research C (22510119)  from the  Japan Society for the Promotion of Science. This work was supported by the  Centre National de la Recherche Scientifique (CNRS) , the  International Center for Frontier Research in Chemistry  (icFRC). AB wishes to thank  JSPS (Japanese Society for the Promotion of Science)  for the Invitation Fellowship in Japan (ID number  L15526 ). The authors would like to also thank  Dr Jane Sosabowski  and  Professor Stephen Mather  from the  Barts Cancer Institute, Queen Mary University of London , for their advice with SPECT/CT imaging and analysis.
a-smooth muscle actin immunofluorescence Cells were fixed with 4% paraformaldehyde in PBS for 15 minutes and permeabilized with 2. 5% Triton X-100 (Euromedex, 2000-B) in PBS for 3 minutes. After saturation with 5% BSA in PBS, cells were stained for alpha smooth muscle actin (aSMA) (Abcam, ab5694) and for DNA (DAPI). As secondary antibody, Cy TM 3 conjugated antirabbit (GE Healthcare, PA43004) was used. Samples were observed with an oil immersion objective (Plan Fluor 40X/1. 30 Oil, Nikon) on a Nikon ECLIPSE Ti (Nikon). Digital images were taken with a digital camera (Cool SNAP HQ 2 , Photometrics) and software (Meta-Morph 7. 5. 4. 0). To estimate the percentage of fibroblast differentiation, myofibroblasts were counted using aSMA staining. Then, Student (t-) and v 2 -tests were realized to evaluate the differential expression of aSMA between the untreated and treated fibroblasts (T2E2).
Exudate characterization TGF-b1, MMP1, MMP2, and MMP9 protein concentrations were determined by ELISA kit assays (respectively Promo-Kine, GE Healthcare, Invitrogen, PromoKine) according to the manufacturers' instructions. Absorbance was read at 450 nm on SpectraMax M5e (Molecular Devices) and protein concentration was calculated using SOFT Max Pro software (Molecular Devices).
Quantitative real-time PCR Quantitative real-time PCR (qPCR) was performed on the LightCycler480 system (Roche) using Maxima SYBR Green qPCR Master Mix (Fermentas, K0252). A final concentration of 500 nM of primer pairs (Eurofins, MWG, designed according to  14  ) was used for each qPCR reaction (sequences of the primers used are presented in Supporting Information Table  S6 ). Mean values of the triplicate relative concentrations were calculated and normalized to the value of the untreated cells (T2E2). For RTqPCR experiments, the "invariant" status of mRNAs of at least 3 housekeeping genes was assessed for each experiment to prevent experimental bias (Supporting Information Figure  S5  and data not shown).
In case of overlapping exons, coordinates flanking the region covered by the overlapping exons were used (Supporting Information Figure  S2A ). We obtained 49. 733 virtual transcripts corresponding to coding and noncoding genes. Raw gene expression is the sum of reads strictly included in each exon of a virtual transcript. Here, we analyzed mRNAs prepared from fibroblast cells obtained from two donors: donor A (two replicates) and B (one sample). The two samples from donor A allow us to limit experimental biases (independently from the donor) and the addition of the sample from donor B allows us to minimize donor-dependent variations. To evaluate the magnitude of potential biases introduced by the excess data from donor A, we tested three different normalization methods: (1) the three datasets are considered individually (triplicate); (2) normalization is performed on the two samples from donor A prior to a second normalization with the sample from donor B (prenormalization method); and (3) normalization is performed on the sum of the two samples from donor A and the sample of donor B (sum method) (Supporting Information Figure  S2 ).
In all cases, the normalization procedure from the DESeq R package  17  was applied using the Eoulsan pipeline. 15 nly genes showing differential expression associated with an adjusted p-value of 10 23 or less after normalization and analysis were retained. To deal with infinite fold change (FC) values caused by genes showing no expression in one condition, we added one read to all the replicates of the condition where at least one sample showed no expression, and repeated the complete analysis (normalization and differential analysis). Values for genes that previously had infinite FC values were modified in this manner, whereas all other genes retained their initial LogFC and adjusted p-values. Only genes with |LogFC| > 2 and Padj < 1Á10 23 by all three normalization methods (171, 409, and 1,006 genes for List I, List II, and List III, respectively) were included in further analyses, unless stated otherwise.
Cellular differentiation is the result of the differential expression of cell-specific genes. However, expression levels of the TFs controlling this process are not necessarily significatively changed as their activities can be modulated post transcriptionally. Thus, we performed an in silico target gene-based network analysis allowing us to identify 23 potential key regulators of fibroblast cell fate either for normal differentiation into myofibroblasts or in the context of chronic wounds. By knockdown approaches, we found that 17 out of 23 of these TFs were strongly involved in differentiation (Figure  5 ). The strength of our analysis comes from the unbiased approach of looking for evolutionarily conserved DNA binding elements common to the regulatory regions of concordantly expressed genes (via the DIRE program  20  ), rather than directly measuring TF transcript levels.
ACKNOWLEDGMENTS The authors thank  Elsa Raban  for technical help for the last sets of experiments. The authors thank  Brigitte Arnaud  and  Fondation Pierre Gilles de Gennes  for administrative support. The authors thank  Groupe Urgo  for the financial support. The authors thank all the members of the " Functional Imaging of Transcription " group for stimulating discussions. The authors thank  Lily Mirels  and  David Gorczyca  for their huge help in editing this manuscript. Source of Funding:  Fondation Pierre Gilles de Gennes  to CDD Conflicts of Interest: The authors declare no conflict of interest.
ACKNOWLEDGMENTS We thank  G. Nowell  ( Durham University, UK ) for technical support;  L. Cottrell ,  S. Guillot ,  S. Klimm , and  N. Malaspina  for constructive reviews; and  J. Brendan Murphy  for his careful editorial handling. This work was supported by a  Natural Environment Research Council (NERC)   Deep Volatiles Consortium Grant  ( NE/M000303/1 ) and a  European Research Council (ERC)   Starting Grant  (HabitablePlanet;  306655 ) to Williams. Williams also acknowledges  NERC Advanced Fellowship   NE/F014295/1. Bouilhol acknowledges support from an  ERC   Starting Grant  (MASE; 279828).
It was found that during the formation of the second layer, TiCl 4 molecules reacted both with either one or two hydroxyl groups; starting from the third layer TiCl 4 molecules reacted predominantly with two hydroxyl groups. HCl was identified as the only reaction by-product. The O/Ti ratio was found to increase from 1. 5 to 2 with the increasing number of cycles, which corresponds to the formation of stoichiometric TiO 2. The presence of anatase in the reaction products was confirmed using IR spectroscopy and XRD, where data obtained from the samples were compared to those obtained from commercial and/or synthesized anatase phase TiO 2. The author also pointed out that four Ti atoms were needed for the formation of the TiO 2 unit cell; therefore, XRD lines corresponding to the anatase phase appear only after four ML cycles.
ACKNOWLEDGMENTS R. L. P. thanks Tuomo Suntola for his support during the VPHA. Aziz Abdulagatov and Annina Titoff are acknowledged for significant help during the initiation of VPHA. The authors are grateful for all volunteers, who in addition to the current authors have shared at least one comment in the ALD-history-evolving-file during VPHA, in alphabetical order (as of December 3, 2016): Jaan Aarik, Ivan Bodalyov, Nikolai Chekurov, Simon Elliott, Aris Goulas, Marcel Junige, Luis Fabi an Peña, Alexander Pyymaki Perros, David C. Smith, Pia Sundberg, Massimo Tallarida, Mikko Utriainen, Timo Weckman, and Thomas W€ achtler. Additionally, Angel Yanguas-Gil has valuably contributed to VPHA by making VPHA-related improvements in Wikipedia and Christian Dussarrat by translating a Japanese original ALD paper.
This dispersion was spincoated for a target thickness of about 90 nm (3000 rpm, 90 s) and baked (90 °C, 90 s). The PEDOT:PSS thus covers the whole glass slide and fills the "wells" defined in the second photolithographic patterning step. Peeling of the sacrificial layer and hard baking the device (125 °C, 1 h) thus define the channel width, the distance between source and drain contact defines the channel length. Immersing the devices in deionized water over night removes excess low molecular weight compounds. Device Characterization: All experiments were done using a NaCl solution (100 mm) as electrolyte and a Ag/AgCl pellet (Warner Instruments) as gate electrode. The IV curves were recorded using a Keithley 2612A dual SourceMeter with customized LabVIEW software. For the precharacterization experiments with the drain load a Voltcraft R-BOX 01 decade resistor box was connected to the OECT and a Keithley 2612A dual SourceMeter was used for the supply voltage, the output voltage was recorded using a National Instruments USB-6251 BNC data acquisition system and customized LabVIEW software.
The ECG recordings were done in a low noise room at the hospital La Timone in Marseille, France. Ambu sensor N medical Ag/AgCl electrodes with 0. 95 cm diameter gel-assisted contact area were used as standard ECG electrodes to make contact with the skin. A battery was used for the supply voltage to reduce the noise coming from building ground and the output voltage was recorded using a Braintronics voltage recording system with Brainbox EEG-1166 amplifiers. The data were treated subsequently using a 49-51 Hz band block fast Fourier transform (FFT) filter, a 100 Hz low pass FFT filter, and a 0. 05 Hz high pass FFT filter.
Data collection and processing Prior to data collection, crystals of HMA8 N were cryoprotected with Paratone-N, while crystals of HMA6 N -AA were cryoprotected by adding ethylene glycol to the reservoir solution to a final concentration of 27% (w/v). The crystals were then flash-cooled to 77K in liquid nitrogen. A complete X-ray diffraction data set was collected on beamline BM14 at the European Synchrotron Radiation Facility (ESRF, Grenoble, France) using a MARCCD 225 detector in case of HMA8 N. A total of 150 frames were collected with a rotation range of 1°and a detector distance of 187. 25 mm. For HMA6 N -AA complete X-ray diffraction data sets corresponding to the peak and inflection point were collected on beamline ID23-1 (ESRF, Grenoble, France) using a PILATUS 6M-F detector. A total of 1210 frames were collected with a rotation range of 0.