dataesr/scientific-paragraphs-categorization huggingface dataset:
The signals were amplified 100Â in DC mode (10Â by Axoprobe 1A and then 10Â by a custom-made DC preamplifier), processed using Digidata 1200, stored on a PC and analyzed using pClamp 10 software (Axon Instruments/Molecular Devices, USA). CAP recordings were analyzed according to their baseline-topeak amplitude, width, refractory period with pair pulse stimulation. The maximal amplitude of the CAPs was recorded at supra-threshold stimulation intensity. The refractoriness of the axons was examined by stimulating the cord by pair pulses with different intervals (starting from 0. 5 ms with an increment of 0. 5 ms), and by examining the recovery of the second CAP in comparison to the first one. To examine the ability of spinal cord axons to conduct signals at high frequency, the cord was stimulated with 20, 50 and 100 Hz (100 pulses in total), respectively.
63-fold increase) (Fig. 5B ). However, no evidence of long-distance CST axon preservation/regeneration at and beyond the lesion was detected (data not shown). The survival of axons traversing the injury site was also assessed by counting the FG-labeled neurons in brainstem nuclei following spinal cord transection and FG impregnation distal (T10) to the injury site. Counts of retrogradely labeled neurons were performed in the red nucleus, vestibular nuclei and the total brainstem (which includes red nucleus, vestibular nuclei, raphe nuclei and reticular formation). Representative sections of FG-labeled neurons in the red nucleus from animals treated with saline and QL6 are shown in Fig. 5C. QL6-injected animals showed higher overall neuronal counts in the red nucleus, vestibular nuclei and total brainstem (Fig.
To assess the refractoriness of the spinal cord, paired stimuli with varied intervals were delivered to the cord, and we measure the minimum time intervals for the second pulse to trigger CAP (absolute refractory period), as well as the full recovery of the CAPs (relative refractory period). Varying the intervals between the two paired pulses successfully yielded a clear estimation of the absolute refractory periods. We observed a significant decrease (P < 0. 01) in the absolute refractory period in the QL6-treated groups in comparison to the injured control (Fig. 8B ). Similarly, QL6-treated cords also exhibited a decreased relative refractory period (Fig. 8C ). Taken together, these data indicate that QL6 treatment significantly reduces axonal refractoriness in injured cords.
Acknowledgements The authors would like to thank  Dr. Jeffrey D. Hartgerink  for the preparation of the fluorescent tagged QL6 peptide,  Jenny Oh  for assistance with the histochemistry experiments,  Behzad Azad  for his help with behavioral testing,  Jian Wang  for help with cell culture,  Giovanni Battista Calvieri  and  Steven Doyle  for assistance with EM experiments and  Madeleine O'Higgins  for her editorial reviews. This study was supported by operating grant from  Canadian Institutes of Health Research and the Gerry and Tootsie Halbert Chair in Neural Repair and Regeneration  (held by  Dr. Michael G. Fehlings ).
5 (1. 0)% for coherent electrons (muons), and 6. 5 (3. 5)% for incoherent electrons (muons), and are taken into account in the systematic error calculation. Transverse polarization is expected from helicity conservation for a quasi-real photon. It is therefore assumed in these calculations that the J/ψ is transversely polarized, as found by previous experiments  [25, 26]. The trigger efficiency was measured relying on a data sample collected in a dedicated run triggered by the ZDCs only. We selected events with a topology having the BUPC conditions, given at the beginning of section 3. 1. The resulting trigger efficiency was compared with that obtained by the Monte Carlo simulation, showing an agreement within - - - f c - - 0. 03±0. 03 0. 47±0. 09 - - λ γγ (GeV -1 c 2 ) - - - - -1. 55±0. 88 -0.
Taking the ratio between the incoherent and coherent cross section provides further constraints on the treatment of the nuclear modifications implemented in the different models. Another advantage is that the photon spectrum is factorized out, so that the comparison directly probes the ratio of the photonuclear cross sections. The ratio obtained from data is 0. 41 +0. 10 -0. 08 sta + sys. This can be compared with 0. 21 from LM, 0. 41 from STARLIGHT, and 0. 17 from RSZ-LTA. Although the RSZ-LTA model is quite close for the coherent cross section at midrapidity, it seems to underpredict the incoherent cross section. The LM model also predicts a too low ratio. STARLIGHT, on the other hand, has about the right ratio of incoherent-to-coherent cross section, although it does not reproduce any of the cross sections individually.
Acknowledgements The ALICE collaboration would like to thank all its engineers and technicians for their invaluable contributions to the construction of the experiment and the CERN accelerator teams for the outstanding performance of the LHC complex. The ALICE collaboration acknowledges the following funding agencies for their support in building and running the ALICE detector:  State Committee of Science, World Federation of Scientists (WFS)  and  Swiss Fonds Kidagan ,  Armenia ,  Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) ,  Financiadora de Estudos e Projetos (FINEP) ,  Fundacão de Amparo à Pesquisa do Estado de São Paulo (FAPESP) ;  National Natural Science Foundation of China (NSFC) , the  Chinese Ministry of Education (CMOE)  and the  Ministry of Science and Technology of China (MSTC) ;  Ministry of Education and Youth of the Czech Republic ;  Danish Natural Science Research Council , the  Carlsberg Foundation  and the  Danish National Research Foundation ; The  European Research Council  under the European Community's  Seventh Framework Programme ;  Helsinki Institute of Physics  and the  Academy of Finland ;  French CNRS-IN2P3 , the  'Region Pays de Loire', 'Region Alsace', 'Region Auvergne'  and  CEA, France ;  German BMBF  and the  Helmholtz Association ;  General Secretariat for Research and Technology, Ministry of Development, Greece ;  Hungarian OTKA  and  National Office for Research and Technology (NKTH) ;  Department of Atomic Energy and Department of Science and Technology of the Government of India ;  Istituto Nazionale di Fisica Nucleare (INFN)  and  Centro Fermi -Museo Storico della Fisica e Centro Studi e Ricerche "Enrico Fermi", Italy ;  MEXT   Grant-in-Aid for Specially Promoted Research, Japan ;  Joint Institute for Nuclear Research, Dubna ;  National Research Foundation of Korea (NRF) ;  CONACYT, DGAPA, México, ALFA-EC  and the  EPLANET Program  ( European Particle Physics Latin American Network) Stichting voor Fundamenteel Onderzoek der Materie (FOM)  and the  Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) ,  Netherlands ;  Research Council of Norway (NFR) ;  Polish Ministry of Science and Higher Education; National Authority for Scientific Research -NASR  ( Autoritatea Nat ¸ionalȃ pentru Cercetare S ¸tiint ¸ificȃ -ANCS) ;  Ministry of Education and Science of Russian Federation, Russian Academy of Sciences, Russian Federal Agency of Atomic Energy, Russian Federal Agency for Science and Innovations and The Russian Foundation for Basic Research; Ministry of Education of Slovakia ;  Department of Science and Technology, South Africa ;  CIEMAT ,  EELA, Ministerio de Economía y Competitividad (MINECO) of Spain, Xunta de Galicia  ( Consellería de Educación ),  CEADEN, Cubaenergía, Cuba , and  IAEA (International Atomic Energy Agency );  Swedish Research Council (VR)  and  Knut & Alice Wallenberg Foundation (KAW) ;  Ukraine Ministry of Education and Science; United Kingdom Science and Technology Facilities Council (STFC) ; The  United States Department of Energy , the  United States National Science Foundation , the  State of Texas , and the  State of Ohio.
Expression microarrays Three replicate array experiments were done for ASCs, LMNA-KD ASCs, and adipocytes using Illumina HumanHT-12 v4 expression BeadChip arrays. The Gene Expression module from Illumina GenomeStudio was used to compute a detection P-value for each probe. Signal intensities between replicates were normalized using the lumi package  (Du et al. 2008 ) and replicate signals combined by using median signal intensity. A gene was considered expressed when probe intensities were significantly stronger (P < 0. 01) than background signals. Adipocyte gene expression data have been Figure  6. Developmental regulation of LMNA association of promoters important for lineage commitment. In undifferentiated adipocyte progenitors (ASCs), master regulator genes of differentiation into adipogenic and nonadipogenic lineages are tethered to LMNA and not expressed.
Adipogenic differentiation results in disengagement of adipogenic loci from LMNA and their transcriptional activation. However, nonadipogenic loci remain associated with LMNA in adipocytes. These include genes important for differentiation into, e. g. , osteogenic or myogenic pathways, endodermal and ectodermal lineages, as well as pluripotency-associated genes. published earlier  (Sørensen et al. 2010)  and are available in NCBI GEO with accession code number GSE19773.
Acknowledgments We thank  K. Vekterud  for technical assistance. This work was supported by the  Centre National de la Recherche Scientifique-University Paris-Diderot  Paris 7, and  Association Franc xaise de lutte contre les Myopathies  (B. B. , I. D. -G. ), and by the  Research Council of Norway, South-East Health Norway , the  Cancer Society (P. C. ) , and the  University of Oslo  (P. C. , R. E. ).
2005 , data version delivery § DR3-S11); Herschel PACS 100 and 160 µm data from the HerMES survey (UDS deep level-3 field; reduced as in  Ibar et al. 2010  but using an improved deglitching approach); SPIRE 250, 350 and 500 µm maps (SMAP v4. 2;  Levenson et al. 2010 ) and catalogues (SCAT SXT iDR1;  Smith et al. 2012 ) retrieved from the Herschel Database in Marseille (HeDaM * ) of the HerMES survey; AzTEC 1100 µm data taken at JCMT  (Austermann et al. 2010). COSMOS: 24 and 70 µm, from the Spitzer coverage of the COSMOS field (S-COSMOS; GO2+GO3a+GO3b Delivery v1 from the NASA/IPAC Infrared Science Archive ‡ ;  Sanders et al. 2007; Le Floc'h et al. 2009; Frayer et al. 2009) ; PACS 100 and 160 µm from the PEP survey; SPIRE 250, 350 and 500 µm from HerMES (SMAP v4. 2 and SCAT SXT iDR1 from HeDaM); AzTEC 1100 µm data taken at ASTE  (Scott et al.
Empirical Calibration To account for possible biases introduced by the way we measure stacked flux densities, we use the released catalogues from each image to find the median and scatter (3 σ clipped) of the ratio between catalogued flux densities (between 5-and 10-σ) and fitted Gaussian peaks (aperture photometry for the PACS case). We call this ratio η = SFIT/SCAT. We note that for Herschel and AzTEC images, η is within 15% from unity, although for Spitzer images η is the value to convert from ster-radians to beams. We apply these normalisation factors to the extracted flux densities in order to make the calibration of each stacked data point dependent on the released catalogues from each of the different images (see Table  1 ). In the cases when we merge the UDS and COSMOS fields, we use the average correction found between both fields (usually within 10 per cent of each other).
In summary, for a given number of UDS (NUDS) and COSMOS (NCOSMOS) sources, the calibrated flux density measured from their co-added stacked signals can be expressed as: MED(S) = η × MED [(Si=1,. ,N UDS -BMC,UDS) + (Sj=1,. ,N COSMOS -BMC,COSMOS)] , (1) where MED stands for the median over all the cut-out map signals Si, and BMC correspond to the Monte-Carlo simulated sky background obtained by randomising the positions around the source sample for each field. We find that the detection significance (fitted peak over local pixel r. m. s. ) of each stacked data point ranges at < 15 σ, where the 24-, 250-, and 350-µm bands provide the clearest detections. Errors in our measurements are estimated using the same Monte-Carlo simulations (100 realisations) to obtain the averaged pixel rms noise for Spitzer, Herschel-SPIRE and AzTEC stacks, and the averaged uncertainty using random aperture photometry on Herschel-PACS stacks.
6). This alternative parametrisation is valid for samples with L(Hα) obs /L(8-1000 µm) ≈ 2/1000, i. e. when both obscured and unobscured component have similar contributions to the total SFR. port from the Netherland Organisation for Scientific research (NWO) through a Veni fellowship. IRS acknowledges support from STFC, a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. RJI acknowledges support in the form of ERC Advanced Investigator programme, cosmicism. The HiZELS data is based on observations obtained using both the Wide Field Camera on the 3. 8-m United Kingdom Infrared Telescope (operated by the Joint Astronomy Centre on behalf of the Science and Technology Facilities Council of the U. K. ) and Suprime-Cam on the 8. 2 m Subaru Telescope, which is operated by the National Astronomical Observatory of Japan.
This research has made use data from the HerMES project (http://hermes. sussex. ac. uk/). HerMES is a Herschel Key Program utilising Guaranteed Time from the. SPIRE has been developed by a consortium of institutes led by Cardiff Univ. (UK) and including: Univ. Lethbridge (Canada); NAOC (China); CEA, LAM (France); IFSI, Univ. Padua (Italy); IAC (Spain); Stockholm Observatory (Sweden); Imperial College London, RAL, UCL-MSSL, UKATC, Univ. Sussex (UK); and Caltech, JPL, NHSC, Univ. Colorado (USA). This development has been supported by national funding agencies: CSA (Canada); NAOC (China); CEA, CNES, CNRS (France); ASI (Italy); MCINN (Spain); SNSB (Sweden); STFC, UKSA (UK); and NASA (USA). PACS has been developed by a consortium of institutes led by MPE (Germany) and including UVIE (Austria); KUL, CSL, IMEC (Belgium); CEA, OAMP (France); MPIA (Germany); IFSI, OAP/AOT, OAA/CAISMI, LENS, SISSA (Italy); IAC (Spain).
Moreover, despite the fact that a large number of TDP-43 RNA targets have been identified  (15 -18) , the initiating events and pathogenic pathways underlying TDP-43mediated neurodegeneration remain to be identified. Here we show that similar to its human homolog, Drosophila TDP-43, TAR DNA binding protein homolog (TBPH), is expressed in neurons, glia and muscle cells. Both loss of function and overexpression of TBPH result in decreased viability, impaired synaptic transmission, defective locomotion and age-related progressive neurodegeneration. Together these data suggest that both increased and decreased levels of TDP-43 initiate a loss-of-function phenotype, resulting in decreased neuronal viability and subsequent degenerative cell loss that characterize motor neuron diseases like ALS and FTLD.
We also recorded electroretinograms (ERGs) from adult TBPH LOF and GOF cases compared with appropriate controls. Both white-eyed TBPH2/2 LOF and w 1118 control revealed similar responses to blue light pulses with no differences in peak -peak amplitude of the ERG. Moreover, the ERG amplitude of red-eyed GMR. TBPH-RNAi and OregonR were indistinguishable, also when compared between 1-and 5-day-old flies (Fig. 4C  and D ). We then examined the off-transient and plotted their size as a function of the maintained photoreceptor response. On average, data points from both TBPH LOF strains, TBPH2/2 and GMR. -TBPH-RNAi flies, were above those from controls (Fig. 4E ). We tested the null hypothesis that data points were distributed evenly above and below the control regression line between maintained ERG potential and off-transient, which revealed significant deviation for both TBPH2/2 and GMR.
-TBPH-RNAi. Moreover, we compared the size of the offtransient recorded in both TBPH LOF lines with that estimated from the control regression line which revealed 15 and 25% reduction in the off-transient in TBPH2/2 and GMR. -TBPH-RNAi, respectively. As positive control, we blocked synaptic transmission in the retina using GMR. Shibire-RNAi, the Drosophila homolog of Dynamin involved in synaptic transmission  (32) , which resulted in completely abolished offtransient (Fig. 4C ) with data points significantly above the wild-type regression line (Fig. 4E ). We also recorded ERGs from TBPH GOF flies where Drosophila TDP-43 was over-expressed in the eye. TBPH/ w-controls showed an ERG in response to blue light pulses like wild-type, whereas GMR/w-flies showed a smaller response. In contrast, GMR.
According to this model, C-terminal, but also RRM mutations may hinder the participation of TDP-43 in ribonucleoprotein complex formation and hence, their function, leading to physiological deficits and eventually neurodegeneration. In summary, our findings demonstrate that both loss and gain of TDP-43 function result in functional deficits whereby impaired synaptic transmission and defective motor behavior precede progressive deconstruction of neuronal connections, ultimately causing age-related neurodegeneration. Our data therefore provide in vivo evidence for common loss-of-function phenotypes underlying TDP-43 dysfunction that likely also characterize TDP-43-mediated ALS and FTLD.
Image acquisition and analysis Images were obtained either with Motic BA400 or Leica TCS SP5 confocal microscope with Leica Application Suite Advanced Fluorescence (LAS AF) version 2. 0. 2 software. For confocal images, channels were scanned sequentially. For comparative images, the same microscope settings were used for the control and experimental genotypes. For Figs  6  and 7 , confocal z-stacks were rendered as 3-D projections. Signal quantification of digital images was carried out using Fiji (FIJI). Significance of GFP and FasII signal intensity was calculated using unpaired Student's t-test. Equal variance assumptions were based on Levene's test for equality of variance.
Video-assisted motion tracking Tracking arenas were modified six-well tissue culture plates (35 mm diameter wells) filled with silicon rubber (Sylguard) to leave a 3 mm space so that flies could walk freely but not hop or fly. 18-24 flies were briefly anaesthetized with CO 2 , placed in separate arenas and left to recover at 258C for 45 min before being placed above an array of white LEDs within a temperature-controlled incubator. Tracking was carried out at 258C. A black and white CCD camera (Hitachi, MP-M1A) positioned above the arenas was connected to a PC via an analog capture card (Integral Technologies, Flashbus MV Lite). Recordings were carried out during the same time slot. Recorded videos were converted to fly movie format using the motmot package  (62)  and loaded into Ctrax software  (63)  to analyze the positions of the flies throughout the video.
Position data for the 30 min file was exported as a Matlab-compatable (Mathworks) matrix file. Errors in the tracking were fixed using Matlab (Mathworks) as well as FixErrors GUI  (63) , which is described in further detail at http://ctrax. sourceforge. net/fixerrors. html. Fixed trajectories were analyzed in Matlab using custom scripts (written by D. M. H). This analysis determined the mean velocity, mean activity, activity over time and mean cumulative distance traveled by the population of flies in the arena. Activity was defined as movement per frame above a velocity of 2 mm/ s. Average activity was the percentage of frames where the fly was active (. 2 mm/s velocity). Mean velocity was the average of velocities in each frame of the recording only when the fly was active. Box-plots were generated in Matlab where the boxes show median, upper and lower quartiles; whiskers contain data 1.
0. 05) for w 1118 and TBPH2/2 larvae, respectively. Resting membrane potentials were 254. 1 + 1. 4 mV (n ¼ 7) and 252. 0 + 1. 5 mV (n ¼ 8, P ¼ 0. 0018) and input resistances were 5. 9 + 0. 2 MV (n ¼ 7) and 6. 4 + 0. 3 MV (n ¼ 8, P , 0. 05) for ELAV/+ and ELAV. TBPH, respectively. Data, filtered at 1 kHz and digitized at 10 kHz, were acquired using an Axopatch 200B amplifier and a Digidata 1320A data acquisition board (Molecular Devices Data) were acquired using pClamp8. 02 (Molecular Devices) and analyzed with Clampfit8. 02 (Molecular Devices) or MiniAnalysis (Synaptosoft). EJP amplitude histograms were constructed by averaging 50 separate events stimulated at 0. 2 Hz from an individual muscle cell and then calculating the mean response from at least six larvae per line. Spontaneous release events were recorded for 120 s without any electrical stimulation.
Acknowledgments We thank  Anne Derbise  and  Elisabeth Carniel  ( Pasteur Institute, Paris, France ) for providing Yersinia pseudotuberculosis strain IP31758,  Arie Geerlof  ( EMBL, Hamburg, Germany ) for vector pETG20A,  Jean-Marc Ghigo  ( Pasteur Institute, Paris, France ) for strain MFDpir, the members of the  Cascales, Lloubes, Cambillau, Bouveret and Sturgis research groups  for helpful discussions,  Isabelle Bringer ,  Annick Brun  and  Olivier Uderso  for technical assistance, the  Sarah Bigot shuttle  for cloning procedures,  Yvan Duach  for encouragements, and the three reviewers for their helpful comments.
This work was supported by the  Centre National de la Recherche Scientifique  and a grant from the  Agence Nationale de la Recherche  ( ANR-10-JCJC-1303-03 ) to E. C. E. G. and E. D. were recipients of post-doctoral fellowships from the  Fondation pour la Recherche Medicale  ( SPF-2009-12-17571  and  SPF-2010-12-21116  respectively). X. -Y. Z. was supported by the  ANR-10-JCJC-1303-03  grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
The function of genes is often evolutionarily conserved, and comparing the annotation of ortholog genes in different model organisms has proved to be a powerful predictive tool to identify the function of human genes. Here, we describe Manteia, a resource available online at http://manteia. igbmc. fr. Manteia allows the comparison of embryological, expression, molecular and etiological data from human, mouse, chicken and zebrafish simultaneously to identify new functional and structural correlations and gene-disease associations. Manteia is particularly useful for the analysis of gene lists produced by high-throughput techniques such as microarrays or proteomics. Data can be easily analyzed statistically to characterize the function of groups of genes and to correlate the different aspects of their annotation.
INTRODUCTION The recent explosion of bioinformatics resources provides an increasing amount of data and an expanding array of tools for researchers. Some of the databases where this information is available are specialized for a specific type of data such as expression data [e. g. Unigene (1), Gene Expression Omnibus (2), Arrayexpress (3)], genomic data [e. g. Ensembl (4), the National Center for Biotechnology Information (NCBI)  (1) ] or genetic disease data [e. g. the Online Mendelian Inheritance in Man database (OMIM)  (5) ]. Several resources have been established gathering the information relevant to specific model organism such as the Mouse Genome Informatics database [MGI  (6) ] and the Zebrafish Information Network database [ZFIN  (7) ]. However, the way the information is formatted and stored in such specialized databases greatly limits the possibilities for combined analysis of multiple data sets.
The information is usually formatted for the system that hosts it, which makes it difficult to correlate and compare different data from different databases. Even in systems that specialize on a particular model organism, the information is usually compartmentalized and can only be explored individually. Conversely, the understanding of events involved in development, physiology and disease requires one to gather a wide variety of experimental observations and to study how events correlate over time. This requires not only a resource that hosts the relevant information, but also a system that provides the right tools to extract and exploit the full range of these data in a coherent environment. When we started this project, the annotation of the chicken genome was poor, yet the first microarrays were becoming available.