dataesr/scientific-paragraphs-categorization huggingface dataset:
, Heppignies,-Belgium) according to the manufacturer's instructions. Statistical analysis. Statistical analysis was performed by using the SPSS 17. 0 package (SPSS Inc. , Chicago, IL). Comparisons of groups were analyzed using the x 2 test of a Fisher exact test (when expected values were below 5). To calculate combined odds ratios (ORs) and 95% confidence intervals (CIs), we used the Cochran-Mantel-Haenszel method implemented in Review Manager RevMan v. 5. 0 (The Nordic Cochrane Centre, Copenhagen, Denmark). p values ,0. 05 were considered statistically significant. The Der Simonian and Laird random effects model was used according to the results of the tests of heterogeneity. A sensitivity analysis was performed to test the relative influence of each study on the results. Studies were sequentially dropped, and the effect on the change in the overall degree of heterogeneity was determined.
All sequencing results were assembled using the CAP3 program  (10). Sequence analysis revealed that PmCV-1 is closely related to members of the Cyclovirus genus in the Circoviridae family. PmCV-1 possesses a 1,777-nucleotide (nt) genome containing three ORFs encoding 266, 255, and 146 amino acids (aa). Numbering starts with the loop in the conserved stem loop. The 266-aa product of the largest ORF, from nt 51 to 851, shared about 30% sequence identity (over 90% of query coverage) with the putative Rep of cycloviruses and contained RCR and SF3 motifs. The 255-aa product of the ORF translated in the opposite di-rection, from nt 1,671 to 904, shared 25% identity with the Cap protein of a Diporeia sp. -associated circular virus (GenBank accession no. KC248415. 1, E value 0. 004), and thus the ORF probably encodes the capsid protein.
The smallest ORF, from nt 1,246 to 1,686, codes for a 146-aa protein that did not reveal any amino acid similarity using Blastx in a protein database with E values of Ͻ0. 01. The 156-nt intergenic region between the 5= ends of putative cap and rep genes encompasses 13-nt inverted repeats (nt 11 to 23 and 1765 to 1777) forming a stem and a 10-nt loop containing a canonical nonanucleotide, TAATATTAC, between nt 2 and 10. The intergenic region between the 3= ends of the cap and rep genes is 53 nt long. The genome structure resembles that of circoviruses and cycloviruses. Metagenomic discovery has particularly impacted the discovery of CRESS-DNA viruses, both in host range and genetic diversity. Although this approach is very powerful, its perils should not be underestimated  (11). Nucleotide sequence accession number.
GENOTYPING The six coding exons and introns boundaries of FHL1 (NM_001159702) were screened for mutations by PCR on DNA from peripheral lymphocytes using primer pairs with a universal sequence (Table on demand). Exon 5 was sequenced with primers: 5PUF: 5 -ACCGTTAGTATGCGAGTTGGATTCAGGCAC TGGATCCTA -3 5PUR: 5 -TCGGATAGTCAGTCGTTTGCTGTCGTGAGG ATGGAATG -3. Analysis of sequences was done with SeqScape software (Applied Biosystem).
, 2014). Membranes were probed with primary antibodies against FHL1 (ab23937 Abcam), LC3 (Thermo Scientific), p62 (Progen Biotechnik), ubiquitin (Cell Signaling Technologies), beclin 1 (Cell Signaling), BNIP3 (Sigma), vinculin (Sigma), or GAPDH (Millipore). Proteins were revealed with anti-rabbit, -mouse (Bethyl), -goat (Santa Cruz Biotechnologies), or -guinea pig (Sigma) HRP-conjugated secondary antibodies using the ECL reagent (Pierce-Thermo Scientific). Densitometric quantification of protein bands was performed by the ImageJ software (US National Institute of Health). Western blotting and quantifications are representative of at least three independent experiments.
Comparative study It is difficult to make a fair comparison between two methods that are so different in nature. In the comparison presented in the following, strong efforts have been made in order to obtain the best results with the inversion-based method. Constant feedback gains K p and K d can be designed so as to achieve some performance properties. For instance, the pole placement technique is used to set the damping ratio and the natural frequency of the tracking error dynamics. For our application, this tuning yielded degraded performances compared to the LPV method. Better results were obtained using recently developed tools that are based on nonsmooth optimization  [28]. They allow synthesizing structured and fixed-order controllers for linear systems. The main tool is the hinfstruct function of MATLAB  [29] , devoted to H ∞ synthesis.
Trans-splicing is efficient on endogenous mRNA in vitro and in vivo We next wanted to address the possibility of obtaining transsplicing on endogenous RNA. As a first step, we analyzed the expression of titin and dysferlin mRNA in a number of cell lines including the myogenic C2 cells at the myoblast stage (D0) and after 1 (D1), 2 (D2), and 7 days (D7) of differentiation (data not shown). Detection of titin and dysferlin RNA was obtained only from C2 at all stages. RT-PCR was performed with a set of oligonucleotides (Mex2F and Mex6R for titin and a and 51R for dysferlin, Supplementary Table  S1 ). The titin set encompasses the alternatively spliced Mex5 exon. As a control for this RT-PCR, TA of WT mouse were amplified and showed the two known alternative spliced isoforms (Mex5+ and Mex5-).
Confirmation of translation from ORF in the PTM Since the observed bands were present even when the PTM was transfected alone (with or without the presence of the BD for titin PTM), they seem related to the presence of the PTM but not dependent on trans events at the location of binding. A bioinformatics analysis indicated the existence of an open reading frame (ORF) for all PTM sequences in-frame with the Flag epitope and for which the ATG start codon was associated with a predicted Kozak sequence as defined by the ATGPR software (http://atgpr. dbcls. jp/) (Figure  5a ). In the titin sequence of PTM Mex6, only one such ORF was identified, starting at an ATG embedded in a sequence with a weak predicted Kozak score (ATGPR score 0. 10). This ORF would lead to a 6 kDa polypeptide if translated, therefore with a size not consistent with the 16 kDa protein seen on WB.
Paired-end sequencing on 100 bp was then run on Illumina HiSEQ 2000. Bioinformatical analysis of the sequencing data was performed as described in ref. 29 in four steps: (i) alignment of the reads on the reference genome (mm 9 ) supplemented by the exogenous sequence of the PTM using the TopHat2 software,  30  (ii) detection, assembling, and quantification of the sequenced transcripts using the Cufflinks software,  31  and (iii) detection of fused transcripts using the TopHat-Fusion software. 32 Examination of the data was performed through the web interface Integrated Genome Viewer (http://www. broadinstitute. org/igv/), and graphic representation of the consensus sequence around junctional sites were obtained using the web-based tool WEBLOGO (http://weblogo. berkeley. edu/logo. cgi).
Quantifications were performed using the Odyssey Application Software. Histological analysis. Cryosections (8 μm thickness) were prepared from frozen muscles injected or noninjected by the AAV-PTM Mex6 or AAV-PTM Dysf. Transverse sections were processed for Hematoxylin-Phloxin-Saffron and imaged using a Nikon Eclipse E600 microscope with a charge-coupled devices camera (Sony, Tokyo, Japan) and a motorized stage for centronucleated fibers evaluation. Centronucleated fibers were quantified using the Histolab software (Microvision, Evry, France). Statistics. Data are presented as means ± SEM. Individual means between two groups were compared using the Mann-Whitney nonparametric test. Differences were considered to be statistically significant at *P < 0. 05.
EXPERIMENTAL PROCEDURES Recombinant RNA Modeling and Synthesis-To predict secondary structures of recombinant RNA and estimate their free energy (dG), the Mfold (  16 ), IDT Sci-Tools OligoAnalyser (ver-sion 3. 1), and ViennaRNA platforms were used. To estimate melting temperatures for DNA-DNA and RNA-DNA duplexes, we used IDT Sci-Tools OligoAnalyser software (version 3. 1)  (17). The recombinant RNAs were obtained by T7 transcription using the T7 RiboMAX Express Large Scale RNA Production System (Promega) on the corresponding PCR products and were gel-purified. For PCR, the following oligonucleotides containing a T7 promoter (underlined) were used: To test recombinant RNA annealing to target mtDNA, fragments of wild type and mutant mtDNA were amplified using primers hmtGluRT (5Ј-GTT CTT GTA GTT GAA ATA C-3Ј) and CRC-F (5Ј-CAT ACC TCT CAC TTC AAC CTC C-3Ј), separated on 1% agarose gel, blotted to Hybond-N membrane, and hybridized with 32 P-labeled recombinant RNAs in 1ϫ PBS at 37 °C.
After PhosphorImager quantification (Typhoon Trio, GE Healthcare), the hybridization signals were normalized to amounts of corresponding mtDNA fragments calculated after ethidium bromide staining of the agarose gel (before transfer to Hybond membrane) by densitometry using G-Box and GeneTools analysis software. Thereafter, hybridization specificity was calculated for each RNA as one minus ratio between normalized signals for wild type and mutated DNA fragments. Thus, for recombinant RNA annealed only to mutant DNA fragment, the hybridization specificity value reached 1, and for RNA annealed equally to mutant and wild type fragments, this value was close to 0. At least three independent experiments were performed for each RNA. Chimeric Oligonucleotide Synthesis-Chimeric oligonucleotides D20L DNA and D20H DNA were synthesized on an automatic ASM-800 RNA/DNA synthesizer (Biosset) at 0.
At different time periods after transfections, living cells were stained with 5 M tetramethylrhodamine methyl ester (TMRM) for 15 min at 37 °C, washed, and imaged in DMEM without red phenol. The LSM 700 confocal microscope (Zeiss) was used in conjunction with Zen imaging software, and images were acquired with a Zeiss 63ϫ/1. 40 oil immersion objective with a resolution of 1024 ϫ 1024. The excitation/emission laser wavelengths were 488 nm (green channel) and 555 nm (red channel). Images were analyzed using ImageJ software  (24)  and JACoP plugin  (25). Co-localization analyses were performed on multiple cells and optical sections. Pearson's and Manders' coefficients were estimated  (26, 27). Pearson's correlation coefficient provides a measure of correlation between the intensities of each channel in each pixel.
Mitochondria Quantification-2-cm 2 wells of 80% confluent cybrid cells and control wild type 143B cells, transfected with FD20H RNA, were stained with 5 M TMRM and 200 nM MitoTracker Green during 15 min in culture medium. The intensity of fluorescence was directly measured in a culture plate in DMEM without red phenol by VICTOR TM X3 multilabel plate reader (PerkinElmer Life Science) at 485 nm (green channel) and 555 nm (red channel) in triplicate for each sample. After fluorescence measurement, cells were detached and quantified by flow cytometry using CyFlow FACS and FloMax software (Partec). Activity of complex I was measured using a MitoSciences kit (Abcam). Statistical Analyses-Pairwise comparisons were performed using two-tailed Student's t test and Excel software (Microsoft). Data are expressed as means Ϯ S.
We suppose that the discrepancy between predictions and experimental data is due to the absence of software adapted to calculate the T m of RNA-DNA duplexes containing a mismatch. Another possible explanation consists in formation of alternative secondary structures in RNA molecules that cannot be predicted by available software. Another interesting issue is that the hybridization of RNA containing an insertion of the same length corresponding to the complementary L-strand of mtDNA (FD20L) was much less selective. This discrepancy can be explained by base mismatches: for FD20H, C-A pairing decreases the T m of hybridization with wild type mtDNA by 10 °C (Table  1 ) compared with mutant mtDNA (predicted by IDT Sci-Tools OligoAnalyser software (version 3. 1) for mismatch containing hybrids).
Acknowledgments-We are grateful to  Massimo Zeviani  ( National Neurological Institute "Carlo Besta" of Milan ) for providing the transmitochondrial cybrid cell lines and to  Jérôme Mutterer  ( Institute of Molecular Biology of Plants, Strasbourg ) for helpful assistance in confocal microscopy analysis. We also thank  Virginie Girault ,  Catherine Murfitt ,  Laure Poirier , and  Charlotte Simonin  for experimental contributions.
* The work was supported by  CNRS , the  University of Strasbourg, Association Française contre les Myopathies ,  Agence Nationale de la Recherche  ( ANR-06-MRAR-37-01 ;  BLAN08-2-309449 ),  Fondation pour la Recherche Médicale  ( DEQ20081214003 ),  ARCUS/Suprachem Collaboration Program and LIA Collaboration Program (ARNmitocure). This work has also been published under the framework of the LABEX  ANR-11-LABX-0057_MITOCROSS  and is supported by the state managed by the  French National Research Agency  as part of the  Investment for the Future program. □ S This article contains supplemental movies. 1 Supported by  Fondation pour la Recherche Médicale  and  Association Française contre les Myopathies Ph. D. fellowships.
The pellets were dried at RT. Duplicate pellets were dissolved in 200 ml of urea 8 M. 2D-DIGE and mass spectrometry identification of proteins of interest were performed by the Cochin Institute (Paris). Spots corresponding to proteins with expression modified between HG001 wt and ÁsprX were subjected to in-gel trypsin digestion, peptide extraction and desalting, followed by MALDI-ToF/ToF analysis. Peptides were analyzed using MASCOT and the NCBInr database to identify the selected protein spots. The average ratio of protein levels was calculated using DeCyder 2D software (GE Healthcare) to determine the change in normalized spot volume between HG001 wt and HG001DsprX samples. The average ratios are shown in Supplementary Table  S3 , although the statistical analysis was based on the log of the true ratio measurements.
In agreement with the 2D-DiGE data, we observed an increase of SpoVG protein levels in the ÁsprX strain (Figure  2A ). Furthermore, the effect of sprX inactivation resulting in an increase in SpoVG protein levels was detected at different phases of growth (Supplementary Figure  S4 ). To confirm that the enhanced expression of SpoVG was linked to SprX inactivation, we performed complementation experiments. Introducing pCN38-sprX into the ÁsprX strain decreased SpoVG protein levels as compared with the ÁsprX strain and also compared with those in the wt strain (Figure  2A ). These results are explained by the overexpression of SprX from pCN38 compared with its endogenous expression levels in the wt strain. Altogether, these data demonstrate that the SprX sRNA lowers SpoVG expression. Because SpoVG protein expression is downregulated by SprX, we monitored mRNA levels to determine whether this occurs at transcriptional and/or translational levels.
ACKNOWLEDGEMENTS We are grateful to  Dr B. Berger-Ba¨chi  ( Zurich, Switzerland ) for the plasmid pSTM33 and the RN4220ÁyabJ-spoVG strain. We thank  Dr M. Hallier  and  Y. Le Pe´tillon  from the lab for the technical assistance and  Pr. P. Y. Donnio  ( Rennes University ) for helpful discussions and advices. FUNDING Institut National de la Sante´et de la Recherche Me´dicale (INSERM) , the  Rennes University (De´fis Scientifiques Emergents) , the  Re´gion Bretagne  ('allocation doctorale', PhD thesis) and the  Fondation pour la Recherche Me´dicale [FRM ;  FDT20130928407  to A. E. ];  Agence Nationale de la Recherche  [ ANR-09-MIEN-030-01  to B. F. ]. Funding for open access charge: Inserm.
OpenCL and GPU implementation For performance reasons, we decided to implement the 2D scheme on recent multicore processor architectures, such as a Graphic Processing Unit (GPU). A modern GPU is made of a global memory (≈ 1 GB) and compute units (≈ 27). Each compute unit (or work-group in the OpenCL terminology) is made of processing elements (≈ 8, also called work-items) and a local cache memory (≈16 kB). The same program (a kernel) can be executed on all the processing elements at the same time. There are some rules to respect. All the processing elements have access to the global memory but have only access to the local memory of their compute unit. The access to the global memory is slow while the access to the local memory is fast. The access to global memory is much faster if two neighboring processing elements read (or write) into two neighboring memory locations, in this case we speak about "coalescent memory access".
This factor is essentially due to the optimized transposition that we perform between x and y update and to the relaxation solver that gives a robust but simple expression of the numerical fluxes. As the computation is very fast, the limiting factor becomes the memory size of a GPU. The MPI version permits to treat very fine meshes. We test the code on R22/Air shock bubble interaction, thanks to a very fine mesh we can observe Rayleigh-Taylor instabilities at the bubble interface.
Matrigel concentration modulates epithelial morphogenesis To allow for high resolution live cell imaging, 3D cultures of MCF10A cells were grown in glass-bottom multiwell plates. This configuration produced a similar distribution of structures to those previously described  [13]. At five days after seeding, the distribution of epithelial structures in the gels was largely uniform (Figure  1A, B  and C ) with the exception of their extreme periphery where ducts organized parallel to the borders of the gel (data not shown). Confocal stacks were acquired in a systematic random sampling to analyze the shape of epithelial structures in each condition. As explained in the experimental procedures, the shape score of each epithelial structure was used to distinguish ducts from acini. Ducts have a higher shape score than acini by definition.
Whole mount analysis After 5 days, gels were mounted on slides, fixed and stained with Carmine  [16]. Confocal stacks of the whole mounted gels were acquired using an automated systematic random sampling method (Leica SP5 software). ImageJ plugins, 3D Object counter  [37]  and 3D ROI manager  [38]  were used for shape analysis of the epithelial structures. To analyze the shape of the structures, we chose the approach of fitting the structure into an ellipsoid. The shape descriptors Elon1 and RatioVolEllipsoid were chosen to analyze the types of structures formed: acini or ducts  [38]. Briefly, Elon1 is the ratio between the major axis and the middle axis of the 3D fitted ellipsoid and RatioVolEllipsoid is the ratio between the volume of the 3D structure and the 3D fitted ellipsoid. Structures smaller than 300 voxels were excluded from the analysis.
Rheology Evaluation of viscoelastic properties was performed using a Kinexus Pro Rheometer (Malvern, UK). Using Parallel-plate geometry (20 mm665 mm), gels were placed onto the lower plate of the rheometer, while the higher plate oscillated on the sample at a gap size of 1 mm. For each of the samples, small deformation linearity (linear viscoelastic region) was identified via strain measurement under the application of controlled stress sweeps. Optimum conditions such as shear strain at 1. 0% of the angular single frequency (1 Hz) were selected. All measurements were performed at a temperature of 3760. 02uC (n = 4, from two independent experiments). Shear modulus (G9) measurements were derived from G9/G0-frequency (v) plots produced by single frequency measure. Data was analyzed using proprietary software (rSpace).
Instead, pixel-wise fiber orientation data were processed for each depth slice spanning the structure (18-31 slices). Fiber direction was averaged across the depth slices at each pixel location to obtain a fiber orientation map for further element-wise analysis. RCM intensities were also averaged through the depth slices at each pixel location and an average intensity threshold of 1 was selected to identify pixel locations containing a collagen fiber through the depth. Similarly, epithelial morphology and cell surface orientations at day-5 were computed from an average intensity projection of the Prewitt-filtered transmission images. Correlation coefficients between epithelial morphology and each fiber measurement were recorded. Those structures with a form factor of less than 0. 3 were classified as ducts at day 5, while structures with a form factor exceeding 0.
Statistical analysis To compare differences in shape score, the Wilcoxon rank test was used. For the analysis of shape score, Hartigans' dip test for unimodality was used to determine whether the distribution departed from unimodality. Levene's test was used to analyze the variance of the average of shape score. Cell proliferation data were analyzed with Cran R by using an analysis of variance (ANOVA) with a linear model. A Chi square test was used to evaluate the differences in the type of structures formed by a single cell tracked by live-imaging for 5 days. The effects of varying Matrigel concentration on gel stiffness and changes over time were evaluated using ANOVA. Regarding the collagen organization analysis, differences in form factor or fiber organization over the first 12 hours following seeding, were assessed through ANOVA.
Introduction In the mid-1960s, the U. S. Air Force started a research project called the Defense Meteorological Satellite Program (DMSP 1  ). The main purpose of this enterprise was to provide the military with daily information on worldwide cloud coverage. After scrutinizing the first results, it was discovered that, besides the initial goal of measuring cloud coverage, nighttime light was also very well captured by the sensors. When the system was declassified in 1972, and the data made publicly available, this unexpected, but very convenient, side-effect, gradually gained more interest from the scientific community. Light emission is a quantity that can be measured instantaneously, objectively and systematically. This is in stark contrast to many widely used economic and demographic indicators, which are often based on estimates and censuses, such as the gross domestic product, energy consumption, population levels, or the degree of poverty.
, 2012). As a result of the noise and unstable light removal, the number of dim pixels, with a DN below 5, is unreasonably low, e. g. in the year 2000 composite of satellite F14 (see Exhibit 1 for an overview), there are no pixels with a Digital Number equal to 1. A second artifact is the occurrence of a saturation, which can be seen in the higher end of the spectrum for pixels with a DN of 60 and above. We have carefully considered these matters during the measurements and data analyses presented in this paper and will discuss them when relevant in our analyses presented below. Following an attentive study of the literature and a consultation with the authors of the dataset, we decided that the Stable Lights product is the most suitable for our research. All the described methods and analyses from here onward refer therefore to the Stable Lights dataset, version 4 (NGDC, 2012).
Tools Dealing with geographical images of up to 3 Gigabytes in size is not trivial. Therefore, all the preliminary data processing is done using the ArcGIS 3  software package; this is the Geographic Information System from ESRI 4. The country boundaries used in this research were downloaded as a polygonal shapefile from CShapes  (Weidmann, et al. , 2010). All countries that ceased to exist (e. g. Yugoslavia, USSR) were removed, such that a total of 194 nonoverlapping countries remained in the dataset. For the geo-location of big cities, the point-based shapefile from  (Nordpil, 2009)  was used. It features the center of the 589 cities with a population larger than 750'000 in 2010. Additional analysis of the data was done using MATLAB 5.