dataesr/scientific-paragraphs-categorization huggingface dataset:
DE Meta-Analysis of TomExpress and TOGE Data A DE meta-analysis was performed for all the biological conditions of the TomExpress and TOGE data sets. For each pair of biological conditions, a DE analysis was done with the DESeq2 R package with default settings and a threshold of 0. 05 to control the FDR. For a given condition, simulated replicates were carried out by a convex linear combination of existing replicates with uniform random coefficients. For this purpose, we used conditions that had two or more replicates. Then, for each simulated replicate, raw counts were randomly carried out with a multinomial distribution with probabilities given by the true observed probabilities of genes, and with library sizes of 5, 10, 15, 20, and 25 M reads. These calculations aim at simulating pseudoreplicates that have almost the same characteristics (means and variances) as the true ones.
DE Meta-Analysis of TomExpress and TOGE Data A DE meta-analysis has been performed with all the TomExpress 4  data plus the TOGE data described above. TomExpress is an RNA-Seq platform that was developed to provide the tomato community with a dedicated browser and tools for public RNA-Seq data handling. Our analysis was performed on 17 projects, each containing from two to 18 biological conditions with up to eight biological replicates and 100 M reads. Two kinds of analyses were performed: a description of all DE analyses performed in each project, and a simulation of all possible DE analyses of all pairwise biological conditions of all projects for different replicate numbers and library sizes. The results of these two analyses are described hereafter. For the first descriptive analysis and for each project, we performed all possible DE analyses of all pairwise biological conditions.
DISCUSSION In the present work, we have conducted a thorough analysis of the impact of both replicate number and library size on an RNA-Seq DE analysis. In this discussion, we will compare our results to those obtained by  Ching et al. (2014) ,  Liu et al. (2014)  and  Schurch et al. (2016) , who are, to our knowledge, the only authors that exclusively and deeply address these questions. After reviewing these three benchmark articles, we can conclude that their main drawback is the lack of generality. Indeed, their analyses were performed on, respectively, one data set with two conditions, six data sets (from mouse and human tissues) with between six and 129 conditions, and one data set with 48 conditions. Clearly, their conclusions cannot be easily generalized. In regards to our study, on the one hand, we performed a study on a single data set (the TOGE data set), the results of which will be compared with those of the three benchmark articles described above.
This new result is in adequacy with the trade-off between replicate number and library size discussed above for the number of DE genes and power. As described above, a meaningful result of the present article comes from the meta-analysis that we made with all 17 projects on the tomato fruit extracted from the TomExpress platform and the TOGE data set. A descriptive analysis of the DE analyses performed within these projects clearly shows the impact of the replicate number and the library size, but also the distance between conditions and the variance of both conditions. Ching et al. (2014)  underline the need for a high replicate number to accurately estimate the variance, and then obtain higher TPR and lower FPR. In the same way, Auer and Doerge (2010) also underline the need to properly estimate the variability.
CON myocytes were depolarized for 50 ms at both 1 and 5 Hz while MCT myocytes were depolarized for 125 ms at 1 Hz and 50 ms at 5 Hz (see  Benoist et al. , 2012). Electrophysiological data was acquired at 2 KHz and analyzed with pClamp (Axon Instruments). Ionic currents were normalized to cell capacitance. Cell shortening was measured by video edge detection (VED-114, Crystal Biotech) from the video image of the cell. Shortening data was sampled at 200 Hz and simultaneously recorded with electrical activity in pClamp. Shortening parameters were measured on the averaged trace of 4-8 contractions at steady state. The amplitude of shortening and the time from peak shortening to 50% relaxation were calculated.
Data Analyses Statistical tests were performed using Graphpad Prism R statistical software (Version 6. 0; La Jolla, CA, USA). Data from the tail immersion, light-dark, and splash tests were analyzed using a two-way analysis of variance (ANOVA) with genotype as a within subject's factor and dose or day of injection as repeated factors. A 2-way ANOVA (genotype by drug) was used to assess each category of withdrawal score. Subsequent comparisons were conducted using Bonferroni post hoc tests. Statistical significance was set at p < 0. 05.
ACKNOWLEDGMENTS This work was supported by the  Université de Strasbourg , the  Investissements d'Avenir Idex , the  Centre National de la Recherche Scientifique (CNRS)  and the  Projet International de Coopération Scientifique (PICS)  from the  CNRS. L-AR was supported by the  Ministère de l'Education Nationale, de la Recherche et de la Technologie  and by  Elia Médical. MO was supported by a  Discovery Grant  from the  Natural Sciences and Engineering Research Council of Canada  (NSERC # 203707 ).
Statistical analyses Statistical analyses were performed using Statistica 9. 0 software (StatSoft, Maisons-Alfort, France). All data were initially checked for normality of distribution using Kolmogorov-Smirnov's test of normality. For all comparisons, values of p < 0. 05 were considered as significant. Statistical significance in behavioral experiments was assessed using three-to four-way analysis of variance (genotype, gender, condition, and training effects) followed by Newman-Keuls post hoc test. Variance was similar between compared groups. We defined sample size (GPower 3. 1) to ensure sufficient statistical power using ANOVA to detect significant effect of our parameters (effect size f = 1. 80, α = 0. 05, σ = 5, n = 8, power = 0. 96). Significance of qRT-PCR results was assessed after transformation using a one-sample t test, as previously described  9.
Acknowledgements We thank  B. Dutray  ( Centre Hospitalier Spécialisé de Rouffach ) and  B. L. Kieffer  for fruitful discussions. We thank  Benoit Piégu  ( Physiologie de la Reproduction et des Comportements ) for technical advice on clustering analysis. We thank  G. Duval  and  D. Memedov  for animal care and technical assistance ( Institut de Génétique et de Biologie Moléculaire et Cellulaire ). We thank the  Experimental Unit   PAO-1297  ( EU0028 ) from the  INRA-Val de Loire Centre  for animal breeding and care. This work was supported by the  Centre National de la Recherche Scientifique (CNRS) ,  Institut National de la Santé et de la Recherche Médicale (Inserm) ,  Université de Strasbourg ,  Institut National de la Recherche Agronomique (INRA) , and  Université de Tours. We thank the  Mission for Interdiciplinarity of the CNRS  for funding through the call  Therapeutic Innovations for Mental Diseases.
We also thank  Région Centre  ( ARD2020   Biomédicament-GPCRAb ) and  LabEx MabImprove  for support in this project. J. L. M. acknowledges postdoctoral fellowship from the  Fondation Université de Strasbourg , generously granted by  Pierre Fabre Laboratories. L. P. P. acknowledges postdoctoral support from the  Marie-Curie/AgreenSkills Program.
Structural Study Data were corrected from absorption using the Twinabs program  [39]  developed for scaling and corrections for twin and area detector data. The structure was determined using SIR2011  [40]  and refined using the program Jana 2006  [41] ; the analysis of the electronic residue allows the location of all the missing atomic sites. Harmonic atomic displacement parameters were considered for Co, P, O, and C species. Hydrogen atoms were geometrically added; distance and angle restraints were introduced for H belonging to water molecules and these H were refined. Twin laws were introduced for the monoclinic phase and the ratio of the possible twin domains was refined. All the details of the refinement are summarized in Table  1. Atomic positions are listed in Table  S1 , thermal parameters in Table  S2 , bond angles in Table  S3 , and interatomic distances in Table  S4.
In order to check that the crystal is representative of the whole powder, a study by powder X-ray diffraction was performed. After analysis with FullProf software  [1] , a simulation of the pattern was realized. All the peaks were indexed and were shown to match with the P21/c space group and lattice parameters found by single crystal X-ray diffraction (Figure  S1 , Supplementary Materials). Weighted R factor 0. 0877 R[F 2 > 2σ(F 2 )] 0. 0462 Rint (internal R-value) 0. 0371 S (Goodness of the fit) 1. 720 The view of the structure along b (Figure  2 ) shows that it consists of chains of CoO4(H2O)2 octahedra running along that direction. Two PO3C-C12H9 groups are grafted on each cobalt chain in "trans" positions with respect to the chain, so that the cobalt chains and the fluorene groups form layers parallel to the (100) plane.
The HSs were calculated on the fluorene moieties of the cobalt phosphonate in very high resolution with a standard void cluster mode (unit cell + 5 Å) and an isovalue of 0. 002 e•au -3. Crystallographic data have been deposited into the Cambridge Crystallographic Data Centre, with deposition numbers CCDC 1853487 for Co(H 2 O) 2 PO 3 C-C 12 H 9 •H 2 O. These data can be obtained free of charge via www. ccdc. cam. ac. uk/conts/retrieving. html (or from the Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK; fax: (+44) 1223-336-033; or deposit@ccdc. ca. ac. uk).
Morphological and cellular analysis To measure leaf area, petal area and silique length, we photographed leaves, petals (stage 14) and siliques and used ImageJ software to analyze the images. To measure cell size, leaves and petals were treated with the clearing solution  [38]  and then photographed under a differential interference contrast (DIC) microscope (Leica DM2500). The middle region of adaxial side of petals and the palisade parenchyma cells in the middle region of the leaves were used for cell size measurement. Dental resin imprints were performed as described before  [13]. The dental resin imprints were taken daily from the abaxial surface of the first leaves from DAG (day after germination) 12 to DAG 14. The surface of the epidermis was copied with Vinyl Polysiloxane impression material.
Accession numbers Sequence data from this article can be found in the EMBL/GenBank data libraries under accession numbers: AT5G35770 (STERILE APETALA [SAP]), AT4G14713 (PEAPOD1 [PPD1]), AT4G14720 (PEAPOD2 [PPD2]), AT3G24150 (KIX8), and AT4G32295 (KIX9).
In addition, to verify if any miRNA off-target effect might be caused by the synthetic antiviral miRNAs, all the sequences of each antiviral miRNA were examined by the miRNA off-target effect prediction software Genome-wide Enrichment of Seed Sequence matches (GESS)  43  , including the passenger strands of each antiviral miRNA; no statistically significant interaction was identified against any transcript of Ae. aegypti. All antiviral miRNA clusters were constructed to place them under either the Aedes Poly-Ubiquitin (AePUB) or Aedes Carboxypeptidase A (AeCPA) gene promoters to elicit constitutive or blood meal-inducible, midgutspecific expression of the effector molecules (Fig. 1 ). Generation of transgenic mosquitoes. A Class II TE mariner MosI system  44  was used to generate transgenic mosquito lines by microinjection in four separate experiments mixtures of the donor plasmids, pMosI_AePUb>4miR:D3 (4miR:D3), pMo-sI_AePUb>6miR:CHIKV (6miR:Chik), pMosI_AePUb>10miR: D3+CHIKV (AePUb>10miR), and pMosI_AeCPA>10miR:D3 +CHIKV (AeCPA>10miR), with the transposase expressing helper plasmid pKhsp82MOS.
Reverse transcription and qPCR were conducted as described in materials and methods. anti-CHIKV_6-4, the fourth anti-CHIKV miRNA; anti-DENV-3_4-1, the first anti-DENV-3 miRNA. Data were normalized to normalized values of aae-miR-1, and presented in relative expression levels to aae-miR-1. Each sample corresponds to two replicates (2 × 12 mosquitoes) mosquitoes were detectable in the midgut and carcass, and a slightly increased expression level was observed 24 h PBM. As the AeCPA promoter is reported to be active in the midgut and salivary glands  45  , the antiviral miRNAs was detected in the midgut and carcass of AeCPA>10miR mosquitoes, and the expression levels were increased 24 h PBM. The two antiviral miRNAs were also detected from the samples of female salivary glands at day 0, 1, and 6 after receiving a viremic blood meal; the results show that both antiviral miRNAs remain detectable in the salivary glands even at day 6 after virus challenge (Fig.
), generating pMOS1_nanos-mimyd88_3xp3-CFP′. The anti-DENV-3 and anti-CHIKV miRNA stem-loop backbones containing 5′-EcoRI/BglII and 3′-XhoI/BamHI were generated by oligo synthesis, and subcloned into pMOS1_nanos-mimyd88_3xp3-CFP with EcoRI and XhoI sites, generating pMOS1_nanos-Den3-4miR_3xp3-CFP and pMOS1_nanos-CHIKV-6miR_3xp3-CFP. The AePUb promoter was amplified from Ae. aegypti genomic DNA by PCR primers pMOS1_fusion_FseI/PstIAePUbpr-F and pMOS1_fusion_BglII/EcoRIAePUb-pr-R, and subcloned into FseI and EcoRI double digested pMOS1_nanos-Den3-4miR_3xp3-CFP and pMOS1_nanos-CHIKV-6miR_3xp3-CFP with In-Fusion ® HD Cloning technology (Clontech), generating pMOS1_AePUb-Den3-4miR_3xp3-eGFP (GenBank accession: MG603748)and pMOS1_AePUb-CHIKV-6miR_3xp3-eGFP (GenBank accession: MG603749). DENV-4miR was extracted from EcoRI and BamHI double digested pMOS1_AePUb-Den3-4miR_3xp3-CFP, and CHIKV-6miR was extracted from BglII and XhoI double digested pMOS1_AePUb-CHIKV-6miR_3xp3-CFP.
The two antiviral miRNA clusters were then subcloned into BglII and XhoII double digested pMOS1_AePUb-Den3-4miR_3xp3-CFP, generating pMOS1_AePUb-Den3-CHIKV-10miR_3xp3-eGFP (GenBank accession: MG603750). AeCPA promoter was amplified from Ae. aegypti genomic DNA by PCR primers pMOS1_fusion_FseI/PstIAeCPA-pr-F and pMOS1_fusion_BglII/EcoRIAeCPA-pr-R, and then subcloned into FseI and EcoRI double digested pMOS1_AePUb-Den3-CHIKV-10miR_3xp3-CFP, generating pMOS1_AeCPA-Den3-CHIKV-10miR_3xp3-GFP. This plasmid was then re-modified by replacing the reporter 3xp3-CFP with BglII and XhoI sites (bolded) disrupted Hr5IE1-DsRed which carried out by In-Fusion ® HD Cloning technology with mutation primers Oxitec_#4573_BglII-mutate-F and Oxitec_#4573_XhoI-mutate-R. By using In-Fusion ® HD Cloning technology with PCR primers pMOS1_fusion_Hr5IE1-DsRed_marker_NotI-F and pMOS1_fusion_Hr5IE1-DsRed_marker_XmaI-R, the Hr5IE1_DsRed was subcloned into NotI and XmaI double digested pMOS1_AeCPA-Den3-CHIKV-10miR_3xp3-CFP, generating pMOS1_AeCPA-Den3-CHIKV-10miR_Hr5IE1-DsRed (GenBank accession: MG603751).
Acknowledgements This study was funded by the  Institut Pasteur and the French Government 's  Investissement d'Avenir program ,  Laboratoire d'Excellence "Integrative Biology of Emerging Infectious Diseases " (Grant No. ANR-10-LABX-62-IBEID ) and the  Ministry of Science and Technology, Taiwan  (Grant No. MOST 105-2325-B-400-006 ;  MOHW105-TDU-M-212-000006 ). P. -S. Y. was supported by the  Pasteur-Paris University (PPU) program. We are grateful  Hervé Blanc  and  Carla Saleh  for technical advice and,  Marie Vazeille  and  Laurence Mousson  for technical help.
Data availability. All data generated or analyzed during this study are included in this published article (and its supplementary information files). The accession codes of the plasmid sequences are MG603748 (pMOS1_AePUb-Den3-4miR_3xp3-eGFP), MG603749 (pMOS1_AePUb-CHIKV-6miR_3xp3-eGFP), MG603750 (pMOS1_AePUb-Den3-CHIKV-10miR_3xp3-eGFP) and MG603751 (pMOS1_AeCPA-Den3-CHIKV-10miR_Hr5IE1-DsRe).
6. Figure  2  and Dataset 2 now include a more reliable visual scoring table instead of intensity profile quantification as we agree it might fail to discriminate a typical distribution of VAMP7 (ie: Golgi-like and peripheral vesicles) from an incorrect one (ie: perinuclear-enriched and peripheral diffuse signal, such as ER localization pattern). We modified legends, methods and text accordingly and specified the criteria used for scoring.
7. Dataset 3 now includes a WB using TG50 antibody in the IP experiment of endogenous protein. Please note that as the same antibody was used for immunoprecipitation and immunoblot, signal of the IgG is therefore more intense. Nevertheless, endogenous VAMP7 can be readily detected in the WT input and not in the KO condition, as expected. In Figure  1  and Dataset 1, the profile scoring for WB was maintained as we think it is a reasonable approach to quantify the band corresponding to VAMP7 out of the total staining. This total staining does not merely reflect noise but also includes non-specific bands and we still think that the index used is quite informative about the Ab quality. Following recent renaming of our institute, affiliation 2 has been amended for authors Beatrice Cholley, Thierry Galli and Sebastien Nola.
Altogether, we showed here that both 158. 2 and TG50 antibodies were able to immunoprecipitate VAMP7 from different species and that immunoprecipitation of endogenous VAMP7 could be performed in mouse tissue extracts using TG50 for IP and 158. 2 (or TG50, see Dataset 3) for subsequent western blotting. recapitulating  visual scoring of indicated antibodies used for immunostaining. Antibodies were scored for yielding a "typical VAMP7 localization pattern" (ie intracellular punctate membranes pattern with perinuclear concentration and peripheral vesicles) and "loss of signal in KO". Characters used in the table indicated whether the above-mentioned criteria are obviously met ("+") or not ("-"). AP, affinity purified.
This is in good agreement with the fact that human, rat and mouse VAMP7 protein sequences share more than 94% identity (alignment with www. uniprot. org website). MAb 158. 2 also immunoprecipitated mouse, rat and human GFP-tagged VAMP7 (Figure  3A ). Altogether, 158. 2 and TG50 thus appeared as suitable antibodies in all species and for all applications. However, 158. 2 antibody may not be very sensitive, as it did not allow for the endogenous detection of low amounts of the protein, particularly in tissues (Figure  3 ) while TG50 performed slightly better (Dataset 3). More generally, further comparative study should be conducted to formally assess the efficiency of this set of antibodies in non-human cell lines or tissues, particularly in immunocytochemistry. However, immunoprecipitation using TG50 (protein A purified serum available from Covalab, ref.
pab01031-P) and 158. 2 or TG50 (Dataset 3) detection appeared as a valid strategy for specific isolation of the endogenous VAMP7. Finally, we proposed here an easy profile comparison of WT and KO western blotting signals and visual scoring criteria for immunocytochemistry staining in order to rank the quality of antibodies directed against membrane-associated proteins as a decision-making tool for more complex studies.
Data availability Dataset 1. Raw images of experimental replicates for Figure  1 , immunoblotting experiments. This dataset includes uncropped blots for all experimental replicates that are represented in Figure  1. Treatments and immunoblot methods were performed as outlined in Figure  1. Blots were probed with indicated anti-VAMP7 antibodies and anti-α-tubulin antibodies was used as a loading control. (A) Dataset used for Figure  1 , with cropped regions in red dashed line. (B) Additional set of raw images of a replicate experiment. Quantification as performed in Figure  1   3 , immunoprecipitation. Uncropped data from Figure  3  (A) and replicate (C) for VAMP7 immunoprecipitation from Cos-7 cell lysate overexpressing GFP-tagged mouse, rat or human VAMP7 constructs. Uncropped immunoblotting data from The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: We have read this submission. We believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. This study has compared the specificity of a panel of antibodies against VAMP7, a member of the SNARE protein family. Using CRISPR/Cas9 to create a HeLa-VAMP7 knockout cell line together with knockout mouse tissues the authors effectively demonstrate that the panel of antibodies are able to recognise the endogenous VAMP7 protein, the majority performing effectively in both WB and IF. Image analysis was performed to profile the signal-to-noise index in both techniques. While this does provide quantitative data with which to prioritise the antibodies, I reached the same conclusions without needing the profiling data. This approach may indeed have utility in other projects but perhaps consideration should be given to incorporating a measure for antibody sensitivity.
Competing Interests: I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. The benefits of publishing with F1000Research: Your article is published within days, with no editorial bias You can publish traditional articles, null/negative results, case reports, data notes and more The peer review process is transparent and collaborative Your article is indexed in PubMed after passing peer review Dedicated customer support at every stage For pre-submission enquiries, contact research@f1000. com.
Raw images of experimental replicates for Figure 1, immunoblotting experiments https://dx. doi. org/10. 5256/f1000research. 15707. d221360This dataset includes uncropped blots for all experimental replicates that are represented in Figure1. Treatments and immunoblot methods were performed as outlined in Figure1. Blots were probed with indicated anti-VAMP7 antibodies and anti-αtubulin antibodies was used as a loading control. (A) Dataset used for Figure1, with cropped regions in red dashed line. (B) Additional set of raw images of a replicate experiment. Quantification as performed in Figure1is shown in lower panel. Note that although signal intensity and background are different within these two replicates, the relative performance of the different tested antibodies remained the same.
Work in our group was funded by grants from  Association Française contre les Myopathies  ( Research Grant   16612 ), the Grant information:  French National Research Agency  (NeuroImmunoSynapse  ANR-13-BSV2-0018-02 ; MetDePaDi  ANR-16-CE16-0012 ), the  Ecole des Neurosciences de Paris (ENP) , the  Fondation pour la Recherche Médicale (FRM) ,  Prix Coup d'Elan pour la recherche française of the Fondation Bettencourt Schueller , awards of the  Association Robert Debré pour la Recherche Médicale  to T. G. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Dataset 1. 1 Raw images of experimental replicates for Figure 1, immunoblotting experiments https://dx. doi. org/10. 5256/f1000research. 15707. d221360This dataset includes uncropped blots for all experimental replicates that are represented in Figure1. Treatments and immunoblot methods were performed as outlined in Figure1. Blots were probed with indicated anti-VAMP7 antibodies and anti-αtubulin antibodies was used as a loading control. (A) Dataset used for Figure1, with cropped regions in red dashed line. (B) Additional set of raw images of a replicate experiment. Quantification as performed in Figure1is shown in lower panel. Note that although signal intensity and background are different within these two replicates, the relative performance of the different tested antibodies remained the same.