dataesr/scientific-paragraphs-categorization huggingface dataset:
We also looked for pan-photoreceptor markers (markers of both cones and rods). Among the markers of Cones or Rods, genes that were found overexpressed in Cones against all other types except Rods and in Rods against all other types except Cones were assigned to pan-photoreceptor. Values indicated in Supplementary Data 3 for panphotoreceptor markers have been computed using the FindAllMarkers function comparing photoreceptor cells against all other cells. Visualization tool. A R-Shiny web-app [https://retinoblastoma-retinamarkers. curie. fr], based on the shiny (v. 1. 6. 0) and shinydashboard (v. 0. 7. 1) Rpackages, was developed to visualize the expression of markers of the retina cell populations, of the two subtypes of retinoblastoma and other genes of interest cited across the manuscript in the two single-cell RNA-seq datasets (from normal human developing retina  38  and from a subtype 2 retinoblastoma, RBSC11 (this report)).
The different plots and tables are made based on the R packages cowplot (v. 1. 1. 1) and the ones included in tidyverse (v. 1. 3. 0). transcriptomic data used in this study are available in the GEO database under accession codes GSE29683 and GSE59983. The public human developing retina scRNA-seq data used in this study are available in the GEO database under accession code GSE138002. The remaining data are available within the Article, Supplementary Information, or Source Data file. Additional data inquiry can be addressed to the Lead contact: francois. radvanyi@curie. fr. Source data are provided with this paper.
Acknowledgements We thank  Cécile Reyes  and  Aude Vieillefon  from the  Genomics platform ,  Benoît Albaud  from the  NGS platform at the Institut Curie (IC) ,  Emmanuel Martin  from  Integragen  for sequencing, and  Nadège Gruel  ( IC ) for her help in the single-cell experiments. We thank  Dr. Jelena Martinovic  and  Prof. Alexandra Benachi  from  Béclère Hospital ,  Dr. M. Eugenia Riveiro  from  OTD Oncology , and  Pr. Daniel Louvard  from  IC  for their help with this work. Me. S. was supported by fellowships from the  French MESRI  and the  IC , D. O. by the  SFCE , the  IC , and the AMCC, J. L. by the Foundation ARC, C. D. by the  Barletta Foundation, Clé. H. by  La Ligue Contre le Cancer. A. M. C. was funded by  ISCiii-FEDER  ( CP13/00189 ). This work was supported by the  Retinostop Association , the  Barletta Foundation , the  INCa , and the INSERM in the framework of an  ICGC  project.
The raw array data are deposited in the Gene Expression Omnibus (GEO) database under accession code GSE58785. The raw whole-exome sequencing data are deposited in the European Genome-Pheome Archive (EGA) database under accession code EGAS00001005248. The raw targeted sequencing data are deposited in the EGA database under accession code EGAS00001005550. The raw single-cell RNA sequencing data are deposited in the EGA database under accession code EGAS00001005178. Data in EGA is available under restricted access, access can be obtained by contacting Retinoblastoma Data Access Committee -Institut Curie (data. office@curie. fr). The public retinoblastoma.
Louis, USA) in DMEM and neutralizing buffer for 10 min in a 37 °C incubator. Growth medium (DMEM, 10% Horse Serum, 0. 5% Chicken Embryo Extract) with 1 μM luciferin (PJK GmbH, Kleinblittersdorf, Germany) was added, the dish was placed on the stage of an inverted microscope (IX83-ZDC, Olympus, Tokyo, Japan) and maintained at 37 °C in 5% CO 2. The nGFP signal from the Pax7 nGFP transgene was used to focus and to track the cells. Bioluminescence was acquired using the EM-CCD camera (Hamamatsu, Shizuoka, Japan). Image analysis and quantification. Image analysis was performed using Fiji software (ImageJ, v. 2. 1) and custom plug-ins  25. The semi-automated tracking approach was used to determine cell locations and the intensity of the signal over time. Cells were identified using differences of Gaussian detection and the nearest neighbor searching approach in successive frames.
This process can be corrected manually according to bright-field images. The mean intensity values of the signal of different single cells over time were recorded. After deduction of the background, 7th order Savitzky-Golay polynominal fitting was used to smooth the image. The oscillation periods were measured as the length of time between two peaks of bioluminescence signals. To define the stability of the oscillations, FFT with Hanning window was used by Origin software (OriginLab, Massachusetts, USA), which transfers a time-dependent function into its corresponding frequencydomain function. The dominant frequency can be identified as a peak. The powers of the frequency bands corresponding to periods between 1. 5 and 3. 75 h were quantified as area under the FFT curve  25. Data from randomly chosen cells that could be followed over at least 10 h were analyzed.
Matlab software (R2016a, MathWorks, Massachusetts, USA) was used to determine the phase relationship of oscillations in two coupled cells. To derive accurate phase differences, we performed the following signal processing steps 51 : (i) detrending (by moving average with a window of 3 h); (ii) normalization (by dividing by a sliding standard deviation with a window of 3 h); (iii) Hillbert transformation analysis. The time at which the oscillatory signal in one cell corresponds to a peak was marked, and time intervals to the next peaks in oscillation of neighboring cells were determined. Mathematical modeling. To model the network of Hes1, MyoD, and Dll1 in single cells, we extended our original qualitative ordinary differential equation (ODE) model of Hes1 and MyoD 25 to incorporate Dll1. In the original model, Hes1 mRNA, Hes1 protein, a Hes1 interacting factor, MyoD mRNA, MyoD protein and MyoD interacting factor are included and it is assumed that Hes1 protein suppresses both MyoD and Hes1 transcription.
Acknowledgements We are grateful to  Petra Stallerow  ( MDC, Berlin ) for help with animal husbandry. We also thank  Hans-Peter Rahn  for advice and help with cell sorting,  Michael Strehle  for providing the drawing shown in Fig. 9 and  Elijah Lowenstein  and  Thomas Müller  for critically reading the manuscript (all from the  MDC, Berlin). This work was supported by grants of  AFM Telethon, DFG  ( FOR 2841 ),  ANR/DFG , and  Helmholtz POF  and AMPro to C. B. , and by a  Grant-in-Aid for Scientific Research on Innovative Areas  from  MEXT, Japan  ( 16H06480 ) to R. K.
These unmet needs in those receiving prophylactic FVIII replacement therapy are incompletely characterised on an individual and population level  [5, 6]. Standardised data on bleeding, FVIII use, and QoL in the setting of routine clinical practice for patients on prophylaxis are needed to better understand the burden of both severe HA and the prophylactic treatment approach. This multinational, prospective, noninterventional study collected standardised real-world data on bleeding episodes, haemophilia medication use, and health-related QoL from a global, heterogeneous population of participants with severe HA on currently available FVIII prophylaxis. This study was also a run-in for the sponsor's phase 3 gene therapy studies (Clinicaltrials. gov NCT03370913/EudraCT 2017-003215-19, NCT03392974/EudraCT 2017-003573-34).
Planned enrolment was up to 250 participants followed for ≥6 months and ≤12 months. After 6 months, potentially eligible participants could be screened for entry into a phase 3 interventional study of valoctocogene roxaparvovec (Clinicaltrials. gov NCT03370913/EudraCT 2017-003215-19, NCT03392974/EudraCT 2017-003573-34). To be eligible, participants had to have received prophylactic FVIII therapy for ≥6 months prior to study entry and been treated/exposed to FVIII concentrates or cryoprecipitate for ≥150 exposure days. Participants could not have a history of detectable FVIII inhibitors. After being initially eligible for enrolment, participants positive for human immunodeficiency virus (HIV) infection were excluded by a protocol amendment-secondary to the development of elevated liver enzyme levels by an HIV-positive participant who was receiving a combination of highly active antiretroviral therapy (HAART) and valoctocogene roxaparvovec-out of caution for the long-term liver health of HIV-positive participants receiving HAART who may be interested in receiving gene therapy.
Additional exclusion criteria, including significant liver dysfunction, chronic or active hepatitis B, and active hepatitis C, are described in detail in (Supplementary S2). High-quality historical documentation concerning bleeding and exogenous FVIII usage over the previous 6 months was required. Retrospectively collected pre-baseline data were compared to and combined with data collected during the study period. There were no minimum requirements of annualised bleeding rates, either before or during this study, that could impact participants' eligibility for the future gene therapy trial. However, the possibility of future enrolment in gene therapy a trial may have been a motivating factor for some participants to enrol in this study. Pre-existing host humoral and cellular immunity against the AAV capsid are known to negatively affect the efficacy of AAV-vector-based gene therapies  [7] ; thus, participants were also screened for pre-existing adeno-associated virus 5 (AAV5).
Although antibody status did not impact eligibility for this trial, participants positive for anti-AAV5 antibodies were not eligible for enrolment in the subsequent gene therapy trial. Study procedures included the review and entry of bleeding episode and haemophilia medication data on at least a monthly basis, as well as the collection of concomitant medications, adverse events (AEs), serious AEs (SAEs), and interim medical history at each visit or during telephone calls on at least a monthly basis. Except for screening/baseline and end-of-study visits, all other study visits occurred according to participants' local standard of care. No clinical intervention or study drug was provided.
Study Assessments and Endpoints After enrolment, participants reported bleeding episodes and haemophilia medication data on a weekly basis for the duration of the study. Details of each bleeding episode were captured, including start date/time, type (e. g. , joint or muscle), location, and whether there was preceding trauma or ensuing treatment. Specific reporting of all administered haemophilia medications was required, including start/date time, product name, dose, and reason for use (e. g. , usual prophylaxis, one-time prophylaxis, or treatment for bleed). As the prescribed frequency of usual FVIII prophylaxis was not captured, the manual review of listings was required to adjudicate the prescribed frequency of infusions and assess adherence. The primary clinical endpoint was the annualised number of bleeding episodes (annualised bleeding rate (ABR)) requiring exogenous FVIII replacement treatment.
Statistical Analysis Baseline and safety analyses included all enrolled participants. Bleeding and FVIII usage were analysed for those with ≥6 months of on-study data (6-Month Analysis Population). ABR was calculated using only treated bleeds for the primary analysis; bleeds due to surgery/procedure were not included. ABR was defined as number of bleeding episodes during the calculation period/total number of calculation period days × 365. 25. ABR and FVIII usage rates were determined for the 6 months before day 1 (pre-baseline), 6 months after day 1 (on-study), and total duration (pre-baseline and on-study). Supportive analyses included all bleeds (treated and non-treated), joint bleeds, problem joint bleeds, spontaneous bleeds, and traumatic bleeds. Results were also evaluated by prophylaxis type (standard half-life (SHL), extended half-life (EHL), or plasma-derived (PD)) and geographic regions in which the sites were located to provide a more nuanced understanding of the data.
0 (20. 0-100. 0). The median (range) HAL summary score for 293/294 (99. 7%) participants was 80. 5 (20. 5-100. 0) points, with higher scores representing better self-perceived functional abilities. For 289/294 (98. 3%) participants, the median (range) WPAI+CIQ:HS Activity Impairment percentage score was 20. 0% (0-90. 0%), with higher percentages indicating greater impairment and less productivity. Most participants (286/294, 97. 3%) completed their diary entries, with a median (range) of 28. 5 (1. 0-95. 0) weeks of data collected. The median (range) percentage of missed days from work (calculated as missed days/expected workdays) for the total population was 0% (0-100%).
Potential study limitations include visits scheduled at irregular intervals following the usual standard of care/routine clinical practice for the study site and the collection of QoL measures at a single time point. The population enrolled in this study was very heterogeneous in terms of age, race, medical history, and access to medical treatment, and it represents a specific cohort that is potentially interested in pursuing gene therapy for HA. This may have resulted in selection bias, as illustrated by the AAV5+ individuals who chose not to enrol after screening. Participants seeking better outcomes than those provided by their current FVIII prophylaxis may have been particularly motivated to enrol. Additionally, the mandated 6 months of high-quality retrospective data may have biased enrolment towards well-informed participants compliant with treatment.
The libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 25 million reads per sample. Reads of 100 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 sequencer (Illumina, Evry, France). After the quality control was performed with FastQC, the reads were mapped to the mm10 genome using STAR software (http://star. mit. edu, accessed on 1 June 2021). Tables of counts were thus generated with HTSeq. The normalisation and differential expression analysis was performed with the R package edgeR, for the genes annotated in the reference genome. We filtered out very lowly expressed genes and normalised data according to the library size (sequencing depth) and the RNA composition (dispersion). The differentially expressed genes were estimated using a general linear model (GLM) approach, negative binomial distribution and a quasi-likelihood F-test.
We identified 2637 transcripts corresponding to 2531 National Center for Biotechnology Information (NCBI)-referenced genes that were regulated by ischemia, by comparing group 2 to group 1 using a bilateral t-test with the FDR cutoff for significance set at 5%. We created a "renal ischemia-reperfusion" gene set with these genes significantly regulated by ischemia. In a secondary analysis, we used a logistic regression pathway analysis (LrPath) in order to identify other known gene sets enriched with ischemia-regulated genes, and used the REVIGO (Reduce + Visualize Gene Ontology) tool to provide a graphical representation of these results. Next, we studied the effect of anaesthesia during renal ischemia on gene regulation by comparing the gene expression in group 3 vs. group 2, using a bilateral t-test.
Acknowledgments: The authors wish to thank  Liliane Louedec ,  Gaëtan Girault ,  Jessy Renciot  and  Claude Kitou  for the care of the animals and  Souhila Ouchelouche  from the renal morphometry platform of the CoRaKID Unit. They also thank  Barry Warbuton  (from  UCL Biological Services ) for the advice, careful reading and correction of the methods related to the animal care and surgery.
Acknowledgements xiii Introductory Essay 1. Law, Culture, and Industry: Toward a History of Intellectual Property for Visual Works in the Long Nineteenth Century Acknowledgements 24 A search of copyright registrations in the online catalogue of the National Archives, UK (http://discovery. nationalarchives. gov. uk/details/r/C5349) reveals that  James Robinson  registered at least eight photographs in his name (as both author of the work and owner of the copyright) between 1863 ( COPY 1/2/493 ) and 1896 ( COPY 1/424/184 ). J. Robinson  and Sons must have existed by 2 September 1882, when the firm registered a photograph of the late  Daniel O'Connell  using the address of 65 Grafton Street, Dublin ( COPY  1/58/394). A pair of photographs registered by  J. Robinson  and Sons in 1884 listed both the Dublin address and 172 Regent Street, London ( COPY 1369 /273-274).
7 For further discussion, seeSimon Stern, 'From Author's Right to Property Right',  University of Toronto Law Journal, 62 (2012), 29-91. A recent study by Douglas Duhaime, drawing from large databases of printed texts, offers valuable new insights into the nature and frequency of reusing material from other sources during the eighteenth century. See Douglas Duhaime, 'Copyright and the Early English Book Market: An Algorithmic Study' (unpublished doctoral thesis, University of Notre Dame, 2019), https://www. earlybookmarket. com/. 8 Advertisement in the Gazetteer (London), 7 May 1741, quoted in Thomas Keymer and Peter Sabor, Pamela in the Marketplace (Cambridge: Cambridge University Press, 2005), p. 59.
Accession number 24366. Handwritten note, 'This picture of my father Wm. Neff was taken in 1856 at my operating room #239 West 3d St. Cinti [Cincinnati, Ohio] when I was perfecting and completing my melainotype -'. This is one of several dozen tintypes acquired from Neff in 1891. 67 Robert Taft, 'The Tintype', Photography and the American Scene (New York: MacMillan Company, 1938), pp. 153-157. 12. New or Improved? polksnashvilleda00nash; NMAH, PHC. Ephemera collections (advertisements, business cards, broadsides, etc. ) reveal the scope of a photographer's business. 66 NMAH, PHC,.
While the cause of the disease in these patients is unknown, they present with the same clinical phenotype as HCM SMP patients albeit at older age. 3  Moreover, recent data from the SHaRe registry (the sarcomeric human cardiomyopathy registry) indicate that HCM SMP has a 2-fold greater risk of adverse outcomes than HCM SMN. 11 hereas LV outflow tract obstruction can be invasively corrected by surgical myectomy, other symptoms can only be managed by pharmacological therapies, which do not halt or reverse cardiac disease. 1  Knowledge about the cellular changes that cause cardiac dysfunction and hypertrophy in patients with HCM is needed to design new therapies. The main goal of this study was to define HCM-and genotype-specific derailments at the protein level, which may explain the heterogeneity in cardiac characteristics and disease initiation and progression.
METHODS The proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD012467 and are publicly available (http://proteomecentral. proteomexchange. org/cgi/ ; patients with MYBPC3 mutations other than the 2373insG mutation of which 81. 8% were truncating mutations as well; patients with MYH7 mutations; patients with mutations in less frequently affected sarcomere genes (TNNT2, TNNI3, and MYL2); and HCM SMN patients. In line with studies in other cohorts,  15  almost all mutations in MYBPC3 were truncating mutations, whereas mutations in other sarcomeric proteins were missense except the truncating mutation c. 814C>T in TNNT2.
Protein Fractionation Proteins were separated using 1D SDS-PAGE. Samples from each group were loaded alternating on the gels to avoid bias. Equal volumes of sample (30 μL protein homogenate per sample, containing ≈20-30 μg of protein) were loaded on a precast 4% to 12% NuPAGE Novex Bis-Tris 1. 5 mm mini gel (Invitrogen). Electrophoresis was performed at 200 V in NuPAGE MES SDS running buffer until the dye front reached the bottom of the gel. Gels were fixed in a solution of 50% ethanol and 3% phosphoric acid and stained with 0. 1% coomassie brilliant blue G-250 solution (containing 34% methanol, 3% phosphoric acid, and 15% ammonium sulfate). Images of all gels are provided in Figure  I  in the Data Supplement. In-Gel Digestion and Nano-LC-MS/MS Each gel lane was cut into 5 pieces, and in-gel digestion was performed as described previously.
Data Analysis MS/MS spectra were searched against a Uniprot human reference proteome FASTA file (Swissprot_2017_03_human_ canonical_and_isoform. fasta, 42161 entries) using MaxQuant version 1. 5. 4. 1 (details to search settings are provided in the Data Supplement). The mass spectrometry proteomics data are provided in Table V in the Data Supplement, and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE  18  partner repository with the data set identifier PXD012467. Beta-binominal statistics were used to assess differential protein expression between groups, after normalization on the sum of the counts for each sample. 19 Proteins with a P value below 0. 05 were considered significantly differentially expressed. Proteins which were present in <25% of the samples or had an average normalized count of  <1.
4  were excluded from further functional analysis. Principal component analysis was performed in R. Therefore, quantile normalization and log2 transformation were performed on the normalized counts. The 95th percentile was taken, the data median centered, and the principal components calculated. Hierarchical clustering was performed after a statistical multigroup comparison. Proteins with a raw P<0. 05 were selected for the pathway analysis. Protein networks were generated using the STRING database (Search Tool for the Retrieval of Interacting Genes/Proteins) and visualized with Cytoscape software. 20 Protein interaction networks were generated with ClusterONE and gene ontology (GO) analysis was performed using the BiNGO application in cytoscape. 21, 22 Heatmaps for a specific GOs were created with ToppGene Suite  23  and Graphpad Prism v7 software.
Animal Experiments The MYBPC3 2373insG mouse model was engineered using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9, details are provided in the Data Supplement). Echocardiographic phenotyping (Vevo 2100, Visualsonics) was performed on 7 homozygous The MYBPC3 772G>A mice were developed previously  25  and maintained on a blackswiss genetic background. Western blot analysis was performed of the cytosolic fraction of LV tissue in 6 homozygous MYBPC3 772G>A mice (2 females and 4 males) and 6 WT littermates (2 females and 4 males). The age of these mice was 55 to 59 weeks.
5 mmol/L, KCl 5 mmol/L, NaH 2 PO 4 1. 2 mmol/L, MgSO 4 1. 2 mmol/L, glucose 11. 1 mmol/L, sodium pyruvate 5 mmol/L; pH 7. 4 at 37 °C) at 37 °C using the MultiCell system (CytoCypher, the Netherlands). The dish was field-stimulated at 2 Hz, 25 V, and a 4 ms pulse duration. Changes in sarcomere length were recorded with a high-speed camera and Ionoptix software (Ionoptix, Westwood, MA). The contractility profiles were analyzed with the automated batch analysis software CytoSolver (CytoCypher, Amsterdam, NL). An R 2 for peak and recovery fit >0. 95 was selected as inclusion criteria for contraction data. For protein analysis, cells were incubated with dimethyl sulfoxide (0. 1% v/v) or 10 μmol/L parthenolide (Sigma) for 2 hours, washed with PBS, and directly lysed in loading buffer.
Samples were grouped based on their genotype and protein expression changes were analyzed in different group-wise comparisons. Table  II  in the Data Supplement lists all group-wise comparisons and the corresponding number of significantly deregulated proteins that contributed to the subsequent cluster and GO analysis. An unbiased principal component analysis of the protein expression data revealed separate clustering of the nonfailing IVS and HCM samples, indicating different protein expression profiles between controls and patients (Figure  1A ). Supervised hierarchical clustering of a multigroup comparison revealed separate clusters for nonfailing IVS and HCM samples (Figure  1B ). However, in both analyses, the HCM samples did not cluster according to their genotypes, indicating that the protein profile at the time of myectomy surgery is relatively homogeneous with differences between genotypes that are not sufficiently large to distinguish them with cluster analysis.