dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgments The authors would like to thank the patients who participated in the HAWK and CONDOR trials, their families, and the investigators and study site personnel. Medical writing support, under the direction of the authors, was provided by  Ward A. Pedersen of Parexel and Laura Park, MSc , of  CMC Connect, Mc-Cann Health Medical Communications , with funding from  AstraZeneca , in accordance with Good Publication Practice (GPP3) guidelines. This study was funded by  AstraZeneca. One of the Editors-in-Chief of Cancer Research Communications is an author on this article. In keeping with AACR editorial policy, a senior member of the Cancer Research Communications editorial team managed the consideration process for this submission and independently rendered the final decision concerning acceptability.
This has led to the concept of IRESome, a multi-partner ribonucleic complex allowing ribosome recruitment onto the mRNA via the IRES. ITAFs often exhibit several functions in addition to their ability to control translation. Many of them play a role in alternative splicing, transcription, ribosome biogenesis or RNA stability  (Godet et al. , 2019). Clearly, a large part of ITAFs are nuclear proteins able to shuttle between nucleus and cytoplasm. Previous data have also shown that a nuclear event is important for cellular IRES activity, leading to the hypothesis of IRESome formation in nucleus  (Ainaoui et al. , 2015; Semler & Waterman, 2008; Stoneley et al. , 2000). Interestingly, several ITAFs are components of a nuclear body, the paraspeckle, formed in response to stress  (Choudhry et al.
, 2019)  (Fig. 1B  and 1C ). Neat1 and Neat1_2 expression in cells was measured by reverse transcription and droplet digital PCR (RT ddPCR), showing an increase of Neat1 and Neat1_2 at 4 h with a peak of expression of Neat1 at 8 h of hypoxia, while the peak of expression of Neat1_2 was observed after 4 h of hypoxia (Fig. 1D ). The same data were also obtained by classical RT-qPCR (data not shown), in agreement with our previous report showing Neat1 induction by hypoxia in HL-1 cells  (Hantelys et al. , 2019). In parallel, paraspeckle formation was studied by fluorescent in situ hybridization (FISH) targeting the non-coding RNA Neat 1, considered as the main marker of paraspeckles. The fluorescent probes targeted either the common part of the two Neat1 isoforms, or only the large isoform Neat1_2 (Fig.
In addition, previous data from the literature support the hypothesis that the IRESome is a multi-partner complex. In order to identify other members of this complex, we analysed the p54 nrb interactome in HL-1 cell nucleus and cytoplasm using a label-free quantitative mass spectrometry approach. For this purpose, cells were transduced by a lentivector expressing an HA-tagged p54 nrb (Fig. 4A ). After cell fractionation (Fig. 4B ), protein complexes from normoxic and hypoxic cells were immunoprecipitated with anti-HA antibody. Immunoprecipitated interacting proteins (three to four biological replicates for each group) were isolated by SDS-PAGE, in-gel digested with trypsin and analysed by nano-liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS), leading to the identification and quantification of 2013 proteins (Table  S6 ).
S4A )  (Godet et al. , 2019). As regards cytoplasmic proteins, we identified Rps25, a ribosomal protein previously described as an ITAF for many IRESs (Fig. S4A )  (Hertz et al. , 2013). Interestingly, p54 nrb also interacted with Rps5, Rps18 and Rps19, and other Rps, mainly from the small ribosome subunit. Only few proteins were enriched when comparing hypoxic versus normoxic extracts. In hypoxic nucleus the enriched proteins are hnRNPM, nucleolin (both previously described as ITAFs)  (Hertz et al. , 2013; Shi et al. , 2016 Shi et al. , , 2017) )  and the ribosomal protein Rps2/uS5 (Fig. 4D ), while the helicase Ddx17, the enolase Eno3 and the heat shock protein Hspa2 are enriched in hypoxic cytoplasm (Fig  4E ). These data showed that p54 nrb interacts in normoxia and hypoxia with several ITAFs known as paraspeckle components, suggesting that the paraspeckle might be involved in the formation of the IRESome.
6D ). According to our data, P54 nrb is an activator of the FGF1 and VEGFC IRESs in normoxia, and of the FGF1 and VEGFAa IRESs in hypoxia. PSPC1 is an activator of the FGF1, FGF2, VEGFAa, VEGFC and IGF1R IRESs in normoxia and of the FGF1 and FGF2 IRESs in hypoxia. Neat1 is an activator of the FGF1, FGF2, VEGFAb, VEGFC, VEGFD, IGF1R and cmyc IRESs but not of the VEGFAa IRES in normoxia while it activates all the cellular IRESs in hypoxia. The EMCV IRES does not belong to any of these groups as it is not regulated by these three ITAFs, suggesting that this viral IRES is not regulated by the paraspeckle. In conclusion, these data suggest that IRESome composition varies for each IRES and with the normoxic or hypoxic conditions. The long non-coding RNA Neat1 appears as the key ITAF for the activation of all the cellular IRESs, suggesting a crucial role of the paraspeckle in IRESome formation and in the control of IRES-dependent translation, at least for cellular IRESs.
It has been reported that Neat1_2 is not expressed in all tissues in vivo, whereas it is found in all transformed or immortalized cell lines (data not shown)  (Nakagawa et al. , 2011). In concordance with this observation, previous reports show that cellular IRESs are active in all cultured cell lines while inactive or tissue-specific in mice  (Créancier et al. , 2000 (Créancier et al. , , 2001)). S7 ). IREScontaining mRNAs (A-B) and ITAF mRNA levels in polysomes (C-D) (polysomal RNA/ total RNA) were analyzed. Relative quantification (RQ) of mRNA level was calculated using the 2-ΔΔCT method with normalization to GAPDH mRNA and to HL-1 tranfected by gapmer control, and is shown as fold change of repression (red) or induction (blue). Our data contrast with the study of Shen et al who showed that Neat1 depletion allows to redistribute p54 nrb and SFPQ/PSF onto the c-myc mRNA, in correlation with an increase in c-Myc protein  (Shen et al.
, 2019). The model of IRESome formation mediated by Neat1 in the paraspeckle, and the absence any impact of Neat1 on the picornaviral EMCV IRES activity, are both consistent with previous reports suggesting that the site of mRNA synthesis is crucial for IRES structure and function  (Semler & Waterman, 2008). For picornaviruses whose mRNAs are synthesized in the cytoplasm, IRES elements would be able to form an IRESome RNP in the cytoplasm. In contrast, cellular mRNAs (as well as DNA viruses and retroviruses mRNAs) transcribed in the nucleus need a nuclear event  (Ainaoui et al. , 2015; Stoneley et al. , 2000). The present data provide a mechanism for this nuclear history and reveal a new function of the paraspeckle, a nuclear body, in IRESome formation. A role of Neat1 in ischemic heart has been recently reported showing that Neat1 downregulation would protect cardiomyocytes from apoptosis by regulating the processing of pri-miR-22  (Gidlöf et al.
ACKNOWLEDGMENTS Our thanks go to  J. J. Maoret  and  F. Martins  from the  Inserm UMR1297 GeT-TQ plateau of the GeT plateform Genotoul (Toulouse) , and  A. Lucas  from the  We-Met Functional Biochemistry Facility (Toulouse). This work was supported by  Région Occitanie (Midi-Pyrénées) ,  Association pour la Recherche sur le Cancer (ARC) ,  Fondation Toulouse Cancer Santé  and  Agence Nationale de la Recherche   ANR-18-CE11-0020-RIBOCARD , European funds ( Fonds Européens de Développement Régional, FEDER) ,  Toulouse Métropole , and by the  French Ministry of Research  with the  Investissement d'Avenir Infrastructures Nationales en Biologie et Santé program  ( ProFI, Proteomics French Infrastructure  project,  ANR-10-INBS-08 ). A. C. G, F. H. and E. R had fellowships from the  Ligue Nationale Contre le Cancer (LNCC).
Apparatus and Procedures The electrochemical characterization was performed by cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and chronoamperometry (CA) using an Autolab PGSTAT204 potentiostat/galvanostat equipped with the FRA32M EIS module and NOVA software, 2. 1. 4 version (Metrohm Autolab, Utrecht, The Netherlands). The disposable SPCEs (reference 110) were acquired from Metrohm Dropsens (Netherlands) with a three-electrode configuration, formed by using two carbon electrodes, i. e. , working (WE) and counter (CE) electrodes, and a reference pseudo-reference electrode (RE) with Ag/AgCl. CV was performed in a potential range between -0. 6 and 0. 6 V, at a scan rate of 50 mV s -1. The EIS measurements were conducted at a frequency range from 10 kHz to 0. 1 Hz at a potential of 0.
| European Union Labour Force Survey (LFS) controls The LFS was used as the first source of general population controls. The LFS is a major source of information for European statistics about the labour market. It is conducted by the national statistical institutes all over Europe and is centrally processed by Eurostat (2019), the statistical office of the European Union. It provides detailed information on topics including employment and education. The sampling is designed in order to ensure representativeness for the overall population. The data is collected based on individual interviews (see https:// ec. europa. eu/eurostat for details). Specific items used in this study are listed in the Supporting Information. Individual participant LFS data from the countries and the period of time corresponding to the LSQ survey was made available by Eurostat for this project.
| Panel controls Two control samples were obtained, one matched and one not matched by the level of education. In the first step, for each survivor a population control was sampled with the same age category  (18-19, 20-21, …, 38-39, 40-44, 45-52 years) , province and level of urbanisation (urban vs. rural area). The level of urbanisation was based on the postal codes of residential addresses. The controls were sampled from a panel of 110,000 individuals in Belgium and 390,000 individuals in France, registered in the database of SurveyEngine, a company specialised in the conduct of surveys (https://surveyengine. com). In case more than one panel member matched a cancer survivor, one panel member was randomly selected to be invited to participate in the study. Between April 2019 and February 2020, the controls were provided with a computer-and mobile-device-based survey through an anonymous link, so that the General Data Protection Regulation was guaranteed.
ACKNOWLEDGEMENTS The authors thank all the  EORTC Children Leukemia Group members  and the clinicians who participated in the studies. We also thank  Caroline Gilotay  and the EORTC HQ Data Management Department members ( Livia Giurgea ,  Bart Meulemans ,  Séraphine Rossi ,  Nicole Duez  and  Gabriel Solbu ) for their essential support. We thank  Teresa de Rojas ,  EORTC CLG Fellow , for her help. We thank the  EORTC Lymphoma Group and Pr. Michel Henry-Amar  who authorised us to adapt the ' Life Situation Questionnaire ' for our project. Finally, we thank  Nancy van Damme  and  Linda Thibaut  ( Belgian Cancer Registry ) and Pr. Jacqueline Clavel  ( Registre National des Hémopa-thies malignes de l'Enfant ) for their support in the update of the vital status and of second neoplasms. This paper uses data from the  European Union Labour Force Survey (Eurostat, European Union ).
These items were dichotomized given the sample is community-based and the data were not normally distributed, aligning with prior research  [15] [16] [17] [18] [19] [20]. Demographic and control variables included selfreported race/ethnicity (White or Caucasian; Black; Latino/a; East/Southeast Asian; South Asian; Middle Eastern; Indigenous; other race/ethnicity; and multiracial), sexual identity (heterosexual; gay/lesbian; bisexual; and queer, questioning, or other), highest education completed (high school diploma or less; college or undergraduate degree; master's degree or higher; other), weight perception (very underweight; slightly underweight; about the right weight; slightly overweight; very overweight) and current weight change behaviors (lose weight; stay the same weight; gain weight; not doing anything about weight).
25 mm i. d, film thickness 0. 20 µm; Varian, France) equipped with a flame ionization detector. Hydrogen was used as the carrier gas (inlet pressure 210 kPa). The oven temperature was held at 60 °C for 5 min, increased at 165 °C with a 15 °C/min rate, held for 1 min and then to 225 °C at 2 °C/min and finally held at 225 °C for 17 min. FAMEs and DMAs were identified by comparison with their commercial and synthetic standards. The data were processed using the EZChrom Elite software (Agilent Technologies, France) and reported as a percentage of total FAMEs and DMAs. Plasmalogen levels were calculated as 2 x (% of total DMAs) as previously described by Acar and collaborators  (Acar et al. , 2007).
Quantitative Analysis of Intercellular Ca2+ Waves Each cell was considered as an individual region of interest (ROI). For each ROI, we obtained a curve representing the 340/380 nm fluorescence ratio. Since the fluorescence intensity of Fura-2AM is proportional to calcium concentrations, changes in cytosolic calcium concentrations were inferred from the fluorescence profile of individual cells. The mask of each ROI was imported on ImageJ software (National Institute of Health, United States, https://imagej. nih. gov/ij) to measure the distance between the stimulated Müller cell and the subsequently activated astrocytes. Astrocytes were considered as activated once they reached a 10% increase of the baseline (0. 1 x Imax + baseline), and the corresponding latency time was evaluated (activation time).
Cell Migration Müller cells migration was evaluated by a wound healing assay. Müller cells were isolated and generated as previously described (see 2. 1 and Figure  1 ). At P2, cells were seeded in a culture-Insert (Ibidi, Germany) at a density of 1 × 10 4 cells/well. Inserts were removed 5 days after the second siRNA transfection (P2), thus creating a cell-free gap of 500 µm. Cell migration was monitored under microscope by recording a picture each hour during 72 h. Three fields per insert were observed and the results were averaged. The cell-free area and the percentage of recovery were measured and calculated using the ImageJ software (National Institutes of Health, United States).
Cell Proliferation Cell proliferation was evaluated by Ki-67 labeling of Müller cells. Briefly, Müller cells were washed with PBS and fixed for 10 min with 4% formaldehyde in PBS. After washes and permeabilization steps with TritonX100 (Sigma-Aldrich), cells were incubated with primary antibodies (mouse anti-ki67, dilution 1:1,000, reference M7248, Dako, Denmark) overnight at 4 °C. Then, secondary antibody (reference A11001, Thermo Fischer Scientific, dilution 1:1,000) and DAPI were added and cells were cover slipped using a fluorescence-mounting medium. Fluorescence microphotographs were taken using a Nikon microscope (Eclipse E600, Nikon, France) and a Nikon digital camera (DS-Ri2, Nikon) equipped with the Nikon Nis BR software. Images were analyzed with ImageJ software. Proliferation was evaluated as a ratio between the numbers of cells stained by Ki-67 to total cells stained by DAPI.
Statistical Analysis Statistical analysis was performed using GraphPad Prism v6. 05 (GraphPad software, United States). For gene and protein expression, comparisons between two groups were performed using a non-parametric Mann-Whitney test. For the calcium wave quantitative analysis, Pearson correlation coefficients were determined to assess linear associations between astrocytes activation time and their distance from the ATP-stimulated Müller cell. Radius-dependent comparisons between groups were performed by Mann & Whitney test. A p value lower than 0. 05 was considered as statistically significant and noted by one star (*). Two (**) and three stars (***) were used for p values lower than 0. 01 and 0. 001, respectively.
ACKNOWLEDGMENTS The authors would like to thank  Laurence Decocq  and  Patrick Cailler  for animal care. The authors thank VISIO Foundation;  National Research Institute for Agriculture, Food and Environment (INRAE) ;  Regional Council of Burgundy  ( PARI Grant );  European Regional Development Fund (FEDER) ;  Agence Nationale de la Recherche  ( ANR-11-LABX-0021-01 );  Fondation de France/Fondation de l'Oeil; Groupe Lipides et Nutrition (GLN)  for their financial support.
Materials and Methods Recruitment and sample description SYT1 variants were identified via exome sequencing (trio or solo) within clinical laboratories or ethically approved research studies. The identification, validation, confirmation of de novo status, and clinical reporting of SYT1 variants were carried out by each participant's clinical center. Authors were notified of diagnosed variants by personal communication, through database searching of ClinVar 11 (https://www. ncbi. nlm. nih. gov/clinvar/) or Decipher  12  (https://www. deciphergenomics. org/), or through Gene-Matcher  13  (https://genematcher. org/statistics/). A total of 51 additional participants with ID of known monogenic origin (excluding synaptic vesicle cycling disorders as listed by John et al 3 ) were recruited as a comparison group for behavioral data.
Molecular dynamics simulations Homology models of SYT1 C2 domains harboring variants were generated from solution structures of the Ca 2+ -bound C2A and C2B domains of rat SYT1 (Protein Data Bank: 1BYN  16  and 1K5W  17  ). Note that amino acid numbering used throughout this paper follows human sequence numbering for simplicity. The wild-type (WT) structure and each variant homology model (with Ca 2+ ions both present and removed) were subjected to 4 individual atomistic molecular dynamics simulations with trajectory lengths of approximately 400 ns each (for full details see Supplemental Methods). Root-mean-square deviation of the backbone and root-mean-square fluctuations (RMSF) of the backbone Calpha atoms of each domain variant were measured over the course of the simulations as readouts of overall and local mobility of the domains.
47; Genome Aggregation Database version 2. 1. 1, 22 https://gnomad. broadinstitute. org/gene/syt1 ?dataset=gnomad_r2_1), the C2A and C2B domains lie within a region that demonstrates significant missense constraint with an observed to expected ratio of 0. 24 (χ 2 = 48. 87; Exome Aggregation Consortium,  22  https://gnomad. broadinstitute. org/gene/syt1?dataset=exac).
Notably, a pathogenic variant has been found at the residue corresponding to Ser309 in the homologous SYT2. 25  In the Ca 2+ -bound simulations, both Met303Val and Ser309Pro increased the mobility of the distal arginine apex (Arg399, Arg400) at the opposite end of the C2B domain (Supplemental Figure  4 ). No structural alterations were detected in simulations of the Asn341Ser variant (Supplemental Figure  4 ), but importantly, Asn341Ser may perturb the interaction between SYT1 and the SNARE complex. Asn341 faces outward on β-5 and is proximate to the primary binding interface between SYT1 C2B and SNAP-25. 26 Crystal structures of the SYT1-S-NARE complex (Protein Data Bank: 5CCH, 5CCG, and 5KJ7)  26  show that Asn341 may interact directly with Asp166 of SNAP-25 or form a hydrogen bond with the neighboring Tyr339 in SYT1, which binds to Asp166 of SNAP-25 (Figure  2I ).
Interestingly, 2 variants at Asp166 have been identified in individuals with SNAP25 developmental and epileptic encephalopathy. Primary interface of the SYT1-SNARE complex (Protein Data Bank: 5CCH; white: SYT1; green: SNAP-25; red: synaptobrevin-2; blue: syntaxin-1A) highlighting the intramolecular (Asn341-Tyr339 in SYT1) and intermolecular (Asn341 SYT1 -Asp166 SNAP-25 ) hydrogen bonds involving Asn341 in yellow. J, K. YRB representations  23  of Ca 2+ -bound WT and variant C2A or C2B domains (at last frame of simulation) that show surface charge and hydrophobicity (red: negative charge; blue: positive charge; yellow: hydrophobic). J. WT and Glu219Gln (inset) C2A domains. K. WT, Gly369Asp (left inset), and Lys367dup (right inset) C2B domains. Ca 2+ ions are represented as orange spheres. Ca 2+ , calcium ion; WT, wild-type.
Broadening the genetic landscape We describe 4 novel variants in the SYT1 C2A domain as well as additional C2B loci. Although the 4 C2A variants and 1 C2B variant remain of uncertain significance according to ACMG/AMP criteria, and functional evidence is required to substantiate pathogenicity, molecular dynamics simulations and existing literature support potential functional impacts. Novel variants may exert dominant-negative effects, as seen for previously identified variants, 8-10 but we cannot preclude haploinsufficiency as a possible pathogenic mechanism. Ca 2+ -binding loops 1 and 3 of the C2B domain seem to be highly sensitive to variation as pathogenic missense variants cluster in these regions in both SYT1 and the homologous SYT2,  25, 33, 34  and no missense SYT1 variants in these loops are recorded in the Genome Aggregation Database version 2.
F-H. Intramolecular interactions that were abolished in simulations of variant domains are shown as yellow dotted lines (see Supplemental Table 4 for details). F. C2A domain showing the Glu209-Thr196 hydrogen bond lost in Glu209Lys. G. C2A domain showing the Glu219-Lys223 salt-bridge lost in Glu219Gln. H. C2B domain showing Ser309-Met303 and Ser309-Asp304 hydrogen bonds lost in Ser309Pro. I. Primary interface of the SYT1-SNARE complex (Protein Data Bank: 5CCH; white: SYT1; green: SNAP-25; red: synaptobrevin-2; blue: syntaxin-1A) highlighting the intramolecular (Asn341-Tyr339 in SYT1) and intermolecular (Asn341 SYT1 -Asp166 ) hydrogen bonds involving Asn341 in yellow. J, K. YRB representations 23  of Ca 2+ -bound WT and variant C2A or C2B domains (at last frame of simulation) that show surface charge and hydrophobicity (red: negative charge; blue: positive charge; yellow: hydrophobic).
Acknowledgments We appreciate the important and generous contributions of each individual with a SYT1 variant, their families, and carers. We appreciate the roles of each clinician and laboratory scientist involved in the diagnostic pathway of each case. Furthermore, we appreciate the involvement of individuals in the comparison intellectual disability group and their families and carers. We acknowledge the  NIHR UK Rare Genetic Disease Research Consortium  for assistance with recruitment to the study. H. M. was supported by an  Australian   Government Research Training Program Scholarship. S. L. G. and H. M. were supported by Grant 2003710 from The  National Health and Medical Research Council of Australia  and a  Florey Fellowship. The  Florey Institute of Neuroscience and Mental Health  acknowledges the strong support from the  Victorian Government, Australia  and, in particular, the funding provided from the  Operational Infrastructure Support Grant.
c. 1113C>G 2 49 x synonymous Tolerated (1) Probably damaging Possibly pathogenic Y 9 PS3, PM1, PM2, May perturb structure of p. Asn371Lys(N371K) change (0. 999) (0. 131) PM6, PP3 Ca 2+ -binding loop 3 of (19 in controls) Pathogenic C2B Variant classification shown in bold. ACMG/AMP, American College of Medical Genetics and Genomics/Association for Molecular Pathology; Ca 2+ , calcium ion; gnomAD, Genome Aggregation Database; M-CAP, Mendelian Clinically Applicable Pathogenicity; N, no; SIFT, Sorting Intolerant From Tolerant; VUS, variants of uncertain significance; Y, yes.