dataesr/scientific-paragraphs-categorization huggingface dataset:
Size Exclusion Chromatography Right-Angle Light Scattering Protein mass measurements were performed on an Agilent HPLC system connected to a Viscotek 305 tri-detector (Malvern) to monitor static light scattering, refractive index, and UV absorbance. 100 mL sample was loaded onto a Superdex 200 HR 10/300 GL column (GE Healthcare) equilibrated in Size Exclusion Chromatography (SEC) buffer at a flow rate of 0. 3 mL min À1. Data were recorded and processed using OmniSEC software (Agilent). Small Angle X-ray Scattering Small angle X-ray scattering (SAXS) data were collected at EMBL beamline P12 at the PETRA III storage ring (DESY, Hamburg, Germany)  (Blanchet et al. , 2015)  using a 2M Pilatus pixel detector (DECTRIS) detector, a distance of 3. 1 m and a wavelength of 1. 24 A ˚(Table  2 ). MbcTA was measured at several protein concentrations in a range between $0.
6 to $7. 1 mg ml À1. Analysis of the scattering data was performed using the programs from the ATSAS 2. 7 package  (Petoukhov et al. , 2012). The data obtained at the lowest and highest concentration were used for further analysis of MbcTA. The forward scattering I(0) and the radius of gyration R g were calculated from the Guinier approximation calculated using PRIMUS GNOM  (Svergun, 1992)  was used to evaluate the pair distribution function, P(r), and to calculate the maximum particle dimension (D max ). Ab initio models for MbcTA were generated with DAMMIN  (Svergun, 1999)  utilizing a relaxed disconnectivity criterion without symmetry restrictions. Validation, resolution estimation and averaging for the final model building were performed with SASRES  (Tuukkanen et al. , 2016)  and DAMAVER  (Volkov and Svergun, 2003).
Circular Dichroism Spectroscopy Samples were diluted to $0. 1 mg ml À1 in buffer containing 250mM NaF and 10mM sodium phosphate (pH 7. 5). Circular dichroism (CD) spectra were recorded between 190 and 320 nm at 10 C in a 1 mm QS quartz cuvette on a Chirascan CD Spectrometer upgraded with an Active Nitrogen Management System (Applied Photophysics). Instrument settings were as follows: 1 nm bandwidth, 1 s response and 0. 5 nm data pitch. For each dataset 5 spectra have been averaged and sample buffer subtracted as background. Data were recorded with the Pro-Data Chirascan software  (version 4. 5. 1833). Isolation of genomic DNA and total RNA For isolation of genomic DNA, E. coli DH5a cells were cultured in LB medium to an OD 600 of 0. 7, collected and washed with PBS buffer. Genomic DNA was obtained using the DNeasy Blood & Tissue kit (QIAGEN) according to the manufacturer's instructions for Gram-negative bacteria, including RNaseA digestion.
Reactions with DNA and RNA or without substrate were analyzed by thin layer chromatography. Thin Layer Chromatography 2 mL of each ADP-ribosylation reaction was spotted on polyethyleneimine (PEI) cellulose plates (Merck Millipore), which were airdried prior to development with 0. 25 M LiCl and 0. 25 M formic acid. After drying, plates were exposed to an image plate (Fujifilm) and analyzed using a Phosphor-Imager (Fujifilm). Raw images are available on Mendeley Data (https://doi. org/10. 17632/ y6ynjm5sf3. 1).
HPLC Reactions were analyzed on an Agilent 1260 Infinity HPLC system using an Agilent Poroshell 120 EC-C18 column (2. 7 um 4. 6 3 50 mm) and monitoring absorbance at 260 nm. Elution was achieved with an isocratic flow of 2 ml/min of 10 mM ammonium phosphate pH 5. 5 with 2. 5% acetonitrile  (Muller-Steffner et al. , 1994). Data were collected and analyzed with OpenLAB CDS Chem-Station (Agilent).
NMR spectroscopy Spectra were acquired in a Bruker Avance III HD spectrometer operating at a 1 H frequency of 700 MHz and equipped with a 5 mm 1 H/ 31 P/ 13 C/ 15 N resonance PFG cryogenic probe. Data were processed and analyzed with Topspin 3. 5. 1D and COSY HMBC NMR spectra are available on Mendeley Data (https://doi. org/10. 17632/y6ynjm5sf3. 1).
Initial rates of the reaction were determined by the linear regression of the plot of NAD + consumption versus time, assuming saturating conditions of inorganic phosphate. Each calculated initial rate was plotted versus the corresponding NAD + concentration. Michaelis Menten kinetics were used to determine K M , V max for MbcT under each condition. K cat was determined from the fit of the plot of K obs (initial rate divided by enzyme concentration) versus NAD + concentration. All calculations were performed using GraphPad Prism software. Western blotting pET28a(+)-MbcT constructs were transformed to E. coli BL21 (DE3) and cultured in LB at 37 C. Protein expression was induced with IPTG (0. 5mM) at an OD 600 of 0. 7 and cells were harvested 1 h after induction by centrifugation. Cells were resuspended in 1x BugBuster lysis reagent (Merck Millipore) supplemented with 0.
13 mg ml À1 protease-inhibitor-mix HP (SERVA Electrophoresis) and 0. 01 mg ml À1 deoxyribonuclease I (Sigma-Aldrich) and incubated at RT for 15 min. Protein lysates were separated by SDS-PAGE, transferred to Immuno-Blot PVDF membrane (Bio-Rad) using a Trans-Blot Turbo (Bio-Rad) and blocked overnight using 5% solution of skimmed milk powder (Carl Roth). Membranes were probed with either Penta His HRP conjugate (QIAGEN) or anti-GroEL (E. coli) monoclonal antibody (clone 9A1/2) (Enzo Life Sciences) as the primary antibody. HRP-linked whole Mouse IgG Antibody (GE Healthcare) was used for detection of GroEL. Blots were developed using SuperSignal West Pico Maximum Sensitivity Substrate (ThermoFisher Scientific) and visualized using a ChemiDoc MP (Bio-Rad). Raw blot images are available on Mendeley Data (https://doi.
QUANTIFICATION AND STATISTICAL ANALYSIS Comparison of survival curves of SCID mice was performed with Log-rank (Mantel-Cox) test in GraphPad Prism software. Significance of variation in CFUs in lungs of infected C57BL/6J mice was performed using unpaired Student's tests in GraphPad Prism software. No animals were excluded from statistical analysis. p values correlate with symbols as follows: ns = not significant, p > 0. 05, * p % 0. 05, ** p % 0. 01, *** p % 0. 001, **** p % 0. 0001.
DATA AND SOFTWARE AVAILABILITY All raw images as well as the 1D and COSY HMBC NMR spectra are deposited on Mendeley Data (https://doi. org/10. 17632/ y6ynjm5sf3. 1). The accession number for the MbcT-MbcA crystal structure reported in this paper is PDB: 6FKG. The accession number for the MbcT-MbcA SAXS data reported in this paper is SASBDB: SASDD33.
aeruginosa NAD + glycohydrolase Tse6 (UniProt: Q9I739), and Streptococcus pyogenes NAD + glycohydrolase SPN (UniProt: D7S065). (D) Structural comparison of the active site in MbcT, Dtox in complex with NAD + (PDB: 1TOX), PARP1 (PDB: 4DQY), and CpnT (PDB: 4QLP). Conserved residues are colored according to their localization in the three distinct regions (cf. C). See also Figures S3 and S4.
ACKNOWLEDGMENTS We thank  K. Aktories  and  S. Ost  for providing CDTa and actin,  M. Jeske  and  K. Temmerman  for help with enzyme assays,  G. Kelly  for NMR data collection analysis, the  IPBS imaging (TRI)  and zootechnics (Anexplo) core facilities,  F. Moreau  and  C. Berrone  for assistance with functional exploration, the  SPC facility at EMBL Hamburg  and the  Proteomics Core Facility at EMBL Heidelberg  for technical support, and  Y. Rombouts ,  F. Rauschel ,  G. R. Stewart , and  S. H. E. Kaufmann  for comments on the manuscript. NMR data were recorded in the  MRC Biomedical NMR Centre  at the  Francis Crick Institute , which receives core funding from  Cancer Research UK  ( FC001029 ), the  Medical Research Council  ( FC001029 ), and the  Wellcome Trust  ( FC001029 ). This work was supported by the  European Union  ( TBVAC2020 ),  Agence Nationale de la Recherche / Programme d'Investissements d'Avenir  ( ANR-11-EQUIPEX-0003  and  ANR-13-BSV8-0010-01 ),  Fondation pour la Recherche Medicale  ( DEQ20160334902  and post-doctoral fellowship to A.
The miniassisting hand assessment will be rated between 10 and 11 months and at 18 months of age. Adverse events will be recorded at least monthly for each child. Ethics and dissemination Full ethical approval for this study has been obtained. The findings will be disseminated in peer-reviewed publications. trial registration number EudraCT: 2015-001402-34 in European Clinical Trial database; NCT03198702 in Clinical Trial database; Pre-results.
Ethics Full ethical approval for this study has been obtained by the ethical committee Ouest 1 of Tours and Agence Nationale de Sécurité du Médicament et des produits de santé (ANSM). The trial has been registered in the European Clinical Trial database (EudraCT: 2015-001402-34) and Clinical Trial database (NCT03198702). All families will be given a written information letter detailing the study and parents or guardians will sign informed consent prior to the child's inclusion. Any modification or amendment to the protocol will be submitted to the ethical committees and ANSM for approval. After approval, investigators and trial participants will be informed of the changes by letter or email. All trial databases will also be updated.
study procedure The study procedure is described in figure  1  and table 1. At visit 1 (between 10 and 11 months of age), the parents or guardians will sign the informed consent form and the baby will be included. The physician or surgeon will carry out a physical examination and will collect sociodemographic data including history of BPBI in a brother or sister, overweight or obesity of the mother, any medical conditions during the pregnancy (eg, gestational diabetes), the birth procedure (caesarean section, vaginal delivery with epidural, induction of labour, instrumental delivery, shoulder dystocia, term and duration), birth weight and length and APGAR score. Visit 2 (at 11 months of age) will involve MRI to confirm the diagnosis of bony deformity (the humeral head on the involved side must be at least 7% more posterior than the humeral head on the contralateral side).
Stratification will be carried out by centre and by microsurgery prior to inclusion, since early surgery could influence the progression of bony deformity. Only the physician who will perform the BTI and the pharmacist will receive the email specifying the randomisation arm of each baby. Neither the parents or guardians nor the clinical and radiological evaluators will be aware of the treatment administered. The doctors carrying out the BTI will not take part in subsequent visits to ensure the blinding of the examiner. A central analysis of MRI data will be carried out in order to ensure blinding of the evaluator to the primary outcome measure.
The chosen doses are based on data in the literature in children and babies with BPBI  20 22 23  : a total of 8 U/kg will be injected (2 U/kg in subscapularis, 3 U/kg in pectoralis major and 3 U/kg in teres major/ latissimus dorsi). Because there is no marketing authorisation for the use of botulinum toxin in children under the age of 2 years, the chosen doses are smaller than the maximal doses authorised for the treatment of spasticity in older children with cerebral palsy. Moreover, the doses chosen correspond with doses used in previous studies. A standardised protocol for the prevention and treatment of induced pain and postinjection pain will be systematically used. This will involve the administration of topical anaesthesia (such as EMLA) and paracetamol (dose according to the baby's weight) 1 hour prior to the injection.
Adverse events related to MRI premedication The risks related to the premedication are the standard risks for the sedation or anaesthesia of children (gastritis, anticholinergic effects, oxygen desaturation, excessive sedation). The child will be examined for potential risks during a routine paediatric or anaesthetic consultation. Independent data monitoring committee and unblinding procedure An independent data safety monitoring committee (DSMC) composed of five independent members will be set up. The purpose of the DSMC will be to provide an independent evaluation of any adverse events that occur during the research, as well as to monitor the benefit/ risk ratio. Should an adverse event that requires different care than that planned in the study occur, unblinding will be carried out. Unblinding will not be carried out in any other condition.
This measurement is quick to carry out and is used in both research and routine clinical practice in children and babies with BPBI to help preoperative decision-making for the type of intervention and postoperative follow-up. 6 8 39 Intrarater and inter-rater reliability have been shown to be excellent, with a 7% estimated measurement error. 38 MRI data will be analysed centrally (at Brest CHRU) by two trained investigators using the same guidelines in order to minimise inter-rater variability and to ensure the blinding of the evaluator.
Locations and data management Each centre will manage their own recruitment of babies and organisation of MRIs, clinical evaluations and treatment. Electronic data will be secured and analysed in a central database managed by the Brest CHRU. Data will be the property of CHRU Brest. In accordance with Good Clinical Practice (GCP) guidelines, the sponsor is in charge of obtaining agreement from all centres involved in the clinical research, in order to guarantee direct access to all the clinical research sites, to all the source data, source documents and all the reports for the purpose of quality control and audit by the sponsor. All information required for the study will be entered in the paper case report forms (CRFs) during evaluations, then transferred to the electronic CRF (Clinsigth).
Items of missing data will be coded. Each centre will be responsible for completing the CRFs for the babies enrolled in their centre. Each investigator will receive an instruction document regarding the use of this tool. The investigator will be responsible for the accuracy, quality and relevance of all the data entered. In addition, the data will be immediately verified as they are entered, using consistency checks. The investigator must validate any changes to the values in the CRF. These modifications will be subject to an audit trail. A justification can be added when applicable, as a comment. Data management and query processing will be carried out by a data manager. A clinical research assistant (CRA) appointed by the sponsor will ensure the good running of the study, data collection on the paper CRF, data recording in the electronic CRF, data saving and reporting in accordance with the sponsor's standardised operating procedures as well as the GCP guidelines and current legislation and laws in force.
Open access The investigator and the members of his/her team will agree to be available during all the routine and planned quality control visits by the CRA. During these visits, the following will be audited: signed informed consent, compliance with the study protocol and procedures, data recorded in the CRF: accuracy, missing data, consistency between these data and their 'source' (medical files, original laboratory results, etc), product management and investigator file. The investigators agree to accept the quality assurance audits carried out by the sponsor as well as the inspections carried out by the competent authorities. All data, documents and reports may be subject to regulatory audits and inspections. Medical confidentiality cannot be invoked in opposition to these audits and inspections.
Any data sent to the sponsor by the investigators (or any other specialised parties) during or after the biomedical research will be anonymised. These data should not reveal any visibly accurate names and addresses of enrolled (involved) individuals. Only the first letter of the subject's name and first name will be saved along with a coded number indicating the order of inclusion of the subjects. The sponsor will ensure that the parent of each research subject has given permission in writing for access to personal information about the baby which is strictly necessary for the quality control of the research.
sample size and statistical analysis No longitudinal data regarding the progression of bony deformities in children with BPBI are available in the literature. Only transversal studies have been carried out, indicating that posterior subluxation is significantly greater on the affected side compared with the healthy side at the age of 4. 8 months (affected side 32. 1%-: SD=19. 7% vs healthy side 49. 8%: SD=7. 3%). 6 The calculation of the number of subjects necessary for this study was based on a difference of the standard deviation at 12 months, for a SD of 5%. In order to guarantee a power of 90%, a sample of 22 babies per group is required, thus a total of 44. In order to account for babies lost to follow-up (10%) and babies who will not be treated because of a lack of true subluxation on MRI, 62 babies will be recruited.
P<0. 05 will be considered as statistically significant. Data analysis will be carried out on an intention to treat basis by a biostatistician after blind review and database freezing at the end of the study. No intermediate analysis is planned during this trial. dIsCussIon This paper presents the background and design for a multicentre double-blind randomised controlled trial to evaluate the effectiveness of BTI in the shoulder internal rotator muscles of 12-month-old babies in limiting the progression of posterior subluxation of the glenohumeral joint, compared with a sham procedure. To our knowledge, this is the first study with a sufficiently robust methodology to allow conclusions to be based on a high level of evidence. The babies included in the study will all receive two sessions of physiotherapy per week.
Acknowledgements The authors acknowledge  Chloe Bureau ,  Bhushan Borotikar ,  Céline Dolou ,  Valentine Guiton ,  Mélanie Pelouin ,  Emmanuel Novak  for their help in building this project and  Johanna Robertson  for her help in revising English. Collaborators POPB-tox group:  Marianne Alison ,  Madeleine Aslan ,  Jennifer Bastien ,  Gilles Dautel ,  Floriane Colin ,  Marion Delpont ,  Bruno Dohin ,  Marie Agnes Galloy ,  Vincent Gautheron ,  Salem Hassan Al Khoury ,  Pascal Jehanno ,  Mélanie Kaas ,  Olivier Prodhomme ,  Mélanie Porte ,  Anne Gaelle Py ,  Helène Rauscent ,  Emilie Rumilly ,  Katherine Sanchez Barr ,  Catherine Tréguier ,  Philippe Violas. Contributors CP and SB conceived the study and defined the original study protocol. CP, FF, NQ and SB developed the intervention parameters.
S4 ), with the main plan representing 43. 8% of the inertia of the data summarized in Table  3. Fatty acid profile in F2 placental intracellular lipid storages (neutral lipids, NL). EC placental intracellular lipid stores (neutral lipids, NL) (Table  4 ) were characterized by lower C14:0 and C15:0 contents (-14. 2%, p = 0. 004 and -12. 1%, p = 0. 035), a tendency for lower di-homo-gamma-linolenic acid contents (DGLA, C20:3n-6, -17. 5%, p = 0. 064), as well as lower PUFA contents (-17. 3%, p = 0. 014), especially arachidonic acid content (AA, C20:4n-6, -31. 7%, p = 0. 026); they were also characterized by higher MUFA (+12. 7%, p = 0. 02), particularly oleic acid (OA, C18:1n-9, +17. 5%, p = 0. 035), compared to the intracellular lipid stores of control placentas. PCA was performed on the fatty acid profiles of placental neutral lipids.
Placental transcriptome. Hierarchical clustering revealed limited differences in the F2 placental transcriptome between the EC and CC groups, as shown by the very short clustering scale (supplementary Fig. S7 ). This close similarity between F2 EC and CC placentas was confirmed by the small number of differentially expressed (DE) probes, transcripts and annotated genes (Supplementary Table  S3 ). The microarray data have been registered in the Gene Expression Omnibus (GEO) under accession number GSE109831. Differential gene expression (adjusted p-value < 0. 05) between EC and CC placentas was observed for F-box protein 32 (FBXO32, +119%, 4 significant probes on a total of 5 probes in microarray), T-cell activation RhoGTPase activating protein (TAGAP, +214%, 2 significant probes on a total of 2 probes) and Interleukin 23 α subunit p19 (IL23A, +275%, 1 significant probe on a total of 1 probe).
After RT-qPCR, statistical significance was only found for one of the three transcripts highlighted by the microarray, FBXO32, confirming this result. For the other two transcripts, TAGAP and IL23A, only a trend going in the same direction was observed. (Fig. 1 ). Gene set enrichment analyses (GSEA) in EC placentas. Because the usual strategy used to analyse transcriptomics is based on a single-gene expression level that becomes inefficient with subtle variations in the same pathway  24  , we further analysed placental transcriptomic data using a GSEA approach as described above. Using GSEA, a total of 58 significantly enriched gene sets were observed after FDR multiple test adjustment (q-value < 0. 25) for the EC group, including 10 terms for the KEGG (the Kyoto Encyclopedia of Genes and Genomes) database, 14 terms for the biological process (BP) category, 19 terms for the cellular component (CC) category and 15 terms for the molecular function (MF) category of the GO (Gene Ontology) database (Supplementary Tables  S4-S7 ).
In the top fifteen terms for all databases, using an enrichment score ranking, most terms defining the placenta-exposed group were related to intracellular organization (nuclear pore and envelope, "integral to organelle membrane", "organelle membrane" and "Golgi vesicle transport") and protein metabolism ("signal sequence binding", "ubiquitin protein ligase activity", "ubiquitin mediated proteolysis" and "proteasome complex") (Fig. 2 ). Gene set enrichment in CC placentas. A total of 69 significantly enriched gene sets were observed after FDR multiple test adjustment in the control group (i. e. , comparatively downregulated pathways in EC placentas), including 16 terms in the KEGG database, 18 terms in the BP, 11 terms in the CC and 24 terms in the MF categories of the GO database (Supplementary Tables  S4-S7 ).
These results are consistent with the molecular changes observed in F2 placentas using GSEA analysis of transcriptomic placental data, showing Expressions were analyzed by microarray (left column) and RT-qPCR (right column). Microarray data were first log2-transformed and then normalized by an intra-array median subtraction. Relative expression of genes obtained by RT-qPCR was normalized by the expression of two housekeeping genes, RPL18 and EIF4E2. Boxplots are representative of the median value and quartiles. Significant differences between conditions were figured out by * (for P value < 0. 05). a downregulation of gene sets involved in inflammation, coherent with the upregulation of gene sets involved in protein metabolism (proteasome) and intracellular signalling. Contrary to what has been shown elsewhere, for example, in the case of maternal lipid over-nutrition in rabbits  35  , suggesting that male and female placental responses differ, this was not the case here.
Foetal sex has been taken into consideration in all of the statistical analyses, as an explicative factor, but no sex-related difference reached statistical significance in any of our datasets. This finding may be explained by the fact that compared with F1 controls, in utero exposure did not lead to observable differences in body weight or blood biochemistry; moreover, in adulthood, the F1 females were all fed with the same balanced and optimal gestation-specific diet. Thus, conditions might not have been met metabolically to induce or highlight different gender-specific responses or that the effects of pollution may have been much stronger than the sex-specific responses that would then have been either smoothed or erased. However, it cannot be excluded that the sample size was too small to highlight sex-specific effects.