dataesr/scientific-paragraphs-categorization huggingface dataset:
Data were collected on births occurring between April 2011 and September 2012; in each region inclusions occurred over 12 months, except in France (six months). Investigators abstracted data from medical records in obstetrical and neonatal units using a pretested standardised questionnaire with common definitions. Gestational age was defined as the best obstetric assessment based on information on last menstrual period and antenatal ultrasound examinations, which are part of routine obstetrical care in all regions. When there were several estimates, we used the following hierarchy to determine gestational age for the study: in vitro fertilisation treatment, ultrasound result based on earliest estimate, last menstrual period, fundal height measurement, and neonatal assessment at birth. We cross checked inclusions against delivery ward registers or another external data source.
study population The study population comprised all infants without severe congenital anomalies born at 24+0 to 31+6 weeks' gestation and admitted to a neonatal unit (n=7336 infants delivered in 335 maternity units and admitted to 242 neonatal units). We excluded infants born before 24 weeks' gestation because there is no consensus across the regions about active treatment for these births  21  (n=301 live births). Infants with severe congenital anomalies were excluded because of regional differences in screening and termination policies (n=126). 22 We also excluded infants who died on the labour ward (n=112 ≥24 weeks' gestation) because the EPICE database does not contain information on the degree of emergency in these cases, condition at birth, or neonatal resuscitation practices, and we were concerned that these cases were often situations where there was no opportunity to provide evidence based care.
Missing data Most variables had low proportions of missing data: less than 1% (gestational age, birth weight, sex, multiple pregnancy, neonatal transport, antenatal corticosteroids), 1-3% (pregnancy complications, mode of delivery, neonatal morbidity), and 4-5% (Apgar score and admission to delivery time). In contrast, admission temperature was missing in 12. 1% of cases (n=886). We used multiple imputations chained equations to impute missing data, based on all variables in the study. 34 We used 100 imputed datasets. 35 Outcomes were not imputed. Results are presented using the imputed data; however, models using list-wise deletion are included as supplementary tables.
Funding: The research leading to these results received funding from the  European Union 's  Seventh Framework Programme  ([FP7/2007-2013]) under grant agreement No  259882. Additional funding is acknowledged from the following regions: France ( French Institute of Public Health Research/Institute of Public Health  and its partners the  French Health Ministry , the  National Institute of Health and Medical Research , the  National Institute of Cancer , and the  National Solidarity Fund for Autonomy ; grant  ANR-11-EQPX-0038  from the  National Research Agency  through the  French Equipex Program of Investments  in the Future; and the  PremUp Foundation) ; Poland (2012-2015 allocation of funds for international projects from the  Polish Ministry of Science and Higher Education); Sweden  (funding by a regional agreement on medical training and clinical research (ALF) between  Stockholm County Council  and  Karolinska Institutet , and by the  Department of Neonatal Medicine, Karolinska University Hospital ); UK (funding for the neonatal survey Neonatal Networks for East Midlands and Yorkshire and Humber regions).
Transmission electron microscope AuNP were visualized using a transmission electron microscope (JEOL 2100, Japan) at an accelerating voltage of 200 kV. The samples were prepared by placing a drop (5 ll) onto ultrathin Formvar-coated 200-mesh copper grids (Tedpella, Inc. ) and left to dry in air at 4 C. For each sample, the size of at least 100 particles was measured to calculate the average and the size distribution. Digital images were analyzed with the IMAGEJ software and a macro performing smoothing (3 Â 3 or 5 Â 5 median filter), manual global threshold and automatic particle analysis provided by IMAGEJ. The macro can be downloaded from http://code. google. com/p/psa-macro. The circularity filter of 0. 8 was used to exclude agglomerates that formed during drying.
D. Circular dichroism Circular dichroism spectra were collected using either a Jasco CD J810 or a Chirascan CD (Applied Biophysics) instrument. A 1 cm pathlength low volume quartz cell was used to analyze low concentration of AuNP-HSA in complex. For each sample 4-9 scans were acquired and averaged according to the quality of the spectra and the concentration of protein. The CD spectra of free HSA and AuNP-HSA samples were baseline-corrected by subtracting the CD spectrum of the buffer (for free HSA) or the CD spectrum of AuNP at the same concentration than in AuNP-HSA samples (for AuNP-HSA complexes). The baseline-corrected spectra were smoothed with Savitzky-Golay smoothing function of six points. CD spectra were analyzed with the DICHROWEB analysis software using the CONTINLL algorithm and the protein dataset 7 (http://dichroweb.
E. Synchrotron radiation circular dichroism SRCD experiments were performed using a nitrogenflushed module B end-station spectrophotometer at the B23 synchrotron radiation CD beamline at the Diamond Light Source (Oxfordshire, UK). Measurements were carried out at 23 C unless otherwise stated with wavelength set between 185 and 260 nm, 1 mm slit equivalent to 1. 5 nm bandwidth, increment of 1 nm, and interval time of 1 s. Data from UV denaturation experiments were collected on protein samples as repeated scans, without any averaging over 30 scans. The cell used has a 10-cm pathlength and a volume of 820 ll. Protein secondary structure was estimated with the B23 software, CDAPPS, available for in-house and remote processing CDAPPS (Ref. 17) using the CONTIN-LL algorithm and the dataset CLSTR.
One of the key parameters in the NP-protein interactions is the surface charge of the NPs (Ref. 18) and its interplay with the surface charges on the proteins. Citrate-stabilized AuNPs are negatively charged at pH 7. 4 and HSA, having an isoelectric point of 4. 7, is also overall negatively charged at that pH. The formation of a stable complex of AuNPs with a layer of HSA on top points to a situation where HSA probably replaces the citrate molecules and acts as a stabilizer for the colloid system. To better understand the damage induced in HSA by UV exposure, we calculated the changes in secondary structure for each one of the 30 SRCD spectra collected for free HSA and AuNP-HSA samples using the integrated software CDAPPS. 19 UV radiation caused a 30% decrease in a-helical structure of free HSA, and a slight increase of $10% in b-strand and unordered structures (Fig.
ACKNOWLEDGMENTS The authors would like to thank  Diamond Light Source  for beamtime on B23 beamline ( SM9836  and  SM9064 ), T amas J avorfi of B23 beamline and  Sylvain D. Vallet  ( ICBMS, Lyon, France ) for technical assistance. This work has been carried out within the  JRC Institutional research action   15524  (Nanobiosciences). The authors thank to  European Commission  for funding.
(The maximal number of such flanking residues for a target protein of unknown structure can be determined empirically, e. g. , by assessing the solubility and thermal stability of a C-terminal truncation series). The junction is optimized by progressively deleting linker and/or flanking residues to reduce the spatial separation between the two fusion partners, thereby restricting the relative mobility of the target subunits. In the ideal case, this procedure generates one or more constructs in which target subunits abut snugly against the scaffold in a uniform orientation, yielding a symmetric particle suitable for cryo-EM analysis (Fig. 1A , bottom). To identify a suitable scaffold, we searched the Protein Data Bank (PDB) for proteins that formed large homo-oligomers and had a sterically accessible N-or C-terminus remote from the oligomerization interface, restricting our search to bacterial proteins so as to facilitate expression in E.
These observations suggest a configuration in which the MBP and GS subunits of construct Δ 2 are approximately aligned along the (6-fold) axial direction, such that adjacent rings of MBP and GS subunits stack with an eclipsed geometry. In contrast, the corresponding Δ 5 subunits appear to be staggered, reflecting a rotational offset between adjacent MBP and GS subunit rings. These findings underscore Comparison of MBP-GS constructs Δ2 and Δ5 by cryo-EM. Based on the above results, we pursued cryo-EM analysis of MBP-GS constructs Δ 2 and Δ 5. To assess which of these was the more promising, we collected preliminary datasets on photographic film using an FEI Tecnai F30 Polara electron microscope. Raw images and class averages recapitulated the characteristic top and side views observed by negative-stain EM (Fig.
Cryo-EM reconstruction of MBP at sub-nanometre resolution. To obtain a higher resolution cryo-EM structure for MBP-GS construct Δ 2 we collected a larger dataset, used an electron-counting direct detection camera and performed 3D classification (Supplementary Fig. S5A-C  and Fig. 4A ). This led to a new reconstruction with an overall resolution of 4. 2 Å (FSC = 0. 143 criterion) and a local resolution that varied from ~4 Å within the GS subunit to between 6 and 10 Å within the MBP subunit (Fig. 4B, C ). This map agreed well with the GS crystal structure, allowing all secondary structure elements and certain large side chains to be visualized (Fig. 4D , Supplementary Fig. S5D  and Supplementary Video S1). A good fit was also observed for MBP: the N-and C-terminal lobes enclosing the active site are clearly defined, several helical elements are well resolved, and the bound maltose ligand is partly visible (Fig.
4D, E  and Supplementary Video S2). To better evaluate the accuracy of the reconstruction, we used program Phenix  34  to calculate real-space correlation coefficients (RSCCs) between MBP and GS residues and the cryo-EM map. The resulting values generally mirrored the local resolution of the map, with the highest and lowest RSCCs associated with GS and MBP residues, respectively (Fig. 5A ). Within MBP, the values were highest for residues close to the N-terminus of GS and decreased with increasing distance from this junction point. This fall-off in map quality is probably due to variations in the MBP subunit orientation relative to the scaffold caused by flexibility of the MBP-GS junction. To verify this hypothesis, we performed normal mode analysis (NMA) of the MBP-GSΔ 2 structure. NMA allows one to evaluate protein flexibility by decomposing large-scale motions such as domain and subunit movements into different vibrational modes and frequencies  [35] [36] [37].
5 °C temperature increment. The dye was excited at 483 nm and fluorescence intensity detected at 568 nm. T m values were calculated as the temperature at which the first derivative of thermograms (dF/dT) displayed a maximum using the integrated Bio-Rad software CFX-manager 2. 1. Dynamic light scattering. DLS experiments were performed on 40 μ M MBP-GS fusion constructs in 50 μ L cuvettes using a DynaPro Nanostar instrument (Wyatt Technology) at 25 °C. A He-Ne laser illuminated the solution at λ = 632. 8 nm and the time-dependent (every 5 μ s) fluctuations in scattering intensity were recorded every 5 μ s. The polydispersity index was calculated using the integrated Dynamics 7 software.
2/1. 3 μ m) at 100% humidity and 20 °C, blotted with filter paper for 2 s and vitrified in liquid ethane using a Mark IV Vitrobot (FEI). Data were recorded on photographic film using a Tecnai F30 Polara electron microscope (FEI) operated at 300 kV at a nominal magnification of 39,000X. Samples were exposed for 1 s for a total dose of 20-25 e-/Å 2. Micrographs were selected by checking their power spectrum and scanned on a Zeiss scanner (Photoscan TD) at a step size of 7 μ m (1. 8 Å on the sample scale). The CTF of scanned micrographs was determined using CTFFIND3  47  and corrected using the bctf routine in Bsoft  48. Particles were selected semi-automatically in boxer (EMAN)  49  , yielding datasets of 16,025 and 8,797 particles (corresponding to ~7400 and ~5000 side views) for MBP-GS constructs Δ 2 and Δ 5, respectively.
Datasets were normalized in IMAGIC  50. Reference models were generated by angular reconstitution using IMAGIC and volumes refined by projection matching using SPIDER  51. As a control to check for possible model bias, we generated an alternative ab initio reference model using RIco  52  , which uses symmetry adapted functions. Volumes derived from the two independent reference structures converged to similar reconstructions. The overall resolution was estimated by dividing the datasets in two halves and calculating the normalized Fourier shell correlation in SPIDER  51. Final reconstruction of MBP-GSΔ2. Grids vitrified as described above were examined using a Tecnai F30 Polara electron microscope (FEI) operated at 300 kV. Images were recorded manually using a K2 Summit direct electron detector (Gatan) in super resolution counting mode at a nominal magnification of 23,000X, which corresponds to a final pixel size of 0.
8155 Å. (Data collection and processing parameters are summarized in Table  S1. ) Exposures were recorded with defocus values ranging from 1. 0 to 3. 5 μ m. For each movie, a total of 40 frames were collected over 6 s, with a total dose of 25 electrons/Å 2. For the initial processing, the 40 frames of each movie were aligned using MotionCorr  53  and combined to generate a single averaged image. CTF parameters were determined using CTFFIND3  47. A total of 39,167 particles selected from 165 averaged images were subjected to 2D classification in RELION  54  , leading to a cleaned dataset composed of 29,976 particles. This dataset was subjected to 3D classification (5 classes) using an angular step size of 7. 5° and a reference model derived from the previous cryo-EM model (obtained from the dataset collected on film) by applying a low-pass filter to 30 Å and imposing D 6 symmetry.
The two most resolved 3D classes (~10 Å in resolution) were combined to yield a dataset of 13,847 particles, which were subjected to 3D refinement in RELION to yield a D 6 symmetry-constrained map at 6. 2 Å resolution as estimated by gold standard FSC in RELION (FSC = 0. 143). Movie processing implemented in RELION improved the overall resolution to 4. 2 Å (FSC = 0. 143). Local resolution was determined with ResMap 55 and confirmed by fitting and visual inspection. Fitting of the MBP and GS crystal structures was performed using Chimera  56. The agreement between the fitted structures and the cryo-EM map was evaluated by calculating real-space correlation coefficients (RSCCs) at 8 Å resolution using Phenix  34. RSCCs were averaged over a sliding window of 5 residues, assigned to the B-factor column of the coordinate file and plotted using PyMOL.
Acknowledgements We thank  M. Bacia ,  D. Fenel ,  E. Neumann  and  I. Gutsche  for guidance using the EM instruments and software,  F. Bernaudat  for biochemical assistance and  S. Karthikeyan  and  P. De Berardinis  for LS and PDH-E2 plasmids. FC was supported by a PhD fellowship from the  Nanosciences Foundation. This work used the platforms of the Grenoble Instruct Center (ISBG:  UMS 3518 CNRS-CEA-UJF-EMBL ) with support from  FRISBI  ( ANR-10-INSB-05-02 ) and  GRAL  ( ANR-10-LABX-49-01 ) within the  Grenoble Partnership for Structural Biology  (PSB); the electron microscope facility is supported by the  Rhône-Alpes Region , the  Fonds FEDER  and the  Fondation pour la Recherche Medicale.
Human adipose tissue SVF preparation and culture Abdominal subcutaneous human adipose tissue was collected from healthy patients as res nullus from surgeries (non-pathologic abdominoplasty) for SVF isolation according to the procedure described for mice (see above). SVF cells were plated and maintained in DMEM containing 10% FCS until confluence. Differentiation of primary cultures in white and brite adipocytes was performed according to the protocol described for hMADS cells previously  [54, 55]. 2. 5. Isolation and analysis of RNA These procedures followed MIQE standard recommendations and were conducted as described previously  [56]. The oligonucleotide sequences, designed using Primer Express software, are shown in Supplementary Table  1. For miRNA analysis, 10 ng of the total RNA were reverse transcribed using Universal cDNA synthesis kit (Exiqon, Denmark).
Further, the raw data was background corrected, normalized by global mean and dyeeswap pairs using ArrayNorm  [58] , and then exported as text-file containing log2 transformed ratios of gene expression. Filtering for present values and differential expression was conducted with Genesis software  [59]. All experimental parameters and raw and processed data files have been deposited in NCBI's Gene Expression Omnibus  [60]  and are accessible through GEO Series accession number GSE80816 (https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc¼GSE80816). Only features that were associated with a RefSeq transcript and detected in 3 or 4 biological replicates were considered for further analysis. miRNA-mRNA interactions were predicted using 10 different prediction tools as described in  [39].
Mitochondrial DNA quantification Genomic DNA was extracted from cell culture using a DNA extraction kit (MachereyeNagel EURL, France). 2 ng of the total DNA were used for qPCR analysis, and data evaluation was performed as described previously  [39, 57]. The mitochondrial DNA copy number was calculated from the ratio of the DNA of the NADH dehydrogenase gene, a mitochondrial gene, to that of lipoprotein lipase gene, a single copy nuclear gene. The oligonucleotide sequences, designed using Primer Express software, are shown in Supplementary Table  1.
Western blot analysis Proteins were extracted from cells or tissues as previously described  [61]. For mitochondrial complex quantification, equal amounts of cellular proteins were separated by electrophoresis using gradient gels (10e20%) and blotted onto nitrocellulose membranes. Following blocking, membranes were incubated overnight with a 1:1000 dilution of total OXPHOS western blot antibody cocktail (#MS601, Mitosciences) before 1 h incubation in 1:10,000 diluted HRP-conjugated anti-mouse immunoglobulins (#7076S, Cell Signaling Technology). Chemiluminescence obtained after adding Clarity ECL western blotting substrate (BioRad, France) was detected using a ChemiDoc MP Imaging System and quantified with Image Lab 5. 0 software (Bio-Rad, France). For other analyses, 40 mg of proteins were blotted using SDS-PAGE basic protocol (10 or 15%).
Primary antibody incubation was performed overnight at 4 C (anti-UCP1, Calbiochem #662045, dilution 1:750; anti-perilipin, Interchim #BP5015, dilution 1:5000; anti-CS, Abcam #ab96600, dilution 1:10,000; anti-b-tubulin, Sigma #T5201, dilution 1:2000; anti-DRP1, Cell Signaling #5391, dilution 1:1000; anti-phosphoDRP1 (ser616), Cell Signaling #4494, dilution 1:1000; anti-LC3, Nanotools #5F10, dilution 1:1000; anti-ATG5, Nanotools #7C6, 1:2000; anti-p62, BD #610833, 1:2000). Primary antibodies were detected with HRP-conjugated anti-rabbit or anti-mouse immunoglobulins (Promega) or anti-guinea pig immunoglobulins (Santa Cruz). Detection was performed using Immobilon Western Chemiluminescent HRP Substrate (Merk-Millipore). OD band intensities were evaluated using PCBas Software.
ACKNOWLEDGMENTS The authors greatly acknowledge IRCAN animal core facility, IRCAN Cytomed,  Bernard Rossi Proteomic  and iBV histology platforms. We thank  Dr. Baharia Mograbi  for helpful discussions. This work was supported by  CNRS ,  EU   FP7  project  DIABAT  ( HEALTH-F2-2011-278373 ), and  French Agence Nationale de la Recherche  ( ANR-10-BLAN-1105  miRBAT). DL is a member of  Institut Universitaire de France. DT is supported by grants from the  German Research Foundation  ( DFG TE912/2-1 ), the  Ministry of Science, Research and Arts of Baden-Württemberg (Boehringer Ingelheim University Ulm Biocenter (BIU) ,  32-7533. -6-10/15/5 )and the  German Association for Pediatric Endocrinology and Diabetes (DGKED). PFP receives funding from  Baden-Württemberg Stiftung , and  Martin Wabitsch  and Uwe Knippschild receive funding by the  Deutsche Forschungsgemeinschaft  ( SFB 1149/B4 ).
Early detection and management of these patients are crucial and involve a close monitoring of CV risk factors, control of blood pressure (BP) and proteinuria (Pu) and use of drugs acting on the renin angiotensin system (RAS) to slow down the progression of the renal disease and prevent CV events and mortality  [14] [15] [16] [17]. Some debate remains as to the BP target to obtain: historically <130/80 mmHg  [18] , or more recently <140/85 mmHg  [19] , <140/80 mmHg  [20]  or <140/90 mmHg  [21] [22] [23]. It is widely accepted that Pu should be decreased under 0. 5 g/day  [18]. Nevertheless, few real-life prospective studies report the proportion of T2DM patients with hypertension and Pu in whom the BP and Pu goals have been achieved and of the incidence of renal and CV events. In this context, we conducted the ALICE-PROTECT observational study.
Methods This is the final analysis of the 2-year follow-up of the French ALICE-PROTECT cohort which was a multicenter, observational, prospective study. Details of the cohort creation, the included patients and the data recorded are described elsewhere  [24]. Briefly, adult outpatients with T2DM, clinical Pu [defined by 24-h Pu ≥ 0. 5 g per day or urinary protein/creatinine ratio (UPCR) ≥ 50 mg/mmol (≥500 mg/g) or urinary albumin/creatinine ratio ≥ 30 mg/ mmol (≥ 300 mg/g)] and an estimated glomerular filtration rate (eGFR by MDRD formula) over 15 mL/min/1. 73 m 2 were recruited by 153 active nephrologists throughout France between January 2010 and February 2011. The planned follow-up for the whole population was 2 years, up to June 2013, with one planned visit per year ± 4 months. No specific assessment was requested for the study.
Data analysis-statistics The statistical analysis plan was defined before the start of the analysis. Descriptive statistics of recruited patient characteristics were performed. Quantitative variables were described in terms of mean, standard deviation, median and outliers, and qualitative variables in terms of absolute frequency and percentage per modality. Depending on the nature of the variables (continuous or discrete) and data availability, t-tests or Wilcoxon tests and chi-squared or Fisher's exact tests were carried out. To evaluate the statistical significance of changes to continuous parameters over time, Wilcoxon signed-rank tests were also adjusted. Multivariate models were also used to determine the predictive factors for BP and Pu control and incidence of CV and renal events. For each event of interest, the relationship with potentially related factors was evaluated using univariate analysis, and then the significant factors at a threshold of p < 0.
10 were entered into a logistic regression using a stepwise method and a maintenance threshold in the model set at p < 0. 05. The factors included in the final model are described in the results with the Odds-Ratio (OR), their 95 % confidence interval (CI), and their p-values. Three analyses were performed: data analysis of the initial questionnaire and the general questionnaire for nephrologists; analysis after the 1-year database lock; and then after the 2 year follow-up. All statistical analyses were performed using SAS 9. 3 software (SAS Institute, Cary, NC, USA). Details about sample size calculation have been published elsewhere  [24].