dataesr/scientific-paragraphs-categorization huggingface dataset:
In the insert is shown the distribution of Rg of the particles, as computed by EOM  34. Panel (c) Superposition of the pair probability distribution functions of SmERp60 (red) and LmPDI (green), as computed with the ATSAS suite  69. Panel (d) Ab initio SAXS envelope of LmPDI, calculated by DAMIN/DAMMIF  72, 73  , with the yeast ScPDI structure (2B5E) docked with Supcomb, all programs were run from the ATSAS suite  69. Panel (e) Superimposed models of the 3 possible conformations of SmERp60 (blue, green and gold) compatible with SAXS data fitting after EOM  34. The crystal structures of HsERp57/PDIA3 (3F8U  33  ) and HsPDIA1 (4EL1 and 4EKZ  36  ) have been used as template models to fit the deconvolved SAXS spectra. 3D images were produced with CCP4MG  75. reaction was both temperature-and concentration-independent.
Indeed a shift of the elution peak of the complex towards molecular mass compatible with a 1:1 stoichiometry was measured; the envelope derived from the corresponding scattering curve (Supplementary Fig. S3 ) was modelled with Gasbor on the ATSAS online server (https://www. embl-hamburg. de/biosaxs/atsas-online/gasbor. php). The structure of HsPDIA3/ERp57 was docked into the envelope leaving enough density for the GAG to be modelled inside (Supplementary Fig. S3 ). The same procedure was repeated with LmPDI in complex with HS and HA (Supplementary Fig. S2 ), here as well a shift in the elution peak was assigned to the complex formation in a bona fide 1:1 stoichiometry. It is interesting to note the change in the Kratky plot of the extrapolated scattering curves of the LmPDI-GAG complexes with respect.
The protein purity was assessed by SDS-PAGE (Supplementary Fig. S7 ). Circular dichroism. Both purified proteins were dialysed vs 10 mM potassium phosphate buffer pH 7. 0 before collecting seven CD spectra for each protein between 185 and 280 nm at 20 °C on a Jasco J-810 instrument. The averaged spectra, after buffer subtraction, were deconvolved and analysed on the DichroWeb website  65. The self-consistent method for analyzing protein CD spectra, SELCON3, and CD secondary structure programme, CDSSTR  66  , were used to estimate the percentage of secondary structure of recombinant PDIs (Table  1 ), by using the reference dataset sp175. Identification of PDI interacting macromolecules by SPRi. SPR binding assays were performed in a Biacore Flexchip system (GE Healthcare, Facility of UMS 3444/US8, Lyon, France).
Data collected from reference spots (gold surface) and from buffer spots were subtracted from those collected on spotted proteins or GAGs to obtain specific binding curves. The binding was confirmed in two independent SPRi experiments for each recombinant protein. Since each biomolecule was spotted in triplicate on each chip, the results were the average of six sensorgrams; any given interaction positive for >4/6 was considered true. Disulfide reductase activity assays. The capability of SmERp60 and LmPDI to reduce disulfide bonds was assessed by two methods: a standard turbidimetric assay using insulin as a substrate  37  ; and a fluorimetric assay using oxidised glutathione conjugated with eosin (di-eosin-GSSG  45  ). Insulin (I6634, SIGMA) was dissolved in 20 mM Tris/HCl buffer pH 8. The solution was then acidified to pH 2-3 and quickly titrated back to pH 8.
Structural analysis by Small Angle X-ray Scattering (SAXS). Data collection for the SAXS studies was initially performed at the BioSAXS beamline P12 of PETRAIII (Hamburg, Germany) using serial dilutions of SmERp60 from 6 to 0. 5 mg/ml and of LmPDI from 2 to 0. 5 mg/ml. Further analysis on new batches of purification was then performed at BioSAXS beamline BM29 of ESRF (Grenoble, France)  68  , where the wavelength was 0. 9998 Å and the sample to detector distance 2. 8 m. Size exclusion chromatography was performed on a HPLC system (Shimadzu) in line with BM29 beamline (SEC-SAXS). Several samples concentrated from 4 to 10 mg/ ml were automatically injected (50 μl) into a Superdex S200 5/150 (GE Healthcare), previously equilibrated with TBS. The column was run at 20 °C with a constant flow of 0.
2 ml/min and 1 image/s was collected. The scattering images were collected on a Pilatus 1 M detector (Dectris) and converted into 1d profiles with BsXCube; the scattering profiles were analysed off-line using the suite ATSAS  69. Scattering of the buffer was subtracted as background from the protein measurements with PRIMUS. HPLC-SAXS data were analysed with CHROMIXS  70  and US-SOMO  71. The evaluation of the radius of gyration (Rg) and the forward scattering intensity (I(0)) were performed using the Guinier approximation. Ab initio analysis was performed either locally with DAMMIF/ DAMMIN  72  or online with GASBOR (https://www. embl-hamburg. de/biosaxs/atsas-online/gasbor. php); validation and averaging was performed with DAMAVER  73  ; rigid body modelling of known structures into SAXS envelope was performed with SUPCOMB  69.
Flexibility was checked with EOM using the default parameters (10000 initial native-like models and constant subtraction allowed)  34  ; the final selection retained 3 final structures, built starting from the a, a′, b-b′ modules of HsPDIA3/ERp57 and HsPDIA1. The model intensities were back computed with CRYSOL  74  and 3D graphics were produced with CCP4MG  75.
Acknowledgements We thank  Marie-Fatoux Ardore , who performed the preliminary trials of L. major PDI cloning,  Francescangelo Vedele  and  Federica Carucci  for testing the long-term storage conditions. We thank  Christophe Marquette  and  Loïc Blum  ( Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, UMR 5246 CNRS, Université Lyon 1, Lyon, France ) and  AxoScience (Villeurbanne, France)  for providing access to the spotter. We are grateful.
The codes within the parenthesis are the UniProtKB accession numbers of each protein 78. HsPDIA1, Homo sapiens PDI isoform A1; HsPDIA3/ERp57, H. sapiens PDI isoform A3, also known as ERp57; LmPDI, Leishmania major PDI; SmERp60, Schistosoma mansoni Endoplasmic Reticulum protein 60; ScPDI, Saccharomyces cerevisiae PDI. Panel (c) Secondary structure analysis of the recombinant proteins by circular dichroism. Spectra of SmERp60 (red) and LmPDI (green) at 25 °C, after buffer subtraction and averaging of seven sequential acquisitions on a Jasco J-810 instrument, are presented.
Statistical analyses We analysed the mass of the uropygial gland in relation to sex, body mass and their interaction. We developed Generalized Linear Models (GLM) for normally distributed data with an identity link function. The models were based on initial analyses of one response variable (mass of uropygial gland) in relation to sex, age and other relevant predictor variables. We report simple bivariate models and models that include a number of potentially confounding variables. We estimated correlations among variables to avoid problems of multi-collinearity. However, variance inflation factors were all less than three, implying that there were no problems of collinearity  (McClave and Sincich 2003). All analyses were made using JPM (SAS 2012).
Bioinformatics Analysis Pipeline for Genomic and Transcriptomic Data Genomic DNA was extracted using the standard phenol-chloroform extraction protocol  [24]. The Affymetrix SNP array 6. 0 (Affymetrix, Santa Clara, CA, USA) was used according to the manufacturer's instructions. One hundred and six samples were normalized with the Genotyping console 2. 0 software (Affymetrix). Total RNAs were extracted as previously described  [21]. RNA quality was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Samples were then analyzed on Human Genome U133 Plus 2. 0 array (Affymetrix), according to the manufacturer's procedures. All expression data obtained are publicly available on https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc=GSE71118.
RNA Sequencing The process from RNA extraction to final BAM files was previously described  [11]. We used SAMtools and BCFtools (v0. 1. 19)   [26, 27]  with custom depths (at least two alternate bases and five total bases) for reporting a candidate variant. These variants were then annotated by ANNOVAR (October 2013)  [28]  with the hg19 genome version, transcriptome annotations (November 2013), and using the databases of the observed variants: dbSNP (v138)  [29] , 1000G project (April 2012)  [30] , ClinVar (September 2014)  [31] , and COSMIC (v70) [32].
Signal was detected using the Fusion Fx7 (Thermo Fisher Scientific, Waltham, MA, USA) imaging system. GAPDH (Santa Cruz Biotechnology, sc-166574, Dallas, TX, USA) was used as a loading and the quantification of protein abundance was performed by blot densitometry using the ImageJ 1. 48v software (Rasband, W. S. , ImageJ, U. S. National Institutes of Health, Bethesda, MD, USA).
Proliferation Assay For this, 5000 cells were seeded in five replicates in 96-well plates. Culture medium was changed every 2 days with or without doxycycline. Every 2 to 3 days, cells were washed, trypsinized, and harvested in a final volume of 200 µL of PBS1X plus 10% of FBS. The number of viable cells was evaluated by flow cytometry (FACS Calibur, BD Biosciences, San Jose, CA, USA) based on their morphological features. Data were acquired using CellQuestPro software (BD FACS Systems, Sunnyvale, CA, USA) and analyzed using FlowJo (Tree Star, Celeza GmbH, Ashland, OR, USA) and GraphPad (La Jolla, CA, USA) software.
Cell Cycle Cells were fixed after 48 h incubation with or without doxycycline. Then, cells were stained with propidium iodide with the FxCycle™ PI/RNase Staining Solution (F10797, Life Technologies) according to the manufacturer's instructions. Data were acquired using CellQuestPro software (BD FACS Systems, Sunnyvale, CA, USA) and at least 10,000 cells per sample were analyzed using FlowJo (Tree Star, Celeza GmbH).
Statistical Analysis Metastasis-free survival (MFS) was defined as the interval between diagnosis and the time of distant recurrence or the last follow-up. Survival rates were estimated using the Kaplan-Meier method and compared using the log-rank test and hazard ratios (HRs). Each experiment was repeated at least three times. To examine the statistical significance of the results, analyses were performed with Prism6 v6. 01 (GraphPad software Inc. , La Jolla, CA, USA) software. Normal distribution of data sets was examined with a Shapiro-Wilk normality test. If data passed the test, the statistical significance between two conditions was assessed with an unpaired t-test, and results were represented as mean ± standard deviation (SD). Otherwise, a Mann-Whitney test was used. Significant differences are represented as * p-value p < 0.
Objective: According to recent European Society of Medical Oncology, European Society of Gynaecological Oncology and European Society of Radiotherapy and Oncology guidelines, adjuvant vaginal brachytherapy (VB) is optional in patients with intermediate risk (IR) and high-intermediate risk (HIR) endometrial cancer (EC). The aim of this French retrospective, multicenter study was to assess the impact of VB in these groups on local recurrence rate, local recurrence-free survival (RFS) and overall survival (OS). Methods: Data of 191 patients with IR and HIR EC who underwent primary surgery with or without VB and no other adjuvant treatment between 2000 and 2016 were extracted from the FRANCOGYN database. Rate of local recurrence, OS and local RFS in these two groups were compared using the Kaplan-Meier method.
Methods This prospective single-center study hypothesized that TORS for skull base would be feasible in the majority of patients, regardless of their anatomical features  [15]. Thus, we studied some anatomical criteria on radiological data from patients requiring a cerebral CT scan for neurological issues. Patients were asked to open their mouth as large as they could during the CT scan, without any retractor. Patients with a history of endonasal surgery, sinus disease, and/ or skull base pathology were excluded. After imaging acquisition, we also excluded patients with mouth opening inferior to 30 mm, as this threshold distance was far from the value with the usual mouth retractor  [14]. CT scans were performed on a Somatom 16, Siemens. A double lecture was performed by one neurosurgeon and one neuroradiologist, who both collected the following data.
Clinical study 4. 1. Methods This prospective clinical study confirms the accessibility of the sella with TORS. It was conducted after validation of the French ethic committee and registration in Clinical Trials NCT02743442. The patients were referred to our institution, Rothschild Foundation, Paris, after the discovery of the sellar tumor, mostly revealed by visual symptoms. Once prolactinoma was excluded, surgical removal was decided, and the patient was informed of dedicated potential TORS risks (mastication difficulties, temporomandibular pain, hypernasal speech, and sore throat). A preoperative "open mouth" skull base CT scan was performed to envision the accessibility of the sella, as previously described  [15]. The setup of the OR was the same than in our cadaveric study (see Figure  1 ).
Closure After removal, oxidized regenerated cellulose was placed against the sellar wall, and the mucosal flap was reapplied and sometimes glued. We did not try to suture the flap in the clinical trial, because preliminary works were mitigated. Outcome measures included several criteria, such as preoperative data (i. e. , visual function, radiological features of the tumor, open mouth CT scan data), intraoperative observations (i. e. , exposure quality on the cavum and the sella, CSF leak occurrence, operative time for each phase, mucosal lesions in the oral cavity at the end of the procedure), and postoperative data. The latter were divided into two categories: TORS side effects (mastication dysfunction, temporomandibular pain, hypernasal speech, sore throat) and usual pituitary adenoma surgery outcomes/complications (vision status, CSF leak, meningitis, diabetes insipidus, hypopituitarism).
[9] he following information were extracted from the patients' charts: Clinical data: Clinical presentation, medical history, complications on admission and during hospital stay, long-term outcomes. Imaging data: X-ray, ultrasound, echocardiography, CT, MRI, and scintigraphy were collected for all patients when available. Microbiological data: These data came from the analysis of blood cultures, pus and sputum cultures. Identification of SA was obtained in French Guiana. Strains were sent for identification of PVL to reference centers for staphylococcal toxemia in Lyon or Strasbourg. Treatment: Information regarding antibiotics received by patients as well as surgery, when performed, were retrieved. Ethical consideration: Patients' medical records were retrospectively reviewed, and all data collected were anonymized according to the French national committee-Commission Nationale de l'Informatique et des Libertés (CNIL)-that oversees research data.
Data analysis Globalisation and economic crises are phenomena that reforming the socio-economic mosaic of cities. The fact that cities today are in intense competition with each other for attracting resources and human resources have discussed in many studies. Moreover, a few scholars have pointed out the competition between cities and countries in some cases. It can be discussed that studies on urban economics themselves are a reaction to the appearance of the new competitive environment between cities, which applies the city branding as a beneficial tool for identifying and increasing the credibility of cities. The prosperity of economic activities in the host city can increase the value added for properties, employment, income and tax levels that are effective in improving the quality of citizens' life.
Cerebral MRI MR examinations were performed at D1 at the FRIM plateform using a 7. 0 Tesla MR unit (PharmaScan, Bruker Biospin, Ettlingen, Germany) equipped with a surface coil with an internal diameter of 10 mm, in thermoregulated and anesthetized (2% isoflurane in O 2 ) mice. T2-weighted imaging [Rapid Imaging with Refocused Echoies (RARE) sequence was used with the following parameters: effective TE: 33 ms, TR: 2742 ms, NEX: 1, Flip angle: 180 • ] was performed in order to measure infarct volume (Medical Image Processing, Analysis and Visualization or MIPAV software, NIH, Bethesda, MD, United States) and T2 *weighted imaging [a Fast Low Angle Shot (FLASH) sequence was used with the following parameters: 15 axial slices 1 mm thick, TE: 8 ms, TR: 600 ms, NEX: 2, Flip angle: 30 • , FOV: 2 cm × 2 cm, MTX: 256 × 256] to verify that there was no hemorrhage in any of these mice.
Open Field Residual sensorimotor deficit and potential anxiety likely to cause the mice to "freeze, " could interfere with the Barnes maze evaluation thus skewing the results. We used the open-field as previously described  (Cifuentes et al. , 2015). Spontaneous activity (distance traveled in cm and mean velocity in cm/s) was measured automatically for 30 min by an EthoVision XT system and analyzed by EthoVision XT 11. 5 tracking software (Noldus, Wageningen, Netherlands). Open field activity was assessed at D28 in all groups that were then tested on the Barnes Maze platform.
Assessment of Infarct Volume At D9, 1 week after hADMSC IV administration, mice were transcardiacally perfused with heparinized saline, followed by 4% paraformaldehyde (PFA). Brain was removed, post-fixed overnight in PFA and cryoprotected in 20% sucrose. Coronal 30 µm-thick sections were cut frozen using a cryostat CM 1950 (Leica Biosystems, Nußloch, Germany). Every eight 30 µmthick floating section was stained with Cresyl violet. Using ImageJ software (National Institutes of Health, Bethesda, MD, United States), the cortical infarct area was measured to calculate the stroke volume (mm 3 ) by integrating measured areas and distances between sections. Measured infarct volume was corrected for edema with the following formula: corrected infarct volume = measured infarct volume × (contralateral hemisphere volume/ipsilateral hemisphere volume) as already described  (Poittevin et al.
Morphological Analysis Cells density assessments were conducted blindly (vascular risk factor and treatment) at D9 and D40 and performed on three coronal brain sections at +0. 80, -0. 80, and -1. 20 mm relative to bregma, that consistently contained the infarct area. Neuroblasts density was assessed by calculating the DCXpositive area (X10) using NIH ImageJ software, in the whole ipsilateral hemisphere to stroke, actually only found in the subventricular zone and along the corpus callosum along which they migrate toward the lesion. Microglial/macrophage density was assessed by calculating the Iba1-positive area (X5) using NIH ImageJ software in the periinfarct area. T-cell density was manually assessed by counting CD3+ cells in each section, actually only present in the infarct area, and expressed as the number of CD3+ cells per section.
ACKNOWLEDGMENTS The authors thank the FRIM platform ( UMS34 ),  University of Paris Diderot , member of  France Life Imaging  (grant  ANR-11-INBS-0006 ) and IDEX Imagerie Du Vivant networks, and in collaboration with the  IAME group  ( UMR1137 ), the  Institut des Vaisseaux et du Sang (Hospital Lariboisière, Paris ).
This approach yielded 92. 5% recall and 99. 8% precision on our manually curated reference set (Fig. 1c , Supplementary Fig. 2  and Supplementary Notes). This detection approach was applied to 56,868 bacterial and archaeal genomes and 6,412 metagenomes publicly available from the Integrated Microbial Genomes (IMG) database  23  (Supplementary Table  2 ). After manual curation of edge cases and removal of detections not based on a clear inovirus-like ATPase, a total of 10,295 sequences were recovered (Fig. 1d , Supplementary Fig. 3  and Supplementary Notes). From these, 5,964 distinct species were identified using genome-wide average nucleotide identity (ANI), and only 38 of these included isolate inovirus genomes. About onethird of these species (30%) encoded an 'atypical' morphogenesis gene, with an amino-terminal instead of carboxy-terminal TMD (Supplementary Fig.
NATURe MICROBIOlOgy have been reported  36. In addition, toxin-antitoxin systems often affect host cell phenotypes, such as motility or biofilm formation  1. Here, similar toxin proteins could be associated with distinct and seemingly unrelated antitoxins and vice versa, suggesting that gene shuffling and lateral transfer occur even within these tightly linked gene pairs (Supplementary Fig. 9 ). All but one toxin-antitoxin pairs were detected in proteobacteria-associated inoviruses, most likely because of a database bias. Thus, numerous uncharacterized iPFs across other candidate families of inoviruses may also encode previously undescribed toxin-antitoxin systems and, more generally, host manipulation mechanisms.
Methods Construction of an Inoviridae genome reference set. Genome sequences affiliated to Inoviridae and ≥2. 5 kb were downloaded from NCBI Genbank and RefSeq on 14 July 2017 (refs. 40, 41 ). These were clustered at 98% ANI to remove duplicates and screened for cloning vectors and partial genomes (Supplementary Table  1 ). Two of these genomes (Stenotrophomonas phage phiSMA9, NC_007189, and Ralstonia phage RSS30, NC_021862) presented an unusually long section (≥1 kb) without any predicted gene, associated with a lack of short genes that are typical of Inoviridae. For these, genes were predicted de novo using Glimmer 42 trained on their host genomes (NC_010943 for phiSMA9 and NC_003295 for RSS30) with standard genetic code. Similarly, genes for Acholeplasma phage MV-L1 (NC_001341) were predicted de novo using Glimmer with genetic code 4 (Mycoplasma/Spiroplasma) and trained on the host genome (NC_010163), followed by a manual curation step to integrate both RefSeq-annotated genes and these newly predicted CDS.
New models were built from these proteins and used in a third round of searches, which did not yield any additional genuine inovirus sequence after manual inspection. An automatic classifier was trained on this extended inovirus genome catalogue, that is, the reference genomes and the 795 manually curated genomes, to detect putative inovirus fragments around pI-like genes, based on 10 distinctive features of inovirus genomes (Supplementary Fig. 2  and Supplementary Notes). These 795 manually curated genomes were identified from 17 host phyla (or class for Proteobacteria) and were later classified into 5 proposed families and 245 proposed subfamilies (see below 'Gene-content-based clustering of inovirus genomes'). Three types of classifiers were tested: random forest (function randomForest from R package randomForest 50 using 2,000 trees, other parameters left as default), random forest with conditional inference (function cforest from R package party 51 using 2,000 trees, other parameters left as default) and a generalized linear model with lasso regularization (function glmnet from R package glmnet  52  ).
The efficiency of classifiers was evaluated via a tenfold cross-validation in which the data set was partitioned into ten equal-sized subsamples, with one retained for validation and the other nine used for training through the ten possible permutations. Results were visualized as a ROC curve generated with ggplot2 (refs. 53, 54 ). The importance of features in the random forest classifier was evaluated using the function 'importance' , from the R package randomForest. On the basis of the inflection point observed on the ROC curves, the random forest classifier was selected as the optimal method as it provided the highest truepositive rate (>92%) for false-positive rates of <1 % (Supplementary Fig. 2 ). This model was then used to classify all putative inovirus fragments that had not been identified as complete genomes previously, using a sliding window approach (up to 30 genes around the putative pI protein), and looking for the fragment with the maximum score in the random forest model (if >0.