dataesr/scientific-paragraphs-categorization huggingface dataset:
, 2013). This convergence of functional traits in bacterial communities highlighted the selection of one major preferential functional strategy in constrained habitats. Macrobenthic assemblages have already exhibited similar patterns, with higher functional divergence and trait dispersion in non-contaminated areas than in sewage contaminated areas  (Gusmao et al. , 2016). However, no significant differences among the three soil types (Fig. S5D ) were found for functional richness (FRic), diversity (FDiv), evenness (FEv), dispersion (FDis) and RaoQ indices, taking into account all the functional traits together. But we must remain cautious in the interpretation of the observed responses of these indices, taking into account the potential bias in calculated values due to the lot of missing data for some traits in BactoTraits.
First, missing exposure assessment at any trimester may be informative of birth outcomes and thus could lead to potential selection bias. For example, women who had a preterm birth may not be available to provide urine samples later in pregnancy. To assess this, we restricted our multiple informant models to the 239 women who provided urine samples at all three trimesters and applied inverse probability weighting to account for potential selection bias because of missing data at any trimester  (62, 63). The weights were the inverse of the predicted probabilities for women providing urine samples at every trimester. The probabilities were predicted using logistic models with covariates being possible predictors of providing urine samples at every trimester. The predictors included study year (continuous), maternal age (continuous), before pregnancy BMI (continuous), education (categorical), race/ ethnicity (categorical), parity (binary), history of pregnancy loss (binary), paternal participation in the study (binary), preterm birth (binary), and a composite prenatal risk variable (categorical) that equaled 1 if the women had any of the following complications as were abstracted from medical records: diabetes (preexisting or gestational), hypertension (preexisting or gestational), preeclampsia, thrombophilia, placental abruption, cervical insufficiency, preterm labor or premature rupture of the membranes, or intrauterine growth restriction.
Triangulation of the two methods showed consistent associations, which may counteract the imprecision of the study. Second, in the fertility treatment setting, gestational age was estimated with high accuracy by using IVF protocol dates, substantially reducing misclassification of preterm birth because of inaccuracies in pregnancy dating  (100). In addition, the EARTH Study allowed for a timely assessment of exposure to BPA replacements such as BPS. This study also had several limitations that should be considered in light of our findings. First, despite our best effort, potential selection bias caused by missingness of any trimester data might not be fully addressed by the inverse probability weighting methods we applied. As such, caution should be taken in interpreting the results for the third trimester.
Acknowledgments: The authors acknowledge all members of the EARTH Study team, including research staff Ramace Dadd, B. S. , and Myra Keller, R. N. , and the physicians and staff at the Massachusetts General Hospital Fertility Center. We are grateful to all study participants and to Xiaoliu Zhou, Ph. D. , Tao Jia, Ph. D. , and Xiaoyun Ye (Ph. D. , deceased) (Centers for Disease Control and Prevention, Atlanta, Georgia) for measuring the urinary concentrations of phenol biomarkers.
5 mM of benzoic acid, and different concentrations of bile salts in 96 deep-well plates. And then follow the same procedures as constructs with constitutive promoters. All chemicals used in this research were purchased from Sigma-Aldrich. Calculation of relative promoter units (RPUs). Fluorescence intensity measurements among different experiments were converted into RPUs by normalizing them according to the fluorescence intensity of an E. coli strain NEB10β containing a reference construct and grown in parallel for each experiment. We used the constitutive promoter J23101 and RBS_B0032 as our in vivo reference standard and placed superfolder GFP as a reporter gene in plasmid pSB4K5. We quantified the geometric mean of fluorescence intensity (MFI) of the flow cytometry data and calculated RPUs according to the following equation: RPU ¼ ðMFI sample Þ=ðMFI reference promoter Þ ð1Þ Flow cytometry analysis.
Flow cytometry was performed using an Attune NxT cytometer coupled with high-throughput autosampler (Thermo Fisher Scientific) and Attune NxT™ Version 2. 7 Software. In all, 30,000 cells were collected for each data point. Experiment on Attune NxT were performed in 96-well plates with setting; FSC: 200 V, SSC: 380 V, green intensity BL1: 440 V (488 nm laser and a 510/10 nm filter). Flow cytometry data were analyzed using FlowJo 10. 0. 8r1 (Treestar Inc. , Ashland, USA). All raw data values are listed in Supplementary Information. The gating strategy is shown in Supplementary Fig. 21. 4 x NNK library construction. Using P9-CadC-TcpP plasmid as a template, the insert with 4 x NNK library was amplified by Phusion Flash High-Fidelity PCR Master Mix (Thermo Fisher Scientific) with the primers I5 and I3; the vector was amplified with the primers V5 and V3 (primer sequence details are listed in Supplementary Table  9 ).
05, **p < 0. 01, ***p < 0. 001, and ****p < 0. 0001, respectively). Dose-response curves were fitted using a nonlinear regression model with Hill Slope (four-parameter dose-response curve). All data analysis was performed on GraphPad Prism (Version 8. 0. 2). Patient samples. Serum samples were consecutively collected from hospitalized or ambulatory liver transplant patients at the Hepatology and Liver Transplantation Unit, Hôpital Saint-Eloi in Montpellier (France) in the month of July 2020. All patients underwent liver transplantation between November 2006 and April 2020. Clinical and biological data were also recorded for every patient included in the study from their medical files. Abnormal liver enzymes were defined by alanine transaminase > 41 U/L, aspartate transaminase > 40 U/L, alkaline phosphatase > 130 U/L, GGT > 60 U/L or total bilirubin (TBil) >21 µmol/L.
) and added UMI barcodes with first round primers (see Supplementary Materials for sequence details). After PCR clean up, the first round PCR products were further amplified by second round PCR primers with NGS index. The PCR products were further purified with AMPure XP paramagnetic beads to remove the contaminants. Samples were sequenced on Illumina PE250 platform at Novogen (Hong Kong, China) with paired-end reads of 250 bases. NGS data processing. The datasets generated and analyzed during the current study are available in the NCBI SRA repository (BioProject ID: PRJNA714981; https://www. ncbi. nlm. nih. gov/bioproject/714981). Sequence counts were converted into amino acid sequences and listed in Supplementary Data 1. The python scripts for NGS data processing are available from Github Page: https://github.
Acknowledgements We thank members of the synthetic biology group and the  CBS  for fruitful discussions. We are grateful to the patients for participating in this study and providing their samples, and to the personnel of the Montpellier CHU hospital for collecting and preparing the samples. This work was supported by an  ERC   starting grant  " COMPUCELL " to J. B. J. B. also acknowledges support from the  INSERM Atip-Avenir program  and the  Bettencourt-Schueller Foundation. The CBS acknowledges support from the  French Infrastructure for Integrated Structural Biology (FRISBI)   ANR-10-INSB-05-01.
Data availability The authors declare that all data supporting the findings of this study are available within the paper, its supplementary information files, or public repositories. NGS data have been deposited in the NCBI SRA database with the BioProject ID: PRJNA714981. The flow cytometry data have been deposited in FlowRepository (https://flowrepository. org), with IDs: FR-FCM-Z3K6 (Fig. 2b ), FR-FCM-Z3KL (Fig. 2d ), FR-FCM-Z3KM (Fig. 2e ), FR-FCM-Z3KT (Fig. 3e_V3_7_11 ), FR-FCM-Z3KU (Fig. 3e_V14_16_18 ), FR-FCM-Z3KV (Fig. 3e_V19_22_78 ), FR-FCM-Z3KR (Fig. S3A ), and FR-FCM-Z3LZ (Fig. S3B ). Source data are provided with this paper.
The hydraulic short-circuit operating mode leads to a change in the flow paths in the penstocks and junctions compared to the normal turbine or pump modes. Indeed, compared to the pump mode, this mode will lead to a flow derivation at the junction between the penstocks directed to the Pelton units and the penstocks directed to the upper reservoir. As this mode have not been scheduled at the beginning of the power plant construction, it is necessary to quantitatively assess the singular head losses generated at the junction to be able to simulate the complete behaviour of the power plant by means of a 1D model. CFD simulations are carried out with the Fluent software for several configurations of hydraulic short-circuit defined by the ratio of flow rate deviated to the Pelton turbines.
A no slip wall condition is imposed at the solid walls with in addition the use of a scalable wall function. The meshes are created with the IcemCFD software. For the 90 degree T-junction, an unstructured tetrahedral mesh with 4 prism layers has been generated with 1. 3 million of cells and 330'000 nodes. On the contrary, for the Grand-Maison junction, two structured meshes have been generated to better control the wall normal expansion ratio of the cells. These two meshes differ only by the number of cells in the domain but share the same height for the first cell layer closed to the solid walls. The first mesh has 4. 4 million of nodes and the second mesh has 8. 2 million of nodes. For a discharge ratio Q T /Q P = 0. 75 and simulations with the RNG k -turbulence model, the averaged, maximum and minimum y + values are gathered in table 1 with in addition the value of the Reynolds number in the pipe linked to the pump-turbines.
The membrane was revealed on a Chemidoc setup with Image Lab Software. Western Blot quantifications were obtained using ImageJ. Integrin activation with manganese. When mentioned, integrin activation was induced by replacing the cell media (Ringer + glucose) with a Ringer+glucose solution with MnCl 2 at 5 mM, at least 5 min before acquisition. Microscopy acquisitions. All acquisitions (except for DONALD modality) were steered by MetaMorph software (Molecular Devices) with an inverted motorized microscope (Nikon Ti) equipped with a temperature control system (The Cube, The Box, Life Imaging Services), a Nikon CFI Apo TIRF 100x oil, NA 1. 49 objective (except cell spreading assays: Nikon CFI Plan Apo Lambda DM 20x objective), and a perfect focus system, allowing long acquisition in TIRF illumination mode.
This spatial resolution depends on the image signal-to-noise ratio and the segmentation algorithm  75  and was determined using fixed mEos2 samples. We analyzed 130 2D distributions of single molecule positions belonging to long trajectories (>50 frames) by bi-dimensional Gaussian fitting, the resolution being determined as 2. 3 s xy , where s xy is the pointing accuracy. For the trajectory analysis, FAs ROIs were identified manually from GFPpaxillin images. The corresponding binary mask was used to sort single-molecule data analyses to specific regions. We analyzed trajectories lasting at least 260 ms (≥13 points) with a custom Matlab routine analyzing the mean squared displacement (MSD), which describes the diffusion properties of a molecule, computed as (1): MSDðt ¼ n Á ΔtÞ ¼ ∑ NÀn i¼1 ðx iþn À x i Þ 2 þ ðy iþn À y i Þ 2 N À n ð1Þ where x i and y i are the coordinates of the label position at time i x Δt.
However, as comparable illumination settings (fixed 561 nm laser power, varying 405 nm laser power) were used between the different experimental conditions, the strong variations in immobilization durations presented here cannot be due to blinking or photobleaching. Direct optical nanoscopy with axially localized detection (DONALD). This method combines super-localization microscopy techniques with detection of supercritical-angle fluorescence emission. This analysis provides an absolute measure of the vertical position of the fluorescent emitter regarding the coverslip. The axial resolution of DONALD enables to localize with 35 nm resolution proteins in the different functional layers. Optical setup. We used an Olympus IX83 inverted microscope with an autofocus system. The excitation path was composed of three laser lines: 637 nm, 532 nm, and 405 nm (Errol lasers) and a TIRF module (Errol lasers) used in combination with a matched 390/482/532/640 multiband filter (LF405/488/532/635-A-000, Semrock).
Image processing. Acquired data were processed using the Nemo software (Abbelight). After removing the background signal, molecules were detected and the numbers of epifluorescence and under-critical angle fluorescence (UAF) photons were measured to extract the corresponding axial positions as described elsewhere  48. Lateral drifts were corrected from the localized data thanks to a crosscorrelation based algorithm. DONALD benefits from the unique property of being free of any axial drift, as the supercritical emission allows one to extract the absolute axial position of the fluorophore regarding the coverslip/sample interface. Image display. Molecules detected 150 nm above the surface were discarded to improve the contrast in the focal adhesions/plasma membrane layer. On the superresolution reconstructed image, each pixel value corresponds to the average axial localization of single molecules detected in this pixel (size: 15 nm).
The expression of the mEos2-kindlin-2 or mutated variants was checked for each cell. Adhesion sites were drawn manually, and quantification of adhesions sites were computed using MetaMorph software (Molecular Devices). Non-isolated cells (i. e. , in contact with other cells) and polynucleated cells were excluded. Between 23 and 42 cells per experiment were used for the kindlin-2-ΔPH or kindlin-2-ΔPH-CAAX conditions (kindlin-2-WT: between 17 and 26 cells per experiment). For each cell used for focal adhesion measurements, the cell area was measured using the TIRF image of GFP-paxillin. Statistical analysis. The indicated P values were obtained with the two-tailed, non-parametric Mann-Whitney rank sum test using the software GraphPad Prism 8. For z distributions, the Mann-Whitney rank sum test was performed using Matlab 2007a due to very high sample size.
Acknowledgements We thank  B. Tessier ,  R. Sterling ,  J. Carrere  for technical assistance and the  IINS Cell culture facility , especially  E. Verdier , for cell culture;  A. Mehidi ,  M. Lagardère ,  C. Saphy  for helpful discussions;  C. Poujol ,  S. Marais  ( Bordeaux Imaging Center, BIC ) for technical help;  F. Cordelières  ( BIC ) for support in kymograph analysis (KymoTool Box). We thank  N. Bourg  and  C. Schietroma  ( Abbelight ) for providing DONALD acquisition system with dSTORM dedicated buffer (Smart kit) and help for the DONALD data analysis. We thank  M. Sainlos  ( IINS, Bordeaux, France ) for providing anti-GFP nanobodies labeled with AlexaFluor-647 used for DONALD experiments;  C. Albiges-Rizo  (IAB,  U. Grenoble Alpes ) and  P. Kanchanawong  ( MBI, NUS, Singapore ) for providing the beta1-integrin- Y795A-mEos2  and the talin1-tdEos plasmid construct, respectively.
We acknowledge financial support from the  French Ministry of Research and CNRS, GDR MIV-ImaBio Bourse AMI  (to O. R. ),  Fondation pour la Recherche Médicale  (to T. O. /O. R. FDM20140630221),  Fondation pour la Recherche Médicale  (to G. G. ),  LABEX Brain  (to T. O. ),  ANR  grant  Integractome  (to G. G. ).
• Quantitative Analysis The concentration of API in the infused solution was quantified by using a highpressure liquid chromatography system (LC-2010HT compact system, Shimadzu, France). Analytical methods and validation data of each API are presented in previously published work  [12]. All three methods possessed mean accuracy, repeatability and intermediate precision coefficients lesser than 5. 0%, excepted for insulin for which a slightly more important variability was noted (mean intermediate precision coefficient of 6. 4%). All samples were diluted to within theoretical calibration curve range, and if beneath quantification limit the samples were reanalyzed after adapting the dilution.
• Statistical Analysis All statistical analyses were performed using Stata statistical software (version 15, StataCorp, College Station, TX, USA). Continuous parameters were expressed as mean and standard-error of mean (SEM) according to statistical distribution. The assumption of normality was studied using Shapiro-Wilk's test. Hedge's effect size was calculated as described in (Equation (  3 )). All the effect sizes were calculated from the standardized values calculated with Equation (1). Statistical analysis was performed by calculating the Hedge's effect size (Equation (  3 )). ES = m 1 -m 2 SD pooled = m 1 -m 2 (n 1 -1)s 2 1 +(n 2 -1)s 2 2 n 1 +n 2 -2 (3) m 1 and m 2 : mean at T8 for Turbo-Flo ® catheters (m 1 ) and other catheters (m 2. n 1 and n 2 : sample sizes, and s 1 and s 2 : standard deviations.
In order to optimize an infusion set in terms of risk of sorption, it is not sufficient to modify the extension line, but it will also be necessary to improve the catheter. The data presented in this work showed that, for the duration of the study, the replacement of the extension set had little impact on the overall sorption, even though the extension set was the medical device with the highest surface contact area. The loss caused by the complete setup followed the same trend as the loss induced by most absorptive tubing in the setup but was not equal to the cumulated loss induced individually by the extension sets and the catheters. It is therefore impossible to precisely deduce complete drug sorption risks possibly caused by a complete setup only by studying individual devices. Indeed, as highlighted by our results, the total drug sorption calculated by summing-up the sorption caused by individual medical devices would be higher than the real impact in a whole clinical setup.
T (H c). The components out of the a * b * (HK) scattering plane could be reached by lifting of the detector. An area detector was used for the mapping of the HK plane (λ = 2. 45 Å). The integrated intensities of the zero field phase were measured by a single counter after a ZFC process, and after a FC process for the 6. 5 T phase (λ = 0. 9 Å). 72 nuclear and 151 magnetic reflections were measured in zero-field (ZF), and, 196 magnetic reflections were measured at 6. 5 T. A nuclear structure refinement yields a volume fraction of 1:1. 10(2) for the twin domains. The Fullprof programm package was used for magnetic structure determination. Direction dependent magnetization measurements on our CoGeO 3 single crystals at low temperatures reveal a sharp step-like increase of the magnetization at H c1 ∼4.
ACKNOWLEDGEMENT We thank  P. Thalmeier  for fruitful discussions. The research in Dresden was partially supported by the  Deutsche Forschungsgemeinschaft  through  SFB 1143  ( Project-Id 247310070 ). The work of D. Kh. was funded by the  Deutsche Forschungsgemeinschaft (DFG, German Research Foundation ) -Project number  277146847 -CRC 1238.
(D) Top: control (DMSO) or MG132-treated (5 mM, 15 h) H1299 cells (preferred system as large nuclear inclusions are formed) were used for immunofluorescence analysis for SUMO-2 (red) and NEDD8 (green). Nuclei were stained with DAPI (blue). Graph indicates the percentage of cells with nuclear inclusions co-stained with SUMO-2 and NEDD8. Data are represented as the mean of three independent experiments ± SD. Approximately 50 cells per condition were counted. Bottom: experiment performed as described above and cells stained for SUMO-2 (red) or for fibrillarin (green). Scale bars, 5 mm. 34, 108635, January 19, 2021 7  Report Diversity between the two modes of NEDDylation was also observed at the modification site level for common targets. In such cases, the same substrate was modified at different lysines under the two modes of NEDDylation.
STAR+METHODS Detailed methods are provided in the online version of this paper and include the following: Peptide fractions were analyzed on a quadrupole Orbitrap mass spectrometer (Q Exactive Plus, Thermo Scientific) equipped with a UHPLC system (EASY-nLC 1000, Thermo Scientific). Peptide samples were loaded onto C18 reversed phase columns (15cm length, 75mm inner diameter, 1. 9mm bead size) and eluted with a linear gradient from 8 to 40% acetonitrile containing 0. 1% formic acid in 2hrs. The mass spectrometer was operated in data dependent mode, automatically switching between MS and MS2 acquisition. Survey full scan MS spectra (m/z 300 -1700) were acquired in the Orbitrap. The 10 most intense ions were sequentially isolated and fragmented by higher-energy C-trap dissociation (HCD). An ion selection threshold of 5,000 was used.
Peptides with unassigned charge states, as well as with charge states less than +2 were excluded from fragmentation. Fragment spectra were acquired in the Orbitrap mass analyzer. d KEY RESOURCES Raw data files were analyzed using MaxQuant (development version 1. 5. 2. 8). Parent ion and MS2 spectra were searched against a database containing 88473 human protein sequences human protein sequences obtained from the UniProtKB released in December 2013 using Andromeda search engine. Spectra were searched with a mass tolerance of 6ppm in MS mode, 20ppm in HCD MS2 mode, strict Lys-C specificity and allowing up to 3 miscleavages. Cysteine carbamidomethylation was searched as a fixed modification, whereas protein N-terminal acetylation, methionine oxidation modification of cysteines (mass difference to cysteine carbamidomethylation) and di-glycine-lysine were searched as variable modifications.
Site localization probabilities were determined by MaxQuant using the PTM scoring algorithm. Peptides with site localization probability above 0. 75 were selected. Approximately 100 sites had a localization probability below 0. 9. For all functional association analysis sites with localization probability R 0. 9 were used. The dataset was filtered based on posterior error probability (PEP) to arrive at a false discovery rate of below 1% estimated using a target-decoy approach. Di-glycine lysine modified peptides with a minimum score of 40 and delta score of 6 are reported and used for the analyses. Bioinformatics analysis STRING network analysis was performed using the online STRING database  (Szklarczyk et al. , 2015)  using NEDDylated proteins as input. Protein interaction enrichment was performed based on the amount of interactions in the networks, as compared with the randomly expected amount of interactions, with both variables directly derived from the STRING database output.
Visualization of the interaction network was performed using Cytoscape version 3. 4. 0 (Shannon et al. , 2003). For NEDDylation, SUMOylation and Ubiquitination site comparative overlap analysis, all NEDDylation sites were analyzed. All MS/ MS-identified Ubiquitination sites and SUMOylation sites were extracted from PhosphoSitePlus (https://www. phosphosite. org) (Hornbeck et al. , 2012). For each dataset, sites from mouse proteins were removed. Perseus software was used to generate a matrix where all proteins from all PTMs were cross-referenced to each other.
ACKNOWLEDGMENTS We are grateful to  Dr. Guillaume Bossis ,  Dr. Rivas Vazquez , and  Dr. Ronald T. Hay  for SUMO-2 reagents and the  Montpellier Rio Imaging (MRI)  facility for the microscopy. The study was supported by an  ATIP/Avenir fellowship  awarded to D. P. X. ; the  Emmy Noether Program  ( BE 5342/1-1 ) and  German Research Foundation  award  SFB1177  to P. B. ; and the  Prematuration program Ubipie  `ges funded by the  Occitanie region, France , awarded to M. S. R. and D. P. X. S. L. -G. was supported by a PhD fellowship awarded by  CONACYT  and C. M. and L. B. were supported by  Labex EpiGenMed , an "( Investissements d'avenir" program , reference  ANR-10-LABEX-12-01.