dataesr/scientific-paragraphs-categorization huggingface dataset:
Quantitative analysis of immunostainings. To analyze IgG transcytosis, z-stacks were taken with an HCX PL APO CS ×63/1. 4 oil objective for confocal microscopy or a ×100 1. 4-NA Olympus UPlanSApo for STED microscopy. Deconvolution was performed for confocal images by Huygens Software (Scientific Volume Imaging). IgG vesicle quantification was performed using Imaris 9. 3. 0 (Bitplane) as described before  41. The 3D vasculature mask was smoothed under surface details (1. 0 µm confocal/0. 4 µm for STED), and spots were identified with an estimated diameter of 0. 5 µm. IgG + vesicles and IgG extravasation were quantified on 10-15 images on one section for each animal (confocal) or three images for each animal (STED). String vessels and their localization in the vascular tree, vessel length, vessel diameter, occludin interruptions and GFAP + astrocytes were analyzed using ImageJ.
Vessel diameter was measured by using the DiameterJ plugin for ImageJ. For the TUNEL analysis, collagen IV + and TUNEL + vessels were counted and normalized to the total image area. GFAP-positive astrocytes were quantified as the percentage of the GFAP + area relative to the total area of the image. Quantifications were obtained from 4-6 images per animal (one section per animal). Images were taken from the cortex if not stated otherwise. Pericyte coverage was analyzed using MotionTracking software (MPI-CBG, v8). In general, the CD13 + area inside the collagen IV + vessels was normalized to the total collagen IV + area. For measuring occludin interruptions, the lengths of occludin and ZO-1 tight junctions were traced manually by using the Simple Neurite Tracer plugin (ImageJ). Then, occludin length was normalized to ZO-1 length for 15 images per animal (one section per animal).
String vessels have a tube-like structure. a, b, c, Super-resolution imaging of human (a), hamster (b) and mouse string vessels (c). In confocal mode with the pinhole closed to 0. 4 AU, the string vessels appeared as solid collagen tubes. However, STED microscopy demonstrated a tube-like structure of string vessels in humans, hamsters and mice. In all species, the apparent diameter of string vessels was about 500 -1,000 nm with the collagen walls having a similar thickness. Images are representative for at least 3 experiments per species. Scale bar, 1 µm. Clustering of human brain cells according to single nuclear RNA sequencing. a, UMAP plot of 35,289 human brain cells. Clusters were annotated according to marker genes for the specific cell types. The dataset has been published (Lake, B. B.
Acknowledgements We thank  W. Brandt ,  I. Stölting ,  V. Hüther ,  A. Wohltmann ,  K. Schulz ,  R. Müller  and  H. Örün  for expert technical help and  G. Hüttmann, Lübeck , for support with STED microscopy. PLX5266 was kindly provided by  Plexxikon  and  RIPKi  was provided by  Sanofi. This work was supported by grants from the  European Research Council  (Synergy grant no. 2019-WATCH-810331  to V. P. , R. N. and  M. Schwaninger ), the  Deutsche Forschungsgemeinschaft  ( SCHW 416/5-3  to  M. Schwaninger ;  WE 6456/1-1  to J. W. ;  STA 1389/5-1  to C. S. ;  INST 392/135-1  to  M. Schwaninger  and P. K. ;  SFB 1403  (project no. 414786233 ) to M. P. ;  SFB 877  to M. G. ;  SFB TRR 296/1  to H. M. -F. and  M. Schwaninger ;  SFB TRR 274  to C. S. and J. F. ; and  EXC 22167-390884018  to H. B.
), the  Marie Skłodowska-Curie European Union 's  Horizon 2020 research and innovation program  (no. 813294  ( ENTRAIN ) to J. W. and  M. Schwaninger ), the research consortium  DEFEAT PANDEMics-National Network University Medicine  funded by the  Federal Ministry of Education and Research  (to M. G. and C. S. ),  Incontinentia Pigmenti France  (to M. Schwaninger), and a  Roche   RiSE fellowship  ( 2017-2018 ; to J. L. ).
5 5 Fig. 1 | SARS-CoV-2 infection is associated with increased string vessels in the brain. a-c, In the brains of SARS-CoV-2-infected patients, empty basement membrane tubes, also known as string vessels (arrowheads), were increased in the frontal cortex. Sections were stained for the basement membrane marker collagen IV (coll IV) and the endothelial marker CD34. Representative images in a and b were obtained from the dataset in c. a, Scale bar, 50 μm. b, Magnified maximal projection of a z-stack of a string vessel with orthogonal views to exclude that these are partial sections of capillaries. Scale bars, 3 μm. c, Quantification of string vessels per image volume. N = 23 control patients, N = 17 COVID-19 patients. d, Immunostaining revealed a higher number of active caspase-3-positive vessels in cortical sections of SARS-CoV-2-infected patients (N = 6) than in controls (N = 6).
IgG and albumin extravasation were determined by immunoblots of brain tissue (N = 8 mice per genotype). d, RIPK3 ablation abolished glial activation. Nemo beKO but not Nemo beKO Ripk3 -/-mice showed a higher number of Iba1 + microglia/macrophages and an increased area of GFAP + astrocytes (N = 7 Nemo fl , 5 Nemo beKO , 6 Ripk3 -/-and 6 Nemo beKO Ripk3 -/-mice). e, Immunostainings of ZO-1 and occludin obtained by expansion microscopy in Nemo fl and Nemo beKO mice, representative of a dataset of three animals for each genotype. Scale bar, 10 µm (corresponding to approximately a 2. 5-µm initial size). We classified tight junction structures as occludin interruptions or disintegrations shown as blurring of the occludin structure (middle). f, Nemo beKO Ripk3 -/-mice showed less IgG extravasation than Nemo beKO mice and a similar decrease in the number of IgG vesicles in brain endothelial cells as Nemo beKO mice.
Extended Data Fig. 1 |. 4 | 6 | 7 | 1467 String vessels have a tube-like structure. a, b, c, Super-resolution imaging of human (a), hamster (b) and mouse string vessels (c). In confocal mode with the pinhole closed to 0. 4 AU, the string vessels appeared as solid collagen tubes. However, STED microscopy demonstrated a tube-like structure of string vessels in humans, hamsters and mice. In all species, the apparent diameter of string vessels was about 500 -1,000 nm with the collagen walls having a similar thickness. Images are representative for at least 3 experiments per species. Scale bar, 1 µm. Clustering of human brain cells according to single nuclear RNA sequencing. a, UMAP plot of 35,289 human brain cells. Clusters were annotated according to marker genes for the specific cell types. The dataset has been published (Lake, B.
General procedure The right knee and hip-joint angles were continuously recorded using bi-axial electrogoniometers (SG150, Biometrics, Newport, UK) firmly secured directly on the skin as previously described  (Alhammoud, Morel et al. , 2020). Briefly, the sagittal plane of the goniometers was calibrated in three positions: seated, standing, crouched (Appendix 1). Data were recorded at 148 Hz by a data logger (TPM, Delsys) and normalised to the cycle as an inside leg (right turn, 0% to 50% of the cycle) plus outside leg (left turn, 50% to 100% of the cycle). The turn switch between legs was automatically identified using the functional minima of the resultant acceleration corresponding to the skier edge's change  (Alhammoud, Morel et al. , 2020). A total of 1602 cycles were analysed, including Slalom (SL, n = 546), Giant Slalom (GS, n = 908), Super Giant (SG, n = 136) and Downhill (DH, n = 12).
Calculations Angles were low-pass filtered (fourth-order Butterworth, cut-off frequencies of 0. 5, 1, 2, and 2. 5 Hz for DH, SG, GS and SL, respectively) and derived to compute the angular velocity  (Alhammoud, Morel et al. , 2020). The MTU length of the RF, vastus medialis (VM), vastus lateralis (VL), biceps femoris long head (BFlh), biceps femoris short head (BFsh), semitendinosus (ST) and semimembranosus (SM) were modelled in Matlab® based on the equations adapted from  Hawkins & Hull (1990). Briefly, linear regression equations using knee and hip angles were used for all muscles except for the single-joint muscles crossing the knee (i. e. , BFsh, VM, VL) for which quadratic regression equations were used. The length was normalised to the resting length (Lr) computed with  Hawkins & Hull (1990)  formulae using the knee and hip slack angles from the literature (Le  Sant et al.
This synchronisation should maintain the RF MTU length but our data showed that it exhibited the lowest quasi-static phase among the quadriceps muscles in SL (17% of the cycle for RF vs. 35% for VM and 32% for VL). Elite skiers stabilise the centre of mass position by postural adjustments of ankle and trunk (LeMaster, 2010), thereby eliciting slight rotations of the hip joint when the knee is locked. Therefore, bi-articular MTUv reflects postural adjustments and stabilisation of the skier (Figure  1 )  (LeMaster, 2010). This finding is in contradiction with previous estimations in free ski-carving predicting a nearly constant length of the RF throughout the ski cycle in recreational skiers  (Kröll et al. , 2010)  who have a more static profile than elite athletes.
Methods The authors retrospectively analyzed the records of 142 patients (142 shoulders) who underwent primary RSA using a hybrid baseplate design by the senior surgeons (L. N. and P. C. ) between May 2014 and December 2018. Patients that underwent revision, resurfacing, stemless, or interposition arthroplasty were not included. The indications for surgery were cuff tear arthropathy (n ¼ 99), primary glenohumeral osteoarthritis with B2/B3 glenoids (n ¼ 28), glenohumeral osteoarthritis secondary to trauma or instability (n ¼ 9), acute trauma (n ¼ 3), locked dislocation (n ¼ 2), or osteonecrosis (n ¼ 1) (Table  I ). All patients were evaluated clinically and radiographically at a minimum follow-up of 2 years. All patients provided informed consent for the use of their data for research, and the study was approved in advance by the ethical board of GCS Ramsay Sant e pour l'Enseignement et la Recherche (COS-RGDS-2021-03-005-NEYTON-L).
Preoperative assessment Preoperative clinical and demographic data were recorded, including the Constant score (CS)  20  and range of motion (ROM), measured using a goniometer. Active forward elevation (AFE) was measured in the scapular plane, while external rotation was measured with the elbow at the side (ER). Internal rotation (IR) was measured using a 10-point scale (greater trochanter, 0; buttock, 2; sacrum-L4, 4; L3-L1, 6; T12-T8, 8; T7-T1, 10). 23.
3 ). A sharp band is observed at 580 nm for [Eu(L1)] 3+ that corresponds to the transition 5 D0 → 7 F0. Its sharpness suggests high symmetry in the coordination sphere of the complex and presence of single site symmetry for Eu III. The 5 D0  Table  2. UV/Vis data of the nitroxide complexes  [a]  Complex  (nm) / (M -1 cm -1 ) [Gd(L1)] 3+ 245 (  30   [a]  In 0. 5 mM CH3CN solutions containing TBAP as supporting electrolyte (0. 1 M). T = 298 K. In order to ensure full nitroxide radical formation the complexes were subjected to electrolysis at a potential intermediate between the TEMPOH/TEMPO and TEMPO + /TEMPO redox couples. Luminescence measurements were also used to determine the lifetimes of the complexes via excitation at 396 nm in both H2O and D2O. For [Eu(L1)] 3+ we determined t=0. 43 s in H2O and t=1.
DFT calculations on model compounds The structure of the lanthanide complexes was investigated by DFT calculations. In order to overcome the prohibitive computational cost on complexes of f-metal ions the optimizations were performed on two models wherein the lanthanide ion was replaced by Y 3+ , namely YL1 3+ and YL2 3+. The yttrium is indeed a common substitute of Gd 3+ in imaging. The number of coordinating water molecules was set to one, in agreement with the luminescence data (see above). For YL1 3+ the optimized structure shows a pendent TEMPO arm, with the hydrogens of the water molecule pointing along but opposite to the TEMPO group. For YL2  3+  we first performed a relaxed potential energy surface (PES) scan along the C-N axis of the alkyne arm to determine its preferred orientation.
X-Ray diffraction. Single crystals were coated with perfluoropolyether, picked up with nylon loops and mounted in the nitrogen cold stream of the diffractometer. Mo-Kα radiation (λ = 0. 71073Å) from a Mo-target rotating-anode X-ray source equipped with INCOATEC Helios mirror optics was used. Final cell constants were obtained from least squares fits of several thousand strong reflections. Intensity data were corrected for absorption using intensities of redundant reflections with the program SADABS. The structures were solved by Patterson methods and subsequent difference Fourier techniques. The OLEX software was used for the refinement. 53 All non-hydrogen atoms were anisotropically refined and hydrogen atoms were placed at calculated positions and refined as riding atoms with isotropic displacement parameters.
Acknowledgements The authors thank the  French National Research Agency  in the framework of the " Investissements d'avenir" program  ( ANR-15-IDEX-02 ),  Labex ARCANE  and  CBH-EUR-GS  ( ANR-17-EURE-0003 ) and the  French National Agency for Research, program Co-Lantha  ( ANR-17-CE07-0034 ) for financial supports. This work was performed under the auspices of the  COST Action   AC15209 , EURELAX. The authors are grateful to  Dr. Pierre Girard  for technical assistance for the DFT calculations and the  Centre de Calcul Intensif en Chimie de Grenoble (CECIC)  for providing the computational resources. The  ICMG Platform  ( FR 2607 ) is acknowledged for the analytical support.
Before catheter insertion, patients were randomly assigned (1:1:1:1) using a secure web-based random-number generator to one of four treatment groups based on skin preparation and type of devices (innovative devices or standard devices; 2% chlorhexidine plus alcohol or 5% povidone iodine plus alcohol). Primary outcomes were the incidence of infectious complications (local infection, catheter colonisation, or bloodstream infections) and time between catheter insertion and catheter failure (occlusion, dislodgment, infiltration, phlebitis, or infection). This study is registered with ClinicalTrials. gov, NCT03757143. Findings 1000 patients were recruited between Jan 7, and Sept 6, 2019, of whom 500 were assigned to the chlorhexidine plus alcohol group and 500 to the povidone iodine plus alcohol group (250 with innovative solutions and 250 with standard devices in each antiseptic group).
Statistical analysis Assuming a 12% infectious complication rate in the povidone iodine plus alcohol group,  16  712 patients were required to detect a 50% reduction of peripheral venous catheter infectious complications with the use of chlorhexidine plus alcohol,  11  with two-tailed α (type-I error) of 5% and a power of 80%. We enrolled 1000 patients to better rule out a potential interaction between the two strategies (+ 30%) and a maximum catheter culture loss of 10%. The analyses were done by two-by-two factorial design on a modified intention-to-treat-basis (all patients except those who withdrew consent). 17 No interim analysis was planned. Demographic data and catheter characteristics were described as number and percentage or median and IQR. For analysis of the primary outcomes, the interaction between two study interventions (antiseptic agent and type of device) was sought first using multivariable logistic regression models.
Secondary outcomes were described as number and percentage or median and IQR and compared with Data are median (IQR) or n (%). CHG=2% alcoholic chlorhexidine. PVI=5% alcoholic povidone iodine. Patients are described twice, once in the antiseptic groups columns and once in the device groups columns. Table  1 : Patient characteristics of the modified intention-to-treat population logistic regression or multiple linear regression, according to the type of variable, to allow interactions terms as for primary outcomes; treatment effects are presented as adjusted relative risk (RR) or adjusted mean difference. All of the tests are two-tailed with no adjustment for multiple testing. Analyses were done with SAS (version 9. 4) and R software (3. 63). The analysis report is presented in accordance with the CONSORT statement.
Exome sequencing identified CFAP61 homozygous variants in patients with MMAF A cohort of 167 patients with MMAF and no other signs of PCD was previously analyzed and permitted to identify harmful variants in known MMAF-related genes in 66 patients  (Martinez et al. , 2020a). After reanalysis of the exomes data from the undiagnosed subjects, we identified one patient with a homozygous variant in CFAP61. This patient (PaCFAP61) had an intronic variant predicted to alter splicing: c. 143+5G>A (NM_015585. 4) (Figure  2A ). The variant was present in the Genome Aggregation Database with a minor allele frequency of 1. 59e-5. Additionally, we found by minigene assay that c. 143+5G>A induced the skipping of CFAP61exon 2 (151nucleotides) and induced a frame-shift shortly after exon1 (Figure  2B  and C ).
Whole exome sequencing (WES) Genomic DNA was isolated from EDTA blood using the DNeasy Blood & Tissue Kits from QIAGEN SA (Courtaboeuf, France) or from saliva using the Oragen DNA extraction kit (DNAgenotech®, Ottawa, Canada) or from saliva using the Oragen DNA extraction kit (DNAgenotech®, Ottawa, Canada). Coding regions and intron/exon boundaries were sequenced on the Novogen platform (agilent v6, HiSeqX,) after enrichment with Agilent kits (Agilent Technologies, Wokingham, UK). Exomes data were analysed using a bioinformatics pipeline developed in-house using two modules, both distributed under the GNU General Public License v3. 0 and available on github: https://github. com/ntm/grexome-TIMC-Primary and https://github. com/ntm/grexome-TIMC-Secondary and as described in part in reference  (Arafah et al.
From the high-resolution MS pre-scan with a mass range of 335 to 1400, the most intense peptide ions were selected for fragment analysis in the orbitrap depending by using a high speed method if they were at least doubly charged. The normalized collision energy for HCD was set to a value of 28 and the resulting fragments were detected with a resolution of 120,000. The lock mass option was activated; the background signal with a mass of 445. 12003 was used as lock mass. Every ion selected for fragmentation was excluded for 30 seconds by dynamic exclusion. Data were processed with MaxQuant software  (version 1. 6. 10. 43)  and Mouse reference proteome from SwissProt database (release 2019_07) using standard parameters. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  (Perez-Riverol et al.
Acknowledgements This work was supported by the  National Key Research and Development Program of China   2016YFA0500902  (to M. L. );  Natural Science Foundation of China  ( 32070842 ,  31771654  and  31530047  to M. L. ); the  Natural Science Foundation of Jiangsu Province  (Grants No. BK20190081  to M. L. ); and  Qing Lan Project  (to M. L. ); the  FLAGEL-OME  project (to P. F. Ray) :  ANR-19-CE17-001.
Purification and Characterization The CH and DHC purifications were performed by flash chromatography on a flashprep PuriFlash ® 4100 LC system from Interchim (Montluçon, France) with prepacked silica columns (30 µm, Interchim PF-Si30-HP) and dual-wavelength collection (λ = 254 and 280 nm). Mixtures of cyclohexane and ethyl acetate were used as eluant. The CHs and DHCs characterizations were realized by NMR and mass spectrometry. 1 H-NMR spectra were recorded on a Brucker Fourier 300 (300 MHz) (Billerica, MA, USA). Residual Acetone-d 6 and DMSO-d 6 protons signals at δ 2. 05 and 2. 5 ppm, respectively, were used for the calibration. Data are reported as follows: chemical shift (δ ppm), multiplicity (s = singlet, d = doublet, t = triplet, dd = doublet of doublets, and m = multiplet), coupling constant (Hz), integration and assignment.
13 C-NMR spectra were recorded on a Bruker Fourier 300 (75 MHz) (Billerica, MA, USA). Residual Acetone-d 6 and DMSO-d 6 protons signals at δ 29. 84 ppm and 39. 52 ppm, respectively, were used for the calibration. Data are reported as follows: chemical shift (δ ppm), assignment. All NMR assignments were made using COSY, HMBC and HSQC spectra. 1D and 2D NMR spectra ( 1 H, 13 C, HSQC, HMBC, and COSY) were recorded using standard Bruker pulse programs. High-resolution mass spectrometry was performed on an Agilent, 1290 system, equipped with a PDA UV detector and a 6545 Q-TOF mass spectrometer (Wilmington, DE, USA). The source was equipped with a JetStream ESI probe operating at atmospheric pressure. The electrospray interface operated with the following parameters: scanning range of 50-1000, nebulizer 35 psi, gas temperature 325 • C, gas flow 8 L/min, sheath da temperature 350 • C, sheath gas flow 11 L/min.
Considering that insulin was unstable in three-in-one PNA, assays were conducted progressively: the influence of each macronutrient (dextrose, amino acids and lipids) was tested. Moreover, each lipid emulsion used in PNA can be composed of one or several oils, coming either from animals or plants, therefore, we hypothesised that the nature and concentration of lipid emulsion could have an impact on the stability of insulin. Nevertheless, neither the nature nor concentration was statistically significant. Lipid peroxydation (leading to the synthesis of malondialdehyde) is a well-known chemical reaction that has already been described in three-in-one PNA  [57] [58] [59]. Consequently, it could explain insulin instability. A stability study was performed with an excessive addition of malondialdehyde (data not shown).
Population. Eligible participants were non-pregnant, nulliparous women attending a visit to our Gynecology unit. The exclusion criteria were as follows: history of previous delivery (vaginal or cesarean section), personal history of PFD, obese women with a body mass index (BMI) higher than 35 kg•m -2 , women with muscular disease, women requiring admission to a psychiatric unit, women under judicial protection, and those who were unable to understand French language. Data collection. Participant characteristics. At the first visit, the participants' age, height, and weight were collected, and their BMI was calculated. Shear wave elastography assessments. The evaluation protocol during the two visits was similar: ultrasound SWE assessment of the LAM at rest, during subjective maximal Valsalva maneuver, and during subjective maximal perineal contraction.
To provide an idea of the temporal changes during measurements, a video clip of an ultrasound SWE assessment of the LAM during the Valsalva maneuver is provided as online supplementary material (Supplementary material 1). Data analysis and statistics. The region of interest was identified and contoured manually using Matlab scripts (The Mathworks, Inc. , 2016). For assessments at rest and during the Valsalva maneuver, the mean SM for the whole acquisition was considered. For assessments during subjective maximal perineal contraction, the maximal SM for the acquisition was considered. In case of limited region within the measurement is not possible, the software automatically excludes it for the analysis. As mentioned in a previous publication, the AIXPLORER device provides a measurement of the Young's modulus that is valid for isotropic tissues.
Ethical and reglementary considerations. The study was approved by an ethics committee (Comité de Protection des Personnes Ile de France 8, ethical committee for human protection from Ile de France) on the 16/07/2018 and is referenced with the ID RCB: 2018-A01422-53. The study was registered on https:// clini caltr ials. gov (NCT03602196) on the 26/07/2018. All methods were carried out in accordance with relevant guidelines and regulations. Written and informed consent was obtained from all subjects before any investigation.