dataesr/scientific-paragraphs-categorization huggingface dataset:
Burosumab treatment in patients with XLH improves alveolar bone and dental features We analyzed clinical data of two patients with XLH treated with burosumab for 4 and 6 years. The first patient, a 20-year-old female, was treated since the diagnosis at the age of 1 year with calcitriol and phosphorus, which was replaced by burosumab at the age of 16. At the onset of burosumab treatment, the patient exhibited enlarged pulp chambers. Measurements of pulp chamber size following this treatment showed a positive outcome on these features (Fig. 1a-e ). The second patient, a 49-year-old male, was treated with calcitriol and phosphorus from 3 to 18 years of age. He resumed conventional treatment at 37 years of age, which was replaced by burosumab at 43 years of age. Evaluation of the bone fraction (BV/TV) showed an improvement during the time of burosumab treatment (Fig.
ACKNOWLEDGEMENTS This work was supported by the  Agence Nationale de la Recherche  grant  Hyposkel 18-CE14-0018-01  to  C Bardet. E Lira dos Santos  was supported by the  Fondation pour la Recherche Médicale  ( SPF202209015771 ). In vivo imaging was performed at the  Life Imaging Facility of Université Paris Cité (Plateforme d'Imagerie du Vivant (PIV)) , supported by  France Life Imaging  (grant  ANR-11-INBS-0006 ) and  Infrastructures Biologie-Santé , and  DIM Thérapie Génique.
We included all women with a live singleton pregnancy in vertex presentation at term (≥ 37 weeks of gestation) who underwent OVD, defined by the placement of at least one blade for forceps or spatula, or a vacuum. Exclusion criteria were multiple gestations, small for gestational age (SGA), defined as less than the 10th centile for gestational age on Hadlock curves  23, 24  , a known congenital anomaly, vaginal breech delivery and women with missing data regarding shoulder dystocia. All women received information about our study. All experiments were performed in accordance with relevant guidelines and regulations. The Research Ethics Committee of the University of Angers, France, approved the study (no. 2008) and confirmed that this study did not require written informed consent from patients.
Statistical analysis. Continuous data were described by their means ± standard deviations and compared by Mann-Whitney tests, and categorical data were described by percentages and compared by Fisher exact tests. A logistic regression model was used both to assess the relationship between the potential risk factors and shoulder dystocia and to build a score of shoulder dystocia risk. The potential risk factors considered were determined based on the literature 2. All factors highlighted in the literature as being associated with shoulder dystocia were included in the model, to be sure not to miss any factor. These covariates were fetal head station at time of OVD (mid vs. low), age (≥ 30 vs. < 30 years), BMI (≥ 25 vs. < 25 kg/m 2 ), gestational diabetes mellitus, gestational age at delivery (≥ 40 vs.
A second analysis was performed by also considering the potential interactions between OVD, on the one hand, and each of the other potential covariates, on the other hand. In this model, only significant interactions were retained due to parsimony considerations. The linear combinations obtained with each of these models were used as different scores of shoulder dystocia risk. Their characteristics and accuracy in identifying women at risk of shoulder dystocia were determined using the area under the receiver operating characteristic curve (AUC). An AUC of at least 0. 80 was considered to represent an accurate prediction  36, 37. STATA 14. 2 software (StataCorp, College Station, TX) was used for all analyses. P values < 0. 05 were considered statistically significant.
Results There were 19,786 deliveries during the study period: 15,836 (80. 0%) were vaginal and 3950 (20. 0%) were cesarean deliveries. A total of 2192 aOVDs resulted in vaginal delivery in 98. 2% of cases (2153/2192) and in cesarean delivery in 1. 8% of cases (39/2,192). Within this cohort, 74 women were excluded: 14 twin pregnancies, 26 preterm deliveries and 14 small-for-gestational-age newborns and 20 women with missing data regarding shoulder dystocia (Fig. 1 ). Therefore, the final sample included 2118 deliveries with an aOVD. Among them, shoulder dystocia occurred in 57 women (2. 7%): 23. 6% (13/55) after mid-pelvic aOVD, 70. 9% (39/55) after low-pelvic aOVD and 5. 5% (3/55) after outlet aOVD. Table  1  details the maternal and labor characteristics and maternal and neonatal outcomes for women who had shoulder dystocia (n = 57) and those who had an OVD without shoulder dystocia after aOVD (n = 2061).
2 mL/min. The injector operated in the spitless mode and its temperature was set at 250°C. The separation of volatile compounds was performed on a SH-Rxi-5 ms column (30 m × 0. 25 mmID, 0. 25 mm; Shimadzu). The oven temperature program started at 40°C (held for 5 min), was raised at a rate of 4°C/ min to 140°C (held for 2 min), raised at a rate of 6°C/min to 190°C (held for 2 min), and then raised at a rate of 15°C/min to 230°C (held for 1 min). The detection was performed by a QP2010 SE mass spectrometer sets in positive electron impact mode (EI) with 70 eV of electron energy. The electron multiplier was set by the auto-tune procedure. MS data were collected in a full scan mode over the m/z range from 35 to 400 (0. 3 s/scan) Transfer line temperature was set at 230°C. At least three independent samples were analyzed for each condition.
Once the raw data had been acquired, the peaks were automatically integrated on the basis of the area. Volatile compounds were identified using the NIST20 spectral library, based on the mass spectrum with the highest similarity score (minimum 87%). This is achieved by comparing the mass fingerprints of the unknown compounds eluted with those of 300,000 references. The identity of 1-undecene has already been confirmed by the use of an analytical standard in one of our previous studies  (Corre et al. , 2021). Only compounds systematically detected in all wild type samples were reported. Frontiers in Microbiology 04 frontiersin. org.
Confocal laser scanning microscopy Biofilm observation and quantification of average thickness and biovolume were performed as described by  Bourigault et al. (2021)  using the Comstat 2. 0 software  (Heydorn et al. , 2000). Surface coverage was determined as described by  Cambronel et al. (2019)  using the ImageJ software  (Schneider et al. , 2012).
The undA deletion impairs 1-undecene emission and Legionella pneumophila aerial inhibition In order to investigate impacts of 1-undecene emission on the physiology of MFE01, we managed to construct a MFE01 mutant unable to emit 1-undecene. The UndA enzyme was previously described in the P. fluorescens Pf-5 strain to catalyze 1-undecene synthesis by oxidative decarboxylation of cytoplasmic lauric acid  (Rui et al. , 2014)  (Supplementary Figure  S1 ). The presence of a single copy of undA gene (GenBank accession number: OQ434583. 1) in MFE01 genome led to the construction of a MFE01 undA in frame deletion mutant, named ΔundA. In LB medium the ΔundA mutant showed no difference in growth compared to the wild type (WT) strain (Supplementary Figure  S2 ). By using HS-SPME/GC-MS analysis, we analyzed VOCs emitted by MFE01 (WT) (Supplementary Figure  S3A ) and the ΔundA mutant.
In our conditions, biofilm maturation seems not AHL dependent in MFE01 A previous work using biosensor strains to detect AHL signals indicated the absence of medium or long chain AHL production by MFE01  (Gallique et al. , 2017b). Since AHL-based QS is considered a key factor for biofilm development for many bacterial species, we wanted to test if MFE01 produced AHL in our conditions. However, biosensors are limited in the range of detectable molecules, and other lactone-containing QS molecules might be produced by MFE01. To challenge this possibility, we performed in silico detection of putative QS system's genes in MFE01 genome using the tblastn software on the Basic Local Alignment Search Tool (BLAST)  (Altschul et al. , 1990). We searched for genes encoding AHLs synthesis proteins. Comparison using tblastn with RhlI (AAC44037.
, 2014)  revealed that the corresponding putative protein contains two domains. The N-terminal domain (amino acids 4 to 166) belongs to the "Transcription factor LuxR-like, autoinducer-binding domain superfamily (IPR036693)" and the C-terminal to the "Winged helixlike DNA-binding domain superfamily (IPR036388)" (Supplementary Figure  S7B ). Thus, it appeared that this gene may encode an autoinducer-binding-domain-containing protein, able to bind to AHLs and to bind to DNA after homodimerization. Interestingly, this putative protein is identical to a protein of Pseudomonas moraviensis (MBH3446738. 1) (Supplementary Figure  S7C ). To determine if biofilm formation is AHLs-dependent in MFE01, under our conditions, i. e. , in the absence of exogenous AHLs, we performed biofilm assays in presence of the lactonase QsdA.
According to our experimental results, despite its hydrophobic part, 1-undecene remains sufficiently soluble in the aqueous phase of the biofilm to modify its maturation. This is coherent with VOCs detection in different sources of water  (Chary and Fernandez-Alba, 2012)  and the 1-undecene solubility in water of 0. 3432 mg/L, corresponding to 2. 22 μmol per liter, accordingly to the PubChem database. 2 Another volatile communication molecule, the 3-hydroxypalmitic acid methyl ester (3-OH PAME), was previously described for its implication in gaseous and water phase communication  (Clough et al. , 1994; Flavier et al. , 1997). This VOC is synthesized by the Ralstonia solanacearum PhcB enzyme and is detected by the PhcR sensor histidine kinase, leading to expression of genes involved in virulence towards Solanum tuberosum  (Clough et al.
Groundwater Suitability for Drinking Quality of groundwater determines its suitability for different purposes depending upon the specific standards. To assess the suitability for drinking, the physicochemical and chemical parameters of groundwater quality of the study area are compared with the standards guidelines values as recommended by the World Health Organization  [24, 25]  for drinking purpose. Furthermore, the water quality index (WQI), total hardness (TH) and total dissolved solids (TDS) which are others important water quality parameter were also used in this study. The physical and chemical water quality parameters of the study area resulting from the chemical water analysis as well as the standard guideline values proposed by the WHO are reported in Table  2. According to the median values of chemical data of groundwater samples, HCO3 -and Na + are respectively the most dominant anion and cation in groundwater samples.
The United States Salinity Laboratory diagram was also used to assess the suitability of groundwater samples for irrigation purpose. The plot of chemical data on the USSL salinity diagram (Figure  6 ) reveals that the majority of the groundwater samples (64. 3%) fall in the field C3S1, indicating high salinity and low sodium water which can be used for irrigation for almost all type soil with little danger of exchangeable sodium  [37, 38]. However this kind of water requires good drainage because the high salinity may affect crop growth and can cause osmotic effects and nutritional disorders. In addition, 16. 7% of groundwater samples fall in C2S1 category indicating medium salinity and low alkalinity water which can be used for irrigation, where moderate amount of leaching occurs and moderate permeability with leaching soil  [20].
Conclusions This study was carried out in the area of West central Senegal in order to assess the quality of groundwater and determine its suitability for irrigation and human consumption. For this purpose, several parameters of groundwater quality evaluation were determined in association with the use of several geochemical plots. The in situ measurements of pH and electrical conductivity indicate respectively that the waters are neutral to slightly basic and the conductivity shows weak to strongly mineralized waters with a maximum value of 8880 µS/cm. The plot of the chemical data on the Piper diagram reveals that several types of facies of which mixte Na-Ca-Mg-HCO3 constitutes the dominant facies. The classification of water according to TH and TDS for human consumption reveals respectively that the majority (73.
Clinical data Characteristics of AMI patients are summarized in Table  1. We collected 415 samples from 178 ST elevation myocardial infarction (STEMI) patients (26 patients from the Hibiscus-STEMI cohort and 152 from the CARIM cohort) and 30 healthy donors. Eighty percent (80%) of patients were male and median age was 60 years. Forty-one percent (41%) were active smokers, 5% had diabetes, 36% had dyslipidemia, and 38% had hypertension at the time of AMI. The observed median of duration of ischemia was 184 minutes. Fifty-two percent (52%) had single, 29% had two-, and 19% had three-vessel disease on coronary angiography. Fourty-nine percent of patients had a 0 TIMI ow score before reperfusion. Hypersensitive Troponin T median concentration was 121. 3 µg/L (N < 14 µg/L) at the time of admission and peak median concentration was 2582 µg/L.
21 pg/mL respectively, p = 0. 0032). Other chemokines were analyzed (CXCL-10, CCL-17, CCL-2, CCL-5, CXCL-11, CCL-4) but did not show any signi cant variation (data not shown). We then analyzed cytokine concentrations in the same plasma samples. Among all 10 cytokines tested (IL-4, IL-2, IL-1β, TNF-α, IL-17A, IL-6, IL-10, IFN-γ, IL-12p70, TGF-β1), only IL-4, IL-6, IL-10 and TNF-α were detectable and signi cantly varied over time (see Supplementary Fig. S1 online ). IL-4 concentration was lower in patients from D3 to M12 as compared to healthy donors (0. 78 vs 10. 1 pg/mL respectively, p = 0. 018), as well as IL-10 (0. 55 vs 2. 54 pg/mL, p = 0. 0195) and TNF-α concentrations (0. 35 vs 4. 04 pg/mL, p = 0. 0105). IL-6 concentration was higher in patients at H0-H48 and D3 as compared to M6-M12 samples (15.
Cohorts inclusion criteria Blood samples of patients admitted at the acute phase of ST-segment elevation myocardial infarction (STEMI) were collected at the Cardiology department of University Hospital of Tours, between January 2019 and September 2021. These patients were enrolled in two prospective cohorts: Hibiscus-STEMI (coHort of patients to Identify Biological and Imaging markerS of CardiovascUlar outcomes in ST elevation myocardial infarction, NCT03070496) and CARIM (CARdioprotection in Myocardial Infarction, NCT02967965). Inclusion criteria were: rst STEMI requiring a primary percutaneous coronary intervention, age 18-90 years, onset of chest pain of less than 12 hours. Exclusion criteria were: diagnosis of STEMI not con rmed by angiography, refusal to participate in the study or to sign the consent, impossibility to give information to the subject about the study, lack of medical social coverage, obvious contraindication to magnetic resonance imaging (claustrophobia, pacemaker, de brillator, renal insu ciency, known allergy to a contrast agent), deprivation of civil rights, participation to another interventional study.
Statistical analyses Data obtained from analyses performed from plasma and PBMC collected from H0 to H48 after AMI were pooled together (H0-H48), as well as samples collected from M6 to M12 (M6-M12) after AMI. The Kruskal-Wallis test was used to compare results from three or more groups of samples, Mann-Whitney test was used to compare two groups. Differences were considered as signi cant at p < 0. 05. Statistical analyses and gures were performed with GraphPad Prism software (GraphPad Software, San Diego, CA, USA).
DATA AVAILABILITY STATEMENT The datasets are available from the corresponding author on reasonable request. Acute myocardial infarction (AMI) is responsible for an increase of P2Y11 expression in PBMC that could lead to a modi cation of immune cells transcriptional pro le resulting in a tolerogenic polarization of dendritic cells and a decrease of Th1/Th2 ratio. P2Y11 receptor could also be involved in PBMC hyporesponsiveness early after AMI and, as a consequence in cytokines and chemokines secretion changes. This immune peripheral response may partly explain the tissue response including differenciation of broblasts in myo broblasts. P2Y11 represents a cornerstone of the control of in ammatory response after myocardial infarction.
( 55 ) Note that, since we consider here that x 1 (t) ∈ [-3, 3] and x 2 (t) ∈ [ -𝜋 2 , 𝜋 2 ] , the obtained N-TS represents exactly the switched nonlinear system (52) on a validity domain  x defined in (7) with: 𝔏 = ⎡ ⎢ ⎢ ⎢ ⎢ ⎢ ⎣ 1 0 -1 0 0 1 0 -1 ⎤ ⎥ ⎥ ⎥ ⎥ ⎥ ⎦ and  = ⎡ ⎢ ⎢ ⎢ ⎢ ⎢ ⎣ 3 3 𝜋 2 𝜋 2 ⎤ ⎥ ⎥ ⎥ ⎥ ⎥ ⎦. ( 56 ) For different values of a ∈ [-1, 3] and b ∈ [-2, 0. 5] with a step of 0. 1, the feasibility regions obtained from Theorem 1 using YALMIP and SeduMi in MATLAB  64  is compared with the ones obtained from the previous related studies. 11, 13, 15, 16 hese results are shown in Figure  1. For these tests, each considered LMI-based conditions are checked over 1066 points (a, b). The feasibility field provided by theorem 1 in Reference 11 (65 solutions, 6. 1%) contains the one provided by theorem 3 in Reference 13 (91 solutions, 8.
We observed that an array of 16 closely spaced Rap1 sites (i. e. , a dense array with 6-bp gaps) led to a 5-fold increase in the occurrence of condensin at the border of the array, relative to the level observed with an array made of mutated DNA sites that are incapable of binding Rap1 12 (Fig. 1C ). This condensin accumulation decreased with the distance from the array, indicating that the accumulation was most strongly localized at the edge of the Rap1 array. We saw a similar local condensin enrichment at the border of a native telomere (Fig. S1B ). These data are in agreement with previous reports of condensin enrichment at the border of telomeres in budding yeast, fission yeast, and vertebrates during mitosis  46- 48   If this higher condensin abundancy resulted from the stalling of condensin-driven loop extrusion at the Rap1 array, a lower density of Rap1 sites could potentially alleviate this higher abundancy, for example by exposing bare DNA segments within the array that condensin could contact during the process of loop extrusion.
18,53,54,63-66 and Dekker et al, Science, to appear on Nov. 10). Second, a stiffer Rap1 array positions the next freely accessible DNA further away from condensin, making it less likely that the SMC can reach beyond the array. While we observed differences between Rap1 arrays of varying length and density, it is difficult to disentangle the effects of density and stiffness, and therefore we cannot unambiguously determine the relative importance of the stiffness. The data call for a detailed mechanistic model and simulations of loop extrusion of DNA with a local array of varying stiffness. Summing up, we conclude that the dense linear protein arrays stall condensin by reducing the amount of freely accessible DNA that can be grabbed and processed by condensin, as well as potentially by inhibiting the incorporation of the array into the loop and by distancing the freely accessible DNA to positions beyond the array.
Distance measurements by microscopy of cells Exponential growing cells (0. 8 OD) in rich medium (YPD) were washed in synthetic medium prior to live-cell imaging with a wide-field inverted microscope (Leica DMI-6000B) equipped with Adaptive Focus Control to eliminate Z drift, a 100×/1. 4 NA immersion objective with a Prior NanoScanZ Nanopositioning Piezo Z Stage System, a CMOS camera (ORCA-Flash4. 0; Hamamatsu), and a solid-state light source (SpectraX, Lumencore). The system is piloted by MetaMorph software (Molecular Device). 2mM Indole-3-acetic acid (IAA) was added to exponential growing smc2-AID cells in YPD for 1 hour prior to imaging. GFP and mCherry two-color images were acquired over 19 focal steps of 0. 2µm using solid state 475 and 575nm diodes and appropriate filters (GFP-mRFP filter; excitation: double BP, 450-490/550-590nm and dichroic double BP 500-550/600-665nm; Chroma Technology Corp.
). Acquisition of both wavelengths was completed on each focal plane with an exposure time of 50ms, before 0. 2µm steps, to minimise the possibility of array movement between acquisitions of each wavelength. A single bright-field image on one focal plane was acquired at each time point with an exposure of 50ms. All images shown are maximum intensity z projections of z-stack images. Image analysis was achieved following processing with ImageJ Fiji software, using scripts written in ImageJ macro language. Briefly, local maxima that define GFP and mCherry fluorescent array positions were determined from 2D maximal projections of three-dimensional data sets. Fluorescent signals within cells were confirmed manually from 3 color merged images. The distance between the two closest GFP and mCherry maxima was calculated using their extracted XY coordinates in R software (v4.
Micro-C datasets were analysed using the Distiller pipeline (https://github. com/open2c/distiller, commit 8aa86e) to implement read filtering, alignment, PCR duplicate removal, and binning and balancing of replicate and sample matrices. Reads were aligned to W303 using bwa 0. 17. 7 and the resulting maps filtered to remove low-quality alignments (MAPQ<30) and cis alignment pairs within 150 bp. Replicates were analysed independently, and their quality assessed before aggregation into sample-level datasets. Maps were visualized and explored using Higlass  78.
The sample was then placed onto the microscope and imaged in buffer. The microscope was a Bruker Multimode, with NanoScope V controller and version 9. 1 Nanoscope software. The imaging mode was PeakForce QNM, with a tapping frequency of 4 kHz and a force setpoint and amplitude manually tuned for optimal image quality, typically 100 pN and 12 nm. Images were acquired with a pixel size of 2 nm, and processed for subtraction of background artifacts using the 'align rows' and 'remove polynomial background' filters in Gwyddion  81. To analyze the contour lengths and array end-to-end lengths, we used a homebuilt Matlab analysis package named DNAcontour. This package in the version that was used to produce the data presented here, is available at https://gitlab. tudelft. nl/allards-matlab-repo/allards-matlab-repo/-/tree/RAP1_paper/DNAcontour.
ACKNOWLEDGMENTS We thank  Milos Tisma ,  Theo Koenig ,  Eric Le Cam ,  Olivier Pietrement ,  Gerard Mazón ,  Armelle Lengronne ,  Jonathan Heuze ,  Olivier Alibert ,  Stéphane Coulon ,  Sylvie Tournier ,  Pascal Bernard ,  Frédéric Beckouet ,  Sabrina Pobieaga  and  Florian Roisné-Hamelin  for discussions,  Anders Barth  for help with determining the Rap1 labelling efficiency, and  Eli van der Sluis  and  Ashmiani van den Berg  for purifying condensin and LacI proteins. Research in the laboratory of S. M. was supported by grants from  Agence Nationale de la Recherche  ( ANR-14-CE10-021 DICENS ,  ANR-15CE12-0007 DNA-Life ),  Fondation ARC pour la Recherche sur le Cancer, Ligue contre le Cancer ,  CEA Radiation biology program  and  GGP CEA EDF program. A. D. was supported by a  PhD fellowship  from  CEA  and a  Ligue contre le Cancer  young researcher grant.
As the cross-sectional area of karst conduits is finite, both pressurized and non-pressurized flow may occur. Equations were therefore adapted for pressurized conditions through considering the Preissmann slot model in MODBRANCH package  (Reimann et al. 2011) , or the Darcy-Weisbach equation in pipe-flow models  (Jeannin 2001) , such as the Storm Water Management Model (SWMM)  (Campbell and Sullivan 2002; Chen and Goldscheider 2014; Peterson and Wicks 2006). However, the use of such models requires detailed distributions of hydraulic parameters which are often unavailable due to the unknown location and geometry of karst conduits.