dataesr/scientific-paragraphs-categorization huggingface dataset:
Phylogenetic signals and tests of the defence escalation hypothesis. We first estimated the phylogenetic signal (Blomberg's K) for all individual VOCs, their sum and their Shannon diversity, and the climatic niche (PCA1) using species-level averages with the function phylosig of the package phytools in R  71. A K value of 1 indicates that trait values are consistent with the tree topology and a random walk model (i. e. , trait similarity is directly proportional to the extent of shared evolutionary history). A K value close to 0 indicates no influence of shared ancestry on trait values (i. e. , phylogenetic independence). When K > 1, the traits have more phylogenetic signal than expected from a random walk model on the given phylogeny  45. Next, to test for the defence escalation hypothesis, we calculated the patristic distance from root to tip (i.
Soil effect on VOCs production and nematode recruitment. To address potential correlations between the soil physico-chemical variables and the whole VOCs matrix we mapped the soil variables (Table  S3 , Fig. S8 ) on the VOCs ordination based on a distance-based redundancy analysis (dbRDA) (function cca in the package vegan). We performed the analysis using both Euclidean and Bray-Curtis distances, and obtained very similar results, and thus used the Euclidean distance results to show. Finally, we performed a multivariate regression analysis for testing the effect of all soil variables on EPNs attraction.
Acknowledgements We thank  Maiann Suhner  for helping with Festuca collection and identification. This work was supported by  Swiss National Science Foundation  grants ( 179481  and  159869 ) to SR, the  Spanish Ministry of Economy  and Competitivity  CGL2012-39953-C02-01grant  to PC. MFM was funded by a  University of Zaragoza /Santander PhD fellowship. Moreover, PC and MFM were partially funded by a  Spanish Aragón Government and European Social Fund Bioflora   A01-17 grant.
HSPC transfection gRNAs were assembled at room temperature with a 90 M Cas9-GFP protein (provided by De Cian) in RNP complexes using a ratio of 2:1 (gRNA:Cas9). Human CD34 + cells (1 × 10 6 to 2 × 10 6 ) were transfected with RNP particles using the P3 Primary Cell 4D-Nucleofector X Kit S or L (Lonza), respectively, and the AMAXA 4D CA137 program (Lonza) together with 90 M transfection enhancer (IDT), unless otherwise stated.
One day after transfection, cells were replated and selected with puromycin (1 g/ml) for 48 hours to enrich for transfected cells. Cells were then collected, and genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen) and sheared to an average length of 500 bp with the Bioruptor Pico Sonication System (Diagenode). Library preparation was performed using the original adapters and primers according to previous work  (27). Libraries were sequenced with a MiSeq sequencing system (Illumina) using an Illumina MiSeq Reagent kit V2-300 cycles (2 × 150-bp paired-end). Raw sequencing data (FASTQ files) were analyzed using the GUIDE-seq computational pipeline  (52). Identified sites were considered bona fide off-targets if a maximum of seven mismatches against the on-target were present and if they were absent in the background control.
RP-HPLC analysis of globin chains RP-HPLC analysis was performed using a NexeraX2 SIL-30AC chromatograph and the LC Solution software (Shimadzu). Globin chains were separated by HPLC using a 250 mm × 4. 6 mm, 3. 6-m Aeris Widepore column (Phenomenex). Samples were eluted with a gradient mixture of solution A (water/acetonitrile/trifluoroacetic acid, 95:5:0. 1) and solution B (water/acetonitrile/trifluoroacetic acid, 5:95:0. 1). The absorbance was measured at 220 nm. HBA F CGGTCAACTTCAAGCTCCTAA R ACAGAAGCCAGGAACTTGTC HBB F GCAAGGTGAACGTGGATGAAGT R TAACAGCATCAGGAGTGGACAGA HBG1 + HBG2 F CCTGTCCTCTGCCTCTGCC R GGATTGCCAAAACGGTCAC HBD F CAAGGGCACTTTTTCTCAG R AATTCCTTGCCAAAGTTGC HBE F CTTTGGAAACCTGTCGTC R CTTGCCAAAGTGAGTAGC GATA1 F GACAGGACAGGCCACTACCTATG R AGTACCTGCCCGTTTACTGACAA ALAS2 F CAGCGCAATGTCAAGCAC R TAGATGCCATGCTTGGAGAG BAND3 F ACCTCTCTCACCTCACCTTCTG R AACCTGTCTAGCAGTTGGTTGG GAPDH F GAAGGTGAAGGTCGGAGT R GAAGATGGTGATGGGATTTC CE-HPLC analysis of Hb tetramers CE-HPLC analysis was performed using a NexeraX2 SIL-30 AC chromatograph and the LC Solution software (Shimadzu).
We used the nuclear dye DRAQ5 (eBioscience) to evaluate the proportion of enucleated RBCs. To determine genome editing efficiency in erythroid subpopulations, cells were labeled with a PE-Cy7-conjugated anti-GYPA antibody (563666, BD Pharmingen) and an FITC-conjugated anti-HbF antibody (552829, BD Pharmingen), as described above. GYPA + cells were sorted on the basis of HbF expression using FACSAria II (BD Biosciences). Flow cytometry analyses were performed using Fortessa X20 (BD Biosciences) or Gallios (Beckman Coulter) flow cytometers. Data were analyzed using the Kaluza software (Beckman Coulter) or the FlowJo software (BD Biosciences).
NSG mouse transplantation Nonobese diabetic severe combined immunodeficiency gamma (NSG) mice (NOD. CgPrkdcscid Il2rgtm1Wj/SzJ, Charles River Laboratories, St Germain sur l'Arbresle, France) were housed in a specific pathogen-free facility. Mice at 6 to 8 weeks of age were conditioned with busulfan (Sigma, St. Louis, MO, USA) injected intraperitoneally (25 mg/kg body weight/day) 24, 48, and 72 hours before transplantation. Control or edited mobilized healthy donor CD34 + cells (10 6 cells per mouse) were transplanted into NSG mice via retro-orbital sinus injection. Neomycin and acid water were added in the water bottle. At 16 weeks after transplantation, NSG recipients were sacrificed. Cells were harvested from femur bone marrow, thymus, and spleen; stained with antibodies against murine or human surface markers [murine CD45, BD Biosciences, Franklin Lakes, NJ, USA; human CD45, Miltenyi Biotec, Bergisch Gladbach, Germany; human CD3, Miltenyi Biotec, Bergisch Gladbach, Germany; human CD14, BD Biosciences, Franklin Lakes, NJ, USA; human CD15, Beckman Coulter, Brea, CA, USA; human CD19, Sony Biotechnologies, San Jose, CA, USA; human CD235a (CD235a-APC), BD Pharmingen]; and analyzed by flow cytometry using a Gallios analyzer and the Kaluza software (Beckman Coulter, Brea, CA, USA).
Acknowledgments: We thank  R. Kurita  and  Y. Nakamura  for contributing the HUDEP-2 cell line,  L. Douay  for the erythroid differentiation protocol,  G. Pavani  for the optimization of editing protocol in HSPCs,  B. Wienert  for providing assistance and protocol for the  LRF ChIP ,  O. Alibeau  and  C. Bole  for the DNA sequencing,  E. Brunet  for the discussion, and  E. Duvernois-Berthet  for the script used for InDel characterization. Funding: This work was supported by grants from the  European Research Council  (ERC-2015-AdG, GENEFORCURE), the  Agence Nationale de la Recherche  ( ANR-16-CE18-0004 ,  ANR-11-INBS-0014-TEFOR ,  ANR-17-CE13-0016 -i- MMEJ , and  ANR-10-IAHU-01  " Investissements d'avenir" program ), the  Paris Ile-de-France Region  under « DIM Thérapie génique» initiative , the  AFM-Telethon  ( 22399  and  22206 ), and  Genopole  (CHAIRE JUNIOR FONDAGEN).
Finally, we assessed the degree of variability in the HAT titration of serum/plasma samples introduced by sourcing O-ve indicator red cells from different donors. Four monoclonal antibodies to the four known binding sites on the RBD  20  and four Fig. 3  Titration of antibodies in the agglutination assay. A Eighteen plasma samples from mild cases were compared for titration in the HAT with 1:40 O -ve whole blood from a seronegative donor and endpoint titre in an RBD ELISA  32. Four samples were negative in both assays. The data point marked with an arrow on the graph (plasma 2 on the plate, Fig. 3B ) was checked with a reagent composed of IH4 without RBD and shown to be dependent on antibodies to the RBD. This sample did score positive for antibodies to full length spike in an ELISA (endpoint titre 1:1123).
Detection of antibodies by HAT on autologous red cells obtained by finger prick has been repeated multiple times in both Oxford and Toulouse, and will be the subject of a future report. Source data are provided as a Source Data file. 20/SS/0028). Patients were recruited from the John Radcliffe Hospital in Oxford, UK, between March and May 2020 by identification of patients hospitalised during the SARS-COV-2 pandemic and recruited into the Sepsis Immunomics and ISARIC Clinical Characterisation Protocols. Time between onset of symptoms and sampling were known for all patients and if labelled as convalescent patients were sampled at least 28 days from the start of their symptoms. Written informed consent was obtained from all patients. All patients were confirmed to have a test positive for SARS-CoV-2 using RT-PCR from an upper respiratory tract (nose/ throat) swab tested in accredited laboratories.
2 g/L), before staining with a goat anti-human IgGAM-FITC polyclonal secondary antibody (Jackson, Cat. No. 109-095-064, used 1/200) for 60 min on ice. Cells were then washed twice more in PFN before analysis on a FACScalibur flow cytometer, using the Cellquest Pro software 5. 2 to calculate the mean geometric fluorescence intensity on 5000 cells within a broad FSC/SSC rectangular gate (see Supplementary Fig. 4 ). Indirect ELISA to detect SARS-CoV-2 specific IgG (Fig. 6 ). A standard indirect ELISA was used to determine the SARS-CoV-2 specific IgG levels in plasma samples. A highly purified RBD protein from SARS-CoV-2 Wuhan strain (NR-52306, BEI Resources, USA), expressed in mammalian cells, was used to capture IgG in the plasma samples. Briefly, ELISA plates (Nunc, MaxiSorp) were coated with 100 µL/well of RBD antigen diluted in PBS (pH 7.
No date restrictions were imposed on the searches, but we removed animal-only and opinion pieces from the results. The medical librarian searched a minimum of two major databases (e. g. , Cochrane Library, PubMed/MEDLINE, or Embase) to identify relevant systematic reviews, clinical trials, and observational studies published through May 1, 2017. As this was the inaugural version of these guidelines for children, all publications up through May 1, 2017 were considered. Key studies published after the conclusion of the initial literature search on May 1, 2017 were incorporated into the evidence synthesis if identified by panel members as important and relevant even if they were not part of the initial literature review. We excluded articles published in abstract form, in a language other than English, and those focused solely on pre-clinical data.
gov NCT03080038). Until further data are available, we consider it reasonable to begin vasoactive infusions after 40-60 mL/kg of fluid resuscitation if the patient continues to have evidence of abnormal perfusion. Additional fluid resuscitation may be concurrently administered if the patient demonstrates physiologic improvement following each fluid bolus and without signs of fluid overload. All vasoactive agents, including norepinephrine, may be initiated through peripheral venous (or intraosseous, if in place) access if central venous access is not readily available to avoid delays in therapy  (229, 230). However, central venous access should be obtained as soon as reasonably practicable. In our practice, 82% of panel members reported at least sometimes administering the initial vasoactive infusion peripherally if central venous or intraosseous access was not readily available, particularly in the emergency department or other non-PICU settings.
Two pediatric RCTs tested the use of prone positioning in PARDS patients  (265, 289). Pooled analyses of these two studies yielded a RR of 0. 99 (95% CI 0. 36, 2. 69) for mortality in prone positioning as compared to supine positioning for this patient population (Supplemental Table  16 , Figure  6 ). Importantly, no serious adverse events were reported in these trials, although the prone positioning methodology was protocolized in each with particular attention to avoid accidental endotracheal extubation and pressure injury. PALICC  (24)  did not recommend routine use of prone positioning in PARDS patients but suggested its consideration in severe PARDS. The panel noted that the National Institutes of Health (NIH) has approved and funded an international RCT of prone positioning in severe PARDS (ClinicalTrials.
Despite these practical limitations, both PALICC  (24)  and PEMVECC  (263)  endorsed cautionary use of HFOV as an alternative type therapy in patients with severe PARDS. In our panel, clinicians who use versus those who do not use HFOV in patients with severe PARDS and refractory hypoxia were nearly evenly distributed. Application of HFOV in adult ARDS patients has yielded concerning results due to a potentially increased mortality observed in the adult OSCILLATE RCT  (301)  and a neutral result in the adult OSCAR RCT  (302). Pediatric data include 2 observational studies with a non-HFOV control group and 3 randomized trials. In the two observational studies, oxygenation improved with HFOV relative to conventional ventilation but there was a non-significant trend toward increased mortality  (Guo et   (303, 304).
Among three small RCTs, however, a trend toward reduced mortality in those managed with HFOV was observed (pooled RR 0. 77, 95% CI 0. 43, 1. 36)  (305) (306) (307). A large, multi-center, international RCT of HFOV compared to conventional mechanical ventilation in severe PARDS patients, including children with and without sepsis, is underway and will seek to address many of these issues (www. clinicaltrials. gov/ NCT02902055). Rationale: Indirect evidence from 3 adult RCTs  (308) (309) (310)  found that early use of neuromuscular blocking agents (NMBAs) for up to 48 hours in adults with severe ARDS, defined as PaO2/FiO2 ratio <150 mmHg, improved 90-day survival and shortened duration of mechanical ventilation without increasing muscle weakness. In a multi-center double-blind RCT (310), 340 patients with early severe ARDS, meeting criteria within 48 hours, were randomized to receive either cisatracurium besylate or placebo once adequately sedated.
We suggest using neuromuscular blockade in children with In pediatrics, there are no prospective data regarding the use of NMBAs in PARDS (with or without sepsis), although there is an ongoing pediatric trial in the Netherlands (Clinical Trials. Gov NCT02902055). In one large retrospective study of 317 children with PARDS, of whom 23% experienced sepsis-induced PARDS  (312) , mortality was lower in those children treated with neuromuscular blockade (8. 8% versus 17. 7%). However, duration of mechanical ventilation was longer in the treatment group and proportion with neuromuscular weakness was not assessed (Supplemental Table  18 ).
After finalizing the searches for each PICO question, panel members screened the titles and abstracts, reviewed full text of potentially relevant articles, and abstracted relevant data using a standardized form. Panel members, with input from methodologists, used the Cochrane risk of bias tool to assess the risk of bias of randomized trials  (25)  and Newcastle-Ottawa Scale to assess risk of bias of non-randomized studies  (26). When applicable, the methodologists used meta-analytic techniques to generate pooled estimates across two or more studies. For meta-analysis of randomized clinical trials (RCTs), we used random-effects model and inverse variance method to pool estimates across relevant studies. We reported relative risks (RR) and 95% confidence interval (CI) for binary outcomes, and mean difference (MD) and 95% CI for continuous outcomes.
In this analysis, only children with moderate hypotension were included because children with severe hypotension were not allocated to the control (no bolus) arm. Fluid bolus therapy in children with moderate hypotension was not beneficial or harmful compared to maintenance fluid only (RR of death = 1. 48, 95% CI 0. 61-3. 66, p=0. 41). Although children who were reclassified as meeting all three WHO shock criteria of cold extremities, prolonged capillary refill >3 seconds, and weak, fast pulse (14)(  14 ) had 48% mortality in the bolus groups versus 20% mortality in the control group, this difference was not statistically significant (p=0. 07). These cases were a very small proportion of the total FEAST trial participants (only 72 [2. 3%] had moderate hypotension and 65 [2%] met the full WHO shock criteria), and no data were provided about differential patient characteristics between these very small post hoc subgroups to assess for potential confounding.
gov NCT03080038). Until further data are available, we consider it reasonable to begin vasoactive infusions after 40-60 mL/kg of fluid resuscitation if the patient continues to have evidence of abnormal perfusion. Additional fluid resuscitation may be concurrently administered if the patient demonstrates physiologic improvement following each fluid bolus and without signs of fluid overload. All vasoactive agents, including norepinephrine, may be initiated through peripheral venous (or intraosseous, if in place) access if central venous access is not readily available to avoid delays in therapy  (229, 230)   (224, 225). However, central venous access should be obtained as soon as reasonably practicable. In our practice, 82% of panel members reported at least sometimes administering the initial vasoactive infusion peripherally if central venous or intraosseous access was not readily available, particularly in the emergency department or other non-PICU settings.
) First, Boriosi et al (282)(281) enrolled 21 children with lung injury, of whom 66% had sepsis, and used incremental PEEP recruitment maneuvers. Patients experienced improved oxygenation as measured by both the partial pressure of oxygen in arterial blood to FiO2 ratio (PaO2/FiO2 or P/F) and alveolarto-arterial oxygen (A-a O2) gradient for the 4 hours after recruitment. Second, Duff et al  (283)   (282)  enrolled 32 children and used the sustained inflation technique, which also resulted in improved oxygenation for the ensuing 6 hours. However, neither study tested the association of recruitment maneuvers with clinical outcomes, such as ventilator days or mortality. Consequently, despite the potential for benefit for some patients coupled with the possibility of harm  (284, 285)   (283, 284) , insufficient data do not allow us to recommend either for or against recruitment maneuvers in sepsis-induced PARDS patients at this time.
Despite these practical limitations, both PALICC  (24)  and PEMVECC  (263)   (262)  endorsed cautionary use of HFOV as an alternative type therapy in patients with severe PARDS. In our panel, clinicians who use versus those who do not use HFOV in patients with severe PARDS and refractory hypoxia were nearly evenly distributed. Application of HFOV in adult ARDS patients has yielded concerning results due to a potentially increased mortality observed in the adult OSCILLATE RCT (301)(299) and a neutral result in the adult OSCAR RCT  (302)   (300). Pediatric data include 2 observational studies with a non-HFOV control group and 3 randomized trials. In the two observational studies, oxygenation improved with HFOV relative to conventional ventilation but there was a non-significant trend toward increased mortality  (Guo et   (301, 302).
Among three small RCTs, however, a trend toward reduced mortality in those managed with HFOV was observed (pooled RR 0. 77, 95% CI 0. 43, 1. 36)(305-307)  (303) (304) (305). A large, multicenter, international RCT of HFOV compared to conventional mechanical ventilation in severe PARDS patients, including children with and without sepsis, is underway and will seek to address many of these issues (www. clinicaltrials. gov/ NCT02902055). Rationale: Indirect evidence from 3 adult RCTs  (308) (309) (310)   (306) (307) (308)  found that early use of neuromuscular blocking agents (NMBAs) for up to 48 hours in adults with severe ARDS, defined as PaO2/FiO2 ratio <150 mmHg, improved 90-day survival and shortened duration of mechanical ventilation without increasing muscle weakness. In a multi-center double-blind RCT (310)(308), 340 patients with early severe ARDS, meeting criteria within 48 hours, were randomized to receive either cisatracurium besylate or placebo once adequately sedated.
In this study, the intervention group received continuous cisatracurium and deep sedation for 48 hours compared to the control arm that received lighter sedation targets (Richmond Agitation Scale of 0 to -1). Both limbs received low tidal volume ventilation with high PEEP strategy. Notably, only 13. 8% of patients enrolled in ROSE had nonpulmonary sepsis as a primary diagnosis. In pediatrics, there are no prospective data regarding the use of NMBAs in PARDS (with or without sepsis), although there is an ongoing pediatric trial in the Netherlands (Clinical Trials. Gov NCT02902055). In one large retrospective study of 317 children with PARDS, of whom 23% experienced sepsis-induced PARDS (312)(310), mortality was lower in those children treated with neuromuscular blockade (8. 8% versus 17. 7%).
Virulence 2017;8:658-672 87. Dierig A, Berger C, Agyeman PKA, et al: Time-to-positivity of blood cultures in children with sepsis. Front Pediatr 2018;6:222 88. Lin GL, McGinley JP, Drysdale SB, et al: Epidemiology and immune pathogenesis of viral sepsis. Front Immunol 2018;9:2147 89. Paul M, Dickstein Y, Schlesinger A, et al: Beta-lactam versus beta-lactamaminoglycoside combination therapy in cancer patients with neutropenia. Cochrane Database Syst Rev 2013;(6):CD003038. doi:CD003038 90. Paul M, Lador A, Grozinsky-Glasberg S, et al: Beta lactam antibiotic monotherapy versus beta lactam-aminoglycoside antibiotic combination therapy for sepsis. Cochrane Database Syst Rev 2014;(1):CD003344. doi:CD003344 91. Sjovall F, Perner A, Hylander Moller M: Empirical mono-versus combination antibiotic therapy in adult intensive care patients with severe sepsis -A systematic review with meta-analysis and trial sequential analysis.
Chemotherapy 1989;35:296-303 157. Lassi ZS, Imdad A, Bhutta ZA: Short-course versus long-course intravenous therapy with the same antibiotic for severe community-acquired pneumonia in children aged two months to 59 months. Cochrane Database Syst Rev 2017;10:CD008032 158. Lin TY, Chrane DF, Nelson JD, et al: Seven days of ceftriaxone therapy is as effective as ten days' treatment for bacterial meningitis. JAMA 1985;253:3559-3563 159. Linder N, Lubin D, Hernandez A, et al: Duration of vancomycin treatment for coagulase-negative staphylococcus sepsis in very low birth weight infants. Br J Clin Pharmacol 2013;76:58-64 160. Martin E, Hohl P, Guggi T, et al: Short course single daily ceftriaxone monotherapy for acute bacterial meningitis in children: Results of a swiss multicenter study. part I: Clinical results.
Crit Care Med 2018;46:1803-1810 299. Gebistorf F, Karam O, Wetterslev J, et al: Inhaled nitric oxide for acute respiratory distress syndrome (ARDS) in children and adults. Cochrane Database Syst Rev 2016;66:CD002787 300. Macrae DJ, Field D, Mercier JC, et al: Inhaled nitric oxide therapy in neonates and children: Reaching a european consensus. Intensive Care Med 2004;30:372-380 301. Ferguson ND, Cook DJ, Guyatt GH, et al: High-frequency oscillation in early acute respiratory distress syndrome. N Engl J Med 2013;368:795-805 302. Young D, Lamb SE, Shah S, et al: High-frequency oscillation for acute respiratory distress syndrome. N Engl J Med 2013;368:806-813 303. Guo YX, Wang ZN, Li YT, et al: High-frequency oscillatory ventilation is an effective treatment for severe pediatric acute respiratory distress syndrome with refractory hypoxemia.