dataesr/scientific-paragraphs-categorization huggingface dataset:
Acknowledgements This work was funded by the  Junta de Andalucía ,  Consejería de Salud y Familias  (Project number  PI-0216-2019 ) and by the  Acción Estratégica en Salud Intramural  (Project number  PI20CIII/00005 ). MD  Fernandez-Garcia  received a Miguel Servet Research Contract ( CP18/00067 ) from the Strategic Action in Health 2018 and funded by  National Institute of Health Carlos III (ISCIII). ESL acknowledges funding from the  INCEPTION programme (Investissements d' Avenir  grant  ANR-16-CONV-0005 ).
The addition of extended antithrombotic treatment at discharge in patients with COVID-19 and previous coronary disease is not currently recommended. Data on the optimal duration and method of anticoagulation for COVID-19 patients postdischarge are currently not available. However, numerous randomized studies are ongoing (e. g. NCT04508439, NCT04372589). Our case emphasizes the high procoagulant state related to COVID-19 and thus raises the issue of an extended (post-discharge) antithrombotic treatment, which could reduce the risk of ischaemic events, at the cost of increase in bleeding events. Pending specific data on COVID-19, it is reasonable to employ individualized risk stratification for both thrombotic and haemorrhagic risks. Before OHCA, the patient was on single antiplatelet therapy since it was 2 years after his last PCI for de novo angina.
rhizogenes in the mixed biofilm, we found the biofilm to have a more thinner structure than the standard R. rhizogenes biofilm formed in the absence of R. erythropolis (Figure  2A ). Moreover, the roughness coefficient of the mixed biofilm, established using Comstat2 software, showed a significant positive change in comparison to the control biofilm, 0. 019 ± 0. 004 for dual species biofilm vs. 0. 006 ± 0. 001 for the rhizobial biofilm, indicating an increase in the biofilm heterogeneity (Figure  S3 ). This alteration of biofilm structure is also illustrated in detail with pixel density analysis in Figure  S4. Indeed, pixel mean values related to GFP fluorescence, representing rhizobial cell density, were lower for each stack of the dual species biofilm than those recorded for the single species biofilm (Figure  S4 ).
0 (Bruker Daltonics, Wissembourg, France) was used for QqTOF-MS operation, and DataAnalysis 4. 3 (Bruker Daltonics, Wissembourg, France) was used for data processing, all from Bruker Daltonics. Chromatographic retention time and m/z at high mass resolution were compared with those of synthetic AHL standards: 3-oxo-C 8 -HSL, 3 OH-C 8 -HSL, 3-OH-C 14:1 -HSL (BertinPharma, Montigny le Bretonneux, France), 3-oxo-C 14 -HSL, and 3-OH-C 14 -HSL (Sigma Aldrich, Saint Quentin Fallavier, France). The concentrations of each AHL were determined by comparison with standards at various concentrations ranging from 0. 05 to 10 mg. L -1.
Confocal Laser Scanning Microscopy (CLSM) Biofilm observations were performed with a Zeiss LSM710 confocal laser scanning microscope (Zeiss, Germany) equipped with a × 63 oil immersion objective. Bacteria were detected by monitoring GFP fluorescence or mCherry fluorescence with the following excitation and emission wavelengths: GFP (excitation at 488 nm and emission at 509 nm; green channel) and mCherry (excitation at 543 nm and emission at 610 nm; red channel). The fluorescence signals of double-labeled specimens were acquired simultaneously. Images were taken at 1 µm intervals throughout the entire depth of the biofilm. Threedimensional (3D) imaging data were visualized and processed with Zen 2. 1 software (Zeiss, Germany), using the same gain and offset parameters for all images. Quantitative analyses of image stacks were performed with ImageJ (https://imagej.
Top view, 3D shadow representation, and side view of the biofilm produced by R. rhizogenes alone (A1), and by a mixed culture of R. rhizogenes and R. erythropolis (A2) analyzed in the green channel. Location of rhodococcal cells was revealed by 3D shadow representation and side view of the biofilm produced by the mixed culture analyzed in the red plus green, green, or red channels (A3) (activation of the green or red channel is indicated by a light spot of the corresponding color). COMSTAT analyses of R. rhizogenes green fluorescence in single-and dualspecies biofilms. R. rhizogenes biofilm biomass and thickness values were normalized (set to 100%) as a reference for a comparison with mixed biofilm conditions (B). The data shown are the means of three measurements from three independent experiments.
Methanogens, the archaea uniquely detoxifying fermentative hydrogen into methane in the digestive tract, are increasingly detected in pathology situations, rendering their rapid identification mandatory. We improved the experimental protocol to identify broth-cultured methanogens by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF-MS). A database incorporating 34 reference spectra derived from 16 methanogen reference strains representative of eight species, supported further identification of 21 Methanobrevibacter smithii and 14 Methanobrevibacter oralis isolates broth-cultured from human stool and oral fluid, respectively, with scores > 2. In addition, MALDI-TOF-MS differentiated five Methanobrevibacter smithii genotypes incorporated in the study. Data here reported found MALDI-TOF-MS as a first line identification method for methanogens recovered from microbiota and clinical samples.
Further clinical isolates were made from mucosa-associated specimens as previously described  [13, 14]. In total, 35 clinical isolates included 21 stool isolates and 14 oral swab isolates, identified by PCR-sequencing targeting 16S rRNA Archaea and cultured in broth for nine days before being assessed by MALDI-TOF-MS against the MALDI-TOF reference database. Furthermore, we performed multispacer sequence typing (MST) of M. smithii 21 clinical isolates. The multispacer sequence typing technique and analysis was performed on each of the M. smithii clinical isolates according to the previously described protocol  [9, [17] [18] [19]. This part of the study was made in agreement with the positive advice of the IHU Méditerranée Infection Ethics Committee (n° 2016-020).
Methanogens MALDI-TOF-MS reference database. We used a protocol of the manufacturer MALDI Biotyper® (Bruker Daltonics, Wissembourg, France), adding two additional washing steps to remove the culture medium as well as extending the centrifugation time after the ethanol addition step. Briefly, one milliliter of archaeal suspension transferred into a sterile Eppendorf tube (Fisher Scientific, Illkirch, France) was centrifuged at 17,000 g for 30 minutes. The pellet was suspended into 500 μL of High Purity Liquid Chromatography water or HPLC water (VWR International, Strasbourg, France), vortexed, and centrifuged at 17,000 g for 10 minutes and this washing step was repeated twice. The pellet was suspended in 300 μL of HPLC water (VWR International), homogenized by pipetting, and 900 μL of ethanol absolute for HPLC Chromanorm (VWR International, Fontenay-sous-Bois, France) were added and homogenized by pipetting.
Blind MALDI-TOF identification and clustering of methanogen clinical isolates. MALDI Biotyper® version 4. 1. 80 software (Bruker Daltonics) was used to create reference spectra for blind identification and to create dendrograms. Spectral references (MSP) are created using Biotyper® MSP Creation Standard Method. Five raw spectra were used for creating an MSP for each species. We performed the experiments in triplicate and a total of 34 MSP were found to be of very good quality and therefore used as a reference database. We compared the 35 clinical isolates to this database.
Results and discussion We improved the MALDI-TOF-MS protocol for identifying cultured methanogens after a specific database was created, allowing for the rapid and routine identification of colonies issued from clinical specimens collected from mucosa-associated specimens and pathological specimens. The data here reported were validated by the negativity of the negative controls introduced in every one of the experimental steps and the reproducibility of data which were correlated with PCR-sequencing molecular identification used as the gold standard. The database was created after three independent runs, each incorporating 10 spots for each one of 16 methanogen reference strains. We obtained a total of 270 spectra and 135 spectra (50%) analyzed of good quality, were incorporated in the database.
We therefore set up a database with 34 reference spectra. We then blindly tested the identification of these 16 reference strains using the updated local database by analyzing five spots for each of them. We obtained a correct identification of these different spots with scores > 2 for each of the reference strains. We observed a unique protein profile for each one of methanogen reference strains studied (Fig. 1  and Fig. 2 ). There are 15 different MST genotypes of M. smithii among M. smithii strains known in humans according to a previous study  [17]. The multispacer sequence typing is used as the first-line method for genotyping M. smithii strains found in humans. It allows the differentiation of M. smithii strains isolated from humans  [17]. We observed a difference in the number and intensity of spectra between M.
smithii strains from different MST genotypes (Fig. 2B ). These observations proved the reproducibility and the inter-species specificity of the method. These data confirmed the ability of MALDI-TOF-MS to identify archaea cultured in broth, as previously reported in a proof-of-concept study using a difficult protein extraction protocol  [11]. We further tested our database against all the MALDI-TOF-MS databases available in our laboratory, incorporating 16,908 spectra representative of 12,290 different microbial species i. e. , 4,335 bacteria, 5,989 parasites and 1,966 fungi, and no identification was observed which proved the specificity of our spectra and an absence of contaminating spectra. Genotyping the 21 clinical isolates of M. smithii revealed five different genotypes. Genotype 1 was found in 10/21 (47.
76%); genotype 2 in 5/21 (23. 80%); genotype 3 in 3/21 (14. 28%); genotypes 5 in 2 /21 (9. 52%) and genotype 6 in 1/21 (4. 76%). These results confirm the predominance of the MST1 genotype in clinical isolates of M. smithii found in the human digestive tract  [9, 18]. We then used the reference database for the identification of clinical isolates of M. smithii and M. oralis obtained by broth culture of human stool and oral fluid, respectively. We obtained a correct identification of all the clinical isolates tested with scores >2 i. e. , 21/21 (100%) for M. smithii and 14/14 (100%) for M. oralis, respectively. We noticed that for a good identification by MALDI-TOF-MS of the M. smithii species, it is necessary to incorporate a larger set of reference spectra of M. smithii of different MST genotype in the reference database due to the diversity observed within this species  [9, 17, 18] , which results in different spectral profiles depending on each MST genotype as obtained in our study.
To confirm this hypothesis, we repeated the blinding test with only two reference strains of M. smithii with different MST genotype i. e. , M. smithii CSURP5816 of MST genotype 3, and M. smithii CSURP5922 of MST genotype 2. We observed that with these two reference strains, we obtained only 23% (5/21) of correct identification with scores> 2 and 19% (4/21) with scores> 1. 7. Our results demonstrate the need for rapid expansion of the MALDI-TOF-MS database to incorporate isolates of clinical interest. The results here confirmed the proof-of-concept study carried out in our laboratory in which MALDI-TOF-MS was able to perfectly identify the methanogens and environmental archaea  [11]. We further observed that MALDI-TOF-MS could differentiate between different genotypes of M. smithii, opening the possibility to use MALDI-TOF-MS as a first line typing method for this species of prime clinical interest.
We are implanting the experimental protocol and MALDI-TOF-MS methanogen database in the workflow of our clinical microbiology laboratory, for the routine, rapid identification of methanogens of clinical interest. The MALDI-TOF MS database created in this study are available on the website of the University-Hospital Institute (IHU) Méditerranée Infection on the link https://www. mediterraneeinfection. com/acces-ressources/base-de-donnees/urms-data-base/, for use by the scientific community.
Collection de Souches de l'Unité des Rickettsies (CSUR, Marseille, France) were used to create a MALDI-TOF-MS reference database. They included M. smithii CSURP5816 of MST genotype 3, M. smithii CSURP5922 of MST genotype 2, M. smithii CSURQ5493 of MST genotype 5, M. smithii CSURQ5497 of MST genotype 1, M. smithii CSURQ5501 of MST genotype 6, M. oralis CSURP5701, M. oralis CSURQ5479, M. oralis CSURQ5481, M. oralis CSURQ5483, M. oralis CSURQ5485, M. stadtmanae CSURP9634, M. arboriphilicus CSURP9635, M. luminyensis CSURP9636, Methanobacterium beijingense (M. beijingense) CSURP9638, M. mazei CSURP9637, and Methanosarcina barkeri (M. barkeri) CSURP9601. While M. arboriphilicus CSURP9635, M. beijingense CSURP9638, M. mazei CSURP9637, M. stadtmanae CSURP9634, and M. barkeri CSURP9601 have been primarily purchased from the German Collection of Microorganisms and Cell Cultures (DSMZ) (Braunschweig, Germany), M.
Search Process and Criteria For the purpose of this review, we considered only genes that are explicitly involved in cholesterol absorption, metabolism, and transport pathways (Figure  1 ). A systematic search was utilized, and gene-diet interaction studies relative to the genes of interest were retrieved, with no restriction on study design, dietary protocol, population, or quality throughout the preliminary search. Searches were performed on articles published between 1 January 2014 (as a follow-up to our previous review on the topic  [8] ) and 30 September 2020 using the MEDLINE (PubMed) database, and searching string variations of the following keywords: (diet OR gene-diet OR dietary) AND (cholesterol) AND (SNP OR polymorphism OR genetic variant). A total of 291 articles were identified and examined individually to exclude research articles that did not report statistically significant cholesterol responses to gene-diet interactions, did not present clear associations, or did not provide data details.
1 y, mean BMI = 26. 3 kg/m 2 )  [55]. GRS of increased TC (74 loci), LDL-C (58 loci), or triglyceride (TG) (39 loci), and decreased HDL-C (71 loci) concentrations were built based on SNPs previously identified following GWAS of circulating fasting lipid concentrations. Dietary habits were estimated following dietary questionnaires and were classified as unhealthy, moderately healthy, and healthy. There was no significant effect of GRS and dietary habit interaction on baseline fasting serum cholesterol concentrations. The effect of specific components of the diet was not investigated. In a secondary analysis of data from the Food4Me study, a multi-country European online randomized controlled intervention exploring the potential for personalized nutrition to enhance nutritional and health outcomes, the authors built a GRS based on 14 SNPs previously identified in GWAS of components of MetS and that showed a significant association with any component of MetS at baseline of the intervention  [56].
Of the individual SNPs reported in this review, six variants are listed by the Single Nucleotide Polymorphism Database (dbSNP) as missense variants (ABCA1 rs9282541 and rs2230806, ABCG5 rs6720173, ABCG8 rs6544718, APOE rs7412, and DHCR7 rs760241), thus describing changes in single nucleotides that result in different amino acid sequences, while others include intron, upstream transcript, synonymous, 5 prime UTR, or 3 prime UTR variants. Considering the type of genetic mutation may provide some mechanistic insight into the interpretation and discussion of findings in association studies, especially when detailed reports on the molecular mechanisms of action in the field are rarely available. Future research, including multi-site intervention trials, should take such clinical and mechanistic aspects into consideration and, furthermore, explore combinatory patterns of genetic variability in order to better understand the impact of gene-diet interactions on serum lipid profiles, and the potential cardiovascular impacts thereof.
Gas chromatography Coupled to Mass Spectrometry (GC-MS) The EO was qualitatively analysed by GC-MS, using an Agilent Technologies Chromatograph 6890N, coupled to an Agilent mass spectrometer, 5973 Inert series, which operated in electron impact mode at a 70 eV and was controlled by an MSD-ChemStation software. Two types of chromatographic columns were used for the analysis: a non-polar column DB-5ms (5% phenyl-methylpolysiloxane; 30 m × 0. 25 mm × 0. 25 μm) and a HP-INNOWax polar column (polyethylene glycol; 30 m × 0. 25 mm × 0. 25 μm); helium was used as the carrier gas in both analyses (at a constant flow of 1. 00 mL/min). The injection system operated in split mode (40:1) at 220 °C. The GC oven temperature was programmed at 60 °C (5 min), then it was increased to 250 °C (10 min) at a rate of 3 °C/min.
Physical Properties The relative density of the EO was determined according to the international standard AFNOR NF T75-111 (ISO 279:1998) guidelines. The refractive index was determined in an ABBE refractometer, according to the international standard AFNOR NF 75-112 (ISO 280:1998) procedure. Each analysis was performed in triplicate. The EO was qualitatively analysed by GC-MS, using an Agilent Technologies Chromatograph 6890N, coupled to an Agilent mass spectrometer, 5973 Inert series, which operated in electron impact mode at a 70 eV and was controlled by an MSD-ChemStation software. Two types of chromatographic columns were used for the analysis: a non-polar column DB-5ms (5% phenyl-methylpolysiloxane; 30 m × 0. 25 mm × 0. 25 µm) and a HP-INNOWax polar column (polyethylene glycol; 30 m × 0.
25 mm × 0. 25 µm); helium was used as the carrier gas in both analyses (at a constant flow of 1. 00 mL/min). The injection system operated in split mode (40:1) at 220 • C. The GC oven temperature was programmed at 60 • C (5 min), then it was increased to 250 • C (10 min) at a rate of 3 • C/min. We injected 1 µL of a solution of the EO in CH 2 Cl 2 (1:100 v/v) in each analysis. The volatile components of the EO were identified by comparing the linear retention indices (LRI) and the mass spectra with the data reported in the literature. Each LRI was calculated according to Van Den Dool and  [27] , from a homologous series of n-alcanes C 9 -C 25 (C 9 , BHD purity 99% and C 10 -C 25 , Fluka purity 99%), which were injected on each of the two columns after the EO, under identical conditions  [17].
This finding strengthens the view that the polyspecificity in multidrug efflux pumps lies in an extended capacity for ligand-binding brought about by few residues arrayed at the periphery of a core-binding space. The substrate-binding pocket of CaCdr1 is reminiscent of human ABCG2, which shares the same reverse topology of the G-subfamily proteins and whose 3D structure has been determined with various ligands  [75] [76] [77]. The substrate binds in a slit-like pocket at the crevice between the TMDs within strongly overlapping pockets, but with additional contacts depending on the nature of the substrate (Figure  2 ). [69]. Right panel: cryo-electron microscopy structures of human ABCG2 in complex with substrates and inhibitors, PDB codes: 6FEQ  [75] , 6FFC  [75] , 6HCO  [76] , 6VXI  [77] , 6VXJ  [77] , 6VXH  [77].
RP received funding from the Department of Biotechnology, Government of India, grant no: BT/PR14117/BRB/10/1420/2015. AB received funding support from the Science and Engineering Research Board, Department of Science and Technology, Government of India, grant no: SRG/2019/000514. PF received funding from the Centre National de la Recherche Scientifique (CNRS), Lyon University and the French Research Agency (ANR-CLAMP2-18-CE11-0002-01). BCM received funding from the Health Research Council of New Zealand (HRC of NZ 19/397). JP's PhD is funded by EDISS school. SS received support in the form of a Senior Research Fellowship (SRF) award from the Indian Council of Medical Research, Government of India. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
Funding: RP received funding from the Department of Biotechnology, Government of India, grant no: BT/PR14117/BRB/10/1420/2015. AB received funding support from the Science and Engineering Research Board, Department of Science and Technology, Government of India, grant no: SRG/2019/000514. PF received funding from the Centre National de la Recherche Scientifique (CNRS), Lyon University and the French Research Agency (ANR-CLAMP2-18-CE11-0002-01). BCM received funding from the Health Research Council of New Zealand (HRC of NZ 19/397). JP's PhD is funded by EDISS school. SS received support in the form of a Senior Research Fellowship (SRF) award from the Indian Council of Medical Research, Government of India. Institutional Review Board Statement: Not applicable. Informed Consent Statement: Not applicable.
Acknowledgments We thank  R. J. Bridges  and  Cystic Fibrosis Foundation Therapeutics  for compounds  P5  and  C18 ,  M. L. Fulcher  and  S. H. Randell  for primary cultures of airway epithelial cells,  N. Pedemonte  and  L. J. V. Galietta  for FRT cells heterologously expressing CFTR and our laboratory colleagues for valuable discussions and assistance.
Aim: This review identifies interventions involving the fathers of preterm infants that have been tested in neonatal intensive care units (NICU). It examines their effects on the fathers and infants and highlights any differences between fathers and mothers who took part in the same interventions. Methods: A systematic search was performed in English from 1995 to 1 September 2020, using the CINAHL, Cochrane Central Register of Controlled Trials, Embase, PubMed and PsycINFO databases. We examined 14 peer-reviewed studies that investigated NICU interventions involving 478 fathers, whose 511 infants were born before 37 weeks of gestation. These included empirical studies with clinical outcomes. Results: Studies on fathers' interventions in NICUs were limited and mainly restricted to basic skin-to-skin contact or tactile interventions.
| Study selection Studies were included if the infants were born preterm, before 37 weeks of gestational age, and the interventions were delivered by fathers during hospitalisation. Studies that did not report outcomes on infants or on fathers were not included. If studies had resulted in multiple papers, the data from the most complete report were used. Discussion papers, qualitative papers, theses, dissertations and reviews were excluded. The searches identified 1604 papers and the titles and abstracts were used to check whether they fell within the remit of this review. Then, the full texts of 36 studies were evaluated by two reviewers (MF, SS) to determine whether they fitted the inclusion criteria. A third reviewer (PK) was involved if their views differed. The studies were excluded if the intervention was not delivered by fathers or there was insufficient information (Figure  1 ).