dataesr/scientific-paragraphs-categorization huggingface dataset:
Aligned reads were then sorted into one of three BAM files: C57BL6 (genome 1), CAST/EiJ (genome 2), or unassigned. The females carrying conditional Dnmt3a/Dnmt3b double knockout (matDKO) were predominantly C57BL6; however, there was approximately 15% of 129 alleles remaining in the strain. Therefore, these data were run through a unique pipeline to allow for a complete mapping of the maternal allele. All datasets generated from matDKO/CAST embryos were first aligned to a B6/CAST N-masked genome, as above, but with the difference that all SNPs which were in common between 129 and CAST (~2 million) had been excluded. The data was then split against C57BL6 and CAST/EiJ, as above. FastQ reads of the unassigned fraction of reads were then recovered from the original FastQ files, and in the second step, these reads were then aligned to a 129S1/CAST genome (generated with SNPsplit_genome_preparation).
Compensation matrices were established using VersaComp Antibody Capture Beads (Beckman Coulter) while Flow-Count Fluorospheres (Beckman Coulter, lot concentration 1,006/µl) were added to each assay to determine MVs concentration (MV/µl of CSF) according to manufacturer's instructions. Unlabeled CSF and CSF labeled using isotype control antibodies (Table  S2 ) were also analyzed to account for CSF potential auto-fluorescence and antibody unspecific binding, respectively. Data were analyzed with Kaluza Analysis software v2. 1 (Beckman Coulter). Statistical analyses were performed with STATA v14. 0 (StataCorp LLC). Kruskal-Wallis test, followed by Bonferroni correction, was used to compare MV concentration among the three HAT groups with significance set at 5%. Univariate linear regression was used to assess the association between MV concentration and demographic or clinical parameters.
Protein Digestion and Data Independent Acquisition Mass Spectrometry (DIA-MS) Analyses Astrocyte proteins were extracted with 0. 1% RapiGest SF (Waters) in 0. 1 M triethylammonium bicarbonate buffer (TEAB), pH 8. 0. Samples were sonicated, incubated for 10 min at 80 • C, spun (14,000 g, 10 min) and finally the supernatant was recovered. The protein concentration was then determined using the Bradford protein assay. For each sample, 9 µg of proteins were reduced with 5 mM Tris (2-carboxyethyl)phosphine hydrochloride (TCEP), alkylated with 15 mM iodoacetamide and digested with sequencing grade-modified trypsin (Promega, 1:50 protease to protein ratio). The peptide mixture was then desalted with C18 spin columns (Harvard apparatus), dried under vacuum, re-suspended in 5% acetonitrile, 0. 1% formic acid (peptide final concentration of 0.
5 µg/µL), and spiked with iRT peptides (Biognosys) 1:20. The equivalent of 2 µg of peptides were analyzed using Liquid Chromatography-Electrospray Ionization-MS/MS (LC-ESI-MS/MS) on an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Fisher Scientific) equipped with a Thermo EASY-nLC following a published protocol  (Dozio and Sanchez, 2018). Briefly, for generating the spectral library full lysates from all samples together with 12 OFFgel fractionated samples were first acquired in data dependent acquisition mode (DDA) and analyzed with Proteome Discoverer 2. 0 (Thermo Scientific) and the Mascot search engine. The search parameters included 10 ppm precursor mass tolerance, 0. 02 Da fragment mass tolerance and two miscleavages. Static modifications included carbamidomethylation (+57.
021 Da) on cysteines, whereas dynamic modifications included oxidation (+15. 995 Da) on methionines. Peptide spectrum matches (PSMs) were verified using the Percolator module (FDR < 0. 01). Proteome Discoverer results were then imported in Spectronaut (Biognosys) and used to generate a spectral library as previously reported  (Dozio and Sanchez, 2018). The 16 samples corresponding to the different study conditions (Figure  2A ) plus a pool of them injected three times over the whole MS analysis to assess the technical variability, were then acquired in DIA mode  (Dozio and Sanchez, 2018)  and the raw DIA MS data matched against the spectral library using Spectronaut. Peptide intensities were finally exported and analyzed using mapDIA  (Teo et al. , 2015). For each condition, a protein fold change (FC) was computed with respect to untreated control cells; proteins with FDR < 0.
05 and absolute |FC| > 1. 2 were considered significantly differentially abundant  (Dozio and Sanchez, 2018). The list of astrocyte proteins differential in at least one study condition was then analyzed with MetaCore TM (Clarivate Analytics) to highlight significantly represented process networks, i. e. , molecular and cellular processes representing pre-defined network of protein interactions characteristic of each process  (Bessarabova et al. , 2012). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE  (Perez-Riverol et al. , 2019)  partner repository with the dataset identifier PXD014945.
ACKNOWLEDGMENTS The authors wish to thank  Dr. Jean-Pierre Aubry-Lachainaye  and  Cécile Gameiro  from the  Flow Cytometry Facility (University of Geneva ) for technical support with flow cytometry analyses; and  Dr. Christoph Bauer  ( BioImaging Center, University of Geneva ) for support with transmission electron microscopy. The authors also thank the  Proteomics Core Facility  of the  University of Geneva, Faculty of Medicine , for assistance with mass spectrometry analyses.
The distance D between the surfaces is measured by white light interferometry [fringes of equal chromatic order (FECO)] with an accuracy of ±1 Å. 43  Back-silvered mica surfaces were rendered hydrophobic by covalently depositing FDTS (see the Supporting Information for details). We brought FDTS-coated mica surfaces into contact in dry nitrogen, which defines the reference zero distance (D = 0). Several consecutive measurements were recorded in Milli-Q H 2 O (resistivity of 18 MΩ/cm, pH 5. 6), followed by D 2 O or vice versa, and the cycle was repeated. H 2 O and D 2 O contained 5 mM potassium chloride (Fisher Scientific, 99. 8%) and were degassed by being stirred with Teflon-coated magnetic bars for 2 h before being injected into the SFA chamber. FECO images were recorded for each force run using the Andor Solis software.
| Statistical analyses All analyses were performed using R software (version 3. 2. 0, R Core Team 2016, https:// www. r-proje ct. org/). Secondary sex ratio was calculated for each litter as the ratio between the number of males and number of females and analyzed with logistic regressions including a logit link and binomial error term [package lme4] and z tests were performed [package lmerTest]. We tested the relationships between secondary sex ratio and water deprivation treatment, female body size and reproductive timing. Reproductive timing was retro-calculated as the day differential between parturition date and the last day of exposure to water restriction, to estimate the embryonic developmental stage when females were exposed to water restriction. For analyses in the Common lizard, we used mixed-effect models to include the random effects of female identity given that some females had repeated contributions between years.
We therefore tested the robustness of each term selected in the final model using a parametric bootstrap analysis [package pbkrtest]. In this analysis, we compared the likelihood ratio test (LRT) of the final model (i. e. , large model) to model without the selected term (i. e. , simple model). For each term, we generated 1,000 samples of the simple model LRT that were either larger (p < 0. 05) or equal (p > 0. 05) than the LRT of the large model. Results are presented as the mean ± SE. In figures, secondary sex ratio was represented as proportion of males in the litter.
To test this hypothesis, we examined data from offspring unambiguously sexed from their reproductive organs once yearling. Our sexing technique caused some errors (8% error rate). However, error rates were similar between hydric treatments (n = 919, χ 2 1 = 2. 86, p = 0. 091) and the discriminant function between number of ventral scales and sex did not differ between hydric treatments (all p > 0. 226). This demonstrates that the biased sex ratio at birth was most likely not caused by a methodological bias. In lizards, the last alternative hypothesis implies a statistical artifact caused by the use of mixed logistic models and unequal litter size among females  (Bolker et al. , 2009). We therefore used a parametric bootstrap method for comparing the observed influence of hydric treatment and reproductive timing to predictions of 1,000 iterations of models under the null hypothesis of a random, balanced sex ratio.
We calculated the reproductive timing as the differences (days) between parturition date and the exposure to water restriction in order to estimate the embryonic developmental stage when pregnant females were exposed to water restriction (0 = parturition date). In both a) V. aspis and b) Z. vivipara, the male proportion increases when exposure to water restriction occurred earlier in gestation. The predictions of the final model were fitted on the data (solid line) together with the 95% confidence interval (dashed lines) of both control (gray lines) and water restricted females (orange lines) responses. In vipers, early growth was similar between sexes (t 1,119 = -0. 9, p = 0. 379, Table  3 ) and increased in juveniles from waterdeprived females (t 1,119 = 2. 8, p = 0. 009, Table  3 ) irrespective of juvenile sex (interaction term, t 1,118 = -1.
Funding information Agence Nationale de la Recherche , Grant/Award Number:  AQUATHERM  ( ANR-17-CE02-0013 ) and  DESTRESS  ( ANR-13-JSV7-0011-01 );  Centre National de la Recherche Scientifique ;  Conseil Régional Nouvelle Aquitaine & Conseil Départemental des Deux Sèvres , Grant/ Award Number: BOCAGE ( 10-RPC-R-056 );  Interreg Poctefa , Grant/Award Number: ECTOPYR ( EFA031/15 );  Conseil Régional Ile de France , Grant/Award Number:  DIM Program   R2DS (I-05-098/R );  Ministry of Environment ;  Agence Nationale de la Recherche , Grant/Award Number:  EFA031  and  15.
Indirect calorimetry Mice were placed in an open-circuit indirect calorimeter system 24 h prior to the start of the experiment with free access to water and food (TSE Systems GmbH, Bad Homburg, Germany). Flow rates were measured and controlled with a mass flow controller. O 2 and CO 2 concentrations of dried inlet and outlet air from each chamber were measured every 10 min. Infrared light-beam frames surrounding the home cage measured activity in the x and y direction. Data were analyzed using LabMaster software (TSE Systems GmbH). Energy expenditure was calculated using the following equation: EE (kcal/h) = [3. 941 × VO 2 (ml/h) + 1. 106 × VCO 2 (ml/h)]/1,000.
A list of significantly changed annotated genes, including FDR-corrected P-values (5%) was generated. All microarray data reported are described in accordance with MIAME guidelines and are available in the GEO database (GSE37248). Identification of overrepresented functional categories among responsive genes and their grouping into functionally related clusters was performed using DAVID 6. 7 functional annotation clustering tool  (37)  and Gene Set Enrichment Analysis (GSEA)  (38). Transcription factor analysis was performed with Metacore, Clarivate Analytics.
Digestion was carried out overnight at 37°C. After digestion, the peptides were extracted from the gel by drying the gel pieces by speed-vac, rehydrating with 0. 1% trifluoroacetic acid, and dehydrating with 0. 1% trifluoroacetic acid in 100% ACN. The extracted peptides were dried by speed-vac and redissolved in a MS-compatible solvent (0. 1% formic acid). Separation of the resulting tryptic peptide mixtures was performed by nanoscale reversed-phase LC-MS/ MS. Protein identification and data analyses were performed as described  (32). Minor adjustments made to this protocol were: 1) Selected mass range of m/z 300-1,100 in Analyst QS 1. 1 software (Applied Biosystems, Carlsbad, CA). 2) Selected three abundant charged peptides were dynamically excluded for 90 s with 50 mmu mass tolerance. 3) ProteinPilot 3.
1E , supplemental Fig. S1C ). Growth curves showed that the body weight difference was  already apparent from weaning onwards (supplemental Fig. S1D ). Surprisingly, the reduced weight of aP2-hFXR mice compared with controls was not only due to a reduction in fat mass; reduced lean body mass accounted for most of the difference (Fig. 1F ). WAT depot weights of chow-fed aP2-hFXR mice were comparable to those in wild-type controls (Fig. 1G ), particularly when normalized to body weight (data not shown). Histological examination of adipose tissues, however, revealed that adipocytes from chowfed aP2-hFXR animals were markedly hypertrophic (Fig. 1H  for eWAT, supplemental Fig. S1E  for rWAT and iWAT). To determine whether adipose tissue appearance is already affected early in development, WAT depots of very young aP2-hFXR mice were examined.
HODEs and HETEs were quantified using a 1290-LC 6490-QqQ system (Agilent Technologies, Les Ulis, France). Briefly, after evaporating the organic phase under a vacuum, lipids were solubilized with 100 µL of a 70/30 v/v methanol/water mixture and 4 µL were injected onto a Zorbax Eclipse Plus C18 column (2. 1 × 100 mm, 1. 8 µm column, Agilent Technologies, Les Ulis, France). Separation was achieved at a flow rate of 0. 3 mL/min at 30 °C using the following linear gradient of 5 mM ammonium acetate (solvent A) and acetonitrile/methanol (95/5, v/v) (solvent B): 23% B for 6. 5 min, up to 50% B in 8. 5 min, up to 52% B in 3 min and maintained at 52% for 5 min. Data were acquired in negative multiple reaction monitoring (MRM) mode (source temperature: 200 °C, nebulizer gas flow rate: 15 L/min, sheath gas flow rate: 11 L/min, temperature: 250 °C, capillary: 3500 V, collision energy: 18 V and 10 V for HODEs and HETEs respectively).
Two microliters of each sample were injected. A 13-min elution gradient was established as follows: from 0 to 0. 5 min, 55% of A (water, ammonium formate 5 mM, formic acid 0. 1%) and 45% of B (acetonitrile/water (95/5, v/v), ammonium formate 5 mM, formic acid 0. 1%); from 3 to 8 min, 100% of B; and from 8. 10 to 13 min, 55% of A and 45% of B. The flow rate was maintained at 0. 4 mL/min throughout the gradient elution process. The mass spectrometer was set in MRM mode. A calibration curve was constructed with increasing concentrations of the external standard 3-OH C14:0. 3-OH C14:0 levels in samples were quantified by calculating the 3-OH C14:0/3-OH C13:0 ratio by using the calibration curve. Chromatograms were analysed with the Agilent MassHunter Workstation software, and calibration curves were created using authentic standards extracted with the same method used for samples.
RNA-seq data were analysed for differentially expressed genes and transcripts using the TopHat and Cufflinks informatics procedures  67. An unsupervised hierarchical clustering analysis was performed using Gene Cluster 3. 0 software and viewed with the Treeview viewer. Values were normalized and centred on the mean. Hierarchical clustering was performed with Euclidean distance measure and complete linkage analyses. Upregulated genes are shown in red and downregulated genes are shown in green. Genes that were significantly upregulated by at least 2-fold (FDR < 0. 05) in mice fed the HF/HS diet compared to mice fed the standard chow and significantly downregulated by the PRPE formulation were further used for gene ontology and enrichment analyses using the Database for Annotation, Visualization, and Integrated Discovery (DAVID v.
Acknowledgements The authors are grateful for the staff who cared for animals at the animal facility of the  University of Bourgogne. The authors thank CellImap and  Small Animal platforms  for providing expert technical assistance,  Philippe Durand  for assessing the blood antioxidant defence capacity with the KRL ™ biological test,  Frederic Prost  for analysing the size distributions of plasma lipoprotein subfractions using Spiragel ™ , and  Christos Tsaconas  for analysing plasma MDA levels. The authors also thank the American Journal Experts for English language editing. This study is part of VITALIM' SENIORS and SYMPPA (SYndrome Métaboliques PolyPhénols Actifs ), two Integrated Projects funded by the  European Union (FEDER) , the  French Government, Regional Council (Bourgogne-Franche-Comté), General Departmental Council (Yonne, Côte d'Or) ,  Grand Dijon  and  Vitagora.
This work was supported by grants from the  University of Bourgogne Franche-Comté , the  Institut National de la Santé et de la Recherche Médicale (INSERM) , and by a  French government  grant managed by the  French National Research Agency  under the  programme 'Investissements d' Avenir'  with reference  ANR-11-LABX-0021  ( Lipstic Labex ). We would like to thank  SENAGRAL -Eurial Ultra Frais  for providing additional funding and the partnership with the VITALIM'SENIORS and SYMPPA projects.
Code Availability The RNA-seq data have been deposited in the NCBI Gene Expression Omnibus (GEO) (http://ncbi. nlm. nih. gov/geo) with accession number GSE120748. Visit https://www. ncbi. nlm. nih. gov/geo/query/acc. cgi?acc = GSE120748 and enter token gbidqeiaxjurvat into the box to review GEO accession number GSE120748.
Introduction: Enterococcus species are associated with an increased morbidity in intraabdominal infections (IAI). However, their impact on mortality remains uncertain. Moreover, the influence on outcome of the appropriate or inappropriate status of initial antimicrobial therapy (IAT) is subjected to debate, except in septic shock. The aim of our study was to evaluate whether an IAT that did not cover Enterococcus spp. was associated with 30-day mortality in ICU patients presenting with IAI growing with Enterococcus spp. Material and methods: Retrospective analysis of French database OutcomeRea from 1997 to 2016. We included all patients with IAI with a peritoneal sample growing with Enterococcus. Primary endpoint was 30-day mortality. Results: Of the 1017 patients with IAI, 76 (8%) patients were included.
Material and methods This study was a retrospective data analysis from the OUTCOMEREA database (OutcomeRea®). Data were prospectively collected daily by senior physicians with research assistants in the participating ICUs. All codes and definitions were established prior to study initiation and have been previously described  [22]. We collected delay between hospitalization, diagnosis, and surgery. Patients' age, sex, and McCabe score were recorded. Severity of illness was evaluated on the first ICU day using the Simplified Acute Physiology Score (SAPS II), Sequential Organ Failure Assessment (SOFA) score, and Glasgow Coma Scale (GCS) score. Knaus' scale definitions were used to record preexisting chronic organ failures including respiratory, cardiac, hepatic, renal, and immune system failures  [23, 24].
Admission category (medical, scheduled surgery, or unscheduled surgery), admission diagnosis (cardiac, respiratory, or neurological failure, infection, and other), invasive procedures (arterial or venous central catheter, Swan-Ganz catheter, or endotracheal intubation), and treatment of organ failures (inotropic support, hemodialysis, and mechanical ventilation) and ICU-acquired infections, bacteriological samples, and daily antimicrobial therapy were also collected. Data collected from hospitalization records were as follows: risk factors for healthcare-associated infections, antimicrobial therapy within the 3 months prior to ICU admission (particularly with cephalosporins), date of diagnosis of IAI according to clinical, biological and radiological findings, anatomical origin of IAI, localized or generalized type of IAI, community-acquired or nosocomial infection, and pathophysiological mechanisms.
Ethical issue The database is in accordance with French legislation concerning biomedical research. Patients or their family gave authorization for collection, conservation, and use of their personal anonymized data. Authorizations were obtained from the CNIL (Commission Nationale de l'Informatique et des Libertés), the CCTIRS (Comité consultatif sur le traitement de l'information en matière de recherche), and the Rhône-Alpes-Auvergne Institutional Review Board.
Definition Enterococcus IAI was defined as an IAI which required surgery or percutaneous drainage and whose intraoperative peritoneal sample was growing with Enterococcus. Day 0 (first day of the IAI) was defined as the day of surgery. Intra-abdominal infections were nosocomial if they appeared after more than 48 h of hospitalization or if there were any risk factor of healthcare-associated infection (hospitalization within 3 previous months, rehabilitation/long-care stay within the 30 previous days, chronic dialysis or chemotherapy within 30 days, or home-care within 30 days). Enterococcus IAI were identified from the infectious data recorded in the database. Medical records were then accessed to confirm diagnosis and details of the surgical procedure. Initial antimicrobial therapy (IAT) was the antimicrobial therapy started on day 0 or day 1 after surgery.
Antimicrobial therapy was considered appropriate or inappropriate according to the antibiogram when available. Otherwise, it was considered appropriate if it used either a penicillin (A or ureido or carboxy) or a carbapenem for Enterococcus faecalis, E. avium, or E. durans, and vancomycin, linezolide, or tigecycline for Enterococcus faecium. Delay between IAI (day 0) and appropriate antimicrobial therapy were extracted from the database separately for Enterococcus spp. and other germs including yeasts. Septic shock was defined according to the Surviving Sepsis Campaign 4th edition (2016)  [25]. For septic shock at diagnosis, we considered septic shock criteria within a 72-h period including the day preceding and the day following IAI diagnosis. Pneumoniae, other bacteremia (other than from intraabdominal origin), and catheter-related bloodstream infections were considered at diagnosis of IAI if they were diagnosed within 48 h preceding the IAI diagnosis.
Statistical analysis Patient characteristics were expressed in numbers (percentages) and median (interquartile interval) for qualitative and quantitative variables, respectively. They were compared using chi-squared and Mann-Whitney tests respectively. The impact on day 30 mortality of Enterococcus species and inappropriate IAT on Enterococcus species were assessed with univariate Cox models. Then, multivariate Cox models adjusted on SAPS score on day 0, acquisition of peritonitis in ICU, and adequacy of IAT on other germs were used. For every analysis, p < 0. 05 was considered significant. All statistics were done using SAS software (v 9. 3, SAS Institute, Cary, NC, USA).
Results Between 1997 and 2016, data of 1017 patients with IAI were analyzed. Only 76 IAI with Enterococcus were included (Additional file 1). Incidence of Enterococcus differed between centers (Additional file 2). Median  [IQR]  age was 72 [59-78]. Fifty-seven percent of patients were male. Median SAPS II score at day 0 was 52. Median time between admission in the hospital or in the ICU and diagnosis of IAI was 8  [5] [6] [7] [8] [9] [10]  and 1  [1] [2] [3] [4]  days, respectively. Eight (10. 5%) patients had a community-acquired IAI. Sixty-eight (89. 5%) patients had a nosocomial IAI, among them 2 were healthcare-associated IAI and 66 were hospital-acquired IAI. Two patients had a percutaneous drainage as an initial treatment, and 7 had a percutaneous drainage secondarily after an initial surgical treatment.