dataesr/scientific-paragraphs-categorization huggingface dataset:
Hence for each metabolite, the modelling process generated distributions for σ, v, μ 0 , σ 0 , μ 1 and σ 1 and -for each subjectdistributions for β 1 and β 0. Our primary interest was in the distributions of μ 1. Non-informative priors were used for all parameters. Remembering that all data were z-transformed prior to analysis, all σ were given a broad prior uniform distribution (with parameters L = 10 -3 and H = 10 3 denoting the low and high limits), and ν a broad exponential distribution with a minimum of 1 and mean of 30 (at which point the distribution is approximately normal). For each normal distribution, μ was given a normal prior with parameters M = 0 and S = 10. Both the individual and group regression were assessed simultaneously and the individual regression lines constrained by the average regression lines.
Bayesian analysis was conducted using R and JAGS (Just Another Gibbs Sampler 51 as described in Kruschke  50  ). All code is available in supplementary materials. Identified metabolites were presented with corresponding identification codes from the human metabolome database (HMDB). In the case of certain lipids where HMDB identification was not available, chemical entities of biological interest (ChEBI) were included. Calculation of Absolute Changes. For the aqueous phase metabolites, the binned 1 H-NMR spectral regions corresponding to an identified metabolite were assessed. The change in spectral intensity between LDN and EBC was calculated and from this the median % change derived. Given that this was a measure of spectral intensity, no absolute value such as concentration/ml plasma could be given for the change, instead arbitrary units were employed.
Statistical analysis. Analysis was performed in GraphPad Prism 7. The LDN and EBC values for SpO 2 and body weight data were abnormally distributed, as assessed using the D' Agostino-Pearson normality test. Therefore, a Wilcoxon matched-pairs signed rank test was employed for analysis. The Δ abundance of metabolites/lipids from LDN to EBC that were identified as undergoing large changes with ascent were plotted against the Δ SpO 2 or body weight from LDN to EBC. For the aqueous fraction metabolites, this specifically refers to the Δ of spectral region intensity undergoing the greatest change, and for lipids, the definitively identified lipid variables. Data that followed a Gaussian distribution were tested using a Pearson Correlation Coefficient. A non-parametric Spearman rank correlation (two tailed) was applied for non-normally distributed data.
Study limitations. In comparison to previous studies examining metabolic acclimatisation of human subjects to high altitude hypoxia both in the field and laboratory, this study is unique in its scale and design. To enable success, it required the adoption of a pragmatic approach, the nature of which precluded the addition of a control group. Whilst the insult of hypobaric hypoxia was undoubtedly severe at the altitude reached, it must be noted that the effects reported may have been influenced by other environmental factors, such as a change in temperature and UV exposure. Other factors that are known to impact metabolic function that may have affected the metabolomic/lipidomic profiles are potential alterations to exercise and diet. Daily activity data was not recorded, however all subjects underwent identical ascent profiles for which the exercise burden each day was low in both intensity and duration, as demonstrated by trekking distance/day detailed in the methods.
Acknowledgements CXE is a research project coordinated by the  Centre for Altitude, Space  and  Extreme Environment Medicine, University College London, UK. The CXE Research Groups members all contributed to the collection of the data described in this study. Membership, roles and responsibilities of the CXE Research Group can be found at http://www. caudwell-xtreme-everest. co. uk/team. The CXE expedition was funded from a variety of sources, none of which are public. The entrepreneur  John Caudwell , whose name the expedition carries, donated  £500 , 000  specifically to support the research. BOC Medical, now part of the Linde Group, generously supported the research early on and continues to do so. Ely-Lilly Critical Care, The London Clinic (a private hospital),  Smiths Medical ,  Deltex Medical  and  Rolex also donated money  to support the research and logistics.
All monies were given as unrestricted grants. Specific research grants were awarded by the  Association of Anaesthetists of Great Britain and Ireland , and the  UK Intensive Care Foundation. The CXE trekkers themselves also kindly donated to support the research. H. E. M. and M. G. M. are supported by the  National Institute for Health Research (NIHR) University College London Hospitals Biomedical Research Centre, London, UK. M. P. W. G. , D. Z. H. L. and K. M. are supported by the  National Institute of Health Research (NIHR) University Hospital Southampton Biomedical Research Centre, Southampton, UK. A. J. M. received an  Academic Fellowship  from the  Research Councils UK  ( EP/E500552/1 ). Work in the JLG lab is funded by the  Medical Research Council  ( Lipid Profiling  and Signalling;  MC_UP_A090_1006 ).
Camera calibration protocol The cameras were calibrated before each trial and the MOCAP camera calibration protocol was adopted for both systems (Table  2 ). For the setup #1 (reference), this protocol required first the acquisition of wand, carrying five markers, which was moved within the working volume and second the acquisition of a calibration frame, located on the floor, according to the method described in  [1]. For the MOCAP, the video acquisitions were automatically processed by proprietary software. For ASC, the captured videos of the same acquisitions were converted to AVI movie format and processed by a custom software environment developed in Matlab 1 2015a (Mathworks, Natick MS) to semi-automatically detect and extract markers from the images processing  [14, 1]. For setup #2 (steady structure), the ASC camera calibration was performed the same way as in the setup #1.
Statistical analysis In order to analyze the overall accuracy of the 3D reconstruction we used the MAE values (D1, D2 and the angle between the markers on the frame). All statistical analysis were performed in Matlab 1 2015a (Mathworks, Natick, MA) assuming statistical significance of p<0. 05. The test to evaluate the data distribution (Lilliefors test) was applied to the absolute errors of the intermarker distance value and of the angle shaped between the three markers of each experimental condition and revealed a non-normal distribution. Thus, the system performance was evaluated in each setup (#1, #2 and #3) applying the non-parametric tests (Wilcoxon rank sum) to compare the ASC and the MOCAP. To analyze the differences between the setups in each systems (ASC and MOCAP, separately), we applied the non-parametric test (Kruskal Wallis, post-hoc Tukey).
To evaluate the human kinematic data computed with the setup #3, we first compared the knee flexion-extension angle curves, obtained by both systems, ASC and MOCAP. Both for the walking and for the running, we applied the Spearman correlation coefficient (ρ) for each cycle, on both lower limbs, in order to analyze the relationship of the waveform pattern of the knee angular variation between the two systems. Second, we applied the Wilcoxon rank sum test to compared the values of the angular (maximum knee angle values of the right and left lower limb) and linear (stride length) parameters obtained in each system. For these comparisons, the effect size (r) was calculated, in which the values above of 0. 8, between 0. 79 and 0. 5, between 0. 49 and 0. 2 and below 0. 19 represented a large, medium, small and insignificant effect, respectively  [19, 20].
Isolation and growth conditions In 2018, we isolated from the human stool an unidentified bacterial strain. The study was validated by the ethics committee of IHU Méditerranée Infection under number 2016-011. Screening was made by MALDI-TOF MS on a Microflex LT spectrometer (Bruker Daltonics, Bremen, Germany) as previously described  [7]. The obtained spectra (Fig. 1 ) were imported into MALDI BIOTYPER 3. 0 software (Bruker Daltonics) and analysed against the main spectra of the bacteria included in the database (Bruker database constantly updated with MEPHI database https://www. mediterranee-infection. com/urms-database/). Initial growth was obtained after 48 h of culture on Columbia agar with 5% sheep blood in anaerobic conditions at 37°C at pH 7. 5.
Strain identification The 16S rRNA gene was sequenced to classify this bacterium. Amplification was performed using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequencing used the Big Dye® Terminator v1. 1 Cycle Sequencing Kit and ABI Prism 3130xl Genetic Analyzer capillary sequencer (Thermofisher, Saint-Aubin, France), as previously described  [8]. The 16S rRNA nucleotide sequences were assembled and corrected using CODONCODE ALIGNER software (http://www. codoncode. com). Strain Clostridium transplantifaecale exhibited a 96. 46% sequence identity with Clostridium symbiosum strain ATCC 14940 (GenBank accession number NR_118730. 1), the  phylogenetically closest species with standing in nomenclature (Fig. 2 ). We consequently classify this strain as a member of a new species within the genus Clostridium, family Clostridiaceae, phylum Firmicutes.
Genome sequencing Genomic DNA was extracted using the EZ1 biorobot (Qiagen, Courtaboeuf, France) with the EZ1 DNA tissue kit and then sequenced using MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera XT Paired end (Illumina), as previously described  [9]. The assembly was performed with a pipeline incorporating different softwares (VELVET  [10] , SPADES  [11]  and SOAP DENOVO  [12] ) on trimmed (TRIMMOMATIC  [13] ) or raw data. GAPCLOSER was used to reduce assembly gaps. Scaffolds <800 bp and scaffolds with a depth value <25% of the mean depth were removed. The best assembly was selected using different criteria (17 scaffolds, 19 contigs). The genome of strain Marseille-P8228 T is 5. 65038 bp long with a 48. 1 mol% G+C content and contains 4705 predicted genes. The degree of genomic similarity of strain Marseille-P8228 T with closely related species was estimated using the ORTHOANI software  [14].
Acknowledgements This work was funded by the  IHU Méditerranée Infection (Marseille, France)  and by the  French Government  under the Investissements d'avenir (Investments for the Future) programme managed by the  Agence Nationale de la Recherche  ( ANR , fr:  National Agency for Research) , (reference: Méditerranée Infection  10-IAHU-03 ). The authors thank  Hitachi Corporation  for providing the TM4000 Plus Tabletop microscope. They also thank  Magdalen Lardière  for reviewing the English and  Aurelia Caputo  for submitting the genomic sequences to GenBank.
We can therefore write N(E) = 2H(m χ -E)/m χ , with the factor 2 accounting for the e ± multiplicity (2) for each mediator and H the Heaviside step function. We assume that mediators can pass through Sun without attenuation. The capture rate has been evaluated with the DARKSUSY code version 6. 1. 0 [21, 22]  assuming the default settings, with a local DM density ρ = 0. 3 GeV/cm 3 , a Maxwellian velocity distribution with average velocity v = 220 km/s and velocity dispersion v rms = 270 km/s, and setting the DM-nucleon cross section to σ = 10 -40 cm 2 (in both spin independent and spin dependent cases). The capture rate scales linearly with both σ and the local DM density ρ. In the second model, a DM particle χ that scatters inelastically off a solar nucleon N will produce an excited state χ * with a slightly heavier mass, i.
Analysis Method For the present work we analyzed the same dataset used in Refs. [6]  and  [8]. Full details on the event selection are given in Ref. [6]. We have implemented a fitting procedure in sliding energy windows to search for possible local peaks (either bumps, box or lines) on the top of a smooth CRE spectrum. In each energy window we model the CRE intensity as I(E) = I 0 (E) + I f (E), where I 0 (E) is the "smooth" part of the spectrum and I f (E) describes the possible feature. Since the energy windows are narrow, we assume that the smooth part of the spectrum can be described by a power-law (PL) model I 0 (E) = k(E/E 0 ) -γ , where γ is the PL spectral index and the prefactor k corresponds the CRE intensity at the scale energy E 0 , fixed to 1 GeV. In our analysis, we assume three models for I f (E): (i) a delta-like (hereafter line model) feature, I f (E) = s δ (E w -E), where s represents the intensity of the line in units of m -2 s -1 sr -1 ; (ii) a box-like (hereafter box model) feature, I f (E) = s H(E w -E), where s represents the intensity of the box in units of GeV -1 m -2 s -1 sr -1 ; (iii) a spectrum produced by DM annihilating into CREs, I f (E) = sI DM (E|m DM , σ v ,.
PoS(ICRC2019)531 and a background control region as cones with fixed angular radius and axis pointing towards the Sun and the anti-Sun respectively, and we fit simultaneously the count distributions from the two regions. To estimate the parameters {k, α, s} which minimize the χ 2 we use the MINUIT code within the ROOT toolkit; the values of the parameters at a 95% confidence limit (CL) are evaluated using MINOS and setting the error confidence level to 2. 71. We have performed our fits scanning an energy range extending from 42 GeV to about 2 TeV. This interval has been divided in 64 bins per decade, equally spaced on a logarithmic scale. We perform the fit in sliding energy windows with a half-width of 0. 35E w , that well contain the possible features. In fact, the LAT energy resolution for the CRE selection at 95% containment ranges from about 15% at 42 GeV to about 20% at 1 TeV and increases up to 35% at 2 TeV, as shown in Ref.
Study design A single-centre study with retrospective matched case-control analysis to evaluate the effects of FMT on the clearance of CPE/A digestive carriage. The study reviewed medical records and laboratory data on FMTs performed between January 14, 2015 and October 20, 2017 in patients whose digestive tract s were colonised by CPE/A, and who were admitted to the institution for initial clustering and decolonisation purpose (cases). Data were also collected from CPE/A-colonised patients who were hospitalised at the University Teaching Hospital between November 1, 2014 and October 27, 2017, but did not receive FMT (controls) and compared the delay in clearance of CPE/A digestive carriage in both populations.
Matching controls Two CPE/A-colonised control patients per case were matched based on sex, age, bacterial species and carbapenemase type. The diagnosing clearance threshold differs for the two groups. The FMT-treated patients were hospitalised in the Infectious Diseases Department, where a protocol is currently available in both terms of treatment and follow-up of CPE/A colonisation. The control patients were hospitalised throughout the University Teaching Hospital and were identified through a database recording the positively tested patients for rectal CPE/A microbiologic identification.
Statistical analysis Statistical analysis was performed using spreadsheet software Calc version 5. 1. 6. 2 (Libreoffice). Student's t -test or χ 2 test, if appropriate, were used to compare the quantitative variables of the two groups (FMT-treated and control). Fisher's exact test was used to compare clearance rates in FMT-treated group and control group at day 14 post-FMT (treated) and day 14 postdocumentation (control). Student's t -test was used to compare mean delays in discharge from the hospital between FMT-treated and control patients. Univariate Kaplan-Meier curve with Log rank analysis was performed using GraphPad Prism Version 4. 03 for Windows (GraphPad software Inc. , La Jolla California, USA). As for the Kaplan-Meier analysis, day 0 of comparison was considered to be FMT for patients who received FMT (second FMT for patients who received two FMTs) and first CPE/A documentation for control patients.
At least three independent biological replicate samples were sequenced and used for downstream analysis. RNA sequencing was performed on Illumina HiSeq2000 platform. The average number of reads per sample was 27 M. Reads from each sample were processed as follows. First, reads were trimmed using an in-house Perl script with a minimum phred quality of 20 per vase and a minimum read length of 30 base pairs. On average, 24% of reads per sample were discarded. The resulting reads were later aligned to the Rattus norvegicus genome assembly 3. 4 (from Ensembl) using Tophat version 2. 0. 10. At least 12 million reads were aligned to the genome for each sample. Gene expression was then quanitifed to obtain read count and FPKM values. The nonadjusted read counts for each gene were used for statistical calculation of global differential expression using DESeq2.
Participant Recruitment and Progression A convenience sample of 41 postmenopausal women aged 50 to 70 y recruited from the University of Limerick Body Composition (ULBC) Study database by invitation. ULBC subjects had preassigned alphanumeric ID codes that continued to the present study. Subject volunteers were free-living, lactose tolerant, and devoid of treatment for osteoporosis or drugs affecting calcium absorption. Dual energy X-ray absorptiometric (DXA; Lunar iDXA™ with enCORE™ 2007 v. 17 software, GE Healthcare, Chalfont St Giles, Bucks. , UK) measurement of AP spine (L1-L4) and dual femur BMD (femoral neck), conducted and analyzed in accordance with the International Society for Clinical Densitometry  [18] , confirmed eligibility (BMD T scores < -1. 0, ≥ -2. 5). Twenty-four volunteers confirmed as osteopenic submitted to a clinical examination, blood screen and 7-day weighed food dietary intake record.
Dietary Intake and Standardized Diets for the Intervention Following instruction from a qualified dietitian, participants recorded their dietary intake for seven consecutive days (5 weekdays, 2 weekend days) using a weighed food and fluid log. Participants reported food type, brand name, quantity, cooking method, type, time, and location of meal preparation. Subsequent coding and analysis was completed using Nutritics ™ Dietary Analysis Software (Nutritics © software version 4. 0 for Ireland). Dietary intake was compared to reference intakes (DRIs) developed by the Food and Nutrition Board (FNB) at the Institute of Medicine (IOM) of The National Academies  [19]. Based on the 7-day dietary intake data a 48 h dietary standardization, representative of the individual's reported habitual dietary patterns of the research population, compliant with dietary recommendations (IOM DRIs) for energy, protein, and calcium, reflective of participants' food preferences and normalized to body mass was prescribed for each participant by a registered dietitian.
Statistical Analysis Shapiro-Wilk test was applied to check for normality of the data that are presented as the mean ± SD unless stated otherwise. Temporal change in serially sampled data was analyzed by repeated measures ANOVA, the level of significance for post-hoc tests subject to Bonferroni correction. Difference between mean change attributed to CON and MBPM was analyzed by paired t-test. Cohen's effect size was calculated using the standard formula (t-score/√n). Statistical significance was set at p ≤ 0. 05. Serum and plasma were separated by centrifugation at 10,000× g at 4 • C for 5 min and frozen at -80 • C until analysis. Sixteen of the 192 blood samples drawn were hemolyzed and not analyzed. This reduced the full analysis from 3 participants. Active plasma GLP-1(7-36) and total GIP (1-42) was measured using the MSD ® metabolic assay kits (Meso Scale Discovery, Rockville, MD, USA) based on sandwich ELISA and according to the manufacturer's instructions.
Conclusions In summary, the reduction in AUC of CTX (-30% compared to CON) confirms our initial hypothesis that a dairy-based protein supplement fortified with calcium (MBPM) fed at bedtime has a potent effect on nocturnal rates of bone resorption in healthy osteopenic postmenopausal women. The synergistic, pluripotent quality of a milk-based protein matrix and timing of ingestion to the nocturnal, peak rate of bone remodeling transiently depressed bone turnover. We conclude that a late-evening supplement of calcium-fortified milk protein affects a beneficial decrease in the homeostatic rate of bone remodeling in persons at risk of degenerative bone disease. A 24-w longitudinal study (clinicaltrials. gov identifier NCT03701113) is currently in progress to assess the efficacy of outcome in bone turnover and BMD in this population.
RT-qPCR on ZIKV-infected mouse eyes was performed as previously published  [47]. Briefly, eyes were enucleated and tissue lysis performed with a Fastprep 24 apparatus (MP Biomedicals) and mRNA extraction with the Altona Diagnostics kit RealStar® Zika Virus RT-PCR Kit 1. 0, according to the manufacturers' instructions. Cycle thresholds were converted to relative charges using ten-fold serial dilutions of a ZIKV culture supernatant extract. Experiments performed previously with similar MOI for ZIKV AF and AS showed equal amplification for both strains (data not shown).
Enzyme-linked immunosorbent assay (ELISA) and multiplex analyses Proteins such as cytokines and survival factors were quantified in supernatants from Mock and ZIKV-infected RPE cells. Multiplexed microbead assays were used according to manufacturer's instructions (Merk Millipore). A first kit aiming to quantify CXCL10 was used in duplicate. Similar approach was undertaken with a second kit consisting of 5 cytokines: IFNα, IFNγ, IFNβ, IFNλ, IL2 and CXCL10. Readings were performed on MAGPIX apparatus from Merck and data were analyzed using the xPONENT program. Mean concentrations (pg/ml) of cytokines were all superior to the detection limits, defined as the mean background value plus 2S. Vascular endothelial growth factor (VEGF) and pigment epitheliumderived factor (PEDF) protein levels were measured by ELISA assays (R&D systems) according to the manufacturer's instructions.
Acknowledgments We thank  Dr. Giles Uzé  for the Ifnar -/-mouse model,  Dr. Marie Pequignot  ( INM ) for bovine POS isolation and assay, and members of our laboratory for technical help and support. We thank  Chantal Cazevieille  ( Comet ) for the processing of electron microscopy sections,  Isabelle Sassetti  ( RHEM ) for cryosections and the  Montpellier RIO Imaging facility  for confocal microscope imaging.
Study design The HELENA study is a population-based multi-centre investigation of the nutritional and lifestyle status among European adolescents. Data were collected from October 2006 to December 2007 and fieldwork took place in ten European cities of nine countries: Vienna (Austria), Ghent (Belgium), Lille (France), Dortmund (Germany), Athens (Greece), Heraklion (Greece), Pécs (Hungary), Rome (Italy), Zaragoza (Spain) and Stockholm (Sweden). The purpose of the study was to obtain standardized, reliable and comparable data from a random sample of European adolescents on a broad battery of relevant nutrition and health-related parameters. This included dietary intake, food choices and preferences, blood indicators of lipid metabolism and glucose metabolism, vitamin and mineral status, anthropometry, physical activity, fitness and genetic markers.