dataesr/scientific-paragraphs-categorization huggingface dataset:
In Nancy, the study was retrospective and lung echo data were acquired as part of usual clinical management; collection of patient files was approved by the Commission Nationale Informatique et Libertés (CNIL), in keeping with French law for single-centre usual care observational studies. Echocardiographic-lung ultrasound study and natriuretic peptides assessment. All patients underwent echocardiography and lung ultrasound examination at rest using a Vivid 7 or a Vivid I (transducer 3S -RS) ultrasound system (GE HealthCare). LV volumes and EF (obtained using the biplane method of disks summation, the modified Simpson's rule), inferior cava (IVC) diameter, and systolic pulmonary artery pressure (PAPs), were assessed according to current recommendations  22. Diastolic function was assessed from the pattern of mitral inflow by pulsed Doppler echocardiography (E/A ratio); the examination was complemented by septal, lateral, and average mitral annular velocity measured by tissue Doppler imaging (E/e' ratio)  19.
Typically, all LUS were performed in 5 minutes, or less. Intra-and inter-observer reliability of lung ultrasound examinations were assessed by the two operators on the recordings of 30 loops, showing intra-and inter-observer correlation coefficients of 0. 95 and 0. 85, respectively. Lung ultrasonographies were performed on the day of discharge in Perugia and during the first 3 days following admission in Nancy, at the end of the standard two-dimensional echocardiogram. Peripheral venous blood samples for BNP analysis were obtained on the day of the echocardiographic assessment except in 9/60 patients evaluated at discharge; in these small subset of patients, data obtained within the 2 days prior to discharge were used.
Introduction Under the influence of strengthening emission regulation  [1] , increasing climate change concern and high fuel price volatility, energy efficiency has become a hot topic in the maritime industry  [2, 3]. If ship specific (e. g. , fishing vessels  [4] [5] [6] ) or equipment specific (e. g. , diesel engines  [7, 8]  or ballast water treatment system  [9] ) energy efficiency studies are quite common, the literature is still limited regarding more comprehensive and global approaches where the totality of the ship is taken into account  [10]. In previous work  [11] , an initial ship energy modeling approach was developed and presented. From this approach, a modeling tool, named SEECAT (ship energy efficiency calculation and analysis tool), and based on the engineering computer language Modelica  [12]  was created.
The new approach also requires new models such as pumps, heat exchangers, and valves, which were not represented in the previous approach (except for the pumps' electrical consumption). The increased number of models implies more links and connections as well as more fluid junctions, and separations; here, the inherent characteristics of the Modelica language are very valuable, as it natively integrates the Kirchhoff's current and voltage laws. In that respect, Modelica proved itself to be a very useful tool for energy modeling. The SEECAT model presented in Section 3. 2 also integrates several proportional integral controllers for temperature regulation. From an "energy" point of view, these regulators are not justified as their energy consumption is negligible. Nevertheless, they are useful for modeling purposes, as they avoid having to laboriously declare start value variables, and they allow computation even when temperature set-points are not achievable: They allow more simulation flexibility.
Finally, it will enable exergy analysis. To do all this, more information needs to be transported through each connector (graphical links between models used in Modelica  [18] ). In the previous approach, only power was transported. In this new approach, the pressure, the mass flow, and the specific enthalpy of the fluid are transported. The new approach also requires new models such as pumps, heat exchangers, and valves, which were not represented in the previous approach (except for the pumps' electrical consumption). The increased number of models implies more links and connections as well as more fluid junctions, and separations; here, the inherent characteristics of the Modelica language are very valuable, as it natively integrates the Kirchhoff's current and voltage laws. In that respect, Modelica proved itself to be a very useful tool for energy modeling.
‚ For T ă 326. 85 ˝C, two possible cases: ‚ if λ ă 8, then: c p " p975. 5 `0. 28¨Tq ´log pλq ¨p11. 92 `0. 06¨Tq ‚ else: c p " 1000 `2. 85¨e 0. 0088¨pT´273. 15q (6) These curves do not perfectly "join" at 326. 85 ˝C and therefore a linear interpolation, between 226. 85 and 426. 85 ˝C, has been added in the Modelica code of the Keenan and Kaye function.
Analysis of mouse gene expression across straing. Mouse gene expression data were downloaded from BioGPS  [31]. Gene expression in mouse epididymal adipose tissue was derived from data presented in  [32]  , based on a customised microarray platform GNF1M. There was one probeset for Fbn1 (gnf1m00711_a_at) and one for Fbn2 (gnf1m02242). Available results were from pooled RNA obtained from mice at 25 weeks of age, of the following mouse strains: C57BL/6J (n=3), C3H/HeJ (n=4), CBA/J (n=2), DBA/2J (n=3). To find genes with similar expressions to Fbn1, the Correlation function in BioGPS was used, with minimal correlation coefficient set at 0. 75. Mouse phenotype data were obtained from the Mouse Phenome Database (MPD;  [33] ) which provides results for mice scanned immediately post-mortem using mouse densitometer dual energy X-ray absorptiometry (PIXImus mouse densitometer (LUNAR, Madison, WI).
Details of the mouse husbandry are available at http://phenome. jax. org/db/q?rtn=projects/docstatic&doc=Jaxpheno1/Jaxpheno1_Animal. Results for MPD data set Jaxpheno1 were downloaded for body weight, body fat tissue weight and body fat percentage for males and females aged 8 and 16 weeks. Results for single nucleotide polymorphisms.
A C C E P T E D M A N U S C R I P T for C57Bl/6J, C3H/HeJ and DBA/2J strains were retrieved from MPD and the Mouse Genome Informatics database (MGI;  [34] ). The mouse Fbn1 transcription start site region was identified using data from the FANTOM3  [35]  and FANTOM5 projects and the coordinates on the current build of the mouse genome (GRC m38. p4) determined by a BLASTN search in Ensembl  [36].
Analysis of human adipose tissue gene expression data. Gene expression data from the adipose tissue of a previously analysed cohort of 30 obese (BMI > 30 kg/m 2 ) and 26 non-obese (BMI < 30 kg/m 2 ) women  [37]  was subjected to Significance Analysis of Microarrays  [38]. Affymetrix microarray data from 114 adult Swedish women without diabetes  [39]  was examined for correlations between markers of adiposity and FBN1 expression with the statistical package Statview (SAS Institute Inc, NC, USA). The human FBN1 transcription start site was identified using data from the FANTOM3 and FANTOM5 projects  [2, 29, 35].
For the present These samples consisted of adipocyte precursor cells isolated from the adipose stromal vascular fraction of four additional donors, differentiated without cell passage and sampled at three time points (day 4, day 8 and day 12). The gene based and promoter based data for these experiments were downloaded from the FANTOM5 website. Gene expression patterns were clustered using BioLayout Express 3D  [44, 45]. Pearson correlation coefficients and MCL inflation values used for different analyses are given in the results. Gene Ontology (GO) term enrichment in the generated clusters was analysed using the Database for Annotation, Visualisation and Integrated Discovery (DAVID) v6. 7  [46]  using total human genes as background. A C C E P T E D M A N U S C.
Fbn1 gene expression correlates with amount of adipose tissue in mouse The expression data available at BioGPS for different mouse strains indicate considerable variation in expression of Fbn1 in epididymal adipose tissue from males of different mouse strains (Figure  1A ). The expression of the fibrillin gene family member Fbn2 was very low in adipose tissue and Fbn1 expression was much lower in other tissues such as liver (Figure  1A ), hippocampus and pancreas across strains. To assess the impact of the variability of Fbn1 expression in adipose tissue, we used data available through MGI. We compared results for four strains of mice: DBA/2J (high expression of Fbn1), CBA/J (moderate to high expression), C3H/HeJ (low to moderate expression) and C57Bl/6J (low expression) (Figure  1A ). At 16 weeks, female C57BL/6J and C3H/HeJ were not different in body weight and nor were female CBA/J and DBN/2J.
A C C E P T E D M A N U S C R I P T The analysis of fibrillin-1 protein suggested that the amount of fibrillin declines rapidly after the onset of adipogenic differentiation (Figure  2B ). Preliminary analysis using gene expression microarary and quantitative reverse transcriptase polymerase chain reaction showed that there was a decline in FBN1 mRNA during the differentiation time course used for immunofluorescence staining (not shown). To examine further the pattern of FBN1 mRNA expression during adipogenesis, we analysed a gene expression dataset which explored a similar but more extensive time course of adipogenic differentiation from mesenchymal stem cells. This study, which has been described previously  [30] , looked at gene expression using Cap Analysis of Gene Expression (CAGE), a quantitative method to assess promoter usage and hence gene expression  [50].
A C C E P T E D M A N U S C R I P T contained the related gene FBN2, also contained other genes often coexpressed with FBN1 (for example, ANTXR1, CALU, COPZ2, FN1, LOX, LTBP2, PTGIS, TIMP3, VGLL3)  [1]. The largest downregulated cluster contained ACTA2, ATOH8, CALD1, LOXL1, PALLD, POSTN, PRRX1, PRRX2, PRSS23, PTX3, TGFB3, TGFB1I1 and THBS1, which have also been shown to be coexpressed with mouse Fbn1  [1]. The coexpression of genes commonly associated with FBN1 indicates that general mesenchymal genes were shut down during adipogenesis, while mesenchymal genes encoding proteins specific to the specialised needs of adipose connective tissue, such as those encoding collagen type IV subunits, were up-regulated, as shown previously  [30]. We analysed the dataset to identify transcription factors that might be involved in regulating the level of FBN1 during adipogenesis.
DISCUSSION In this study we have analysed several publicly available databases and a cell culture model of adipogenesis to examine the possible role of fibrillin-1 in adipogenesis. Firstly we showed that Fbn1 level in mouse strains is correlated with the amount of adipose tissue (measured as total adipose or as percent fat). This relationship was true although the mRNA was derived from epididymal fat from male mice at 25 weeks and the weight and body fat composition were from both male and female mice at 16 weeks, indicating that it is likely to be a general feature of mouse adipose tissue and that fibrillin-1 is important to the synthesis and/or maintenance of adipose tissue in vivo. There was no similar relationship with the fibrillin family member Fbn2 (not shown), so this association appeared to reflect a specific role of fibrillin-1.
ACKNOWLDEGEMENTS The  Roslin Institute  (MRD and KMS) is supported by  Institute Strategic Programme Grants  from the  Biotechnology and Biological Resources Council (BBSRC)  of the United Kindgom, grant numbers  BB/J004235/1  and  BB/J004316/1. EA was supported by a  Research Grant  from  MEXT  to the  RIKEN Center for Life Science Technologies. PA and ID receive support from the  Swedish Research Council. We thank  Dr Christopher West  for provision of the stromal vascular fraction from adipose tissue. Ethical approval for the collection of adipose tissue and subsequent research was granted by the  South East Scotland Research Ethics Committee  (Reference 10/S1103/45 h).
Single lepton channel at √ s = 8 TeV The ATLAS collaboration released a preliminary result for the measurement of the inclusive t t production cross-section in the single lepton channel using pp collisions data delivered in 2012 by the LHC, corresponding to an integrated luminosity of 5. 8 fb -1 at a centre-ofmass energy of √ s = 8 TeV  [1]. Signal event candidates are selected using single isolated electron or muon triggers. The offline selection in the electron (muon) channel requires the presence of exactly one electron (muon) with p T > 40 GeV and |η| < 2. 5, 1 and satisfying tracker and calorimeter isolation requirements, together with three or more jets satisfying p T > 25 GeV and |η| < 2. 5, at least one of which is required to be identified as likely to have originated from a b-quark (b-tagged), using a multivariate discriminant such as the b-quark jets tagging efficiency is approximately 70%.
eμ channel at √ s = 7 TeV and 8 TeV The inclusive production cross-section is measured at 7 and 8 TeV in the eμ dilepton channel, using the full datasets recorded by the ATLAS detector in 2011 and 2012, corresponding to integrated luminosities of 4. 6 fb -1 and 20. 3 fb -1 respectively  [15]. Signal event candidates are selected using single isolated electron or muon triggers. The offline selection requires the presence of exactly one electron and one muon with p T > 40 GeV and |η| < 2. 5 with opposite electric charge, and satisfying tracker and calorimeter isolation requirements. Jets are selected such as to satisfy p T > 25 GeV and |η| < 2. 5, and are b-tagged using a discriminant with a 70% b-tagging efficiency. The distributions of the number of b-tagged jets for events satisfying the above described pre-selection are shown on Figure  1 , without any requirement on the number of additional jets failing the b-tagging requirement.
The ratio R t t = σ tt (8 TeV)/σ tt (7 TeV) of the two total cross-sections is measured to be: R t t = 1. 326 ± 0. 056,  (7)  in comparison with the QCD NNLO+NNLL predicted value of 1. 430 ± 0. 013. Furthermore, the ATLAS collaboration provides measurements of the inclusive t t cross-sections for the two centre-of-mass energies in a fiducial volume, in order to separate the systematic uncertainties due to the modelling of the signal in the fiducial volume from the ones due to the extrapolation to the total cross-section. Thanks to the theoretical dependence of the total cross-sections on the top quark mass, the measurement of the cross-sections is also used to determine the pole mass of the top quark. The measured value is: m pole t = 172. 9 +2. 5 -2. 6 GeV, (8) combining the datasets at 7 and 8 TeV, providing the best measurement of the top-quark pole mass so far.
Differential cross-section measurement in the sin- gle lepton channel at √ s = 7 TeV ATLAS provides a measurement of the t t differential cross-section as a function of different kinematic variables at a center-of-mass energy of 7 TeV  [22]. This measurement is performed in the single lepton channel, using the whole pp collision data recorded in 2011 by the ATLAS detector, corresponding to an integrated luminosity of 4. 6 fb -1. Signal event candidates are selected using single isolated electron or muon triggers. The offline selection in the electron (muon) channel requires the presence of exactly one electron (muon) with p T > 25 GeV and |η| < 2. 5, and satisfying tracker and calorimeter isolation requirements, together with four or more jets satisfying p T > 25 GeV and |η| < 2. 5, at least one of which is required to be b-tagged, using a multivariate discriminant such as the b-quark jets tagging efficiency is approximately 70%.
(C15), det   A A -B C A -B A -B -α i /ω 2 C + E C C + E D -2/β i   = 0, (2) where A = 1 + T 0i T 0e + σ T 0i T 0σ Γ 0 (α σ ) ξ σ Z (ξ σ ) B = 1 + T 0i T 0e - σ T 0i T 0σ Γ 0 (α σ ) C = 1 e σ q σ Γ 1 (α σ ) ξ σ Z (ξ σ ) D = 2 σ T 0σ T 0i Γ 1 (α σ ) ξ σ Z (ξ σ ) E = 1 e σ q σ Γ 1 (α σ ) , using the same notation as in Ref. [8]. A Python program is used to solve for the complex frequencies fulfilling this dispersion relation, with very similar algorithms as in the recently introduced HYDROS code for the hybrid-kinetic system (see next section).
Acknowledgments D. T. is grateful to  V. Bratanov  for pointing out a mathematical subtlety in the gyrokinetic dispersion relation. J. C. was supported by the  NSF REU  Grant No. PHY-1460055. The research leading to these results has received funding from the  European Research Council  under the European Union's  Seventh Framework Programme  ( FP7/2007-2013)/ERC Grant  Agreement No. 277870. Furthermore, this work was facilitated by the  Plasma Science and Technology Institute at the University California, Los Angeles , and by the  Max-Planck/Princeton Center for Plasma Physics.
ArrayPro 4. 5 (Media Cybernetics Inc. , Silver Spring, MD) was used to analyze slide images; processing and normalization were performed using MicroPrep software  (31, 32)  as described previously  (32). Gene expression was considered to be significantly altered when the Cyber-T Bayesian p value was Յ0. 001. Transmission Electron Microscopy-Pellets of bacteria (A 600 0. 5 for MG1363, MG1363 ϩ uracil, and ⌬pyrB mutant ϩ uracil and A 600 0. 2 for the ⌬pyrB mutant) were fixed with 2% glutaraldehyde in 0. 1 M sodium cacodylate buffer, pH 7. 2, for 3 h at room temperature. Samples were contrasted with 0. 5% oolong tea extract in cacodylate buffer, fixed with 1% osmium tetroxide that contained 1. 5% potassium cyanoferrate, gradually dehydrated in ethanol (30 -100%), substituted gradually in a mixture of propylene oxide-Epon, and embedded in Epon (Delta Microscopie, Labège, France).
Acknowledgments-We are indebted to  A. Gruss ,  V. Fromion , and  J. Martinussen  for valuable discussions. We thank  Carmen Bulbarela-Sampieri ,  Valerija Mikalaeva ,  Aurelie Bobillot , and  Pascal Quenée  for help in different phases of the work. The work of P. C. , S. F. , P. V. , J. A. , M. S. , M. -P. C. -C. , and S. K. benefited from the facilities and expertise of  Microscopie et Imagerie des Micro-organismes, Animaux et Aliments Microscopie Électronique à Transmission, UMR 1313 Génétique Animale et Biologie Intégrative, Equipe Plateformes, Institut National de la Recherche Agronomique, Jouy-en-Josas, France.
_____________________________________________________________________________________________________ the course of a fractionated radiotherapy treatment or during a PET study. This work examines how transient perfusion of vessels may influence tissue radiosensitivity (including reoxygenation) and FMISO image contrast, as a guide for dose painting. Material and Methods: Microscopic oxygen and FMISO distributions are simulated in tissue using bespoke MATLAB software which solves coupled partial differential equations by finite difference methods. Dynamic vasculature is modelled by opening and closing individual vessels at random, with time spent in each state sampled from a normal distribution. Oxygen enhancement ratios are calculated from the resulting PO2 maps. The optimal prescription dose is found by simulating a range of dose levels and determining radiobiological cell kill using the linear-quadratic model with repopulation.
1E , Supplementary Fig. S1 ). We additionally detected a pronounced peak of lactate in cerebrospinal fluid from the patient (Supplementary Fig. S2 ) which indicated a less efficient oxidation of pyruvate (the oxidized form of lactate) in mitochondria. These observations suggested that a mitochondrial dysfunction was possibly at the origin of, or contributed to, the disease process. This led us to analyze the mtDNA of the patient. No visible rearrangement (deletion) (Fig. 2A ) and depletion (Fig. 2B ) were observed. However, a point mutation (G8969> A) that was absent in 2704 controls in databases as well as in 100 age-matched controls from the same geographic region, was detected in the ATP6 gene (Fig. 2C , Supplementary Table  S3 ). This mutation leads to the replacement of a serine residue by asparagine at position 148 in the a-subunit of ATP synthase (aS148).
Total genomic DNA was isolated from blood, urine sediments and renal samples using the QIAamp DNA extraction kit (QIAGEN). The 16. 5 kb mtDNA was amplified using 15 polymerase chain reaction (PCR) primer pairs and then sequenced. The sequencing data were compared against the revised Cambridge Reference Sequence (rCRS) of human mtDNA (GenBank NC_012920. 1). For detection of mtDNA deletion, long range PCR was amplified using two primer pairs and the amplified DNA fragments were separated by electrophoresis on a 0. 8% agarose gel. Real-time quantitative PCR was used to determine mtDNA copy number, relative to the nuclear 18S rRNA gene, using two primers specific of the mitochondrial COX1 locus and two primers specific of the nuclear 18SrRNA locus. The Pyromark Q24 platform (Qiagen) was used to assess the levels of heteroplasmy of the G8969> A mutation.
TMHMM 2. 0 and PSIPRED 3. 3 servers were used to predict transmembrane segments and secondary structures, respectively. Figure  5A  was drawn using the ESPRIPT program. The homology model of human ac8 complex is based on the atomic model build in the cryo-electron microscopy density map of the bovine ATP synthase (pdb:5ARH; emdb:3166)  29  and the bovine c8-ring crystal structure (pdb:2xnd)  32. It was built using Phire2, energy minimized using Phenix, Fig. 5B, C  was drawn using Pymol. Statistics. Data are expressed as means ± S. D. or S. E. M. SPSS software (16. 0), unpaired t test and analysis of variance (ANOVA) were used for comparison between groups of data. A p value < 0. 05 was considered as statistically significant. Publisher's note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Acknowledgements This work was supported in part by  National Basic Research Program of China 973 Program  No. 2012CB517600  (No. 2012CB517606 ) (to Z. L. ),  National Natural Science Foundation (NSF)  Grant  81370788 & 8151101098  (to H. C. ) and  Scientific Research Foundation for the Returned Overseas Chinese Scholars, SEM  (to H. C. , 2012). This work was also funded by grants from  FRM  ( Fondation pour la Recherche Médicale)  and  AFM (Association Française contre les Myopathies)  to J. -P. dR,  Agence Nationale de la Recherche  to M. -F. G. and A. D. ( ANR-12-BSV8-024 ), and by  National Science Center of Poland  ( UMO-2013/11/B/NZ1/02102 ) to R. K. We thank for  Professor Bin Lu  ( Wenzhou Medical University ) for technical support for the ρ 0 cell construct and Seahorse XF96 Extracellular Flux Analyser.
Genome resequencing Draft genomes of the R. solanacearum strains UW163 and IBSBF1503 were generated in a previous study  (Ailloud et al. , 2015). For this study, we resequenced these strains using long reads generated on a PacBio platform (RS II) at GATC biotech facilities (Konstanz, Germany) and short paired reads generated on an Illumina platform (MiSeq) by UWBC. Long reads were assembled using the SMRT Portal tool (HGAP 3 pipeline) and subsequently corrected with the short paired reads using the PALOMA pipeline  (Cruveiller, 2015, unpublished)  with stringent parameters for the ''SNP calling'' step (allelic frequency was set to 0. 8 with at least 10 reads mapping the position and a balance of forward reads to reverse reads was set to 0. 33). UW163 BioProject accession number: PRJNA297400; IBSBF1503 BioProject accession number: PRJNA297402.