dataesr/scientific-paragraphs-categorization huggingface dataset:
Winter temperature was also analyzed from the available data sets. The spatial pattern shows agreement between the CRU and UDEL databases and ERA-Interim, and the interannual variability from reanalysis is bounded by the gridded data. Note that UDEL shows systematic colder temperatures than CRU over the entire period. The analysis of the spatial distribution of trends indicates that ERA-Interim shows significant warming in a much larger region than indicated by CRU and UDEL. In particular, in the northern regions of the box, the large positive trends in ERA-Interim are opposite to the significant cooling trends shown in both CRU and UDEL. The vertical structure of ERA-Interim in the region was evaluated using radiosonde data available on either side of the Andes (only one station on each side), compared with the nearest grid point of ERA-Interim.
2. Spatial distribution in the southern central Andes. ERA-Interim exhibits a different frequency distribution than gridded data sets, overestimating the modal frequency, underestimating the frequency of lowintensity events (1 mm/d) and overestimating the frequency of large intensity events (>5. 5 mm/d). The trends in precipitation determined using ERA-Interim were not significant. The interannual variability of the mean winter temperature in the region is represented well by ERA-Interim and the magnitude bounded by CRU and UDEL (which is systematically colder in the box). The positive trends estimated in surface temperature from ERA-Interim show significance in the northern regions of the SCA box, where gridded data sets indicate significant cooling. 3. Height of the 0°C isotherm. ERA-Interim overestimates the height by 200-300 m compared with radiosonde data, which could be important in the partition of liquid and solid precipitation and the estimation of the extent of the snowpack in the Andes.
Temporal correlations of winter temperature between ERA-Interim, CRU, and UDEL for the period 1979-2010 are presented in Figure 9. Note the general pattern of positive, significant correlations with only smaller values found in northwest Argentina, the same region where precipitation correlations are almost zero. The mean winter temperature averaged over the SCA region is shown in Figure 10 for the three gridded databases. During almost the entire period UDEL shows systematically lower values than CRU and ERA-Interim in most of the years. Reanalysis data have more coincidences with CRU, especially in the last decade, and, overall, ERA-Interim satisfactorily captures the interannual variability of temperature. Correlations between ERA-Interim winter temperature in the SCA region and the observational data sets for the period 1979-2010 (not shown) are.
Acknowledgments This work was funded by the  Universidad de Buenos Aires  through the  UBA-20020100100789  project, the  Consejo Nacional de Investigaciones Científicas y Técnicas of Argentina  through  CONICET PIP 227  project, the  Consejo Nacional de Ciencias y Tecnología  through grant  Sep-Conacyt 154729 , and the  Universidad Nacional Autonoma de Mexico. We acknowledge the institutions that made available the data sets used in this study. The GPCC precipitation, University of Delaware air temperature and precipitation, and GPCP precipitation data were provided by the  NOAA/OAR/ESRL PSD, Boulder, Colorado, USA , from their website at http://www. esrl. noaa. gov/psd/. TRMM data were obtained from the  IRI/LDEO  Climate Data Library from the website http://iridl. ldeo. columbia. edu/. CRU data were obtained from http://badc.
Dietary intake assessment Patients in both groups were instructed to fill in a one-day dietary record of the day before the visit. The UC patients gave their record to the staff of the centre and the UC+IC gave theirs to the study dietician who needed it to adapt counselling. Any intake was taken into account, including oral nutritional supplements and artificial nutrition. Nutrisoft Billnut software (Tours, France) was used to calculate intake by the coordinating centre  [17]. Percent of patients achieving the goal in energy or protein intake were shown.
Outcomes The main outcome was one-year mortality recorded in centres. Causes of death were recorded. General practitioners and patients' relatives were contacted if needed. Chemotherapy management (dosage, changes and arrest), grade 3-4 toxicities including severe infections, weight changes, prescription of enteral or parenteral nutrition, and hospitalization for reasons other than chemotherapy were considered as secondary outcomes. These data were collected by investigators during the chemotherapy period. Two-year mortality was also assessed.
Statistics Analyses were performed on an intention-to-treat basis. Comparisons of dietary intake between groups were performed using a mixed linear model accounting for repeated measures. The Kaplan-Meier method was used to estimate survival probabilities and mortality was compared using the Wald Chi2 test in a Cox model adjusted on the recruiting centre of the participants. Proportions were used to describe qualitative variables of the secondary outcomes. Comparisons were made with the Chi2 test. For the outcomes that were recorded at several visits such as infections, the outcome was considered absent when the data was not available in the main analysis. In a robustness analysis, we used the missing = failure strategy. Quantitative variables were described with mean and standard deviation (SD) or Inter-Quartile Interval (IQR) and compared using Student's t test or the Wilcoxon test according to the distribution of the analysed variable.
The reason why increased energy intake fails to change body mass may involve the activation of anti-anabolic pathways during cancer cachexia  [23, 24]. It is likely that pharmaconutrition targeting cachexia related metabolism alterations should be tested. This trial cannot however provide hypothesis to drive pharmaconutrition related to cancer cachexia. In patients receiving chemotherapy, increase in dietary intake just before treatment may also not be favourable. Indeed, it has been reported that short-term fasting (48 hours) can protect normal cells but not cancer cells from chemotherapy agents in mice and in cell culture  [25]. An interventional study in patients undergoing chemotherapy for breast or prostate cancer is ongoing to test the effects of a controlled low calorie diet on the side effects and response to treatment (NCT01802346).
We present Herschel/PACS 100 and 160 µm integrated photometry for the 323 galaxies in the Herschel Reference Survey (HRS), a K-band-, volume-limited sample of galaxies in the local Universe. Once combined with the Herschel/SPIRE observations already available, these data make the HRS the largest representative sample of nearby galaxies with homogeneous coverage across the 100-500 µm wavelength range. In this paper, we take advantage of this unique dataset to investigate the properties and shape of the far-infrared/sub-millimeter spectral energy distribution in nearby galaxies. We show that, in the stellar mass range covered by the HRS (8 < ∼log(M * /M ⊙ ) < ∼12), the farinfrared/sub-millimeter colours are inconsistent with a single modified black-body having the same dust emissivity index β for all galaxies.
In order to ascertain the dust properties of galaxies in the local Universe, and to provide new constraints to theoretical models, we have carried out the Herschel Reference Survey (HRS,  Boselli et al. 2010b) , a Herschel guaranteed time project focused on the study of the interplay between dust, gas and star formation in a statistically significant sample of ∼300 galaxies spanning a wide range of morphologies, stellar masses (8 < ∼log(M * /M⊙) < ∼12), cold gas contents (-3 < ∼log(MH I /M * ) < ∼1), metallicities (8. 2 < All raw PACS data were processed from Level-0 to Level-1 within HIPE (v10. 0. 0, Ott 2010) using the calibration file v48. This pre-processing includes, among the other tasks, pixel flagging, flux density conversion and coordinate assignment. To remove the 1/f noise which, at this point, still dominates the timelines, the Level-1 data were fed into Scanamorphos (version 21, Roussel 2013), an IDL algorithm which performs an optimal correction by exploiting the redundancy in the observations of each sky pixel.
No noise modelling is hence needed. The pixel size of the final maps was chosen to sample at the best the point-spread-function, at the respective wavelengths, typical of the data taken at medium scan speed: 1. 7 and 2. 85 arcsec pixel -1 at 100 and 160 µm, respectively (i. e. , FWHM/4). The typical pixel-bypixel noise in the map varies between ∼0. 1 and ∼0. 25 mJy pixel -1 at 160 µm and between ∼0. 04 and ∼0. 1 mJy pixel -1 at 100 µm. In order to show the data quality of the new observations presented here, in Fig. 1  we compare the PACS images for three of our targets with the RGB Sloan Digital Sky Survey  (Abazajian et al. 2009 ) optical and SPIRE 250 µm  (Ciesla et al. 2012)  images. We show an example of an early-type galaxy with dust lanes (HRS45, top row), late- type galaxy (HRS48, middle row) and un-detected elliptical and its spiral companion (HRS244/245, bottom row).
PACS 100 and 160 µm integrated photometry Integrated 100 and 160 µm photometry has been performed following very closely the technique used by  Ciesla et al. (2012)  for the SPIRE data of HRS galaxies. This is crucial to properly combine the two datasets, and to characterise the shape of the SED across the entire 100-500 µm wavelength range. Thus, whenever possible, we determined integrated flux densities within the same apertures adopted in  Ciesla et al. (2012). The aperture sizes are adapted to include the entire extent of the FIR emission from the galaxies, and they correspond to ∼1. 4, ∼0. 7 and ∼0. 3 times the optical diameter for late-type, lenticular and elliptical galaxies, respectively. Only for 36 galaxies (∼11% of the sample) we choose different sizes than those used for SPIRE.
Column 13: 160 µm flux density measurement flag. Column 14: Integrated 160 µm flux density, or upper limit in Jy. Column 15: Total uncertainty on the 160 µm flux density measurement in Jy. Columns 16-18: Major, minor semi-axis (in arcseconds) and position angle (in degrees) of the aperture used for the photometry. Column 19: Herschel Proposal ID. This table, as well as all the reduced PACS maps, are publicly available on the Herschel Database in Marseille (HeDaM, http://hedam. oamp. fr/).
Auld et al. (2013)  recently published PACS flux density measurements for all the VCC galaxies in the HeViCS footprint. A comparison between the flux density estimates for the 65 detected galaxies in common reveals a nice correlation between the two estimates with a standard deviation of just ∼12% and ∼7% at 100 and 160 µm, respectively. However,  Auld et al. (2013)  measurements are systematically ∼12% and ∼15% lower than ours. After various tests, we concluded that there are two main reasons for this discrepancy. First, a different flux density estimate technique. Auld et al. (2013)  used apertures on average significantly smaller than ours (e. g. , see their Fig. 3 ), and then applied aperture corrections. Indeed, by using our own apertures on the  Auld et al. (2013)  dataset, we find no systematic offset with our 100 µm data, whereas at 160 µm there is still a difference of ∼12%.
(2012)  for the 49 galaxies in common. These are based on an early HeViCS data release and are measured on apertures much more similar to the ones we used. Our flux density measurements agree very well with these estimates (∼+2±22% and ∼+2±14% at 100 and 160 µm, respectively). The scatter is larger than in the case of  Auld et al. (2013) , but consistent with the typical uncertainty given in  Davies et al. (2012). It is likely that, in this case, the different calibration between the two datasets compensates for the intrinsic differences between photProject and Scanamorphos, providing a set of measurements consistent with our own. Spitzer/MIPS 160 µm flux densities for 103 galaxies in the HRS have been published by  Bendo et al. (2012). In order to perform a proper comparison with our data, we removed those galaxies which were flagged as problematic due to incomplete coverage, or simply being confused with other nearby galaxies of similar surface brightness in  Bendo et al.
FITTING THE DUST SED WITH A SINGLE MODIFIED BLACK-BODY 4. 1 How well do colours trace the average dust temperature? The results presented in the previous section show that FIR/sub-mm colours may not always represent a proxy for the average underlying dust temperature. In order to investigate this issue in more detail, it is interesting to quantify how the FIR/sub-mm colours correlate with the parameters obtained from a single modified black-body fitting. We assume either a constant value of β=2, or keep this as a free parameter. The model functions were convolved with the PACS and SPIRE filter response functions and fitted to the relative spectral responsivity function-weighted flux density measurements. Best-fit parameters and their 1σ uncertainties are determined via a χ 2 minimisation using the Python version of the minimisation library MINUIT  (James & Roos 1975).
2010a (Boselli et al. , 2012;; Rémy-Ruyer et al. 2013). Our findings overall reinforce the results already presented in  Boselli et al. (2010a Boselli et al. ( , 2012)). However, it is important to note that the discovery of a clear variation in the shape of the SED across the HRS has only been possible thanks to the large wavelength coverage obtained by combining both PACS and SPIRE data. Indeed, with SPIRE or PACS data only, it would be not only much more difficult to show under which conditions a simple modified black-body approach does not work, but it would also be nearly impossible to quantify how model assumptions can affect the correlation of dust temperature with star formation, galaxy structure and chemical enrichment. 22. 9 +0. 9 -0. 9 6. 69.
ACKNOWLEDGMENTS We thank an anonymous referee for his/her very useful comments and suggestions which have significantly improved this manuscript. LC thanks  B. Draine  for useful discussions, and  B. Catinella  for comments on this manuscript. We thank all the people involved in the construction and the  launch of Herschel. The research leading to these results has received funding from the  European Communitys Seventh Framework Programme  ( /FP7/2007-2013/)  under grant agreement No  229517 , and was supported under  Australian Research Council's Discovery Projects funding scheme  (project number  130100664 ). IDL is a postdoctoral researcher of the  FWO-Vlaanderen (Belgium). PACS has been developed by a consortium of institutes led by  MPE (Germany)  and including  UVIE (Austria) ;  KU Leuven, CSL, IMEC (Belgium) ;  CEA ,  LAM (France) ;  MPIA (Germany) ;  INAF-IFSI/OAA/OAP/OAT ,  LENS ,  SISSA (Italy) ;  IAC (Spain).
This development has been supported by the funding agencies  BMVIT (Austria) ,  ESA-PRODEX (Belgium) ,  CEA/CNES (France) ,  DLR (Germany) ,  ASI/INAF (Italy) , and  CICYT/MCYT (Spain). SPIRE has been developed by a consortium of institutes led by  Cardiff University (UK)  and including  Univ. Lethbridge (Canada) ;  NAOC (China) ;  CEA ,  LAM (France) ;  IFSI ,  Univ. Padua (Italy) ;  IAC (Spain) ;  Stockholm Observatory (Sweden) ;  Imperial College London ,  RAL ,  UCL-MSSL ,  UKATC ,  Univ. Sussex (UK) ; and  Caltech ,  JPL ,  NHSC ,  Univ. Colorado (USA). This development has been supported by national funding agencies:  CSA (Canada) ;  NAOC (China) ;  CEA ,  CNES ,  CNRS (France) ;  ASI (Italy) ;  MCINN (Spain) ;  SNSB (Sweden) ;  STFC (UK) ; and  NASA (USA). Part of the HRS data was accessed through the Herschel Database in Marseille (HeDaMhttp://hedam.
Angular momentum conservation is explicitly imposed by a modified stress-free boundary condition. Aubert (A): Spectral simulation using the code PARODY-JA, which uses spherical harmonics for the angular component and a second-order finite differences in radius (see  Dormy et al. 1998; Aubert et al. 2008). The time marching is done with a semi-implicit Crank-Nicolson/Adams-Bashforth scheme. The radial mesh includes a gridpoint exactly at the centre of the sphere. Spectral toroidal and poloidal components of order l behave like r l at the centre. Angular momentum conservation is achieved by correcting for solid-body rotation at each time step. Schaeffer (S): Spectral simulation using spherical harmonics for the angular component and second-order finite differences in radius  (Monteux et al. 2012).
The (unstructured) mesh is made of prisms in the boundary layer and tetrahedrons in the bulk. The incompressibility is imposed using a penalty method. The time stepping uses the Implicit Differential-Algebraic solver (IDA solver), based on variable-coefficient Backward Differencing Formulae (e. g. Hindmarsh et al. 2005). The integration method in IDA is variable-order, the order ranging between 1 and 5. At each time step, the system is solved with the sparse direct linear solver PARDISO (www. pardiso-project. org) or a multigrid GMRES iterative solver. This is all implemented via the commercial code COMSOL Multiphysics R. Nore, Luddens and Guermond (NLG): Hybrid Fourier and finite element method using a Fourier decomposition in the azimuthal direction and the standard Lagrange elements P1-P2 in the meridian section (with P1 for the pressure and P2 for the velocity field).
A C K N O W L E D G E M E N T S This work was partly funded by  ERC  grant  247303  'MFECE' to AJ. AJ and PM acknowledge  SNF  grant  200021-113466 , and are grateful for the provision of computational resources by the  Swiss National Supercomputing Centre (CSCS)  under project ID s225. PM acknowledges the support of the  NSF CSEDI Programme  through award  EAR-1067944. For this work, DC was supported by the  ETH Zurich Post-doctoral fellowship  programme as well as by the  Marie Curie Actions for People COFUND Programme. JLG acknowledges support from the  University Paris-Sud , the  National Science Foundation  (grants  NSF   DMS-1015984  and  DMS-1217262 ), the  Air Force Office of Scientific Research , (grant  FA99550-12-0358 ) and the  King Abdullah University of Science and Technology  (Award No.
The motility test was negative and the cells were not sporulating. Colonies were translucent and 1 mm in diameter on bloodenriched Columbia agar. Cells were Gram-positive rods (Figure  2 ). In electron microscopy, the bacteria grown on agar had a mean diameter and length of 0. 63 and 1. 22 μm, respectively (Figure  3 ). Phylogenetic tree highlighting the position of Corynebacterium jeddahense strain JCB T relative to other type strains within the genus Corynebacterium. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximumlikelihood method in the MEGA software package. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree.
Genome project history The organism was selected for sequencing on the basis of its phylogenetic position, 16S rDNA similarity and phenotypic differences with members of the genus Corynebacterium and is part of a culturomics study of the human digestive flora aiming at isolating all bacterial species within hu-man feces  [2]. It was the 96th genome from a Corynebacterium species. The EMBL accession number is CBYN00000000and consists of 244 contigs. Table  3  shows the project information and its association with MIGS version 2. 0 compliance  [41].
Genome annotation Open Reading Frames (ORFs) were predicted using Prodigal  [60]  with default parameters. However, the predicted ORFs were excluded if they spanned a sequencing gap region. The predicted bacterial protein sequences were searched against GenBank  [61]  and Clusters of Orthologous Groups (COG) databases using BLASTP. The tRNAs and rRNAs were predicted using the tRNAScanSE  [62]  and RNAmmer  [63]  tools, respectively. Lipoprotein signal peptides and numbers of transmembrane helices were predicted using SignalP  [64]  and TMHMM  [65] , respectively. ORFans were identified if their BLASTP E-value was lower than 1e -3 for alignment length greater than 80 amino acids. If alignment lengths were smaller than 80 amino acids, we use an E-value of 1e -5. Such parameter thresholds have already been used in previous works to define ORFans.
Artemis  [66]  and DNA Plotter  [67]  were used for data management and visualization of genomic features, respectively. The Mauve alignment tool (version 2. 3. 1) was used for multiple genomic sequence alignments  [68]. To estimate the mean level of nucleotide sequence similarity at the genome level between C. jeddahense and another 4 members of the Corynebacterium genus (Tables  6  and 7 ), we used the Average Genomic Identity Of gene Sequences (AGIOS) home-made software  [35]. Briefly, this software combines the Proteinortho software  [69]  for detecting orthologous proteins between genomes compared two by two, then retrieves the corresponding genes and determines the mean percentage of nucleotide sequence identity among orthologous ORFs using the Needleman-Wunsch global alignment algorithm.
Using Api Zym (BioMerieux), alkaline and acid phosphatases and Naphtol-AS-BI phosphohydrolase activities are positive, but esterase (C4), esterase lipase (C8), lipase (C14), trypsin, α-chemotrypsin, α-galactosidase, β-galactosidase, β-glucuronidase, α-gluco- The G+C content of the genome is 67. 2%. The 16S rRNA and genome sequences are deposited in GenBank under accession numbers HG726038 andCBYN00000000, respectively. The habitat of the microorganism is the human digestive tract. The type strain JCB T (= CSUR P778 = DSM 45997) was isolated from the fecal flora of a Saudi male who suffered from morbid obesity.
Figure1. Phylogenetic tree highlighting the position of Corynebacterium jeddahense strain JCB T relative to other type strains within the genus Corynebacterium. GenBank accession numbers are indicated in parentheses. Sequences were aligned using CLUSTALW, and phylogenetic inferences obtained using the maximumlikelihood method in the MEGA software package. Numbers at the nodes are percentages of bootstrap values obtained by repeating the analysis 500 times to generate a majority consensus tree. Mycobacterium avium was used as outgroup. The scale bar represents 1% nucleotide sequence divergence.
Polysaccharide utilization Both Hrd. species contain high numbers of CAZyme genes, i. e. genes for enzymes that synthesize, modify or breakup glycosides  (Henrissat and Coutinho, 2001). Halorhabdus tiamatea SARLB T has in total 50 glycoside hydrolase genes (15. 9 GHs Mbp -1 ), 42 on its chromosome and eight on its putative plasmid (Supporting Information Table  S1 ) -the highest numbers so far observed in Archaea (Supporting Information Fig. S2 ). Halorhabdus utahensis has 44 GH genes (14. 1 GHs Mbp -1 ) according to the CAZy database as of 10 December 2013  (Cantarel et al. , 2009; Lombard et al. , 2013). Halorhabdus tiamatea features genes for the degradation of xylan, arabinan, arabinoxylan and galactancontaining hemicelluloses, pectin and likely cellulose. These polysaccharides occur in land plant cell walls, algae  (Popper et al.
5 kbp for plasmid). DNA curvature and bending were calculated with the program banana from the EMBOSS package  (Rice et al. , 2000). TETRA  (Teeling et al. , 2004)  was used for the calculation of the deviation from the average tetranucleotide composition (sliding windows: 5 kbp for chromosome; 1 kbp for plasmid). decorating L-arabinose side chains from arabinoxylans and arabinogalactans. Arabinoxylans are likely degraded by concerted action of GH10 xylanases and GH51 arabinosidases. The resulting L-arabinose is then likely taken up, isomerized to L-ribulose and subsequently funnelled into the PP pathway. Halorhabdus tiamatea lacks any obvious galactanase and thus probably cannot use the backbones of galactans and arabinogalactans. However, its genome codes for a GH4 α-galactosidase and a GH42 β-galactosidase, which likely enable H.