dataesr/scientific-paragraphs-categorization huggingface dataset:
within each POLDER superpixel via a nearest pixel approximation collocation. The final joint products thus provide all coincident POLDER and MODIS cloud products at the same spatial resolution of about 20 × 20 km 2. Note that the official cloud phase products from MODIS use index values representation (1 for ice, 2 for liquid, 3 for mixed). In PM dataset, this cloud product is reproduced by counting the number of ice, liquid and mixed pixels in the POLDER super-pixel. If all of MODIS pixels in the POLDER superpixel have ice (liquid or mixed) phase, the final phase is directly labeled as ice (liquid Discussion Paper | Discussion Paper | Discussion Paper |.
Conclusions Although they are independent modelling approaches, both tectonic reconstructions and convection models with plate-like behaviour and continental lithosphere converge to support that seafloor spreading fluctuates significantly over 200 My. Indeed, the shape of the area-age distribution is time-dependent and changes from rectangular-like in periods of tectonic quietness, to skewed in periods of generation of new plate boundaries. The triangular-like distribution of the present-day Earth corresponds to an intermediate state. In the past 200 My, aggregation of Pangaea led to a quiet period and dispersal phases involved subsequent skewed distributions. The convection models show that seafloor spreading dynamics itself, without significant continental drift, can lead to such time-dependence.
allowing us to track the properties of the plates themselves through time. In the Triassic, the vast Panthalassic and the smaller Tethys Ocean sur-rounded the supercontinent, Pangaea. Panthalassa, modeled as a simple three plate spreading system between the Izanagi, Farallon and Phoenix plates dominated the planet, accounting for over half iof ts surface area. The expansion of the Tethys Ocean at the expense of the palaeo-Tethys (which was being consumed along the Tethyan subduction zone) was accommodated by the Meso-Tethys spreading ridge system. The predominant plate boundary regime operating in the Triassic/Jurassic was subduction, particularly around the rim of Panthalassa and along the northern Tethyan margin. By 200 Ma, Pangaea was undergoing slow continental break-up centered along a rift zone extending along the north and central Atlantic, through eastern Africa and southern South America (Figure 3) leading to the onset of a progressive increase in ridge lengths and increasing crustal production (Figure 4).
The initial break-up separated Pangaea into Laurentia, Laurasia and the China/Amuria block in the northern hemisphere and Gondwanaland in the southern hemisphere. The birth of the Pacific plate within Panthalassa at 190 Ma and the change from rift to drift along the central Atlantic initiated a period of younging of the ocean floor and increase in the global ridge length. The final break-up of Pangaea was established by 160 Ma, dividing Gondwanaland into its eastern and western portions via rifting and seafloor spreading between Africa, India, Antarctica, Madagascar and east Gondwana. The closure of the palaeo-Tethys, composed of mature oceanic crust was completed by around 170 Ma and the Mongol-Okhotsk Ocean by 150 Ma. The continual growth of the Pacific plate at the expense of the Izanagi, Farallon and Phoenix plates led to an increasing length of mid ocean ridges and production of young ocean crust in the Pacific domain (Figure 3).
The higher proportion of new crust produced at the mid ocean ridges compared to old crust being destroyed along the subduction zones of the northern Tethys and circum-Panthalassa is reflected in the change from a rectangular-like area-age distribution during Pangaea amalgamation towards a triangular distribution, reflecting a scenario consistent with a near constant production of oceanic lithosphere compared to what is destroyed, similar to the present-day state of the planet (Figure 3).
Growth curves and parameter determination The nine strains were grown in MMB plus 0. 15% yeast extract, with 2% glucose or 2% oleic acid, in 500-ml Erlenmeyer baffled flasks, to improve the dispersion of alkanes and oxygen supply  [30]. Cells from overnight YPD cultures were used to inoculate the culture at an initial OD 600 of 0. 5. Biomass production was followed by measuring OD 600nm every two or three hours. Cells grown in the presence of oleic acid were washed twice with 0. 5% bovine serum albumin and then once with 0. 9% NaCl before OD determination. We used a custom-developed R software script  [31]  to derive parameters from the growth curves: length of the lag phase l, growth rate corresponding to the maximum slope (mmax) and maximum cell density.
Use of non hydrophobic carbon sources Carbon assimilation tests have been performed for identification of the different species of the Yarrowia clade  [18, 19, 20, 21, 22, 23]. However, to obtain a homogeneous set of data, we assessed the ability of the nine strains to use 31 compounds. API galleries were initially used, for 30 compounds. The results were compared with the data available from the CBS (http://www. cbs. knaw. nl/). For 11 carbon sources, our observations were not consistent with those of the CBS for some strains, possibly reflecting differences in experimental procedures (API galleries, microtiter plate or agar plate tests) or carbon source concentration. Thus, liquid cultures in microtiter plates were used for these substrates, with glucose and sucrose used as positive and negative controls, respectively.
The results of these tests indicated that some hydrophobic substrates neither supported nor inhibited cell growth. The two exceptions were the two C6 compounds (hexanoic acid and methyl hexanoic acid), which strongly inhibited all strains, although YAPH and YAHI were able to grow on YP-methyl hexanoic after 20 days. Similarly, on MMB-methyl decanoate, no growth defect was observed at low cell density, whereas growth was strongly inhibited at high cell density. No such growth inhibition was observed on YP-methyl decanoate (Figure  2 ). Morphology on plates was very variable, ranging from smooth to rough colonies, and from superficial to agar-invasive forms, depending on the medium (see figures 2, 3 and data not shown). The presence of a halo around cells grown on plate containing insoluble substrates generally reflects the secretion of surfactants or of extracellular enzymes, such as lipases or esterases  [39].
10 OD 600 units after about 23 h of growth, with a generation time of 2. 06 h. By contrast, YAGA seemed be assimilate oleic acid much less efficiently, with a generation time almost twice that of YAHI. We were therefore unable to use the standard protocols for estimating lipid storage in Y. lipolytica. Thus, to ensure that the data obtained were comparable, we had to identify similar physiological stages not necessarily corresponding to the same time in culture. We estimated the maximal level of lipid storage, by determining cellular lipid content at various time points. Based on the growth curves obtained, we selected three time points between the beginning of the exponential phase and the deceleration phase. These time points corresponded roughly to the time required to obtain one fifth of the maximum OD 600 (OD max), half the OD max and the OD max.
Discussion We analyzed eight closely related species of the Yarrowia clade, to obtain preliminary data concerning their physiology and, in particular, their ability to grow on and to assimilate HS, before beginning comparative genomic and transcriptomic studies. All the data discussed below were obtained from a single isolate per species and may, therefore, not be representative of the entire species. As expected on the basis of published findings, despite their isolation from highly diverse environments (Table  1 ), these strains displayed a very limited range of non hydrophobic substrate used, with low levels of variability  [18, 19, 20, 21]. Glucose, fructose and glycerol were the only non hydrophobic carbon sources used by all strains of the clade. The screening of these strains for the detection of enzymatic activities useful for the exploitation of agricultural byproducts, such as xylose degradation, does not therefore appear to be pertinent.
SM has a PhD fellowship funded by the  French Minister of Research  via the ABIES doctoral school. This work was supported in part by the  Institut National de la Recherche Agronomique (INRA)  and additionally by the  SAS PIVERT , in the frame of the  French Institute of Excellence  in the field of  Low-Carbon Energies (IEED) P. I. V. E. R. T (www. institut-pivert. com)selected as an  Investment for the Future ("Investissements d'Avenir" ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
We comment further on this below when discussing comparisons against the ARCTAS data. Comparing FULL and DDEP shows that the best correlation occurs when emissions, enhanced deposition and chemical production terms, are included in the simulation. Figure  8  shows the corresponding comparison against the PEM-tropics B data for RONO 2 for BASE and DDEP. Here the measurement data represents the sum of different alkyl nitrates, namely C 2 H 5 ONO 2 , i-C 3 H 7 ONO 2 , n-C 3 H 7 ONO 2 and 2-C 4 H 9 ONO 2. For discussion regarding the chemical production of RONO 2 in BASE, the reader is referred to Sect. 4. As for CH 3 ONO 2 , the introduction of oceanic emissions of RONO 2 has little effect away from the source region but improves the quality of the comparison in the tropics between 10 • S-10 • N, especially at the surface.
Determination of Pulmonary Function Pulmonary function was estimated from the spirometric data FEV1, representing the forced expiratory volume in one second. To assess the variation of pulmonary function versus time during the first six months after transplantation, FEV1 ratios were calculated from the ratio of the difference between two spirometric values obtained approximately 1 month apart to the number of days between two spirometric measurements. We expressed these ratios in liters per second per day. Because we considered positive FEV1 ratios as a normal evolution of pulmonary function, only null and negative values of FEV1 ratios, which reveal a negative alteration of pulmonary function were taken into account for the study.
Statistical Analysis The values are expressed as the means6SD or the medians and percentiles. For the evaluation of the relationship between CNa and acute rejection, CN-a values were censored when patients received a first IV bolus of steroids. Kernel smoothing curves were generated and the dispersion of extreme CN-a values was determined. For the evaluation of the relationship between CNa and pulmonary function, we compared the rates of negative altered FEV1 at different CN-a levels. The survival without BOS, overall survival and the occurrence of adverse events were estimated by the Kaplan-Meier method. Other potentially associated risk factors of BOS occurrence were evaluated by using a stepwise logistic regression model. Analyses were performed by using SAS 9. 2 and Graphpad Prism softwares.
A large dispersion of CN-a values was observed, and since no reproducible pattern in CN-a could be discerned, we chose to express the CN-a data using their quartile range. For the We compared CN-a expression prior to transplantation in patients with or without cystic fibrosis (CF) since it is the main initial end-stage lung disease that led to lung transplantation in this cohort of patients and a similar dispersion of the CN-a values was found in CF+ and CF-patients (p = 0. 77, Mann-Whitney test). Subsequently, a relationship between extreme values of calcineurin activity and acute rejection was investigated. (B) Comparison across time of the median CN-a levels in patients displaying or not acute rejection: Kernel smoothing curves were generated. The 2 groups of patients displayed similar profiles of CN-a which consist of a phase of enzyme inhibition within the first 10 weeks after transplantation followed by a phase in which enzyme activity is restored.
Molecular docking of TC-AMP into the active site of PaKae1 Molecular docking was performed as blind docking by using the Autodock Vina 1. 1. 2 software (35) from the MGLTools 1. 5. 6 package (Molecular Graphics Laboratory of The Scripps Research Institute). This method refers to the use of a grid box that is large enough to encompass any possible ligand-receptor. The PDB file 2IVN related to Pa-Kae1 (19) devoid of its AMP-PNP ligand and TC-AMP substrate were used, respectively, as receptor and ligand for docking. A rectangular cuboid grid box with dimensions of 15 Â 10 Â 15 A ˚, along the x, y and z axes, respectively, was defined around the active site of Pa-Kae1 to circumscribe it entirely, and to accommodate free motion of ligands. All rotatable bonds within the ligand were allowed to rotate freely and the receptor was considered rigid.
Interestingly, whereas the ATPase activity of the whole PaKEOPS complex is stimulated by the presence of tRNA, the ATPase activity of the Kae1-Bud32 complex is independent of tRNA, suggesting that Pcc1 and/or Cgi121 were required for the response to tRNA. To test this hypothesis, we compared the ATPase activity of Kae1-Bud32-Cgi121 complex with that of the mixture of the Pcc1-Kae1 and Kae1-Bud32 binary complexes (Figure  3B ). In both cases, we recorded a significant ATPase activity that was independent of tRNA. However, when Kae1-Bud32-Cgi121 was combined with Pcc1-Kae1, or Cgi121 was added to the Pcc1-Kae1 and Kae1-Bud32 assay, we observed the wild-type tRNA-stimulated ATPase activity. Taken together, these data indicate that the simultaneous presence of both Pcc1 and Cgi121 is required for the tRNA-stimulated ATPase activity of PaKEOPS.
In line with this observation, the analysis of the same reaction mixture by TLC revealed the release of free inorganic phosphate, indicative of an ATPase activity. These results indicated that the autophosphorylation activity of Bud32 is modified in the context of the PaKEOPS complex. Because Bud32 interacts with Kae1 in the PaKEOPS complex, we hypothesized that Kae1 might be responsible for the modification of the kinase activity. We thus measured the autophosphorylation activity of Bud32-Cgi121 in presence of increasing concentrations of Pcc1-Kae1 complex. As predicted, the decrease of the phosphorylated Bud32 was proportional to the increase in concentration of Pcc1-Kae1 and was accompanied by an increase in the amount of produced free inorganic phosphate (Figure  5 ). In conclusion, our data demonstrated that in the context of PaKEOPS complex, Kae1 switches the activity of Bud32 from kinase into ATPase.
Consistent with our data, the structural study of KEOPS complex reported only the purification of the Kae1-Bud32-Cgi121 ternary complex (2). The structure of this complex revealed that interaction of Cgi121 with Bud32 altered significantly the conformation of Bud32, suggesting that binding of Cgi121 to Bud32 might provoke a chain reaction of conformational changes necessary for the formation of the whole KEOPS complex. Taken together, these observations indicate that Cgi121 does not participate directly in the catalytic activities of KEOPS; instead, it regulates these activities by acting as an allosteric effector. Consistent with this notion, Cgi121 has a short half life in the cells of S. cerevisiae ($30 min) and its average abundance is 10-fold lower as compared with Kae1 and Bud32 (PaxDb database) (2,37).
coli ThrRS numbering). This suggests that the metal-based mechanism for the recognition of threonine was acquired independently in two unrelated protein lineages and thus illustrates another case of convergent evolution. Kae1 and Pcc1 form the tRNA binding core of the KEOPS complex Using EMSA experiments, we showed that the tRNA binding profile of the Pcc1-Kae1 complex was comparable with that of the whole KEOPS complex. Moreover, the Bud32-Cgi121 complex showed low affinity for tRNA, whereas Cgi121 did not bind at all to tRNA. Taken together, these data indicate that the Pcc1-Kae1 complex is mainly responsible for tRNA binding, whereas Bud32 possibly plays a minor role. The predicted function of Kae1 in transfer of threonylcarbamoyl moiety implies that the anticodon loop of tRNA carrying the A37 nucleotide binds in the active site of Kae1.
cerevisiae carrying the same mutation exhibited a severe growth phenotype  (2). Taken together, these observations are compatible with a possible role of the Bud32 tail in regulating tRNA binding to the KEOPS complex. Putative mechanistic model for the catalysis of the threonyl-carbamoyl transfer to tRNA by KEOPS Based on the combination of biochemical data presented in this work and previous structural studies of the KEOPS complex, we propose a putative modus operandi for the catalysis of the last step in the biosynthesis of t 6 A modification (Figure  8 ). The TC-AMP intermediate produced by Sua5 is delivered into the active site of Kae1 probably during a transient interaction between Sua5 and Kae1. The metal ion bound in the active site of Kae1 participates in binding and recognition of the TC-AMP intermediate by forming coordination bonds with the side-chain hydroxyl group of threonine.
Sarcopenia was defined according to the ASD EWGSOP. The ASD combines an estimate of muscle mass and function, in addition to physical performance. Muscle mass was assessed by means of calf circumference, with a cut-off point of 31cm or less for diminished muscle mass, as described by Rolland et al  (16). Muscle function was measured by means of grip strength, with cut-off points adjusted for gender: 20kg for women and 30kg for men, meaning low muscle functioning, according to EWGSOP recommendations for grip strength. Finally, physical performance was defined according to gait speed by means of the 4-meter walking test, with a cut-off point of less than 0. 8m/s for low physical performance  (9). Cognition was assessed with the Mini-Mental Status Exam (MMSE), analyzing the data as a continuous variable (score 0 to 30)  (17).
The LHC is currently stopped for accelerator upgrade and should restart beginning 2015 for a period of three years. An integrated luminosity of 75-100 fb -1 at a center of mass energy from 13 to 14 TeV (Run 2) is expected. Afterwards, two data taking periods called LHC (approved) and HL-LHC (not approved yet) are expected to start in ∼2019 and ∼2023. The two periods should deliver 300-350 fb -1 (incorporating the Run 2 data) and 3000 fb -1 at √ s=14 TeV. During the two shutdowns prior to these periods, the two experiments will upgrade their detectors [6] [7] [8] to keep similar detector performance as Run 1 but under more severe conditions (more radiation, more pileup, higher trigger rate,. ). Based on the current experience with data analysis at Run 1 and the expected detector performance during the 300 and 3000 fb -1 campaigns, the ATLAS and CMS collaborations have recently provided expected precisions on the measurements of the Higgs boson properties and the accessible parameters for the search of new physics beyond the Standard Model (BSM).
Supersymmetry The observation of the Higgs boson with a mass of 125 GeV increases the need of finding a solution to the stability of its mass to large quantum corrections (the so-called hierarchy problem). Natural supersymmetry is one of the most effective and popular solutions to this problem. No evidence of this model has been found yet. The ATLAS [14] and CMS [11] collaborations searched for three particle families : generic squarks and gluinos, light top squarks (stop) and SUSY partners of the electroweak gauge bosons (EWKinos). Assuming a mass equal to zero for the Lighest Supersymmetric Particle, the current 95 % exclusion limits with Run 1 data are respectively ∼ 1. 8 TeV for g in a simplified squark-guino model (assuming m g=m q), ∼480 and ∼640 GeV for the top squark depending on the decay channel and ∼320 GeV EWKinos.
INTRODUCTION Titan's atmosphere is composed mainly of N 2 with a few percent of CH 4. Knowledge of the distribution of these constituents with altitude, latitude, and longitude is key to constraining the atmospheric structure and dynamics, and thereby investigating energy and momentum balance in the upper atmosphere. This knowledge is used to develop and constrain models investigating atmospheric chemistry, aerosol production, thermal balance, and escape processes. Measurements by instruments on the Cassini spacecraft provide data necessary to study these processes. At present there are uncertainties about the absolute magnitude of the N 2 densities in the upper atmosphere, with large disagreements among values inferred from in situ measurements by the Cassini Ion Neutral Mass Spectrometer (INMS)  (Cui et al.
Flyby T53 took place on 20 April 2009. We retrieved reliable data for densities in the 849 -1404 km region, near the evening terminator. The geometry of observation, including the tangent altitude or shortest distance between the UVIS line of sight and Titan's surface, was calculated by using the SPICE system developed by the Navigation and Ancillary Information Facility (NAIF)  (Acton 1996). The Sun subtended an angle of 1 mrad in the field of view. Based on this and the imaging performance of the instrument  (McClintock et al. 1993) , the spectral resolution is estimated to be 3. 6 Å. The size of the Sun projected onto the atmosphere is slightly larger than the altitude sampling interval (see Table  1 ). Therefore we choose to average every 2 samples to produce a net sampling distance of ∼8 km.
2002; Samson et al. 1987 ) not included in the calculations described above. These N 2 and CH 4 cross sections are measured only at room temperature; therefore the variation of absorption coefficient with temperature is not accounted for in this study. This variation is expected to be small in the wavelength region used. For CH 4 this argument is based on the behavior of the absorption cross section near 1200 Å  (Chen & Wu 2004). We used the number densities to derive the scale height and temperature. Fitting a straight line to the natural logarithm of our CH 4 number densities between 920 and 1302 km we found a scale height of (100 ± 2) km. The scale height for the range 849 -910 km is (56 ± 3) km. The change in scale height is also evident in the stellar occultation data from  Koskinen et al.
The temporal and spatial variability of the N2 densities precludes us from providing strong constraints on the INMS calibration. Nevertheless, the agreement between our profiles and the INMS profiles shown suggests that the scaling factor of 2. 9 is appropriate for N2. Interestingly, our CH 4 profile differs from the UVIS stellar occultation profile, measured for a different latitude of 39 • N on the dayside during T53  (Koskinen et al. 2011) , by a factor of about 1. 5 above 950 km. The profiles are closer at lower altitudes and coincide near 850 km. It is possible that the factor of 1. 5 arises because the stellar and solar occultations probed different latitudes. Although the CH 4 densities derived from UVS data differ from ours by a factor 0. 8 to 2. 5, our profile falls above their low uncertainty limit (not shown for clarity).