dataesr/scientific-paragraphs-categorization huggingface dataset:
Operating space and projected fusion performance The operating space covered in the dataset at q 95 ~ 3 is shown in figure  20 , where the achieved β N in stationary discharges is plotted against the internal inductance l i (3). All four machines occupy roughly the same region of this parameter space and lie within the specified range for the ITER poloidal field coils for 15 MA operation (0. 6 < l i (3) < 1. 2). DINA-CH and an advanced transport modelling code, CRONOS were used  [54]  for simulations of the 15 MA ELMy H-mode inductive scenario, considering PF coil current and voltage limits. These studies showed that application of early heating and current drive is required in ITER to obtain plasma inductance  to values of l i (3) ~ 0. 72-0. 74 throughout the fusion burn phase, allowing plasma configurations to be maintained within the PF coil limits.
73, even discharges at the highest β N values achieved in AUG and JET only approach l i (3) = 0. 75. The data may indicate that it could be challenging to obtain the predicted (and required) edge pedestal pressure in ITER with a Be/W wall, but care should be taken comparing l i (3) values for different plasma shapes. Moreover, the plasma inductance is not a measure of the pedestal pressure, for this the dataset needs to be extended to include pedestal values for plasma density and temperature. The data show that values of β N ~ 3 can be achieved in stationary conditions at q 95 = 2. 7-3. 3 for a range of devices (AUG, JET and DIII-D). More data are available at high plasma beta for experiments with a carbon wall, but there seems to be no difference in plasma MHD stability related to the use of different wall materials.
The database does not document the limiting events to the β N values that can be obtained. H-mode discharges at q 95 ~ 3 limited by the appearance of an n = 1 tearing instability, after the discharge has run at constant pressure for several confinement times, are reported from DIII-D  [58]. The database presented here however does not contain MHD onset data to provide a survey across several devices. Experimental values of the stationary H-modes included in the database certainly exceed the values required for ITER (β N = 1. 8), showing that with potentially more favourable energy confinement at high beta (compared to IPB98(y,2) scaling), or with an increase of additional heating power, ITER could obtain Q > 10. Hence, the performance of ITER can be improved significantly; in terms of fusion power, P fus ∝ β 2 N /q 2 95 or duration by operating at higher average plasma temperatures and higher bootstrap current fractions (∝ q 95 /β N ).
7-3. 3 in the database, but more importantly because of variations in energy confinement with β N. Also, there is a marked difference between carbon wall devices and high-Z metal wall devices in that G ⩾ 0. 4 is only obtained for β N > 2 for high-Z metal wall devices, using dominant co-current NBI heating (AUG and JET). The figure of merit G uses the total plasma energy, including the fast particle pressure W fast. Only discharges with carbon walls can obtain W fast more than 20% of the total stored energy (W). However, analyses of the data show that the best performance is obtained for W fast /W in the range 5%-20%, which is the predicted fast particle content of ITER plasmas. The objective of achieving Q = 10 in ITER at 400-500 MW of fusion power seems achievable as shown by the simulations provided by the ITER team.
Moreover, the data from devices with carbon walls show that this objective could even be exceeded with the heating power available at ITER. However, as shown in figure  21  from high-Z metal wall devices achieve ITER requirements. This is demonstrated in more recent results with the Be/W wall at JET, not part of the database as entries are restricted up to December 2014, to allow sufficient time for publication of the data. JET obtained operation at a plasma current of 3 MA at q 95 = 3, reaching β N ~ 2. 15 and H 98y2 ~ 1. 1 in stationary conditions  [61].
Discussion The strongly negative beta dependence is a general feature of most energy confinement scaling laws derived from multimachine databases. A much weaker, in many cases negligible, beta dependence has been observed in dedicated experiments on both DIII-D  [34, 62]  and JET  [36] , where β th was varied whilst the other dimensionless parameters were held constant. This discrepancy has been explained in terms of correlations in the multi-machine database, most notably between β and the aspect ratio and differences in the energy transport dependency between core and edge of the plasma. This was illustrated in β scan experiments in H-mode plasmas with type-I ELMs in ASDEX Upgrade, which were at higher collision frequency compared to experiments in DIII-D and JET  [63]. These results suggest that degradation of global confinement with β is a plasma edge effect.
In addition, non-dimensional transport experiments in JT-60U show a beta degradation of energy confinement. Combining these JT-60U data with subsets of ASDEX Upgrade and JET data in the ITPA H-mode confinement database show that the shaping of the plasma cross section, as well as the fuelling condition of the H-mode discharges are possible candidates for causing the beta dependence of energy confinement, as well as causing variation of the beta dependence among different devices  [64]. The disagreement between single scan experiments of the dimensionless parameters and the scaling expressions based on database analyses for the dependencies on both β and ν C have been investigated before  [65]. Thomsen et al  [66]  showed that the condition of the datasets used to obtain the ELMy H-mode scaling in the late 1990s, such as the IPB98(y,2) scaling, is critical in view of their sensitivity to errors in the absorbed heating power and stored energy.
Moreover, the bias in ordinarily least squares regression due to measurement errors of the ELMy H-mode database is sufficient to explain the discrepancy in the β and ν C dependences provided that the error on the loss power and thermal stored energy is sufficiently large. In addition, no account is taken of the additional loss terms such as radiation and charge exchange. The analyses of Cordey et al  [65]  of using a reduced dataset for scaling closer to ITER parameters, has β and ν C dependencies closer to the dedicated dimensionless parameter scan experiments of β 0. 0 and ν -0. 3 C , similar to the results reported here. In obtaining an indication on a dimensional scaling with a minimum number of variables, a similar study for the thermal energy confinement time using only three fit param eters (I p , P loss , R geo ) was performed for the advanced inductive database from the ITPA-IOS TG, concentrating on data at high plasma beta for a range of q 95 values, but typically q 95 > 3  [26].
The regression for these data obtained τ scaling (s) = 0. 16P -0. 67 loss I 1. 41 p R 1. 04 geo and only gives a small reduction in the quality of the fit when applied to the dataset at q 95 ~ 3, with RMS error = 34%, compared to the fit given in equation (  10 ) that obtains RMS error of 30%. It demonstrates that the principle thermal confinement parameters for 0D data are similar for the two regimes. The database presented in this paper contains global scalar variables, no data are available (or included) that separate core and edge or pedestal contributions to plasma confinement. Most devices only give the total radiated power from the plasma without separating bulk and edge or divertor radiation. However, the separatrix crosses the area of strongest radiation, such that realistic assumptions on the radial error of the separatrix itself and on the errors of the radial uncertainty of the power deconvolution give rise to large errors on the power outside the separatrix compared to the total power.
Information on the pedestal and an agreed formalism to compute core and edge radiation should be included in future database activities coordinated by the ITPA as it may improve predictions to ITER for core confinement, pedestal pressure, and effect of core or edge radiation on plasma performance. Concerning core and edge separation for predicting confinement, Cordey et al  [67]  showed that models for the core and edge can be combined to provide a good fit to the ELMy H-mode database used for the IPB98(y,2) scaling. The resulting two-term scaling expressions are shown to give very similar predictions for the confinement time, in the next step devices such as ITER with a predicted stored energy in the pedestal that is 28%-50% of the total stored energy. The scaling of the thermal stored energy of the core plasma with dimensionless variables was found Bτ th ∝ ρ * -3.
02 β 0. 05 th to be an almost pure gyro-Bohm form. Maggi et al  [68]  showed results for a multimachine database for the edge pedestal, with the pedestal top pressure increasing moderately with power in all tokamaks, in broad agreement with the power dependence of the IPB98(y,2) scaling. Also showing a robust correlation between the total and the pedestal thermal stored energy, with the pedestal stored energy between 30% and 50% of the total stored energy. The inclusion of data with high-Z wall from more recent experiments, would warrant another analysis of the pedestal and core confinement scaling. Regarding the total radiated power, the scaling of the thermal confinement does not include the radiated power loss from the bulk of the plasma, nor does the scaling for the H-mode threshold by Martin et al  [41]  include the radiated power to provide a scaling with P net = P loss -P rad,bulk , rather than with P loss only.
Hence, in predictions for ITER, the core radiation should not be subtracted in the computation of H 98y2 or τ th to allow comparisons of the confinement with experimental data. Even after restricting the dimensionless parameters in the trends shown in figures 5-7 in this paper, substantial variation in the normalised thermal confinement remains at fixed values of any of the dimensionless parameters. This variation may arise from changes not captured by the database, such as the ratio of the ion to electron temperature (T i /T e ), E × B shearing of turbulence, magnetic shear in the plasma centre and fast particle fractions. Especially, T i /T e > 1, plasma rotation and fast particle pressures might influence the results obtained at low collision frequency as they have been obtained at low plasma density with co-neutral beam heating in current day devices.
The dataset does contain information on T i /T e and fast particle stored energy, but not consistently across the five devices to draw any conclusions. More work is needed to broaden the data available q 95 ~ 3, supported dedicated experiments on electron heating and variations of the torque input as reported by DIII-D  [69]  and by AUG  [70]. Beurskens et al  [71]  showed that Type I ELMy H-mode operation in JET with the ITER-like Be/W wall generally occurs at lower pedestal pressures compared to those with the full carbon wall and that changes in the pedestal stability may have contributed to the reduced pedestal confinement in JET-ILW plasmas. The data presented in this paper, show that the performance potential of devices with a carbon wall is higher and only the best results from devices with a high-Z wall show that ITER should be able to obtain Q ~ 10 at P fus ~ 500 MW.
Summary and main conclusions A database with global parameters of stationary H-mode discharges at q 95 = 2. 7-3. 3 with data from AUG, C-Mod, DIII-D, JET and JT-60U provides a unique overview of the operational range of the baseline scenario proposed for ITER. Sufficient data are obtained to study plasma confinement trends with proxies for the dimensionless variables, such as normalised gyro-radius (ρ * ), collision frequency (ν C ) and beta ( βth ), with one dimensionless variable while restricting the range of the other two. The ITER values for ρ * are significantly lower than the existing dataset, while ITER values for νC are obtained in experiments today and ITER values for βth have been exceeded (figure  4 ). The data show trends of Bτ th with ρ * between gyro-Bohm ρ * -3 and Bohm dependence ρ * -2.
Discharges at the lowest values of νC show confinement trends closest to gyro-Bohm scaling (figure  5 ), the dataset does have values for νC that approach ITER values only for discharges obtained with carbon walls. Devices with high-Z metal walls have (so far) not found a way to access the low collision frequencies routinely. AUG can only achieve low collisionality for a few discharges following a boronisation of the high-Z walls, with the fresh boronisation mimicking a beryllium first wall in ITER. The dependence on collision frequency is weakly negative, with Bτ th increasing at lower νC values (figure  6 ). The dependence of Bτ th with beta is not negative as suggested by the IPB98(y,2) scaling (figure  7 ). A good fit to the trends is no dependence on beta ( β0 th ). Hence, the IPB98(y,2) scaling written in dimensionless form Ä Bτ th ∝ ρ * -2.
2-0. 45 (figure  15 ). The ITER reference configuration has a design value δ x = 0. 49, experiments targeted in obtaining data at q 95 ~ 3 for triangularities >0. 5 at f GW > 0. 8 and H 98y2 > 0. 95 are recommended to give more confidence that the required confinement can be achieved at high plasma density in ITER. AUG and JET with high-Z walls cannot obtain stationary H-modes at low input power without mitigation strategies for avoiding tungsten accumulation, such as gas dosing for maintaining high enough ELM frequency with low tungsten sputtering. Hence, H 98y2 = 1 is only obtained at β N ~ 2 or higher, with P in /P LH ~ 2 (figure  16 ). H 98y2 ⩾ 1 can be obtained in discharges with dominant RF heating for the full range of P RF / (P NB + P RF ) from 0% to 100% (figure  17 ). Bulk radiation fractions observed in both carbon and metal wall devices are similar to ITER simulations (figure  18 ).
Moreover, requirements for ELM mitigation and tungsten accumulation may lead to poorer H-mode confinement H 98y2 ~ 0. 8-0. 9 at β N < 1. 8. From the data presented here, it is likely that in ITER the energy confinement time will not increase with plasma density and will have no degradation with plasma beta. These observations should be used in simulations for ITER, rather than assuming H 98y2 = 1. The implications of this reduced confinement for tungsten divertor operation together with the lack of beta dependence of the energy confinement on the required additional heating to meet the ITER high Q objectives in the DT phase need to be assessed. The database presented here could be improved by a better separation of the core and pedestal region for the stored energy and radiation of the plasmas.
Nevertheless, the current database represents a wealth of data for the ITER baseline, collected by the IOS TG of the ITPA. The analyses and projections discussed here indicate that operation at 15 MA at q 95 ~ 3 in ITER can fulfil the primary objective of Q = 10 operation at 500 MW fusion power for 400 s to 500 s, while guiding further experiments and simulations for ITER. necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.
Acknowledgment Discussions with the Integrated Operation Scenario Topical Group of the ITPA are appreciated. This material is based upon work supported by the  U. S. Department of Energy (DoE)  award  DE-FC02-99ER54512  using  Alcator C-Mod  and award  DE-FC02-04ER54698  using DIII-D, as  DoE Office of Science User Facilities. This work has been carried out within the framework of the  EUROfusion Consortium  and has received funding from the  Euratom  research and training programme  2014-2018  under grant agreement No  633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission or the ITER Organisation. DIII-D data shown in this paper can be obtained in digital format by following the links at https://fusion. gat. com/global/D3D_DMP. This report was prepared as an account of work sponsored by an agency of the  United States Government.
, 2017). The turbopause and exobase are observed to move together in response to the warming of the lower atmosphere  (Jakosky et al. , 2017) , and the Mg + layer is expected to follow suit. Therefore, altitudes considered here are relevent for the stated observing conditions and are not intended to represent the Mg + layer generally. The Mars Climate Database v. 5. 2 (http://www-mars. lmd. jussieu. fr/mcd_python/) (Forget et al. , 1999)  is used to provide vertical profiles of temperature, pressure, and the mixing ratios of CO 2 , O 2 , O 3 ,O, O 2 , and CO (Figure  S1 ). The electron density profile is also taken from the Climate Database, and electrons are assumed to be balanced by O 2 + ions  (González-Galindo et al. , 2013). Daytime low-latitude conditions are used (local noon, latitude = 0°, solar longitude L s = 85°).
This dataset was retained for further analysis (Fig. 1a ). Half-lives have been determined with classical linear model fitted on log concentration of mRNA (see example of a set of 50 randomly selected mRNAs in Additional file 2: Figure  S2 ). The half-lives obtained (Fig. 1 , median value > 13 min) were higher than previously published in the rph-1 control strain and the rph-1 Δpnp double mutant  [2, 29, 34] , however our growth conditions were different (prolonged stationary phase versus exponential phase), and this could justify in part the discrepancy in the results. We also hypothesized that a delay in the transcription arrest during the mRNA half-life measurement could lead to an increase in the determination of the general values of half-lives. Such a delay, probably due to RNA polymerase elongation activity in presence of rifampicin, was first demonstrated by Chen and coworkers  [34]  and modelled more recently  [35].
We have combined on Fig. 3 , the three plots of the degradation rate constant k (k = ln2/ half-life) versus the mRNA concentration obtained for the rph-1 control strain and the rph-1 Δrnr and rph-1 Δpnp double mutants, respectively. This figure allowed the visualization of a global negative relationship between degradation rate constant and the mRNA concentration for each individual strain but the level of correlation differed with the mRNA concentration. Three correlation phases were differentiated using a K-means clustering algorithm on the combined three datasets (see the correlation coefficients and p-values in the legend of Fig. 3 ). In phase I, for the lowest mRNA concentrations, the correlation was very strong; in phase II for intermediary mRNA concentrations, the correlation was less strong and in phase III for the highest mRNA concentrations, the correlation was not significant.
Microarray procedures A double-stranded cDNA synthesis kit (InvitroGen) was used to produce cDNA from 2 μg aliquots of total RNA. Aliquots of 1 μg of cDNA were labeled using the one color DNA labeling kit and 2 μg of labeled cDNA were hybridized onto E. coli K-12 gene expression arrays (Nimblegen, Roche) for 17 h at 42 °C according to the manufacturers' instructions. Arrays were washed and then scanned with a MS200 Microarray Scanner (Nimblegen, Roche). The images were analyzed with DEVA 1. 2. 1 software. Only raw data were used for further analyses. All array procedures were performed by the GeT-Biopuces platform (http://get. genotoul. fr).
Transcriptome and genome-wide mRNA half-life measurements For transcriptomic analysis, raw probe intensities were processed and analyzed with the R computing environment using the affy  [53]  and limma  [54]  packages of Bioconductor. Raw data were submitted to a RMA-based background correction  [55]. After background correction, intra-replicate quantile normalization was performed for each strain. A set of probes in the background for which the ranks were roughly invariant across all nine arrays was selected. The median value of the invariant probe set intensities in each condition was used as a scaling factor for normalization between the three strains. After normalization, the intensity of a transcript was calculated by a RMA-summarization procedure  [55]  within each condition. Intensity values were multiplied by the total RNA extraction yield (in μg total RNA per mg of dry cell weight) to provide the mRNA concentration value in arbitrary units per mg of dry cell weight.
The rRNA depleted RNAs were then fragmented with RNase III and the 5'PPP structures were removed using RNA 5' Polyphosphatase (Epicentre). Afterwards, the RNA fragments were poly(A)-tailed using poly(A) polymerase and a RNA adapter was ligated to the 5′-phosphate of the RNA fragments. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to about 30 ng/μl using a high fidelity DNA polymerase and sequenced. The reads were mapped against E. coli genome (NC_000913 downloaded from NCBI genome database). The ncRNAs expression was quantified using Artemis  [57]  and the Log2 Fold change was calculated for each of the ncRNAs.
Confirmation of mRNA half-life data by northern blot Three genes osmB, ompA and nlpl were selected for additional calculation of their associated mRNA half-life using Northern blot method. Northern blots were performed using the total RNA samples extracted for microarrays. Briefly, 10-30 μg of total RNA were fractionated under denaturing conditions in 1. 2% agarose formaldehyde gel in MOPS buffer. RNAs were transferred onto Hybond-N+ membrane (GE Healthcare) and cross-linked by UV irradiation using a UVC 500 apparatus (Amersham Biosciences). Membranes were hybridized overnight with radiolabeled specific probes in PerfectHyb Plus Hybridization Buffer (Sigma Aldrich) at 68 °C. Specific probes (primers are given in Additional file 4: Figure  S4 ) were obtained by in vitro transcription reactions with PCR DNA templates carrying a T7 promoter sequence through the use of 32P-UTP and T7 RNA polymerase (Promega).
Funding This work was supported by grants from the collaborative INTERREG  Interbio  project ( 2011-2012 ). This work was also supported by  Fundação para a Ciência e Tecnologia (FCT-Portugal ), Project  LISBOA-01-0145-FEDER-007660  ( Microbiologia Molecular ,  Estrutural e Celular -R&D Unit ,  UID/CBQ/04612/2013 ) funded by  FEDER  funds through  COMPETE2020 -Programa Operacional Competitividadee Internacionalizacao (POCI)  and project  PTDC/BIA-MIC/1399/ 2014. This work also received funding from the  European Union 's  Horizon 2020 research and innovation program  under grant agreement No  635536. Clémentine Dressaire  and Vânia Pobre were recipient of  FCT Post-Doctoral Fellowships  ( SFRH/BPD/65528/2009  and  SFRH/BPD/87188/2012 , respectively).
1  A and Fig. S1 A ). HSCs also express significant levels of two other movable REs, SINE B1 and IAP (Fig. S1 A ). Quantitative PCR (qPCR) analysis performed on RNA samples before reverse transcription gave very low or undetermined cycle threshold (Ct) values, indicating that the higher RE expression found in HSCs was not a result of genomic contamination (data not depicted). In addition, expression of L1s and IAP was much lower in myeloid progenitor populations than in HSCs even though all the samples were prepared and tested together. L1 fragments are frequently embedded into genes. The limited numbers of HSCs precluded us from performing Northern blot analysis. Thus, to confirm that HSCs express full-length L1 mRNA rather than truncated forms that would be transcribed from other genomic sites, purified RNA was reversed transcribed using a sense-strand L1-specific primer recognizing the 3′ end of ORF2 (Fig.