dataesr/scientific-paragraphs-categorization huggingface dataset:
As shown in the present work, the simple extrapolation of 14 NH 3 gain medium to the 15 NH 3 isotopologue directly allows to double the number of laser lines, while using strictly identical experimental conditions. Obviously, with some instrumental effort, pump frequencies can be adjusted to different spectral regions in order to access other fundamental bands of various molecules, as well as overtones and combinations bands providing even more possibilities to generate THz lasers lines. Such opportunities require to sort out and organize molecules and their energy levels allowing the generation of THz laser processes. Our study demonstrates, using the NH 3 molecule, that the generation of such database is of great help to guide the experimental production of new laser lines. To increase the number of entries in our laser database, we set-up a very versatile code interrogating HITRAN molecular spectroscopy database in order to extract all necessary information (energy levels, intensities, and Einstein coefficients of MIR and THz transitions) to generate new THz lines for any molecules already reported in HITRAN.
The description of the method used to generate the code is given in Section 4. However, such laser database relies entirely on the accuracy of the spectroscopic molecular characterization. Even though a few lines are currently missing for  15  NH 3 , our work reveals that the HITRAN database, which is constantly improving, is well suited to predict the position and strength of ammonia laser lines. Finally, deuterated isotopologues of ammonia are other good candidates for generating new THz laser lines. In particular, as for the H isopotologues, the rotational transitions will allow access to numerous frequencies higher than 1 THz. [44, 45]. Establishing their THz line catalogs, however, requires an investment from the spectroscopy community to record and analyze their FIR spectra in order to update the spectroscopic databases.
For a given J, the "a" level lies at higher energy than the "s" one (e. g. , see Figure  1 ). Selection rules for the ro-vibration transitions within the v 2 ¼ 1← GS (IR absorption) are: ΔJ ¼ 0, AE 1; ΔK ¼ 0; a ← s; s ← a (5) It is worth noting that "forbidden" ΔK ¼ 3 transitions exist and exhibit intensities about two orders of magnitude lower than the corresponding ΔK ¼ 0 transition. [46] These transitions are beyond the scope of this article, in part because in their current state, databases do not allow to reproduce them satisfactorily,  [46]  and because the expected G m values should be rather small. A schematic representation of the energy-level diagram of the lowest rotational states of NH 3 is displayed in Figure  1  for the ground and v 2 ¼ 1 states, the latter containing less than 1% of the ground state population at room temperature.
Establishment of a Catalog of Ammonia THz Laser Transitions Assuming the population inversion criterion is met for all pumped energy levels (and that the levels in the upper vibrational state are empty prior to pumping), one needs to possess several parameters in order to predict the list of possible THz laser frequencies using various IR pump transitions, and to calculate their molecular gain factors: 1) a list of vibrational transitions of the species (ν 02 and involved quantum numbers); 2) their corresponding spectral line strengths (S 0 02 ); 3) a list of pure rotational transitions within the lasing state (ν 21 and involved quantum numbers); and 4) the Einstein coefficient B 21 of these rotational transitions. In the case of 14 NH 3 and 15 NH 3 , all these parameters can conveniently be retrieved from the HITRAN online database  [37]  which was used to build the two catalogs in the present work.
Listing all possible pairs of pump/laser lines by identifying all pump and laser transitions sharing the same upper state, is rather trivial; calculating the G m values, however, require some care. Firstly, all entries in the HITRAN database are in CGS units. Secondly, the Einstein absorption coefficient A 21 is reported for each transition and the corresponding B 21 coefficient thus must be calculated. Thirdly, the S ij (S ij ¼ S 0 ij =c Â 10 2 ) values are reported at T ¼ 296 K thus, for a laser operating at a significantly different temperature, the spectral line intensities have to be recalculated (see Ref. [48]). Here, all G m calculations have been performed at T ¼ 296 K. Finally, the S ij values reported in HITRAN are weighted according to the natural terrestrial isotopic abundances I a while in the present work the molecular gain factor is established for a given isotopologue (thus at 100 % abundance).
Expressed as a function of parameters directly extracted from HITRAN, Equation (  13 ) becomes: G m ¼ S 02 A 21 ν2 02 ν3 21 10 À15 M 16π 2 hI a N A k B T (15) with G m in uG m , S 02 in cm molecule À1 (HITRAN unit), A 21 in s À1 , ν in cm À1 , M in g mol À1 , and I a unitless (I a < 1). In our catalogs, we also report the polarization axis of the THz laser beam relative to the IR pump polarization. If jΔJj 02 ¼ jΔJj 21 , the THz polarization axis is parallel to the IR pump one; otherwise it is perpendicular. [49] The frequencies of the THz laser transitions given in our tables correspond to the values given in HITRAN database. The corresponding uncertainty depends on the particular line and isotopologue, and typically ranges from 0. 3 to 300 MHz for 14 NH 3 and 15 NH 3. Specific values can be retrieved from the HITRAN database.
One can estimate the molecule-molecule collision rate as Γ NH 3 ÀNH 3 ¼ u 0 =l ¼ 1. 8 Â 10 5 s À1. To consider the collision between two identical molecules, we use the reduced mass μ ¼ m=2 rather than m to calculate the average relative speed u 0 ¼ ffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffiffi 8k B T=πμ p which leads to u 0 ¼ ffiffi ffi 2 p u. Thus, the global relaxation rate can be estimated to Γ NH 3 Àwall þ Γ NH 3 ÀNH 3 ¼ 2. 6 Â 10 5 s À1 , which is in agreement with the value extracted from the fit in Figure  4. supported by the ANR project HEROES (ANR-16CE30-0020), the CPER "Photonics for Society" and the Hauts de France regional council. This study was undertaken as part of the Terafood project, which is financially supported by the European Regional Development Fund and the province Oost-Vlaanderen (1.
3373. 6128 sR(3,0) 1046. 4055 4. 6 E-18 ⋆ 3332. 3527 sR(3,0) 1041. 0901 5. 2 E-18 ⋆ 1067. 6770 sQ(2,2) 967. 7384 4. 6 E-18 ⋆ 1030. 1163 sQ(2,2) 962. 5199 5. 0 E-18 2035. 4532 aR(4,0) 1034. 2448 4. 6 E-18 ⋆ 2064. 9399 aR(4,0) 1030. 1412 4. 9 E-18 ⋆ a)These lines are absent from our catalogs because one of the two lines is not reported in the HITRAN database. The reported frequencies are taken from ref. [51]. For these transitions, the G m factor of the corresponding pair of transitions in 14 NH 3 was scaled by the ratio of molar masses between the two species.
2b ; Table  2 ). Regionally, the same three strategies deliver the greatest benefit, though higher benefits are generally predicted for the Antarctic Peninsula region than the continent (S2 Fig. ), possibly due to the greater projected changes there. While the above summarises the number of taxa that would benefit and the total amount of benefit predicted under each management strategy for all taxa, it does not provide information on the amount of benefit to an individual taxon (where some taxa may benefit far more from a management strategy than others). Responses to management strategies vary amongst taxa in both scale and direction (see benefits for individual taxa shown on the Australian Antarctic Data Centre; https://doi. org/10. 26179/5da8f8e7a2256), for example Adélie penguins are predicted to increase intactness by ~45% with the 'Influencing external policy' strategy (RCP8.
g. ,  Chown and Convey 2007; Convey 2011; Cannone et al. 2016; Convey and Peck 2019). Such taxa expanding beyond current intactness may also have consequential negative impacts on other species, such as the grass Deschampsia antarctica's predicted ability to outcompete native mosses due to more efficient nitrogen acquisition  (Hill et al. 2011). Intactness estimates were recorded by biodiversity experts using an online tool created with JavaScript and HTML and hosted by a NodeJS web server on Amazon Web Services. The tool effectively functioned as a survey where biodiversity experts could select the taxon they wished to assess and then proceed through the questions estimating the benefits for both regions (Antarctic Peninsula and continental Antarctica) and for both climate forcing scenarios (RCP4.
RNA-sequencing and data preparation Total RNA was extracted from leaves and inflorescences with a cetyl-trimethyl-ammonium-bromide-based method (Methods S4), modified from  Chang et al. (1993). Sequencing libraries were prepared by the SNP&SEQ Technology Platform in Uppsala, using the Illumina TruSeq Stranded mRNA (poly-A selection) kit, and sequenced on three NovaSeq 6000 S4 lanes, with pair-end reads of 150 bp. One library was prepared for each diploid sample, and two libraries were prepared for each tetraploid sample. The RNA-sequencing reads of the same individual were later combined. All RNA-sequencing data are stored on SRA BioProject PRJNA848625. The quality of the raw RNA-sequencing reads (FASTQ format) was inspected with FASTQC  (Andrews, 2010)  and MULTIQC  (Ewels et al. , 2016).
The RNA-sequencing reads were then mapped to the reference genome of C. rubella  (Slotte et al. , 2013)  with STAMPY v. 1. 0. 32  (Lunter & Goodson, 2011). For mapping, the expected divergence from the reference (-substitutionrate) was set to 0. 02, 0. 04, and 0. 025 for C. grandiflora, C. orientalis, and hybrids, respectively. We used the same substitution rate for tetraploids and the corresponding diploids. SAMTOOLS v. 1. 5 (Danecek et al. , 2021)  was used for format conversion between steps. The mapping quality was then checked by QUALIMAP v. 2. 2. 1  (Okonechnikov et al. , 2016). The number of reads mapped to each transcript (total gene expression of both homeologs) was determined by HTSEQ v. 0. 12. 4  (Anders et al. , 2015). Only the reads that were unambiguously mapped to a single transcript were counted (mode 'union' in HTSEQ).
TE abundance To test whether a TE-mediated genomic shock occurred in the newly generated hybrids or polyploids, we compared the TE abundance in transcriptomes among the seven plant groups. If there is an ongoing large-scale TE-reactivation and proliferation in hybrids or polyploids, we expect both autonomous and passive TE transcription to increase and, therefore, a higher TE abundance in transcriptomes. Repeat sequences were first identified and annotated in the C. rubella reference genome  (Slotte et al. , 2013)  with the software REPEATMASKER v. 4. 1. 0 (Smit et al. , 2015) , using Brassicaceae repeat sequences from DFAM_3. 1  (Storer et al. , 2021)  and REPBASE-20181026  (Bao et al. , 2015)  as the reference repeat database. Simple repeats were excluded by the '-nolow' option. Then, the number of reads mapped to genes and TEs was quantified simultaneously with the TECOUNT package v.
Statistical analysis The difference in stem length, flowering time, number of pollen grains per flower, and extremely expressed genes per individual among the seven plant groups was tested by one-way analysis of variance (ANOVA) and Tukey's HSD test (R package 'AGRICO-LAE',  de Mendiburu & Yaseen, 2020). To test the effect of WGD and hybridization on the ratio of viable : nonvariable pollen grains, normal : abnormal seeds, or reads mapped to TEs : genes, generalized linear models (GLMs) were fitted to the data in the R software environment v. 3. 6. 3 (R Core Team, 2020), using both ploidy level (29/49) and hybrid state (hybrid/nonhybrid) as categorical factors. For all GLMs, a quasi-binomial error distribution with a logit link function was used to account for overdispersion. The effect of the factors and their interaction were then tested with F-tests using the CAR R package  (Fox & Weisberg, 2019).
2e, f ). All hybrid or tetraploid groups had fewer normal seeds per fruit than diploid parental groups (one-way ANOVA, F 6,181 = 94. 9, P < 0. 001; Tukey's HSD test, a = 0. 05). Both hybridization and WGD significantly affected the proportion of normal and abnormal seeds, and the interactions between the two variables were significant (Table  S3 ). WGD decreased the proportion of normal seeds among the nonhybrid groups but increased it for hybrid groups. The proportions of normal seeds of the F, Allo-h, and Allo-d groups were 0. 57 AE 0. 03, 0. 78 AE 0. 02, and 0. 70 AE 0. 04, respectively. Transcriptome-wide expression pattern was determined by hybridization, not WGD Gene expression was compared across the seven groups using RNA-sequencing data from leaves and flowers. Each tissue of each group was represented by six individuals, resulting in 84 RNA-sequencing libraries (Table  S4 ).
Acknowledgements The study was supported by grant  2019-00806  from the  Swedish Research Council  to ML and  Nilsson-Ehle  research grant from the  Royal Physiographic Society in Lund  to TD. ML also acknowledges support from the  Erik Philip-S€ orensen Foundation. TD was supported by the  Sven and Lilly Lawski Foundation. Computation and data handling were provided by the  Swedish National Infrastructure for Computing (SNIC)  at  Uppmax , partially funded by the  Swedish Research Council  through grant agreement no. 2018-05973. Finally, we thank  Elsa Sundkvist  for her help with seed counting.
Instrumentation The six wells were equipped with a water-level data logger U20-001-04 in 2018 and replaced with a U20l-04 in 2019 (HOBO, Onset, USA) for continuous measurements of the water table depth (WTD) and temperature from June 2018 to October 2020. Water temperature was recorded hourly in pools M11 to M15 using HOBO TMC50 probes coupled with a HOBO U12-008 data logger (Onset, USA) from June 2019 to August 2020. A water-level data logger was installed in pool M11 (Fig. 1 ), and water-level variations were measured from 20 May to 28 August 2020. Height variations (in cm) between the peatland surface at wells P5 and P6 and adjacent pool M11 were measured using a ZIPLEVEL Pro-2000 (Technidea, USA). Those measurements allowed the water levels in the pool to be compared with those in the two wells (Fig.
Statistical analyses All statistical tests were performed on R (CRAN project) through the RStudio interface (RStudio inc. , USA), and all figures were realized with the package ggplot2  (Wickham, 2016). Comparisons of variance tests were performed, and in the following sections, the mention of significant differences refers to statistical tests using the following method. First, normal distribution was tested using the Shapiro and Wilk test, and a normal distribution was considered true when the p value was >0. 05. If the distribution was not normal, a Kruskal and Wallis test was performed to compare the averages, and significant differences were considered true when the p value was <0. 05. Dunn tests were performed as post hoc pairwise comparison tests to determine which group was significantly different (when the p value <0.
90, with p values <0. 05. Therefore, the DOC : DON ratio (DOC : DON ∼ DOC, r = 0. 90, p value <0. 0001), %CAR_MIC (%CAR_MIC ∼ deoxyC6 : C5 ratio, r = 0. 99, p value <0. 0001), and f MIC (f MIC ∼ MIC : VEG ratio, r = 0. 98, p value <0. 0001) were excluded from the PCA data set. The PCA was performed with the package Fac-toMineR  (Lê et al. , 2008). The ellipses in the representation of the first two axes of the PCA correspond to the function addEllipses from the R package FactoMineR used to add concentration ellipses to the plot.
Acknowledgements. We thank  Katherine Velghe  and  Alice Parks  from  GRIL  for their laboratory training and assistance in absorbance and fluorescence analyses, as well as  Paul Del Giorgio  for access to his laboratory. Marine Liotaud, from  Géosciences Rennes , is acknowledged for performing THM-GC-MS analyses, and  Frederic Julien ,  Virginie Payre-Suc , and  Didier Lambrigot , from  Laboratoire Ecologie Fonctionnelle et Environnement , are acknowledged for performing DOC/TN and cations/anions analyses. We thank  Roman Teisserenc  ( Ensat, Toulouse ) and  Charles Bonneau ,  Charles-Élie Dubé-Poirier ,  Camille Girard ,  Pénélope Germain-Chartrand ,  Léonie Perrier ,  Guillaume Primeau ,  Khawla Riahi , and  Karelle Trottier  for their assistance in the field. Financial support. This research has been supported by the  Natural Sciences and Engineering Research Council of Canada and Hydro-Québec  funding to  Michelle Garneau  (grant no.
We therefore purified the full-length YukC and subjected the protein to crystallization trials. Unfortunately, YukC resisted all attempts at crystallization. We reckoned that the last 38 residues at the C terminus, mostly positively charged, could interfere with crystallization. We therefore produced a YukC 413 construct lacking these residues, which promptly crystallized. Its structure was solved by molecular replacement on a 2. 6-Å-resolution data set (PDB identifier [ID] 6Z0F) (Fig. 3A , Table  1 ) using the coordinates of the soluble domains from G. thermodenitrificans EssB as search models (PDB IDs 2YNQ and 4ANO). In the crystal, YukC organized as a pseudosymmetrical dimer with chains A and B revolving around a virtual central axis (384 and 377 residues assigned, respectively). The final stretch of residues could not be traced due to the lack of supporting electron density (Fig.
We tested whether this region might be involved in the interaction with YueB, which is the only T7SSb subunit having a large extracellular domain. Our bacterial twohybrid assay results show that YukC still interacts with a variant of YueB that is missing 90% of its extracellular domain (YueB INT , lacking residues 31 to 817) (Fig. S3E ). Since the other loops of YueB are relatively short, this result suggests that YukC and YueB may interact primarily through their TM regions, as proposed for the S. aureus homologs  (45). The pseudokinase domain. Structural comparisons between the PK domains of YukC and the homologous regions of EssB proteins from S. aureus (PDB ID 4ANN) and G. thermodenitrificans (PDB ID 4ANO) indicated a closer similarity to the latter (Fig. S3F ), reflecting their levels of sequence identity (15% with S.
The most important motifs characterizing Hankstype kinases are partially missing in YukC pseudokinases (Fig. S4A ). These include the glycine-rich P-loop coordinating the ATP band g-phosphate, the VAIK motif, and the catalytic, Mg-binding, and activation loops  (72). The structural comparison of YukC with PknB in complex with ATP (PDB ID 1O6Y) (RMSD = 4. 2 Å for their pseudokinase domains) shows that YukC has an additional a-helix in the ATP-binding pocket, with a large side chain (F 26 ) partially occluding the ATP binding site (Fig. S4B ). In agreement with this, microscale thermophoresis assays show that YukC cannot bind ATP in vitro, in contrast to PknB (Fig. S4C ). Taken together, these sequence and structural analyses, as well as in vitro ATP-binding assays, suggest that YukC is unable to bind ATP (and to hydrolyze it).
4C ). Altogether, these data show that the effector's secretion through the T7SSb is affected by the mutation of the central transmembrane residue P 231 , potentially involved in signal transduction. Interestingly, in the YukC structure, the orientation of the monomers diverges below the b-swap. This asymmetry is related to the different orientations of helix a8 in the two PK domains, favoring the H-bond between residues K 205 of chain A and A 80 of chain B (Fig. S4D , red asterisk). As a consequence, the PK domain of one monomer (chain B) is closer to the membrane plane than the other (Fig. S4E ). This further supports structural flexibility in the region of YukC surrounding the b-swap. In the future, it will be interesting to investigate the physiological effects of mutating these residues.
2C  and D ). FHA domains usually recognize and bind phospho-threonine residues on several eukaryotic and prokaryotic proteins  (38, 86). However, the phosphorylation of the threonine residues on YukC's domain requires a eukaryotic-like Ser/Thr kinase (eSTK) (or Hanks-type kinase), such as PrkC in B. subtilis  (87). Since the YukC-YukB FHA interaction was tested in E. coli, in which, to our knowledge, no typical eSTK is present  (88) , this suggests that the FHA-PK interaction in T7SSb is phosphorylation independent. Indeed, residues responsible for the binding of phosphorylated targets are not conserved in either the FHA of YukB  (38)  or those of EssC from S. aureus and G. thermodenitrificans (PDB IDs 1WV3 and 5FWH, respectively)  (37, 39). YukC's structure and its functional implications.
YukC crystallization and structure determination. Crystals of the YukC 413 construct were obtained by hanging-drop vapor diffusion in 0. 4 mL with a 1:1 ratio between the protein solution (20 mg/mL YukC 413 , 25 mM HEPES, pH 8, 175 mM NaCl, 0. 04% Cymal-6) and the crystallization solution (0. 1 M MgCl 2 , 50 mM HEPES, pH 7. 5, 15% [wt/vol] polyethylene glycol  [PEG 2000] ). Two-hundred-nanoliter drops were dispensed by a mosquito crystal robot (TTP Labtech) at 4°C, and crystals appeared within 3 days. The crystals were frozen in liquid nitrogen with a 50% Paratone N (Hampton Research), 50% paraffin oil solution as the cryoprotectant. A 2. 6-Å-resolution data set was collected on beamline ID30A-3 at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. Data were processed with autoPROC  (98) , and the structure (PDB ID 6Z0F) was solved by a two-step molecular replacement approach with PHASER (99).
RMSDs were calculated with MolProbity (100) within the PHENIX crystallographic software suite. A first molecular-replacement search was performed using the coordinates of the dimeric extracellular portion of G. thermodenitrificans EssB (PDB ID 2YNQ) as the probe, followed by a new search using the coordinates of the pseudokinase domain from the same protein (PDB ID 4ANO). Once a solution including both the intracellular and extracellular domains was identified, the missing part of the molecule, including the transmembrane domain, was modeled by combining automated tracing with Phenix AutoBuild (101) and manual rebuilding with Coot  (102). The overall model was then subjected to alternating cycles of inspection with Coot and refinement with BUSTER  (103). Analysis of the YukC dimer interface.
The selected protein sequences were aligned with the web tool T-COFFEE  (105) , and the structures were superimposed with the software UCSF Chimera  (106). Nanoscale differential scanning fluorimetry (nanoDSF). Thermal denaturation was performed on the Prometheus NT. 48 (NanoTemper) from 20 to 95°C with 80% excitation laser power and a heating rate of 2°C/min. The tryptophan fluorescence emissions were monitored at 330 nm and 350 nm as a function of increasing temperature. The purified YukC 413. strep construct and PknB were diluted to a concentration of 1 mg/mL in the presence or in the absence of 1 mM ATP in 25 mM HEPES, pH 8, 175 mM NaCl, 2 mM MgCl 2 , 0. 04% Cymal-6. The sample was filled into the capillaries, and the emissions at 350 nm and 330 nm were measured. The intrinsic fluorescence signal expressed by the 350-nm/330-nm emission ratio was plotted as a function of temperature.
Three replicates were performed for each protein. The average values of the replicates were calculated and are plotted in Fig. S4C. Analyses of YukC conservation and stability. The conservation of YukC was evaluated using HMMER software (http://hmmer. org). The sequence logo reported in Fig. S5C  is based on this alignment, and it was created at https://weblogo. berkeley. edu/logo. cgi. Analysis of the stability of YukC. His P231A was performed by expressing wild-type YukC (YukC. His) and the mutant (YukC. His P231A ) in E. coli, together with the membrane protein TseB as a control. Cell samples were collected at different time points after protein synthesis was blocked by chloramphenicol and were analyzed by Western blotting using antibodies directed against the His tag (for YukC) or against TseB.