dataesr/scientific-paragraphs-categorization huggingface dataset:
The measurement noise amounts to 0. 6 ppb, calculated as the standard deviation of the averaged measurements of The Glade (E) and Za Miastem (N) from 07:00 to 10:00 UTC on 28 May 2018 (see top panel in Fig. 7 ). W is a diagonal matrix with elements 1 x a,j , j = 1,. , m, which renders the second cost term dimensionless  (Butz et al. , 2012). Technically, we transform the Phillips-Tikhonov regularization problem into a plain least-squares fit using the definitions  (Hansen and O'Leary, 1993; Hansen, 1999; Golub and Von Matt, 1997 ) C = S -1 2 K λ W and d = S -1 2 y λ W x a , (2) which transforms Eq. (1) to x λ = argmin C x -d 2 2 , (3) and is treatable by a standard least-squares solver (e. g. , python module scipy. optimize. lsq_linear). The a priori information x a for each ventilation shaft is taken from the annual E-PRTR emission inventory updated by  Gałkowski et al.
Beside excluding data at the start of the daily time series due to the travel time, we also exclude data that we diagnosed to be affected by systematic forward model errors. The periods before 10:00 and after 13:30 UTC on 28 May (Fig. 8 , upper panel) are an illustrative example. For these periods, we find substantial deviations between the measured and modeled time series that the optimization cannot resolve by adjusting emission rates. We expect that such patterns originate from systematic errors in the wind fields that drive FLEXPART. If we include these periods in our optimization scheme, we end up with distorted L-curves (Fig. 9 , upper panel, grey dashed line). Thus, inspection of the L-curve provides us with a diagnostic tool to identify periods that are affected by forward model errors, which we then exclude.
The other excluded periods are around noon on 6 June and the beginning of 7 June (faint colors in Fig. 8 ). After selecting the data periods well represented by the FLEXPART simulations and choosing a suitable regulariza- tion parameter, we estimate the compatible shaft-wise emission rates illustrated in Fig. 10. Before evaluating the estimates, it is mandatory to inspect the emissions averaging kernels (upper sub-panels in Fig. 10 ), which encode the information on whether individual shafts or groups of shafts can be resolved. For 28 May (upper panel in Fig. 10 ), the emissions averaging kernels are greater than 0. 7 and well positioned for the two Silesia shafts, while, for the Brzeszcze shafts, the emissions averaging kernels are small, indicating that there is very little measurement sensitivity to these shafts.
Acknowledgements. The Heidelberg team acknowledges support by the  Heidelberg Center for the Environment  and funding by the  Excellence Strategy  -a funding program of the  Federal and State Governments of Germany. Further, we acknowledge funding for the CoMet campaign by  BMBF  ( German Federal Ministry of Education and Research)  through  AIRSPACE  (grant no. FKZ:  01LK1701A ). We thank  DLR VO-R  for funding the young investigator research group "Greenhouse Gases". This work used resources of the  Deutsches Klimarechenzentrum (DKRZ)  granted by  its Scientific Steering Committee (WLA)  under project IDs  1104  and  1170. Financial support. This research has been supported by the  Bundesministerium für Bildung und Forschung  (grant no. FKZ:  01LK1701A ), the  Deutsche Forschungsgemeinschaft  (excellence strategy grant), and the  Deutsches Klimarechenzentrum  (grant nos.
Data availability. WRF v4. 0 can be downloaded from https: //www. mmm. ucar. edu/weather-research-and-forecasting-model (University Corporation for Atmospheric Research, 2020). FLEXPART-WRF can be downloaded from https://www. flexpart. eu/ (Zentralanstalt für Meteorologie und Geodynamik, 2019). Model setups for both models employed are available upon request. Data are available from https://doi. org/10. 5281/zenodo. 6512078 (Luther, 2022).
Acknowledgments This project has received funding from the  European Union 's  Horizon 2020 research and innovation programme  under grant agreement No  872102. The authors at  Tianjin University  acknowledge financial support from the  National Key R&D Program of China  ( 2019YFE0123200 ), the  National Nature Science Foundation of China  (No. 21878219 ), and the  Haihe Laboratory of Sustainable Chemical Transformations.
Our survey with the NOEMA (NOrthern Extended Millimeter Array) interferometer consists of several observing runs starting from 2012 with the latest datasets arriving in January 2022 and covers the line and continuum emission in the 100-200 GHz frequency range of more than 16 northern FUors reaching spatial resolutions of around 1000 au. In each case, the main targeted lines are transitions of 13 CO and C 18 O in order to map both the more di↵use and denser gas and assess excitation temperatures, opacities and possibly column densities around the objects. On-the-fly observations with the IRAM 30 m telescope are merged to exhibit an accretion rate of 10 -4 M year -1 compared to the typical rate of 10 -8 M year -1 for T-Tauri stars. The length of these FUor-type eruptions can reach years or decades, have been observed at all stages of star formation and theorized to be quasi-recurring, together with their shorter-timescale, fainter counterparts called EXor-outbursts (named after EX Ori) which show accretion rates of at most 10 -7 M year -1 during eruptions.
Our survey with the NOEMA (NOrthern Extended Millimeter Array) interferometer consists of several observing runs starting from 2012 with the latest datasets arriving in January 2022 and covers the line and continuum emission in the 100-200 GHz frequency range of more than 16 northern FUors reaching spatial resolutions of around 1000 au. In each case, the main targeted lines are transitions of 13 CO and C 18 O in order to map both the more di↵use and denser gas and assess excitation temperatures, opacities and possibly column densities around the objects. On-the-fly observations with the IRAM 30 m telescope are merged to Figure  1. NOEMA CO and continuum maps of northern FUors (adapted from  [7]  and  [8] ). Left: 13 CO integrated intensity map of V1735 Cyg. The cross marks the optical position of the FUor, the black contours are the 2.
7 mm continuum emission in units of Jy beam -1 at the 10. 90% of the peak. The dashed contour is the blue-shifted (integrated between -0. 2-2 km s -1 ) and the dotted contour is the red-shifted lobe (integrated between 7-9. 4 km s -1 ) of the outflow at 50, 70 and 90% of their peak emission. Right: 13 CO integrated intensity map of RNO 1B/C. The black contours are the 2. 7 mm continuum emission at the 10. 90% of the peak. The two crosses are the members of the binary FUorsystem (RNO 1B is at the center) and the star symbol marks an IRAS source. The letters mark clumps identified on the CO map and circles mark some of the other IR/sub-mm/mm sources in the vicinity. these datasets to correctly detect the large-scale gas emission the interferometer would filter out. Our maps revealed extended, fragmented gas clouds around all our targets on a few thousand au spatial scales with local peaks at or close to the FUors  [7].
Numerical implementation Because of the geometrical symmetry of hollow sphere model, only a quarter is considered, which is discretized by 1500 quadratic axisymmetric elements in Abaqus software (Fig. 3 ). The velocity field  =  ⋅ is prescribed on the external surface, which can be achieved by a MPC (Multi-Points Constraints) user subroutine in Abaqus/Standard  (Smith, 2009). The implementation of such MPC program was firstly provided in void interaction and coalescence study of polymeric materials  (Cheng and Guo, 2007) , and has been successfully used in the studies of porous media  (Cheng et al. , 2014; Shen et al. , 2018; Zhang et al. , 2017). Hence, the enforced macroscopic triaxiality  =   ∕  can be maintained during each loading cycle. The step-by-step path-following elastic-plastic incremental simulations of the considered structure under variable loads is a intuitional manner to analyze the corresponding responses of the transient phase until shakedown or collapse occurs.
Introduction Guiana extended-spectrum (GES) enzymes are a widely distributed family of class A β-lactamases  [1]  , which is commonly segregated according to their hydrolysis spectrum against β-lactams into carbapenemases (functional subgroup 2f) and extended-spectrum β-lactamases (ES βLs; functional subgroup 2de)  [2]. The GES carbapenemases possess a serine or asparagine at Ambler position 170, as opposed to glycine in the ES βL-type variants  [ 2 , 3 ]. This substitution is associated with the enhancement of the hydrolytic activity towards carbapenems  [2]. To date, 49 GES variants have been described, and at least 14 are carbapenemases according to the Beta-Lactamase DataBase -Structure and Function ( http://bldb. eu/ ). Furthermore, the genes encoding GES-type βlactamases are carried by class 1 and 3 integrons frequently associated with mobile genetic elements (MGEs)  [ 4 , 5 ] , which explains the widespread distribution of these enzymes reported worldwide  [2] [3] [4].
Bacterial strain and antimicrobial susceptibility testing In 2009, as part of a national surveillance study  [6]  , a carbapenem-resistant P. aeruginosa strain (P-10. 226) was recovered from a blood culture of a 47-year-old female patient hospitalised in an intensive care unit (ICU) at a tertiary hospital located in the city of Brasília, Federal District, Brazil. Species identification was performed by MALDI-TOF MS using the Microflex LT mass spectrometer and Biotyper 3. 3 software (Bruker Daltonics), according to the manufacturer's recommendations. Minimal inhibitory concentrations (MICs) were determined by cation-adjusted broth microdilution, except for ceftazidime/avibactam, which was tested by Etest gradient strip (bioMérieux, France) following manufacturers' recommendations. The MICs were interpreted according to Brazilian Committee on Antimicrobial Susceptibility Testing and EUCAST breakpoints ( http://brcast.
For short-and long-read hybrid genome assemblies we used a customised Python ( https: //github. com/wshropshire/flye _ hybrid _ assembly _ pipeline ). Raw assemblies are created with Flye v. 2. 7  [8]  , and then undergo a series of error correction steps using first an interactive long-read polish step with Racon v. 1. 4. 5  [9]  followed by Medaka v. 0. 11. 5 ( https://github. com/nanoporetech/medaka ). The consensus Medaka assembly then underwent a series of Racon short-read polishing steps with a final error correction step using a modified Python script ( https://github. com/powerpak/pathogendb-pipeline/ tree/master/scripts ) that fixes regions with low, short-read coverage. AMR and plasmid determinants and virulence markers were identified using the ABRicate v. 0. 8. 10 ( https://github.
com/ tseemann/abricate ) tool using the Comprehensive Antibiotic Resistance Database (CARD -https://card. mcmaster. ca/ ), PlasmidFinder ( https://cge. cbs. dtu. dk/services/PlasmidFinder ) and Virulence Factor DataBase ( http://www. mgc. ac. cn/VFs/ ), respectively. In silico MLST was done using mlst v. 2. 15. 1 ( https://github. com/tseemann/ mlst ). Sequence data were deposited in the NCBI database under the Biosample accession number SAMN21357977.
1 A ). Besides this, six other copies of IS Pa157 were also detected in the genome of the P-10. 266 strain, as well as in five genomes of P. aeruginosa strains deposited in GenBank belonging to the Brazilian epidemic ST277 clone carrying the metallo-β-lactamase (M βL) encoding gene bla SPM-1 with 2 to 3 copies of the IS in each one  [ 21 , 22 ]. Remarkably, each IS Pa157 copy in the genome of P-10. 226 was flanked by distinct DRs ( Fig. 1 A ). These results demonstrated that IS Pa157 is a high-copy-number MGE that is distributed within P. aeruginosa genomes in Brazil, especially those belonging to ST277. Analysis of the region downstream of orf5 -IS5564::IS Pa157 genetic structure revealed the presence of a full copy of IS 6100 followed by a partial copy consisting of the last 321-bp of IS 6100 ( ) ( Fig.
(A) Distribution of GES-type variants in distinct GNB species according to each Brazilian geographic region [ 2 , 4 , 26-39 ] and (B) genetic structural comparison of class 1 integrons carrying bla GES-1 , bla GES-5 , and bla GES-16 described in Brazil. ( * ) Indicates those variants with carbapenemase activity. ( §) Integrons that have not a number assigned by the INTEGRALL database ( http://integrall. bio. ua. pt/ ).
2. 2 (A) Distribution of GES-type variants in distinct GNB species according to each Brazilian geographic region [ 2 , 4 , 26-39 ] and (B) genetic structural comparison of class 1 integrons carrying bla GES-1 , bla GES-5 , and bla GES-16 described in Brazil. ( * ) Indicates those variants with carbapenemase activity. ( §) Integrons that have not a number assigned by the INTEGRALL database ( http://integrall. bio. ua. pt/ ).
In conclusion, this wealth of data continues to demonstrate the interest of versatile and multivalent molecular tools for chemical biology investigations, in general, and of biomimetic, TASQ-based G4 ligands for G4-focused research, in particular. The biotinylated TASQ used here can indeed be implemented in various in vitro manipulations (affinity capture, optical imaging) to sharpen our knowledge about G4 biology. The technicality of TASQs is in considering their chemical access, that we have tried to improve here by using click chemistry for the key conjugation step between the PNA G units and the cyclen-based template. Overall, this strategy turned out to be synthetically advantageous and also revealed that changes to the TASQ scaffold result in a subtle modification of the G4interacting properties of the resulting TASQs, as exemplified by the differential ability to pull down G4-DNA (BioCyTASQ) or G4-RNA (BioTriazoTASQ).
Image Processing Images were processed with ImageJ (https://fiji. sc); for statistical hypothesis tests, Student's t-test and Welch's unequal variances t-test were used depending on variances equality. The automated foci quantification was made according to homemade FIJI add-ons, which can be download (free of charge) at https://github. com/ICMUB/TASQ/blob/main/ macro-eng_quantif-foci-int_TASQ-gH2AX. ijm.
The tube curvatures are positioned in the same plane in the aligned robot configuration, as shown in Figure  4A. The configuration was chosen because the planar robot shape is perpendicular to the camera view. To compare the robot's experimental backbone to that of the constant-curvature CTR model, MATLAB software was used to run the simulation and postprocessing analysis. Comparing the experimental results to the model revealed a similarity along the robot's backbone, as shown in Figure  4A. There was a mean deviation of μ x ¼ 0. 30 mm, a standard deviation of σ x ¼ 0. 17 mm, and a percentage error of 0. 83%. The same process was used for the case of antialigned robot configuration (where the two tube curvatures are aligned in opposite directions), as shown in Figure  4B. The experimental robot's backbone closely matches the backbone of the model (see Figure  4B ); comparing the two revealed a mean deviation of μ x ¼ 0.
Numerical Simulation and Evaluations For the numerical modeling and data processing simulation analysis, MATLAB software was used. The analysis included the arc geometry approach to piecewise constant-curvature (Figure  4A ,B), the closed-form geometric approach to IKM (Figure  4C ), and the stability evaluation (Figure  4D ). In addition, the software was used for data processing of the fabrication process characterization (Figure  6B ) and other analyses in the Supporting Information. For the FKM, the use of piecewise constant-curvature approximation simplified the kinematic modeling of continuum robots using two mapping decompositions. It was simplified by treating it as a discretized link section made of arc parameters. The CTR kinematics was usually mapped between: the actuator space [the joint variable consisting of the translation and rotation of each individual tube of the robot (q)], the configuration space [which are the robot backbone parameters (κ, ϕ, l)], and the task space [the tip pose due to the resultant shape of the robot backbone (x)], as shown in Figure  S3 , Supporting Information.
Acknowledgements The authors thank  Pierre Roux  for assisting in the prototyping of the robot and  Michaël Gauthier  for his valuable suggestions about the manuscript. This work was supported by the  Région de Bourgogne-Franche-Comté , the  ANR  project  μRoCS  ( ANR-17-CE19-0005 ), the  ROBOTEX network  ( TIRREX ANR-21-ESRE-0015 ), and by  EUR EIPHI program  ( ANR-17-EURE-0002 ).
| Library for metabarcoding The 18S ribosomal RNA gene (rDNA) amplicon library preparation and sequencing were performed at the sequencing facility of Genes Diffusion according to the standard metabarcoding workflow of the facility. The V2-V3 region of eukaryotic 18S rDNA was amplified by using adapter-tagged primers 18S-82F (5′-GAAACTGCGAATGGCTC-3′)  (López-García et al. , 2003)  and Euk-516r (5′-ACCAGACTTGCCCTCC-3′;  Amann et al. , 1990). 18S amplicon libraries were sequenced with the Illumina MiSeq pairedend system (Illumina). Raw sequence reads were deposited in the NCBI sequence read archive (SRA, BioProject PRJNA789723).
| Library for metatranscriptomics The cDNA library preparation and sequencing were performed at the Plateforme de Genomique LIGAN-PM (Université Lille, CNRS-UMR8199, Lille, France) following the Illumina TruSeq standard mRNA library preparation workflow (Illumina). The cDNA library was sequenced with the Illumina HiSeq 2500 system (Illumina). Raw sequence reads were deposited in the NCBI SRA (BioProject PRJNA789723).
| Data analyses: rDNA Sequence processing All 18S rDNA sequences were processed together using mothur version 1. 34. 0  (Schloss et al. , 2009)  following the standard operating procedure including normalization  (Kozich et al. , 2013). The data set was dereplicated to unique sequences and aligned against the SILVA 108 database (http://www. arb-silva. de). Suspected chimeras were removed by using uchime  (Edgar et al. , 2011). After quality filtering, an average of 100,646 rDNA reads per sample were clustered into operational taxonomical units (OTUs) at 97% similarity threshold  (Edgar, 2010) , using the average neighbour method in mothur. Single singletons, referring to OTUs that have a single representative sequence in the whole data set, were removed as these are probably erroneous sequencing products  (Behnke et al.
, 2011; Kunin et al. , 2010; Reeder & Knight, 2009). After normalization of the entire data set, all remaining (964 OTUs) sequences were searched against the PR2 curated database  (Guillou et al. , 2012)  and SILVA 132 database  (Quast et al. , 2013)  by using blastn  (Altschul et al. , 1990). blastn results were carefully examined and manually curated before putative taxonomic affiliation was assigned to each OTU. To categorize the impact of the chytrid epidemic on microbial community members, patterns of relative read abundances for each OTU during the studied period were grouped into "beneficiary," "victim," "opportunist" and "neutral/unclassified. " The relative read abundance of each OTU was.
Based on the resulting alignment files, tables with counts for each feature were generated by using the htseq-count script in htseq  (Anders et al. , 2015). These count tables were then taken in as inputs for the differential expression analysis (step iv) that was carried out with deseq2  (Love et al. , 2014). According to the results of step (iv), differentially expressed feature sequences were annotated on the protein database using blastx  (Altschul et al. , 1990)  in order to infer their functions (step v). blastx annotation results were manually curated to categorize the function of genes.
| Cladogram analysis for chytrid affiliation A cladogram analysis was performed to provide an overview of taxonomic affiliation and specific subgroup assignments for chytrid OTUs found in this study, along with chytrid reference sequences that were previously found in Lake Pavin and public databases. Sequences of 68 OTUs affiliated with chytrids were aligned using muscle (version 3. 8. 31) (Edgar, 2004 ) and all positions containing gaps were eliminated using bioedit version 7. 2. 5  (Hall, 1999). The cladogram analysis was performed on 465 sites that could be unambiguously aligned, using maximum-likelihood (MCL) methods implemented in mega7  (Kumar et al. , 2016)  based on the Tamura-Nei model  (Tamura & Nei, 1993). The initial tree for the heuristic search was obtained by applying the neighbour-joining method to a matrix of pairwise distances estimated using the MCL approach.
| Active functions in Chytridiomycota during chytrid epidemics According to the results of blastx analyses, putative functions of transcripts were assigned. During the chytrid epidemic, functions of 546 up-regulated transcripts in Chytridiomycota were identified (Table  4 ). They could be generally categorized as: 69 stress-tolerancerelated, 17 host-invasion-related, 45 host nutrient processing, 52 colonization-related, 342 other cell functions and 21 unknown/ hypothetical proteins. Around one-third of these transcripts appeared relevant to the parasite lifestyle. Stress-tolerance-related functions include proteins in response to reactive oxygen species (ROS), heat/cold-shock proteins, chaperons, and DNA damage-repair proteins. Host-invasion-related functions include cell adhesions, toxins and proteases/peptidases.
TA B L E 3 Summary of blastx annotation for metatranscriptomics analyses Bacillariophyta (diatoms) is a phylum in the kingdom Chromista. b Numbers in parentheses represent the number of up-regulated genes that were identified as Chytridiomycota genes by the blastx analysis. Chytridiomycota (chytrids) is a phylum in the kingdom Fungi. belonged to these two diatoms. Among the few diatom species  granulata and As. formosa (representing over 98% of all diatom reads), it is highly likely that diatom transcripts abundantly expressed during the spring bloom (9651 transcripts, Table  5 ) represented active functions of these two diatoms. Comparatively, transcripts/functions involving lipases, transporters, histone, vacuolar systems, proteasome, proteases, DNA/RNA polymerases, and caspases/metacaspases were more abundant during the diatom bloom (Table  5 ).
| Active functions in "beneficiaries" during chytrid epidemics In addition to active functions in diatoms, the functions of other "beneficiary" organisms during chytrid epidemics were also extensively explored based on blastx results and available genome information. A diverse ciliate protozoa class, Spirotrichea, had 1658 transcripts identified as more abundant during the chytrid epidemic (Table  6 ). Besides ribosomal proteins and hypothetical proteins, transcripts of protease/peptidase (including proteasomerelated protease and ubiquitin) were particularly abundant (176 transcripts, Table  6 ). Other abundant functions include 54 energy/ ATP-related transcripts, 48 carbohydrate metabolism-related and 11 lipid metabolism-related (Table  6 ). The abundance of functions related to protein, carbohydrate and lipid metabolism and energy suggests that "beneficiary" Spirotrichea were active and possibly consuming chytrid zoospores.
| A panorama of active functions in a eukaryotic microbial community One major advantage of metatranscriptomics is that it provides a snapshot of all active functions in a microbial community at the time of sampling. During the diatom bloom, 12,062 up-regulated transcripts had probable functions identified. During the chytrid epidemic, 23,427 up-regulated transcripts had probable functions identified. Generally categorized by functions, details of these transcripts are presented in Table  7. Comparing the two sampling points, a higher proportion of upregulated transcripts were categorized as hypothetical/uncharacterized proteins during the diatom bloom, with most of them belonging to Bacillariophyta (diatoms). This is probably due to the lack of complete Asterionella and Aulacoseira genome sequences in the database.