dataesr/scientific-paragraphs-categorization huggingface dataset:
ACKNOWLEDGMENTS. We thank  Florent Goussard  for assistance with 3D datasets. We also thank  Paul Tafforeau  and the  European Synchrotron Radiation Facility  for help in scanning the original specimens. We are grateful to the two anonymous reviewers who gave valuable and highly constructive feedback on the manuscript. This work was funded by a  Paris Île-de-France   Region grant  ( Domaine  d'int  erêt majeur [DIM]  " Mat eriaux anciens et patrimoniaux ") awarded for the  DIM PHARE (Pharyngeal Evolution: illuminating its formed function in early jawed vertebrates)  project. R. P. D. is now supported by  Leverhulme Trust  Grant  RPG-2021-271  "Feeding without jaws. " A. P. is supported by the  Agence nationale de la recherche  (Grant CE02)  Terre vivante ,  jeunes chercheurs ou des jeunes chercheuses ,  MACHER  ( Mechanical Adaptation to Crushing in the Holocephalan Evolutionary Radiation ).
Environmental flow modelling can be achieved either by using wind-tunnel studies or via the utilization of Computational Fluid Dynamics (CFD) techniques. Conducting wind-tunnel studies may be expensive and time consuming, particularly in the event of additional test requirements with modified building and/or environmental configurations. On the other hand, CFD can provide significant cost benefits for assessing and optimizing engineering design solutions related to environmental concerns and appear attractive as a potential alternative tool. By using CFD in this manner it is anticipated that these types of advanced performance-based studies will be a useful tool and essential aid for urban designers and environmental planners. This paper discusses ongoing development and application of CFD simulations through a case study using CFD software for simulating air flow around a specific vernacular urban fabric of Ghardaïa.
The potential of CFD for prediction of wind speeds around a complicated urban environment and a complex fabric structures is investigated. As the 3D solid model of the geometry was not available a captured Google Earth image of the fabric structure was used as a backdrop in the AC3D software, supplied as a utility to Phoenics. The outlines of the buildings were then traced to create polygons, which were then extruded to produce the individual buildings. Finally, the entire scene was exported to the VR-Editor as a single Phoenics object. Résumé -La modélisation des écoulements dans l'environnement extérieur autour des bâtiments soit par la voie expérimentale en soufflerie ou par l'utilisation de la mécanique des fluides numériques (Computational Fluid Dynamics, 'CFD'). Les expérimentations en soufflerie peuvent êtres longues et coûteuses, en particulier dans le cas des configurations urbaines complexes où il est souvent nécessaire de faire de nombreux essais de modifications de paramètres et configuration de l'environnement.
INTRODUCTION There is a need to properly develop the application of Computational Fluid Dynamics 'CFD' methods in support of air quality studies. CFD models are emerging as a promising technology for such assessments, in part due to the advancing power of computational hardware and software  [Neophytou, 2005]. CFD, simulations have the potential to yield more accurate solutions than other methodologies because it is a solution of the fundamental physics equations and includes the effects of detailed threedimensional geometry and local environmental conditions. The results of CFD simulations can both be directly used to better understand specific case studies as well as be used to support the development of better-simplified algorithms that may be generally applied  [Jal, 2003]. The city of Ghardaïa, in the M'Zab valley, was taken as the case study with its dense fabric which demonstrates the ideas of building cool, shaded, airy structures in a hot dry climate.
Physical model The Phoenics 3. 5 CFD program was used in this research  [Cham Phoenics, 2005 ]. The turbulence model was the modified ε k model by MMK. The standard ε k model is known to yield unsatisfactory predictions when applied to flow around bluff bodies as encountered for example in wind-engineering applications. The model fails to reproduce well the surface pressure distribution around a body because of the tendency to overestimate turbulent production in the impingement region on the frontal area of the body  [Tsuchiya et al. , 1997]. All the objects that will be included in the simulation must be prepared in a step-bystep procedure starting with the capture of the area of investigation using Google Earth 4. 2 Professional [Google Earth, 2007]. The image is then imported in the AC3D software where the outlines of the buildings were traced and then extruded to produce the individual buildings  [AC3D, 2009].
The dimensions and the geometry of the objects are scaled to fit the real size of the configuration. It is well known that the CAD files created or generated by CAD packages do not necessarily guarantee that the facets are consistent with each other in respect of inwardand outward-looking direction or define closed volumes. Phoenics requires that facets should have a direction sense in order that it can know on which side is the fluid and on which the solid; and of course facets which share an edge should be in agreement on the matter. In most cases there a need to fix and repair the overlapping surfaces in order to simulate complicated configurations. In the present case, Magics 12. 0 software [Materialise Magics, 2007] has been used to correct the file containing the urban geometry of the case study as shown in figures 3 and 4.
Using plasmid similarity networks to understand mechanisms of gene spread is tantamount to using parasite-sharing networks as a proxy for potential parasite transmission across multi-species host communities in disease ecology  [42, 45] , or networks that describe contacts between individuals. Essentially, any "transmission network" describes potential pathways for pathogen transmission, and there are multiple ways to estimate these pathways  [44]. In the case of gene transmission across plasmids, this approach requires that plasmid genetic information is collected within the same system. However, nearly all studies used plasmid sequences originating from diverse and geographically distant environments because they were mined from databases  [33, 34, 37, 39, 40]. Using plasmids from different systems is inadequate for determining pathways of genetic exchange or dispersal on finer spatial and temporal scales; for instance, between and within animal hosts.
The network is characterized by asymmetric and nonrandom pathways of gene transmission Although the plasmid similarity network is highly sparse, it may still contain major pathways of gene exchange. In epidemiology and disease ecology, areas of potential transmission in networks can be detected using community detection algorithms, loosely referred to as modularity  [41, 52]. Modularity is a mesoscale property in which parts of the network are denser compared to others  [53]. We detected modules using Infomap, an algorithm based on the movement of a random walker on the network. Infomap is explicitly designed for multilayer networks and also measures the amount of flow contained within each node (the total flow across state nodes in the network sums to 1)  [54] [55] [56]. Flow measurement is particularly suitable for our purposes because it is directly related to the idea of gene exchange  [56].
Comparison of node-and module-level metrics between plasmids and modules with (n = 235) and without (n = 1109) mob genes based on the Mann-Whitney-Wilcoxon test. We show the median values for plasmids or modules with and without mob genes, U, and p value. Significant p values (<0. 05) are indicated in bold. The magnitude of the differences in these measures is small, possibly due to the low number of plasmids for which mob-related ORFs were detected. and percent identity. Identical plasmids were those with the same length and 100% identity over 100% of their length with no gaps in the alignment. We then confirmed that these plasmids were identical by aligning them in the software Geneious (v. 11). A total of 314 sequences were identified as identical to at least one other sequence in the data set and were consequently grouped in 138 identical plasmids.
Scale Because contigs were assembled from samples individually, we mapped the reads from each individual cow back to the full set of plasmid contigs using bbmap with the parameter "ambig" set to "all" to determine whether additional plasmids from the data set not detected in the original assembly were present in individual cows. Based on read mapping, we measured the coverage of each plasmid sequence in each cow. We considered plasmids to be present in a cow if they had 100% coverage in that cow.
Plasmid annotations We used previously published annotations for plasmid ORFs  [30]. These ORFs were annotated by comparing them to the NCBI-NR protein database using a maximum E value cut-off 10 -5. For each ORF, the hit with the lowest E value was chosen unless it was a hypothetical protein, in which case we chose the next lowest E value. If all five of the lowest E value hits were hypothetical proteins, the ORF was annotated as hypothetical. Annotated functions were then manually curated into functional categories such as "plasmid", "phage" and "sugar metabolism" based on their description in the database. We conducted additional bioinformatic analyses on all plasmids in the data set using the Resistance Gene Identifier (https://github. com/arpcard/ rgi). We did not detect additional AMR genes, but those already in our data set were reverified, corroborating our previous analyses  [30].
Moreover, for all plasmids in the data set, we predicted the ORFs using Prokka and used KofamScan to identify KEGG orthologies, which resulted in 15 KOs across 40 plasmids. We specifically blasted the plasmids in module #1 (the largest module). Because blast results of entire plasmids had no hits, we also manually looked for conserved domains of the plasmids in module #1 and module #2 (which contained the plasmids with the beta-lactam-carrying plasmids) using the Conserved Domain tool with NCBI (https:// www. ncbi. nlm. nih. gov/Structure/cdd/wrpsb. cgi?RID=3FEF4TF8013&mode =all). These results can be found in the Supplementary Information.
Modularity using Infomap We obtained network partitioning to modules using the infomap algorithm  [54, 80]  implemented in the infomapecology R package  [56]. In brief, infomap minimizes a function called the map equation using a modified and extended Louvain algorithm to partition the network into modules in a way that minimizes the amount of information needed to describe the movements of a random walker across the network. Modules indicate groups of nodes in the network that are more connected to each other than to other nodes. Infomap is a useful tool for analyzing this type of network because it explicitly accounts for multilayer network structure, and is computationally efficient  [56]. Because Infomap is based on flow, it is particularly relevant for this study, which aims to look for signatures of gene flow  [56].
ACKNOWLEDGEMENTS This work was supported by an  Israel Science Foundation (ISF)  research grant  1281/ 20  to SP, DIP ( 2476/2-1 ) to IM, ISF ( 1947/19 ) to IM, and  ERC  ( 866530 ) to IM. JTS was supported by a  Zuckerman STEM Leadership Program postdoctoral  fellowship. VJO was supported by a  Margarita Salas grant  funded by the  Spanish Ministry of Universities  and the " European Union -Next GenerationEU ".
Context. Cold cores are one of the first steps of star formation, characterized by densities of a few 10 4 -10 5 cm -3 , low temperatures (15 K and below), and very low external UV radiation. In these dense environments, a rich chemistry takes place on the surfaces of dust grains. Understanding the physico-chemical processes at play in these environments is essential to tracing the origin of molecules that are predominantly formed via reactions on dust grain surfaces. Aims. We observed the cold core LDN 429-C (hereafter L429-C) with the NOEMA interferometer and the IRAM 30 m single dish telescope in order to obtain the gas-phase abundances of key species, including CO and CH 3 OH. Comparing the data for methanol to the methanol ice abundance previously observed with Spitzer allows us to put quantitative constraints on the efficiency of the nonthermal desorption of this species.
2016)  were searched for unsuccessfully. The source has been proposed to be on the verge of collapsing by  Stutz et al. (2009) , based on 70 µm observations with Spitzer. Based on observed molecular line profiles, both  Lee et al. (2004)  and  Crapsi et al. (2005)  classified this source under a possible "infall" category, although the authors also discussed the possibility that the line asymmetry could be due to other types of motion. Herschel observations of this cold core are available from the Herschel database 1. We used the temperature and optical depth maps at 353 GHz(τ 353 ) derived by  Sadavoy et al. (2018)  from SPIRE 250, 350 and 500 µm and PACS 160 µm, with a resolution of 36 ′′. Those authors fitted spectral energy distributions to these maps in order to obtain temperature and τ maps on more than 50 globules.
The other crosses represent different positions where the spectra were studied (see Fig. 2 ). Right: computed molecular hydrogen density (n H 2 in cm - 3  ) map. On both maps, the white contours are the dust temperatures. Pickett et al. 1998) , coupled with CLASS. The NOEMA data reduction was performed using the Gildas package CLIC, the standard pipeline provided by IRAM, to create the UV tables. We then used MAPPING to produce the data cubes, using a natural weighting for the synthesized beam. Residuals of the cleaning residuals were systematically checked. The rms sensitivity on these maps was on average between 0. 15 and 0. 25 K. The NOEMA data cube does not show any signal at any frequency. This indicates that there is a spatial filtering with no molecular emission smaller than approximately 30 ′′.
Molecular transitions and integrated intensity maps Among the targeted molecules, we detected 19 lines (listed in Table  1 ), corresponding to 11 different molecules, with a A141, page 3 of 19 A&A 670, A141 (2023) peak intensity greater than three times the local rms. The integrated intensity maps have been constructed from the data cubes with the Spectral Cube python package  (Ginsburg et al. 2019 ). In Fig. B. 1, we present the integrated intensity maps of all detected molecules; when several lines were observed, we only show the most intense ones. The molecules (and transitions) in the following list were targeted but not detected: OCS (9-8), HNCO (4,0-4,4), and c-C 3 H 2 (4,3-1,0). These non-detections are discussed in Appendix E. 5 6 7 8 9 V LSR [km. s 1 ] 0 1 2 3 4 T mb [K] CH 3 OH CS C 18 O 5 6 7 8 9 V LSR [km.
Method For all detected molecules, when the collisional rate coefficients were available in the LAMDA database 5   (Schöier et al. 2005) , we estimated the observed column density with an inversion procedure and the RADEX radiative transfer code  (van der Tak et al. 2007). We first computed a theoretical grid of line integrated intensities, using external constraints on the temperature, line width, and H 2 density. Then, comparing this grid of theoretical values with our observed ones through a χ 2 minimization, we constrained the molecular column densities at each pixel. We assumed a gas temperature equal to that determined from Herschel observations (see Fig. 1 ). The resolution of the Herschel observations (36 ′′ resolution, from  Sadavoy et al. 2018 ) is similar to our 30 m data (23-26.
These maps of the abundances with respect to H 2 are shown in Figs. 4  and 5. For CO, we computed the main isotopologue abundance from the C 18 O abundance multiplied by 557  (Wilson 1999). We also computed it from the C 17 O abundance multiplied by 2005  (Lodders 2003 ) and obtained the same abundance of the main isotopologue. The maps of CCS and HC 3 N were computed at LTE because no collisional coefficients are available. Similar to CN, the lines are only detected in a small portion of the map. For the non-detected molecules, we computed upper limits on their column densities (given in Appendix E). Finally, the optical depth for each detected molecule (that has an entry in the LAMDA collisional database) was computed. To do so, we used the four positions shown in Fig. 1  and for each associated pixel, we collected the kinetic temperature, the H 2 density, the line width, and the column density.
-LTE radiative transfer code RADEX (van der Tak et al. 2007), with the LAMDA database to obtain a grid of integrated intensities for one or multiple transitions per molecule (for the latter, a grid was computed for each line). Collision rates used are: SO from Lique et al. (2005), CS from Lique et al. (2006), CN from Lique et al. (2010), CO from Yang et al. (2010), H 2 S from Dubernet et al. (2009), CH 3 OH from Rabli & Flower (2010), and HC 3 N from Faure et al. (2016).
Acknowledgements. A. T. , V. W. , P. G. , J. N. , E. D. , and M. C. acknowledge the  CNRS program  " Physique et Chimie du Milieu Interstellaire " (PCMI) co-funded by the  Centre National d'Etudes Spatiales (CNES). We would like to thank  Lars Bonne  and  Sylvain Bontemps  for their help on the dynamical study and for sharing with us Planck data of the cloud. D. H. is supported by  Center for Informatics and Computation in Astronomy (CICA)  grant and grant number  110J0353I9  from the  Ministry of Education of Taiwan. D. H. also acknowledges support from the  National Science and Technology Council of Taiwan  through grant number  111B3005191.
Observations MIRI data of NGC 6552 was obtained on May 7, 2022, during the commissioning of JWST, as part of the persistence characterisation of the MIRI detectors (PID 1039, P. I. D. Dicken). NGC 6552 was selected because is one of the brightest mid-IR source in the northern continuous viewing zone of JWST. Aditionaly, NGC 6552 was used as a calibrator of WISE and Spitzer, offering the possibility of cross-checking the MRS absolute photometry. The aim of this program was to investigate aspects of persistence after long observations of NGC 6552 on the MIRI Imager and MRS detectors and to analyze any artefacts and their decay for up to 25 min. The magnitude of the detector persistence is a function of flux of the source of origin, as well as the time spent observing that source on the same detector pixel  (Rieke et al.
The nucleus of NGC 6552 was able to saturate the imaging data in the third detector readout. Visit 5 was on-target MRS observations with exposure times of 505 s in each of the MRS bands. The MRS observations did not saturate. Visit 6 was used as a reference image and to study persistence decay in the MIRI Imager detector, if any. Finally, MRS observations from visits 2, 3, and 4 have been used for background characterisations purposes. Since the MRS is spatially undersampled, the MIRI instrument team recommends using four-point dithering 1 on every MIRI observation to maximise the spatial and spectral sampling and the scientific return of the MIRI observations. Due to the nature of this program, the MRS on-target observations did not use dithers, as the programme was designed to investigate artefacts in the detector image rather than on sky.
MIRI image The MIRI imaging data were reprocessed with the v1. 6. 3 JWST pipeline, using the latest reference files available 2. After the level 1 detector processing, we applied a fix to the pipeline to re-create rate images averaging only valid data, as a bug in the pipeline affected the pixels that are saturating in after the third group, which is the case for some of the central pixels of NGC 6552. For those pixels, only the first three frames were used. We note that this fix will be implemented in a future version of the pipeline. Then, the level 2 pipeline was run with the default parameters and using the sky flats computed from the LMC data taken during commissioning (PID 1040). These preliminary flats contain image artifacts caused by MIRI reset anomaly (see  Ressler et al. 2015 , for a discussion of this effects), such as tree-ring shaped structures.
However, most of these image artifacts are removed by the master background subtraction (explained below), as the features are stable. Since the calibration of the image is still preliminary, the MIRI Imager data are only used in this paper to illustrate the MRS pointings, crossmatch the MIRI Imager and the MRS photometry, and illustrate the optical quality (in particular the low persistence) and dynamical range of the imager. A master sky background image was created from the first visit file and subtracted from all the images. This sky image was created by sigma clipping all the images from the visit 1 aligned in instrument coordinates. We note that this injects residual small scale variations at a percent level in the background, which are not critical for our analysis. The left panel Fig.
MRS data calibration The MRS observations were processed with the JWST calibration pipeline (release 1. 8. 3). This release uses the build 8. 4. 2 of the Data Management System (DMS) and context 1017 of the Calibration References Data System (CRDS). The MRS pipeline is divided into three different processing stages  (Labiano et al. 2016; Bushouse et al. 2022)   3. The first stage performs the detector-level corrections, identification, and correction of the cosmic ray (CR) impacts and then transforms the ramps 4  into slope detector products  (Morrison et al. , in prep. ). The second stage assigns the coordinate system, performs the straylight, fringe flat, residual fringe correction, and photometric calibrations to generate fully calibrated individual exposures  (Argyriou et al. , in prep.
). The third stage combines the different dithered exposures to create 3D spectral cubes and 1D extracted spectra  (Law et al. , in prep. ). In the process, it allows for the performance of an outlier rejection and a background matching. The background could be subtracted in stage 2 or 3 of the pipeline depending of the methodology selected by the user. The third stage was not used in this work as the MIRI data were not dithered, and the 1D spectral extraction and background subtraction were performed outside of the JWST calibration pipeline. We found that the standard pipeline identifies and corrects most of the CR events, but the so-called CR 'showers' and/or high energetic CRs still leave some relevant residual effects even using the large CRs events function. Also, the current in-flight darks and reset anomaly corrections inject a vertical striping pattern in the slope detector data (see Footnote 3 for examples).
Their strength depends on the length of the ramp, where long ramps (>150-200 groups in FASTR1 readout mode, ∼500 s) minimise this effect. These effects, along with others such as hot or bad detector pixels, are vastly reduced in four-point dithered observations allowing to obtain the optimal MRS spatial and spectral resolution. The MRS observations of NGC 6552 were taken with no dithers, as the goal of this commissioning activity was not to obtain a final optimised cube. Then, the 3D cubes could still have a small number of spaxels affected by the lack of data due to bad or hot pixels in the detector. These have been identified, masked and interpolated in the 1d extracted spectra presented in Sect. 4. 2. We generated 12 3D cubes, that is, one for each of the MRS sub-channels, with spatial sampling of 0.