dataesr/scientific-paragraphs-categorization huggingface dataset:
MLVA-14 genotyping of a world collection of Xpm strains We compared the discriminatory power of MLVA-8 with the previously reported MLVA-14 microsatellite scheme. MLVA-14 scheme was able to distinguish 89 haplotypes out of the 93 Xpm strains. All loci were highly polymorphic with a mean allelic richness of A = 13. 5 leading to high discriminatory index (HGDI = 0. 999) and Nei's gene diversity index (H E = 0. 863), which were much higher than those estimated from the MLVA-8 dataset (Tables  3  and S4 ). Strains sharing the same haplotype originated from the same country and, when the information was available, they were isolated the same year in the same locality (S1 Table ). The minimum spanning tree describing the relationships between the 89 haplotypes produced ten small clonal complexes grouping only two or three SLVs (S1 Fig).
Nine CCs contained strains originating from the same country among which six consisted of strains isolated the same year in the same region probably corresponding to the same outbreak. Five CCs grouped strains from the same continent either South America (CCs 6, 11 and 16, each with strains from two different countries) or Africa (CCs 1 and 2, both with strains originated from Mali, Burkina Faso and Togo). Most of these CCs are tightly related as they differ by variations in two loci. We used DAPC to delineate seven clusters in our dataset (Fig  3 ). The assignation probability to clusters was > 0. 99 for all strains in the dataset. Interestingly, the large polymorphism revealed for strains from South America split them in the seven clusters. Strains originating from Argentina (n = 4), Brazil (n = 12), Colombia (n = 28) and Venezuela (n = 21) were assigned to three (Argentina) or four (other countries) distinct clusters.
The MLVA-8 dataset confirmed (i) a more extensive genetic diversity for the South American strains than for the African strains and (ii) the hypothesis of some genetic links between African strains and some South-American strains as previously shown using four RFLP probes and SNPs based-phylogeny  [26, 37]. The MLVA-8 scheme alone lacked discriminatory power and therefore did not reveal a fully meaningful epidemiological perspective at a global scale. The relatively low number of minisatellite loci identified and their low mutation rates both are factors favoring homoplasy  [51, 52]. In contrast, 89 out of 93 Xpm strains genotyped using the MLVA-14 scheme were separated as unique haplotypes clearly confirming the high mutation rate of this genotyping technique, consistent with a previous study and suitable for small scale epidemiology  [40].
The pathogenic bacterium was likely introduced in this continent through transportation of infected plant material after multiple introduction events into both Eastern and Western African coasts. Three strains isolated in New-Zealand during outbreaks in 1960s or in 1980 were distributed in two different DAPC clusters, one of them sharing an MLVA-12 haplotype with a strain from Venezuela and the others were SLVs of Colombian and Brazilian strains. This result supports the occurrence of multiple introduction events of Xpm in this country. No clear correlation between the MLVA profiles and virulence patterns occurred. The different haplotypes representative of the genetic variability of observed within our world Xpm collection from MLV8-dataset produced different pathological patterns though all the isolates were virulent on the Colombian cassava varieties.
We thank the  Faculty of Sciences from Universidad de los Andes-Bogota, Colombia  ( INV-2021-128-2283 ), the  UMR Interactions Plantes Microorganismes Environnement , and the  Agropolis Foundation  (project  PAIX , grant no. 1 403-073 ),  Montpellier, France , for financial support. The  Ecos Nord programme supported inter-laboratory mobility  (grant no. C15A01 ). Leidy Rache  was supported by  Colciencias  with a doctoral fellowship (call No. 528 , 2011). Olivier Pruvost acknowledges the  European Union  (ERDF contract  GURDT I2016-1731-0006632 ) and Reunion regional council for support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
12 scheme proposed for large scale epidemiology Four VNTRs (2-31,2-6, 2-7, 2-38) among the least discriminant of the MLVA-14 scheme were combined to the eight VNTRs (2-22, 2-18, 2-35, 2-20, 2-3, 2-23, 2-5, 2-33) of the MLVA-8 scheme to slightly increase its discriminatory power. The mean allelic richness and HGDI produced by the MLVA-12 dataset were estimated to 4. 75 and 0. 995, respectively (Table.
Each of these n T x acquisitions corresponded to the emission of ultrasound by one of the n T x = 10 elements depicted in Fig. 1c  (red stars). For each of the N sequences, M = 10 sets of photoacoustic RF data, corresponding to M wave- lengths, were acquired at 100 Hz (limited by the laser repetition rate) in an interleaved manner with ultrasound RF data. Ultrafast ultrasound sequences of n T x acquisitions (0. 56 ms total duration each) were repeated every 5 ms (200 Hz repetition rate), twice faster that photoacoustic acquisitions. In principle, ultrafast sequences could have been acquired with a repetition rate higher than 200 Hz, but at the cost of more data to handle and process. 200 Hz turned out to be sufficient to perform quantitative Doppler measurement in chicken embryo without significant aliasing.
In summary, a complete acquisition resulted in a set of N × M multispectral photoacoustic RF dataset (100 Hz rate) and N × 2 × M ultrafast ultrasound sequences (200 Hz rate). For all the results presented in this work, the number N of sequences was of the order of a few hundreds, corresponding to a total acquisition time of the order of a few tens of seconds (10-s acquisition time for N = 100). Data processing. The various data processing steps leading to 3D ultrasound Doppler and photoacoustic fluctuation images from RF data are summarized in Fig. 7. All data processing steps were performed with Matlab 2020 (https:// www. mathw orks. com/), which was also used to drive all the instruments. Image reconstruction. All acquired real-valued RF signals were transformed into complex-valued RF signals through a Hilbert transform, before further processing.
Three-dimensional data were visualized either through maximal intensity projections (MIP) computed with Matlab 2020 (https:// www. mathw orks. com/) or 3D rendering produced with AMIRA 6. 7 (https:// www. therm ofish er. com/ fr/ fr/ home/ elect ron-micro scopy/ produ cts/ softw are-em-3d-vis/ amira-softw are. html). For non quantitative images such as in the Fig. 2 , colorbars ranged between the minimum and the maximum of each 3D images. SO 2 values in 2D images are computed at the pixels corresponding to the MIP through the fluctuation image (computed at the wavelength leading to the strongest signal-to-noise ratio). In addition, a gaussian mask, computed from a 2D gaussian filtering of the binarized MIP image (with a width of 1. 5 pixels), was applied to the 2D SO 2 map to smooth the borders of the vessels.
Mopsa is a multilanguage static analysis platform relying on abstract interpretation. It is able to analyze C, Python, and programs mixing these two languages; we focus on the C analysis here. It provides a novel way to combine abstract domains, in order to offer extensibility and cooperation between them, which is especially beneficial when relational numerical domains are used. The analyses are currently flow-sensitive and fully context-sensitive. We focus only on proving programs to be correct, as our analyses are designed to be sound and terminating but not complete. We present our first participation to SV-Comp, where Mopsa earned a bronze medal in the SoftwareSystems category.
Verification Approach: the Mopsa platform Mopsa is an open-source static analysis platform relying on abstract interpretation  [4]. The implementation of Mopsa aims at exploring new perspectives for the design of static analyzers. Mopsa has a triple objective: -To allow developers to define abstract domains in a modular fashion -that is, as independently of each other as possible. In particular, this means that each abstract domain can easily be enabled or disabled to customize an analysis. -To allow different abstract domains to cooperate and communicate in a relational way. Previous analyzers were able to combine domains in tree-shaped structures  [5, Fig. 1]. Mopsa allows sharing between abstract domains, meaning schematically that the domains can be combined into an acyclic graph. -To support the analysis of multiple languages while reusing existing abstractions.
Mopsa is able to analyze C  [16] , Python  [13] , and multilanguage Python/C programs  [14]. The Michelson smart contract language is being added  [1]. Other safe analyzers, such as Astrée  [5] , Frama-C  [6] , Goblint  [19] , and TAJS  [8]  are specialized in analyzing a single language. These aims are achieved through a dynamic expression rewriting mechanism, and a unified signature for abstract domains and iterators. Journault et al. [9]  describe the core Mopsa principles, and Monat  [12, Chapter 3]  provides an indepth introduction to Mopsa's design. The C analysis which we rely on for this competition is based on the work of Ouadjaout and Miné  [16]. The analysis works by induction on the syntax, is fully context-and flow-sensitive, and committed to be sound. It targets complete programs that have not been modified: Mopsa can be seamlessly integrated in standard build systems (such as make), it supports main functions with symbolic arguments, and it includes precise stubs for most of the standard C library.
Software Architecture: the SV-Comp driver By default, the C analysis of Mopsa detects all the runtime errors that may happen in the analyzed program (NULL pointer dereferences, integer overflows,. ), while SV-Comp tasks focus on a specific property at a time (reachability of a function, validity of memory accesses,. ). We thus created an SV-Comp specific driver. It takes as input the task description (program, property, data model). It runs increasingly precise C analyses defined in Mopsa until the property of interest is proved or the most precise analysis is reached. Each analysis result is postprocessed by the driver to check if the property is proved. An analysis configuration defines the set of domains used, as well as their parameters allowing modifications of the precision-efficiency ratio.
Strengths and Weaknesses Mopsa participated in all categories targeting reachability, memory safety and overflow properties: ReachSafety, MemSafety, NoOverflows and SoftwareSys-tems. It did not compete in the datarace and termination categories. The competition report  [2]  details all results. Mopsa relies on over-approximations to guarantee soundness and termination of its analyses. As such, Mopsa scales well on SV-Comp benchmarks: the successive analyses described in Section 1 yield a result within the allocated resources in 91% of the tasks (and 98. 5% of the cases for our cheapest analysis). We show the detailed precision benefits of each analysis for the benchmarks in Figure  2. Thanks to Mopsa's scalability and commitment to soundness, we have been able to discover and fix defects within SV-Comp benchmarks which were not discovered by previous tools.
In particular, we fixed 164 task definitions, as well as 23 programs with unintended issues in their source code. 5 Mopsa is especially competitive in the SoftwareSystems category, focusing on verifying real software systems: it ranked third for our first participation. Our approach is scalable but not complete: we can only prove programs correct. In other cases, we cannot decide if the issues we found are real bugs or false alarms: we return "unknown" in all these cases to avoid yielding incorrect results. Thus, we can only obtain points on correctness verification tasks, which represents around 58% of the current tasks. Our future work includes finding approaches to exhibit real counterexamples when they exist. In addition, our analyses are not precise enough for some small but intricate benchmarks (for exemple, on arrays).
Software Project and Contributors Mopsa is currently available on Gitlab  [17] , and released under an open-source license (GNU LGPL v3). Mopsa was originally developed at LIP6, Sorbonne Université following an ERC Consolidator Grant award to Antoine Miné. Mopsa is now developed in other places, including Inria, Airbus, and Nomadic Labs. We thank Matthieu Journault for being one of the initial contributors to Mopsa. This first participation to SV-Comp has spurred a lot of interesting discussions within our development team, and lead to 20 bugfixes and new features.
The galaxy group NGC 6338 is one of the most violent group-group mergers known to date. While the central dominant galaxies rush at each other at 1400 km s -1 along the line of sight, with dramatic gas heating and shock fronts detected, the central gas in the BCGs remains cool. There are also indications of feedback from active galactic nuclei, and neither subcluster core has been disrupted. With our deep radio uGMRT data at 383 and 650 MHz, we clearly detect a set of large, old lobes in the southern BCG coinciding with the X-ray cavities, while the northern and smaller BCG appears slightly extended in the radio. The southern BCG also hosts a smaller younger set of lobes perpendicular to the larger lobes, but also coinciding with the inner X-ray cavities and matching the jet direction in the parsec-resolution VLBA image.
2020a). This paper is structured as follows. In Section 2, we describe the setup and data reduction of the recent uGMRT observations. Several other data sets have been included in this study, such as archival VLA and VLBA observations, as well as our recent Submillimeter Array (SMA 7  ) and IRAM observation at high frequencies, which are also described in Section 2. Our results, such as the description of past feedback cycles in the southern BCG and the current state of the AGN and connected jets, are presented in Section 3. Section 4 provides a discussion of the radio and submm results, including the age of past feedback cycles and opportunities for future X-ray missions. We summarize our findings in Section 5. Throughout this paper, we assume a flat ΛCDM cosmology with the following parameters: Ω m = 0.
Observations The main goal of the dedicated uGMRT observations was to find signatures of feedback, which is ideal for this instrument, with its decent spatial resolution at low frequencies (below ∼1 GHz). We decided to expand this by including higherfrequency data from the VLA and several other published values, to construct and fit an SED over three orders of magnitude in frequency, which reveals the emission mechanisms. At the high-frequency end, we included our recent SMA continuum observation at 230 GHz, to complete the SED. Repeated VLA observations indicate the radio variability of the central radio source in the southern BCG, and the IRAM 30 m CO measurements can quantify the reservoir of cold molecular gas.
uGMRT Data Reduction The upgraded Giant Metrewave Radio telescope (uGMRT) is equipped with four wideband receivers. We observed NGC 6338 in bands 3 (300-500 MHz) and 4 (550-850 MHz) (see Table  1 ). Both observations were recorded with 5. 37 s integration time, 4096 channels, and two Stokes parameters. The hardware-based removal of radio frequency interference (RFI) 8  was not enabled. For band 3, 27 of 30 antennas were available, while for the band 4 observation, only 26 antennas were operational. Each observation ends with a 10-minute scan of 3C48, which was used as a flux calibrator for both data sets (more details on the observations are given in Table  1 ). The reduction of uGMRT data utilized the SPAM pipeline  (Intema et al. 2009) , and the processing is analogous to the description in  Schellenberger et al.
VLA Data Reduction NGC 6338 has been observed many times in the past with the VLA at frequencies higher than those observed by the GMRT (see Table  2 ). We selected observations with frequencies higher than 1 GHz (at least L band), which can easily determine the flux of the compact radio source in the southern BCG in NGC 6338. The survey data from FIRST  (Becker et al. 1994) , NVSS  (Condon et al. 1998) , and VLASS  (Lacy et al. 2020 ) have only been downloaded from the archive -not reprocessed-and are listed for completeness in Table  2. We reduced the archival VLA data before 2012 using the Astronomical Image Processing System (AIPS version 31DEC22  ; Greisen 1990 Greisen , 2003) )  and the vlaprocs module. We load the raw VLA files into AIPS and apply the flux scale to the corresponding flux calibrator observation with SETJY, including the options OPTYPE = CALC.
SMA Data Reduction We observed NGC 6338 at 230 GHz with the SMA to measure the current high-frequency flux (project 2021B-S068,  PI Schellenberger). Seven of the total eight 6 m antennas were operational during the observations performed in the compact configuration on 2022 January 15 and 2022 January 17, with total observing times of 1h 33 minutes and 2 hr 4 minutes, respectively. A reliable flux calibration was ensured through a scan of Ceres during each track. The time dependence of the complex gain was calibrated through frequent observations of 1740 + 521. The total on-target time sums to 139 minutes. Data reduction was performed using the IDL package MIR 10   (Gurwell et al. 2007) , and the important steps include the flagging of unusable visibilities, a system temperature calibration, and a baseline-based bandpass calibration using scans of 3C345 and 3C279 with the pass_cal task.
VLBA Data Reduction To better understand the current state of the southern BCG in NGC 6338, we analyzed the archival VLBA observation (Project BE063/F, PI A. Edge) in C band taken in 2013 May. The scan of NGC 6338 has data taken from nine antennas (SC missing) and a spectral setup of eight spectral windows, with each window having a 32 MHz bandwidth. We used the VLBARUN task in AIPS to perform the VLBA calibration, using the scan of 3C345 as fringe finder and bandpass calibrator and J1722+5856 for phase referencing. The solution interval was set to 10 minutes, and the selected reference antenna is Pie Town (PT). After exporting the 19minute calibrated target scans, we applied five phase-only selfcalibration cycles, reaching an r. m. s. 74 μJy bm -1 and a restoring beam of 4. 0 × 1. 1 mas. The integrated source flux yields 26 mJy at 5 GHz.
IRAM 30m We observed NGC 6338 with the IRAM 30 m on 2020 July 21-24 (project 066-20) using the E0 and E2 bands of the EMIR receivers and both horizontal and vertical polarizations. We observed the redshifted CO(1-0) and CO(2-1) lines simultaneously, at  112. 194 GHz and 224. 388  GHz respectively. Both the FTS and WILMA backends were used. Weather conditions made about half the approved time unusable, but we were able to observe the target for a total of ∼8 hr. The focus and pointing of the telescope were calibrated using observations of bright quasars or planets, and the data were reduced using the GILDAS 11  CLASS software  (Pety 2005; Gildas Team 2013). Figure  1  shows the summed CO(1-0) and CO(2-1) spectra for NGC 6338. Although neither line was detected, we are able to place strong upper limits on the CO emission from the source.
Results We describe the results obtained from the data that have been analyzed: The new uGMRT data cover low frequencies (below 1 GHz) at higher spatial resolution compared to existing LOFAR data (13 7 × 8 7 versus 7 9 × 5 6 for the band 3 uGMRT data), allowing us to look at feedback cycles of the AGNs in the northern and southern BCG in detail. With the multifrequency radio coverage from 142 MHz to 20 GHz, the SED is parameterized by a self-consistent model, which can even be expanded to 230 GHz. The archival VLBA data give a glimpse at the current state of the AGN.
Feedback Cycles in the Southern BCG There are strong indications that the southern BCG has established a feedback cycle that is maintained by the central AGN: O'Sullivan et al. (2019) found X-ray cavities around the core (inner cavities and a potential outer cavity in the E), a strong radio point source in the center of the BCG, and Hα filaments. These features are either absent or less pronounced in the northern BCG, which we describe in more detail in Section 3. 4. O'Sullivan et al. (2019)  did not find extended radio emission in a GMRT pointed observation at 1. 39 GHz in the southern BCG of NGC 6338, at least not beyond a small extension of the core to the southwest. However, assuming a typical spectral index for aged radio lobes we expect our new uGMRT data sets to be at least five times deeper and able to detect any signs of past feedback.
We find some other (distant) radio sources in the nearby field that we can identify using NED (see Figure  2  middle panel) and confirm the accuracy of our astrometric corrections. We do not find other extended sources in the center of this merging group, and none in the outskirts that are related to NGC 6338. The brightest source in the field (136 mJy bm -1 in band 3) is about ¢ 20 to the west. The depth of the uGMRT data in both bands allows us to create a spectral index map from 383 to 650 MHz for the southern BCG. Figure  2  (right) shows a map of the spectral index α, which we define as S ν ∝ ν α , where S ν is the flux density at frequency ν. We show the associated error map of the spectral index in Figure  11. The core of the region exhibits an inverted spectrum with α 383-650 MHz = 0.
NGC 6338 has also been observed with the GISMO bolometer camera on the IRAM-30 m telescope in 2012 October by  Hogan et al. (2015). The authors showed NGC 6338 to have a flux of 7. 3 ± 1. 5 GHz at 150 GHz. The authors interpreted the GISMO flux as "flickering at high frequencies or variability. " It is also slightly inconsistent with the reobservation in 2019 by  Rose et al. (2021)  with the NIKA2 bolometer on the IRAM-30 m telescope, which found the flux to be 4. 5 ± 0. 5 mJy at the same frequency as GISMO. It should be noted that here we averaged the two NIKA2 measurements, which were about 7 months apart and are consistent with each other. Figure  7. Modeling of the high-frequency spectrum of the southern BCG. The dashed power law is consistent with all data points except the IRAM/GISMO measurement, which requires an additional ADAF component that does not match the current SMA flux.
larger SE-NW lobes that have a slightly steeper spectral index than the smaller SW-NE lobes (-1. 3 versus -1. 1), and the spectral index steepening of the larger lobes points toward a radiative age of about 200 Myr; 5. a small, parsec-scale jet in the VLBA image, with a direction similar to those of the new radio lobes, which strengthens the assumption of a recent shift in feedback direction and that the newly inflated cavities might still be powered; 6. radio emission in the core that is consistent with typical spectral index of -0. 58 and currently shows no indications of steepening. For a complete picture of the feedback processes, especially on the galaxy group level, we need to understand the current and past AGN feedback cycles in various environments. Through the wealth of high-quality, multiwavelength data from radio to X-rays, NGC 6338 offers the possibility to look at the feedback process in a violent group-group merger in the pre-corepassage phase.