dataesr/scientific-paragraphs-categorization huggingface dataset:
B05. 10, Sl3 and Vv3 strains show different repertoires and densities of transposable elements Different subfamilies of Transposable Elements (TEs) were identified in the B05. 10, Sl3 and Vv3 strains. The complete annotation of TEs in the Sl3 and Vv3 genomes was carried out using a de novo approach with the REPET package  (Flutre et al. , 2011; Amselem et al. , 2015). Consensus sequences representing all possible TEs among the Sl3 and Vv3 genomes were identified. After manual curation, 19 and 33 consensus TE sequences were retained for Sl3 and Vv3, respectively (Sup. File S1). They were classified based on their structure and sequence similarities to characterized eukaryotic transposons  (Hoede et al. , 2014; Wicker et al. , 2007). Fifteen consensus were previously identified in the B05. 10 genome using the same pipeline and parameters as in the present study  (Porquier et al.
As only the helicase domain was clearly identified in the TE found in Vv3, it was called a Helitron-like element (Sup. Fig. S9 ). Helitrons are also known for their capacity to capture genes, which increases their size  (Castanera et al. , 2014). In addition to a helicase-coding gene, the 15. 5 kb sequence of the Helitron-like element found in Vv3 revealed two captured genes as well as relics of Boty (i. e. Long Terminal Repeats). For one of the captured genes, the predicted protein was a secreted pectate-lyase (IPR002022), similar to enzymes involved in the maceration and soft rotting of plant tissue. Notably, 33 complete or uncomplete copies of the Helitron-like TE carried this putative virulence gene in the genome of Vv3. Unlike most TEs that were randomly distributed along chromosomes, the Helitron-like TEs were mainly localized at the chromosome ends (Sup.
cinerea specialized on grapevine or on tomato  (Mercier et al. , 2021)  and the production of some of these small RNAs. The study was extended to a total of six strains from the T population, four strains from the G1 population and three strains from the G2 population, as well as to reference B05. 10. All strains were grown on grape juice medium and small RNAs were investigated as described above. Principal component analysis of small RNA repertoires (Sup. Fig. S12, B ) differentiated samples from the G1 population from samples from the G2 and T populations. To compare the repertoires of TE-derived small RNAs from the 14 strains, we mapped the reads on the TEs identified in B05. 10, Sl3 and /or Vv3 strains (Table  2 ; Sup. Table  S4 ). Mapping data indicated that the same seven retrotransposons that produced small RNAs in B05.
0. 1) (https://github. com/PacificBiosciences/) and CANU v1. 6  (Koren et al. , 2017). HGAP4 was run with the set of parameters recommended for fungal genomes (https://pbfalcon. readthedocs. io/en/latest/parameters. html). CANU was run with default parameters and an expected coverage of 42Mb. HGAP assemblies were polished with pilon  (Walker et al. , 2014)  using Sl3 or Vv3 Illumina reads  (Mercier et al. , 2021). CANU assemblies were polished with both arrow (https://github. com/PacificBiosciences/) and PILON. Mitochondrial, ribosomal and small redundant contigs were removed, and final versions of assemblies were manually compiled from polished runs of HGAP and CANU assemblies. Both genome assemblies were evaluated and compared with B05. 10 referent genome (van Kan et al. , 2017) using QUAST  (Gurevich et al.
Transposable elements prediction Transposable elements (TEs) were annotated using the REPET package (https://urgi. versailles. inra. fr/Tools/REPET ;  (Amselem et al. , 2015)  as previously described in  Porquier et al. , 2016  for the genome of the B. cinerea reference strain B05. 10. Briefly, the TEDENOVO pipeline  (Flutre et al. , 2011)  was used to detect repeated elements in the genome and to provide a consensus sequence for each family. Consensus sequences were then classified using the PASTEC tool  (Hoede et al. , 2014) , based on the Wicker hierarchical TE classification system  (Wicker et al. , 2007). After manual correction, the resulting library of consensus sequences was used to annotate TE copies in the whole genome using the TEANNOT pipeline  (Quesneville et al. , 2005). Consensus sequences identified from different genomes were compared and considered as the same subfamily based on a bidirectional best hit approach (blastn with evalue < 1e-10 and coverage > 70%).
Funding This work was supported by a grant overseen by the  French National Research Agency (ANR)  as part of the " Investments d'Avenir" Programme (LabEx BASC ;  ANR-11-LABX-0034 ) and by the  INRAE department SPE. The BIOGER unit also benefits from the support of " Saclay Plant Science-SPS"  ( ANR-17-EUR-0007 ). AM was supported by a grant from the  Doctoral School « Sciences du Végétal », Université Paris-Saclay.
Availability of data and materials The genomic raw data were deposited into the NCBI SRA under the accessions PRJNA752967 for Sl3 and PRJNA752962 for Vv3. Genome assemblies were deposited at NCBI under the accessions CP080979-CP080996 for Sl3 and CP080961-CP080978 for Vv3. Small RNAs raw data and the matrix of sequence counts were deposited into the NCBI GEO under accession GSE181592. Furthermore, the genomic and annotation (gene/TE) fasta and gff files, as well as Sl3 and Vv3 genome browsers are available at the INRAE BIOGER Bioinformatics platform (https://bioinfo. bioger. inrae. fr/).
FTIR microimaging FTIR microspectroscopy was performed at IPGP on a Thermo Fisher Scientific iN10 MX microscope (Ever-Glo conventional infrared source) equipped with a 15× objective (numerical aperture = 0. 7) and a liquid nitrogen-cooled MCT-A detector. The incident beam was collimated to a sample area of 20 m by 20 m. The thinned rock sample was deposited on a BaF 2 window without any Downloaded from https://www. science. org on March 31, 2023 9 of 11 treatment. FTIR hyperspectral maps were acquired in transmission in the range 4000 to 675 cm -1 using step size of 20 m, and 64 accumulations per spectrum per pixel and the spectral resolution was set to 8 cm -1. Spectrum analyses and reconstructions based on band areas were performed using OMNIC software (Thermo Fisher Scientific). A second derivative was applied to raw data to remove baseline variations using the Stavitsky-Golay method (polynomial order, 2; filter width, 15).
Second derivative maps were obtained from unit vector-normalized maps using MATLAB and PLS_Toolbox software (Eigenvector Research Inc. ). Curve fitting in the absorbance region of the aliphatic moieties (i. e. , 2800 to 3000 cm -1 ) was computed with Wire 3. 2 software (Renishaw). Five mixed Lorentzian/ Gaussian functions were used to account for all the symmetric and asymmetric C─H stretching bands. The methyl-to-methylene ratio (R CH2/CH3 ) was computed as the area ratio of the fitted asymmetric C─H stretching bands of CH 2 to CH 3 at ~2930/2960 cm -1 , respectively. R CH2/CH3 allows rough assessment of the length and degree of branching of side groups associated with aliphatic chains  (70).
Acknowledgments: This research used samples and data provided by the  International Ocean Discovery Program (IODP). Funding: Financial support was provided by  LabEx UnivEarthS Frontier MYSTHIC  ( ANR-10-LABX-0023  and  ANR-18-IDEX-0001 ), the  INSU Syster program , a  NERC Moratorium Award  (no. NE/P020860/1 ), the F. N. R. S. , the  Fondation Wiener Anspach  ( RG97553 ), and the  Deep Carbon Observatory. Part of this work was supported by the  IPGP multidisciplinary program  PARI and by  Région Ile-de-France SESAME  grant no. 12015908.
g. ,  Nakada and Fujii, 1993; Loughlin et al. , 2002a Loughlin et al. , , 2002b;; Dufek et al. , 2015; Jenkins et al. , 2016). As a result, surges can unexpectedly inundate built areas outside of pre-existing channels, where people are present. Here we present new detailed data connecting the geology and dynamics of the distal (>10 km) 5 November 2010 unconfined PDCs at Merapi, focussing on their deposit characteristics, generation mechanisms and impacts to buildings, vegetation and victims, who were caught in the process of evacuating. We then use lessons drawn from the analysis of the Merapi 2010 eruption to assess PDC dynamics and impacts from the deadly June 2018 eruption of Volcán de Fuego in Guatemala. Using the same techniques as for Merapi 2010, we use satellite and media images to investigate loss of life and damage to structures caused by unconfined PDCs, supplemented by field studies focused on the deposits, and infer their types and dynamics.
Despite their ability to cause serious impacts, unconfined PDCs have been previously described on a limited number of occasions, often tied to specific case studies in notable eruption sequences (e. g. ,  Abdurachman et al. , 2000; Loughlin et al. , 2002b; Charbonnier and Gertisser, 2008; Macorps et al. , 2018). The lack of a broader comparative study of the different types of unconfined PDCs, and the relationships between their occurrence, deposits, dynamics and the impacts they cause, leaves a gap in the literature that we aim to fill with this study. We review the physical characteristics and devastating impacts associated with unconfined PDCs and provide new geological, impact and casualty data on a subset of these unconfined PDCsslow overspill flows and low-energy detached surges during the Merapi 2010 eruption, Indonesia.
The 2010 Merapi eruption The full spectrum of confined and unconfined PDCs can occur within one eruption, affecting multiple places at the same time, or the same place at different times. PDCs produced during the 2010 eruption of Merapi in Indonesia provided one such example. Post-eruption field studies of the PDC impacted areas offered a unique opportunity to characterise the range of PDC types, their dynamics, deposits and interaction with populated areas to the south of the volcano. Here, we synthesise the sequence of PDC events and their impacts and present new data for key villages along the Gendol river. We focus on slow overspill flows and low-energy detached surges, as these two unconfined PDC end-members and their impacts are poorly documented in the literature. After approximately one year of unrest, Merapi volcano began a new eruptive sequence on 26 October 2010 with the explosion of a cryptodome and associated high-energy PDCs laterally directed towards the south.
5 km in the Gendol valley in the south, with flow overspills and low-energy detached surges extending 700 m from the channel and up to 200 m from the parent flow  (Charbonnier et al. , 2013; Komorowski et al. , 2013; Jenkins, et al. , 2016). PDC overspill and detachment along the more distal parts of the Gendol channel (>8 km from source) during this paroxysmal phase killed ~170 people  (Jenkins et al. , 2013 (Jenkins et al. , , 2016) )  and damaged (n = 395), severely damaged (removed the roof: n = 108) or destroyed (n = 645) 1148 buildings. This event was termed a 'centennial' eruption  (Surono et al. , 2012) , as this magnitude and style of eruption is seen approximately every 100 years at Merapi. Field visits to the Merapi area three weeks after the 5 November 2010 event, and several times over the years that followed, allowed some of the authors [SFJ, SJC, JCK, and PJB] to collect detailed field data on confined and unconfined PDCs produced during the eruption.
Discussion and conclusions In this study, we reviewed the physical characteristics and devastating impact associated with unconfined PDCs. We identified four unconfined PDC end-member types: i) Fast overspill flow; ii) Slow overspill flow; iii) High energy surge; and iv) Low energy detached surge, all four of which were produced by the 2010 Merapi eruption, Indonesia. We used previously unpublished data on the deposits and impacts of slow overspill flows in Bakalan village, 12. 6 km from the summit, and LEDS in Bronggang village, 13. 5 km from the summit, to infer some key characteristics of their emplacement dynamics. Using the lessons learned from Merapi, we then applied the same approach using remotely sourced imagery (satellite images, social and professional media) and field studies to assess impacts and infer the dynamics of unconfined PDCs produced during the Fuego 2018 eruption.
Human modification of the landscape must also be accounted for, as data from the Merapi 2010 eruption reveals that in some cases river channel engineering structures (e. g. , sabo dam, valley walls, paved valley sides) can modify the dynamics of primary PDCs and favour the generation of damaging and especially lethal LEDS even near the distal PDC flow terminus. Volcanic hazard and risk assessment relies upon empirical data from past eruptions and their impacts. However, we are often limited in the amount of data that can be collected shortly after an event, while deposits and impacts are preserved, because of safety and access limitations. This preservation is what makes extracting quantitative data about a PDC from its deposit and impact such a valuable effort despite its difficulty. Despite uncertainties caused by the fact that this information is collected after the event, the variability in amount and detail of data obtainable, the extrapolated rather than observed nature of this information, and the difficulty researchers face when collecting this data as shortly as possible after a disaster with casualties and widespread damage, these techniques are paramount to improve the understanding of past events and to refine the parametrization of complex physical models that allow the elaboration of a range of deterministic as well as probabilistic scenarios of potential future crises.
Acknowledgements The authors are grateful to  Eric Breard  and an anonymous reviewer for highly constructive feedback which resulted in improvements to the manuscript. The authors thank JVGR editor  James Gardner  for his handling of our manuscript. GAL and SFJ acknowledge funding from  AXA  and  Singapore National Research Foundation  ( NRF2018NRF-NSFC003ES-010 ). This research was supported by the  Earth Observatory of Singapore  via its funding from the  National Research Foundation Singapore  and the  Singapore Ministry of Education  under the  Research Centres of Excellence initiative. This work comprises EOS contribution number  371. SFJ, PJB and JCK are grateful for funding from the  European Union (MIAVITA)  and  Agence Nationale de la Recherche  (CASAVA). PJB acknowledges funding from the  Pan American Health Organisation.
In this study, we describe a new crystal form that lacks the unknown ligand, leading to an essentially symmetric and unusually compact conformation of the dimer. This compact conformation is also observed in solution by means of small-angle Xray scattering (SAXS). Furthermore, we have repeated the crystal structure determination of the asymmetric, ligand-bound dimer at a higher resolution (1. 89 A), providing more detailed insight into the nature of the small molecule, a possible polyamine. Taken together, our data suggest that a novel allosteric mechanism underlies the ligand response of SCO3201.
SCO3201 adopts the closed conformation in solution The markedly different conformations observed in our crystal structures prompted us to characterise SCO3201 in solution by means of SAXS (Fig. 4 ). Comparison of the extrapolated forward scattering (I 0 ) to that of a bovine serum albumin (BSA) reference sample suggests a particle mass of 46. 4 kDa, while the concentration-independent Bayesian method of Hajizadeh et al. [22] , yields a value of 46. 7 kDa. These results are in excellent agreement with the predicted mass of the SCO3201 homodimer (46. 7 kDa). A more detailed analysis of the data using CRYSOL  [23]  (Fig. 4A ) indicates that the scattering from SCO3201 is explained almost to within experimental error (v 2 = 1. 2) by the CD dimer from the ligand-free crystal structure. In contrast, using the asymmetric liganded structure as a model (either with or without the small molecule) leads to a considerable lack of fit (v 2 = 2.
6). The same is true for a symmetrical 'doubly liganded' model, constructed by superimposing a copy of the A chain of the liganded structure onto the dimerisation interface of the B chain and combining that with the original A chain (v 2 = 2. 5). An ab initio model calculated from the experimental data using the program DAMMIN  [24]  closely matches the dimer from 5EFY (Fig. 4B ). We therefore conclude that, in our SAXS experiments, SCO3201 predominantly adopts a closed conformation similar to the one seen in the ligand-free crystal structure. Several things may explain why the ligand-induced conformation is not observed here. In the first place, the basic conditions (pH 8. 5) might favour dissociation of the complex, as the pH of the solution could have a considerable impact on the protonation state of both the ligand and the glutamate residue it is in contact with.
And finally, our SAXS data corroborate the existence of the closed conformation in solution. Intriguingly, the compact arrangement of the two HTH-motifs, with their recognition helices at less than  25  A from each other, would preclude binding to consecutive instances of the major groove on one face of the promoter. This DNA-binding mode, which is a hallmark of the TetR/AcrR family  [10] , requires an a3-a3 distance very close to 35 A  [16]. This implies that the SCO3201 dimer has to undergo a major conformational change if it is to interact with the operator. Although DNA binding by members of the TetR/ AcrR family is typically accompanied by appreciable structural changes in the regulatory domain  [10] , all currently known cases involve DNA-binding domains that are far apart in the free repressor and need to be brought into closer proximity to enable promoter binding.
The rationale behind this approach was that the oil, which was used as a cryoprotectant in the determination of the earlier structure (4CGR), might contain the unknown ligand, in which case pre-equilibration might increase occupancy and improve crystal quality. The solution, without the organic phase, was subsequently concentrated to 50 lL (40 mgÁmL À1 ) and used for crystallisation. The reservoir solution in these experiments contained 1 M of (NH 4 ) H 2 PO 4 and 0. 1 M of Tris/HCl pH 5. 0. Again, paraffin oil was used for cryoprotection. A dataset with a resolution of 1. 86 A was collected at beamline P13, operated by EMBL Hamburg at the PETRA III storage ring (DESY, Hamburg, Germany)  [51]. All diffraction data were processed with XDS  [52, 53]. Both crystal structures were solved using PHASER  [54] , in combination with the CCP4 suite  [55].
For the ligand-free form, chain B of protein data bank (PDB) entry 4CGR was used as the molecular replacement search model. Searches with chain A or the complete homodimer (AB) did not yield meaningful solutions. For the liganded form, the dimer was used as the search model. The structures were refined using the CCP4 suite  [55]  and REFMAC5  [56, 57]. All molecular graphics illustrations were produced with PYMOL 0. 99rc6 (DeLano Scientific LLC, Palo Alto, CA, USA). Centres of mass and angles between helices were determined using CALCOM  [58]  and QHELIX  [59] , respectively. Data collection and refinement statistics can be found in Table  1.
, 2012). Dubois et al. (Dubois et al. , 2008)  measured P1 conduction velocity of visual evoked potentials (VEPs) using EEG data and transverse diffusivity in various WM tracts using DTI data from full-term infants. They demonstrated that FA and transverse diffusivity are structural markers of myelination. They related the increase in P1 conduction velocity of VEPs to maturation of optic radiations and the transfer time between hemispheres to maturation of the visual callosal fibers. Microstructural changes in these areas reflect the pattern of growth in children that continues toward adulthood  (Gomez et al. , 2017). A joint S-F study (using MRI and MEG) assessed the age-related correlation between gamma band responses of the primary visual cortex and structural measures including the cortical thickness, volume and surface area of pericalcarine and cuneus  (Gaetz et al.
Despite providing complementary information, higher dimension of joint S-F features makes their clinical usage (e. g. in prediction of diseases) questionable. Using dimensionality reduction strategies and accessing larger datasets are the eventual solutions to this problem. Fortunately, different projects, such as the human connectome project (HCP), have been launched in order to collect more accessible data for neuroscience research. To estimate the normal developmental model and introduce new informative biomarkers, increasing the dataset size is favored over dimension reduction techniques. One method for developing a joint S-F temporal atlas is to use age-related changes for each structural, functional, and S-F feature and combine them. The other applicable and ideal solution, however, is to use suitable informative biomarkers to construct a joint S-F atlas.
3(c) ). On the one hand, some studies considered preterm born neonates as a slight deviation from normal development  (Adibpour et al. , 2020; Benders et al. , 2015; Daneshvarfard et al. , 2020)  and reported their age-related changes as the evolution of the brain before birth. On the other hand, few researches tried to reveal their different structural and functional patterns in comparison with terms  (Baldoli et al. , 2015; Barnes-Davis et al. , 2020; Rogers et al. , 2018). More works will need to be done to determine the evolution of brain S-F coupling after birth, and how preterm birth may deviate natural brain maturation. Are the reported deviations just temporary and negligible changes that will be compensated by the brain's plasticity nature? Or will preterm birth affect the brain and behavior in the future? Do these explanations help to decide whether preterm birth is an important factor in prognosis or not? The multimodal longitudinal dataset of preterm born subjects in different age stages is ideal for such study.
Data collection The data on malaria were collected from the Regional Health Direction of the Hauts-Bassins. They were collected during the year 2017, from January to December from the health facilities: CSPS, CM, MCA and CHU. These data assess number of cases for both simple and severe malaria, the number of deaths, information on awareness sessions as well as the number of people reached. Malaria cases were confirmed by rapid diagnostic test (RDT) or thick blood smear and registered in the consultation registry (Ministère de la Santé, 2020). Data pre-processing Due to the variety of sources, formats and resolutions, the data have been pre-processed. This treatment allowed us to harmonize the data format in order to prepare the modelling. Thus, Thiessen polygons were plotted to delineate the HCA of each health care facility.
Then, the contours of the Thiessen polygons define the area closest to each health centre considering all other surrounding health centres. This technique assumes that patients use the nearest health centre despite the results of studies which have shown that the use of care follows other spatial logics  (Cisse, 2007). This choice is justified by the non-availability of a layer of HCA boundaries. Then, the total number of malaria cases as well as the total population of villages within the HCA were reported to the health centre layer to calculate malaria prevalence. Finally, potential explanatory variables were prepared. Thus, the land-use units contained in the New Land Use Database (NBDOT) were reclassified according to the vegetation density using a visual interpretation of the photographs contained in the database user guide.