dataesr/scientific-paragraphs-categorization huggingface dataset:
Only for the experiments with dilute samples, were the quantity of D2O in samples reduced to 4%, to decrease deuterium isotopic effects that affect the exchange rates  [41]. The CEST experiments were recorded on the 15 N-labeled NCp7 protein at 700 and 950 MHz and at 25 and 35 • C. The data recorded at 700 MHz comprised a series of 2D spectra with the 15 N offset ranging between 102. 2 and 132. 61 ppm and obtained with increments of 0. 41 ppm (25 Hz) or of 0. 205 ppm (12. 5 Hz). The 15 N B1 field applied during the relaxation time (T ex ) was 25 and 12. 5 Hz, respectively. The T ex was set to 0. 4 s. At 950 MHz, the data were recorded as 2D spectra with the 15 N offset ranging between 103. 3 and 133. 41 ppm and obtained with increments of 0. 5 ppm (40 Hz) and 0. 25 ppm (20 Hz). In agreement with these frequency increments, the 15 N B1 field forcefield applied during the relaxation time (T ex = 0.
4 s) was 40 and 20 Hz, respectively. CPMG and CEST relaxation data were analyzed with two-state and three-state models using the program ChemEx (https://github. com/gbouvignies/chemex, accessed on 14 February 2022), which numerically integrates the Bloch-McConnell equations  [42]  and allows the extraction of k ex_AB , k ex_AC , and k ex_BC (kinetic rates of exchange between states A and B, A and C, and B, and C respectively), p A , p B , and p C (populations of the different conformers), and ∆ω AB and ∆ω AC (chemical shift differences between the major and minor conformers). In the case of a three-state equilibrium between a major state A and two minor states B and C (p A >> p B or p C ), the three states could mutually interconvert (Supplementary Figure  S1 ). These values were extracted for each residue of ZK2 in NCp7, NCp9, and NCp15.
Viruses 2022, 14, x FOR PEER REVIEW 9 of 14 Figure  4. 15 N-CEST intensity profiles for C39, G40, Q45, and W37 residues obtained at 600 MHz and 25 °C with a B1 field of 25 Hz and Tex = 0. 4 s. The main dip is at the resonance frequency of the major state and minor dips were observed at the frequency of the minor states. For the figure, the ChemEx software was used to fit the data, using an individual fit for each residue. All fitted parameters associated with the exchange processes that were extracted using chemEx (pA, pB, pC, kex_AB, kex_AC,and kex_BC, ΔωAB, ΔωAC) are similar to those previously measured for NCp7  [33] , particularly the values for Δω, confirming that the same minor conformers, originating from a defect in the coordination of the zinc ion in ZK2, were observed. Table  2. Populations and kinetic rate constants obtained from the fit of CPMG data or/and CEST data for NCp7 at 35 °C.
The best model was a three-state model (in which A is the major form and B and C are the minor forms) with interconversion between the three states. Different sets of data have been used for these calculations: in the first column, CEST data are shown in combination with CPMG data for the residues H44, W37, C39. In the second column, CEST data are shown for the residues H44, W37, C39 with CPMG data for ten residues of ZK2; the third column comprises only the CPMG data (similarly to the calculations of Table  1 ). In the fourth column, only CEST data have been used. In the fifth column, CEST data for the residues H44, W37, C39, G40, and E42 with CPMG data for the residues H44, W37, C39 have been used. 1 N-CEST intensity profiles for C39, G40, Q45, and W37 residues obtained at 600 MHz and 25 • C with a B1 field of 25 Hz and T ex = 0.
CESTH44,W37 All fitted parameters associated with the exchange processes that were extracted using chemEx (p A , p B , p C , k ex_AB , k ex_AC ,and k ex_BC , ∆ω AB, ∆ω AC ) are similar to those previously measured for NCp7  [33] , particularly the values for ∆ω, confirming that the same minor conformers, originating from a defect in the coordination of the zinc ion in ZK2, were observed. The results of the calculations are shown in Table  2  and Supplementary Table  S1. The calculations were performed with different sets of data, including only CEST data for residues featuring the largest ∆ω AB , either a set of three (CEST H44,W37,C39 ) or five (CEST H44,W37,C39,G40,E42 ) residues. CPMG data was included for three residues (CPMG H44,W37,C39 ) or for a larger set of 10 ZK2 residues (CPMG 10residues ).
In Table  2 , the populations and kinetic rate constants obtained with the different sets of data are similar, with a major state A populated at around 94-95% and two minor states quasi-equally populated at ~2% each, showing that the different sets of data converge to the same results. Concerning the kinetic rate constants, only one significant difference was observed for the rate constant k ex_BC , which is is higher for the CEST data. We think that the CEST data contain more information since the minor species were explicitly observed. Therefore, kinetic rate constants determined using CEST data that are notably related to the interconversion between the minor species, k ex_BC , are more accurate. C. The best model was a three-state model (in which A is the major form and B and C are the minor forms) with interconversion between the three states.
Different sets of data have been used for these calculations: in the first column, CEST data are shown in combination with CPMG data for the residues H44, W37, C39. In the second column, CEST data are shown for the residues H44, W37, C39 with CPMG data for ten residues of ZK2; the third column comprises only the CPMG data (similarly to the calculations of Table  1 ). In the fourth column, only CEST data have been used. In the fifth column, CEST data for the residues H44, W37, C39, G40, and E42 with CPMG data for the residues H44, W37, C39 have been used. CEST experiments also permit researchers to evaluate the relaxation rates R2 of the individual states, in contrast to the calculations using only CPMG data that are made with the hypothesis that the intrinsic relaxation rates of the various states are similar  [31, 32].
Results Invasive origins. The total number of individuals used in this study was 177 (99 from native populations and 78 from invasive populations) from 12 geographic populations (Fig. 1A  and Table  1 ), making this dataset the largest and most comprehensive to date. The identified strain had an almost perfect correlation with host plants (Fig. 1B ) according to the TPI marker. When the mitochondrial COX1 marker was used, almost all samples from rice or grasses were sfR, but sfR was also often observed from corn plants. The mitochondrial COX1 phylogenetic tree recovered two clades corresponding to sfC and sfR mitochondrial strains with high bootstrap confidence scores (bootstrap support value of 97. 3%) (Fig. 2A ). The existence of two mitochondrial strains in invasive populations suggests a possibility of multiple introductions from the Americas to the Old World, as shown by Tay et al.
Adaptive evolution contributed to the second and third steps, potentially through insecticide resistance or host plant adaptation. for whole genome resequencing were constructed from 1. 0 μg of DNA per sample using the NEBNext DNA Library Prep Kit. We performed whole genome sequencing from FAW samples collected in Benin (39 individuals), India (14), Mexico (26), Florida (24), French Guiana (3), and Guadeloupe (4) using the NovaSeq 6000 System with 20X coverage on average with 150 bp paired-end and 300 bp insert length. Then, we combined resequencing data from Santa Isabel in Puerto Rico (15) (NCBI SRA: PRJNA577869), Stoneville in Mississippi (17) (PRJNA494340), and from Citra and Jacksonville in Florida (USA) (24) (PRJNA639296), which were generated for our previous studies  45, 47, 48. The resequencing data from Kunming in China (2)  44  was also included in the analysis.
Variant calling. Nucleotides with a Phred score less than 20 and adapter sequences were removed from the reads using AdapterRemoval v2. 1. 7  72. Reads were mapped against the ver7 reference genome (https:// bipaa. genou est. org/ sp/ spodo ptera_ frugi perda_ pub/ downl oad)  48  , which had chromosome-sized scaffolds, using bow-tie2 v2. 3. 4. 1 with the -very-sensitive-local preset  73. The read depth of mapping of resequencing data was 17. 72X in the median. Then, we performed local re-assembly of haplotypes using GATK v4. 1. 2. 0  74. The resulting gvcf files were merged into one gvcf file with CombineGVCFs command and variant calling was performed with GenotypeGVCF command in the same software. Filtering was performed from the resulting VCF (variant calling format) file if QD is lower than 2.
0, FS is higher than 60. 0, MQ is lower than 40. 0, or MQRankSum is lower than -12. 5, or ReadPosRankSum is lower than -8. 0. The total number of genetic variance is 158,277,530, which includes 89,387,997 SNVs (single nucleotide variations). After filtering, 27,117,672 SNVs remained. Strain identification. FAW strains were identified using a phylogenetic tree reconstructed from the mitochondrial COX1 gene, which is the universal barcode gene and is also commonly used for FAW strain identification  75. We first mapped the Illumina reads against mitochondrial genomes (NCBI: KM362176) using bowtie2 v2. 3. 4. 1 with -very-sensitive-local preset  73  , followed by extracting mitochondrial reads using samtools v1. 9  76. Mitochondrial genomes were assembled from these reads, and mitochondrial genes were annotated using MitoZ using the default options  77.
13  85. First, a new VCF file with individuals from native populations was generated by subsetting the original VCF file with 177 individuals. Second, S. litura (Fabricius), which is one of the most closely related species to FAW in the Spodoptera genus  86  , was used as an outgroup, and a VCF file was generated by mapping S. litura Illumina reads (NCBI SRA, SRX2446353) against the FAW reference genome using bowtie2 with -very-sensitive-local preset  73  and by variant calling using GATK v4. 1. 2. 0  74. Third, these two VCF files were merged using VCFtools v0. 1. 15  83 , while missing data of S. litura was not allowed. The number of used SNVs is 697,498. Fourth, the newly merged VCF file was converted to TreeMIX format using vcf2treemix. sh (https:// github. com/ speci ation genom ics/ scrip ts/ blob/ master/ vcf2t reemix.
sh). Fifth, we ran a TreeMIX binary with the number of migration edges ranging from three to six while the resulting tree was rooted by S. litura. The number of SNVs per block was 500 to estimate covariance matrices. Finally, the resulting file was visualized using the internal R library (plotting_funcs. R) in the TreeMix software. We also used the VCFphylo approach  47  to infer phylogenetic relationships at the level of individuals out of whole genome sequences. First, the euclidean distance of allele frequency between each pair of individuals was calculated from the biallelic variant positions in which genotypes are determined from all individuals using VCFphylo  47. Transversional variants were weighted to two. Then, bootstrapping distance matrices were generated with 1,000 replications, and we generated BIO-NJ trees for each matrix using FastME v2.
1. 5  87. Then, a consensus tree was made using consense in the Phylip package v3. 697  88. The tree was visualized using iTOL v6  52. The inference of loci under selective sweeps. Potential targets of selective sweeps were identified from the composite likelihood of being targeted by selected sweeps from the site frequency spectrum using SweeD v3. 2. 1  54  from the largest 29 scaffolds, which are believed to be chromosome-sized. The proportion of the assembly covered by these 29 scaffolds is 93. 52%. The number of grids in which composite likelihood was calculated was 1,000 per scaffold. Based on the assumption that most genomic sequences were not targeted by selective sweeps, outliers of composite likelihood were identified as loci targeted by selective sweeps. The annotation of Cytochrome P450 genes was manually curated, as described in Gouin et al.
Acknowledgements This work ( ID 1702-018 , given to KN) was publicly funded through  ANR  (the  French National Research Agency)  under the " Investissements d'avenir " programme with the reference  ANR-10-LABX-001-01 Labex Agro  and coordinated by  Agropolis Fondation  under the frame of I- SITE MUSE  ( ANR-16-IDEX-0006 ). In addition, a grant from the  department of Santé des Plantes et Environnement at Institut national de la recherche  agronomique for KN (adaptivesv). This work was also financially supported by  EUPHRESCO  (FAW-spedcom, given to  Anne-Nathalie Volkoff ) and by  CSIRO Health  & biosecurity (given to WTT, TW, and KG). SY was supported by a  CIRAD-INRAE  PhD fellowship. We are grateful to the genotoul bioinformatics platform  Toulouse Occitanie  ( Bioinfo Genotoul , https:// doi.
The 64 angular sectors of the "d1" data product each cover a solid angle of 22. 5° × 22. 5°. This data product accumulates ion counts over a time period of 4-32 s, depending on the instrument operational mode. McFadden et al. (2015)  detail the known caveats of STATIC operations and measurements. In particular, protons can be reflected by the surfaces of MAVEN's spacecraft and by surfaces and grids of the STATIC instrument itself. In both cases, this background flux has an intensity of 10 -5 to 10 -3 times the solar wind flux and can be misidentified as Phobos-related protons if not carefully considered. We follow a 2-step approach to identify the origin of the protons observed by STATIC close to Phobos and to figure out if STATIC detected any Phobos-related signal.
Identifying Reflection by the Artificial Surfaces of MAVEN and STATIC The yellow rectangle on Figure  1a  identifies an area of significant 500-1,000 eV proton flux. A flag provided in the STATIC data product indicates that most of these sectors were, at this time, blocked at more than 50% by MAVEN spacecraft parts. Figure  1c  shows the energy-time spectrogram corresponding to the angular sector A10D3 (red square on Figure  1a ) and reveals a steady signature with protons having an energy equal to or lower than the solar wind energy measured by SWIA of around 1 keV. The direction-resolved flux intensity of this steady signature is 10 -3 times the SWIA solar wind flux. These protons are likely solar wind protons reflected by MAVEN. Similar steady signatures are observed for solar wind protons reflected by STATIC grids and surfaces.
Data Availability Statement The public AMDA science analysis system of the French data center for Plasma Physics (CDPP) provided the ephemeris of Phobos (AMDA, 2022c, Automated Multi-Dataset Analysis (AMDA). This dataset is available at http://amda. irap. omp. eu by clicking on "Public Access" and then going in the subdirectory "AMDA Database > Astronomical Objects Ephemerides > Planets and Moons > Mars moons > Phobos -1 sec. " Alternatively, the MSO position of Phobos can be directly retrieved with the following link, in which the start and end times should be set as needed: http://amda. irap. omp. eu/service/hapi/data?id=mars-phobos-orb1s%26parameters=xyz_ phobos1s%26time. min=2020-09-02T00:00:00. 000Z%26time. max=2020-09-02T01:00:00. 000Z%26attach=false) and MAVEN (AMDA, 2022b, Automated Multi-Dataset Analysis (AMDA).
This dataset is available at http://amda. irap. omp. eu by clicking on "Public Access" and then going in the subdirectory "AMDA Database > MAVEN > Ephemeris > orbit Mars -1 sec. " Alternatively, the MSO position of MAVEN can be retrieved with the following link, in which the start and end times should be set as needed: http://amda. irap. omp. eu/service/hapi/data?id=maven-orb-marsobs1s%26parameters=mav_xyz_mso1s%26time. min=2020-09-02T00:00:00. 000Z%26time. max=2020-09-02T01:00:00. 000Z%26attach=false), the MAVEN-SWIA solar wind velocity vectors (AMDA, 2022d, Automated Multi-Dataset Analysis (AMDA). This dataset is available at http://amda. irap. omp. eu by clicking on "Public Access" and then going in the subdirectory "AMDA Database > MAVEN > SWIA > ions: key parameters. " Alternatively, the solar wind velocity vector can be directly retrieved with the following link, in which the start and end times should be set as needed: http:// amda.
irap. omp. eu/service/hapi/data?id=mav-swia-kp%26parameters=mav_swiakp_vmso%26time. min=2020-09-02T00:00:00. 000Z%26time. max=2020-09-02T01:00:00. 000Z%26attach=false) and the MAVEN-MAG (AMDA, 2022a, Automated Multi-Dataset Analysis (AMDA). This dataset is available at http://amda. irap. omp. eu by clicking on "Public Access" and then going in the subdirectory "AMDA Database > MAVEN > MAG > 1 sec. " Alternatively, MAG data can be directly retrieved for a given period of time with the following link, in which the start and end times should be set as needed: http://amda. irap. omp. eu/service/hapi/data?id=mav-mag-all%26parame-.
exposure of fossiliferous layers, sedimentary deposits are often inconveniently reworked. Yet, within the available dataset, only the latest dating  15  is in fact difficult to reconcile with the others. While the large uncertainties and the overdispersion of the data revealed by the mean square weighted deviation (Fig. 3  in  15  ) may explain this outlier, their study indisputably revives the controversy. In addition, most previous dating methods suffer from large uncertainties arising from the poor constraints on the pre-burial history. Instead, Terrestrial Cosmogenic Nuclide dating (TCN) is, to our knowledge, the only available method to focus on the burial time and thus to minimize uncertainties associated to the pre-burial history. For that reason, this technique is increasingly applied in archaeology and paleoanthropology, and sheds new lights on hominin dispersal  [16] [17] [18] [19] [20] [21].
I. Table  3 ). Acid attacks were repeated until the maximum amount of pure SiO 2 was retrieved, within the availability limit of materials. All samples (besides SAN18-7 to SAN18-9) yielded enough quartz to perform suitable measurements. After purification, the quartz content was dissolved in HF 48% after addition of 150 µl of a 3025±9 ppm  9  Be solution. Natural Al content was determined by ICP-OES using an ICAP6500 from Thermo. BeO and Al 2 O 3 were respectively mixed with niobium and silver powders prior to measurements. Beryllium data were directly calibrated against the STD11 standard 66 with a 10 Be/ 9 Be ratio of (1. 191±0. 013) x 10 -11. Aluminum measurements were performed against in-house standard SM-Al-11, with a 26 Al/  27  Al ratio of (7. 401±0. 064) x 10 -12 , previously cross-calibrated against the primary standards certified by a round-robin exercise  67, 68.
Sundaland physical landscape reconstruction ca. 1. 8 Ma. In order to reconstruct the landscape at 1. 8 Ma, we first compiled rates of vertical land motions inferred from geomorphological indicators, stratigraphic, and seismic data (S. I. Fig. 1a  adapted from  6, 7, 33  ). This dataset provides discrete informations that we interpolated in order to obtain a continuous map of uplift rates over the region, which backward integration in time provides a paleo-elevation map. To reconstruct a realistic landscape at 1. 8 Ma, we ran the Landscape Evolution Model (LEM) goSPL 32 over a 10,000 years period starting from an adjusted paleo-elevation surface (1 km resolution) derived from the uplift map and past absolute sea level, set to -30 m during Early Pleistocene sea level highstands  71. Continuity of mass is the main equation of the model, and is expressed by: where z is surface elevation (m), t is time (yr), U is vertical land motion ( m/yr ) and κ the diffusion coefficient for soil creep (set to 5 × 10 -3 m 2 /yr).
Acknowledgements Authors are grateful to  Nandang  from  LIPI Geotek  for his continued involvement in the field, to the people of Sangiran for their assistance, and to the  Museum Situs Manusia Purba Sangiran and Tanto  for their guidance. The authors thank  J. Arief  for his help in the field,  F. Semah  and  C. Falguères  for discussions,  L. Léanni  for her valuable assistance during chemical treatments and ICP-OES measurements, and  D. Daddi-Addoun  for her support. J. Louys  and two anonymous reviewers greatly help improving the manuscript. Our colleague and friend  Didier L. Bourlès , who passed away in 2021, instigated this study.
The oceans represent 97% of all water on Earth and contain microscopic, drifting life, plankton, which drives global biogeochemical cycles. A major hurdle in assessing marine plankton is the planetary scale of the oceans and the logistical and economic constraints associated with their sampling. This difficulty is reflected in the limited amount of scientifically equipped fleets and affordable equipment. Here we present a modular hardware/software open-source strategy for building a versatile, re-configurable imaging platform -the PlanktoScope -that can be adapted to a number of applications in aquatic biology and ecology. We demonstrate high-throughput quantitative imaging of laboratory and field plankton samples while enabling rapid device reconfiguration to match the evolving needs of the sampler.
, 2004) , Tara Oceans  (Karsenti et al. , 2011; Duarte, 2015). In particular, Tara Oceans (2009 -2013)  has applied a standardized, eco-systems biology strategy to explore plankton diversity from genes to communities, from viruses to animals, and across coarse but planetary spatial and seasonal scales  (Sunagawa et al. , 2020). The combination of global ocean DNA metabarcoding, metagenomic, and metatranscriptomic datasets [e. g. (de Vargas et al. , 2015 )  (Sunagawa et al. , 2015)   Carradec et al. (2018) ] has unveiled the basic structures of open ocean plankton taxonomic diversity and generated hypotheses about its interactions  (Chaffron et al. , 2021) , biogeography  (Ruuskanen et al. , 2021) , and roles in critical ocean processes such as the carbon pump  Guidi et al. , 2016. However, understanding the eco-evolutionary dynamics of plankton will require far more information across the four dimensions of the world ocean.
foldscope. com/). Plankton ecology would greatly benefit from a low-cost portable quantitative microscope that can be used directly at sea or on the shore by the vast community of mariners enjoying and/ or living from the ocean. Here, we used modularity -a natural way to make complexity manageable and accommodate uncertainty in the evolution of design  (Efatmaneshnik and Ryan, 2016)  -to construct the PlanktoScope, a miniaturized modular open-source imaging platform for quantitative imaging of micro-plankton that matches the quality of much larger and more expensive commercial instruments, for costs that are affordable for personal assembly and use. Even though we develop the canonical versions of the PlanktoScope for a global homogenous measure of plankton life, every module encapsulates a simple function allowing scientists and makers to adopt the platform for their needs.
Designs of Two PlanktoScope Prototypes To design the modular version of the PlanktoScope (v. 1) made of six units that can be stacked on top of each other (Figures  1A-D ), we used Autodesk Fusion 360 (v2. 0. 5688) to create a parametric design optimizing the physical interface common to all modules. Different parameters define the interface's areas, such as the electronic connection area, the magnetic linkage, and the optical path. The thickness of the material and the outer dimensions of all the electronics used inside the instrument were critical to characterizing the interface. The shareable online 3D environment provided by Fusion 360 contains the main 3D model, together with other models that form the electronic and optical parts. Most of these models have been generated by measuring existing objects but some have been downloaded from the online GrabCad library (https://grabcad.