dataesr/scientific-paragraphs-categorization huggingface dataset:
As a result, several technical aspects of the proposed schemes such as amplitude saturation and fiber-ground coupling during strong shaking cannot be fully evaluated. However, unlike commonly used empirical EEW approaches  [32] [33] [34]  , the proposed scheme is theoretical and relies on a well-established source model  41  that was found to adequately describe the far-field radiation of a large range of earthquakes. Thus, showing that the proposed methods work for the current earthquake dataset is sufficient to demonstrate their validity. In addition, considering small magnitude earthquakes, as we do here, demonstrates the robustness of the system to false alarms. Analyzing near field records is a troublesome issue for EEW; since a complete theoretical framework is yet to be developed  57  , other approaches such as resolving line sources  58  or extrapolating peak ground motions away from the earthquake source 59 may need to be adapted to DAS data in order to address this gap.
The approach allows for continuous update of magnitude and ground motion predictions, key for analyzing large earthquakes with long durations. In addition, using a holistic magnitude estimation and ground motion prediction that are derived from the same earthquake model reduces the impact of stress drop related magnitude biases on ground motion predictions and enhances the overall robustness of the system. The computational costs of the presented approaches are low. While DAS acquisitions typically provide very large data volumes, for EEW, data can be largely down-sampled in both time and space, limiting both the volume of data and processing times. For instance, to obtain timely and robust magnitude estimates, it is sufficient to use preselected well-coupled fiber portions at spacings of several kilometers.
For the purpose of this study, we analyzed 180 s long recordings of preselected DAS fiber segments (33 channels), down-sampled to ~ 20 Hz, in ~ 136 s using a Python code on an Intel Core i7 laptop with 32 GB RAM using a single thread. These computation times indicate that the method is valid for real-time. For future implementation as part of an operational EEW system, several aspects of the code can be optimized and run in parallel. For example, slant-stack computations, which are the most time-consuming (~ 4 s per channel), can be parallelized, in addition to computations for different fiber segments. The latter can also increase the number of fiber segments used for magnitude estimation. For few earthquakes, strain amplitudes exhibited a small degree of saturation. Nevertheless, magnitude estimations still allow for reliable ground motion predictions (Fig.
Real-time strain-rates to ground accelerations conversion. The slant-stack  62  based strains to ground motions conversion scheme  37  accounts for apparent phase velocity variations in both time and space. The conversion is applied for each DAS channel along the fiber using short, approximately linear, fiber segments. Here, this recently presented approach  37  is modified and optimized for real-time performance. The semblance (coherency) as a function of apparent slowness p x and time t, for a DAS channel located at x 0 along the fiber, can be written as: where L is the number of DAS channels used for slowness estimation, g(t) is the DAS strain-rates time-series, and x j -x 0 is the distance between station j and the reference channel (at x 0 ). Equation (  2 ) can be regarded as the causal slant-stack, where only data samples of g(t) that have already been recorded are considered.
The conversion procedure is performed as follows. For computational efficiency, recorded strain-rates are down-sampled to 20 Hz (or slightly higher, depending on the original signals' sampling-rate). Data is lowpass filtered at 5 Hz using a 4-pole Butterworth filter to diminish high frequency instrumental noise. The applied down-sampling and filtering did not decrease the robustness of the conversion and subsequent magnitude estimation. The local slant-stack transform is applied using fiber segments of ~ 380 m length  37  , with channel spacings of ~ 20 m, skipping several channels for densely spaced measurements. The used fiber segments are long enough to resolve long seismic wavelengths with fast velocities of several km/s, and short enough so that seismic waves are coherent and fiber sections are approximately linear  37.
Synthetic ground motions. The GMPEs in Eq. (  10 ) are used to generate synthetic PGV and PGA for different seismic moments, stress drops and hypocentral distances. Synthetic A rms are generated by calculating the rms of the acceleration spectra (Supplementary Fig. 9 ). These spectra are produced for a specific seismic moment, stress drop and hypocentral distance using Eq. (  3 ) and (  4 ), subject to a lowpass filter. The filter is modeled in two manners: as a clean cutoff (dashed black curve in Supplementary Fig. 9 ) as used for the model derivation (See "Magnitude estimation from bandlimited ground accelerations" in Methods), or as an ideal 4-pole Butterworth filter (solid black curve in Supplementary Fig. 9 ), similar to that used for DAS signal processing. Earthquake dataset. DAS measurements in Greece were conducted using a Febus A1 DAS interrogator between 18-19 and 19-25 April 2019 on 13.
Seismometer and accelerometer recordings were used to calculate PGV and PGA for the different earthquakes as follows. Data for Greece, France and Chile were obtained from the National Observatory of Athens, the RESIF repository and IRIS, respectively. The two horizontal components of point-sensors were demeaned and highpass filtered at 1 Hz using a 4-pole Butterworth filter, followed by a simple gain correction. Velocity-meter signals were differentiated to obtain ground accelerations and accelerometer records were integrated to obtain ground velocities. An additional highpass filter was applied after differentiations and integrations. PGV (PGA) were then calculated as the geometric mean of the maximum of the absolute value of the two velocity (acceleration) components. PGV and PGA that are smaller than 5 times the standard deviation of the associated time-series are discarded as they may be biased by noise.
Acknowledgements This project has received funding from the  European Research Council (ERC)  under the European Union's  Horizon 2020 research and innovation program  (grant agreement No. 101041092 ), from the  UCA JEDI Investments  in the  Future  project managed by the  National Research Agency (ANR)  with the reference number  ANR-15-IDEX-01 , and from the  Observatoire de la Côte d' Azur. We thank  GTD Grupo  SA who provided access to the infrastructure, and el  Centro Sismologico Nacional  staff who helped in the logistics.
Similarly, there is little existing published work on the use of conservation actions to reduce direct impacts of climate change or severe weather: for example, 173 studies specifically address this in the Conservation Evidence database, compared to 1972 relating to agriculture  (Sutherland et al. , 2021). Stakeholder engagement is particularly important to capture the latest impacts of, and responses to, a developing threat like climate change. Third, climate change interacts with other drivers and pressures in complex ways (Schulte to  Bühne et al. , 2021) , and many climate change impacts are indirect  (Gissi et al. , 2021; Mitchell et al. , 2020). Seabirds were chosen as they are a highly threatened and relatively well-studied group of organisms suffering substantial impacts from climate change  (Dias et al.
Each participant was categorized as focused on research, practice, or policy based on their primary organizational affiliation. Any participants who did not fall into these three categories were classed as "other. " We also wished to partially quantify how much and in what ways the comments from the workshops contributed to the overall guidance. One researcher (HH) manually recorded meta-data related to each comment in a separate database. Each comment was assessed against one (or several) of the following categories: (a) new information that could form a major new point in the guidance; (b) new evidence to support a point already present in the guidance; (c) information based on personal or unpublished data; (d) information specific to the participant's study area; (e) a new study not previously included in the guidance; (f) a new study in a language other than English; (g) information that changed species' range maps; (h) a new climate change impact; (i) new evidence that supported an existing impact; (j) a new conservation action not already in the guidance; (k) new evidence to support an existing conservation action.
ACKNOWLEDGMENTS The authors would like to thank  José Manuel Arcos ,  Elmar Ballstaedt ,  Adrien Lambrechts ,  Szabolcs Nagy ,  Aðalsteinn Örn Snaeþ  orsson, and  Ram unas  Žydelis for their valuable contributions to the project concerning seabird conservation in the face of climate change, and for their feedback during the development of our guidance documents. This work has been funded by  Stichting Ave Fenix Europa. NP is funded by  Research England. SOP and WJS are funded by The  Arcadia Fund , The  David and Claudia Harding Foundation , and The  MAVA Foundation.
Sample and chemical species selection Out   2017). A total of 178 chemical species were measured for each filter. Species displaying irregularities in their time series were excluded from the analysis, as were those with over 25 % of the data falling below the quantification limit (< QL, which is defined as the mean field blank concentrations measured per species, plus 2 times the standard deviation). From the remaining 86 species, the ones that were measured through both ion chromatography (IC) and inductive coupled plasma-mass spectrometry (ICP-MS), only the ICP-MS metals were included in order to avoid duplicative counting, except for K + , for which the IC measurements were used, since water-soluble K + is a known tracer for biomass burning (BB), soil resuspension, and fertilizers  (Li et al.
Multisite PMF Initial parallel runs of single-site PMF analysis revealed similar main sources contributing to particulate matter. Increasing the number of factors showed the potential for the separation of the traffic profile, although this meant compromising on the statistical stability of the solution. Motivated by these findings, a multisite PMF analysis was conducted. Such an approach has proven its ability to reduce the rotational ambiguity in factor analyses  (Dai et al. , 2020; Hopke, 2021; Pandolfi et al. , 2020; Hernández-Pellón and Fernández-Olmo, 2019) , increasing the statistical robustness through an increased number of samples. To combine both datasets into a single dataset (EA-LP) the dates in the La Paz dataset were shifted in time by 2 years and then appended to El Alto's dataset.
The factors associated with secondary aerosol particles (secondary sulfate, secondary nitrate, and MSA rich) were responsible for nearly 22 % and 24 % of total PM (La Paz and El Alto, respectively), and only a slight difference can be observed between the cities, except for the nitrate-rich profile. Finally, the biomass burning factor was responsible for an average of 9 % and 8 % of the total measured PM 10 (in LP and EA, respectively). The chemical profiles and seasonality of each factor are displayed in Figs. 4  and 5 , respectively, and one of the advantages of performing a multisite PMF in the present study is the possibility of differentiating between two traffic profiles that could hardly be observed in the individual solutions. Similarly, some factor profiles that remained mixed in the single-site solution for one site were polished as a result of combining both datasets.
For the multisite solution, the indirect information of the mixing of sources during transport is lost. -The average molar ratio of sulfate and ammonia concentrations differs between the two cities (2. 05 and 1. 63 in El Alto and La Paz, respectively), indicating a lower availability of ammonium to neutralize the sulfate and nitrate ions in the city of La Paz. However, this distinction is no longer evident in the multisite analysis, which yields a median molar ratio of 1. 96 that is representative of both cities. -The MSA-rich profile in El Alto exhibits strong mixing with metallic species, among them crustal material, which hinted at its path through the Altiplano towards the city of El Alto. This mixing pattern is no longer evident in the multisite analysis. Considering that the advantages of a more specific characterization of sources provided by the multisite approach outweigh the associated drawbacks, we believe it was the most appropriate technique to apply in the metropolitan region of La Paz and El Alto with such a database at hand.
Conclusions This study presents innovative information and a unique analysis of air pollution sources in the high-altitude urban environment of the fast-growing cities of La Paz and El Alto in Bolivia. It also provides a detailed description of the chemical profiles of 11 identified source types, resolved by the multisite PMF method, along with their temporal and spatial variability. The extensive and comprehensive dataset, combined with the inclusion of inorganic and organic species in the analysis, enabled an advanced source apportionment beyond classical solutions, allowing for the identification of several biogenic and combustion-related factors that would have remained unresolved otherwise. Notably, waste burning was separated from biomass burning, and traffic exhaust emissions were separated into two independent profiles.
Gene retrieval Trimmomatic was used to remove adapter sequences, poorquality base calls and poor-quality reads from sequencing reads with the settings: illuminaclip 2:30:10, leading 30, trailing 30, sliding window 4:2:30, minimum length 36 and Phred-33 base quality encoding  (Bolger et al. , 2014). Exon sequences were assembled using the HybPiper v1 pipeline for nucleotide data  (Johnson et al. , 2016). Trimmed reads were mapped against the Sapindales subset of the mega target file, which led to a substantially higher recovery for Sapindales than with the standard Angiosperms353 target file  (McLay et al. , 2021). Exons and supercontigs were retrieved using the HybPiper script retrieve_sequences. py, and summary gene recovery statistics for each sample were generated for each sample with the HybPiper scripts get_seq_lengths.
Data cleaning and paralogy characterization We cleaned loci or samples where the multiple copies are uninformative (i. e. , are likely due to contamination or laboratory error), and retained paralogous loci where the cause is more likely to be gene duplication events. This enabled maximum retention of data, and the identification of lineages in the phylogenetic tree where gene duplication events (such as polyploidization or hybridization) could have played a role. It is uncertain whether Angiosperms353 baits differ in their ability to hybridize with paralogous copies of genes across lineages at the ordinal scale, and theoretically, this could result in an underestimation of paralogy in cases where gene copies are highly divergent or lost. Nevertheless, we suggest that the characterization of paralogy is useful for gaining a general understanding of where genes have been duplicated and retained in Sapindales, how these patterns may differ across the order, and where gene duplication events may affect evolutionary inference from phylogenetic trees and morphology.
It is possible that the use of ambiguities in sequences could depress branch lengths relative to the use of a tree estimated with consensus sequences; however, we consider the use of ambiguities to be the most conservative and accurate way to code SNPs from paralogous loci, as it avoids the analysis of chimeric contigs assembled from reads of paralogous loci as orthologous loci, and places more weight on the regions of the locus that are conserved across copies within the same sample in the phylogenetic analysis. Reads were remapped to the contig for each gene generated with the HybPhaser script Generate_consensus_sequences. sh. Information on length and coverage of sequences from all samples and loci was collated with the HybPhaser script Rscript_1a_count_snps_in_consensus_seqs. R. Following visual inspection of the outputs which summarised heterozygosity in the raw Angioperms353 data and manual inspection of the remapped.
bam files, HybPhaser scripts R1b_optimize_dataset. R and Configure_1_SNPs_assessment. R were used to clean the data by removing samples with >50% missing loci and loci with <30% locus recovery, >21% missing samples, as well as samples and loci with outlying heterozygosity (> 1. 5x the inter-quartile range for heterozygosity, which we considered more likely to be contaminated). Tables of heterozygosity and allele divergence were collated with the script Rscript_1c_summary_table. R, and the cleaned consensus sequences with ambiguities exporte d with Rscript_1d_generate_sequence_lists. R. A summary of final sample coverage, sequence length, heterozygosity, and allele divergence after cleaning is given in Supplementary Material 2. We examined SNP patterns in the cleaned Angiosperms353 dataset and determined the proportion of heterozygous loci and the proportion of loci with more than 0%, 0.
5%, 1%, and 2% SNPs, as well as mean allele divergence for each sample. While heterozygosity (as indicated by the presence of SNPs, i. e. , any locus with > 0% SNPs) can be expected in any homologous locus due to allelic variation, loci with a high proportion of SNPs (e. g. , >1% SNPs per locus) more likely result from multiple gene copies. Therefore, we consider that any locus with >1% SNPs in the cleaned dataset is likely to be paralogous, with paralogy caused by biological processes such as gene duplication, polyploidization, and hybridization, rather than by allelic variation, sequencing error or contamination.
Divergence time estimation To date the Sapindales phylogenetic tree, 29 fossils were selected from the literature as calibrations (Table  1 ). The reliability of each fossil's identification and age was rigorously assessed and scored following the approach used in a previous angiosperm-wide fossil calibration dataset  (Ramıŕez-Barahona et al. , 2020)  and using best practices for justifying fossil calibrations  (Parham et al. , 2012; Supplementary Material 3). A conservative approach to calibration was employed, with fossils assigned to the stem node of the taxon or clade the fossil was assigned to. Full justification of node assignment for each fossil calibration is given in Supplementary Material 3. Computational efficiency of the dating analysis was optimized through gene-shopping, as implemented in SortaDate  (Smith et al.
Locus recovery and paralogy The final Sapindales dataset comprised 472 species (including 24 outgroup representatives) with an average of 324 loci recovered per sample and 74% target coverage per locus (Supplementary Material 2). On average, 15 (0-44) loci with an outlying proportion of SNPs were removed per sample in the cleaning steps of HybPhaser. In the cleaned Sapindales dataset, 63% (15-99) of loci contained one or more SNP, and the mean allele divergence was 1. 33% (0. 89-7. 52). While the presence of a low number of SNPs can be expected in any orthologous locus, a high proportion of SNPs in a locus (e. g. >1% SNPs per locus) in the cleaned dataset is more likely to be indicative of multiple copies of that locus in the data (i. e. , paralogy). Therefore, to differentiate allelic variation from paralogy, we consider loci with >1% SNPs to be paralogous (i.
The rapid divergence of Simaroubaceae, Rutaceae, and Meliaceae could explain the difficulty of reconstructing familial relationships with the smaller datasets of previous studies. Ancient hybridization in the early history of these families could also explain contrasting family topologies in previous studies based on plastid data, and may be supported by the high degree of paralogy in Rutaceae and Meliaceae detected in this study relative to other Sapindales families. Given that our study includes an order of magnitude more data and denser sampling than previous phylogenetic studies of the order, we suggest that it is the most reliable representation of family relationships published to date. However, future research should be conducted with short-and long-read sequences to investigate whether ancient hybridization could be driving contrasting topologies between nuclear and plastid phylogenetic trees.
Acknowledgments We would like to thank  G. Brown ,  L. Simmons ,  D. Murphy ,  K. Shepherd ,  B. Lepschi  and  R. Fowler  for the contribution of data for GAP samples, and the support of  M. Lum  and  L. Simpson  in facilitating their acquisition. EJ is grateful to  M. Harrison ,  R. Cowan  and  L. Frankel  for laboratory assistance,  B. Wannan  for helpful discussions on Anacardiaceae and  S. Manchester ,  P. Wilf  and  A. Rozefelds  for paleobotanical advice. We also thank  C. J. Rothfels  and three reviewers for their feedback which greatly improved this manuscript.
Funding This work was supported by grants from the  Calleva Foundation  to the Plant and  Fungal Trees of Life (PAFTOL)  project at the  Royal Botanic Gardens, Kew. We also acknowledge the contribution of the  Genomics for Australian Plants (GAP) Framework Initiative consortium in the generation of data  for some samples used in this publication. GAP is supported by funding from  Bioplatforms Australia  (enabled by NCRIS), the  Ian Potter Foundation ,  Royal Botanic Gardens Foundation (Victoria) ,  Royal Botanic Gardens Victoria , the  Royal Botanic Gardens and Domain Trust , the  Council of Heads of Australasian Herbaria, CSIRO ,  Centre for Australian National Biodiversity Research  and the  Department of Biodiversity, Conservation and Attractions ,  Western Australia. This research was also supported by an  Australasian Systematic Botany Society   Hansjörg Eichler Research Grant  and a  Wet Tropics Management Authority   Research Grant  to EJ.
Our results are summarized in a catalog of convective vortex encounters through sol 415 of the mission. The catalog summarizes properties such as the duration and magnitude of the pressure excursion, detection of dust or not, and thermal properties of the environment during the event. The catalog is complemented by a larger catalog of pressure drops containing additional long and turbulent events, physical parameters of a selection of vortices, and DDs from model fits and a movie of the LES, all available online  (Hueso et al. , 2022). The structure of this paper is as follows. Section 2 describes MEDA data sets and the analyses conducted to identify vortices and DDs, the results of which are shown in Section 3. Section 4 describes the variability of this activity, including its seasonal evolution, variations associated with the dust storm, and effects linked to different terrains.
Data and Data Analysis MEDA acquires data in measurement sessions that can extend from 5 min to a few hours and that typically cover 54% of a sol. The data is obtained with a cadence of 1 Hz in most sensors (including pressure), and up to 2 Hz in the five Atmospheric Temperature Sensors (ATSs) and the two WSs. Gaps in the data are due to a combination of minor hardware issues and mission operations. The WSs were required to be off during orbiter communication passes, and as a result, some observed vortex encounters do not have simultaneous wind data. In addition, one of the two WSs was partially damaged on sol 313 by a DD that will be described in Section 7. Wind data obtained afterward requires modified wind retrievals which were not yet available at the time of writing this paper. Figure  S1  in Supporting Information S1 shows the cadence of MEDA observations.