dataesr/scientific-paragraphs-categorization huggingface dataset:
Long-Period Waves (Period >1 sol) We next examine the excursions of mean daily temperature on timescales between diurnal and seasonal. Oscillations in atmospheric variables on timescales larger than a sol are generally related to planetary scale waves or the passage of weather fronts. Battalio et al. (2022)  examined planetary waves from multiple meteorological variables measured by Perseverance and MSL, including temperatures, and compared their results with the Ensemble Mars Atmospheric Reanalysis System (EMARS) data set. According to this work, traveling waves of baroclinic nature with periods of ∼3 sols are found in the temperature data from Perseverance, MSL, and EMARS, being further supported by their analysis in pressure, whereas waves with periods above 8 sols are attributed to barotropic instabilities and possible weather fronts.
We study oscillations in mean daily temperatures from MEDA ATS data at 1. 45 m and MCD predictions. For this analysis, the MCD data set differs from the one in Figure  7. The MCD data shown here reconstructs the effects of large-scale perturbations on a typical Martian year adding synthetic perturbations to the averages of Mars GCM simulations that define the MCD. These perturbations are added using Empirical Orthogonal Functions (EOFs) that are calculated from the original Mars GCM simulations and that are representative of the typical variations in the Mars GCM. EOFs are a statistical technique that examines the covariance of atmospheric variables in the Mars GCM as a function of both height and longitude generating a set of functions and coefficients that are later used to reconstruct the typical effects of large-scale perturbations in the model  (Lewis et al.
The changes in the vertical distribution of the dust between sols 315 and 316 might have been driven by the strong reduction in the vertical thermal gradient on sols 314-315 (Figures  12c  and 12d ) producing a negative feedback on the maintenance of vertical motions and storm activity. The thermal effects observed during this dust storm can be compared with in situ data during previous dust storms. Two Global Dust Storms (GDS) were observed by the Viking Landers on MY12. These storms reached atmospheric dust opacities of τ = 3 and τ = 6, respectively  (Pollack et al. , 1979) , and maximum air temperatures were observed to decrease by ∼19 K  (Ryan & Henry, 1979). The REMS instrument on the Curiosity rover obtained meteorological data of the 2018/MY34 GDS, which reached values of τ ∼ 8. 5 and resulted in decreases of surface and air temperatures of 35 and 30 K, respectively  (Guzewich et al.
Comparison With Previous Missions Several surface missions (VL1, VL2, MPF, PHX, M2020, and InSight) have recorded near surface atmospheric temperatures on Mars  (Banfield et al. , 2020; Davy et al. , 2010; Gómez-Elvira et al. , 2014; Hess et al. , 1977; Martínez et al. , 2017; Schofield et al. , 1997; Sutton et al. , 1978). Of all these missions, only VL1 and MPF obtained data at latitudes comparable to that of Jezero (at latitudes between 18 and 22°N). Figure  13  shows daily averaged air temperatures from Mars 2020 compared with VL1 and MPF. During the brief period of time it was active, MPF obtained temperature data that resemble those of Mars 2020. Temperature data of Mars 2020 and VL1 show that Mars 2020 temperatures are systematically higher than those of VL1 by ∼6. 5 K. This difference is well above the uncertainty in absolute temperatures of both missions, which is 1.
Acknowledgments We are very grateful to the entire Mars 2020 science operations team. We would like to thank two anonymous reviewers for comments and suggestions that helped us to improve the quality of the manuscript. A. Munguira is supported by the grant  PRE2020-092562  funded by  MCIN/ AEI/10. 13039/501100011033  and by " ESF Investing  in your future. "  R. Hueso  and  A. Sánchez-Lavega  are supported by Grant  PID2019-109467GB-I00  funded by  MCIN/AEI/10. 13039/501100011033/  and by  Grupos Gobierno Vasco   IT1742-22. US coauthors have been funded by  NASA's STMD, HEOMD , and  SMD.
Data Availability Statement The MEDA data used in this study are available via the NASA Planetary Data System (PDS) (de la Torre Juarez & Rodriguez-Manfredi, 2021). Derived MEDA ATS temperatures at 0. 84 and 1. 45 m and the program to derive these data from RAW MEDA ATS data are available in Hueso et al. (2022). Albedo and thermal inertia values from MEDA data are available in  Martínez et al. (2023). Atmospheric opacities at Jezero are calculated from publicly available data from the ZCAM instrument via the PDS  (Bell & Maki, 2021). Reduced meteorological data from Viking Lander 1 (J. Tillman, 1989)  and Mars Pathfinder  (Murphy, 1998)  are publicly available via the PDS. The Mars Climate Database (MCD) is accessible at http://www-mars. lmd. jussieu. fr/mcd_python/.
We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median H E = 0. 70-0. 81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.
Effective estimation of identity by descent with microhaplotype panels A formal evaluation of the accuracy of the three panels to estimate IBD between monoclonal P. vivax infections was first conducted using simulated data generated on pairs of infections across a range of relatedness ‫)ݎ(‬ values using the paneljudge package  22. All data were simulated under the model used to estimate relatedness. In each geographic region, the 95% confidence intervals (CIs) around the estimate ‫̂ݎ‬ were calculated as a measure of the informativeness of a given marker panel (Figure  2 ). In all geographic regions and for all marker panels, the CI intervals were shortest when r=1 (identical infections), closely followed by ‫0=ݎ‬ (strangers), and highest when ‫5. 0=ݎ‬ (siblings) indicating lowest accuracy in predicting sibling relationships.
These results indicate that panels of ~100 uniformly spaced microhaplotypes provide more accurate estimation of IBD than the current single SNP panel used for P. vivax infections; this advantage may be more pronounced in certain geographic regions, possibly reflecting the geographic representation informing SNP selection. In addition to the simulated data, the efficacy of the three panels in estimating IBD between infections was also evaluated using 'real' data from sequenced pairs of primary and recurrent P. vivax infections. These samples came from a range of clinical trials, as well as from returning travellers  [23] [24] [25] [26]. A total of 14 infection pairs satisfied the criteria for selection which required monoclonal infections with high-quality genomic data at both time points. The infection pairs originated from a range of geographic locations in the Asia-Pacific and exhibited a range of durations between the primary and recurrent episode (Table  2 ).
Using thresholds of COI = 1 and F WS ≥ 0. 95 to define a monoclonal infection, there were no significant differences in the proportion of polyclonal infections defined by the microhaplotype and genome-wide data in any geographic region (Table  4 ). Furthermore, as illustrated in Figure  4 , the F WS scores of the infections with COI=1 was significantly larger than those with COI>1 in all regions, demonstrating a strong alignment between the microhaplotype and genomic data (Table  4 ). The capacity of the High-diversity SNP microhaplotype panel to capture spatial transmission patterns including differentiation of geographically distinct populations was also assessed, using Principal Coordinate Analysis (PCoA) and IBD-based networks. The microhaplotype-based PCoA trends were consistent with spatial trends observed with genome-wide datasets 20.
vivax cases by determining an infection's country of origin. Using the data from 21 countries with a minimum sample size of 4 from the available P. vivax global dataset, we determined the accuracy of the 494 SNPs within the microhaplotype panel in predicting country of origin using a recently developed Bi-Allele Likelihood (BALK) classifier  28. The predictive accuracy of the 494 microhaplotype SNPs was compared to the 38-SNP Broad barcode and three recently identified P. vivax geographic barcodes selected specifically for determining country of origin (GEO33, GEO50 and GEO55 comprising 33, 50 and 55 SNPs respectively).
Discussion Our study provides the first description in silico of P. vivax microhaplotype panels which can be used to estimate "identity by descent" relatedness between pairs of acute and recurrent infection isolates, and thus help to discriminate between different causes of vivax malaria recurrence. A systematic genome-wide selection process was used to identify panels of 100 globally diverse microhaplotypes using an expansive P. vivax genome dataset. The utility of these panels was assessed against a pre-existing P. vivax SNP panel using both simulated and whole genome data. These relatively parsimonious panels have significant potential to improve the interpretation of clinical trials and surveillance data. Further details on the integration of microhaplotype data in the proposed use cases, and areas requiring further research and development are described herein.
The impact of miss-specified allele frequencies, miss-classified multiclonal infections, etc. was not evaluated. In addition, it should be acknowledged that genotyping errors and failures (missing data) were not included in our simulations. However, we anticipate that genotyping failures should be infrequent with NGSbased amplicon sequencing methods, where each locus is typically covered by hundreds of reads  19. Data from pairs of P. vivax isolates, collected from recurrent infections in clinical trials, confirmed the ability of the high diversity microhaplotype panel to estimate pairwise IBD. High correlations were observed between microhaplotype and genome wide IBD estimates in a set of 14 paired P. vivax isolates from the same patient before and after treatment. Using our assigned IBD thresholds, only one of 14 pairs of infections had mismatching classifications of 'stranger' versus 'distant relative', which are both likely to reflect either reinfections or relapses.
The accuracy in pairwise IBD estimation using the microhaplotype data also demonstrates a unique potential for tracking infection spread at micro-epidemiological spatial resolution, to inform the dispersal of infections within and between communities. For example, the microhaplotype data from Malaysia effectively captured a previously described clonal expansion, as well as more subtle population structure reflecting different foci of infection. The spatial analyses conducted here used biallelic SNP data at the microhaplotypes; whilst the high density of SNPs (n=494) provided rich genetic information, even greater information content can be achieved using multiallelic microhaplotypes once new software to deal with these complex datasets becomes available. Some global regions are not well represented in the Pv4 genomic dataset that were used for marker selection, such as the Indian subcontinent, Central and South America.
It is therefore unclear how well the microhaplotypes described here will capture IBD in these regions. However, the informatics pipeline that was established for the microhaplotype selection can be applied readily to update the panel as needed once additional whole genome data become available from new geographical regions. The pipeline can also be used to select country-or regionspecific panels where needed. Information on within-host infection complexity is important to capture epidemiologically relevant transmission dynamics. We observed high concordance in the proportion of polyclonal infections captured by microhaplotypebased COI and genome-wide F WS measures when thresholds of COI=1 and F WS ≥0. 95 were applied. Only a few of infections displayed differences in classification of polyclonality between the microhaplotype and genomic datasets.
In interpreting these differences, it should be acknowledged that the 0. 95 F WS threshold is only a guideline, and that population distributions of within-host diversity generally reflect a continuum, not discrete clusters of monoclonal and polyclonal infections. Within-host diversity at SNP barcodes also follows a continuum, but this is less marked owing to the lower genetic resolution. When monoclonal thresholds were only applied to the COI data, the F WS demonstrated significantly larger values in the COI=1 (monoclonal) vs COI>1 (polyclonal) infection group in all geographic regions investigated, highlighting consistency between the two data sets. Further work is needed to determine how to phase microhaplotype profiles in highly complex infections where any number of clones may be present in varying proportions, but tools such as the Dcifer software provide an important step forward  31.
Data preparation The initial dataset comprised 1,816 samples from 17 countries derived from the P. vivax community study (Pv4. 0) in the vivax and Malaria Genomic Epidemiology Networks (vivaxGEN and MalariaGEN)  20  , as well as previously published external studies 32-34. Of the 1,895 samples described in Pv4. 0 data note, the 1,816 samples reflect data for which we had access prior to the open release. All genomic datasets were generated using Illumina short-read sequencing platforms. Sequence alignment, SNP discovery and variant calling, population assignments, and Fws (within-sample F statistic) calculations for within-host allele infection complexity were undertaken using previously described methods within the MalariaGEN framework, producing a dataset referred to as P. vivax Genome Variation Project release 4.
0 (Pv4. 0). The F WS estimates the fixation of alleles within each infection relative to the diversity observed in the total population on a scale from 0 to 1 and were provided as part of the Pv4 dataset 20,35. Using a threshold of F WS ≥0. 95 as a proxy to identify a monoclonal infection, all polyclonal infections were excluded from subsequent analysis. High-quality samples were selected using a threshold of ≥50% core genome, notated by the "analysis-set" flag in the MalariaGEN Pv4 dataset. The patient metadata provided by the contributing VivaxGEN partner studies was used to identify independent isolates for marker selection, and recurrent isolates for downstream evaluation of selected marker sites. The MalariaGEN curated metadata was used to define 7 regional-level geographic assignments with the following categories: Africa (AF), South and Central America (SAM), West Southeast Asia (WSEA), East Southeast Asia (ESEA), Maritime Southeast Asia (MSEA), Oceania (OCE) and West Asia (WAS).
Evaluation of IBD estimation with the microhaplotype panel The 2 selected microhaplotype panels (Random microhaplotype panel and High-diversity microhaplotype panel), as well as the 42-SNP Broad barcode panel, were evaluated with paneljudge package for their ability to estimate relatedness (IBD) using a range of simulations to compute the uncertainty (error rate) in estimations of relatedness (r) ranging from 0 (strangers) to 1 (identical) under varying allele frequency distributions in different geographic regions. Details of the equations, assumptions, and parameter options in the paneljudge package can be found on GitHub (https://github. com/aimeertaylor/paneljudge). Briefly, for each of a range of data-generating r values (r = 0, 0. 25, 0. 5, 0. 75 and 1. 0), data were simulated on a pair of haploid genotypes, generating 100 haploid genotype pairs.
0 software  40. As the version 3 software does not enable adjustments in the genotyping error rate for polyallelic markers (which may reduce artificially the IBD estimates between infections) the microhaplotype data were run as biallelic SNP markers rather than polyallelic markers. Sample pairs were run in geographically defined batches using allele frequency estimates based on the regional estimates from the baseline samples (high-quality, monoclonal, independent infection) using default parameters. Genome-wide and microhaplotype-based recurrence classifications were assigned using the following infection pair IBD thresholds; clone (pairwise IBD ≥0. 95), close relative (0. 25≤ IBD <0. 95), distant relative (0. 05≤ IBD <0. 25), stranger (IBD <0. 05). The concordance between the microhaplotype and genome wide IBD estimates was evaluated by the correlation coefficient between the datasets, and the proportion of recurrence classification mismatches.
The consortium in based on the network of collaborators coming from more than 20 laboratories and research team in France. It involves national infrastructures such as Huma-Num and C. I. N. E. S. (Centre Informatique National de l'Enseignement Supérieur). It is providing recommendation from the creation, up to the publication and archiving of such data. It is developing the national 3D data repository for Human Sciences together with the required metadata scheme and a companion software to simplify the documentation process. It aims at implementing FAIR principles  [Wilkinson et al. 2016 ].
Proposal Since 2017, a fully integrated solution for the long-term archiving and online publication of 3D data in the humanities has been available to researchers in France. The service is divided into a web interface called "The French National 3D Data Repository for Humanities" (CND3D in French -https://3d. humanities. science) for publication purposes and a desktop software called a Long Term Archive Generator for 3D (aLTAG3D -https://altag3d. huma-num. fr) for archive package creation. During 5 years of successful service, the provenance of the 3D data has gradually broadened, initially focusing on archaeological issues, then opening up to cultural heritage elements in general, and more recently to all areas of the humanities: psychology, theatre, literature, etc. To accommodate these new types of data and their description, domain-specific metadata, data production processes and data types have been updated.
The absence of any physical source object creates a major conceptual gap between heritage fields and these new disciplines. Figure  1  describes the macro process that is nowadays used by all the French communities when digitizing, modeling, manipulating virtual heritage objects. In this article, we present a new metadata schema, a more complete and exhaustive documentation of this schema, a mapping of this schema to the Europeana Data Model (EDM), and the integration of these new descriptors into our two existing tools: CND3D, our online platform, and aLTAG3D, our desktop tool.
RELATED WORKS 2. 1 Metadata schema Since the 2000's, numerous vocabularies have been developed, sometimes at a high level, sometimes more specific to the fields of archaeology or cultural heritage. CIDOC-CRM  [Doerr 2005 ] is the reference for the description of data in these fields. Vocabularies dedicated to cultural heritage or other disciplinary fields (psychology, theatre, etc. ) complement our work. These vocabularies provide a precise description of the content in terms of concepts and relationships between these concepts. These descriptors and their associated semantics are not included in our proposal. However, CIDOC-CRM, which is very complete, covers our entire schema on a top level. A mapping to CIDOC-CRM and DublinCore ensures strong interoperability with our records. Specialized schemas for the description of 3D data have also been published.
At the crossroads of the humanities and 3D, CARARE [D'  Andrea and Fernie 2013b] , from the 3D ICONS project [D'  Andrea and Fernie 2013a] , offers a very flexible and lightweight metadata schema, widely recognized at European level. CARARE is a bundle of other standards (EDM, MIDAS, LIDO, DublinCore). This schema is too light for our archiving constraints based on the file content. Nevertheless, inspired by CARARE, the high-level and administrative parts of our schema overlap with its requirements. Thus, and similar to  [Niccolucci et al. 2022] , our schema remains interoperable through a mapping. In addition, the Europeana Data Model (EDM) has inspired the architecture of our schema with core and contextual classes. Mapping to reference schemes for disciplines other than archaeology and heritage will be defined as needs arise and data is ingested, depending on the needs, uses and skills of the members of the emerging discipline of our consortium.
These classes are mapping more easily with the EDM contextual Classes Agent, Place and TimeSpan. The new physicalObject class helps mapping data with the EDM ProvidedCHO classe with separate metadata related to the physical object. To map the EDM WebResource class, we align metadata from our 3dObject class and other information from deposit part of the schema. Concept information is provided by the use of interoperable thesaurus, PACTOLS. At last, most of the information of the Aggregation EDM class are computed from information provided by the deposit management class (dm_Rights,. ) as see in Figure  4. The final mapping document will soon be available online, as soon as Europeana has validated it.
Documentation and tool integration aLTAG3D  [Dutailly et al. 2023 ] reads an XSD file and provides a visual programming interface to create and organize XML elements. An XSD validation of the user input content is processed in real time. This flexibility allows the user interface to be easily updated for the new schema with very few changes on the software side. Many automated process reduces the amount of information that the researcher will have to fill in manually. In the Figure  5  red boxes indicates mandatory data in the updated metadata schema. CND3D publishes part of the package in an online format. The update of the metadata schema will affect the online platform by providing more details when available. The CND3D creates a DOI for the package and a web page with basic public information about it.
It exposes the metadata via an OAI-PMH endpoint. Depending on the depositor's choice, it may display some of the package's 3D files online via its 3DHOP  [M. et al. 2015]  or Potree  [Schütz 2016 ] viewer instance. CND3D stores the packages on secure servers for cold data (Huma-Num Box) and is the sole data provider for the CINES. Based on the XSD file, an exhaustive documentation of the schema has been created (not yet online in production), so to give everyone the possibility to create an SIP by their own, contribute, and create new tools or plugins for aLTAG3D.
APPLICATION The whole process, from 3D creation to long term preservation and publication has been successfully experimented for a few years now, thanks to aLTAG3D software and CND3D platform. A schema in Figure  6  explain the complete workflow. Once integrated in the CND3D platform, documented 3D data can be harvested by other portals like OpenArchaeo http://openarchaeo. huma-num. fr/ explorateur/home in France. Thanks to linked references in the new metadata schema, data can be cross referenced in CND3D and other portals of online publication. An example is exposed in Figure  7.