dataesr/scientific-paragraphs-categorization huggingface dataset:
The malaria prevalence in the pre/post surveys was assessed by multiplex real-time PCR derived from Shokoples et al. [15]  , to take into account the submicroscopic carriers, which were predominant in the pre-intervention surveys  [2]. The detection threshold was of one parasite/μl of blood for the five species of malaria, after DNA extraction of 200μl of whole blood with QIAamp® DNA kit (Qiagen). • The impact on malaria incidence in the region was assessed by using data from the surveillance systems of Brazil and Suriname. • Safety follow-up was implemented to monitor potential adverse events (data collection process presented in Suppl. Mat. 2). An independent Data Safety Monitoring Board (DSMB) was created to advise the sponsor on safety of the intervention during the project. The four international malaria experts gathered once a year to assess the data and the reports produced by the project coordination team.
Data collection Questionnaires were administered by the facilitators for socio-economic data and behavior during the last malaria episode. They were collected on paper or with the help of tablets that transferred the anonymized data to a secure online database, Clinsight. A venous blood sample was taken for each participant to perform a PCR-Plasmodium at the Pasteur Institute of FG. A RDT was performed on site and participants who tested positive were referred to the nearest health facility for confirmation by microscopy, notification and treatment. During each visit, facilitators administered a questionnaire and filled out the electronic form with the open-source ODK Collect application on Android tablets. Each completed questionnaire generated a record that was immediately encrypted and sent to a server managed by Ona when an Internet connection was available.
Analyses We presented categorial variables as frequencies and proportions, and continuous variables as median and interquartile range. Comparisons used chi2 or student tests, respectively. Longitudinal data collected at follow-up visits during the intervention was used to assess appropriate kit use. Some participants reported several kit use events (i. e. performing an RDT and/or using AL from a kit), the indicator of correct kit use was thus calculated by participant and by kit use event. For each participant, the first kit use event of the most recent visit was selected to ensure that the participant had a complete kit before use. Three levels of analysis were conducted, in order of thoroughness: raw analysis, intermediate analysis, 'per protocol' analysis (Suppl. Mat. 3). For cross-sectional data, the comparison of the main indicator before and after the intervention was based on the odds-ratio calculated by univariate unconditional logistic regression.
Safety data No serious adverse events were reported by participants, facilitators or health centers (Suppl. Mat. 4). Treatment interruption for adverse effects was rare (1. 0%). The circulation of kits outside the Malakit study was limited. Very few people (7/631) attended follow-up visits to get a new kit over five times. Among Malakit participants, 1. 1% had already acquired a kit before inclusion. The reported cost on the blackmarket was stable throughout the project (on average 2. 6 g of gold (about 80 USD) for a complete malakit).
𝐵 of the marginal posterior distribution for each pixel of s  given the data {d  ,d  }: G({𝒅 𝐸 , 𝒅 𝐵 }) = ∫ 𝒔 2 𝐵 -𝝁 2 𝐵 𝑝(𝒔 𝐵 | 𝒅 𝐸 , 𝒅 𝐵 , M) d𝒔 𝐵. (7) In this work we show the result for s  here as it is the most significantly contaminated by polarized dust foregrounds. Both stages of the Moment Network use a UNet convolutional neural network from the DeepMass 1  package (Jeffrey et al. 2020) -see section 3.
WAXS experiments Wide Angle X-rays Scattering (WAXS) experiments were performed on the Xenocs Nano-inXider SW system in transmission mode using Cu Kα radiation ( = 1. 54 Å) from an X-ray microsource (GeniX3D) operating at 50 kV-0. 6 mA (30 W). Patterns were collected on a detector Pilatus3 (Dectris) allowing a 2 range between 5° and 62°, the collimation was chosen at 800 m to maximize intensity. The reduction of 2D datasets from the Pilatus3 detectors to 1D was achieved by radially averaging the raw data detector counts using Foxtrot data reduction software  [54]. WAXS intensities were corrected for the flat field and for the Ewald sphere solid angle. WAXS spectra, I(2), were fitted using the Fityk0. 9. 8 software  [55]  in the full 2θ range. With this software, each WAXS spectrum is decomposed into crystalline and amorphous contributions.
Dielectric spectroscopy Dielectric measurements were achieved on an Alpha-Analyser (Novocontrol) spectrometer. Annealed samples were placed between two circular titanium electrodes (1 cm diameter). A sinusoidal tension (1 V amplitude at 10 2 , 10 3 , 10 4 , 10 5 and 10 6 Hz) was applied to determine the complex relative permittivity ε (ε', ε'' and tan δ = ε''/ ε'). At the same time, temperature ramps at 1 °C/min were applied using a Quatro Cryosystem (Novocontrol). A first heating until the annealing temperature was performed to ensure a good thermal contact between the electrodes and the terpolymer films. Data were recorded during the cooling back to  50 °C and upon the second heating. 1a ) as well as annealed films (Figure  1b ) was measured as a function of applied electric field, E, to investigate the effects of annealing (conditions listed in Table  1 ) on the electro-active properties of terpolymers.
Crystalline structure WAXS spectra were recorded on each terpolymer film, after solvent evaporation (as-cast sample) and after annealing 1h00 at a temperature 15-20 °C below the melting point. We analyzed all WAXS spectra using Fityk software  [55]  in order to separate the crystalline and amorphous contributions. Decomposition in crystalline and amorphous components is shown in Figure  2  for the two specific composition 2. 2 mol% and 7 mol% of CTFE, after solvent casting (Figure  2-a  and b ) and after annealing (Figure  2-d  and e ). WAXS spectrum presents an asymmetrical crystalline peak around 2 = 19° (Fig. 2 a, b  and d ) which can be decomposed in two peaks: one contribution (red or orange peak) at small 2DFE/RFE, with the higher inter-reticular distance (dDFE or dRFE) and the second one (blue peak), for higher 2FE, which corresponds to a smaller distance, dFE.
Acknowledgments The authors are grateful to  French National Agency of Research and Technology (ANRT)  and  Arkema  for supporting this work during the PhD thesis of  F. Bargain  at the  MMC laboratory  (CIFRE convention no. 2014/0573 ) and for the financial support from the  Industrial Chair HOMERIC (Arkema/ANR)  within the grant agreement n°AC-2013-365. Part of this work was performed within the framework of the  Equipex ELORPrintTec   ANR-10-EQPX-28-01  with the help of the  French state's Initiative d'Excellence IdEx   ANR-10-IDEX-003-02. Michel Cloitre  and  Ilias Iliopoulos  are warmly thanked for enlightening and stimulating discussions. Authors are grateful to the  LEM laboratory (Arkema, Serquigny, France)  for facilitating SAXS-WAXS experiments and dielectric spectroscopy measurements, especially  Sylvie Lebreton ,  David Deperrois  and  Stéphane Bizet  for technical helps and discussions.
Acknowledgements The authors are grateful to CNRS and to the  Agence Nationale de la Recherche (ANR) :  CARBENOPOL  Project ( ANR-19-CE06-0015 ) for financial support. This research was also supported by  LabEx AMADEus  ( ANR-10-LABEX-0042-AMADEUS ). We thank  Ms. A. -L. Wirotius  ( LCPO ) for NMR analysis and  Dr. B. Kauffmann  ( IECB ) for X-Ray diffraction analysis. G. Pino  and  G. Pécastaing  are warmly acknowledged for their help in evidencing the formation of stable films using AFM and optical microscopies. UPPA,  MCIA  ( Mesocentre de Calcul Intensif Aquitain ), and  CINES  under allocation A009080045 made by " Grand Equipement National de Calcul Intensif" (GENCI)  are acknowledged for computational facilities. CDAPP is also thanks for funding part of the post-doctoral contract of  E.
Data availability The X-ray crystallographic coordinates for structures reported in this study have been deposited at the Cambridge Crystallographic Data Centre (CCDC), under deposition numbers 1973046 for 7a 1973048 for 3a, 1973057 for 3b, 1973059 for 3c, 1973049 for 4a, 1973058 for E-3b(HOTf) 2 and 1973060 for E-3a(HOTf) 2. These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via www. ccdc. cam. ac. uk/data_request/cif. The authors declare that all other data supporting the findings of this study, including computational details, are available within the article and.
, 2014). This characterization includes their gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) identifier (ID) and closest Arabidopsis thaliana homologue. Only primary hits assigned to the reverse strand were included in the raw gene counts (-s 2 -p ÀÀprimary options). The gene count data was used to identify significantly differentially expressed genes (DEGs) using DESEQ2 v. 1. 30. 0 in RSTUDIO v. 4. 0. 3 (Love et al. , 2014). Relative log 2 -fold change was calculated through pairwise comparison of each timepoint to axenic plant-only controls using DESEQ2. These values were then sorted by significance whereby a DEG was deemed to have a log 2 -fold change of greater than 1 and a P-value (adjusted for false-discovery; P adj ) of ≤ 0. 05. Normalized, rlog transformed count data was used to perform principal component analysis (PCA) using the MIXOMICS package v.
Eucalyptus grandis root metabolism changes over the course of P. microcarpus colonization The metabolic pathways regulated in E. grandis over the course of colonization were identified using annotated GO terms within our datasets (Table  1 ). During the integration stages, genes associated with the flavonoid and phenylpropanoid biosynthesis pathways were significantly repressed while the latter became positively regulated during functional symbiosis at 2 wk post-contact. Beyond KEGG pathway enrichment, we also considered the enriched biological processes at each of the timepoints and found that genes involved in defence or response to abiotic stress were typically upregulated during the integration stages of colonization (i. e. 24 h and 48 h post-contact timepoints through 1 wk post-contact) after which they were repressed at 2 wk (Table  1 ).
Discussion The accommodation of a fungal symbiont within root tissues requires the coordination of a large number of plant metabolic and developmental pathways  (Martin et al. , 2016). Along with morphological changes, differential host gene expression has been previously linked to the stage of colonization in other model EcM interactions  (Duplessis et al. , 2005; Le Qu er e et al. , 2005; Sebastiana et al. , 2014; Bouffaud et al. , 2020). In this article, we have identified how gene expression changes over time within E. grandis roots undergoing P. microcarpus colonization. Within our current dataset, the pre-symbiotic and functional stages exhibited the least amount of DEGs as compared to axenic roots, while New Phytologist (2022) 233: 966-982 www. newphytologist. com each of the timepoints during fungal integration showed a high number of unique DEGs.
, 2015b; Liao et al. , 2016). Most prominent within our defence-related gene dataset were 163 significantly regulated LRR/PR proteins, a class highlighted by  Liao et al. (2016)  to also be differentially regulated in various Pinus species in response to colonization by members of the Suillus genus. Sebastiana et al. (2014)  report that these defence-related DEGs might be involved with fungal species recognition. There were, also, a number of dirigent-like defence genes that were downregulated throughout the fungal integration stage; these genes are associated with cell-wall reinforcement and their repression may be required to enable growth of P. microcarpus into the root apoplastic space  (Sebastiana et al. , 2014; Li et al. , 2017). In terms of the biosynthesis of metabolic products, using GO, we found that genes involved in the synthesis of phenylpropanoids, terpenoids, and flavonoids were also enriched within our transcriptional profiling of E.
Acknowledgements The authors thank  M Mikhael  and  D Wojtalewicz  at the  Western Sydney University Mass Spectrometry  facilities for assistance with the carotenoid and hormone analyses, and the  Western Sydney University Confocal Bio-Imaging Facility  for access to its instrumentation. This research was funded by the  Australian Research Council  for a  Discovery grant  to ICA, JMP and FM ( DP160102684 ) and the  US Department of Energy Joint Genome Institute  ( CSP1953 ). This research was also supported by the  Laboratory of Excellence ARBRE  ( ANR-11-LABX-0002-01 ) and the  Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Programme , the  Office of Biological and Environmental Research in the US Department of Energy (DOE) Office of Science. The work conducted by the  US Department of Energy Joint Genome Institute , a  DOE Office of Science User Facility , is supported by the  Office of Science of the US DOE  under contract no.
Expression of hormone receptor (HR) for estrogens (ER) and progesterone (PR) and HER2 remains the cornerstone to define the therapeutic strategy for breast cancer patients. We aimed to compare phenotypic profiles between matched primary and metastatic breast cancer (MBC) in the ESME database, a National real-life multicenter cohort of MBC patients. Patients with results available on both primary tumour and metastatic disease within 6 months of MBC diagnosis and before any tumour progression were eligible for the main analysis. Among the 16,703 patients included in the database, 1677 (10. 0%) had available biopsy results at MBC diagnosis and on matched primary tumour. The change rate of either HR or HER2 was 27. 0%. Global HR status changed (from positive = either ER or PR positive, to negative = both negative; and reverse) in 14.
ESME (Epidemio-Strategy-Medical-Economical)-MBC is the largest available multicentre, nationwide, real-life, retrospective but prospectively maintained database of metastatic breast cancer patients, with a long follow-up  18, 19. The present study aimed at (i) comparing tumour immunophenotypic profiles between matched breast cancer primaries and metastatic sites in ESME-MBC, and (ii) assessing the impact of potential discordances on patient outcome.
DISCUSSION The ESME-CSM platform is one of the largest real-life database for MBC, providing description of therapeutics and various ways of MBC management in France. ESME allowed the present very large evaluation of HR and HER2 discordance between primary tumour and metastatic disease. This study first establishes that, at MBC diagnosis, HR status changed (from positive = either ER or PR positive, to negative = both negative; and reverse) in 14. 2% of the cases (expression loss in 72. 5% and gain in 27. 5%) and HER2 status in 7. 8% (amplification loss in 45. 2%). Factors associated with HR discordance are metastasis to bone, both HR+/HER2-and HER2 + MBC subtypes as well as endocrine therapy in adjuvant setting. For HER2, factors associated with discordance are both HR+/HER2-and HER2 + MBC subtypes as well as endocrine therapy in adjuvant setting.
Nevertheless, generalization of guidelines and development of quality controls have greatly improved the reproducibility of IHC assays and their level of performance. Therefore, these technical limitations are not sufficient to explain the discordance rates observed in HR and HER2 status. The second and better explanation relies on intratumor and intertumor heterogeneity and the ability of tumours to generate tumour clones and subclones with different molecular properties, either spontaneously or following the selection pressure imposed by the treatments  13. The ESME-CSM platform provides a large database representing real-life practice at the scale of a country, allowing to answer or generate some research questions. Such large cohorts are useful to provide data on uncommon subtypes or phenotypes.
For example, the prevalence of ER-/PR+ cases in this database is low (n = 213, 1. 7% in the whole ESME cohort), as reported in the literature with a prevalence ranging from 0. 3 to 3. 4%  [27] [28] [29]. The ER-/PR+ phenotype is still a controversial molecular subtype, as some data suggest that this phenotype might be mainly due to technical artifacts  20, 30  , while other studies confirmed it as a true but rare biologic subtype  [27] [28] [29]. Moreover, the largest studies to date on this rare phenotype reported a trend for a poorer prognosis (early recurrence, poorer overall and disease free survival) as compared with ER+/PR+ tumors, and more similar to ER-/PR-tumors  28, 29. Albeit we cannot rule out that some of these cases in the ESME cohort might be due to a technical artifact, further exploration of these 213 cases might be of interest.
METHODS ESME database The ESME-MBC (NCT03275311) cohort is an ongoing national cohort collecting real-life information from all consecutive MBC patients aged ≥18 year-old who initiated their MBC treatment in one of the 18 French Comprehensive Cancer Centers  19. Data collected include patient and tumour characteristics at primary and metastatic settings, outcomes and treatment patterns. All data are updated annually. For the present study, we used data collected for MBC patients who entered the cohort from 2008/01/01 to 2014/12/31.
Definitions All immunohistochemistry (IHC) assessments were performed locally as per routine practice in each institution and were reported in the central database. All 18 Comprehensive Cancer Centres used the same guidelines (i. e. updated ASCO-CAP recommendations and their adaptation issued by the French GEFPICS Group) for tumour testing regarding ER, PR and HER2  22, 34  , and were participating to mandatory external proficiency tests Fig. 5  Overall survival according to HR modification status. performed each year in the frame of quality assurance programs (AFAQAP, UKNEQAS). Tumours were reported as ER-positive and PR positive, respectively, if ER and PR expression was observed in ≥10% of tumour cells by IHC, following French guidelines  35. A global HR-positive (HR+) status was considered if ER and/or PR were expressed.
A global HRnegative (HR-) status was defined by absence of both ER and PR detectable expressions. HER2-positive (HER2+) breast cancer was defined by a 3+ HER2 IHC score, or a 2+ IHC score associated with HER2 gene amplification by in situ hybridization. Multifocal heterogeneous tumors showing a different status for a given biomarker (either HR or HER2) between the different primary tumors were excluded from the analysis only for this biomarker. The primary tumour status was defined on the first surgical histology sample available. In the absence of surgery of the primary tumour, pathological data from the initial core needle biopsy were selected. The first metastatic HR/HER2 status was obtained on the first available sample within the first 6 months of metastatic diagnosis and prior to any tumour progression.
ACKNOWLEDGEMENTS We thank the 18  French Comprehensive Cancer Centers  for providing the data and each ESME local coordinator for managing the project at the local level. Moreover, we thank the  ESME Scientific Group and Strategic Committee  for their ongoing support. The  ESME-MBC  database receives financial support from an  industrial consortium (Roche ,  Pfizer ,  AstraZeneca ,  MSD ,  Eisai  and  Daiichi Sankyo ). Data collection, analysis and publication are managed entirely by  UNICANCER  independently of the industrial consortium.
DATA AVAILABILITY The data generated and analysed during this study are described in the following data record: https://doi. org/10. 6084/m9. figshare. 14248691  36. All data are contained in the ESME database, which is managed by Unicancer (http://www. unicancer. fr/). However, the ESME database is not publicly available for the following reason: in the ESME Research program, public data sharing is not automatic in order to ensure that only trained users can analyse the ESME datasets. The analysis datasets will be made available only under data transfer and use agreements executed between Unicancer, ICR (https://www. icr. ac. ukx/) and the potential licensee. Interested parties should contact the corresponding author.
Unfortunately, research on how ethnic perception establishes and evolves at both individual and community or social levels in modern societies is seriously limited by the scarcity of integrative databases comprising genetic, phenotypic, socio-cultural and socio-economic data. Departing from the comprehensive approach of the Consortium for the Analysis of the Diversity and Evolution of Latin Americans-CANDELA database  1, 2, [29] [30] [31] [32] [33]  , here we analyze the relationship between genomic ancestry and ESP, as well as its among-country variation and its putative biases caused by both, biological and non-biological factors. Specifically, we use multivariate and multifactorial analyses to explore the combined effect and the relative weight of variables differing in scale and nature, such as socio-economic status and skin pigmentation, among others.
The contribution of different kinds of variables to ESP. Multiple Factorial Analyses (MFA) approaches are useful to attempt a comprehensive picture of the relative importance of phenotypic and sociocultural factors underlying the individual building of self-perceived identity. MFA provides the advantage that the complex interactions among self-perception, physical factors such as external appearance and socio-cultural traits such as access to formal education and/or welfare can be studied on a single analytical framework, making the unravelling of specific interactions more accessible. To develop such analyses, large and comprehensive databases are needed, with different types of variables measured on each individual. Here we used the CANDELA database to explore further questions regarding the determinants of ESP, such as what is the relative weight of very different variables.
Multiple factor analysis (MFA). The data compiled in the CANDELA database differs, by its own nature, in types and scales, which turns difficult comprehensive analyses of complex phenomena. To overcome this problem we used Multiple Factor Analysis (MFA), a method that analyzes a given set of observations described by several "blocks" or sets of variables that can differ in their nature (e. g. nominal or quantitative)  49, 50. Of course, variables within a given block must belong to the same type (quantitative or categorical) but blocks of variables can vary in nature from one to another. Our interest in this method is due to its being able to analyze a mix data table as a whole, but also its ability to simultaneously compare information provided by various information sources. In fact, MFA can be seen as a type of Principal Component Analysis on a weighted matrix that balances information provided by different groups of variables.
The resulting four categories were used as dependent variables on a MFA design  49, 51. The variables in our dataset are either quantitative (e. g. melanin values, wealth index, etc. ) or qualitative/categorical (e. g. levels of balding, categories of hair shape, level of formal education, etc. ), and all these variables describe either physical or socio-cultural phenotypic traits. To run the MFA, we arranged these variables into four blocks of our interest: phenotypic traits measured in a quantitative scale, which were averaged for each self-perception categories (e. g. stature, etc. ); phenotypic traits measured in a qualitative scale (e. g. eye color, hair shape, etc. ), which were entered to the analysis as frequencies for each self-perception categories; the wealth index described before was arbitrarily partitioned into three levels (low, medium, high) and were entered to the analysis as frequencies of individuals at these levels for each self-perception categories; finally, the information of level of formal education achieved by the individual was also codified as low, medium or high and entered to the analysis as frequencies (see Supp.