dataesr/scientific-paragraphs-categorization huggingface dataset:
Data Analysis The normalized NMR dataset was unit variance scaled to highlight changes in low abundance metabolites. Initially, the principal component analysis (PCA) of the 1 H NMR spectral data was carried out to identify any outliers within the dataset. Following PCA, orthogonal partial least squares discriminant analysis (OPLS-DA) was applied to optimize the separation between the different groups. The model robustness was evaluated through the calculation of R 2 Y (fraction of variance), Q 2 (model predictability), and p-values. Close to 1, R 2 Y, and Q 2 values indicate an excellent model, whereas low values are indicative of model over-fitting. The statistical model was tested for robustness with a Y-permutation performed using PLS-DA, which confirmed the observed metabolic variations.
Study Design To answer our research questions, we surveyed the members of twelve health professional organisations around the world to assess their views about climate change as a human health issue. 4] [25]  All procedures described below received the Institutional Review Boards' approval before data collection (IRBNet #1629592). To ensure clarity and that the length was appropriate, the instrument was pilot tested with members (n=176) of an organisation of medical professionals who work on public engagement on climate change and health. The median time to complete the survey was 11 min. A copy of the questionnaire is provided in the appendix (pp 1 -41). Participants had the option to take the survey in English, Spanish, French, or Arabic.
Peripheral services include attributes such as the gift shop, food and beverage (F and B) services, audio, audio-guide, staff, ticketing, and activities. Identification of attributes of the Thyssen-Bornemisza Museum was carried out by downloading 2500 reviews in English and 2500 reviews in Spanish from TripAdvisor using WebHarvy. From this database, keywords were extracted, and the attributes identified among these keywords were manually coded using Nvivo12. The ambiance is a vital fact, and this category of attributes comprises "queue", "crowding" and "photos", among others. The attributes were The first phase includes a previous study's identification of attributes by applying text-mining methods. Previous research has used reviews to identify attributes in the field of tourism  [58]. The study by Zanibellato et al.
[17]  presents an essential key aspect of the classification of attributes that we employed to develop this research: (1) core offering; (2) external services; (3) ambiance. This empirical analysis is following this classification. The core offering evaluates the permanent collection and temporary exhibitions. Peripheral services include attributes such as the gift shop, food and beverage (F and B) services, audio, audio-guide, staff, ticketing, and activities. Identification of attributes of the Thyssen-Bornemisza Museum was carried out by downloading 2500 reviews in English and 2500 reviews in Spanish from TripAdvisor using WebHarvy. From this database, keywords were extracted, and the attributes identified among these keywords were manually coded using Nvivo12. The ambiance is a vital fact, and this category of attributes comprises "queue", "crowding" and "photos", among others.
The second part of the questionnaire concerns attribute evaluation using a Likert scale. These attributes were previously selected by analyzing eWom data (5000 reviews). In this way, it was possible to justify the selection of attributes included in the survey. A Bayesian design of attribute sets and attribute levels (Table  1 ) is performed, employing the combination of choice sets. The full factorial design was combined with utility balance to avoid a dominant alternative. This type of choice experiment design has previously been applied in tourism-focused research  [59, 60]. Therefore, 120 (i. e. , 5 × 4 × 3 × 2 × 1) possible permutations are produced. The options were assigned, and then, a preference level (from 1 to 5) is chosen. Participants' willingness to pay is also assessed based on the different options proposed, evaluated from EUR 0 to 100, considering the price of similar services in worldwide museums that are highly ranked.
Choice Experiments and Willingness to Pay The results derived from the analysis of choice experiments and willingness to (Table  6 ) show that option E, which consists of taking a personalized 1-hour guided of the temporary exhibitions (M = 3. 46), stands out as of greater value for the intervie tourists. This attribute is also the highest result of direct WTP (M = 20. 212). These data connected to the attributes of the temporary exhibition (A13) and activities (A3). Howe the interviewed residents' perception of the value of the different options differs from results obtained from the sample of tourists. The local population values option B ( 3. 25) and E (M = 3. 25) equally. The attributes included in option B are the perma collection (A9), temporary exhibitions (A13), and having a meal included (A5).
1% Tween 20 containing 3% BSA. Primary antibodies were incubated overnight at 4 • C in TBST-0. 02% azide. After incubation with HRP-labelled secondary antibodies for 1 h at RT in TBST-3% BSA, membranes were developed with the ECL system (GE Healthcare) and exposed to autoradiographic film (Kodak, Rochester, NY, USA); for quantification, images were acquired and quantified using ImageJ software. Primary and Secondary antibodies used were: rabbit anti-UCP1 1/1000 (ab10983; Abcam), mouse anti tubulin 1/1000 (T9026-100ul; Sigma-Aldrich), mouse anti pan-ERK 1/1000 (610123; Transduction Laboratories), rabbit Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) 1/1000 (9101; Cell Signaling), rabbit p38 MAPK 1/1000 (9212; Cell-Signaling), rabbit Phospho-p38 MAPK (Thr180/Tyr182) 1/1000 (9211; Cell Signaling), rabbit active β-catenin 1/1000 (4270; Cell-Signaling), mouse total β-catenin 1/1000 (610154; BD Biosciences, San Jose, CA), goat anti-rabbit 1/3000 (ab6721; Abcam) and goat anti-mouse 1/3000 (Cat # 170-6516; Bio-Rad Laboratories, Hercules, CA, USA).
A thermic shock was delivered by heating the stool sample to 80°C during 20 minutes; the sample was then preincubated for 10 days in anaerobic conditions at 37°C in an anaerobic blood culture bottle (bioMérieux, Marcy l'Etoile, France). Then colonies were obtained by subculture on 5% sheep's blood-enriched Columbia agar (bioMérieux) at 37°C and pH 7. 5 in anaerobic atmosphere generated using AnaeroGen (bioMérieux) after 48 hours. The identification of strain Marseille-P5551 T by MALDI-TOF MS using a Microflex spectrometer (Bruker Daltonics, Bremen, Germany) was unsuccessful. The obtained spectra (Fig. 1 ) were imported into MALDI Biotyper 3. 0 software (Bruker Daltonics) and analysed against the main spectra of the bacteria included in the database (Bruker database constantly updated with MEPHI database) (https:// www.
Strain identification The 16S rRNA gene was sequenced in order to identify this strain. Amplification was performed using the primer pair fD1 and rP2 (Eurogentec, Angers, France) and sequencing using the Big Dye Terminator v1. 1 Cycle Sequencing Kit as previously described  [12]. The 16S rRNA nucleotide sequences were assembled and corrected by CodonCode Aligner software (https://www. codoncode. com/). Strain Marseille-P5551 T exhibited a 91. 87% sequence identity with Faecalicatena orotica strain DSM 1287 (GenBank accession no. NR_117129. 1) (Fig. 3 ). We consequently classify this strain as a new genus within the Lachnospiraceae family and the Firmicutes phylum.
Genome sequencing Genomic DNA was extracted using the EZ1 biorobot (Qiagen, Courtaboeuf, France) with the EZ1 DNA tissue kit, then sequenced on the MiSeq technology (Illumina, San Diego, CA, USA) with the Nextera Mate Pair sample prep kit and Nextera XT Paired end (Illumina), as previously described  [13]. The assembly was performed with a pipeline incorporating different software packages (Velvet  [14] , Spades  [15]  and Soap Denovo  [16] ) and trimmed (MiSeq and Trimmomatic  [17]  software) or untrimmed data (only MiSeq software). GapCloser was used to decrease assembly gaps. Scaffolds with <800 bp and those with a depth value of <25% at mean depth were removed. Therefore, the best assembly was chosen by using different criteria (number of scaffolds, N50, number of N). The genome of strain Marseille-P5551 T is 4.
14 Mb long with a 44. 4 mol% G + C content and contains 3940 predicted genes. The degree of genomic similarity of strain Marseille-P5551 T with closely related species was estimated by OrthoANI software  [18]. OrthoANI values among closely related species ranged from 67. 56% between Robinsoniella peoriensis and strain Marseille-P5551 T to 84. 42% between Blautia marasmi and Blautia producta (Fig. 4 ). When strain Marseille-P5551 T was compared to these closely related species, values ranged from 67. 56% with R. peoriensis to 74. 92% with Faecalicatena contorta (Fig. 4 ).
Description of Luxibacter massiliensis sp. nov. Luxibacter massiliensis gen. nov. , sp. nov. (mas. si. li. en'sis, N. L. fem. adj. massiliensis, 'to Massilia', the Latin name of Marseille, where the type strain was first isolated and characterized) is classified as a member of the family Lachnospiraceae in the phylum Firmicutes. Strain Marseille-P5551 T is the type strain of the new species 'Luxibacter massiliensis' gen. nov. , sp. nov. It is an anaerobic Gram-positive bacterium and is motile. Colonies of strain Marseille-P5551 T observed on blood agar medium are cream coloured with a mean diameter of 0. 75 mm and are catalase negative and oxidase positive. The genome size of Luxibacter massiliensis strain Marseille-P5551 T is 4 142 938 bp with 44. 4 mol% G + C content. The GenBank accession number for the 16S rRNA gene sequence of strain Marseille-P5551 T is LS488978 and for the whole genome shotgun project is UWOE00000000.
Acknowledgements Supported in part by the  Institut Hospitalo-Universitaire  ( IHU) Méditerranée Infection, RHU Torino-Lumiere   ANR-16-RHUS-0008 , the  National Research Agency  under the  programme 'Investissements d'avenir'  (reference  ANR-10-IAHU-03 ) and the  Région Provence Alpes Côte d'Azur , as well as European funding via  FEDER PRIMI. The authors thank  Hitachi  for providing the TM4000Plus tabletop microscope. We also thank  Aurelia Caputo  ( Aix-Marseille Université, IRD, AP-HM, MEPHI ) for submitting the genomic sequences to GenBank and the members of the genomics team for sequencing.
Material and methods (a) Sample collection Forty-three individuals across 10 species and seven families were sampled (electronic supplementary material, table  S1 ). Leaf tissue was collected from wild individuals and desiccated using silica gel to preserve DNA. Approximately 20 mg of dried tissue was used for DNA extractions. The majority of samples were collected in Andasibe, Madagascar, and palm species were collected across the island (figure  1 ). Location data are detailed in electronic supplementary material, table  S1. All samples were collected and exported with prior informed consent of Madagascan authorities under all necessary permits, including CITES permits where appropriate. Permit numbers can be found in electronic supplementary material, table  S1.
(d) Inference of N e For each species, the fasta format output from the Stacks pipeline containing all aligned loci was used to estimate effective population size. We first estimated the population scaled mutation rate (ϴ = 4N e µ) using a Bayesian method implemented in the R package thetamateR, which permits rate variation between loci and makes use of all ddRAD loci per species. The estimated ϴ value for each species was converted to N e assuming the average mutation rate in angiosperms (5. 35 × 10 -9 sites year -1  [36] ) and a generation time of either 10 or 50 years. Estimates of N e converted from ϴ are dependent on the mutation rate (µ) used. Ideally, we would use µ estimated specifically for the species of interest or their close relatives but such information is not yet available for the vast majority of species, so a general rate for angiosperms is applied here.
(e) Extended Bayesian skyline plots To infer changes in population size through time, we used the extended Bayesian skyline plot (EBSP)  [37]  approach in BEAST v. 2. 4. 2  [38] , following the methodology outlined by Trucchi et al. [39] , for each species separately. A custom R script  [39]  was used to select only those loci with high numbers of SNPs (three or more per locus) to maximize the amount of information per marker to increase the accuracy and reliability of our inference. Datasets used for EBSP differed from thetamateR, for which all ddRAD loci were used. Due to computational restraints of the EBSP approach, 50 loci were selected randomly to use in the EBSP analysis. One haplotype was chosen at random for each individual at heterozygous loci to minimize bias in haplotype frequencies and reduce bias caused by undiscovered heterozygote samples  [39].
(f ) Simulations of anthropogenic population decline We used fastsimcoal2 (v. 2. 6)  [41]  to simulate sequence data for genetic bottlenecks at 100, 250 and 500 generations ago (equivalent to 1000, 2500, 5000 years). We simulated four strengths of bottleneck: 90%, 50% and 10% reductions and a 10% increase in effective population size with ancestral population size set to 25 000. We generated 40 000 DNA sequences matching the length of the corresponding empirical RAD tags (147 bp, 380 bp) and selected loci with the same distribution of SNPs in the empirical Dypsis procumbens dataset (i. e. each SNP category contained the same number of tags). We then used these loci as input for our pipeline for EBSP, replacing the output of populations. We repeated simulations for each decline severity at least three times to assess consistency in demographic patterns across different simulations.
Results and discussion (a) Effective population size greatly exceeds census size in palms We used four palm species (all of which have decreasing or small populations) as our 'training' dataset-their red list assessments provide prior expectations for the demographic patterns we estimate from genetic data. Two of these have been assessed as near threatened with decreasing population trends-R. robustior  [42]  is estimated to have fewer than 1000 mature individuals in the wild, while D. procumbens is more common but restricted to 32 locations and is exploited for timber  [43]. Dypsis rabepierrei has yet to be redlisted but is expected to be considered critically endangered with no more than 20 individuals known from a single location  [44]. Satranala decussilvae is endangered with fewer than 200 mature trees in the wild  [45].
However, the Stacks pipeline limits over-merging of loci through filtering high coverage loci and the number of paralogous sites  [46]  present will only be inflated if the choice of M (maximum distance between stacks) is too high, here we chose an intermediate value  [47]. Heterozygosity does not appear to have been inflated (electronic supplementary material, table S2 and figure  S1 ), although we have few samples in each dataset to assess this fully. Likewise, when working with rare species it may be difficult to accurately estimate census sizes for this comparison, but given the sizable disparity between N e and N c in all palm species (electronic supplementary material, table  S3 ) it is unlikely that unaccounted individuals, or paralogy, would alter the inferred pattern.
(c) Simulations reveal declines at anthropogenic time scales To validate whether our approach has the power to detect anthropogenic population decline, we simulated sequence datasets at a range of population declines of varying severity that took place 250 generations (2500 years ago). We then inferred N e over time using EBSP, as for empirical data. We found that the number of demographic events ('sum(indicators. alltrees)') was greater than one for all declines simulated at 90% severity. The lower 95% HPD of these simulations did not overlap with 0, indicating that population size was not constant over time (electronic supplementary material, table  S5 ). As the severity of the decline decreased (i. e. when N e was more stable), we were unable to reject constant size more often. Constant sizes were consistently rejected at all severities for 147 bp simulations, even at smaller simulated changes in population size.
(e) Diverse demographic histories across species from seven plant families To investigate the prevalence of population decline in less well-studied Madagascan species, we repeated the above analyses for the remaining six species in our dataset (figure  4 )-only one of which has a known census population size. Among this group, just four species have been red list assessed and three are categorized as of least concern: Psiadia altissima and D. cordifolia have stable populations (P. altissima is a slash-and-burn successor), while Dilobeia thouarsii is decreasing due to agriculture, harvesting for timber and traditional medicine  [52, 53]. Chrysophyllum boivinianum is also exploited for timber and malarial medicine and is suspected to be declining rapidly  [54]. Little is known about the extent of exploitation and biology of the undescribed species of Psychotria.
(g) Genomic data can help target conservation effort Our ddRADseq approach is a relatively cheap and accessible way to rapidly assess past demographic changes with a handful of specimens. It holds great potential to screen species at a much higher rate than is possible with observation-based red listing assessments. At present, there are too many potentially at-risk species and limited resources in terms of time, money and scientific expertise for the species of interest for a detailed conservation assessment at the level of quality required for the IUCN redlist. One way our approach might be useful is to identify species that are in urgent need of more thorough assessment so that other types of conservation efforts are better placed. Likewise, a species that has recently become rare might benefit from a breeding and reintroduction programme to increase its numbers, while a micro-endemic species that has always been rare would not benefit from this.
Our results suggest that rapid decline has affected 70% of the species we assessed and it seems likely that many of the micro-endemic species in Madagascar have not always been so rare. Instead, we propose that the radical environmental changes that have taken place in Madagascar since the arrival of humans have driven rapid population decline in Madagascan plants. Our approach can predict extinction risk from demographic patterns inferred from genomic data and has the potential to act as an important tool for rapidly assessing the threat status of poorly known species in need of further study and conservation efforts, particularly for tropical flora and fauna. Ethics. All samples were collected and exported with prior informed consent of Madagascan authorities under all necessary permits, including CITES permits where appropriate.
Statistics The sample size was chosen based on feasibility, i. e. the number of new eligible patients in the study center over the duration of the study. Patient's EQ-5d scores were calculated by using the EQ-5d crosswalk index value tool with French weighting (version 2. 0). For QLQ-C30, we used the PROscorer R package for calculation. Descriptive analysis was reported with means and standard deviations, medians and ranges. Student t test and chi-squared test were used to test for differences between OH and combined OH/HaH care, at the 0. 05 type I risk level. Statistical analysis was performed with SAS 9. 4 software. Sensitivity analysis was represented as con dence ellipses on the cost-effectiveness plane. These ellipses represent the different credible region for the cost-effectiveness coordinates (at 95%, 75%, and 50%).
Secondary antibodies: anti-rat, anti-mouse and anti-rabbit conjugated to 488, 568, 647 Alexa-Fluor (1:500 to 1:1000, Life Technologies). Images were acquired on a Leica SP5 confocal microscope using 40X (1. 25 N. A. ) and 63X (1. 40 N. A. ) objectives, controlled with Leica LAS software and analyzed on Fiji or Imaris.
The microscope was controlled by the Inscoper Imaging Suite and the dedicated software (Inscoper). Alternatively, a CSU-X1 spinning-disk unit mounted on an inverted microscope (Elipse Ti; Nikon) equipped with a 60X (1. 4 N. A. ) oil objective, a sCMOS ORCA Flash 4. 0 (Hamamatsu) and controlled by MetaMorph; was also used for some experiments. Images were processed with Fiji or Imaris softwares.
A metagenomics survey based on a comprehensive sampling of termites is required to answer these questions. In this study, we sequenced whole gut metagenomes of 145 termite samples representative of the phylogenetic and ecological diversity of termites, including many lineages that have remained undocumented. We also sequenced the gut metagenome of one sample of Cryptocercus, the sister group of termites  [81]. We used the assembled prokaryotic contigs of this dataset to determine  (1)  when important gut prokaryotic pathways involved in nutritional functions were acquired by termites;  (2)  to which extent termite phylogeny is predictive of gut prokaryote taxonomic and functional composition; and (3) the taxonomic and functional changes experienced by gut prokaryote communities following the acquisition of a diet of soil.
These discrepancies are likely the result of variation in 16S rRNA gene copy numbers  [41, 143] , which are higher in these lineages or are possibly artifacts generated during 16S rRNA gene amplicon PCR cycles. They might also reflect the incomplete coverage of our metagenomes or, to a certain extent, the differences in the databases used for classification. In total, we identified 114 bacterial families and familylevel lineages represented in the marker genes of more than 5% of our 129 termite gut metagenome assemblies (Table  S3 ). These 114 bacterial family-level lineages belonged to 19 phyla. An additional 193 other bacterial family-level lineages were recorded from the gut of no more than a few termite species and were possibly transient and not strictly associated with termite guts. We calculated the Moran I index on the abundance of these 114 family-level bacterial lineages to test whether bacterial abundance is correlated with termite phylogeny.
The carbohydrate-active enzymes of termite gut prokaryotes We investigated the evolution of prokaryotic carbohydrate-active enzymes (hereafter: CAZymes) using the same 129 gut metagenome assemblies used to investigate gut prokaryotic composition. The de novo assemblies of these 129 gut metagenomes contained an average of 127,159 prokaryotic open reading frames (ORF). We identified ORFs coding for CAZymes using Hidden Markov model searches against the dbCAN2 database [157]. As a first step, we investigated the evolution of enzymes derived from prokaryotes with no consideration of their taxonomic origin. In total, we found 346 CAZyme categories in 129 gut metagenomes that consisted of 205 glycoside hydrolases (GHs), 57 glycoside transferases (GTs), 18 enzymes with carbohydrate-binding modules (CBMs), 16 carbohydrate esterases (CEs), 41 polysaccharide lyases (PLs), and nine redox enzymes with auxiliary activities (AAs) (Table  S5 ).