dataesr/scientific-paragraphs-categorization huggingface dataset:
Using a large dataset encompassing 142 species across 31 families collected in French Polynesia, we test how phylogeny, body morphology, and diet relate to three intestinal morphological traits: intestinal length, diameter, and surface area. 4. We demonstrate that phylogeny, body morphology, and trophic level explain most of the interspecific variability in fish intestinal morphology. Despite the high degree of phylogenetic conservatism, taxonomically unrelated herbivorous fishes exhibit similar intestinal morphology due to adaptive convergent evolution. Furthermore, we show that stomachless, durophagous species have the widest intestines to compensate for the lack of a stomach and allow passage of relatively large undigested food particles. 5. Rather than traditionally applied metrics of intestinal length, intestinal surface area may be the most appropriate trait to characterize intestinal morphology in functional studies.
| Data collection A total of 1,208 individuals from 142 species were collected from reefs around Mo'orea, French Polynesia, in the lagoon, pass, and K E Y W O R D S Bayesian phylogenetic comparative method, convergent evolution, digestive traits, evolutionary conservatism, fish diet, gut length outer reef slope (Appendix S2: Table  1 ), between 2018 and 2019. We primarily targeted adult fishes, but a wider size range was collected for a subset of species. The selection of species cover all the major trophic guilds of coral reef fishes (i. e. , corallivores, herbivores, invertivores, piscivores, and planktivores). All individuals were collected by spearfishing between 10:00 and 15:00 hours and transferred to the laboratory on ice. In the laboratory, each individual was measured and weighed, and the intestine was unraveled and photographed on a tray, using a ruler for a size reference.
A minimum of three individuals per species was examined. The collection of fishes for this project was approved by the Ministry of the Environment of French Polynesia (permit #681/MCE/ENV). We measured the length and the external diameter of the intestine using the software Fiji/ImageJ  (Schindelin et al. , 2012). The length was measured from the pyloric outlet to the anus in the presence of a stomach and from the esophagus to the anus in stomachless fishes  (Elliott & Bellwood, 2003; Karachle & Stergiou, 2010; Kramer & Bryant, 1995a , 1995b). The average diameter was calculated with measurements taken at ten equal intervals along the entire length of the intestine  (Elliott & Bellwood, 2003). The external intestinal surface area (IS) was used as a proxy for mucosal surface area  (Cleveland & Montgomery, 2003; Lassuy, 1984; Montgomery, 1977) , and it was estimated using the following formula: where r is the mean outer radius of the intestine, and IL is the intestinal length.
In contrast, sac-like stomachs (e. g. , Tetraodontidae) were considered nonfunctional stomachs. Furthermore, species were classified as either durophagous or not durophagous depending on whether their diet consisted of hardshelled prey items (e. g. , corals, crabs, molluscs, and sea urchins). We compiled this dataset according to the literature  (Fagundes et al. , 2016; Koide & Sakai, 2021; Ray & Ringø, 2014; Sorenson et al. , 2013; Wilson & Castro, 2010) , authors' knowledge, and direct observation of the dissected fishes. We used trophic level as a continuous measure of diet. Data were retrieved from FishBase using the R package rfishbase version 3. 0. 4 (Boettiger et al. , 2012). In FishBase, a species' trophic level is calculated by adding one to the mean trophic level of all food items consumed, weighted by their contribution  (Froese & Pauly, 2000).
These results are consistent with previous observations  (Kline & Pauly, 1998)  and suggest that food item-based trophic level is a reasonable indicator of diet, thus supporting its use in our analysis. FishBase was also used to retrieve species-level data on body elongation (i. e. , standard length divided by maximum body depth). Similar to trophic level, when elongation was unavailable, the mean value of the genus (n = 1) was used. We used body elongation to account for body shape as it is the major axis of body shape variation among reef fishes  (Claverie & Wainwright, 2014). Moreover, body elongation is strongly related to abdominal cavity depth and the space available to accommodate the intestine and other organs  (Burns, 2021).
All intestinal traits, fish SL, and elongation were natural-log-transformed prior to the analyses. All continuous predictors were centered and scaled to provide a meaningful interpretation of the intercept (i. e. , it represents the intestinal trait at the mean body size, trophic level, and elongation for stomachless, non-durophagous species) and allow comparison between the slopes. For each intestinal trait, we mapped the predicted mean values onto a phylogenetic tree, including the 139 species with verified phylogenetic positions, using the R package ggtree version 2. 2. 4  (Yu et al. , 2017). We further visualized the predicted intestinal traits in two-dimensional morphospace to characterize the length and diameter of fish intestines and observe the partitioning of intestinal morphology among reef fish families and trophic guilds, which were determined using an unbiased, reproducible trophic categorization scheme  (Parravicini et al.
| D ISCUSS I ON We investigated the relationship between reef fish intestinal morphology and phylogeny, body morphology, and diet using a large dataset of 142 species and 1,208 individuals. Our results indicate F I G U R E 3 Relationship between three intestinal traits and body elongation (a, c, e) and trophic level (b, d, f) for 142 species of coral reef fishes. Thick, darkened lines represent the mean predicted fits of Bayesian phylogenetic hierarchical linear models after controlling for the remaining fixed and random effects. Categorical variables were set to their most common value (stomach = present, durophagy = non-durophagous). Thin lines represent 1,000 draws randomly chosen from the posterior fits and show model fit uncertainty. Model predictions are for natural-log intestinal traits, but are transformed here to show the fitted function on the original scale of the data.
For instance, the two most distinctively elongated species in our dataset, Aulostomus chinensis and Fistularia commersonii, both of which are strict piscivores, had the lowest values across all intestinal traits. Regardless of taxonomic identity, body size, and elongation, trophic level strongly influences intestinal morphology. The negative relationship between intestinal length and trophic level is consistent with previous work on marine and freshwater fishes  (Elliott & Bellwood, 2003; Kramer & Bryant, 1995b; Wagner et al. , 2009). Furthermore, we found that the same negative relationship holds true for other intestinal traits, providing the first quantitative evidence that intestinal diameter, as well as length, varies as a function of trophic level. However, while carnivores and herbivores have the widest intestine and corallivores the narrowest across three reef fish families  (Elliott & Bellwood, 2003) , a clear relationship between intestinal diameter and diet has not yet been established.
Therefore, the intestinal traits presented herein could be used to explore relationship with these functions in future studies. In the present study, we mainly focused on interspecific variability in intestinal morphology. However, in Mo'orea, the fishes were collected around the entire island, including a great span of habitats (lagoon and slope; coral-dominated and algae-dominated reefs), and across multiple seasons. While these variables were not explicitly accounted for in our analysis due to limited replication, our models explained 85% to 92% of the variation in the data, demonstrating that intraspecific variability, independent of body size, was minor compared to interspecific variability in our dataset. Nevertheless, spatial and temporal variation in food availability and/or nutritional quality may lead to intraspecific variability  (Olsson et al.
This research was funded by the BNP Paribas Foundation (Reef Services Project) and the French National Agency for Scientific Research (ANR; REEFLUX Project; ANR-17-CE32-0006). This research is product of the SCORE-REEF group funded by the Centre de Synthèse et d'Analyse sur la Biodiversité (CESAB) of the Foundation pour la Recherche sur la Biodiversité (FRB) and the Agence Nationale de la Biodiversité (AFB). MG was partially supported by the Campus World scholarship program from Polytechnic University of Marche (Ancona, Italy), VP was supported by the Institut Universitaire deFrance (IUF), and JMC was supported by a Make Our Planet Great Again Postdoctoral Grant (mopga-pdf-0000000144). We thank three anonymous reviewers for their helpful comments. Open Access funding enabled and organized by Projekt DEAL.
(2000). This case is particularly interesting to study because its associated ridge building led to the onset of a synoptic-scale Scandinavian blocking in early October 2016  (Schäfler et al. 2018; Maddison et al. 2019). It has been observed during three aircraft flights: two flights of the French Falcon operated by Service des Avions Français Instrumentés pour la Recherche en Environnement (SAFIRE) and one flight of the German Falcon operated by the Deutsches Zentrum für Luft-und Raumfahrt (DLR). The structure of the paper is as follows. Section 2 is dedicated to the description of the NAWDEX case study and the methodology. It first includes information about the model and its detailed bulk microphysical schemes ICE3 and LIMA. It also includes a synoptic overview of the NAWDEX case study and a description of the observational datasets.
2018; Sánchez et al. 2020; Steinfeld et al. 2020 ) that had a weaker synoptic forcing. This case, which is referred to as the Thor ridge case in  Schäfler et al. (2018) , led to more numerous WCB trajectories in ICE3 than LIMA (55% more) that lead to a more rapidly amplified ridge building with ICE3 (not shown). Other sensitivity experiments have been made by changing the starting times of the simulations of the two cyclones and by using ECMWF datasets to initialize and force the model and this did not change the main picture provided in the present study. While the intensity of the PV anomaly may depend on the starting times and the domain extension, the previously mentioned tests provide confidence in the general character of our comparison between LIMA and ICE3. The comparisons with observations emphasize the important issue of the large underestimation of the reflectivity and ice water content in the model.
Acknowledgments. We thank  David Flack  for proofreading an early version of the manuscript and correcting the English spelling and grammar. This work was funded by several projects:  EARTHCARE RALI NAWDEX-EPATAN ESA  Contract  4000119015/NL-CT/gp ,  CNES AEOLUS/EECLAT ,  F-NAWDEX  of the  French national programme INSU/LEFE , and  ANR DIP-NAWDEX  ( ANR-17-CE01-0010 ). Data availability statement. Data are available on request from the authors.
Background: A recent world health report suggests that there is a growing rehabilitation human resource crisis. This review focuses on capacity-building needed to meet present and future rehabilitation challenges in low-and middle-income countries (LMICs). Capacity building is the process by which individuals and organizations obtain, improve, and retain the skills, knowledge, tools, equipment, and other resources needed to do their jobs competently. The objectives of this review are; 1) to determine how capacity-building has been de ned, implemented, and evaluated in LMICs; and 2) to provide an overview of the effectiveness of capacity-building initiatives. Methods: In the rst of seven stages, we will re ne and delimit the research. Then, we will identify relevant studies by searching ve biomedical databases, two rehabilitation databases, three regional databases, and three databases of grey literature.
Two independent reviewers will then select the studies using a priori selection criteria. We will exclude incomplete records, records published prior to 2000 for databases and 2010 for grey literature, and records written in languages other than English or Spanish. We will also exclude records focusing on entry-to-practice programs in academic settings. For Objective 1, using qualitative analysis software we will extract and analyze text from included records which de nes or explains capacity building. For Objective 2, using an online le sharing platform, one reviewer will extract data describing the effectiveness of capacity building interventions and a second reviewer will verify accuracy, with disagreements resolved by consensus. The results will be collated using tables and charts. After synthesizing the results, we will discuss the practicality and applicability of ndings with partners from Honduras and Colombia.
Search Strategy An experienced information specialist will develop and test the search strategy in consultation with the review authors. Keywords and controlled vocabulary terms will be selected to maximise sensitivity and speci city of the search. The information specialist will be instrumental in choosing and applying search terms to comply with several databases in the health and social sciences. The complete and nal search strategy will be provided in a follow up publication. Upon completion, the results from each database will be documented and the references will be imported into a bibliographic management software to eliminate duplicates. References will then be imported to a review software for screening. We will search all databases from inception to the date of search. We will include a geographical EPOC lter for low and middle income countries.
As "rehabilitation" is a narrow area to search, we will review the records left behind when the lter is applied. If we nd records of interest, we will remove the lter and run the search strategy without it. We will search in the following databases: Biomedical: PubMed (medline), Embase Classic+Embase 1947 to present (OVID), Web of Science Core Collection (Thomson Reuters) 1900 to present, Cochrane Library (Wiley) and Epistemonikos. Rehabilitation: CINAHL (EBSCO) 1937 to present, PEDro (https://www. pedro. org. au/) Regional: Bireme-Lilacs, Scielo, LA Referencia.
Exclusion: Records with no abstract or full text available after exhausting all possible sources Records written in languages other than English and Spanish. Date of publication prior to 2000 for research reports and prior to 2010 for grey literature Records focusing on an entry-to-practice program (diploma or degree) in an academic setting Following the search, the identi ed records will be collated and uploaded in Zotero bibliographic software (18) for deduplication. The nal unique record set of potentially eligible studies will be exported to Qatar Computing Research Institute's internet-based software, Rayyan  (19) , through which screening of records will be carried out. Prior to the screening, reviewers will pilot the eligibility criteria on a random sample of 15 titles/abstracts and full text, with further pilot rounds if necessary.
Data Extraction Data extraction forms will be developed a priori by the rst author to capture information on each document included in the review. The forms will be piloted by members of the review team and re ned based on feedback from the exercise. Team members (DD, AJB JB, EPA) will carry out data extraction in the following manner: data will be extracted by one reviewer and a second reviewer will verify the data for all records. Disagreements between reviewers will be resolved by consensus. We will use online le sharing (e. g. Drop box, Google Drive) to facilitate collaboration during study selection and data extraction. For data extraction related to Objective 1, the pdf or text version of the included study will be uploaded into a qualitative analysis tool. We will extract blocks of text from the full text articles dealing with the de nition (concepts, frameworks or models), description (when, where, what, how), and motives (why) which describe rehabilitation capacity building in LMICs for later coding and qualitative analysis using constant comparative methods.
fundyense, A. minutum, A. catenella, and/or A. pacificum. These isoforms consist of one "short" isoform encoding three catalytic domains (sxtA1-3) (excluding a 4th domain that has no homolog in existing databases [amino acids 822-976,  (Le Gac et al. , 2016) ] and a "long" one encoding four catalytic domains (sxtA1-4)  (Stüken et al. , 2011; Wang et al. , 2020a). Based on the presence of the sxtA4 domain, it is thought that the two isoforms are also present in A. affine, A. australiense, A. ostenfeldii, A. tamarense and the toxic dinoflagellates G. catenatum and P. bahamense  (Stüken et al. , 2011; Suikkanen et al. , 2013; Murray et al. , 2015; Wang et al. , 2020a). The sxtA4 domain is also found in the transcriptome of two non-toxic dinoflagellates, Prorocentrum micans and Cochlodinium polykrikoides, but is composed of a different sequence than those found in toxic Alexandrium species  (Wang et al.
Sequence Analysis and Primer Designs The nucleotide and protein bioinformatic analyses of the recombinant plasmids were performed using Vector NTI 9. 1. 0 (Invitrogen, Invitrogen Corporation, Carlsbad, CA, United States). Similarity searches between the sequenced recombinant plasmids were done with BLASTN and BLASTX sequence alignments against the nucleotide and protein sequences in the available databases from GenBank 1. Specific qPCR primers sxtA4 were designed with Primer Express 3. 0 (Applied Biosystems, Carlsbad, CA, United States) in the clone similarity sequence between A. minutum and A. pacificum, respectively (Supplementary Table  4 ). The sequence data from this article can be found in the GenBank/EMBL databanks and are listed in Supplementary Table  4  with their accession numbers.
According to the linear regression equation, the copy numbers in each reaction (CPNr) were calculated as described by  Stüken et al. (2015) , with CPr corresponding to the crossing point of the individual reaction. Subsequently, the copy numbers in each reaction per ng (CPNng) were estimated as follows: CPNng = CPNr DNAin where DNAin is the amount of input DNA in ng. The copy numbers per genome (CPN G ) were calculated as follows: CPN = CPNng × Gsize 1000 where Gsize is the measured genome size of the strain in pg. sxtA4 Analyses in the A. minutum Transcriptomic Database The A. minutum strain-specific sequence and expression levels of sxtA4 were obtained from a previously published RNAseq dataset  (Le Gac et al. , 2016). Each strain was collected at the end of the exponential phase and the mRNA was sequenced on an Illumina Hiseq PE 2× (100 bp).
Normalized expression values are calculated as 2ˆrlog (coverage). The FreeBayes software  (Garrison and Marth, 2012)  was used to identify genetic variants. As A. minutum strains are haploid in our culture conditions, allelic variants within strains reflect the presence of genetically divergent gene copies within a given strain. Biallelic variants were considered when displaying a quality criterion >40 and when covered more than 20 times in each strain. For each variant site, the reference allelic frequency was calculated as the number of reads corresponding to the reference allele (i. e. , as in the reference transcriptome) divided by the total number of reads covering the site. In the A. minutum reference transcriptome (https://doi. org/10. 17882/45445), the sxtA4 reference sequence was comp112540_c0_seq1 (Supplementary Figure  3 ).
tamarense CCMP1771; and the mutant A. pacificum ACHK-NT)  (Murray et al. , 2011; Stüken et al. , 2011; Zhang et al. , 2014). In the European A. minutum and A. pacificum strains, the genomic copy number of sxtA4 also appears to be a good indicator of the toxin production level, tough it remains an ambiguous marker for other species. Moreover, given that there is a potential relationship between the genome size, the gene copy number and toxin quotas in dinoflagellates, the compilation of a larger dataset on PST-producing strains of dinoflagellates is encouraged so as to further assess this observation. sxtA4 Expression and Isoforms in A. minutum The nine toxin-producing strains with several (>9) sxtA4 copies were genetically polymorphic, with several divergent sxtA4 copies co-occurring within a given strain.
ACKNOWLEDGMENTS We are authors are grateful to the  IFREMER Institute and the Regional Council of the Région des Pays de La Loire for the Ph. D. funding of SG. We would like to thank,  Enora Briand  for their assistance in the design of experimentation and their support in molecular biology,  Estelle Masseret  and  Ester Garces  for providing several A. pacificum strains. We also acknowledged  Eric Abadie ,  Nicolas Chomérat  and  Gwenaël Bilien  from  IFREMER  for the isolation and identification of several Alexandrium strains.
10 4 and 8. 10 5 copies, were used as internal standards to verify qPCR efficiency. Three biological replicates were performed, each in four technical replicates. A negative control without DNA was included for each PCR mix. All of the assays showed a R 2 > 0. 98 with mean efficiency of 104% (min 102%, max 109%). 1 https://www. ncbi. nlm. nih. gov/genbank/ sxtA4 Copy Number Determination.
Methods CESM1-LENS datasets. The North Pacific region from 20° N to 60° N and 100° E to 90° W is considered here. The CESM1-LENS is specifically designed to provide information on internal climate variability  36. All the ensemble members use the same model parameters; however, each member represents a distinctive climate trajectory. This is achieved by initializing the simulations with small round-off differences in the air temperature  50. Here the daily and monthly SLP, surface air temperature, precipitation, sea surface temperature and net heat flux from 36 members of both the historical and RCP8. 5 scenario simulations of the CESM1-LENS from 1920 to 2100 are used. Despite the slightly different initial atmospheric conditions, the ensemble members share the same external historical and future RCP8.
e. SLP and net heat flux) of a large (order of 1000) surrogate dataset with the same AR(1)  78. The Morlet wavelet used in the wavelet analysis is defined as where ψ 0 (η) is the wavelet function, i is the imaginary unit, ω 0 is dimensionless frequency and η is dimensionless time. The Continuous Wavelet Transform of a time-series x n ( n = 1,. , N) with uniform time steps δ t is the convolution of x n with the scaled and normalized wavelet: where W X n (s) 2 is defined as the wavelet power which can be interpreted as the local phase and represents the variance with respect to the frequencies in the signal, ψ 0 is the normalized wavelet, s is the wavelet scale, n is the localized time index, and n ′ the translated time index of the time ordinate x. The global power refers to the time integration of all the local wavelet spectra, if we considered a vertical slice through the wavelet plot as a local measure of the spectrum  80.
The Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S.