dataesr/scientific-paragraphs-categorization huggingface dataset:
Sample preparation Ground beef was obtained from Société Convivial (Gannat, France). The meat was certified from Charolais cattle and contained 11% fat. Stored at -80 • C, it was thawed overnight in the fridge at 4 • C the day before preparation. As the aim of this work was to evaluate the sensory impact of the addition of the 4 natural ingredients rich in phenolic antioxidants evidenced by  Meurillon et al. (2020) , the same formulations were chosen. The four natural products rich in phenolic antioxidants were purchased from the local supermarket and were comprised of: 'Extra Fine Capers' from Maille, Pinot Noir Burgundy wine bottles (red wine), organic green tea in bags from Naturela and dried oregano from Ducros. They were added in two ways: marinated or blend in. Marinade durations were chosen according to literature data on marinated meat  (Busquets, Puignou, Galceran, & Skog, 2006; Melo et al.
Some of them were coherent with cooked meat aromas but others seemed to originate from the addition of natural ingredients. Sour, salty, bitter and umami were the four gustatory attributes recorded. Typical aroma and odor descriptors from cooked meat were described with grilled, fat-like, mushroom, caramel, bloody, rancid and meaty and matched the data displayed by Adhikari et al. in the lexicon for beef flavor  (Adhikari et al. , 2011). Other attributes were also included as "aromatic plants", "winy" and "fruity". In addition, the panelists included two physical attributes: "juiciness" and "cohesiveness". In the second session, semi-trained panelists received the concentrations chosen in the hedonic step, including two standards (unmarinated and water marinated) and were instructed to rate the intensity of each term using a 10 cm unstructured linear scale from 'no perception' to 'strong perception'.
Dynamic headspace-gas chromatography-mass spectrometry/ multibooth olfactometry (DH-GC-MS/8O) Olfactometric data were acquired and processed with AcquiSniff® software  (Tournayre & Berdagué, 2003). After running the DH-GC-MS/ 8O  (Berdagué et al. , 2007)  on the six samples, over 600 terms were generated by the 8 panelists. Panelists were free to choose any terms but given the congruence of some descriptors and for a better representation of the results on the aromagram, the vocabulary was classified into 12 odor poles (Table  1 ). By its coupling with a mass spectrometer, the DH-GC-MS/8O enabled to identify the odor-active compounds and to assess their contribution to the overall odor/aroma of the product. The matching of the resulting candidate compounds and the odor descriptors generated by the trained panelists was assessed thanks to a library of aroma descriptors and retention time found at thegoodscentscompany.
For example, the miRNA database miRbase (www. mirbase. org) contains 326 known miRNAs (accessed on 1 December 2022) in Arabidopsis thaliana, 604 in Oryza sativa, 247 in Physcomitrella patens, 594 in Picea abies, 2654 in Homo sapiens, 1978 in Mus musculus, 437 in Caenorhabditis elegans, and 469 in Drosophila melanogaster. These genes are grouped in families represented by a number in reference to similarities between their mature miRNA sequences. The various homologs within one multigene miRNA family are distinguished with different letters. Unlike animal miRNAs, which frequently target hundreds of genes, plant miRNAs usually have fewer than 10 targets, typically key regulators such as transcription factors (TFs), hormonal receptors, and nutrient sensors  [5]. By downregulating key regulators, which in turn modify the expression of several genes, miRNAs thus act as developmental switches capable of modulating entire signaling networks.
This was recorded continuously by oxygen probes (Firesting O2, PyroScience, Germany) and associated software (PyroScience Oxygen Logger). Oxygen consumption (MO 2 ) was then calculated using a custom script on R software, to transform oxygen saturation (in %) into oxygen concentration, based upon established values of oxygen solubility as a function of temperature and salinity (measured twice a day in each tank). The slopes of decreasing oxygen concentration over time were estimated through a linear model using an automated R script. The first and last minute of measurement were removed before.
Journal of Experimental Biology • Accepted manuscript estimating the slopes, and only slopes with an R² > 0. 8 were retained. Measurements collected during fish handling, feeding or any intervention on the tanks were removed. Thus only routine respiration was considered, including spontaneous activity and the postprandial period. The MO 2 was calculated in mg O 2 h -1 g -1 of fish, from the decline in water O 2 concentration and considering the total volume of water and the total biomass of the fish  (McKenzie et al. , 2007; McKenzie et al. , 2012). The changes of the total biomass of each tank were taken into account in MO 2 calculations. The cyclical measures were then summed up into daily median rates of oxygen uptake. Because of the data distribution, the number of cycles measured per day was not homogenous (due to interventions on tanks, etc.
Fish were then dissected to assess sex, maturity stage (97% of fishes were mature) and total mass of red muscle and white muscle. White muscle samples were stored at -80°C for subsequent analyses. Gonad mass and proportion are reported in the Supplementary Data (Table  S2 ). Respiration of red muscle fibres was measured using Oxygraph-2K high resolution respirometers (Oroboros® Instruments -WGT Austria), with measurements carried out at the relevant acclimation temperature of the fish. Muscle samples were transferred to respirometer chambers containing 2 mL of MiR05, and mitochondrial function was measured at the acclimation temperature, with a substrate-uncoupler-inhibitor titration protocol adapted from OXPHOS respiration). Oligomycin (1. 25 µg mL -1 ) was then added to inhibit ATP synthase to obtain the basal non phosphorylating respiration rate (i.
Statistical analysis Effects of food deprivation, temperature and time were evaluated for all physiological and morphometric characteristics by linear-models (LM), or linear mixed-models (LMM) to account for dependency of the data when there was more than one measure per individual (i. e. for analyses of the relative change in body mass). Temperature (12°C or 20°C), treatment (control or food deprivation), time (30 or 60 days) as well as their triple interaction and the 3 double interactions were included in models as fixed effects. The model was then simplified according to a stepwise procedure by removing non-significant interactions and fixed effects (only when not involved on any remaining interactions). Groups were then compared through post-hoc tests, using the emmeans-or glht-function, when any of the interactions were significant (P < 0.
and var. borneensis, are genetically differentiated, or whether differences between them in morphological traits are due to phenotypic plasticity. Genome (Abu Bakar et al. , 2016)  and plastome (Wee et al. , 2022)  datasets of cultivated mangosteen are now available for reference for Single Nucleotide Polymorphism (SNP) calling. Analysis of both nrDNA and cpDNA markers in a large number of samples from across the region would enable inferences about several open questions: (i) patterns of genetic variation in mangosteen and its wild relatives; (ii) whether gene flow occurs between them, and whether any gene flow detected is unidirectional (from wild pollen donors to mangosteen), as expected from results of crossing experiments (Hambali & Natawijaya, 2016) ; (iii) whether mangosteen originated from numerous initial progenitors that arose from independent events of sexual reproduction.
Plant Materials and Management Field experiments were conducted in a randomized block design with three replications in 2019 and 2020, at Danyang Experimental Base of Nanjing Agricultural University, Jiangsu Province, China (31°54′31″ N, 119′28′21″ E). The size of plot was 7 m × 10 m. According to our previous data  (Jiang et al. 2021) , two homozygous largepanicle rice cultivars, CJ03 and W1844, were selected to analyze the deep relationship of sink strength and source leaves during grain filling. These two cultivars were coming from the State Key Laboratory of Rice Genetics and Germplasm Innovation, Nanjing Agricultural University. Seeds were sown on May 21 in 2019 and May 23 in 2020. The 25-d old seedlings were transplanted with two seedlings per hill, at a hill spacing of 13. 3 cm × 30 cm.
Analysis of Photosynthesis On 8 DPA of inferior spikelets, the photosynthesis of the flag leaves was measured with a portable photosynthesis system (LI-6400; Li-Cor) at 10 am. On sunny day, the measurement was conducted in 9 tagged rice in each replicate plot with a constant saturated light level of 1500 μmol m -2 s -1 provided by red/blue light-emitting diodes. Leaf temperature was maintained at 30 °C and relative humidity in the chamber at c. 0-6 (humidity deficit c. 1. 1 kPa). Before using gas-exchange measurements for data analysis, the flag leaves were allowed to equilibrate nearly 20 min at each setting.
Females of most species exhibit few stable morphological interspecific differences, and females are therefore not considered in the species descriptions below. About 500 specimens were examined for this study. Identifications of the previously described species were made by comparison with type specimens and study of the original descriptions. Label data of name-bearing types are reported verbatim, with consecutive lines separated by a slash and data from a single label enclosed by double quotation marks. Additional information and interpretations appear between square brackets. The format of the label data of other specimens is standardised. Valuable additional bio-ecological information was obtained from the Coleoptera field collection books of the Ditsong National Museum of Natural History (the former Transvaal Museum) in Pretoria (TMSA).
92° S, 18. 42° E in decimal-degree notation. We retained historic notations in label data citations of name-bearing types, but in all other cases we standardised such coordinates to the degrees-minutes notation. Following Article 50. 1 and Recommendation 50A of the Code (ICZN 1999), JMH is responsible for the new names introduced in this paper. The lectotype designation is in accordance with Article 74. 1  (ICZN 1999). Larvae and pupae used for morphological descriptions were preserved in 80% ethanol. Habitus photos of the larvae were taken with a JVC KY-F75U camera associated with a Leica MZ16f stereo microscope. The pupa was photographed with a Keyence ® VHX-5000 imaging system. Larvae were dissected and slide-mounted for microscope study under high magnification, basically following the technique of  May (1993 May ( , 1994)).
Nucleotide sequences were aligned and manually checked using CodonCode Aligner ver. 3. 7. 1. (CodonCode Corporation, Centerville, MA, USA) to verify the absence of pseudogenes. Uncorrected p-distance values of pairwise genetic distances between species were computed with Mega 7  (Kumar et al. 2016). Reconstruction of phylogenetic trees was carried out with COI and EF1 sequences (658 and 517 base pairs, respectively) using PhyML  (Guindon & Gascuel 2003)  with 1000 bootstrap replicates. The trees were rooted with three species of two tribes of Brachycerinae sensu  Oberprieler (2014) , Brotheus crenelatus  Marshall, 1907 (JHAR01250_0101) , Synthocus hopei Boheman, 1842 (JHAR02578_0101) (both Brachycerini) and Ocladius baccicollis Boheman, 1838 (JHAR02406_0101) (Erirhinini), as well as with a species of the brentid genus Episus Billberg (JHAR02469_0101) (Microcerinae).
Life history Specimens of C. estriatus were found on the ground or feeding on vegetation, but no precise data of its host plants are known. A series of adults was found feeding on leaves of Moraea by S. Neser near Nieuwoudtville in 1995, and they also fed on this plant in captivity  (Oberprieler et al. 2007 : fig. 17 ), but, in view of the wide use of Oxalis as larval host in Cryptolarynx, the larvae of C. estriatus probably also develop in bulbs of an Oxalis species rather than on Moraea. Adults were collected in July, September and November.
Acknowledgements We thank  Max Barclay  (NHMUK), Simon van Noort (SAMC) and  Ruth Müller  ( TMSA ) for providing loans of specimens and  Werner Strümpher  ( TMSA ) for access to the Coleoptera field collection books of the  Ditsong National Museum of Natural History. We thank the  Western Cape Nature Conservation Board  (Permit No. CN44-30-4229 ) and the  Cape Research Centre ,  South African National Parks  (Permit No. CRC/2019-2020/012-2012/V1 ) for permission to collect specimens in areas under their control. We acknowledge  Paula Strauss ,  Gary Beukman  and  Michael Lutzeyer  for access to the  Grootbos Private Nature Reserve  and their friendly assistance with our collecting efforts. AEM´s research was supported by the  National Agency of Promotion of Science of Argentina (ANPCyT , grant  PICT 2016-2798 ), and by the  National University of La Plata  ( UNLP , grant  11/N852 ).
[27]. The swelling index (SWE) was measured using the bed volume technique. The bed volume was recorded and expressed as mm of swollen sample per g of dry initial sample  [28]. Hygroscopicity (H y ) was determined according Cai and Corke  [29]. Samples were placed in a petri dish at 25 • C, in an airtight plastic container containing Na 2 SO 4 saturated solution (81% relative humidity). After 7 days, each sample was weighed and the hygroscopicity (H y ) was expressed as g of water gained per 100 g dry solids  [29]. Texture properties were measured using puncture tests (TA-XT2 Texture Analyzer, Stable Micro Systems Ltd. , Godalming, UK) and software (Texture Exponent, version 6. 1. 12. 0)  [30]. From a force-time curve, the area under the curve plot, which represented the work done for a time of displacement of the puncturing device, was obtained.
Statistical Analysis Statgraphics Centurion XVII Software, version 17. 2. 04 was used for Analysis of Variance (ANOVA), with a confidence level of 95% (p < 0. 05). ANOVA was applied to evaluate the differences among mixtures, pellet and expanded snacks. The method used to discriminate between means was Fisher's least significant difference procedure. Pearson correlation analysis (Statgraphics Centurion XVII), with a 95% significance level was conducted to establish the relationships among the studied parameters.
Microwaving Expansion Kinetics Microwave dehydration curves of pellets with different moisture (25% and 30%) and % beetroot byproduct (0, 5, and 10) were obtained by plotting the moisture ratio (MR) vs. time. The experimental data were fitted to the Page, Logarithmic, and Midilli-Kucuk models. Figure  2  shows the MR microwave process experimental data at different studied times. The kinetic parameters and the accuracy of the fit determined for the three models are presented in Table  1. These models fit well with the experimental data, as seen from the adjusted regression coefficient (R 2 ) and the root mean square error (RMSE) values (Table  1 ). The best fit (higher R 2 ) was the Page model for all samples except C30. In this sample, the Midilli-Kucuk model presented the best fit. Therefore, in general terms, the Page model provided the best fit with the experimental data.
Transcript analysis using BUSCO v5 (ref. 15) showed that the transcripts' annotations match 88. 6% of the transcripts in the apicomplexa_odb10 database (80. 5% single-copy and 8. 1% duplicated), whereas 5. 8% are fragmented and 5. 6% are missing. BUSCO analysis further showed that the B. duncani protein annotations match 87. 7% of the proteins in the apicomplexa_odb10 database (79. 6% single-copy and 8. 1% duplicated), whereas 5. 6% are fragmented and 6. 7% are missing. Only 1. 2% of the genome is considered repetitive by RepeatMasker.
1% of the gene models in the apicomplexa_odb10 database (85. 2% single-copy and 9. 9% duplicated). Long-range chromatin contact frequency information using Hi-C allowed creation of contact maps for B. duncani WA1 (shown on Figs. 1a  and 2b ). The contact maps show that the assembly does not contain large mis-joints or mis-assemblies and is consistent with that of other apicomplexan parasites  16. The centromeres interact strongly with each other (as illustrated in Fig. 1b (bottom)). Chr I was found to have a metacentric centromere; Chr II and III have a telocentric profile, and Chr IV and V have acrocentric centromeres (Supplementary Fig. 3 ). A similar organization was previously observed in three of the four chromosomes of Babesia bovis  17. The chromosomal organization of the B. duncani nuclear genome was further validated using pulsed field gel electrophoresis https://doi.
The components of each of the gene families and their properties are available in the supplementary datasets. The chromosomal location of the genes in the three largest BdUMGF and BdOMGF families, as well as the activator protein (AP) family, is illustrated in Fig. 3c. Our analysis showed that genes in the BdUMGF1 strongly co-localize and are on the telomeres of Chr I and IV, which also appear to be in close proximity in the 3D genome model (Fig. 3c  and also Fig. 4a  and Supplementary Fig. 4 ). All genes in the BdUMGF3 family (shown in blue) are clustered together on the same strand in the The distribution of BdUMGF1 gene family members near the telomeres as determined by Hi-C analysis (Fig. 4a ) suggests a possible heterochromatin clustering associated with transcriptional silencing surrounding these genes as described for the var or SICAvar gene families of P.
DNA prep for PacBio sequencing Genomic DNA was isolated from 100 ml in vitro culture of B. duncani (15% parasitemia and 5% haematocrit) using DNeasy Blood and Tissue kit (Qiagen, 69506), and quality control and concentration determination were performed using nanodrop and qubit. DNA integrity was evaluated using Blue Pippin pulse gel and the DNA was then used for library preparation using Pacific Biosciences SMRTbell Express template prep kit 2. 0 (100-938-900) according to manufacturer instructions. The Pacific Biosciences Smart Link software was used to determine loading concentration and proper stoichiometric measurements. The gDNA library was then annealed to the Pacific Biosciences V5 primer for 1 h at 20 °C. The annealed library was then bound to polymerase using Pacific Biosciences Polymerase 2.
2 for 1-4 h at 30 °C and loaded onto the Sequel II Instrument as an adaptive sequencing run. At least one smart cell was sequenced for each gDNA library with a move time of 30 h and a pre-extension of 2 h. After the DNA library sequencing was completed, the loading metrics were evaluated by mean read length, polymerase read length, data yield and P1 values (a productive zero-mode waveguide (ZMW) with a high quality (HQ) sequencing region detected within the read) to ensure the sample ran as expected and data had met Yale's gold standards (polymerase read length between 50-60 kb, data yield (HiFi) of around 2-4 million reads of a total of 10-20 Gb and P1 between 60-70%).
DNA preparation for Bionano optical mapping A total of 60 ml in vitro culture of B. duncani at 15% parasitemia and 5% haematocrit was collected and centrifuged at 500 × g to obtain a packed pellet. For analysis, pellet was used to isolate ultra-high molecular weight gDNA for use in genomic optical mapping by Histogenetics using the Bionano Prep Blood and Cell Culture DNA Isolation kit (Bionano Genomics, 80004). Following this, DNA was quantified using Qubit dsDNA BR Assay kit. A total of 0. 75 g of high molecular weight DNA was then labelled using the Bionano Prep direct label and stain method (Bionano Genomics, 80005) and loaded onto a flow cell to run on the Saphyr optical mapping system (Bionano Genomics). Approximately 1,177 Gb of data were generated per run. Raw optical mapping of molecules in the form of BNX files were run through a preliminary bioinformatics pipeline that filtered out molecules less than 150 kb in size and less than 9 motifs per molecule to generate a de novo assembly of the genome maps.
Genome sequencing and assembly An in vitro culture of B. duncani (100 ml) in hRBCs was propagated to a parasitemia of 10% at 5% haematocrit. DNA was isolated from infected hRBCs and sequenced at the Yale Center for Genome Analysis using Illumina HiSeq 2500 and PacBio HiFi (CCS) sequencing. A total of 177,189 PacBio HiFi reads were obtained. The average HiFi read length was 8,814 bp, and the longest read was 29,067 bp. The HiFi reads totalled 1. 56 B bases, which translated to an expected ~156x coverage of the B. duncani genome (assuming a ~13 Mb genome). HiFi reads were mapped using Minimap2 47 to the B. duncani mitochondrion and apicoplast. Only 0. 41% of the reads mapped to these organelles, which were then discarded to enrich the data for nuclear DNA. HiFi reads were also mapped to the human genome to determine possible host contaminations, but only 1.
48% of them were flagged. Cleaned reads were assembled using HiCANU v2. 2 13 using default parameters. HiFi reads were also tested on HiFiASM v0. 16  48  and Wengan  49  , but they generated slightly inferior assemblies (based on assembly statistics, comparison with the optical map and transcript isoform annotations). The Bionano Hybrid Scaffolding pipeline v1. 7 was used to compare the draft assembly with the Bionano optical map to detect possible mis-joins and create scaffolds. The scaffolded assembly was polished using two rounds of PolyPolish  14. At every step of the assembly (draft, scaffolds, polished), a series of quality control steps were carried out to ensure that no imperfections were introduced. The quality control steps included (1) mapping of all the Illumina WGS and HiFi reads to the assembly, (2) carrying out a BUSCO  15  completeness analysis (at the genome level) and (  3 ) determining the number of detected gene loci from the mapping of RNA-seq IsoSeq reads.
Hi-C data processing The Illumina sequencing of the four B. duncani clones (WA1, A6, B7 and B1) yielded over one billion Hi-C paired-end reads in total. Hi-C reads were processed using the command-line version of the HiCExplorer pipeline. HiCExplorer is a comprehensive and versatile pipeline that processes Hi-C reads and generates normalized chromatin conformation contact maps. The pipeline started by mapping all Hi-C single reads to the B. duncani assembly using 'BWA mem -A1 -B4 -E50 -L0'  51. The percentage of reads mapped ranged between 83% and 96%. After sorting and merging the reads from the four data sets, the command 'hicBuildMatrix' was used with default parameters and a bin size of 10 Kb. A diagnostic plot created using 'hicCorrectMatrix diagnos-tic_plot' indicated that a threshold of -4.
PacBio IsoSeq processing PacBio IsoSeq reads were mapped to the B. duncani genome using Minimap2  47  with options 'splice:hq -uf -secondary=no -C5'. The resulting SAM files were sorted using 'sort -k 3,3 -k 4,4n', then fed into the PacBio cDNA_Cupcake ToFU pipeline (https://github. com/Magdoll/ cDNA_Cupcake) using the Python code 'collapse_isoforms_by_sam. py' to collapse redundant isoforms (more details about this pipeline can be found at https://github. com/Magdoll/cDNA_Cupcake/wiki). The resulting isoform sequences were used in the gene finding pipeline below.
Gene prediction and annotation The genome was first soft masked with RepeatMasker (http://www. repeatmasker. org), then processed using the FunAnnotate (v1. 8. 9) gene annotation pipeline (https://github. com/nextgenusfs/funannotate). As transcript evidence, we provided the IsoSeq-based isoforms computed via the cDNA_cupcake pipeline (see PacBio IsoSeq processing). As protein sources, we provided the annotated protein sets of B. bigemina, B. bovis, B. microti, P. falciparum, T. gondii, T. orientalis, T. parva as well as all the UniProt/SwissProt protein models. FunAnnotate was run with default parameters and weights (augustus:2 hiq:4 transcripts:4 proteins:4). Functional annotations were obtained via InterProScan (v5. 55-88) with default parameters  54. The output of InterProScan was parsed by custom scripts for the downstream analyses.