dataesr/scientific-paragraphs-categorization huggingface dataset:
Salinity and crab burrow mapping J o u r n a l P r e -p r o o f A field survey was conducted in March 2015 to collect data on WW dispersion and crab burrow density in the Malamani mangrove. Four 80 m-long transects covering the impacted area as well as the control zone were established parallel to the shore. For each transect, 8 plots (1 m 2 , located approximately 10 m from each other) were monitored after one day without rain. Thirty two plots were divided in 3 areas: one subjected to WW release and two control areas (one northern and one southern area, located respectively on each side of the impacted area). These plots were in all cases established on flat bottoms only, since it is where WW flows and infiltrates the sediment through the crab burrows. The geographical coordinates of these plots were recorded using a GPS system (Garmin GPSMAR®78S).
Acknowledgements The authors are thankful to the  Syndicat Intercommunal d'Eau et d'Assainissement de Mayotte (SIEAM)  and especially  Kissimati Abdallah  for her help on the field. This study was partly funded through the  Marie Curie Actions EU  grant  FP7-PEOPLE-2013-IEF  (grant number  622087 -" IAS-Life ") awarded to GRI and by the  French National Agency for Water (ONEMA) , which is now part of the  French Agency for Biodiversity (AFB).
Instead, population immunity can be directly measured by serology. Crucially, this has proven successful in predicting the risk of measles outbreaks in a few settings. A cross-sectional population serological survey was harnessed to launch a vaccination campaign and thus avert a post-honeymoon outbreak in England and Wales  [7]. More recently, analysis of a serological convenience sample, taken from fever/rash surveillance, estimated a large susceptible population in Madagascar, suggesting that the country had been experiencing a 'honeymoon period' and was at considerable risk of a measles outbreak  [8]. This subsequently occurred (Figure  1A ). In practice, serological data necessary for such predictions are rare. We can approach this problem via two immediately available sources of samples, allowing increasing granularity of prediction; there is also potential for a much more comprehensive approach.
Materials and methods Dates of first fungicide treatment. SSP survey. Pesticide use on vines in the Bordeaux region was surveyed by SSP during the 2010, 2013 and 2016 growing seasons, on 606, 576 and 459 vineyards (n = 1641), respectively. Information about product names, dates and rates of pesticide application were collected in each vineyard and the date of first fungicide application to control downy mildew was determined for all vineyard*year combinations. Survey conducted by the French Vine and Wine Institute. In spring 2018, IFV published an online questionnaire to collect data from vine growers on the timing of the first anti-GDM treatment applied. Vine growers in the Bordeaux region (n = 94) were asked to report the frequency of treatments against GDM for each 10-day interval between March 1 and July 31.
The protocol of the farm survey was approved by the IFV to ensure that the data source is valid and that the data is used correctly and ethically. The responses received were used to plot histograms and to determine likely dates of first treatment. A continuous probability distribution was fitted to each histogram with the fitdist() function of version 1. 4. 0 of the SHELF package  50  of R 51 (version 3. 3). The distribution yielding the best quality of fit was selected for estimation of the median date of first GDM spray for each vine grower. Dates of GDM onset. Survival analysis. Dates of GDM onset were estimated by analyzing epidemiological data collected from untreated plots in vineyards of the Bordeaux region. GDM incidence data were collected from 266 vineyards in the Bordeaux region from 2010 to 2017 by the technical staff of the IFV.
In each vineyard, at least one untreated row of vine stocks was monitored for the detection of GDM symptoms. The number of vine stocks with GDM symptoms was determined by visual inspection. Visual observations stopped when the proportions of infected vine stocks and bunches were close to 100%. In total, 1 to 19 GDM incidence data were collected in each vineyard. Cox survival models  52  were fitted to estimate the dates at which the epidemiological threshold of 1% of vines infected was reached in the sample of untreated vines surveyed. The results obtained with the fitted Cox model were used to derive three distributions of dates of GDM onset: a common distribution for all years, and two separate distributions for years characterized by dry spring (rainfall in March-May < 1. 51 mm/day) and years with a wet spring (rainfall in March-May > 5.
Each elicitation was carried out with MATCH Tool ® 53 and resulted histograms were analyzed using the fitdist() function of version 1. 4. 0 of the SHELF package  50  of R  51 (version 3. 3). This procedure was applied by each expert, each year, between April 15 and May 15, generating one distribution of dates of GDM onset per expert*year combination. Number of fungicide treatments. For each distribution of dates of first anti-GDM treatment or of disease onset dates, we calculated a mean number of fungicide sprays in vineyards of the Bordeaux region. Each distribution was used to compute the proportion of vineyards in which fungicide treatment begins for each week, between cw 12 (mid-late March) and cw 33 (mid August). These proportions were then multiplied by the duration of the treatment period (number of weeks) and by the treatment frequency.
The final form of the equation for each term depends on the pesticide mixing/loading and application scenarios considered. Terms relating to dermal exposure (including the head, body and hand terms) and inhalation are used for the calculation of dermal exposure (DE O ) and inhalation exposure (IE O ) to an active substance, respectively. The assessment of DE O and IE O also takes into account absorption through the skin or by inhalation (according to the term assessed) of the active substance, the default body weight of the operator (i. e. 60 kilograms) and a risk mitigation factor corresponding to the use of PPE (if indicated). The model then estimates overall operator exposure (in mg per kg of body weight per day) as the sum of DE O and IE O. Based on new exposure datasets from 34 unpublished studies  23  , the AOEM model is representative of current agricultural practices, including PPE use, in EU member states  12.
Main active substances used in Bordeaux vineyards against GDM. Use frequencies of the most common fungicides applied to control GDM in the Bordeaux region were calculated from the SSP surveys. Each fungicide product was characterized in terms of the mean number of sprays in a given vineyard and the number of vineyards in which it was used during each of the growing seasons surveyed (2010, 2013 and 2016). The composition of each fungicide (i. e. names of active substances and amount of each molecule in the fungicide) was obtained from the ANSES E-Phy database  54. Substances and fungicide products were paired, and the number of applications of each pair in the region was calculated by multiplying the mean number of treatments with the fungicide by the number of vineyards receiving these treatments.
Acknowledgements We thank the  French Wine and Vine Institute  ( Institut Français de la Vigne et du Vin ) and its technical partners for collecting data and allowing us access to these data and to the EPIcure web platform (https://www. vignevinepicure. com). This work received funding from the  French Ministry of Agriculture  (reference: CAS DAR,  SMART-PIC  project), the  Institut Carnot Plant2Pro  (project  L-i-cite ) and the  Bordeaux Vine Council (CIVB). This work is part of the # DigitAg  project ( ANR-16-CONV-0004 ). It is supported by a public grant overseen by the  French National Research Agency (ANR)  as part of the  "Investissements d'avenir" program  (reference:  ANR-10-EQPX-17 -Centre  d' accès sécurisé aux données -CASD).
Species distribution and identification Although species distribution data is limited for the current samples collected in the Wallis and Futuna volcanic region, we know that at least some specimens of A. kojimai and A. strummeri were taken from single gastropod patches, recorded for the first time (co-occurring less than a metre apart). Unfortunately, data on the proximity of A. boucheti and A. kojimai when co-occurring are unavailable, as specimens were a pooled collection from multiple sampling locations during a dive where both species were found (though still only several metres apart). Nucleotide sequence data from 106 specimens targeting the 1228 bp fragment of the mitochondrial gene, cytochrome-c oxidase subunit I (COI), have been deposited in GenBank (see Table  1 ). Anatomical descriptions detailed below are listed by functional system.
Material examined Specimens collected from the Fatu Kapa vent field (within EEZ of Wallis and Futuna Islands) during the Futuna 3 cruise with the HOV Nautile. When measured (n = 3), SH ranged from 46. 1-69. 9 mm (A. strummeri specimens were smallest of three SW-pacific species, occurring in much lower numbers). Periostracal-bristle arrangement examined in 7 specimens (two in ethanol, five frozen). Dissections performed on 6 specimens (1 in ethanol, 5 frozen). Of these, histology carried out on multiple tissues from one specimen. SEM analyses of radulae extracted from two frozen specimens. CT analyses were on remaining ethanol-fixed voucher specimen with code MNHN-IM-2014-7973 and GenBank# MT010489, which has been deposited at the Muséum National d'Histoire Naturelle, Paris (SH 69. 9 mm). This specimen was collected live from the Aster'x vent site by HOV Nautile during dive # PL18-1839 of the Futuna 3 cruise (14°45′ 6"S, 177°9' 8"W, 1571-m depth on June 14th, 2012), fixed and stored in 96% ethanol at room temperature (~5 yrs), then contrast-stained in 1%-Lugol's iodine (I 2 /KI) and following CT scanning, returned to 96% ethanol at room temperature for storage.
Material examined Specimens originate from the Fatu Kapa vent field found within the French EEZ of the Wallis and Futuna Islands during the Futuna 3 cruise with HOV Nautile. For those measured (n = 13), SH in current study ranged from 49. 4-77. 6 mm. All specimens were frozen (branchial filaments from a subset of specimens were fixed for microscopic analyses). Periostracal-bristle arrangement was examined in 32 specimens. Detailed dissections performed on 4 frozen specimens. Histology carried out on formalin-fixed gill tissue from 2 specimens. SEM analyses of radulae extracted from three frozen specimens. CT analyses were on frozen voucher specimen postfixed in 4% formalin with code MNHN-IM-2014-7974 and GenBank# MT010510, which has been deposited at the Muséum National d'Histoire Naturelle, Paris (SH 71.
Species identification and shell characteristics Genus was assigned based on morphological observations, after which total DNA was extracted for COI barcoding (Additional file 7). Resulting sequence chromatograms were visualized, assembled and edited using Geneious v. 10. 0. 5  [53]. Finally, sequences were matched to publicly available databases using the NCBI blastn algorithm  [54]. All sequences are deposited in GenBank (Table  1 ).
Dissections Dissections were performed using heat and UV-sterilised tools on frozen (n = 28, all species), formalin-(A. kojimai only n = 2) and ethanol-fixed specimens (A. kojimai n = 1, A. strummeri n = 2) by first removing the shell and then dissecting and separating organs and tissue samples for further investigation. Ethanol-and formalin-preserved adults were initially dissected based on the limited anatomical data available from similar species  [2, 3]  with subsequent, more meticulous dissections following preliminary histological analyses. Certain regions were targeted; 1) the ctenidium (gill) and enveloping pallial epithelium (which includes the rectum); 2) the buccal mass (i. e. dorsal folds, salivary ducts, odontophore and contractile musculature, radula and radular sac); 3) oesophagus, salivary glands and granular cephalopedal tissue; 4) the gonad (when present); 5) lower posterior oesophagus, the stomach, and associated digestive glands; 6) the cardio-renal complex (i.
Histology Preliminary dissections were used to determine which organs would be investigated histologically and from where the tissue samples would originate in each. Resin choice depended on tissue sample size (large being > 2mm cutting diameter, embedded in PEG stearate; small tissue was embedded in LR white, see Additional file 7). PEG-embedded tissue was stained using standard histological protocols for Harris' Haematoxylin (aqueous) and Eosin-Y (in alcohol). Semi-thin sections of LR-white embedded tissue required extended staining times and the use of aqueous Eosin-Y (after  [56] , see Additional file 7). Slides were viewed and photographed under a Zeiss AxioImager-Z2 microscope. Multiple micrographs were captured (Zeiss AxioImager. Z2) and stitched to form image mosaics using the Tiles module in the associated microscope software Zen 2 (Blue edition).
The projection data was aligned and registered as a voxel matrix: effectively a rasterised 3D map of signal, where pixel values ultimately define voxel greyscale data. This data was transformed into a RAW image stack. Raw image stacks were converted into a series of 8-bit greyscale images (henceforth 'volume') in Fiji (Image-J), based on the associated metadata generated during the scan. Initial and final image slices containing no tissue were excluded to reduce subsequent memory demand of volume manipulation. Volumes were then imported into the open-source 3D rendering software Slicer (v. 4. 10). For details on software application see Additional file 7 and Figs. 1, 2, 3, 4 within. Physical dimensions of volumes were specified by imputing scan-specific imaging resolutions as scaling factors, obtained from scan metadata (i.
Acknowledgements Our thanks to:  Alex Ball ,  Vincent Fontanez  and  Brett Clark  of the  Natural History Museum (London)  for providing access and technical assistance during CT imaging, to  Nicolas Gayet  (Ifremer) for scanning electron microscopy analyses and to  Fabien Noël  (formerly at Ifremer) for COI sequencing. Many thanks also to  Dr. Roxanne Beinart  ( University of Rhode Island, USA ) for independent corroboration of certain morphoanatomical findings detailed in the current study. We also thank the captain and crew of  L'Atalante , as well as operation teams for Nautile and AUV AsterX, for their pivotal role in realising highly technical exploratory cruises in the Wallis and Futuna area. Finally, we thank the reviewers for insights and constructive criticisms, which improved the manuscript considerably.
Funding The 2012 Futuna cruise during which the Fatu Kapa vent field was discovered was financed through a public/private consortium comprising the French government, Ifremer and industrial groups Eramet and Technip. Laboratory analyses were also supported by the Ifremer REMIMA program. SRL is supported by project REDEEM (02/SAICT/2017) funded by FEDER, within the framework of COMPETE2020 -Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (OE), through FCT/MCTES (UIDP/50017/2020 + UIDB/50017/2020).
| Analysis of genetic relatedness between MLGs To estimate the relationship between MLGs, a matrix of shared allele distances (D AS ) was constructed  (Jin & Chakraborty, 1994)  using the software POPULATIONS 1. 2. 31 (http://bioin forma tics. org/~tryph on/popul ation s/). Distance trees were calculated with the obtained values and then plotted as a neighbor-joining tree using FigTree v1. 4. 3 (http://tree. bio. ed. ac. uk/softw are/figtr ee/).
| D ISCUSS I ON In this study we used A. pisum aphids collected from alfalfa fields located in a latitudinal transect of about 4,000 km and covering various climates, to test for an ecological short-term advantage of sex in cold environmental conditions. Both phenotypic and genetic data provided evidence for signs of sexual reproduction only in the southernmost climatic zone, where winter conditions are harsh and extreme in comparison to northern localities (Table  1  and Figure  4a ). The highest clonal diversity, the closest observed to expected heterozygosity, and the production of cold-resistant eggs only by lineages from the southernmost locality provides evidence for sexual reproduction in an invasive range and its link with cold conditions. In contrast, obligate parthenogenesis with no male production, and obligate parthenogenesis but with male production were found in northern and central areas of Chile, respectively (Tables  3  and 4 ; Figures  2  and 4 ).
Funding information  CONICYT  fellowship, Grant/Award Number:  21150761 ;  Fondo Nacional de Desarrollo Científico y Tecnológico , Grant/Award Number:  1170943  and  1190007 ;  ANID PIA/ BASAL , Grant/Award Number:  FB0002 ;  FIA, Grant/Award Number :  PYT-2018-0058 ;  ANR Sexaphid, Grant/Award Number :  ANR-17-CE20-0010.
Query Process of Literature Data Our bibliographic search aimed to collect relevant data associated with microbiological spoilage of meat products from scientific literature. A preliminary search from the Science Direct database, based on three main keywords ("meat" AND "microbiology" AND "spoilage") in full-text, provided more than 8000 records. However, these records were mostly not relevant, since many of them were studies on pathogens in meat or in other food products (seafood, vegetables, etc. ). Thus, an alternative procedure, combining expert opinion and data mining, was adopted for identifying the relevant keywords for search query functions. The procedure used to extract relevant keywords for query functions is detailed in Figure  1. First, 63 publications were initially provided by experts.
Afterwards, the keyword extraction from the full text of these 63 publications was done using a text mining approach  [14, 15]  using the tm R package  [16]. This approach extracted the most relevant terms after different text treatment steps (filtering, categorization) based on correlations between terms, i. e. , the occurrence frequency of multiple keywords in the same article  [15]. The extraction was carried out following the procedure outlined by  Williams (2016)   [17]. The text mining of 63 publications provided an output of 18 relevant keywords. The data searches were carried out afterwards using advanced searches of full texts in two scientific platforms: Science Direct and Web of Science. While query functions required the "AND" function for the three principal keywords, ("meat", "microbiology" AND "spoilage"), all supplementary extracted keywords were added with the "OR" option.
The keyword and search function used were thus written as follows: FULL-TEXT (meat * AND spoil * AND microbiology * AND (Brochothrix OR community OR data OR food OR lactate OR "lactic acid bacteria" OR "modified atmosphere packaging" OR odor OR psychrotroph * OR Pseudomonas OR volatile OR salt OR sodium OR refrigerated OR yeast)). The latest query process using those above-mentioned keywords was performed on the 7 July 2019 and identified 1622 records. Afterwards, these records were filtered in accordance with the PRISMA Statement Guidelines  [18]  (Figure  1 ). Different criteria were used to exclude non-relevant publications after several stages of screening: (i) selecting from databases: only research journal articles were kept (book chapters, short communications and other article types were excluded) and duplicates from databases were removed; (ii) screening using titles: only studies on meat products in research articles were kept; (iii) screening using abstracts: review articles, studies exclusively on pathogenic bacteria in meat products and ready-to-eat foods were excluded; and (iv) removing duplicates already provided by experts.
Afterwards, these records were filtered in accordance with the PRISMA Statement Guidelines  [18]  (Figure  1 ). Different criteria were used to exclude non-relevant publications after several stages of screening: (i) selecting from databases: only research journal articles were kept (book chapters, short communications and other article types were excluded) and duplicates from databases were removed; (ii) screening using titles: only studies on meat products in research articles were kept; (iii) screening using abstracts: review articles, studies exclusively on pathogenic bacteria in meat products and ready-to-eat foods were excluded; and (iv) removing duplicates already provided by experts.
Microbiological Data Microbiological data associated with spoilage were collected from the selected studies. High throughput sequencing data were provided in some studies, but this type of information was not available often enough to be considered for the present study. Therefore, we considered only enumeration data acquired by conventional cultural methods for the five most studied microbial indicators, i. e. , total mesophilic aerobic counts, lactic acid bacteria (LAB), Brochothrix spp. , Pseudomonas spp. and Enterobacteriaceae. For each initial experimental condition, we determined the count of each microbial indicator observed at the spoilage occurrence time. If experimental sampling was carried out daily, we considered the bacterial count as the value observed at the sampling time point.
Otherwise, if spoilage was observed after a two-or three-day interval between consecutive sampling times, the bacterial count at the spoilage occurrence time was considered as the average count observed at the two sampling time points. The gathered dataset used for quantitative analyses included the following for each initial experimental condition: meat type, storage temperature ( • C), initial composition of the atmosphere packaging (initial percentage of dioxygen and carbon dioxide), the corresponding spoilage occurrence time (days) and the bacterial count observed at the spoilage occurrence time (log CFU/g).
Measurement of Spoilage in Meat Products The exploration of all studies suggested a very important number of possible approaches for measuring spoilage. The most common methods of spoilage assessment were found to be classified in different categories: microbiological analysis, sensorial analysis and physicochemical analyses. Figure  2  illustrates the evolution of spoilage measurement among publications over the years. It appears that microbiological analyses remained the preferred strategy of spoilage assessment over the years. It especially concerns enumeration of bacterial groups. In recent years, recent highthroughput technologies involving 16S DNA amplicon sequencing has emerged but regarding our dataset, it still corresponds to a limited number of publications. Besides, sensory analyses have always represented a large part of the responses studied while considering spoilage.
Isolate identification was performed in 70 studies plates mainly by genotyping methods such as molecular fingerprinting approaches using restriction enzymatic profiles such as Denaturing Gradient Gel Electrophoresis (DGGE); Restriction Fragment Length Polymorphism (RFLP) or ribotyping; or DNA amplification such as Random Amplified polymorphic DNA (RAPD) and Amplified Fragment Length Polymorphism (AFLP). These methods have been gradually replaced by sequencing of the 16S It appears that microbiological analyses remained the preferred strategy of spoilage assessment over the years. It especially concerns enumeration of bacterial groups. In recent years, recent high-throughput technologies involving 16S DNA amplicon sequencing has emerged but regarding our dataset, it still corresponds to a limited number of publications.