dataesr/scientific-paragraphs-categorization huggingface dataset:
Control of relative humidity. RH was controlled with two mass flow controllers [MKS 1179 A -1,000 sccm and 10,000 sccm], using LabView ® , to regulated the flow of nitrogen (to dry) and water vapor (to humidify) at different ratios into a glass chamber. Calculation of optical shutter intensity. MATLAB ® was used for calculating the light intensity from each frame of a video from the optical shutter. The intensity was calculated as the average gray-scale intensity of pixels corresponding to the circular optical window.
Acknowledgements M. M. H. acknowledges support from  Marie Curie IOF   FP7 for project nanoPAD  (Grant Agreement Number  330017 ). P. R. acknowledges support from  MRSEC  ( DMR 14-20570 ). F. G. thanks  German Research Foundation  ( GU 1468/1-1 ) for research support. D. C. C acknowledges support from  Defense Threat Reduction Agency  (award number  HDTRA1-14-C-0037 ). Received: ((will be filled in by the editorial staff)) Revised: ((will be filled in by the editorial staff)) Published online: ((will be filled in by the editorial staff)).
Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades.
To provide a stronger empirical foundation for this debate, here we provide a preliminary checklist of all valid tree species collected to date in Amazonia. We then analyse the list to explore why some Amazonian tree species are more frequent in herbaria and other floristic datasets than others. Does a species' frequency in these datasets reflect its abundance and range size, the date it was first discovered in Amazonia, the spatial pattern of Amazonian exploration, or some combination of those factors? Answering these questions will allow us to discuss the dynamic behind the discovery of new species and consequently the best approach to complete the inventory of the Amazonian tree flora.
The grid cell in which Manaus is located has 24,598 collections (Fig. S1 ). At the poorly collected end of the spectrum, half of all grid cells contain fewer than 200 collections. Eleven grid cells contain no tree collections at all, and together these cover an area of approximately 320,000 km  2. The vast majority of the Amazonian tree species in our preliminary checklist (96%) come from our initial collections database (GBIF, SpeciesLink, INPA, MG, and COAH). Roughly 41% of all Amazonian tree species (4657) have been recorded in ATDN tree plots to date (Appendix S1) and 104 of these were not found in the herbarium databases we examined. Additional species (i. e. , species not in the initial collections dataset or ATDN) were added from checklists, catalogues, and IPNI (385). Correcting all names of Annonaceae with Maas et al.
7% of all tree species in the collections dataset. Estimated population size had a moderate effect on the number of collections per species (Fig. 2 , linear regression R 2 = 22%, p ≪ 0. 001). Only 139 of the 227 hyperdominants, sensu ter Steege et al. 11  , were among the most frequently collected species that accounted for 50% of all collections. Among species with population sizes ranging from 10 5 to 10 7 individuals, the mean number of collections was nearly constant at 14 collections per species. For species with estimated populations between 1 and 10 6 individuals  11  , the mean number of collections was also around 14 (data not shown, see Appendix S1). Among species with population sizes over 10 8 , the mean number of collections rose sharply to 200 collections per species, for a final average of close to 700 for species with populations over 10 9 individuals.
S4 ). A historical perspective on the discovery of the Amazonian tree flora. 1700. Our data suggests that the earliest collections of Amazonian trees were mainly made in the three Guianas (Figs S5 and S6). More than half of the collections (3562) before 1900 came from this area. By area the Guianas are still the best collected countries in Amazonia by far (Table  1 ). Jean Baptiste Christian Fusée Aublet may have been the first serious Figure  3. The number of first-time collections of Amazonian tree species each year between 1707 and 2015. The red line (loess regression) suggests 3 peaks in discovery. The decline after 1980 is partly the effect of decreasing efficiency in the rate of new species per number of collections (see Fig. 6 ) and partly the effect of the lag time between the collection of new species, the description of new species, and the appearance of new species in herbarium databases.
Jørgensen 18 estimated that 50,000 plant collections were made in Ecuador prior to 1900, while ten times that number were made in the 20 th century. Collecting in Ecuador initially focused on the Pacific lowlands; the Amazonian lowlands were explored much later, most notably by a group of botanists associated with the National Herbarium (David Neill, Walter Palacios, Carlos Cerón, Alberto Dik). By 1993 the total number of plant collections in Ecuadorian Amazonia was estimated at 61,000  27. In our dataset the total number of tree collections for Amazonian Ecuador is 16,202 (Appendix S2, Table  S1 ). While this makes the region the fourth-best collected in Amazonia (Table  1 ), our data suggest that much more collecting will be needed to record the full tree flora. With 2366 tree species collected to date, just 35% of the estimated total number of tree species in the Ecuadorian Amazon have been recorded there.
A new catalogue of all plants of Colombia was published in 2015  28. In our dataset the total number of tree collections for Amazonian Colombia is 35,277 (Appendix S2, Table  1 ). With 3511 tree species collected, 35% of the estimated number of tree species have been collected in the Colombian Amazon. Brazil. Brazil is the country with the highest number of collections (278,165) for an average density 6. 8 collections/100 km  2. The first peak of collections occurred very early in the century (Fig. S6F ), when the herbarium of the Museu Paraense Emílio Goeldi em Belém (MG) was created. Later, many Amazonian expeditions organized by the Rio de Janeiro Botanical Garden contributed to the increase of collections thanks to Jacques Huber (1867-1914), João Geraldo Kuhlmann (1882-1958), and especially Adolpho Ducke (1876-1959)  29.
In our dataset the total number of tree collections for Amazonian Brazil is 278,165 (Appendix S2, Table  1 ). With 7696 tree species collected, 61% of the estimated number of tree species have been collected in the Brazilian Amazon. Peru. Twentieth-century botany in Peru was initiated by the work of Augusto Weberbauer and Ignatz Urban, which led to an immediate increase in the number of species  19  (Fig. S6F ). The 'Flora of Peru' project was started in 1922 by Francis Macbride, who added greatly to Peruvian collections himself and attracted many other collectors. Specimens generated from this project provided the Field Museum herbarium (F) with one of the world's best overall collections of Peruvian plants; however, most of those collections have not yet been digitized. Collectors from the Missouri Botanical Garden, especially Alwyn Gentry and Rodolfo Vásquez, also contributed large numbers of Amazonian tree collections in the period 1970-2000.
In 1993 another major step was completed with the 'Catalogue of the flowering plants and gymnosperms of Perú'  34. In our dataset the total number of tree collections for Amazonian Peru is 39,851 (Appendix S2, 1). With 4422 tree species collected, 47% of the estimated number of tree species have been collected in the Peruvian Amazon. Venezuela. Botanical collecting picked up in the 1940s and then increased steeply in the 1970s (Fig. S6G ), yet Huber  20  considers lowland Venezuela to still be severely under-collected. The 'Flora of the Venezuelan Guayana' , initiated by Julian Steyermark in the early 1980s and completed under the guidance of Paul Berry, Kay Yatskievych, and Bruce Holst, has helped the latest increase in the cumulative number of species. In our dataset the total number of tree collections for Amazonian Venezuela is 16,356 (Appendix S2, 1).
With 3189 tree species collected, 49% of the estimated number of tree species has been collected in the Venezuelan Amazon. Bolivia. With just 2. 4 tree collections per 100 km 2 , Bolivia is by far the most under-collected Amazonian country for trees (Table  1 ). Remarkably, for every 1 tree specimen collected per unit area in Bolivia, 31 tree specimens have been collected in French Guiana (the best-collected country). This partly reflects a much later start in botanical exploration. At the beginning of the 20 th century, four independent projects were undertaken but the flora of Bolivia received virtually no study between the 1920s and 1946  35. In our dataset the total number of tree collections for Amazonian Bolivia is 11,721 (Appendix S2, 1). With 2404 tree species collected, 40% of the estimated number of tree species has been collected in the Bolivian Amazon.
1 , Fig. S5 ). This is a well-known bias, which is understood to reduce the value of collection databases for describing patterns of diversity and planning conservation  6, [43] [44] [45]. What we were surprised to find is that the estimated population size of a species in Amazonia is a poor predictor of the number of times it has been collected, and of the date it was first collected in Amazonia (Figs  2  and S3 ). This appears to be the result of how trees have been collected. Collecting started from a limited number of points, where many or perhaps most species, both common and rare, were collected. The fact that many collectors tend to maximize the number of species for a given number of collections  44  causes a strong disconnect between local abundance and local number of collections of tree species (Fig.
2 ). When new areas are visited the same pattern repeats itself. The data of one of the first Amazonian collectors, Aublet, is a good example of the efficiency of collectors. Aublet collected 211 tree species in French Guiana (Appendix S1). These species differ in estimated population size by 5 orders of magnitude and 12 of them have not been encountered in tree inventory plots in French Guiana. Because in most areas common as well as rare species are collected, range size affects the number of collections much more than abundance, since wide-ranging species are likely to be collected in many local inventories. This effect is so strong that after accounting for range size, population size did not add a significant amount of explained variation. That plant collectors have recorded nearly 12,000 species with a collection effort of fewer than 10 collections per 100 km 2 likewise reflects their high efficiency at capturing rare taxa  44.
The third and fourth errors occur at the first stage of data collecting (i. e. , at the individual stem level) and are very difficult to find and correct after data have been aggregated. (1) Taxonomy: This error is independent of data collection. New taxonomic treatments of families and genera will move species currently on our checklist into synonymy. The impact on our list was relatively small in the case of a nomenclatural treatment of all Annonaceae (~3%, see above) but much greater in the full systematic treatment of the genus Guatteria (of the same family)  16. Further study of specimens will also add to the checklist via the formal description of new species, as shown by the several new species added from IPNI but not yet present in the herbarium databases and the 10 new species of Guatteria described in  16.
mobot. org/W3T/ Search/vast. html) and we checked all these new species on their protologue and on herbarium labels for their habit. Because life form can be fluid within a species, it is possible that our checklist includes a small number of species that are primarily shrubs or lianas. We believe the amount of non-tree species in our list is quite small. (3) Species identifications: An unknown but significant number of specimens in our collections dataset are incorrectly identified  55, 56. Incorrect identifications in herbaria have a tendency to snowball, as botanists match unidentified specimens to wrongly identified material. In some cases, duplicates of the same collection may receive different names in different herbaria. In public repository data such errors are difficult to check and may have slightly increased our species list.
(4) Location: Many digitized collections contain location errors, many of which we were able to correct. Errors in location data lead to errors in species richness prediction and tend to overestimate local richness as species are wrongly positioned outside their actual range. With many species these errors add up  8. As we constructed one large list and checked quite substantially for errors in geography, removing data with dubious location, we believe this is not a major problem in our list. (5) Incomplete digitization: Many large herbaria have not digitized their collections and deposited the data in GBIF, and their collections are only partially represented in our checklist. For example, most collections from the major expeditions outside the Guianas before 1900 were deposited in P and M (Paris and München), and records from these two herbaria were not present in GBIF when we downloaded our data.
This bias might potentially explain why our dataset shows that early collecting was focused on the three Guianas (Figs  S5  and S6 ). However, the patterns and species counts reported here for the period before 1900 are likely robust to this potential shortcoming, since most historical collectors made numerous duplicates that were widely distributed among or sold to herbaria and private collectors. Collections from the 20 th century are probably less vulnerable to this type of bias, since they have more complete label data, label data in English, and were collected under more established herbarium practices that make digitization easier and more likely (including the sharing of duplicates with multiple herbaria). We have shown that collecting of trees is not random in Amazonia, consistent with  44.
Specimens need to be identified, inserted in herbaria, databased, and in some cases described as new species, and then the data need to be uploaded to an online aggregator (such as SpeciesLink or GBIF). The latter is done on a regular basis by most large herbaria, but not on short time intervals and not by many smaller herbaria. Many undescribed species may also be found in recent  47  or older 46 collections. As an example, the 10 newly described Guatteria species in ref. 16 were collected for the first time in Amazonia between 1943 and 1991 (Appendix S1). Second, the decline could reflect a shift from general collection and plot work to more phylogenetic research, which targets specific groups and does not lead to broad collections. Third, it may reflect a decrease in collecting expeditions due to increased difficulties in getting permits and funding.
We recommend focusing on data exchange and curation, digitization of specimens, support of taxonomic descriptions and monographs of families, in addition to field collecting that targets specific areas or taxa. 1) Digitize all Amazonian herbarium specimens. It has been estimated that perhaps 50% of all undescribed species are already present in natural history collections  46. If this is true, then several hundred Amazonian tree species have been collected and deposited in herbaria but not yet 'discovered' or described, as was shown in the recent example of Guatteria  16. Discovering those new species in herbaria is a slow process -because huge numbers of specimens remain overlooked by taxonomists. Digitization efforts combined with search engines will quickly inform taxonomists about the specimens of the focal taxon available in the different herbaria, helping the choice of material to study and facilitating the spotting of possible new species that should be studied more carefully.
To resolve these problems, we recommend aggressive digitization of herbarium collections combined with data curation by specialists, such as proposed in Reflora (http://floradobrasil. jbrj. gov. br/). Naturalis's recent advances at the Naturalis Biodiversity Center in the Netherlands may serve as a model  [60] [61] [62]. With a grant of €13 million, and over a period of two and a half years, 4. 4 million herbarium specimens (and 4. 1 million other specimens) were digitized at an average price of €1. 52 per specimen  61. In three automated 'herbarium digistreets' 22,000-24,000 herbarium sheets were imaged per day, with a record of 35,000 on a single day. Label data was then added into a database using the digital images. The digital material is available through Naturalis' Bioportal (http://bioportal.
g. IPNI  69. Wen et al. 62  provide an outline for the workflow of e-monographs. It would be an asset for the Amazonian tree flora if 'Flora of Ecuador' , 'Flora of the Guianas' , 'Flora Neotropica, ' and similar floras were online with electronic keys, links to collections, and image databases. Such floras democratize floristic and taxonomic information and are updatable 'on the fly'. It should be noted that, while e-floras and e-monographs will speed access to floristic and systematic information, it will not make taxonomic work much faster (see point 2). We have started to amass all information known on Amazonian tree species. Based on the checklist in this paper, we created a platform (http://amazoniantreeflora. myspecies. info) where descriptions, images, DNA barcodes (GenBank, BOLD, new sequences) can be added by a growing and open community of Amazonian tree specialists.
Methods Data sets. All plant collection records for the nine Amazonian countries available at GBIF (http://www. gbif. org; 1. 5 million records) and SpeciesLink (http://splink. cria. org. br/; 300,000 records) were retrieved in May 2014. We complemented these two large datasets with all collection records from the 2015 institutional databases of three primarily Amazonian herbaria (INPA, MG, and COAH; 170,000; 180,000, and 28,000 records respectively). We also included a previously compiled dataset of plant collections in all herbaria in Guyana, Suriname, and French Guiana, containing data from these three countries; at the time of the study these records had not been added to GBIF  22  (190,000 records). All families and genera that do not contain any tree species were removed. A tree was defined as a species with a woody trunk of at least 10 cm diameter at breast height (DBH, where breast height = 1.
30 m). Tree-like species that may have a trunk but that are not always taken into account when establishing tree plots (e. g. , tree ferns, Montrichardia, Phenakospermum, bamboos, Zamia) were removed. Hereafter we refer to this first database as the collections dataset. In order to determine which names in the collections dataset are considered taxonomically valid tree species, we independently produced a list of all known tree species (including synonyms) for South America, based on three literature sources  11, 53, 54. We checked the spelling and synonymy of all ~56,000 names gathered in this preliminary tree species list with the Taxonomic Name Resolution Service (http://tnrs. iplantcollaborative. org/TNRSapp. html), the Plant List (http://www. theplantlist. org/), and the Brazilian flora checklist (http://reflora.
jbrj. gov. br), to achieve a standard taxonomy (e. g. , APG3 plant families) and yield a list of all South American trees synchronized with the ATDN (http://atdn. myspecies. info/) plot database  11. This required the merging of Crepidospermum and Tetragastris into Protium  50. Hereafter we refer to this second database as the South American trees reference list, or reference list. All names in the collections dataset were compared with the corrected names in the South American trees reference list. Species in the collections dataset that matched a species in the reference list were considered a tree species with a valid name or a proper synonym and added to a third database, which is the preliminary checklist of Amazonian trees we present in Appendix S1 (hereafter the checklist). Species in the collections dataset that did not match any species in the reference list were checked against TNRS and then re-matched with the reference list.
After this automated procedure, remaining problems were assessed one by one and solved by literature search and with the Plantminer (http://www. plantminer. com/), which mines various sources through the Plant List. If after inspection some of the unmatched tree species names in the collections dataset were indeed correct, they were added to the reference list and to the checklist. All doubtful names (unresolved, illegitimate, invalid) were checked against the original sources where possible and added to the checklist if they had been published correctly and removed if not. Annonaceae names were standardized to the most recent index to this family  15  and Guatteria was standardized to the most recent monograph of the genus  16. In order to keep only the Amazonian collections in our collections dataset, we checked all coordinates, corrected them where possible, and removed doubtful coordinates.
We accepted as Amazonian all collections located inside Amazonia 11 , as well as all collections without coordinates, but arguably made inside Amazonia based on country (Guyana, Suriname, French Guiana, all collections) or departments that are fully or mainly Amazonian (e. g. Pará, Rondônia, Roraima and Amapá, in Brazil; Amazonas, in all countries). At this point, the new collections dataset consisted of all Amazonian herbarium records identified to a valid species name. However, because a given herbarium record may occur in GBIF, SpeciesLink, and our herbarium databases, our collections dataset contained a large number of duplicate records. To select unique collections we pulled out all unique combinations of species, collection number, year, country, and province. While this may have omitted some collections that lack a collection number, we believe this number is relatively small.
Acknowledgements We thank thousands of naturalists, botanists, ecologists and all others who collected thousands of collections of trees and the hundreds of herbaria that made their data available through GBIF and SpeciesLink. Special thanks to  Mike Hopkins  who made available the latest version of the collection database of INPA. HtS and RS are supported by grant  407232/2013-3 -PVE -MEC/MCTI/CAPES/CNPq/ FAPs; AA is supported by grants from the  Swedish Research Council , the  European Research Council  under the European Union's  Seventh Framework Programme  (FP/2007-2013,  ERC  Grant Agreement n. 331024), and a  Wallenberg Academy Fellowship. We thank  Miles Silman  and one anonymous reviewer for very constructive comments that helped to improve the manuscript.