cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.a2ccus
title: Occurrence Download

description: A dataset containing 37291 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Metidiocerus dzhungaricus (Mitjaev, 2014), Kybos copula (DeLong, 1931), Kybos coronatus (Hamilton, 1972), Kybos empusa (Hamilton, 1972), Kybos rossi (Hamilton, 1972), Populicerus laminatus (Flor, 1861), Agrilus pseudocyaneus Kiesenwetter, 1857, Agrilus tschitscherini Semenov, 1895, Agrilus horni Kerremans, 1900, Nematus papillosus (Retzius, 1783), Titaeosporina tremulae (Lib.) Luijk, Pilophorus neoclavatus Schuh & Schwartz, 1988, Speranza occiduaria (Packard, 1874), Deraeocoris borealis (Van Duzee, 1920), Hydriomena perfracta Swett, 1910, Platarctia parthenos Harris, 1850, Anathix puta Grote & Robinson, 1868, Brachylomia algens Grote, 1878, Ufeus satyricus Grote, 1873, Clostera strigosa Grote, 1882, Notodonta torva (Hübner, 1803), Odontosia elegans Strecker, 1885, Meroptera abditiva Heinrich, 1956, Apotomis infida (Heinrich, 1926), Wockia asperipunctella (Bruand, 1850), Catocala briseis W.H.Edwards, 1864, Furcula modesta Hudson, 1891, Phyllonorycter apparella (Herrich-Schäffer, 1855), Framinghamia helvalis Walker, 1859, Gonioctena americana (C.Schaeffer, 1924), Acronicta noctivaga Grote, 1864, Dicerca callosa Casey, 1909, Gypsonoma adjuncta Heinrich, 1924, Operophtera bruceata (Hulst, 1886), Archips fervidana (Clemens, 1860), Poecilonota ferrea (Melsheimer, 1845), Acleris robinsoniana (Forbes, 1923), Glena cribrataria (Guenée), Lobophora montanata Packard, 1874, Protitame hulstiaria (Taylor, 1906), Egira dolosa Grote, 1880, Cerura scitiscripta Walker, 1865, Acleris maccana (Treitschke, 1835), Olethreutes deprecatoria Heinrich, 1926, Acronicta quadrata Grote, 1874, Palonica tremulata Ball, Macropsis bifasciata (Van Duzee, 1889), Erythroneura rosa Robinson, 1924, Populicerus lunaris (Ball, 1902), Kybos incidus (DeLong, 1931))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 37291 records from 271 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015670-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.48502/6n7k-cn12
title: Functional structure of an arid steppe plant community

description: Abstract Questions (1) How do community‐weighted mean (CWM) trait values of 23 functional traits measured on 34 plant species vary along a gradient of aridity under grazed and ungrazed conditions in an arid steppe? (2) How does variation in our CWM trait values differ from those of more mesic grasslands? Location Eastern Morocco. Methods We measured relative abundance and functional traits along a short aridity gradient over two consecutive years at five heavily grazed sites, each with an exclosure preventing grazing. We analysed the relationship between aridity, grazing, and the expression of CWM trait values using ordination methods and a fourth‐corner analysis. Results Unconstrained and constrained ordinations identified three distinct suites of temporally consistent functional traits that co‐varied with aridity and grazing, and the fourth‐corner analysis identified a number of significant but weak trait–environment associations. Grazing selected for short, fast‐growing annual species with high SLA, high pastoral value and low seed mass, while aridity selected for species possessing succulent leaves with high δ13C leaf content, spines, low LDMC and short stature, although the relative importance of precipitation and grazing changed between years. Conclusions Although distinct from more mesic grasslands, our study sites exhibited patterns of trait correlations that were similar to the worldwide leaf economics spectrum. These correlation patterns represented three groups that were reminiscent of Grime’s C‐S‐R model. Direct ordinations supported this interpretation. Temporal variation in our results was due in part to precipitation fluctuations. Our results also indicated selection for a grazing avoidance strategy under heavy grazing. Integrating plant functional traits in conservation and management of arid ecosystems represents a novel and challenging task to ensure more sustainable use of these lands.
DOI: 10.48502/8bb5-pk85
title: Kakila database of marine mammal observation data around the French archipelago of Guadeloupe in the AGOA sanctuary - French Antilles

description: Database collected as part of the Lorraine Coché master's 2 internship "Inventory and structuring of marine mammal observation data around Guadeloupe" in 2020 (Master Tropical marine ecosystems at the University of the Antilles). This database centralizes and harmonizes the data collected by the team of the Agoa Sanctuary (Aire Marine Protégée), the OMMAG (Observatory of Marine Mammals of the Guadeloupe Archipelago), the NPO BREACH, and whale-watching companies Cétacés Caraïbes, Guadeloupe Evasion Découverte et Aventures Marines.
DOI: 10.48502/cg6n-1103
title: Kakila database of marine mammal observation data around the French archipelago of Guadeloupe in the AGOA sanctuary - French Antilles

description: Database collected as part of the Lorraine Coché master's 2 internship "Inventory and structuring of marine mammal observation data around Guadeloupe" in 2020 (Master Tropical marine ecosystems at the University of the Antilles). This database centralizes and harmonizes the data collected by the team of the Agoa Sanctuary (Aire Marine Protégée), the OMMAG (Observatory of Marine Mammals of the Guadeloupe Archipelago), the NPO BREACH, and whale-watching companies Cétacés Caraïbes, Guadeloupe Evasion Découverte et Aventures Marines.
DOI: 10.48502/cm04-5040
title: Abundance and biological traits of fish sampled by electrofishing (except specific abundance indices) on the River Oir since 1988 (France).

description: Since 1988, an annual campaign is conducted to quantify by electrofishing the abundance of fishes in the Oir basin. Originally, the main target species were salmon and trout. Beginning in 2000, eels were monitored in the same way as salmonids. The inventory of the entire fish community has been carried out on a network of seven sites. It is usually done in September and october. Two sites are also monitored in May for all species The data consist of 1738 electrofishing operations and 138765 fish caught. Biological traits measured on the fish sampled are sex, maturity status, length, weight and age. Some of the salmon, trout and eels are identified individually with a pit tag. Scale sampling is carried out on a sample to estimate the age of the fish. The survey is carried out under the Research Observatory on Diadromous Fish in Coastal Streams (ERO DiaPFC) program. The data are stored in the database of the ERO. They are used to develop predictive models and tools for providing scientific advice to improve the management of this heritage species.
DOI: 10.48502/g9et-qa61
title: Ex de données PAMPA

description: Le jeu de données correspond à des données de vidéo sous-marine collectées en Nouvelle-Calédonie. Il a été utilisé dans le projet PAMPA (Indicateurs de la Performance d’Aires Marines Protégées pour la gestion des écosystèmes côtiers, des ressources et de leurs usAges). Rapport scientifique final du projet PAMPA. PAMPA/WP1/Coord/5. 58 p. Synthèse et Annexes. http://archimer.ifremer.fr/doc/00385/49601/ Le rapport qui contient les tableaux de bord pour l’ensemble des données est: Wantiez Laurent, Dominique Pelletier, Emmanuel Coutures, Elodie Gamp, Emeline Rolland, Delphine Mallet, Yves Reecht, Pascal Dumas, Isabelle Jollit, Laurent Vigliola. 2011. Rapport du site Nouvelle-Calédonie. Document PAMPA/WP1/NC/1. Version du 26 mai 2011. 92 p. http://archimer.ifremer.fr/doc/00351/46171/
DOI: 10.48502/hssh-5194
title: Assessing the importance of field margins for bat species and communities in intensive agricultural landscapes - Data

description: Landscape simplification and degradation through agricultural intensification is widely recognized as a main driver of biodiversity loss. In intensively used agricultural landscapes, patches of semi-natural habitats and particularly connections between them are of high importance for many taxa. Vegetated connections like hedgerows are especially important for foraging and commuting of mobile taxa such as bats. However, the interest of another treeless linear habitat – herbaceous field margins – remains unstudied for insectivorous bats. Field margins are nevertheless known as an important habitat for other taxa, including bat prey. Here we assessed the importance of field margins for bats compared to other landscape variables. We measured bat activity based on a repeated passive acoustic monitoring during 17 complete nights in summer on 112 study sites in an intensively used agricultural landscape. Each night, we sampled bat species activity and community metrics (i.e. species richness and community habitat specialization index) at different distances to field margins, and along a gradient of relative density of field margins. To compare field margin effects with other landscape variables, the sampled sites were selected by keeping a large variability in these other variables (land-cover Shannon diversity index, forests, hedgerows, water bodies, main roads, urban areas, grasslands, number of crops and rapeseed percentage). Only Myotis sp. were affected by herbaceous field margins. Specifically, the Myotis group activity decreased with the distance to herbaceous field margins (i.e. towards field crop cores), and positively correlated with relative density of herbaceous field margins, for which the effect size was comparable to other landscape variables. However, other landscape variables such as the proportion of and the distance to forests, the relative density of and the distance to hedgerows or land-cover Shannon diversity index, affected species richness, community specialization index, and bat activity of species from open, edge and narrow-space foragers, including the Myotis group as well. Our results highlight that herbaceous field margins have a positive effect on the activity of narrow-space bat foragers as Myotis species, but do not replace other landscape variables that drive the activity of the whole community.
DOI: 10.48502/knrh-2r52
title: Data associated with the paper "Contrasting effects of grasses and trees on microbial N-cycling in an African humid savanna"

description: General description of the data set This data set corresponds to a soil sampling in Lamto savanna (Ivory Coast) and to the results of various physico-chemical and microbiological analyses. The general objective was to test the effect of various vegetation features (presence of different perennial grass species, different tree species, a tree clump), interactions between these features (i.e. between grasses and trees), and termite mounds and termitaria on nitrification, denitrification, the microbial communities responsible for these two processes, and the abundances of bacteria, archaea and fungi.
DOI: 10.48502/rtsn-m167
title: Sauvages de ma Rue
DOI: 10.48502/t4cd-0c46
title: Water Interdisciplinary Biology and Ecology database “WIBE”: Towards FAIR, open and interdisciplinary data on biomarkers to monitor the ecological status of coastal waters.
DOI: 10.48502/v7kb-8m05
title: Vigie-Chiro

description: Population monitoring of bats, recorded by ultrasound. Standardized data are collected by naturalists through a Vigie-Chiro participatory science program.
DOI: 10.48502/wk0d-gm05
title: Relevés d'invertébrés sur la Nonette à Gouvieux par la méthode IBG-DCE

description: This dataset is collected as part of the process of monitoring river quality for the implementation of the Water framework directive. It describes the number of invertebrates observed in July 2010 at the station of river Nonette in Gouvieux (Picardie).
DOI: 10.48502/xcah-3w89
title: African rice population genomics dataset or title of the article : "The Rise and Fall of African Rice Cultivation Revealed by Analysis of 246 New Genomes"

description: African rice (Oryza glaberrima) was domesticated independently from Asian rice. The geographical origin of its domestication remains elusive. Using 246 new whole-genome sequences, we inferred the cradle of its domestication to be in the Inner Niger Delta. Domestication was preceded by a sharp decline of most wild populations that started more than 10,000 years ago. The wild population collapse occurred during the drying of the Sahara. This finding supports the hypothesis that depletion of wild resources in the Sahara triggered African rice domestication. African rice cultivation strongly expanded 2,000 years ago. During the last 5 centuries, a sharp decline of its cultivation coincided with the introduction of Asian rice in Africa. A gene, PROG1, associated with an erect plant architecture phenotype, showed convergent selection in two rice cultivated species, Oryza glaberrima from Africa and Oryza sativa from Asia. In contrast, a shattering gene, SH5, showed selection signature during African rice domestication, but not during Asian rice domestication. Overall, our genomic data revealed a complex history of African rice domestication influenced by important climatic changes in the Saharan area, by the expansion of African agricultural society, and by recent replacement by another domesticated species.https://doi.org/10.1016/j.cub.2018.05.066
DOI: 10.15468/dl.wewkmr
title: Occurrence Download

description: A dataset containing 188 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Material sample, Occurrence evidence)",
 "Continent is Asia",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Channa micropeltes (Cuvier, 1831)"
 ]
}

 The dataset includes 188 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015673-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dcv323
title: Occurrence Download

description: A dataset containing 9517096 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Isodontia nigella (F.Smith, 1856), Mimeusemia vilemani Hampson, 1911, Limenitis phylaca (Bates, 1866), Historis odius (Fabricius, 1775), Tangara inornata (Gould, 1855), Sporophila corvina (P.L.Sclater, 1860), Saltator maximus (P.L.S.Müller, 1776), Ramphocelus sanguinolentus (R.Lesson, 1831), Brotogeris jugularis (Statius Muller, 1776), Chrysonotomyia lapierrei Hansson, 2004, Chrysonotomyia phenacapsia (Yoshimoto, 1972), Chrysonotomyia auripunctata (Ashmead, 1894), Micronycteris megalotis (Gray, 1842), Platyrrhinus helleri helleri, Setophaga pinus (Linnaeus, 1766), Helmitheros vermivorum (J.F.Gmelin, 1789), Historis acheronta (Fabricius, 1775), Tigridia acesta (Linnaeus, 1758), Phylloderma stenops Peters, 1865, Sturnira koopmanhilli McCarthy, Albuja V. & Alberico, 2006, Choeroniscus godmani (Thomas, 1903), Platyrrhinus nitelinea Velazco & Gardner, 2009, Platyrrhinus dorsalis (Thomas, 1900), Rhinophylla alethina Handley, 1966, Glossophaga morenoi Martínez & Villa-R., 1938, Seiurus aurocapilla (Linnaeus, 1766), Carollia subrufa (Hahn, 1905), Setophaga pensylvanica (Linnaeus, 1766), Geothlypis formosa (A.Wilson, 1811), Ramphocelus passerinii Bonaparte, 1831, Glossophaga commissarisi Gardner, 1962, Setophaga castanea (A.Wilson, 1810), Noctilio albiventris Desmarest, 1818, Arremon assimilis (Boissonneau, 1840), Penelope barbata Chapman, 1921, Artibeus rosenbergi (Thomas, 1897), Platyrrhinus albericoi Velazco, 2005, Platyrrhinus dorsalis chocoensis Alberico & Velasco, 1991, Sturnira bidens (Thomas, 1915), Sturnira bogotensis Shamel, 1927, Iridosornis analis (Tschudi, 1844), Myiarchus cephalotes Taczanowski, 1880, Pyrrhura hoematotis Souance, 1857, Rupicola peruvianus (Latham, 1790), Platyrrhinus infuscus (Peters, 1880), Sphenopsis frontalis (Tschudi, 1844), Artibeus bogotensis K.Andersen, 1906, Elaenia albiceps (Orbigny & Lafresnaye, 1837), Chlorospingus parvirostris Chapman, 1901, Sturnira erythromos (Tschudi, 1844))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 9517096 records from 987 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015659-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.x5dhmg
title: Occurrence Download

description: A dataset containing 3507 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Opuntia monacantha Haw."
 ]
}

 The dataset includes 3507 records from 159 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015669-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14288361
title: Data used in SeuratIntegrate paper

description: This repository stores the data used to generate hepatocellular carcinoma analyses in the paper presenting SeuratIntegrate. It contains the scripts to reproduce the figure 1 presented in the article.To be able to fully reproduce the results from the paper, one shoud:



download all the files

install R 4.3.3, with correspondig base R packages (stats, graphics, grDevices, utils, datasets, methods and base)

install R packages listed in the file sessionInfo.out

install the provided version of SeuratIntegrate. In an R session, run:


remotes::install_local("path/to/SeuratIntegrate_0.4.0.tar.gz")



install (mini)conda (we used version 23.11.0) if not already

install conda environments:


conda create -n SeuratIntegrate_bbknn –file SeuratIntegrate_bbknn_package-list.txt
conda create -n SeuratIntegrate_scanorama –file SeuratIntegrate_scanorama_package-list.txt



make them usable by SeuratIntegrate by opening an R session and:


library(SeuratIntegrate)

UpdateEnvCache("bbknn", conda.env = "SeuratIntegrate_bbknn", conda.env.is.path = FALSE)
UpdateEnvCache("scanorama", conda.env = "SeuratIntegrate_scanorama", conda.env.is.path = FALSE)

 

Once done, the file integrate.R should produce reproducible results. Note that lines 3 to 6 from integrate.R should be adapted to the user's setup.
DOI: 10.15468/dl.tuw3bj
title: Occurrence Download

description: A dataset containing 842 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Pristidactylus Fitzinger, 1843"
 ]
}

 The dataset includes 842 records from 39 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015677-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mjmv95
title: Occurrence Download

description: A dataset containing 3299 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Tessaratoma papillosa, Tessaratoma papillosa (Drury, 1770), Tessaratoma papillosa, Tessaratoma papillosa (Drury, 1770), Tessaratoma papillosa (Drury, 1770), Tessaratoma papillosa, Tessaratoma papillosa (Drury, 1770), Tessaratoma papillosa (Drury, 1770), Anastatus (Anastatus) shichengensis Sheng and Wang 1997, Anastatus shichengensis Sheng & Wang, 1997, Anastatus formosanus Crawford, 1913, Anastatus (Anastatus) formosanus Crawford 1913, Anastatus (Anastatus) fulloi Sheng and Wang 1997, Anastatus (Anastatus) dexingensis Sheng and Wang 1997, Anastatus fulloi Sheng & Wang, 1997, Anastatus dexingensis Sheng & Wang, 1997, Anastatus shichengensis Sheng & Wang 1997, Anastatus (Anastatus) japonicus Ashmead 1904, Anastatus japonicus Ashmead, 1904)",
 "BasisOfRecord is one of (Specimen, Human Observation, Observation, Living Specimen, Machine Observation, Literature Occurrence)",
 "Geometry POLYGON((-180 -90,180 -90,180 90,-180 90,-180 -90))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3299 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015674-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.14288360
title: Data used in SeuratIntegrate paper

description: This repository gathers the data and code used to generate hepatocellular carcinoma analyses in the paper presenting SeuratIntegrate. It contains the scripts to reproduce the figures presented in the article. Some figures are also available as pdf files.To be able to fully reproduce the results from the paper, one shoud:



download all the files

install R 4.3.3, with correspondig base R packages (stats, graphics, grDevices, utils, datasets, methods and base)

install R packages listed in the file sessionInfo.txt

install the provided version of SeuratIntegrate. In an R session, run:


remotes::install_local("path/to/SeuratIntegrate_0.4.1.tar.gz")



install (mini)conda if necessary (we used miniconda version 23.11.0)

install the conda environments (if it fails with the *package-list.yml files, use the *package-list-from-history.yml files instead):


conda env create --file SeuratIntegrate_bbknn_package-list.yml
conda env create --file SeuratIntegrate_scanorama_package-list.ymlconda env create --file SeuratIntegrate_scvi-tools_package-list.ymlconda env create --file SeuratIntegrate_trvae_package-list.yml



open an R session to make the conda environments usable by SeuratIntegrate:


library(SeuratIntegrate)

UpdateEnvCache("bbknn", conda.env = "SeuratIntegrate_bbknn", conda.env.is.path = FALSE)
UpdateEnvCache("scanorama", conda.env = "SeuratIntegrate_scanorama", conda.env.is.path = FALSE)UpdateEnvCache("scvi", conda.env = "SeuratIntegrate_scvi-tools", conda.env.is.path = FALSE)UpdateEnvCache("trvae", conda.env = "SeuratIntegrate_trvae", conda.env.is.path = FALSE)

 

Once done, running the code in integrate.R should produce reproducible results. Note that lines 3 to 6 from integrate.R should be adapted to the user's setup.integrate.R is subdivided into six main parts:



Preparation: lines 1-56

Preprocessing: lines 58-74

Integration: lines 76-121

Processing of integration outputs: lines 126-267

Scoring of integration outputs: lines 269-353

Plotting: lines 380-507


Intermediate SeuratObjects have been saved between steps 3 and 4 and 5 and 6 (liver10k_integrated_object.RDS and liver10k_integrated_scored_object.RDS respectively). It is possible to start with these intermediate SeuratObjects to avoid the preceding steps, given that the Preparation step is always run before.