cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.c7d7rp
title: Occurrence Download

description: A dataset containing 25904258 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Alcedo atthis (Linnaeus, 1758), Sylvia communis Latham, 1787, Ficedula albicollis (Pallas, 1811), Jynx torquilla Linnaeus, 1758, Sylvia curruca (Linnaeus, 1758), Scolopax rusticola Linnaeus, 1758, Larus michahellis J.F.Naumann, 1840, Acrocephalus arundinaceus (Temminck & Schlegel, 1847), Ardea cinerea Linnaeus, 1758, Bufotes viridis (Laurenti, 1768), Barbastella barbastellus (Schreber, 1774), Passer domesticus (Linnaeus, 1758), Cerambyx cerdo Linnaeus, 1758, Passer montanus (Linnaeus, 1758), Pelobates fuscus (Laurenti, 1768), Spatula clypeata (Linnaeus, 1758), Saxicola rubetra (Linnaeus, 1758), Locustella naevia (Boddaert, 1783), Locustella fluviatilis (Wolf, 1810), Locustella luscinioides (Savi, 1824), Milvus milvus (Linnaeus, 1758), Caprimulgus europaeus Linnaeus, 1758, Vanellus vanellus (Linnaeus, 1758), Emberiza calandra Aerc Tac, 2003, Cinclus cinclus (Linnaeus, 1758), Oriolus oriolus (Linnaeus, 1758), Porzana porzana (Linnaeus, 1766), Porzana parva (Scopoli, 1769), Apus apus (Linnaeus, 1758), Felis silvestris Schreber, 1777, Rana dalmatina Bonaparte, 1840, Oenanthe oenanthe (Linnaeus, 1758), Ophiogomphus cecilia (Fourcroy, 1785), Anas crecca Linnaeus, 1758, Bombina variegata (Linnaeus, 1758), Emberiza citrinella Linnaeus, 1758, Myotis mystacinus (Kuhl, 1817), Gallinago gallinago (Linnaeus, 1758), Spatula querquedula (Linnaeus, 1758), Muscicapa striata (Pallas, 1764), Pipistrellus pipistrellus (Schreber, 1774), Pipistrellus kuhlii (Kuhl, 1817), Emberiza schoeniclus (Linnaeus, 1758), Gallinula chloropus (Linnaeus, 1758), Coturnix coturnix (Linnaeus, 1758), Parus montanus Conrad von Baldenstein, 1827, Crex crex (Linnaeus, 1758), Myotis brandtii (Eversmann, 1845), Hyla arborea (Linnaeus, 1758), Ficedula albicollis (Temminck, 1815))",
 "Year is not null",
 "Year is one of (2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021, 2022, 2023)",
 "HasCoordinate is TRUE",
 "DecimalLatitude is greater than or equal to 44.95782311925129",
 "DecimalLatitude is less than or equal to 58.30331634439415",
 "DecimalLongitude is greater than or equal to -10.001896207643075",
 "DecimalLongitude is less than or equal to 30.31691447027875",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 25904258 records from 7781 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013859-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yeps5e
title: Occurrence Download

description: A dataset containing 307 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Aquilaria malaccensis Lam."
 ]
}

 The dataset includes 307 records from 27 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013855-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.15479736
title: Harmonised methylation array matrix related to the article Fluctuating DNA Methylation Tracks Cancer Evolution at Clinical Scale

description: Contains "QC_2204_ssNob.tsv.zip", a zipped tsv file containing the harmonised, filtered and processed methylation matrix used in the manuscript "Fluctuating DNA Methylation Tracks Cancer Evolution at Clinical Scale", Gabbutt et al, 2025. Also contains "QC_2204_metadata.csv", a csv file containing the sample metadata.
DOI: 10.5281/zenodo.15479737
title: Harmonised methylation array matrix related to the article Fluctuating DNA Methylation Tracks Cancer Evolution at Clinical Scale

description: Contains "QC_2204_ssNob.tsv.zip", a zipped tsv file containing the harmonised, filtered and processed methylation matrix used in the manuscript "Fluctuating DNA Methylation Tracks Cancer Evolution at Clinical Scale", Gabbutt et al, 2025. Also contains "QC_2204_metadata.csv", a csv file containing the sample metadata.
DOI: 10.5281/zenodo.14812414
title: tACS 10 Hz promotes oligodendrogenesis and reduces g-ratio after cuprizone-induced demyelination

description: Results of the novel object location task.
DOI: 10.5281/zenodo.16846017
title: tACS 10 Hz promotes oligodendrogenesis and reduces g-ratio after cuprizone-induced demyelination
DOI: 10.15468/dl.xre6rh
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Galaxias aequipinnis)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 27 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025387-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gsb4bx
title: Occurrence Download

description: A dataset containing 3799 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Eriococcus coriaceus Maskell, 1893, Megastigmus tasmaniensis Girault, 1913, Terobiella flavifrons Ashmead, 1900, Aprostocetus eucalypti (Girault, 1929), Amerostenus varidentatus Girault, 1929, Moranila comperei (Ashmead, 1904), Cirrospilus flavitibia (Girault, 1929), Ditropinotella compressiventris Girault, 1915, Schedotrioza eucalypti (Froggatt, 1901), Lasiopsylla bullata Froggatt, 1900, Glycaspis particeps Moore, 1970, Blepharocosta minima Taylor, 1992, Glycaspis cameloides Moore, 1985, Acantholybas kirkaldyi Bergroth, 1909, Schedotrioza marginata Taylor, 1987, Glycaspis fuliginis Moore, 1970, Cardiaspina jerramungae Taylor, 1992, Glycaspis lacustris Moore, 1970, Anoeconeossa assimilis (Froggatt, 1900), Zanda funerea xanthanota (Gould, 1838), Doratifera oxleyi (Newman, 1855), Ardozyga mesochra (Lower, 1894), Glycaspis rivalis Moore, 1961, Glycaspis permista Moore, 1961, Blastopsylla moorei Taylor, 1985, Glycaspis mellialata Moore, 1961, Blastopsylla brunnea Taylor, 1985, Glycaspis pilata Moore, 1961, Cardiaspina brunnea (Froggatt, 1923), Glycaspis kurrajongensis Moore, 1961, Anoeconeossa pectinata Taylor, 1987, Euselasia melaphaea (Hübner, 1816), Cardiaspina vittaformis (Froggatt, 1923), Dendrophthoe vitellina (F.Muell.) Tiegh., Acrocercops laciniella (Meyrick, 1880), Menurella scotodes (Hoarean Nieukerken, 2013) van Nieukerken et al., 2016, Glycaspis seriata Moore, 1961, Glycaspis hirsuta (Froggatt, 1903), Glycaspis cyta Moore, 1961, Glycaspis pervagata Moore, 1970, Platyobria adustalata Taylor, 1987, Glycaspis whitei Moore, 1970, Dasypsylla brunnea Froggatt, 1900, Lasiopsylla rotundipennis Froggatt, 1900, Cardiaspina albicollaris Taylor, 1962, Glycaspis temenicola Moore, 1970, Glycaspis dreptodria Moore, 1970, Glycaspis longaeva Moore, 1970, Zelotypia stacyi Scott, 1869, Aroa melanoleuca Hampson, 1905)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 3799 records from 61 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009674-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7291/d1nx0t
title: Data from: Leaf litter arthropod responses to tropical forest restoration

description: Soil and litter arthropods represent a large proportion of tropical
 biodiversity and perform important ecosystem functions, but little is
 known about the efficacy of different tropical forest restoration
 strategies in facilitating their recovery in degraded habitats. We sampled
 arthropods in four 7‐ to 8‐year‐old restoration treatments and in nearby
 reference forests. Sampling was conducted during the wet and dry seasons
 using extractions from litter and pitfall samples. Restoration treatments
 were replicated in 50 × 50‐m plots in four former
 pasture sites in southern Costa Rica: plantation – trees
 planted throughout the plot; applied
 nucleation/islands – trees planted in patches of different sizes;
 and natural regeneration – no tree planting. Arthropod
 abundance, measures of richness and diversity, and a number of functional
 groups were greater in the island treatment than in natural regeneration
 or plantation treatments and, in many cases, were similar to reference
 forest. Litter and pitfall morphospecies and functional group composition
 in all three restoration treatments were significantly different than
 reference sites, but island and plantation treatments showed more recovery
 than natural regeneration. Abundance and functional group diversity showed
 a much greater degree of recovery than community
 composition. Synthesis and applications: The less
 resource‐intensive restoration strategy of planting tree islands was more
 effective than tree plantations in restoring arthropod abundance,
 richness, and functional diversity. None of the restoration strategies,
 however, resulted in similar community composition as reference forest
 after 8 years of recovery, highlighting the slow rate of recovery
 of arthropod communities after disturbance, and underscoring the
 importance of conservation of remnant forests in fragmented landscapes.
description: We sampled arthropods in four 7-8-yr old restoration treatments
 and in nearby reference forests (forest). Sampling was conducted during
 the wet and dry seasons of 2012 using extractions from litter and pitfall
 samples. Restoration treatments were replicated in 50 ◊ 50 m plots in four
 former pasture sites in southern Costa Rica: plantation - trees planted
 throughout the plot; islands ñ trees planted in patches of different
 sizes; and natural regeneration - no tree planting.
DOI: 10.7291/d1j679
title: Data from: Tropical forest restoration enriches vascular epiphyte recovery

description: Vascular epiphytes constitute a large proportion of tropical forest plant
 biodiversity, but are among the slowest plants to recolonize secondary
 forests. We asked whether tree planting for ecological restoration
 accelerates epiphyte community recovery. Does the spatial configuration of
 tree planting matter? What landscape contexts are most suitable for
 epiphyte restoration? Location: Restored pastures in premontane
 Coto Brus County, Puntarenas, Costa Rica.
description: We surveyed vascular epiphyte species growing on the lower trunks
 of 1083 trees in thirteen experimental restoration sites in southern Costa
 Rica. Each site contained three 0.25-ha treatment plots:
 natural regeneration, trees planted in patches or "islands", and
 tree plantations. Sites spanned elevational (1100-1430 m)
 and deforestation gradients (4-94% forest cover within a 100-m radius
 around each site).
DOI: 10.7291/d1dd40
title: Surrounding forest cover dataset 2005

description: Forest cover within 100 and 500 m radii from the center of each
 experimental plot was hand digitized from ortho-rectified 2005 aerial
 photographs and comprehensively ground checked. Forest cover spans a range
 from &lt;1% to 66% within a 100-m radius surrounding the plots and
 from 9% to 89% in a 500-m radius.
description: Used in varous publications. Research plots described in Holl, K.
 D., J. L. Reid, R. J. Cole, F. Oviedo-Brenes, J. A. Rosales, and R. A.
 Zahawi. 2020. Applied nucleation facilitates tropical forest recovery:
 Lessons learned from a 15-year study. Journal of Applied Ecology
 57:2316-2328.
description: See readme file for more details.
DOI: 10.7291/d18q3g
title: Data from: Seed dispersal limitations shift over time in tropical forest restoration

description: Past studies have shown that tropical forest regeneration on degraded
 farmlands is initially limited by lack of seed dispersal, but few studies
 have tracked changes in abundance and composition of seed rain past the
 first few years after land abandonment. We measured seed rain for 12
 months in 10 6–9‐year‐old restoration sites and five mature, reference
 forests in southern Costa Rica in order to learn (1) if seed rain
 limitation persists past the first few years of regeneration; (2) how
 restoration treatments influence seed community structure and composition;
 and (3) whether seed rain limitation is contingent on landscape context.
 Each restoration site contained three 0.25‐ha treatment plots: (1) a
 naturally regenerating control, (2) tree islands, and (3) a mixed‐species
 tree plantation. Sites spanned a deforestation gradient with 9–89% forest
 area within 500 m around the treatment plots. Contrary to previous
 studies, we found that tree seeds were abundant and ubiquitous across all
 treatment plots (585.1 ± 142.0 seeds·m−2·yr−1 [mean ± SE]),
 indicating that lack of seed rain ceased to limit forest regeneration
 within the first decade of recovery. Pioneer trees and shrubs comprised
 the vast majority of seeds, but compositional differences between
 restoration sites and reference forests were driven by rarer, large‐seeded
 species. Large, animal‐dispersed tree seeds were more abundant in tree
 islands (4.6 ± 2.9 seeds·m−2·yr−1) and plantations (5.8 ± 3.0
 seeds·m−2·yr−1) than control plots (0.2 ± 0.1 seeds·m−2·yr−1),
 contributing to greater tree species richness in actively restored plots.
 Planted tree species accounted for &lt;1% of seeds. We found little
 evidence for landscape forest cover effects on seed rain, consistent with
 previous studies. We conclude that seed rain limitation shifted from an
 initial, complete lack of tree seeds to a specific limitation on
 large‐seeded, mature forest species over the first decade. Although total
 seed abundance was equal among restoration treatments, tree plantations
 and tree islands continued to diversify seed rain communities compared to
 naturally regenerating controls. Compositional differences between
 regenerating plots and mature forests suggest that large‐seeded tree
 species are appropriate candidates for enrichment planting.
description: Seed rain was collected twice per month from 15 Feb 2012 ñ 14 Feb
 2013 in 420 0.25-m2 traps. In each restoration and reference plot, we
 established four trapping stations along permanent vegetation transects
 (Fig. B1). Each station had three traps. In island plots, we placed two of
 the twelve traps (16%) in the planted patches and the remainder in
 unplanted areas to match the proportion of the area that was initially
 planted (18%). All traps were located &gt;5 m from the plot edge and
 restoration plots were separated by =5 m.
DOI: 10.6084/m9.figshare.30082183.v2
title: A spatial transcriptomics comparison of the adult versus metamorphosed axolotl brain

description: The Mexican axolotl (Ambystoma mexicanum) is an established model for studying tetrapod regeneration and development. Notably, axolotls exhibit remarkable brain regeneration as adults, a trait rarely observed in other adult vertebrates. Adult axolotls can undergo metamorphosis, a process that induces dramatic remodeling of multiple organs and is accompanied by a gradual decline in regenerative capacity and lifespan. However, systematic studies on whole-brain cellular dynamics and molecular mechanisms in both adult and metamorphosed individuals remain lacking. Here, we profiled five representative brain regions (olfactory bulb, telencephalon, diencephalon/mesencephalon, rhombencephalon, and pituitary) of the axolotl brain via spatial transcriptomics in both adult and metamorphosed individuals. Our work reveals metamorphosis-associated changes in cell types and molecular profiles across brain regions.
DOI: 10.7291/d14x1j
title: Forest Survey data 2012-2013

description: Vegetation composition of 6 representative forest fragments adjacent to
 restoration study plots in the Islas Project.
description: Data collected during two time periods: 
 Apr-June 2007: These data were collected laying out four 16 X 16
 m plots at each site and applying the same sampling methodology used in
 the restoration project (see Zahawi et al. 2013 for more details).
   May-July 2012: These data were collected laying out
 four 20 X 20 m plots at each site and applying the same sampling
 methodology used in the restoration project (see Zahawi et al. 2013 for
 more details).  
description: See readme files for more information.
DOI: 10.7291/d11681
title: Data from: Testing applied nucleation as a strategy to facilitate tropical forest recovery

description:   Active forest restoration typically involves planting trees
 over large areas; this practice is costly, however, and establishing
 homogeneous plantations may favour the recruitment of a particular suite
 of species and strongly influence the successional trajectory. An
 alternative approach is to plant nuclei (islands) of trees to simulate the
 nucleation model of succession and accelerate natural recovery. We
 evaluated natural tree recruitment over 4 years in a restoration
 study replicated at eight former pasture sites in the tropical premontane
 forest zone of southern Costa Rica. At each site, two active restoration
 strategies were established in 50 × 50 m plots:
 planting trees throughout, and planting different‐sized tree islands
 (4 × 4, 8 × 8,
 12 × 12 m) within the plot. Restoration plots
 were compared to similar‐sized controls undergoing passive restoration.
 Sites were spread
 across c. 100 km2 and distributed
 along a gradient of surrounding forest, allowing us to compare the
 relative importance of adjacent forest to that of within‐site treatment on
 tree recruitment. Recruitment of animal‐dispersed tree species was more
 than twofold higher in active
 (μ = 0·45 recruits m−2) as compared to
 passive restoration; recruitment was equivalent in plantation and island
 treatments, even though only 20% of the area in island plots was planted
 originally. The majority of recruits (&gt;90%) represented early
 successional species (n = 54 species total). Density of
 animal‐dispersed recruits was greater in large
 (0·80 ± 0·66 m−2) than small
 (0·28 ± 0·36 m−2) islands and intermediate in
 medium‐sized islands. Seedling recruitment
 (&lt;1 m tall) was greater in the interior of
 islands as compared to plantations, whereas sapling recruitment was
 similar, suggesting that island interiors may develop greater density of
 woody recruits as succession proceeds. Surrounding forest cover did not
 influence density or species richness of recruits among sites, although
 this factor may become more important over time. Synthesis and
 applications. Applied nucleation is a promising restoration strategy that
 can accelerate forest recovery to a similar degree as plantation‐style
 restoration but is more economical. Appropriate island size is on the
 order of c. 100 m2. Practitioners should
 consider the methodology as an alternative to large‐scale plantings.
DOI: 10.7291/d1wd5q
title: Data from: Landscape Context Mediates Avian Habitat Choice in Tropical Forest Restoration

description: Birds both promote and prosper from forest restoration. The ecosystem
 functions birds perform can increase the pace of forest regeneration and,
 correspondingly, increase the available habitat for birds and other
 forest-dependent species. The aim of this study was to learn how tropical
 forest restoration treatments interact with landscape tree cover to affect
 the structure and composition of a diverse bird assemblage. We sampled
 bird communities over two years in 13 restoration sites and two old-growth
 forests in southern Costa Rica. Restoration sites were established on
 degraded farmlands in a variety of landscape contexts, and each included a
 0.25-ha plantation, island treatment (trees planted in patches), and
 unplanted control. We analyzed four attributes of bird communities
 including frugivore abundance, nectarivore abundance, migrant insectivore
 richness, and compositional similarity of bird communities in restoration
 plots to bird communities in old-growth forests. All four bird community
 variables were greater in plantations and/or islands than in control
 treatments. Frugivore and nectarivore abundance decreased with increasing
 tree cover in the landscape surrounding restoration plots, whereas
 compositional similarity to old-growth forests was greatest in plantations
 embedded in landscapes with high tree cover. Migrant insectivore richness
 was unaffected by landscape tree cover. Our results agree with previous
 studies showing that increasing levels of investment in active restoration
 are positively related to bird richness and abundance, but differences in
 the effects of landscape tree cover on foraging guilds and community
 composition suggest that trade-offs between biodiversity conservation and
 bird-mediated ecosystem functioning may be important for prioritizing
 restoration sites.
description: We sampled bird communities in 13 restoration sites and two
 old-growth forests in southern Costa Rica (Coto Brus County). Restoration
 sites were located between Las Cruces and the town of Agua Buena (8∞
 44' N, 82∞ 56' W). Study sites were 1100-1400 m a.s.l., and the
 dominant natural ecosystem was premontane moist forest. Most study sites
 were on the Fila Cruces, but one old-growth site was at similar elevation
 in the Talamanca mountains. Precipitation across the study areas varies
 with microtopography but is ~4 m y-1 at Las Cruces. Mean annual
 temperature at Las Cruces is 21∞ C.