cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.n7r0qk8
title: Data from: Effect of lianas on forest-level tree carbon accumulation does not differ between seasons: results from a liana removal experiment in Panama

description: 1. Lianas are prevalent in Neotropical forests, where liana-tree
 competition can be intense, resulting in reduced tree growth and survival.
 The ability of lianas to grow relative to trees during the dry season
 suggests that liana-tree competition is also strongest in the dry season.
 If correct, the predicted intensification of the drying trend over large
 areas of the tropics in the future may therefore intensify liana-tree
 competition, resulting in a reduced carbon sink function of tropical
 forests. However, no study has established whether the liana effect on
 tree carbon accumulation is indeed stronger in the dry than in the wet
 season. 2. Using six years of data from a large-scale liana removal
 experiment in Panama, we provide the first experimental test of whether
 liana effects on tree carbon accumulation differ between seasons. We
 monitored tree and liana diameter increments at the beginning of the dry
 and wet season each year to assess seasonal differences in forest-level
 carbon accumulation between removal and control plots. 3. We found that
 median liana carbon accumulation was consistently higher in the dry ( 0.52
 Mg C ha-1 yr-1) than the wet season (0.36 Mg C ha-1 yr-1), and
 significantly so in three of the years. Lianas reduced forest-level median
 tree carbon accumulation more severely in the wet (1.45 Mg C ha-1 yr-1)
 than the dry (1.05 Mg C ha-1 yr-1) season in all years. However, the
 relative effect of lianas was similar between the seasons, with lianas
 reducing forest-level tree carbon accumulation by 46.9% in the dry and
 48.5% in the wet season. 4. Synthesis: Our results provide the first
 experimental demonstration that lianas do not have a stronger competitive
 effect on tree carbon accumulation during the dry season. Instead, lianas
 compete significantly with trees during both seasons, indicating a large
 negative effect of lianas on forest-level tree biomass increment
 regardless of seasonal water stress. Longer dry seasons are unlikely to
 impact liana-tree competition directly; however, the greater liana biomass
 increment during dry seasons may lead to further proliferation of liana
 biomass in tropical forests, with consequences for their ability to store
 and sequester carbon.
description: van_der_Heijden_seasonal_liana_stem_biomass_2011_2017Liana stem biomass (kg C) for all stems occurring in the 8 control plots of the liana removal experiment. Stems were measured at the beginning of the wet and the dry season from 2011 to 2017 and biomass calculated using established allometric equations.van_der_Heijden_seasonal_tree_stem_biomass_2011_2017Tree stem biomass (kg C) for each tree stem &gt;= 10 cm occurring in the 16 plots of the liana removal experiment. Stem measurements took place at the beginning of the wet and the dry season from 2011 to 2017. Diameter values were converted into biomass using accepted allometric equations.
DOI: 10.5061/dryad.8b9j040
title: Data from: Dispersal syndromes can impact ecosystem functioning in spatially structured freshwater populations

description: Dispersal can strongly influence ecological and evolutionary dynamics.
 Besides the direct contribution of dispersal to population dynamics,
 dispersers often differ in their phenotypic attributes from
 non-dispersers, which leads to dispersal syndromes. The consequences of
 such dispersal syndromes have been widely explored at the population and
 community level, however, to date, ecosystem-level effects remain unclear.
 Here, we examine whether dispersing and resident individuals of two
 different aquatic keystone invertebrate species have different
 contributions to detrital processing, a key function in freshwater
 ecosystems. Using experimental two-patch systems, we found no difference
 in leaf consumption rates with dispersal status of the common native
 species Gammarus fossarum. In Dikerogammarus villosus, however, a
 Ponto-Caspian species now expanding throughout Europe, dispersers consumed
 leaf litter at roughly three times the rate of non-dispersers.
 Furthermore, this put the contribution of dispersing D. villosus to leaf
 litter processing on par with native G. fossarum, after adjusting for
 differences in organismal size. Given that leaf litter decomposition is a
 key function in aquatic ecosystems, and the rapid species turnover in
 freshwater habitats with range expansions of non-native species, this
 finding suggests that dispersal syndromes may have important consequences
 for ecosystem functioning.
description: Suppdata1_G_fossarum_bodyweightsBody weights of Gammarus fossarum individuals used in the experimentSuppdata1_G_fossarum_dispnet_bodyweights.csvSuppdata2_GF_weight_and_survivalLeaf consumption rates by Gammarus fossarum individuals, and their survival, over a roughly two-week experimentSuppdata3_DV_weight_and_survivalLeaf consumption rates by Dikerogammarus villosus individuals, and their survival, over a roughly two-week experimentSuppdata4_D_villosus_bodyweightsBody weights of Dikerogammarus villosus individuals used in the experimentSuppdata4_D_villosus_dispnet_bodyweights.csv
DOI: 10.5281/zenodo.18350513
title: KEYS_BRAND8_300F_5_23C_0k_EDLC_single
DOI: 10.5061/dryad.mt6552d
title: Data from: Bacterial community dynamics during embryonic and larval development of three confamilial echinoids

description: Development of some animals is influenced by and, in some cases, dependent
 on the associated microbiota. The timing of when associated bacterial
 communities are established during the development of marine invertebrates
 and their subsequent dynamics across stages are known for only a few
 species. Here, we compared the bacterial communities of 3 confamilial
 echinoids from egg to juvenile using sequence-based approaches. Bacterial
 communities are established on unfertilized eggs and change gradually
 during embryonic and larval development. Despite the differences amongst
 these pre-metamorphic stages, approximately 30% of operational taxonomic
 units (OTUs) identified in association with unfertilized eggs were present
 in the juveniles. During embryonic development, host-associated
 communities diverged from the environmental microbiota but later converged
 following the onset of larval feeding. Taken together, the data presented
 here support the hypothesis that bacterial communities are established
 prior to fertilization and community composition shifts gradually
 thereafter, all the while remaining distinct from the environment. Future
 work will need to determine the relative influence of the host and
 bacteria–bacteria interactions in shaping the associated bacterial
 community to more broadly determine the potential functional importance of
 bacteria during the development of larval sea urchins and benthic marine
 invertebrates.
description: CarrierReitzel_FSW_RawData_DryadRaw read files (In FASTQ) for environmental samples relating to this study. Samples labels are: FSW_DevelopmentalTimepoint_BiologicalReplicate. Within each folder are forward (*_R1_*)and reverse (*_R2_*) files.CarrierReitzel_Sp_RawData_DryadRaw read files (in FASTQ) for Strongylocentrotus purpuratus (Sp) samples relating to this study. Samples labels are: Sp_DevelopmentalTimepoint_BiologicalReplicate. Within each folder are forward (*_R1_*)and reverse (*_R2_*) files.CarrierReitzel_Mf_RawData_DryadRaw read files (in FASTQ) for Mesocentrotus franciscanus (Mf) samples relating to this study. Samples labels are: Mf_DevelopmentalTimepoint_BiologicalReplicate. Within each folder are forward (*_R1_*)and reverse (*_R2_*) files.CarrierReitzel_Sd_RawData_DryadRaw read files (in FASTQ) for Strongylocentrotus droebachiensis (Sd) samples relating to this study. Samples labels are: Sd_DevelopmentalTimepoint_BiologicalReplicate. Within each folder are forward (*_R1_*)and reverse (*_R2_*) files.
DOI: 10.5281/zenodo.18350512
title: KEYS_BRAND8_300F_5_23C_0k_EDLC_single
DOI: 10.5061/dryad.734q42p
title: Data from: The rate of environmental fluctuations shapes ecological dynamics in a two-species microbial system

description: Species interactions change when the external conditions change. How these
 changes affect microbial community properties is an open question. We
 address this question using a two-species consortium in which species
 interactions change from exploitation to competition depending on the
 carbon source provided. We built a mathematical model and calibrated it
 using single-species growth measurements. This model predicted that low
 frequencies of change between carbon sources lead to species loss, while
 intermediate and high frequencies of change maintained both species. We
 experimentally confirmed these predictions by growing co-cultures in
 fluctuating environments. These findings complement more established
 concepts of a diversity peak at intermediate disturbance frequencies. They
 also provide a mechanistic understanding for how the dynamics at the
 community level emerges from single-species behaviors and interspecific
 interactions. Our findings suggest that changes in species interactions
 can profoundly impact the ecological dynamics and properties of microbial
 systems.
description: Growth_curvesGrowth curves associated to Figure S4. Data correspond to optical density (OD) measurements from plate reader experiments. Abbreviations: "BA600" is Benzyl Alcohol 600µM; "Ben1000" is Benzoate 1000µM; "Ci1000" is Citrate 1000µM.Batch_culture_experimentsBatch culture data associated to Figure 1, Figure 3, Figure S3 and Figure S7. Data correspond to colony-forming units per ml (CFU/ml) from batch culture experiments.Metabolite_measurementsMetabolite data associated to Figure S5. Data correspond to metabolite concentrations (mM) measured using high performance liquid chromatography (HPLC) and to colony forming units (CFU/ml) for Acinetobacter's bacterial growth.OD_CFU_conversion_FigS2Data used to convert optical density (OD) values to cell density values (CFU/ml) shown in Figure S2.
DOI: 10.5061/dryad.rh66vg2
title: Data from: Large neotheropods from the Upper Triassic of North America and the early evolution of large theropod body sizes

description: Large body sizes among non-avian theropod dinosaurs is a major feature in
 the evolution of this clade, with theropods reaching greater sizes than
 any other terrestrial carnivores. However, the early evolution of large
 body sizes among theropods is obscured by an incomplete fossil record,
 with the largest Triassic theropods represented by only a few individuals
 of uncertain ontogenetic stage. Here, I describe two neotheropod specimens
 from the Upper Triassic Bull Canyon Formation of New Mexico and place them
 in a broader comparative context of early theropod anatomy. These
 specimens possess morphologies indicative of ontogenetic immaturity (e.g.,
 absence of femoral bone scars, lack of co-ossification between the
 astragalus and calcaneum), and phylogenetic analyses recover these
 specimens as early-diverging neotheropods in a polytomy with other early
 neotheropods at the base of the clade. Ancestral state reconstruction for
 body size suggests that the ancestral theropod condition was small (~240
 mm femur length), but the ancestral neotheropod was larger (~300–340 mm
 femur length), with coelophysoids experiencing secondary body size
 reduction, although this is highly dependent on the phylogenetic position
 of a few key taxa. Theropods evolved large body sizes before the
 Triassic-Jurassic extinction, as hypothesized in most other ancestral
 state reconstructions of theropod body sizes, but remained rare relative
 to smaller theropods until the Jurassic.
description: Supplementary
 InformationThis file includes:
 Table S1, Figures S1–S6, List of apomorphies within Saurischia, Dataset
 S1–2 captions, Taxon scorings, ReferencesNMMNH
 theropod_SI.docxDataset
 S1NEXUS file of all
 terminal taxa used in these phylogenetic analysesDatasetS2NEXUS file of all terminal taxa used in the phylogenetic analysis based on the Ezcurra (2017) matrix
DOI: 10.5061/dryad.gk1r3s5
title: Data from: Environmental gradients determine the potential for ecosystem engineering effects

description: Understanding processes that determine biodiversity is a fundamental
 challenge in ecology. At the landscape scale, physical alteration of
 ecosystems by organisms, called ecosystem engineering, enhances
 biodiversity worldwide by increasing heterogeneity in resource conditions
 and enhancing species coexistence across engineered and non-engineered
 habitats. Engineering-diversity relationships can vary along environmental
 gradients due to changes in the amount of physical structuring created by
 ecosystem engineering, but it is unclear how this variation is influenced
 by the responsiveness of non-structural abiotic properties to engineering.
 Here we show that environmental gradients determine the capacity for
 engineering to alter resource availability and species diversity,
 independent of the magnitude of structural change produced by engineering.
 We created an experimental rainfall gradient in an arid grassland where
 rodents restructure soils by constructing large, long-lasting burrows. We
 found that greater rainfall increased water availability and productivity
 in both burrow and inter-burrow habitats, causing a decline in local
 (alpha) plant diversity within both of these habitats. However, increased
 rainfall also resulted in greater differences in soil resources between
 burrow and inter-burrow habitats, which increased species turnover (beta
 diversity) across habitats and stabilized landscape-level (gamma)
 diversity. These responses occurred regardless of rodent presence and
 without changes in the extent of physical alteration of soils by rodents.
 Our results suggest that environmental gradients can influence the effects
 of ecosystem engineering in maintaining biodiversity via resource
 heterogeneity and species turnover. In an era of rapid environmental
 change, accounting for this interaction may be critical to conservation
 and management.
description: Grinath_et_al_2019_Oikos_Quadrat_DataThese data are from Grinath et al. 2019. Quadrat data are from 1 m² sampling quadrats located within paired 100 m² plots at each of 18 experimental sites (n = 282 quadrats in 36 plots).Grinath_et_al_2019_Oikos_Plot_DataThese data are from Grinath et al. 2019. Plot data represent variables across whole plots (including within or across burrow and inter-burrow habitats). Soil nitrogen mineralization was measured at the plot level, but other soil properties were averaged across quadrats within plots. At this level, plant species quadrat data (pin hits) were summed and then used to obtain rarefied measures of alpha, beta and gamma diversity.
DOI: 10.25418/crick.31056790
title: Quality assessment evaluation.

description: This table summarizes data collated for quality assessment for a systematic review.<br><br>We assessed data quality and risk of bias using approved tools from the Joanna Briggs Institute. We downloaded a standard data collection proforma, and populated this alongside data extraction to include: were criteria for inclusion of samples to be clearly defined? Were subjects and settings described in detail? Was exposure measured in a valid and reliable way? Were objective, standard criteria used for the measurement of the condition? Were confounding identified and what strategies were put in place to deal with confounders? Were outcomes measured in a valid and reliable way? and lastly was the appropriate statistical tool used?
DOI: 10.25418/crick.31056790.v1
title: Quality assessment evaluation.

description: This table summarizes data collated for quality assessment for a systematic review.<br><br>We assessed data quality and risk of bias using approved tools from the Joanna Briggs Institute. We downloaded a standard data collection proforma, and populated this alongside data extraction to include: were criteria for inclusion of samples to be clearly defined? Were subjects and settings described in detail? Was exposure measured in a valid and reliable way? Were objective, standard criteria used for the measurement of the condition? Were confounding identified and what strategies were put in place to deal with confounders? Were outcomes measured in a valid and reliable way? and lastly was the appropriate statistical tool used?
DOI: 10.5061/dryad.dr7d18t
title: Data from: Deep-tissue optical imaging of near cellular-sized features

description: Detection of biological features at the cellular level with sufficient
 sensitivity in complex tissue remains a major challenge. To appreciate
 this challenge, this would require finding tens to hundreds of cells (a
 0.1 mm tumor has ~125 cells), out of ~37 trillion cells in the human body.
 Near-infrared optical imaging holds promise for high-resolution,
 deep-tissue imaging, but is limited by autofluorescence and scattering. To
 date, the maximum reported depth using second-window near-infrared
 (NIR-II: 1000–1700 nm) fluorophores is 3.2 cm through tissue. Here, we
 design an NIR-II imaging system, “Detection of Optically Luminescent
 Probes using Hyperspectral and diffuse Imaging in Near-infrared”
 (DOLPHIN), that resolves these challenges. DOLPHIN achieves the following:
 (i) resolution of probes through up to 8 cm of tissue phantom; (ii)
 identification of spectral and scattering signatures of tissues without a
 priori knowledge of background or autofluorescence; and (iii) 3D
 reconstruction of live whole animals. Notably, we demonstrate noninvasive
 real-time tracking of a 0.1 mm-sized fluorophore through the
 gastrointestinal tract of a living mouse, which is beyond the detection
 limit of current imaging modalities.
description: Sample Dataset for
 HyperSpectral Imaging (HSC data)This is a sample
 dataset, obtained using Hyperspectral Imaging of a label-free, healthy
 nude mouse, using the DOLPHIN imaging system, using a wavelength-tunable
 laser (from 690 - 1040 nm). As a sample, only the 980 nm excitation
 wavelength data has been provided in this archive. Details of the DOLPHIN
 imaging system and the image processing techniques used for Hyperspectral
 Imaging are described in the aforementioned paper.Sample Dataset for
 HyperDiffuse Imaging (HDC data)This is a sample
 dataset, obtained using Hyperdiffuse Imaging of the passage of a 100
 µm-sized Er-NP cluster probe through the GI tract of a healthy nude mouse,
 using the DOLPHIN imaging system, using a fixed wavelength of excitation
 (980 nm laser). Details of the DOLPHIN imaging system and the image
 processing techniques used for Hyperdiffuse Imaging are described in the
 aforementioned paper.
DOI: 10.5061/dryad.0j4kg0t
title: Data from: Toxic diffuse isolated cerebellar edema from over-the-counter health supplements

description: [No abstract entered]
description: Figure e-1. Pathology
 images of the cerebellar biopsy sample.(Panel A) Biopsy shows
 cerebellar cortex with dark Purkinje neurons and Purkinje neuron dropout.
 There is microvacuolation of neuropil and white matter. Features are
 consistent with ischemic neuronal changes with surrounding edema.
 Luxol-fast blue/hematoxylin-eosin (Bar = 50 microns). (Panel B)
 Neurofilament immunohistochemistry highlights collapsed basket cells which
 emphasize the Purkinje neuron dropout. (Bar = 50
 microns).Supplementary
 Figure.tifTable e-1. Labelled
 ingredients of each herbal or naturopathic product that was taken by the
 patient at the onset of neurological symptoms.List of the various
 products the patient was taking at the time of symptom
 onset.Table
 e-1.docxFigure e-1
 LegendLegend for the Figure
 e-1 image.
DOI: 10.5061/dryad.js4s24f
title: Data from: Latitudinal gradients of parasite richness: a review and new insights from helminths of cricetid rodents

description: The latitudinal diversity gradient (LDG), or the trend of higher species
 richness at lower latitudes, has been well documented in multiple groups
 of free‐living organisms. Investigations of the LDG in parasitic organisms
 are comparatively scarce. Here, I investigated latitudinal patterns of
 parasite diversity by reviewing published studies and by conducting a
 novel investigation of the LDG of helminths (parasitic nematodes,
 trematodes, and cestodes) of cricetid rodents (Rodentia: Cricetidae).
 Using host‐parasite records from 175 parasite communities and 60 host
 species, I tested for the presence and direction of a latitudinal pattern
 of helminth richness. Additionally, I examined four abiotic factors (mean
 annual temperature, annual precipitation, annual temperature range, and
 annual precipitation range) and two biotic variables (host body mass and
 host diet) as potential correlates of parasite richness. The analyses were
 performed with and without phylogenetic comparative methods, as necessary.
 In this system, helminths followed the traditional LDG, with increasing
 species richness with decreasing latitude. Nematode richness appeared to
 drive this pattern, as cestodes and trematodes exhibited a reverse LDG and
 no latitudinal pattern, respectively. Overall helminth richness and
 nematode richness were higher in areas with higher mean annual
 temperatures, annual precipitation, and annual precipitation ranges and
 lower annual temperature ranges, characteristics that often typify lower
 latitudes. Cestode richness was higher in areas of lower mean annual
 temperatures, annual precipitation, and annual precipitation ranges and
 higher annual temperature ranges, while trematode richness showed no
 relationship with climate variables when phylogenetic comparative methods
 were used. Host diet was significantly correlated with cestode and
 trematode species richness, while host body mass was significantly
 correlated with nematode and trematode species richness. Results of this
 study support a complex association between parasite richness and
 latitude, and indicate that researchers should carefully consider other
 factors when trying to understand diversity gradients in parasitic
 organisms.
description: Appendix 4:
 D175Appendix 4 is a dataset
 (D175) compiled from published helminth surveys of cricetid rodents
 (Rodentia: Cricetidae), WorldClim, and other sources. Descriptions of
 column headings and references are included in the README
 file.Appendix4_2.xlsx