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Depth-dependent anisotropy in the Earth's inner core linked to chemical stratification
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Linked collectors and determiners for: eDNA‑based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity.
Natural history specimen data linked to collectors and determiners held within, "eDNA‑based detection of the invasive crayfish Pacifastacus leniusculus in streams with a LAMP assay using dependent replicates to gain higher sensitivity". Claims or attributions were made on Bionomia by volunteer Scribes, <a href="https://bionomia.net/dataset/ea16e238-4e23-41fb-9eee-c1ea4f0caa63">https://bionomia.net/dataset/ea16e238-4e23-41fb-9eee-c1ea4f0caa63</a> using specimen data from the dataset aggregated by the Global Biodiversity Information Facility, <a href="https://gbif.org/dataset/ea16e238-4e23-41fb-9eee-c1ea4f0caa63">https://gbif.org/dataset/ea16e238-4e23-41fb-9eee-c1ea4f0caa63</a>. Formatted as a Frictionless Data package.
Fig 2 in Docosahexaenoic Acid (DHA) Reduces LPSInduced Inflammatory Response Via ATF3 Transcription Factor and Stimulates Src/ Syk Signaling-Dependent Phagocytosis in Microglia
<p>Proteome profiler arrays (A and B) and expression of ATF3 gene (C) in microglia. Representative array membranes (A) and the relative levels of cytokines and chemokines (B) in microglia preincubated with 20 μM DHA and next treated with 10 ng/ml LPS.</p>
Fig 1 in Docosahexaenoic Acid (DHA) Reduces LPSInduced Inflammatory Response Via ATF3 Transcription Factor and Stimulates Src/ Syk Signaling-Dependent Phagocytosis in Microglia
<p>Viability of microglia incubated with various concentration of DHA for 12 h (A) and LPS for 2.5 h (B). Viability of microglia incubated with 20 μM DHA followed by 10 ng/ ml LPS treatment (C).</p>
Sequence-dependent activity and compartmentalization of foreign DNA in a eukaryotic nucleus
<p>In eukaryotes, DNA-associated protein complexes co-evolve with genomic sequence to orchestrate chromatin folding. Here, we investigate the relationship between DNA sequence and the spontaneous loading and activity of chromatin components in the absence of co-evolution. Using bacterial genomes integrated into S. cerevisiae, which diverged from yeast 1.5 billion years ago, we show that nucleosomes, cohesins and the transcriptional machinery can lead to the formation of two different chromatin archetypes, one transcribed and the other silent, independently of heterochromatin formation. These two archetypes also form on eukaryotic exogenous sequences, depend on sequence composition, and can be predicted using neural networks trained on the native genome. They do not mix in the nucleus, leading to a bipartite nuclear compartmentalization, reminiscent of the organization of vertebrate nuclei. </p> <p> </p>
Disturbance-mediated invasions are dependent on community resource abundance
<p>Here is the data for the manuscript entitled "<em>Disturbance mediated invasions are dependent on community resource abundance</em>."</p> <p>The dataset columns are:</p> <ul> <li><strong>disturb</strong> - dusturbance frequency (1 = everyday, 2 = every two days etc)</li> <li><strong>kb</strong> - resource abundance. 0.01 = low, 0.1 medium and 1.0 high.</li> <li><strong>invader</strong> - nill = no invader added (not used in the manuscript), sm shows microcosms invaded by the Smooth invader and ws by the Wrinkly Spreader invader</li> <li><strong>smooth</strong> - the final number of resident smooths</li> <li><strong>wrinkly</strong> - the final number of resident wrinkly spreaders</li> <li><strong>fuzzy</strong> - the final number of resident fuzzy</li> <li><strong>iden</strong> - the final number of invader cfu</li> <li><strong>cfu/6ml</strong> - the number of resident cfu on day four</li> </ul> <p> </p> <p>Smooth, wrinkly, fuzzy and iden columns are cfu counts per 25uL</p>
Data from: Microbe-dependent heterosis in maize
<p>Data and statistical code associated with the manuscript "<strong>Microbe-dependent heterosis in maize" </strong>Wagner, Maggie R.; Tang, Clara; Salvato, Fernanda; Clouse, Kayla M.; Bartlett, Alexandria; Vintila, Simina; Phillips, Laura; Sermons, Shannon; Hoffmann, Mark; Balint-Kurti, Peter J.; Kleiner, Manuel (2021) PNAS July 27, 2021 118 (30) e2021965118; https://doi.org/10.1073/pnas.2021965118</p> <p><strong>19 October 2020: </strong>new version posted to add <strong>fum_16S_ITS.zip</strong></p> <ul> <li>Archive containing processed 16S and ITS amplicon data (i.e., ASV tables) from the soil fumigation experiment. In addition, it contains all code and accessory files used to process and analyze the sequence data. The archive contains its own readme.txt with details on the files and their usage.</li> </ul> <p><strong>27 July 2021: </strong>new version 3 posted to add <strong>Expt4_data.xlsx</strong> and <strong>SynCom_colonization_data.xlsx</strong> . New version 4 posted to include the updated README and analytical code (mdh_analysis_revised.R)</p> <ul> <li><strong>Expt4_data.xlsx </strong>= Raw data from Experiment 4 (Kansas field experiment, summer 2020)</li> <li><strong>SynCom_colonization_data.xlsx</strong> = Raw measurements of colonization rates of SynCom bacterial strains in 4 maize genotypes</li> </ul> <p>Funding: National Science Foundation, IOS-2033621</p>
Dataset - Lagain et al., 2021. Latitudinal dependency of the impact rate: any room for a recalibration of crater chronologies ?
<p>data related to the following article: Lagain A. et al. (2021). Latitudinal dependency of the impact rate: any room for a recalibration of crater chronologies ? submitted to <em>EPSL </em>(July 2021).</p>
Structure-Dependent Influence of Moisture on Resistive Switching Behavior of ZnO Thin Films - Dataset
<p>This is the dataset of "Structure-Dependent Influence of Moisture on Resistive Switching Behavior of ZnO Thin Films"</p>
Data accompanying arXiv:2112.07341, "Euclid: Covariance of weak lensing pseudo-Cl estimates. Calculation, comparison to simulations, and dependence on survey geometry"
<p>Data accompanying <a href="https://arxiv.org/abs/2112.07341">arXiv:2112.07341, "<em>Euclid</em>: Covariance of weak lensing pseudo-Cl estimates. Calculation, comparison to simulations, and dependence on survey geometry"</a>.</p> <p>Code available at <a href="https://github.com/robinupham/shear_pcl_cov">https://github.com/robinupham/shear_pcl_cov</a>.</p>
Data Repository - Thermal-electrochemical parametrisation of a lithium-ion battery: mapping Li concentration and temperature dependencies
<p>Datasets from "Thermal-electrochemical parametrisation of a lithium-ion battery: mapping Li concentration and temperature dependencies" - Journal of Electrochemical Society.</p> <p>This repository contains parameter values for the electrode solid-state diffusivity, entropic term, exchange current density, electronic conductivity, specific heat capacity, and thermal conductivity.</p>
Data for: Context-dependent effects of glucocorticoids on the lizard gut microbiome
<p><strong>Data from: Context-dependent effects of glucocorticoids on the lizard gut microbiome </strong>(provisionally accepted, Molecular Ecology 2021) </p> <p>Metadata is in Sheet 2. Address queries to kirstyjmacleod@gmail.com.</p> <p><strong>Publication abstract:</strong> The vertebrate gut microbiota (bacterial, archaeal, and fungal communities of the gastrointestinal tract) can have profound effects on physiological processes of their hosts. Although relatively stable, changes in microbiome structure and composition occur due to changes in the environment, including exposure to stressors and associated increases in glucocorticoid hormones. Although a growing number of studies have linked stressor exposure to microbiome changes, few studies have experimentally explored the specific influence of glucocorticoids on the microbiome in wild animals, or across ecologically-important processes (e.g., reproductive stages). Here we tested the response of the gut microbiota of adult female Sceloporus undulatus across gestation to ecologically relevant elevations of a stress-relevant glucocorticoid hormone (CORT) in order to determine a) how experimentally elevated CORT influenced microbiome characteristics, and b) whether this relationship was dependent on reproductive context (i.e. whether females were gravid or not, and in those that were gravid, gestational stage). We show that the effects of CORT on gut microbiota are complex and depend on both gestational state and stage. CORT treatment altered microbial community membership and resulted in an increase in microbiome diversity in late-gestation females, and microbial community membership varied according to treatment. In non-gravid females, CORT treatment resulted in inter-individual variation in microbial communities, but this effect was not observed in late-gestation females. Our results highlight the need for a more holistic understanding of the downstream physiological effects of glucocorticoids, as well as the importance of context (here, gestational state and stage) in interpreting stress effects in ecology.</p>
The evolution of size-dependent competitive interactions promotes species coexistence
<p>1. Theory indicates that competing species coexist in a community when intraspecific competition is stronger than interspecific competition. When body size determines the outcome of competitive interactions between individuals, coexistence depends also on how resource use and the ability to compete for these resources change with body size. Testing coexistence theory in size-structured communities, therefore, requires disentangling the effects of size-dependent competitive abilities and niche shifts.</p> <p>2. Here, we tested the hypothesis that the evolution of species and size-dependent competitive asymmetries increased the likelihood of coexistence between interacting species.</p> <p>3. We experimentally estimated the effects of size-dependent competitive interactions on somatic growth rates of two interacting fish species, Trinidadian guppies (Poecilia reticulata) and killifish (Rivulus hartii). We controlled for the effects of size-dependent changes in the niche at two competitive settings representing the early (allopatric) and late (sympatric) evolutionary stages of a killifish-guppy community. We fitted the growth data to a model that incorporates species and size-dependent competitive asymmetries to test whether changes in the competitive interactions across sizes increased the likelihood of species coexistence from allopatry to sympatry.</p> <p>4. We found that guppies are competitively superior to killifish but were less so in sympatric populations. The decrease in the effects of interspecific competition on the fitness of killifish and increase in the interspecific effect on guppies' fitness increased the likelihood that sympatric guppies and killifish will coexist. However, while the competitive asymmetries between the species changed consistently between allopatry and sympatry between drainages, the magnitude of the size-dependent competitive asymmetries varied between drainages.</p> <p>5. These results demonstrate the importance of integrating evolution and trait-based interactions into the research on how species coexist.</p>
Fig. 1 in Dependence of the sperm number on the adult age of the male black field cricket Teleogryllus commodus W ALKER (Insecta: Orthoptera)
Fig. 1: Shape and morphology of the spermatophore (total length: ca. 5 mm) separated from males of the black field cricket Teleogryllus commodus.
Fig. 2 in Dependence of the sperm number on the adult age of the male black field cricket Teleogryllus commodus W ALKER (Insecta: Orthoptera)
Fig. 2: Results of sperm quantification of male crickets belonging to different age categories: (a) Age-dependence of the percentage of filled/unfilled spermatophores (N = 80); (b) Age-dependence of the number of sperm per spermatophore (N = 80). The asterisk indicates a significant difference (p <0.05) between adjacent mean values.
Condition-dependent sexual reproduction is driven by benefits, not costs of sex
<p>Facultative sexual organisms must allocate resources to both asexual and sexual reproduction. Optimal patterns of investment in sex depend on the relative costs and benefits of each reproductive mode, and may consequently be context- and condition-dependent. Two proposed explanations for the observed variation in investment in sex among facultative sexual lineages invoke alternative condition-dependent scenarios. Under the 'fitness-associated sex' hypothesis, sex is predicted when individuals are in poor condition or experience stressful environments. Under the 'resource-demanding sex' hypothesis, sex is only affordable to individuals in good condition experiencing favourable environments. Direct tests of these contrasting hypotheses are rare; moreover, investment in different components of sexual reproduction responds differently to cues promoting sex, and may be subject to different energetic constraints. Using genotypes of facultative sexual Daphnia carinata that differ in their level of investment in sex, we manipulated resource availability while accounting for day length (a seasonal cue for sex) to evaluate these hypotheses. The sexual response to day length depended on resource availability: increased day lengths and reduced food availability increased the production of sexual eggs, and relative investment in males, in a manner consistent with the fitness-associated sex hypothesis. The pattern of condition-dependence was specific to each component of reproductive investment – while male production covaried with asexual fecundity across genotypes, increased sexual egg production was associated with reduced asexual reproduction. Our results suggest that investment in sex is determined largely by its context-dependent advantages, and that this investment is not moderated by immediate costs to asexual reproduction.</p>
Fig. 4 in Dependence of daily oviposition activity and total fecundity on body mass in the house cricket Acheta domesticus (L.) (Insecta: Orthoptera)
Fig. 4: Total fecundity (mean + sd) measured for female crickets belonging to mass category (MC) 1, 2, and 3. Asterisks indicate highly significant differences between adjacent mean values (p <0.001).
Fig. 3 in Dependence of daily oviposition activity and total fecundity on body mass in the house cricket Acheta domesticus (L.) (Insecta: Orthoptera)
Fig. 3: Temporal course of daily fecundity (mean + sd) in Acheta domesticus and its dependence on body mass. Three mass categories (MC) have been distinguished: MC1 ‒ 600-800 mg, MC2 ‒ 801- 100 mg, MC3 ‒ 1001-1200 mg; (a) 1st to 7th day of oviposition period; (b) 8th to 14th day; (c) 15th to 21st day, (d) 22nd to 28th day, (e) 29th to 35th day. Between most adjacent values significant differences (p <0.05) could be determined.
Fig. 2 in Dependence of daily oviposition activity and total fecundity on body mass in the house cricket Acheta domesticus (L.) (Insecta: Orthoptera)
Fig. 2: Equipment for the culture of the house cricket Acheta domesticus: (a) climate chamber with plastic boxes containing cricket nymphs, (b) glass vessels containing adults separated by gender, (c) small oviposition vessels for the investigation of daily fecundity.
Fig. 5 in Size composition, monthly condition factor and morphometrics for fishery-dependent samples of Rioraja agassizi (Chondrichthyes: Rajidae), off Santos, Southeast Brazil
Fig. 5. Relationships between total (black symbols) and gutted weight (g) (grey symbols) for male (above) and females (below) of Rioraja agassizi.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.