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Dataset results
482 results for “Digital data”
Synthesis of Digital Readiness Dimensions Over Four Frameworks and Four Data Driven Indexes
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Data for "Observation of the non-Hermitian skin effect and Fermi skin on a digital quantum computer"
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Data from: Digit ratio predicts the number of lifetime recruits in female collared flycatchers
The early environment in which an organism grows can have long-lasting impact on both its phenotype and fitness. However, assessing this environment comprehensively is a formidable task. The relative length of the second to the fourth digit (2D:4D) is a broadly studied skeletal trait that is fixed for life during ontogeny. 2D:4D has been shown to indicate various early effects including the perinatal steroid milieu in both humans and non-human animals. However, the fitness relevance of the early effects indicated by 2D:4D remains unknown. Here, we investigated hindlimb 2D:4D and measures of lifetime performance in wild collared flycatcher (Ficedula albicollis) females. We found that females with higher 2D:4D had a greater number of recruiting offspring to the breeding population. This was the case despite the fact that such females did not lay more eggs or breed more times during their reproductive life. Our results support that 2D:4D, known to be a retrospective marker of perinatal development, positively associates with female quality in the collared flycatcher.
Data from: Different evolutionary paths to complexity for small and large populations of digital organisms
A major aim of evolutionary biology is to explain the respective roles of adaptive versus non-adaptive changes in the evolution of complexity. While selection is certainly responsible for the spread and maintenance of complex phenotypes, this does not automatically imply that strong selection enhances the chance for the emergence of novel traits, that is, the origination of complexity. Population size is one parameter that alters the relative importance of adaptive and non-adaptive processes: as population size decreases, selection weakens and genetic drift grows in importance. Because of this relationship, many theories invoke a role for population size in the evolution of complexity. Such theories are difficult to test empirically because of the time required for the evolution of complexity in biological populations. Here, we used digital experimental evolution to test whether large or small asexual populations tend to evolve greater complexity. We find that both small and large—but not intermediate-sized—populations are favored to evolve larger genomes, which provides the opportunity for subsequent increases in phenotypic complexity. However, small and large populations followed different evolutionary paths towards these novel traits. Small populations evolved larger genomes by fixing slightly deleterious insertions, while large populations fixed rare beneficial insertions that increased genome size. These results demonstrate that genetic drift can lead to the evolution of complexity in small populations and that purifying selection is not powerful enough to prevent the evolution of complexity in large populations.
Data from: Examining community stability in the face of mass extinction in communities of digital organisms
Digital evolution is a computer-based instantiation of Darwinian evolution in which short self-replicating computer programs compete, mutate, and evolve. It is an excellent platform for addressing topics in long-term evolution and paleobiology, such as mass extinction and recovery, with experimental evolutionary approaches. We evolved model communities with ecological interdependence among community members, which were subjected to two principal types of mass extinction: a pulse extinction that killed randomly, and a selective press extinction involving an alteration of the abiotic environment to which the communities had to adapt. These treatments were applied at two different strengths, along with unperturbed control experiments. We examined how stability in the digital communities was affected from the perspectives of division of labor, relative shift in rank abundance, and genealogical connectedness of the community's component ecotypes. Mass extinction that was due to a Strong Press treatment was most effective in producing reshaped communities that differed from the pre-treatment ones in all of the measured perspectives; weaker versions of the treatments did not generally produce significant departures from a Control treatment; and results for the Strong Pulse treatment generally fell between those extremes. The Strong Pulse treatment differed from others in that it produced a slight but detectable shift towards more generalized communities. Compared to Press treatments, Pulse treatments also showed a greater contribution from re-evolved ecological doppelgangers rather than new ecotypes. However, relatively few Control communities showed stability in any of these metrics over the whole course of the experiment, and most did not represent stable states (by some measure of stability) that were disrupted by the extinction treatments. Our results have interesting, broad qualitative parallels with findings from the paleontological record, and show the potential of digital evolution studies to illuminate many aspects of mass extinction and recovery by addressing them in a truly experimental manner.
Data Table Digital Scholarship Plan
<p>Summary of the types of data linked to my doctoral project. </p>
Raw data - Digital scans - Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature
<p>Raw data of the manuscript "<em>Sepsis Induces Heterogeneous Transcription of Coagulation- and Inflammation-Associated Genes in Renal Microvasculature</em><em>"</em> as published in Thrombosis Research (<a href="https://doi.org/10.1016/j.thromres.2024.03.014" target="_blank" rel="noopener">doi.org/10.1016/j.thromres.2024.03.014</a>) is included. Types of included data are:</p> <p> </p> <p>- NDPI files of digital scans showing immunohistochemical (IHC) protein staining in mouse kidney</p> <p>- NDPI files of digital scans showing Martius Scarlet Blue staining (MSB) in mouse kidney</p>
Raw data - Digital scans - Sepsis-Associated Acute Kidney Injury in Mice and Humans Elicits Heterogeneous Renal Microvascular MicroRNA Responses
<p>Raw data of the manuscript "<em>Sepsis-Associated Acute Kidney Injury in Mice and Humans Elicits Heterogeneous Renal Microvascular MicroRNA Responses" </em>as published in Scientific Reports (https://doi.org/10.1038/s41598-025-17319-0) are included. Types of included data are:</p> <p> </p> <p>- NDPI files of digital scans showing miRNA in situ hybridization in mouse kidney</p>
Cognitive and Mood Assessment Data in Major Depressive Disorder Using Digital Wearable Technology
ClinicalTrials.gov study NCT03067506. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Using Digital Data to Predict CHD
ClinicalTrials.gov study NCT04574882. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Digital Data in Mental Health Therapy
ClinicalTrials.gov study NCT04011540. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Digital Auscultation Test - IPF Data Collection
ClinicalTrials.gov study NCT03503188. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Remote Digital Physiologic Data Collection in Cancer: An MSK Registry Protocol
ClinicalTrials.gov study NCT05390827. IPD Sharing: YES. Countries: 1. Publications: 0.
Cardiovascular Digital Health Data Observatory
ClinicalTrials.gov study NCT05316025. IPD Sharing: Not stated. Countries: 0. Publications: 7.
Carestream Digital Radiography Long Length Imaging Software Data Collection Protocol
ClinicalTrials.gov study NCT01592435. IPD Sharing: NO. Countries: 1. Publications: 0.
Data from: Selective press extinctions, but not random pulse extinctions, cause delayed ecological recovery in communities of digital organisms
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Data from: Context matters: sexual signaling loss in digital organisms
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Data from: Challenges with using names to link digital biodiversity information
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Data from: Different evolutionary paths to complexity for small and large populations of digital organisms
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Data from: Interaction effects of cell diffusion, cell density and public goods properties on the evolution of cooperation in digital microbes
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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.