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57 results for “Long-term Adaptation”
DELTA: Dense Electromyography for Long-Term Adaptive control
<p>The <em><strong>DELTA </strong></em>dataset, namely ”<strong>D</strong>ense <strong>E</strong>lectromyography for <strong>L</strong>ong-<strong>T</strong>erm <strong>A</strong>daptive control”, holds significance in the realm of prosthetic applications, featuring High Density surface Electromyography data collected over an extended duration. It serves as a valuable resource for training data-driven models and testing them under conditions that closely emulate real-world prosthetic applications. Recognizing the temporal variability in EMG data, constructing models that are agnostic to such fluctuations could significantly enhance the efficacy of machine learning models in prosthetic applications</p>
Dataset for the paper "Combining near-term benefits of climate adaptation with long-term benefits of emissions abatement"
<p>This repo archives all data used in Duan et al. (2024), including model codes, raw model outputs, and post-processing scripts. </p> <p>A Readme file describes the data and structure included here. If you have any questions, please contact the lead author (Lei Duan: leiduan@carnegiescience.edu). </p> <p>We have updated the post-process codes to reflect changes in the revised manuscript</p> <p>==</p> <p>Paper associated with this dataset can be found at: https://www.nature.com/articles/s43247-024-01976-6#:~:text=Adaptation%20deployed%20in%20conjunction%20with,adaptation%20reducing%20near%2Dterm%20damage. </p>
Data from: Maintaining local adaptation is key for evolutionary rescue and long-term persistence of populations experiencing habitat loss and a changing environment
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Exo-Metabolomics Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Exo-Metabolomics Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Illumina Sequencing Data for "Phocaeicola vulgatus shapes the long-term growth dynamics and evolutionary adaptations of Clostridioides difficile"
<p>Illumina Sequencing Data for "<em>Phocaeicola vulgatus</em> shapes the long-term growth dynamics and evolutionary adaptations of <em>Clostridioides difficile</em>"</p>
Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host
<p>Scripts and data used in the work "Evolved transcriptional responses and their trade-offs after long-term adaptation of Bemisia tabaci to a marginally-suitable host".</p> <p><strong>Abstract: </strong>Although generalist insect herbivores can migrate and rapidly adapt to a broad range of host plants, they can face significant difficulties when accidentally migrating to novel and marginally-suitable hosts. What happens, at both the performance and transcriptional levels, if these marginally-suitable hosts must be used for multiple generations before migration to a suitable host can take place, largely remains unknown. In this study, we established multigenerational colonies of the whitefly <em>Bemisia tabaci</em>, a generalist phloem-feeding species, adapted to a marginally-suitable host (habanero pepper) or an optimal host (cotton). We used reciprocal host tests to estimate the differences in performance of the populations on both hosts under optimal (30 <sup>o</sup>C) and mild-stressful (24 <sup>o</sup>C) temperature conditions, and documented the associated transcriptomic changes. The habanero pepper-adapted population greatly improved its performance on habanero pepper but did not reach its performance level on cotton, the original host. It also showed reduced performance on cotton, relative to the non-adapted population, and an antagonistic effect of the lower-temperature stressor. The transcriptomic data revealed that most of the expression changes, associated with long-term adaptation to habanero pepper, can be categorized as “evolved” with no initial plastic response. Three molecular functions dominated: enhanced formation of cuticle structural constituents, enhanced activity of oxidation-reduction processes involved in neutralization of phytotoxins and reduced production of proteins from the cathepsin B family. Taken together, these findings indicate that generalist insects can adapt to novel host plants by modifying the expression of a relatively small set of specific molecular functions.</p>
Data from: Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform
<p>The majority of cancer deaths are caused by solid tumors, where the four most prevalent cancers (breast, lung, colorectal and prostate) account for more than 60% of all cases (1). Tumor cell heterogeneity driven by variable cancer microenvironments, such as hypoxia, is a key determinant of therapeutic outcome. We developed a novel culture protocol, termed the Long-Term Hypoxia (LTHY) time course, to recapitulate the gradual development of severe hypoxia seen in vivo to mimic conditions observed in primary tumors. Cells subjected to LTHY underwent a non-canonical epithelial to mesenchymal transition (EMT) based on miRNA and mRNA signatures as well as displayed EMT-like morphological changes. Concomitant to this, we report production of a novel truncated isoform of WT1 transcription factor (tWt1), a non-canonical EMT driver, with expression driven by a yet undescribed intronic promoter through hypoxia-responsive elements (HREs). We further demonstrated that tWt1 initiates translation from an intron-derived start codon, retains proper subcellular localization and DNA binding. A similar tWt1 is also expressed in LTHY-cultured human cancer cell lines as well as primary cancers and predicts long-term patient survival. Our study not only demonstrates the importance of culture conditions that better mimic those observed in primary cancers, especially with regards to hypoxia, but also identifies a novel isoform of WT1 which correlates with poor long-term survival in ovarian cancer.</p>
Data from: Is adaptation associated with long-term persistence beyond a geographic range limit?
<p>Adaptation to new habitats might facilitate species' range shifts in response to climate change. In 2005, we transplanted experimental populations of coastal dune plant <em>Camissoniopsis cheiranthifolia </em>into four sites within and one site beyond its poleward range limit. Beyond-range transplants had high fitness and often delayed reproduction. To test for adaptation associated with experimental range expansion, we transplanted descendants from beyond and within-range populations after 10 generations <em>in situ</em> into two sites within the range, one at the range edge, and two sites beyond the range. We expected to detect adaptation to beyond-range conditions due to substantial genetic variation within experimental populations and environmental variation among sites. However, individuals from beyond-range experimental populations were not fitter than those from within the range when planted at either beyond-range site, indicating no adaptation to the beyond-range site or beyond-range environments in general. Beyond-range descendants also did not suffer lower fitness within the range. Although reproduction was again delayed beyond the range, late reproduction was not favored more strongly beyond than within the range, and beyond-range descendants did not delay reproduction more than within-range descendants. Persistence in beyond-range environments may not require adaptation, which could allow a rapid response to climate change.</p>
Long-Term Physiological Adaptations Induced by Short-Interval High-Intensity Exercises
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Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
<p>Organic ultraviolet filters (UVFs) are contaminants of concern, ubiquitously found in many aquatic environments due to their use in personal care products to protect against ultraviolet radiation. Research regarding the toxicity of UVFs such as avobenzone, octocrylene and oxybenzone indicates that these chemicals may pose a threat to invertebrate species; however, minimal long-term studies have been conducted to determine how these UVFs may affect continuously exposed populations. The present study modeled the effects of a 5-generation exposure of <em>Daphnia</em> <em>magna</em> to these UVFs at environmental concentrations. Avobenzone and octocrylene resulted in minor, transient decreases in reproduction and wet mass. Oxybenzone exposure resulted in > 40% mortality, 46% decreased reproduction and 4-fold greater reproductive failure over the F0 and F1 generations; however, normal function was largely regained by the F2 generation. These results indicate that <em>Daphnia</em> are able to acclimate over long-term exposures to concentrations of 6.59 μg/L avobenzone, ~0.6 μg/L octocrylene or 16.5 μg/L oxybenzone. This suggests that short-term studies indicating high toxicity may not accurately represent long-term outcomes in wild populations, adding additional complexity to risk assessment practices at a time when many regions are considering or implementing UVF bans in order to protect these most sensitive invertebrate species.</p>
Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation : simulated data
<p>Data simulated with Aevol (<a href="http://www.aevol.fr">www.aevol.fr</a>), a software available on gitlab ( <a href="https://gitlab.inria.fr/aevol/aevol">https://gitlab.inria.fr/aevol/aevol</a> ), for our paper submitted to Molecular Ecology entitled "Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation".</p>
Can short-term data accurately model long-term environmental exposures? Investigating the multigenerational adaptation potential of Daphnia magna to environmental concentrations of organic ultraviolet filters
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Data from: Long-term severe hypoxia adaptation induces non-canonical EMT and a novel Wilms Tumor 1 (WT1) isoform
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Data from: Local adaptation is highest in populations with stable long-term growth
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Phenotypic, fitness and environmental data in support of the publication: selection favors adaptive plasticity in a long-term reciprocal transplant experiment
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Data from: Is adaptation associated with long-term persistence beyond a geographic range limit?
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Data from: Long-term dynamics of adaptation in asexual populations
Experimental studies of evolution have increased greatly in recent years, stimulated by the growing power of genomic tools. However, organismal fitness remains the ultimate metric for interpreting these experiments, and the dynamics of fitness remain poorly understood over long timescales. Here, we examine fitness trajectories for 12 Escherichia coli populations during 50,000 generations. Mean fitness appears to increase without bound, consistent with a power law. We also derive this power-law relation theoretically by incorporating clonal interference and diminishing-returns epistasis into a dynamical model of changes in mean fitness over time.
Long-term adaptation of lymphoma cell lines to hypoxia is mediated by diverse molecular mechanisms that are targetable with specific inhibitors - Supplemental Data Tables
<p><strong>Supplemental Data Table - Metabolome.xlsx</strong> - a complete list of measured metabolites for Ramos and HBL2 cell lines. Peak area values for normoxic and hypoxia-adapted cells in triplicates. Mean log 2 fold change and adjusted P values are provided for all metabolites except those under the limits of detection.</p> <p><strong>Supplemental Data Table - Transcriptome Differential Expression.xlsx</strong> - the tables of all transcripts detected in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls. Fold change and log 2 fold change, log 2 CPM, F statistic, P value and False Discovery Rate (FDR) were calculated using EdgeR package. Last column shows if a transcript was significantly <em>up</em>- or <em>down</em>regulated or not (<em>ns</em>).</p> <p><strong>Supplemental Data Table - Transcriptome Gene Set Analysis.xlsx</strong> - the tables of the gene set enrichment analysis of Reactome pathways in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Proteome Differential Expression.xlsx</strong> - the tables of proteins detected and differentially expressed in hypoxia-adapted HBL2 and Ramos lymphoma cell lines compared to normoxic controls.</p> <p><strong>Supplemental Data Table - Cell lines SNV characterization.xlsx</strong> - the tables of mutations (single nucleotide variations and short indels) detected in four tested lymphpoma cell lines and corresponding primary tumor (PT) samples. AF_CTRL - allelic frequency (0..1) in healthy control DNA from the patient, AF_PT - allelic frequency in primary tumor, AF_PDCL - allelic frequency in patient-derived cell line. DP - total sequence depth, TLOD - Log odds that the variant is present in the tumor sample relative to the expected noise. Gencode and HGNC annotation columns are output of the Funcotator analysis. SNVs were detected using Mutect2 as a part of GATK 4.6.0.0 somatic variat calling pipeline.</p>
Thermal adaptation of microbial respiration persists throughout long-term soil carbon decomposition
<p>The microbial respiration data supporting the main findings of the study titled 'Thermal adaptation of microbial respiration persists throughout long-term soil carbon decomposition'. Mass-specific microbial respiration was consistently lower under higher long-term incubation temperatures, suggesting the occurrence and persistence of microbial thermal adaptation in long-term soil carbon decomposition.</p>
Immediate and Long-term Effects of an Adaptation of the "Balloon-blowing Exercise"
ClinicalTrials.gov study NCT04737824. IPD Sharing: UNDECIDED. Countries: 1. Publications: 3.
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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.