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1,947 results for “fate”
Meta-analysis data for Microcystin as a Biogeochemical Cycle: pools, fluxes, and fates of the cyanotoxin in inland waters
We constructed a conceptual biogeochemical model for microcystin through a comprehensive literature synthesis, identifying four major pools and nine major fluxes in lakes that also connect to the terrestrial environment. We also performed a literature synthesis, collating measurements of various pools and fluxes of microcystin in inland waters from the literature. A subset of those values were used in an analysis of microcystin detection for field surveys of waterbodies and a random effects model to estimate the mean and 95% confidence interval for various microcystin pools and fluxes in lakes.
Fate and Toxicity of Engineered Nanomaterials in the Environment: a Meta-analysis
Engineered nanomaterials (ENMs, particles less than 100 nanometers) are being manufactured at increasing levels for a variety of reasons including cosmetics, food packaging and preservation, fertilizers, and medical technology. Thousands of metric tons of ENMs are released to soils, water bodies, air, and landfills each year. These particles have distinct properties owing to their small size and relatively large surface area to volume ratio. These characteristics can result in these materials having higher reactivity and toxicity in biological systems - especially because ENMs are small enough to enter cells. However, studies on environmental and ecological effects of ENMs have shown mixed results. The goal of this project is to address three primary research questions using meta-analysis of existing literature: 1) Which ENMs have been studied and in what context? 2) How do particle identity, size, concentration, and study duration influence toxicity (as estimated by response ratios, lethal concentration (LC50), and effective concentration (EC50)) in different organisms related to the role they play in the environment? 3) What are bioaccumulation, biomagnification, and bioconcentration factors of ENMs as a function of ecosystem role and trophic level in different organisms? We collected data from 191 published scientific papers and extracted 2102 unique observations that are used to address the questions outlined above. We calculated response ratios related to biological responses of biomass, diversity, growth, metabolism, and survival to evaluate how these are influenced by ENM exposure. Values of LC50 (concentration at which 50% of test organisms died) and EC50 (concentration at which 50% of test organisms showed an effect) were collected to estimate concentrations at which toxicity occurs. Bioaccumulation (BAF), bioconcentration (BCF), and biomagnification (BMF) factors were recorded to estimate environmental accumulation and trophic transfer. This work is a resu
Supporting data for "Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision" by Chevalier et al., 2020
<p>Code, data, and notebooks used for the synthesis and simulations of ensembles of Boolean networks for the tumor invasion model introduced in <a href="https://doi.org/10.1371/journal.pcbi.1004571">(Cohen et al, 2015)</a></p> <p>Visualize online:</p> <ul> <li><a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3938904/files/Simulations%20-%20Mutant%20analysis.ipynb">Simulations - Mutant analysis.ipynb </a></li> <li> <a href="https://nbviewer.jupyter.org/urls/zenodo.org/record/3938904/files/Tumour%20-%20Synthesis%20with%20BoNesis.ipynb">Tumour - Synthesis with BoNesis.ipynb</a></li> </ul> <p>The notebooks can be executed within the <a href="http://colomoto.org/notebook">CoLoMoTo Docker</a> image 2020-07-01:</p> <pre><code>pip install -U colomoto-docker colomoto-docker -V 2020-07-01 --bind . </code></pre> <p>The synthesis additionally requires executing the following command (within the Docker image):</p> <pre><code>pip install --user bonesis-preview-20200514.zip </code></pre> <p>The ensembles have been generated with the following commands.</p> <pre><code>python synthesis.py synthesis --exact-pkn --globalfps python synthesis.py synthesis --exact-pkn --globalfps --mutant p53 --mutant NICD </code></pre> <p> </p> <ul> </ul>
The fate of interstellar objects during the collapse of molecular clouds - animations
<p>Animations of collapsing molecular clouds containing a population of interstellar objects.</p>
Data from: Random sperm use and genetic effects on worker caste fate in Atta colombica leaf-cutting ants
Sperm competition can produce fascinating adaptations with far-reaching evolutionary consequences. Social taxa make particularly interesting models, because the outcome of sexual selection determines the genetic composition of groups, with attendant sociobiological consequences. Here, we use molecular tools to uncover some of the mechanisms and consequences of sperm competition in the leaf-cutting ant Atta colombica, a species with extreme worker size polymorphism. Competitive PCR allowed quantification of the relative numbers of sperm stored by queens from different males, and offspring genotyping revealed how sperm number translated into paternity of eggs and adult workers. We demonstrate that fertilisation success is directly related to sperm numbers, that stored sperm are well mixed and that egg paternity is constant over time. Moreover, worker size was found to have a considerable genetic component, despite expectations that genetic effects on caste fate should be reduced in species with a low degree of polyandry. Our data suggest that sexual conflict over paternity is largely resolved by the lifetime commitment between mates generated by long-term sperm storage, and show that genetic variation for caste can persist in societies with comparatively high relatedness.
Data from: Effects of biochar on fate and toxicity of herbicide fenoxaprop-ethyl in soil
The biochar as soil amendment in agriculture has attracted considerable attention. In the study, the fate and toxicity of the herbicide fenoxaprop-ethyl were evaluated in soils with and without 5% rice husk biochar amendment. Fenoxaprop-ethyl and metabolite fenoxaprop degraded followed first-order kinetics in the two soils. Fenoxaprop-ethyl decreased fast with half-lives less than 2 days. Large amounts of fenoxaprop formed and remained in control soil. However, fenoxaprop was much lower in biochar-amended soil with reduction over 85% at the 35th day. The estimated half-lives of fenoxaprop were 56.9 and 1.5 days in control and biochar-amended soils, respectively. Biochar restrained the formation and promoted the dissipation of fenoxaprop. Biological indicator earthworms (Eisenia fetida) were used in a 14-day acute toxicity test. Fenoxaprop-ethyl shown low toxic to earthworms with LC50 value of 322.9 μg/g. Biochar amendment was nontoxic to earthworms and effectively reduced the toxicity. The results suggested that the application of biochar may reduce the risks of fenoxaprop-ethyl in the soil environment.
Data from: Using quantum dots as pollen labels to track the fates of individual pollen grains
1. Despite a long history of significant advances in understanding natural selection and evolution, the field of plant reproductive biology has largely studied plant mating without directly tracking pollen movement due to a lack of suitable pollen-tracking methods. 2. Here, we develop and test a novel pollen-tracking technique using quantum dots as pollen-grain labels. Quantum dots are semiconductor nanocrystals that are so small, they behave like atoms. When exposed to UV light, they emit extremely bright light in both visible and infrared wavelengths We tested the suitability of non-toxic CuInSexS2-x/ZnS (core/shell) quantum dots with oleic acid ligands as pollen-grain labels.Using a micropipette, we dispensed quantum dots dissolved in hexane in minute volumes (0.15–0.5 µl) directly onto dehisced anthers of four different plant species from four different families [Wachendorfia paniculata (Haemodoraceae), Sparaxis villosa (Iridaceae), Arctotheca calendula (Asteraceae), Oxalis purpurea (Oxalidaceae)]. 3. After application, the hexane solvent evaporated immediately, leaving behind quantum dots that remained attached to pollen grains of the four different plant species even after agitation in a polar solvent. This suggests a lipophilic interaction between oleic-acid ligands on quantum dots, and pollenkitt surrounding pollen grains. We also showed that most pollen grains within anthers of the same four plant species were labelled with quantum dots after applying a volume of quantum-dot solution sufficient to cover an individual anther. To test whether quantum-dot pollen-labels influenced pollen transport, we conducted pollen transfer trials (one donor, ten sequential recipients) on S. villosa using captively-reared honey bees to ensure bees were free of external pollen prior to experiments. We found no difference in pollen transport to recipients from donor flowers with labelled or unlabelled pollen grains. 4. We demonstrate that quantum dots can be used as pollen labels allowing subsequent tracking of pollen fates. This method is relatively inexpensive (<$500 for equipment and ca. $0.02 per labelled anther thereafter) and can be simply and directly applied to anthers of most flowers in the lab and field. The ability to track pollen grain movement in situ, may help to address an historically neglected aspect of plant reproductive ecology and evolution.
Data from: Small and ugly? Phylogenetic analyses of the "selfing syndrome" reveal complex evolutionary fates of monomorphic primrose flowers
One of the most common trends in plant evolution, loss of self-incompatibility and ensuing increases in selfing, is generally assumed to be associated with a suite of phenotypic changes, notably a reduction of floral size, termed the selfing syndrome. We investigate whether floral morphological traits indeed decrease in a deterministic fashion after losses of self-incompatibility, as traditionally expected, using a phylogeny of 124 primrose species containing nine independent transitions from heterostyly (heteromorphic incompatibility) to homostyly (monomorphic self-compatibility), a classic system for evolution of selfing. We find similar overall variability of homostylous and heterostylous species, except for diminished herkogamy in homostyles. Bayesian mixed models demonstrate differences between homostylous and heterostylous species in all traits, but net effects across species are small (except herkogamy) and directionality differs among traits. Strongly drift-like evolutionary trajectories of corolla tube length and corolla diameter inferred by Ornstein-Uhlenbeck models contrast with expected deterministic trajectories toward small floral size. Lineage-specific population genetic effects associated with evolution of selfing may explain that reductions of floral size represent one of several possible outcomes of floral evolution after loss of heterostyly in primroses. Contrary to the traditional paradigm, selfing syndromes may, but do not necessarily evolve in response to increased selfing.
The fate of Meconopsis species in the Tibeto-Himalayan region under future climate change
<p>High-mountain areas such as the Tibeto-Himalayan region (THR) host cold-adapted biota expected to be sensitive to anthropogenic climate change. <i>Meconopsis</i> is a representative endangered genus confined to alpine meadow or subnival habitats in the THR. To obtain occurrence data for <i>Meconopsis</i> species found in the THR and adjacent regions, we used records from the Chinese Virtual Herbarium (CVH: <a href="http://www.cvh.org.cn/"><span>http://www.cvh.org.cn/</span></a>), the Global Biodiversity Information Facility (GBIF: <a href="http://www.gbif.org/">http://www.gbif.org/</a>), and the published literature (He et al., 2019). We only used occurrence data collected after 1950, and removed duplicate records found within a 5-kilometer diameter. Our dataset for ten species of <i>Meconopsis </i>are the numbers of records per species ranging from 17 to 228. For these ten <i>Meconopsis</i> species, we identified potential future climate refugia and determined optimal routes for each species to disperse to the proposed refugia. Our results indicate that for the ten <i>Meconopsis</i> species the regions with low vulnerability to climate change in the THR are the central Qinghai-Tibet Plateau, the Hengduan Mountains (HDM), the eastern Himalayas, and the West Qinlin Mountain (WQL), and can be considered potential future climate refugia. Under future climate change, we found for the ten <i>Meconopsis</i> species potential dispersal routes to three of the four identified refugia: the HDM, the eastern Himalayas, and the WQL. <i> </i>Furthermore, climate change may affect the threat ranking of Red Listed Species for <i>Meconopsis</i> species, as Least Concern species were estimated to become more vulnerable to climate change than the only Near Threatened species.</p>
Empirical single-cell tracking and cell-fate simulation reveal dual roles of p53 in tumor suppression
<p>The tumor suppressor p53 regulates various stress responses via increasing its cellular levels. The lowest p53 levels occur in unstressed cells; however, the impact of these low levels on cell integrity remains unclear. To address the impact, we used empirical single-cell tracking of p53-expressing and silenced cells, and developed a fate-simulation algorithm. Here we show that p53-silenced cells underwent more frequent cell death and cell fusion, which further induced multipolar cell division to generate aneuploid progeny. Those results suggest that the low levels of p53 in unstressed cells indeed have a role to maintain the integrity of a cell population. Results of a cell-fate simulation that provides a flexible and dynamic virtual culture space confirmed that these aneuploid progeny could propagate. However, p53-silenced cells were unable to propagate in a virtual cell population that was mainly comprised of p53-expressing cells, supporting the notion that p53 acts as a tumor suppressor. In contrast, when DNA damage responses were repeatedly induced in 53-expressed cells, p53-silenced cells became the major cell population, as the growth of p53-expressed cells was more tightly suppressed by the response than that of p53-silenced cells. In this context, the p53-mediated damage response that is supposed to suppress tumor formation has a pro-malignant function. The cellular microenvironment could thus be a major factor to determine the fate of cancer cells and the fate-simulation algorithm can be used to reveal the fate. </p>
Data for: Origin and fate of the pseudogap in the doped Hubbard model
<p>Data for publication "Origin and fate of the pseudogap in the doped Hubbard model"</p>
Dataset: Fate Therapeutics, Inc. (FATE) Stock Performance
This dataset provides historical stock market performance data for specific companies. It enables users to analyze and understand the past trends and fluctuations in stock prices over time. This information can be utilized for various purposes such as investment analysis, financial research, and market trend forecasting.
The evolution and fate of super-Chandrasekhar mass white dwarf merger remnants
<p>MESA inlists associated with <a href="http://adsabs.harvard.edu/abs/2016MNRAS.463.3461S">Schwab et al. (2016)</a>. MESA version r6596.</p>
Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.
Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.
Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions
<p>This is the supplementary data archive for our study showing that:</p> <p><em><strong>Calpain DEK1 acts as a developmental switch gatekeeping cell fate transitions</strong></em></p> <p><strong>Abstract:</strong> Calpains are cysteine proteases that control cell fate transitions. Although calpains are viewed as modulatory proteases displaying severe, pleiotropic phenotypes in eukaryotes, human calpain targets are also directed to the N-end rule degradatory pathway. Several of these destabilized targets are transcription factors, hinting at a gene regulatory role. Here, we analyze the gene regulatory networks of <em>Physcomitrium</em> <em>patens</em> and characterize the regulons that are deregulated in <em>DEK1</em> calpain mutants. Predicted cleavage patterns of regulatory hierarchies in the five DEK1-controlled subnetworks are consistent with the gene’s pleiotropy and the regulatory role in cell fate transitions targeting a broad spectrum of functions. Network structure suggests DEK1-gated sequential transition between cell fates in 2D to 3D development. We anticipate that both our method combining phenotyping, transcriptomics and data science to dissect phenotypic traits and our model explaining the calpain’s role as a switch gatekeeping cell fate transitions will inform biology beyond plant development.</p>
The fate of icy pebbles undergoing sublimation in protoplanetary discs
<p>The images in this folder are the data of the paper: "The fate of icy pebbles undergoing sublimation in protoplanetary disks". <a href="https://doi.org/10.1093/mnras/stab3196">https://doi.org/10.1093/mnras/stab3196</a></p> <p>In the paper, two pebbles models are described: PA (with 50% mass composed of ice) and PB (15% of mass composed by ice, the rest is dust). We used two dust minerals commonly found in protoplanetary disks: olivine and pyroxene. We sieved the dust in three size ranges: less than 50 um (fine component), 500-100 um (medium component) and 100-300 um (coarse component). </p> <p>The result of the sublimation experiment can be obtained by measuring the area of the pebbles before and after the sublimation of the ice. If they disrupt, then the area of the disrupted pebble is bigger than the starting one. The images before and after the sublimation are labelled "before" and "end" at the end of the file name. The sample description is in the files with "label" at the end.</p> <p>The SEM images are the one displayed in figure 1 of the paper.<br> <br> The .txt file provides the spectrum of the olivine and pyroxene used in the experiment (Fig. 2 in the paper). The first column is wavelength (in nanometers) and the second one is reflectance factor.</p> <p> </p>
Data from: Effects of biochar on fate and toxicity of herbicide fenoxaprop-ethyl in soil
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Data from: All-trans retinoic acid disrupts development in ex vivo cultured fetal rat testes. I: altered seminiferous cord maturation and testicular cell fate
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Data from: A recently transferred cluster of bacterial genes in Trichomonas vaginalis –lateral gene transfer and the fate of acquired genes.
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Data from: Risk of cache pilferage determines hoarding behavior of rodents and seed fate
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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.