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282 results for “data engineering”
Data from: Modification of plant-induced responses by an insect ecosystem engineer influences the colonization behaviour of subsequent shelter-users
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Data from: Experimental study on diesel engine EGR performance and Optimum EGR Rate Determination Method
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Data from: Collective aggressiveness of an ecosystem engineer is associated with coral recovery
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Data from: Genome engineering allows selective conversions of terephthalaldehyde to multiple valorized products in bacterial cells
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Data from: Ecosystem engineering strengthens bottom-up and weakens top-down effects via trait-mediated indirect interactions
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Data from: Enhancing the efficiency of planar heterojunction perovskite solar cells via interfacial engineering with 3-aminopropyl trimethoxy silane hydrolysate
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Data from: Engineering repressors with coevolutionary cues facilitates toggle switches with a master reset
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Data from: Optimized modelling and application of exhaust gas recirculation performance evaluation of turbocharged diesel engine
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Expression data from cyclically stretched engineered neonatal rat ventricuar myocyte (NRVM) tissues
GEO Series GSE43846. Rattus norvegicus. 51 samples. Type: Expression profiling by array.
Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [Pilot_Data]
GEO Series GSE241839. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing data of Candida albicans white, opaque, and white engineered cells under mating conditions
GEO Series GSE103674. Candida albicans. 10 samples. Type: Expression profiling by high throughput sequencing.
Expression data from genetically engineered mouse models (GEMMs)
GEO Series GSE39557. Mus musculus. 15 samples. Type: Expression profiling by array.
Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells [CROPSeq_Data]
GEO Series GSE241882. Homo sapiens. 3 samples. Type: Expression profiling by high throughput sequencing.
RNAseq data for mouse mammary tumors from three novel genetically engineered mouse models combining loss of Brca1, p53 and Rb supression
GEO Series GSE206068. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Research Data Supporting "Engineering synthetic breath biomarkers for respiratory disease"
<p>Raw research data supporting the publication:</p> <p>Chan L., et al., 2020, Nature Nanotechnology, In press</p>
VEGFA dependent endothelial lumen formation in scaffold-free tissue engineering: a hybrid in vitro and in silico approach to improve vascularization of tissue: Spheroid simulation data
<p>Vascularization is a tightly regulated process involving a complex interplay of multiple bio-signaling events. Among these events, lumen formation is a crucial rate-limiting step in successful anastomosis of tissue engineered constructs in a host. We have developed scaffold-free endothelial-fibroblast based constructs with preformed microvessel networks that are a promising approach to rapid host-implant anastomosis. However, rapid formation of a continuous endothelial lumen within the microvessels remains elusive. We propose that pretreatment of these constructs with vascular endothelial growth factor A, a potent proangiogenic molecule, can improve large caliber lumen formation within constructs during <i>in vitro</i> self-assembly.</p> <p>Here, we present a hybrid <i>in vitro </i>and <i>in silico </i>approach to evaluating endothelial-fibroblast spheroid self-assembly and the effects of VEGF-A on lumen formation. Our VEGF-A dosing experiments ultimately demonstrated that our endothelial cells responded to VEGF-A by increased clustering tendency and hollow lumen formation. This behavior was coincident with an increase in polarization markers as well as a time and dose dependent increase in diameter of lumens. We used these observations to develop a simulation model using the Cellular Potts framework, a modeling framework that is well-adapted to tissue self-assembly. The model explores how changes in interfacial energy costs between cell types in our model as well as changes in basic cell parameters such as response to VEGF-A, growth and proliferation can alter dynamics of lumen formation within a construct. From our model, we ran a series of simulated experiments to generate tissues with an optimal distribution of large caliber vessels. Our analysis of the resulting regression model identified several statistically significant modifiable factors that could be mapped back to potential spheroid pretreatment strategies. These strategies could augment VEGF-mediated lumen formation and provide rationale for alterations in the design of our constructs.</p>
Data from: An insect ecosystem engineer alleviates drought stress in plants without increasing plant susceptibility to an above-ground herbivore
Climate change models predict more extreme rainfall patterns, ranging from droughts to deluges, which will inevitably affect primary productivity in many terrestrial ecosystems. Insects within the ecosystem, living above- and below-ground, may modify plant responses to water stress. For example, some functional groups improve soil conditions via resource provision, potentially alleviating water stress. Enhanced resource provision may, however, render plants more susceptible to herbivores and negate beneficial effects. Using a model system, we tested how plants (Brassica oleracea) responded to drought, ambient and increased precipitation scenarios when interacting with both a soil conditioning ecosystem engineer (dung beetles; Bubas bison) and an above-ground herbivore, the major crop pest diamondback moth (Plutella xylostella). Dung beetles enhanced soil water retention by 10% and promoted growth in plants subjected to drought by 280%, relieving the impacts of water stress on plants. Under drought conditions, plants grown with dung beetles had c. 30% more leaves and were over twice as tall as those without dung beetles. Dung beetles produced a 2·7-fold increase in nitrogen content and more than a threefold increase in carbon content of the shoots, though shoot concentrations of nitrogen and carbon were unchanged. Carbon concentrations in roots, however, were increased by dung beetles under both ambient and increased precipitation regimes. Increased precipitation reduced root and shoot nitrogen concentrations by 16% and 30%, relative to plants under ambient regimes, respectively, most likely due to dilution effects of increased plant growth under increased precipitation. Soil carbon and nitrogen concentrations were largely unaffected. While dung beetles enhanced plant growth and nitrogen content in plants experiencing drought, the anticipated increase in plant suitability to herbivores did not arise, possibly because shoot nitrogen concentrations and C:N ratio were unaffected. To our knowledge, this is the first report of an insect ecosystem engineer alleviating the effects of predicted drought events on plants via physical manipulation of the soil matrix. Moreover, their effects did not change plant suitability to an above-ground herbivore, pointing to potential beneficial role for insect ecosystem engineers in climate change adaptation and crop protection.
Data from: Engineered action at a distance: blood-meal-inducible paralysis in Aedes aegypti
Background: Population suppression through mass-release of Aedes aegypti males carrying dominant-lethal transgenes has been demonstrated in the field. Where population dynamics show negative density-dependence, suppression can be enhanced if lethality occurs after the density-dependent (i.e. larval) stage. Existing molecular tools have limited current examples of such Genetic Pest Management (GPM) systems to achieving this through engineering 'cell-autonomous effectors' i.e. where the expressed deleterious protein is restricted to the cells in which it is expressed – usually under the control of the regulatory elements (e.g. promoter regions) used to build the system. This limits the flexibility of these technologies as regulatory regions with useful spatial, temporal or sex-specific expression patterns may only be employed if the cells they direct expression in are simultaneously sensitive to existing effectors, and also precludes the targeting of extracellular regions such as cell-surface receptors. Expanding the toolset to 'non-cell autonomous' effectors would significantly reduce these limitations. Methodology/Principal Findings: We sought to engineer female-specific, late-acting lethality through employing the Ae. aegypti VitellogeninA1 promoter to drive blood-meal-inducible, fat-body specific expression of tTAV. Initial attempts using pro-apoptotic effectors gave no evident phenotype, potentially due to the lower sensitivity of terminally-differentiated fat-body cells to programmed-death signals. Subsequently, we dissociated the temporal and spatial expression of this system by engineering a novel synthetic effector (Scorpion neurotoxin – TetO-gp67.AaHIT) designed to be secreted out of the tissue in which it was expressed (fat-body) and then affect cells elsewhere (neuro-muscular junctions). This resulted in a striking, temporary-paralysis phenotype after blood-feeding. Conclusions/Significance: These results are significant in demonstrating for the first time an engineered 'action at a distance' phenotype in a non-model pest insect. The potential to dissociate temporal and spatial expression patterns of useful endogenous regulatory elements will extend to a variety of other pest insects and effectors.
Tissue-engineered oral epithelial barrier for dental material testing: towards establishing in vitro biomimetic models - Underlying data
<p>Underlying CT data of "<strong>Tissue-engineered oral epithelial barrier for dental material testing: towards establishing <em>in vitro </em>biomimetic models</strong>"<br><a href="https://doi.org/10.1089/ten.tec.2024.0154">https://doi.org/10.1089/ten.tec.2024.0154</a></p> <p>Foteini Machla a, Paraskevi Kyriaki Monou b, c, Chrysanthi Bekiari d, Dimitrios Andreadis e Evangelia Kofidou d, , Emmanouel Panteris f, Orestis L. Katsamenis g, h, Maria Kokoti a, Petros Koidis a, Imad About i, Dimitrios Fatourosb, c, Athina Bakopoulou a</p> <p>a Department of Prosthodontics, Tissue Engineering Core Unit, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>b Department of Pharmaceutical Technology, School of Pharmacy, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>c Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Thessaloniki 57001, Greece</p> <p>d Laboratory of Anatomy and Histology, Veterinary School, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>e Department of Oral Medicine/Pathology, School of Dentistry, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>f Department of Botany, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece</p> <p>g μ-VIS X-ray Imaging Centre, Faculty of Engineering and the Environment, University of Southampton, Southampton SO17 1BJ, United Kingdom</p> <p>h Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom UK</p> <p>i Centre National de la Recherche Scientifique, Institute of Movement Sciences, Aix Marseille University, Marseille 13385, France</p> <p> </p> <p><strong>Measurement of ΤΕΟΕ thickness</strong></p> <p>X-ray computed micro-tomography (μCT) as employed to examine the microstructure of the paraffin-embedded tissue engineered oral epithelium (TEOE), enabling comprehensive 3D assessment of thickness using volumetric analysis (cf. supplementary for imaging parameters) (11). Imaging was conducted using an isotropic voxel-edge of 6.0 μm. Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software (cf. supplementary), allowing for the visualization and quantification of the spatial distribution and variability of tissue thickness.</p> <p>Imaging was conducted at the University of Southampton’s μ-VIS X-ray Imaging Centre ( https://muvis.org ) / 3D X-ray Histology facility, utilizing a customised μCT scanner optimisedfor intricate histological analyses(1), based on Nikon’s XTH225ST system (Nikon Metrology, UK). Operating parameters were set at 80 kVp / 86 μA (6.88 W), with a source-to-object distance of 37.5 mm and a source-to-detector distance of 937.4 mm, resulting in a magnification factor of 25x and an isotropic voxel-edge of 6.0 μm. Imaging acquisition involved the collection of 4001 projections using a 2850 x 2850 dexels detector, by averaging 4 frames per projection, with an exposure time of 500 ms per projection.</p> <p>Visualisation and analysis of the reconstructed dataset was done using Dragonfly software (Comet Technologies Canada Inc.; software accessible at http://www.theobjects.com/dragonfly). Assessment of Local Thickness was carried out in 3D using the “Volume Thickness Map” tool within Dragonfly software, following segmentation of the tissue layer. Local thickness analysis allowed for the visualization and quantification of the spatial distribution and variability of thickness within the tissue engineered oral epithelium (TEOE).</p> <p>Visual representation of local thickness histograms was employed to elucidate the distribution of thickness throughout the TEOE. These histograms effectively illustrate the number of voxels associated with specific cross-sectional thickness, offering both a graphical depiction of the variation in thickness across the tissue sample, and a quantitative measure of the average thickness of the specimen.</p> <p>It's worth noting, the volumetric and non-destructive nature of the technique enabled whole-block imaging, which proved crucial in addressing challenges arising from tissue sample shrinkage. This shrinkage, a consequence of dehydration during the fixation process, can occur in some cases and lead led to the specimen wrapping. While wrapping is not a common occurrence, this analysis method allowed for the evaluation of challenging-shaped specimens, such as the wrapped one presented in Figure 4. Unlike conventional 2D methods such as classical histology, which rely on the angle of slicing and encounter limitations when dealing with non-perfectly perpendicular slicing, μCT-based XRH enables analysis of all specimens, including those with complex shapes.</p> <p> </p>
Data from: Northern flickers only work when they have to: how individual traits, population size and landscape disturbances affect excavation rates of an ecosystem engineer
Woodpeckers are considered ecosystem engineers because they excavate tree cavities which are used subsequently by many species of secondary cavity nesters for breeding. Woodpeckers have the choice of excavating a new hole or reusing an existing one, and this propensity to excavate (e) may affect community dynamics but has rarely been investigated. Using 18 years of data on a population of northern flickers Colaptes auratus, I tested six hypotheses to explain the propensity to excavate (e) in a landscape which experienced two types of disturbance: pine beetles and wildfires. Woodpecker age, breeding experience and mate retention had little influence on e which varied between 13-39% annually and averaged 23% for 1843 first nests over the 18 years. Body size and body condition of males and females were not associated with e but rates of excavation declined seasonally, suggesting time rather than energy costs limited excavation effort. Reduced cavity availability mediated through high conspecific density coupled with wildfires triggered relatively high excavation rates, up to 39% but e decreased to baseline levels three years after the landscape disturbances. Nearly 2/3 of males did not excavate in their lifetime but apparently, e is great enough to balance the average rate of cavity tree loss in this forest which is 11% annually. Excavation propensity in flickers is flexible, but the birds reduce their work levels if there is a surplus of holes available.
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.