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1,930 results for “Matrix”
Census demographic data for the InMAP Source-Receptor Matrix (ISRM) dataset
<p>The InMAP Source-Receptor Matrix (ISRM) estimates the air quality impacts of emissions released from any source location in the contiguous United States to any receptor location. Specifically, the values in the ISRM dataset are the change in PM<sub>2.5</sub> concentration (µg m<sup>-3</sup>) in any receptor grid cell per unit of emissions (µg sec<sup>-1</sup>) in any source grid cell. ISRM was created from repeated runs of the Intervention Model for Air Pollution (<a href="http://spatialmodel.com/inmap/">InMAP</a>), isolating the impact of emissions from every grid cell in InMAP and from three emission heights representing ground-level, low-stack, and high-stack emissions. A file of the marginal impacts of emissions from each source location is also included ("marginal_values.csv"), which summarizes the estimates in ISRM by each source grid cell in terms of monetary damages ($ tonne<sup>-1</sup>), increased mortality (deaths tonne<sup>-1</sup>), and population exposure (population*µg m<sup>-3</sup> tonne<sup>-1</sup>).</p> <p>These files join US Census demographic information to the ISRM to facilitate future analyses. The original ISRM file can be found here: <a href="https://zenodo.org/record/3590127#.Xt0Z4GhKhPb">https://zenodo.org/record/3590127#.Xt0Z4GhKhPb</a></p>
ToxicoDB: an integrated database to mine and visualize large-scale toxicogenomic datasets (drug matrix dataset)
<p>This data was generated by Ganter B, Snyder RD, Halbert DN, Lee MD. Toxicogenomics in drug discovery and development: mechanistic analysis of compound/class-dependent effects using the DrugMatrix database. Pharmacogenomics [Internet]. 2006 Oct;7(7):1025–1044. Available from: http://dx.doi.org/10.2217/14622416.7.7.1025 PMID: 17054413. The data have been curated and analyzed using our open-source R package, <em>ToxicoGx</em> (<a href="https://cran.r-project.org/web/packages/ToxicoGx/">cran.r-project.org/web/packages/ToxicoGx</a>) and are available publicly in the <em>ToxicoDB </em>web application (<a href="http://www.toxicodb.ca">www.toxicodb.ca</a>).</p> <p> </p> <p> </p>
The Ubiquitin Ligase WWP1 Contributes to Shifts in Matrix Proteolytic Profiles and a Myocardial Aging Phenotype with Diastolic Heart Failure
<p><strong><em>Aims</em></strong>. Ubiquitylation is a key event that regulates protein turnover, and induction of the ubiquitin ligase E3 WWP1 has been associated with age. Left ventricular hypertrophy (LVH) commonly occurs as a function of age and can cause heart failure with a preserved ejection fraction (EF; HFpEF). We hypothesized that overexpression (O/E) of WWP1 in the heart would cause LVH as well as functional and structural changes consistent with the aging HFpEF phenotype.</p> <p><strong><em>Methods and Results.</em></strong> Global WWP1 O/E was achieved in mice (n=11) and echocardiography (40 MHz) performed to measure LV mass, EF, Doppler velocities (early-E, late/atrial-A), myocardial relaxation (E’), and isovolumetric relaxation time (IVRT) at 4, 6, and 8 weeks. Age matched wild type animals (n=15) were included as referent controls. LV EF was identical (60+1% vs 60+1%, p>0.90) with no difference in LV mass (67+3 vs 75+5, p>0.25) at 4 weeks. However, at 8 weeks of age, LV mass increased by over two-fold, E/A fell (impaired passive filling), and E/E’ was lower and IVRT prolonged (impaired LV relaxation) - all p<0.05. Collagen percent area increased by over two-fold and fibrillar collagen expression (rtPCR) by over 1.5 fold (p<0.05) with WWP1 O/E. WWP1 with an anti-WWP1 antibody could be identified in isolated cardiac fibroblasts with WWP1 increased by over two-fold in O/E fibroblasts (p<0.05).</p> <p><strong><em>Conclusion.</em></strong> Inducing WWP1 expression caused LVH, preserved systolic function, but impaired diastolic dysfunction, consistent with the HFpEF phenotype. Targeting the WWP1 pathway may be a novel therapeutic target for this intractable form of HF associated with aging.</p>
Composite amine mixed matrix membranes for highpressure CO2-CH4 separation: synthesis, characterization and performance evaluation
<p>The key challenge in composite mixed matrix membrane (MMMs) synthesis is the incompatible membrane fabrication using porous support in the dry-wet phase inversion technique. The key objective of this research to synthesis thin composite ternary (amine) mixed matrix membranes on microporous support by incorporating 10 wt. % of carbon molecular sieve (CMS) and 5-15 wt. % of diethanolamine (DEA) in polyethersulfone (PES) dope solution for the separation of carbon dioxide (CO<sub>2</sub>) from methane (CH<sub>4</sub>). The developed membranes were evaluated for their morphological structure, thermal and mechanical stabilities, functional groups, as well as the CO<sub>2</sub>-CH<sub>4</sub> separation performance at high pressure (10-30 bar). The results showed that the developed membranes have asymmetric structure, and mechanically strong at 30 bar. A new class of PES/CMS/DEA composite MMMs exhibited improved gas permeance compared to pure PES composite polymeric membrane. The permselectivty of CO<sub>2</sub>/CH<sub>4</sub> enhanced from 8.15 to 16.04 at 15 wt.% of DEA at 30 bar pressure. The performance of amine composite MMMs is theoretically predicted using a modified Maxwell model. The predictions were in good agreement with experimental data after applying the optimized values with AARE % = ~ less 2 % and R<sup>2</sup> = 0.99.</p>
Aligned DNA sequence matrix for phylogenetic analyses in the article "Three new species of frogs of the genus Pristimantis (Anura: Strabomantidae) with a redefinition of the P. lacrimosus species group"
<p>Aligned DNA sequence matrix for phylogenetic analyses of the article "Three new species of frogs of the genus Pristimantis (Anura: Strabomantidae) with a redefinition of the P. lacrimosus species group". The matrix is in NEXUS format.</p> <p>Gene partitions are arranged as follows (tRNAs are included as part of larger adjacent genes):</p> <p>RAG1 codon position 1 = 1-625\3;<br> RAG1 codon position 2 = 2-626\3;<br> RAG1 codon position 3 = 3-627\3;<br> 12S rRNA = 628-1440;<br> 16S rRNA = 1441-3071;<br> ND1 codon position 1 = 3072-3972\3;<br> ND1 codon position 2 = 3073-3973\3;<br> ND1 codon position 3 = 3074-3974\3;</p>
Data and R code for What you see is where you go: visibility influences movement decisions of a forest bird navigating a 3D structured matrix
<p>Animal spatial behaviour is often presumed to reflect responses to visual cues. However, inference of behaviour in relation to the environment is challenged by the lack of objective methods to identify the information that effectively is available to an animal from a given location. In general, animals are assumed to have unconstrained information on the environment within a detection circle of a certain radius (the perceptual range; PR). However, visual cues are only available up to the first physical obstruction within an animal's PR, making information availability a function of an animal's location within the physical environment (the effective visual perceptual range; EVPR). By using LiDAR data and viewshed analysis, we model forest birds' EVPRs at each step along a movement path. We found that the EVPR was on average 0.063% that of an unconstrained PR and, by applying a step-selection analysis, that individuals are 1.57 times more likely to move to a tree within their EVPR than to an equivalent tree outside it. This demonstrates that behavioural choices can be substantially impacted by the characteristics of an individual's EVPR and highlights that inferences made from movement data may be improved by accounting for the EVPR.</p>
Telychian Bryozoa, Matrix (Bryozoans from the lower Silurian (Telychian) Hanchiatien Formation from southern Chongqing, South China)
<p>Eight bryozoan species are described from the Hanchiatien Formation (lower Silurian, Telychian) of southern Chongqing, South China. Four species are new: the trepostomes <i>Asperopora sinensis </i>n. sp., <i>Trematopora jiebeiensis</i> n. sp., and <i>Trematopora tenuis </i>n. sp., and the fenestrate <i>Moorephylloporina parvula</i> n. sp. One species, a cystoporate <i>Hennigopora</i> sp. is described in open nomenclature. <i>Moorephylloporina parvula</i> n. sp. is eurytopic, occurring in all types of facies within the bioherms. Erect <i>Moorephylloporina</i>, <i>Trematopora</i> and <i>Leioclema</i> form pioneering communities on weakly cemented substrates, whereas encrusting <i>Fistulipora</i>, <i>Hennigopora</i> and <i>Asperopora</i> occur on hardgrounds and form densely compact framestones. Robust branched <i>Trematopora</i> and <i>Leioclema</i> tend to occur out of the reef core (framework) where they may have formed reef-flank thickets in more agitated conditions. The generic composition of the studied fauna correlates with other localities in South China, and they show general palaeobiogeographic relations to Siberia and Indiana, USA.</p>
Table 8: Pairwise comparison matrix – driver and motorcyclist perceptions
<p>Pairwise comparison matrix for driver and motorcyclist perceptions</p>
Crosstalk between Mast Cells and Lung Fibroblasts Is Modified by Alveolar Extracellular Matrix and Influences Epithelial Migration
<p>Datasets for the data generated and presented in the article: https://doi.org/10.3390/ijms22020506</p>
Three-dimensional biofilm growth supports a mutualism involving matrix and nutrient sharing - related scripts and data
<p>This dataset contains the supporting scripts and data used to analyze co-culture fluorescent colony images in high-throughput. It contains some example images that can be used in the scripts.</p> <p>It also contains the script used to plot and determine the maximum growth rates of growth curves of some of the mutants and the script used to stitch overlapping microscope images.</p>
Data from: Tomato Sl3-MMP, a member of the Matrix metalloproteinase family, is required for disease resistance against Botrytis cinerea and Pseudomonas syringae pv. tomato DC3000
Background: Matrix metalloproteinases (MMPs) are a family of zinc-dependent endopeptidases. MMPs have been characterized in detail in mammals and shown to play key roles in many physiological and pathological processes. Although MMPs in some plant species have been identified, the function of MMPs in biotic stress responses remains elusive. Results: A total of five MMP genes were identified in tomato genome. qRT-PCR analysis revealed that expression of Sl-MMP genes was induced with distinct patterns by infection of Botrytis cinerea and Pseudomonas syringae pv. tomato (Pst) DC3000 and by treatment with defense-related hormones such as salicylic acid, jasmonic acid and ethylene precursor 1-amino cyclopropane-1-carboxylic acid. Virus-induced gene silencing (VIGS)-based knockdown of individual Sl-MMPs and disease assays indicated that silencing of Sl3-MMP resulted in reduced resistance to B. cinerea and Pst DC3000, whereas silencing of other four Sl-MMPs did not affect the disease resistance against these two pathogens. The Sl3-MMP-silenced tomato plants responded with increased accumulation of reactive oxygen species and alerted expression of defense genes after infection of B. cinerea. Transient expression of Sl3-MMP in leaves of Nicotiana benthamiana led to an enhanced resistance to B. cinerea and upregulated expression of defense-related genes. Biochemical assays revealed that the recombinant mature Sl3-MMP protein had proteolytic activities in vitro with distinct preferences for specificity of cleavage sites. The Sl3-MMP protein was targeted onto the plasma membrane of plant cells when transiently expressed in onion epidermal cells. Conclusion: VIGS-based knockdown of Sl3-MMP expression in tomato and gain-of-function transient expression of Sl3-MMP in N. benthamiana demonstrate that Sl3-MMP functions as a positive regulator of defense response against B. cinerea and Pst DC3000.
Data from: What affects the predictability of evolutionary constraints using a G-matrix? The relative effects of modular pleiotropy and mutational correlation
Phenotypic traits do not always respond to selection independently from each other and often show correlated responses to selection. The structure of a genotype-phenotype map (GP map) determines trait covariation, which involves variation in the degree and strength of the pleiotropic effects of the underlying genes. It is still unclear, and debated, how much of that structure can be deduced from variational properties of quantitative traits that are inferred from their genetic (co)variance matrix (G-matrix). Here we aim to clarify how the extent of pleiotropy and the correlation among the pleiotropic effects of mutations differentially affect the structure of a G-matrix and our ability to detect genetic constraints from its eigen decomposition. We show that the eigenvectors of a G-matrix can be predictive of evolutionary constraints when they map to underlying pleiotropic modules with correlated mutational effects. Without mutational correlation, evolutionary constraints caused by the fitness costs associated with increased pleiotropy are harder to infer from evolutionary metrics based on a G-matrix's geometric properties because uncorrelated pleiotropic effects do not affect traits' genetic correlations. Correlational selection induces much weaker modular partitioning of traits' genetic correlations in absence then in presence of underlying modular pleiotropy.
Data from: Local predation risk and matrix permeability interact to shape movement strategy
In fragmented landscapes, the reduced connectivity among patches drives the evolution of movement strategies through an increase of transience costs. Reduced movements may further alter heterogeneity in biotic and abiotic conditions experienced by individuals. The joint action of local conditions and matrix permeability may shape emigration decisions. Here, we tested the interactive effects of predation risk and matrix permeability on movement propensity, movement costs and movers' phenotype in the common toad Bufo bufo. In a full-crossed experimental design, we assessed the movement propensity of juveniles in three connectivity treatments (from poorly to highly permeable matrix), with or without predation risk in their living patch. We also assessed the relationships between movement propensity and morphological traits (i.e. body and leg length) and how it affected the movement cost (i.e. mass loss). Movement propensity increased in presence of predation risk, while matrix permeability had no effect. However, matrix permeability interacted with predation risk to influence movers' phenotype and the physiological cost they endured while moving. In particular, a well-known movement syndrome in toads (i.e. movement propensity positively related to longer legs) depended on the interaction between matrix permeability and predation risk and resulted in differences in mass loss among matrix types. Movers lost more mass on average than residents except when they also displayed longer legs or when they crossed the most permeable matrix in the presence of predation risk. Our results show that matrix permeability shapes the physiological cost of dispersal by changing the identity of individuals moving away from local conditions. As the movers' phenotype can importantly alter (meta)population dynamics, context-dependency of dispersal syndromes should be considered in studies predicting the functioning of human-altered natural systems.
Data from: Environmental effects on the structure of the G-matrix
Genetic correlations between traits determine the multivariate response to selection in the short term, and thereby play a causal role in evolutionary change. While individual studies have documented environmentally induced changes in genetic correlations, the nature and extent of environmental effects on multivariate genetic architecture across species and environments remain largely uncharacterized. We reviewed the literature for estimates of the genetic variance-covariance (G) matrix in multiple environments, and compared differences in G between environments to the divergence in G between conspecific populations (measured in a common garden). We found that the predicted evolutionary trajectory differed as strongly between environments as it did between populations. Between-environment differences in the underlying structure of G (total genetic variance and the relative magnitude and orientation of genetic correlations) were equal to or greater than between-population differences. Neither environmental novelty nor the difference in mean phenotype predicted these differences in G. Our results suggest that environmental effects on multivariate genetic architecture may be comparable to the divergence that accumulates over dozens or hundreds of generations between populations. We outline avenues of future research to address the limitations of existing data and characterize the extent to which lability in genetic correlations shapes evolution in changing environments.
Data from: Many-to-many mapping of phenotype to performance: an extension of the F-matrix for studying functional complexity
Performance capacity influences ecology, behavior and fitness, and is determined by the underlying phenotype. The phenotype-performance relationship can influence the evolutionary trajectory of an organism. Several types of phenotype-performance relationships have been described, including one-to-one relationships between a single phenotypic trait and performance measure, trade-offs and facilitations between a phenotypic trait and multiple performance measures, and redundancies between multiple phenotypic traits and a single performance measure. The F-matrix is an intraspecific matrix of measures of statistical association between phenotype and performance that is used to quantify these relationships. We extend the F-matrix in two ways. First, we use the F-matrix to describe how the different phenotype-performance relationships occur simultaneously and interact in functional systems, a phenomenon we call many-to-many mapping. Second, we develop methods to compare F-matrices among species and compare phenotype-performance relationships at microevolutionary and macroevolutionary levels. We demonstrate the expanded F-matrix approach with a dataset of eight phrynosomatine lizard species, including six phenotypic traits and two measures of locomotor performance. Our results suggest that all types of relationships occur in this system and that phenotypic traits involved in trade-offs are more functionally constrained and tend evolve slower interspecifically than those involved in facilitations or one-to-one relationships.
Data from: Using matrix and tensor factorizations for the single-trial analysis of population spike trains
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons. This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension (differences in stimulus tuning across neurons at different locations), in their temporal dimension (temporal neural response variations), or in their combination (temporally coordinated neural population firing). Here we investigate the utility of tensor factorizations of population spike trains along space and time. These factorizations decompose a dataset of single-trial population spike trains into spatial firing patterns (combinations of neurons firing together), temporal firing patterns (temporal activation of these groups of neurons) and trial-dependent activation coefficients (strength of recruitment of such neural patterns on each trial). We validated various factorization methods on simulated data and on populations of ganglion cells simultaneously recorded in the salamander retina. We found that single-trial tensor space-by-time decompositions provided low-dimensional data-robust representations of spike trains that capture efficiently both their spatial and temporal information about sensory stimuli. Tensor decompositions with orthogonality constraints were the most efficient in extracting sensory information, whereas non-negative tensor decompositions worked well even on non-independent and overlapping spike patterns, and retrieved informative firing patterns expressed by the same population in response to novel stimuli. Our method showed that populations of retinal ganglion cells carried information in their spike timing on the ten-milliseconds-scale about spatial details of natural images. This information could not be recovered from the spike counts of these cells. First-spike latencies carried the majority of information provided by the whole spike train about fine-scale image features, and supplied almost as much information about coarse natural image features as firing rates. Together, these results highlight the importance of spike timing, and particularly of first-spike latencies, in retinal coding.
Data and Codebase on Extracellular Matrix Remodeling from Embedded Spheroid Fluidization Experiments
<p>raw data: 52_025.zip, 52_100.zip, 54_025.zip, 54_100.zip, 56_025.zip, 56_100.zip, 58_025.zip, 58_100.zip</p> <p>analysis data: Archive.zip, README.MD</p> <p>codebase: codebase.zip</p>
Data set for "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories"
<p>Data accompanying the paper "A large-scale integrated vector–matrix multiplication processor based on monolayer molybdenum disulfide memories" </p>
Removal of contaminants of emerging concern from the supernatant of anaerobically digested sludge by O3 and O3/H2O2: Ozone requirements, effects of the matrix, and toxicity
<p>Digestate is a rich source of nutrients that can be applied in agricultural fields as fertilizer or irrigation water.<br>However, most of the research about application of digestate have focused on its agronomic properties and<br>neglected the potential harm of the presence of contaminants of emerging concern (CECs). Aadvanced oxidation processes (AOPs) have proved to be effective for removing these compounds from drinking water, yet there are some constrains to treat wastewater and digestate mainly due to their complex matrix. In this study, the feasibility to remove different CECs from digestate using O3 and O3/H2O2 was assessed, and the general effect of the matrix in the oxidation was explained. While the lab-scale ozonation provided an ozone dose of 1.49 mg O3/mg DOC in 5 h treatment, almost all the compounds were removed at a lower ozone dose of maximum 0.48 mg O3/ mg DOC; only ibuprofen required a higher dose of 1.1 mg O3/mg DOC to be oxidized. The digestate matrix slowed down the kinetic ozonation rate to approximately 1% compared to the removal rate in demineralized water. The combined treatment (O3/H2O2) showed the additional contribution of H2O2 by decreasing the ozone demand by 59–75% for all the compounds. The acute toxicity of the digestate, measured by the inhibition of Vibrio fisheries luminescence, decreased by 18.1% during 5 h ozonation, and by 34% during 5 h O3/H2O2 treatment. Despite the high ozone consumption, the ozone dose (mg O3/mg DOC) required to remove all CECs from digestate supernatant was in the range or lower than what has been reported for other (waste-)water matrix, implying that ozonation can be considered as a post-AD treatment to produce cleaner stream for agricultural purposes.</p>
Supplementary data to BANMF-S: a blockwise accelerated non-negative matrix factorization framework with structural network constraints for single cell RNA-seq data imputation
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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.