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168 results for “Complex systems”
An efficient CRISPR-mediated genome editing system in diploid and polyploid Tragopogon (Asteraceae) enables functional studies of complex phenotypes and polyploid genome evolution
<p>Polyploidy or whole-genome duplication (WGD) is a significant evolutionary force, especially in angiosperms. However, the underlying mechanisms governing polyploid genome evolution remain unclear, limited largely by a lack of functional analysis tools in organisms that best exemplify the earliest stages of WGD. <em>Tragopogon</em> (Asteraceae) includes an evolutionary model system for studying the immediate consequences of polyploidy. In this study, we significantly improved the genetic transformation of <em>Tragopogon</em> and obtained genome-edited <em>T. porrifolius</em> (2<em>x</em>) and <em>T. mirus</em> (4<em>x</em>) primary generation (T<sub>0</sub>) individuals. Using CRISPR/Cas9, we knocked out the dihydroflavonol 4-reductase (<em>DFR</em>) gene, which controls anthocyanin synthesis, in both <em>T. porrifolius</em> and <em>T. mirus</em>. All transgenic allotetraploid <em>T. mirus</em> individuals had at least one mutant <em>DFR</em> allele and 71.4% of the plants had all four <em>DFR</em> alleles (from both homeologs) edited, indicating a high efficiency of the CRISPR system in polyploid <em>Tragopogon</em>. The anticipated absence of the anthocyanin was observed in both leaf and floral tissues from <em>T. porrifolius</em> and <em>T. mirus</em> mutants. In addition, the mutations were inherited in the T<sub>1</sub> generation. This study demonstrates a highly efficient CRISPR platform producing genome-edited <em>Tragopogon</em> individuals that have successfully completed their life cycle. The approaches used and challenges faced in building the CRISPR system in <em>Tragopogon</em> provide a framework for building similar systems in other nongenetic models. Genome editing in <em>Tragopogon</em> paves the way for novel functional biology studies of polyploid genome evolution and the consequences of WGD on complex traits, which holds enormous potential for both basic and applied research.</p>
Word frequencies and text data for the study of Statistical Laws in Complex Systems
<p>The files contain the data reported in the manuscript "Statistical Laws in Complex Systems" and in the repository <a href="https://github.com/edugalt/StatisticalLaws">https://github.com/edugalt/StatisticalLaws</a></p> <p>The files contain list of word frequencies and filtered word texts, computed from the data provided in <a href="https://gutenberg.org/">Project Gutenberg</a>, <a href="https://en.wikipedia.org/wiki/Wikipedia:Database_download">Wikipedia</a>, and the <a href="https://books.google.com/ngrams/">Google N-gram database.</a></p>
Embracing fine-root system complexity in terrestrial ecosystem modelling
<p>Model outputs for manuscript " <strong>Embracing fine-root system complexity in terrestrial ecosystem modelling</strong>".</p>
Data for: Complex cross incompatibility in morning glories is consistent with a role for mating system in plant speciation
<p><span>Reproductive isolation between selfing and outcrossing species can arise through diverse mechanisms, some of which are directly associated with differences in mating system. We dissected cross incompatibility between the highly selfing morning glory <em>Ipomoea</em> <em>lacunosa</em> and its mixed-mating sister species <em>I. cordatotriloba</em>. We found that cross incompatibility is complex, with contributions acting both before and after fertilization. We then investigated whether the transition in mating system may have facilitated the evolution of these reproductive barrier components through mismatched floral morphology, differences in reproductive context, or both. We found evidence that morphological mismatch likely contributes to reproductive isolation in at least one cross direction and that other pollen-pistil interactions are present. We also identified hybrid seed inviability consistent with the predictions of the weak-inbreeder, strong-outbreeder hypotheses, suggesting endosperm misregulation plays an important role in cross incompatibility. In contrast, we did not find evidence consistent with the pre-zygotic weak-inbreeder, strong-outbreeder hypothesis. Our study highlights the complexity of reproductive isolation between outcrossing and selfing species and the extent to which evolutionary consequences of mating system transitions can facilitate speciation.</span></p>
Dataset for the SIAM MPI23 project "Model inversion for complex physical systems using low-dimensional surrogates"
<p>This dataset contains 20,000 synthetic simulations of a simplified two-dimensional confined aquifer model of the Hanford Site. The inputs are the Kosambi-Karhunen-Loève expansion (KKLE) coefficients of the input log-transmissivity field. The outputs are the corresponding stationary pressure responses observed at 323 observation wells. Also included are the arrays necessary to reconstruct the log-transmissivity inputs from the KKLE coefficients.</p>
Data from: Pest management science often disregards farming system complexities
<p><span>Since the 1940s, pesticide-intensive crop protection has sustained food security but also caused pervasive impacts on biodiversity, environmental integrity and human health. Here, we employ a systematic literature review to structurally analyze pest management science in 65 developing countries. Within a corpus of 3,407 publications, we find that taxonomic coverage is skewed towards a subset of 48 herbivores. Simplified contexts are commonplace: 48% of studies are performed within laboratory confines. 80% treat management tactics in an isolated rather than integrated fashion. 83% consider no more than two out of 15 farming system variables. Limited attention is devoted to pest-pathogen or pest-pollinator interplay, trophic interactions across ecosystem compartments or natural pest regulation. By overlooking social strata, the sizable scientific progress on agroecological management translates into slow farm-level uptake. We argue that the scientific enterprise should integrate system complexity to chart sustainable trajectories for global agriculture and achieve transformative change on the ground.</span></p>
The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
<p>Circadian clocks are pervasive throughout nature, yet only recently has this adaptive regulatory program been described in non-photosynthetic bacteria. Here, we describe an inherent complexity in the <em>Bacillus</em> <em>subtilis</em> circadian clock. We find that <em>B. subtilis</em> entrains to blue and red light and that circadian entrainment is separable from masking through fluence titration and frequency demultiplication protocols. We identify circadian rhythmicity in constant light, consistent with Aschoff's Rule, and entrainment aftereffects, both of which are properties described for eukaryotic circadian clocks. We report that circadian rhythms occur in wild isolates of this prokaryote, thus establishing them as a general property of this species, and that its circadian system responds to the environment in a complex fashion that is consistent with multicellular eukaryotic circadian systems.</p>
Interdimensional radial discrete diffraction in Mathieu photonic lattices - Control and manipulation of light in complex photonic systems (CompsLight)
<p>Experimental and numerical data from the journal paper published in Optics Express Vol. 31, Issue 18, pp. 28946-28953 (2023) (https://doi.org/10.1364/OE.497795). Experimental data contains original results in .jpg format, presenting intensity distributions of probe beam after propagation in a 2cm long Mathieu photonic lattices optically induced in cerium doped strontium barium niobate (Ce:SBN61) crystal. Numerical data are intensity distributions (I) that correspond to experimental data as Matlab files (.m format) as well as contain information about numerical space in micrometers (x, y). Data for Figure 5 contains probe beam intensity distributions (I) and lattice intensity distributions (L). </p> <p>We demonstrate transitional dimensionality of discrete diffraction in radial-elliptical photonic lattices. Varying the order, characteristic structure size, and ellipticity of the Mathieu beams used for the photonic lattices generation, we control the shape of discrete diffraction distribution over the combination of the radial direction with the circular, elliptic, or hyperbolic. We also investigate the transition from one-dimensional to two-dimensional discrete diffraction by varying the input probe beam position. The most pronounced discrete diffraction is observed along the crystal anisotropy direction.</p>
Levonorgestrel-Releasing Intrauterine System in Treating Patients With Complex Atypical Hyperplasia or Grade I Endometrial Cancer
ClinicalTrials.gov study NCT00788671. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effects of a Tissue Selective Estrogen Complex (TSEC) on Depression and the Neural Reward System in the Perimenopause"
ClinicalTrials.gov study NCT03740009. IPD Sharing: NO. Countries: 1. Publications: 34.
Study to Evaluate the Efficacy & Safety of the INTERCEPT Blood System for RBCs in Complex Cardiac Surgery Patients
ClinicalTrials.gov study NCT03459287. IPD Sharing: YES. Countries: 1. Publications: 2.
Care Coordination for Complex Cancer Survivors in an Integrated Safety Net System
ClinicalTrials.gov study NCT02943265. IPD Sharing: NO. Countries: 1. Publications: 1.
Ancestral complexity and constrained diversification of the ant olfactory system
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Data from: Complex cross incompatibility in morning glories is consistent with a role for mating system in plant speciation
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Data from: The role of red coloration and song in peacock spiders: insights into complex signaling systems
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Data from: Pest management science often disregards farming system complexities
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Data from: Maize-field complexity and farming system influence insectivorous birds’ contribution to arthropod herbivore regulation
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The circadian clock of the bacterium B. subtilis evokes properties of complex, multicellular circadian systems
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The role of secondary pollinators in the evolution of complex colour signals in a bimodal pollination system
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Data from: Strict monandry in the ponerine army ant genus Simopelta suggests that colony size and complexity drive mating system evolution in social insects
Altruism in social insects has evolved between closely related full-siblings. It is therefore of considerable interest why some groups have secondarily evolved low within-colony relatedness, which in turn affects the relatedness incentives of within-colony cooperation and conflict. The highest queen mating frequencies, and therefore among the lowest degrees of colony relatedness, occur in Apis honeybees and army ants of the subfamilies Aenictinae, Ecitoninae, and Dorylinae, suggesting that common life-history features such as reproduction by colony fission and male biased numerical sex-ratios have convergently shaped these mating systems. Here we show that ponerine army ants of the genus Simopelta, which are distantly related but similar in general biology to other army ants, have strictly monandrous queens. Preliminary data suggest that workers reproduce in queenright colonies, which is in sharp contrast to other army ants. We hypothesize that differences in mature colony size and social complexity may explain these striking discrepancies.
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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.