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253 results for “functional organization”
Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe
<p>Cephalopods are highly visual animals with camera-type eyes, large brains, and a rich repertoire of visually guided behaviors. However, the cephalopod brain evolved independently from that of other highly visual species, such as vertebrates, and therefore the neural circuits that process sensory information are profoundly different. It is largely unknown how their powerful but unique visual system functions, since there have been no direct neural measurements of visual responses in the cephalopod brain. In this study, we used two-photon calcium imaging to record visually evoked responses in the primary visual processing center of the octopus central brain, the optic lobe, to determine how basic features of the visual scene are represented and organized. We found spatially localized receptive fields for light (ON) and dark (OFF) stimuli, which were retinotopically organized across the optic lobe, demonstrating a hallmark of visual system organization shared across many species. Examination of these responses revealed transformations of the visual representation across the layers of the optic lobe, including the emergence of the OFF pathway and increased size selectivity. We also identified asymmetries in the spatial processing of ON and OFF stimuli, which suggest unique circuit mechanisms for form processing that may have evolved to suit the specific demands of processing an underwater visual scene. This study provides insight into the neural processing and functional organization of the octopus visual system, highlighting both shared and unique aspects, and lays a foundation for future studies of the neural circuits that mediate visual processing and behavior in cephalopods.</p>
Similar Enzymatic Functions in Distinct Bioluminescence Systems: Evolutionary Recruitment of Sulfotransferases in Ostracod Light Organs
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Reactivity, fate and functional roles of dissolved organic matter in anoxic inland waters
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Data from: Climatic water availability mainly drives context-dependency of tree functional diversity effects on soil organic carbon storage in European forests
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Programmable assembly of mechanically robust and functional polymer–spore biocomposites in organic solvent
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Calcium imaging data from: Functional organization of visual responses in the octopus optic lobe
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Functional morphology of the Ediacaran organism Tribrachidium heraldicum
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Supporting data: Functional plasticity of the swim bladder as an acoustic organ for communication in a vocal fish
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Data from: Organic matter and nutrient inputs from large wildlife influence ecosystem function in the Mara River, Africa
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Data from: Contrasting patterns of functional diversity in coffee root fungal communities associated with organic and conventionally-managed fields
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Phytoplankton assemblage shifts with dissolved organic matter properties: a functional perspective for sentinel lakes
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Organic compounds drive growth in phytoplankton taxa from different functional groups
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Data and Scripts for "Real-Time Time-Dependent Density Functional Theory Implementation of Electronic Circular Dichroism Applied to Nanoscale Metal-Organic Clusters"
<p>The xyz files were used for the ECD calculation in the paper :https://arxiv.org/abs/2007.08560<br> gsrun.py: ground-state calculation<br> td_calc.py: time -propagation for ECD<br> cdspecX.py: get rotatory strength for plotting</p>
Functional organization of woody plant assemblages along precipitation and human disturbance gradients in a seasonally dry tropical forest
<p>Chronic anthropogenic disturbances (CAD) and rainfall are important drivers of plant community assembly, but little is known about the role played by inter and intraspecific trait variation as communities respond to these pervasive forces. Here we examined the hypothesis that lower precipitation and higher CAD reduce both intra and interspecific trait variation in Caatinga dry forests. We sampled woody plants across 15 plots along precipitation and CAD gradients and measured resource-use traits. Effects of precipitation and CAD on RaoQ functional diversity were decomposed into species turnover and intraspecific variability. We used "T-statistics" to assess the trait sorting from the regional pool to local communities (i.e. external filtering), and within-community forces leading to low trait overlap (i.e. internal filtering) at individual- and species-level. Intraspecific variability explained at least one third of the total trait variation and 46% of variation in multitrait diversity across communities. Increasing disturbance reduced multitrait diversity, while precipitation affected some particular traits, such as wood density. Overall, precipitation determined species sorting across communities, while disturbance relaxed internal filters, leading to higher trait overlap within communities due to higher intraspecific variability.<b> </b>Our results suggest that<b> </b>the woody Caatinga flora contains a substantial amount of both inter and intraspecific trait variation. This variation is not randomly distributed within and across communities, but varies according to rainfall conditions and disturbance intensity. These findings reinforce the emerging idea that human-disturbances can reorganize plant communities at multiple scales and highlight trait variability as a key biological asset for the resilience of dry forests.</p>
Data from: Towards a functional understanding of species coexistence: ecomorphological variation in relation to whole-organism performance in two sympatric lizards
1. We examined intra- and interspecific variation in functional morphology and whole-organism performance in a sympatric lizard species pair, Iberolacerta horvathi and Podarcis muralis, in the area with a high potential for competition. 2. The biggest variation between species was found in two functional traits, bite force and climbing speed, linked with corresponding morphological traits. 3. The species with larger and taller heads, P. muralis, exhibited correspondingly stronger bite forces. The other species exhibited smaller and flatter head. Both traits may potentially promote segregation between species in trophic niche (stronger bites relate to harder prey) and in refuge use (flatter heads allow using narrower crevices, hence, influencing escaping from common predators). Stronger bites and larger heads also provide one species with a dominant position in interspecific agonistic interactions. 4. Females had longer trunks that impacted negatively on climbing speed, which may lower anti-predator escape abilities of the more trunk-dimorphic species, but positively influence reproductive effort. 5. Our results exemplify how the joint examination of morphological and functional traits of ecologically similar and sympatric species can provide a mechanistic background for understanding their coexistence, namely syntopic populations that are frequent in the study area. 6. The identified roles of functional morphology in this system of sympatric rock lizards support the contribution of functional diversification for the complexity of community structure via coexistence.
Data from: The function and organization of the motor system controlling flight maneuvers in flies
Animals face the daunting task of controlling their limbs using a small set of highly constrained actuators. This problem is particularly demanding for insects such as Drosophila, which must adjust wing motion for both quick voluntary maneuvers and slow compensatory reflexes using only a dozen pairs of muscles. To identify strategies by which animals execute precise actions using sparse motor networks, we imaged the activity of a complete ensemble of wing control muscles in intact, flying flies. Our experiments uncovered a remarkably efficient logic in which each of the four skeletal elements at the base of the wing are equipped with both large phasically active muscles capable of executing large changes and smaller tonically active muscles specialized for continuous fine-scaled adjustments. Based on the responses to a broad panel of visual motion stimuli, we have developed a model by which the motor array regulates aerodynamically functional features of wing motion.
Data from: Warming reduces the effects of enrichment on stability and functioning across levels of organization in an aquatic microbial ecosystem
Warming and nutrient enrichment are major environmental factors shaping ecological dynamics. However, cross-scale investigation of their combined effects by linking theory and experiments is lacking. We collected data from aquatic microbial ecosystems investigating the interactive effects of warming (constant and rising temperatures) and enrichment across levels of organization and contrasted them with community models based on metabolic theory. We found high agreement between our observations and theoretical predictions: we observed in many cases the predicted antagonistic effects of high temperature and high enrichment across levels of organization. Temporal stability of total biomass decreased with warming but did not differ across enrichment levels. Constant and rising temperature treatments with identical mean temperature did not show qualitative differences. Overall, we conclude that model and empirical results are in broad agreement due to robustness of the effects of temperature and enrichment, that the mitigating effects of temperature on effects of enrichment may be common, and that models based on metabolic theory provide qualitatively robust predictions of the combined ecological effects of enrichment and temperature.
Data from: Feedbacks between nitrogen fixation and soil organic matter increase ecosystem functions in diversified agroecosystems
Nitrogen (N) losses from intensified agriculture are a major cause of global change, due to nitrate (NO3-) export and the eutrophication of aquatic systems as well as emissions of nitrous oxide (N2O) into the atmosphere. Diversified agroecosystems with legume cover crops couple N and carbon (C) inputs to soil and reduce N pollution, but there is a need to identify controls on legume N2 fixation across ecosystems with variable soil conditions. Here, I tested the hypothesis that N mineralization from turnover of soil organic matter (SOM) regulates legume N2 fixation across 10 farms that spanned a gradient of SOM levels. I separated soil samples into two SOM fractions, based on size and density, which are indicators of soil nutrient cycling and N availability (free particulate organic matter and intra-aggregate particulate organic matter (POM)). This study indicates downregulation of legume N2 fixation in diversified agroecosystems with increasing N availability in intra-aggregate POM and increasing N mineralization. Intercropping the legume with a grass weakened the relationship between N in POM and N2 fixation due to N assimilation by the grass. Further, mean rates of N and C mineralization across sites increased with two seasons of a legume-grass cover crop mixture, which could enhance this stabilizing feedback between soil N availability and N2 fixation over time. These results suggest a potential mechanism for the diversity-ecosystem function relationships measured in long-term studies of agroecosystems, in which regular use of legume cover crops increases total soil organic C and N and reduces the environmental costs of crop production.
Research Data supporting "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures"
<p>Raw research data supporting the article A. Sarkar, T. Behera, R. Sasmal, R. Capelli, C. Empereur-mot, J. Mahato, S. S. Agasti, G. M. Pavan, A. Chowdhury, S. J. George "Cooperative Supramolecular Block Copolymerization for the Synthesis of Functional Axial Organic Heterostructures".</p>
Topographic deep neural networks predict the functional organization of the primate ventral visual pathway
<p>Recording of presentation at the Neuroscience 2021 annual meeting (held virtually). The abstract follows:</p> <p> </p> <p>The primate ventral visual pathway is organized into functional maps, including pinwheel-like arrangements of orientation-tuned neurons in primary visual cortex (V1) and patches of category-selective neurons in higher visual cortex. While deep convolutional neural networks (DCNNs) trained for object recognition accurately predict neural representations throughout the ventral pathway, they have no spatial layout for features at a given retinotopic location and are thus unable to predict the rich topographic organization of visual cortex. Here, we close this gap by first assigning each DCNN unit a position in a 2D cortical sheet, then training the network to minimize a cost function with two components: one encouraging accurate object recognition, and another favoring correlated responses among nearby units in each model layer (Figure 1A, 1B). </p> <p>We find that training with this composite spatial loss produces brain-like topographic maps in both early and later model layers (Figure 1B). Early layers contain smooth orientation preference maps with pinwheels, clusters of units preferring the same spatial frequency, and color-preference domains resembling V1 “blobs”. In a later layer of the same model, we observe clusters of category-selective units, e.g., face patches, whose spatial organization largely matches that found in primate higher visual cortex. Our model thus leverages local response correlations, which have been linked to theories of wire-length minimization, to accurately predict neuron responses and functional organization throughout the ventral visual pathway. In support of the wire-length minimization hypothesis, we find that our topographic DCNN would require shorter connections than a standard DCNN to support connections between similarly-tuned neurons within early (38% reduction) and later (31% reduction) model layers (Figure 1D). These results suggest that the functional organization of visual cortex can be explained by two constraints: the need to perform object recognition and pressure for local populations of neurons to have correlated responses.</p>
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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.