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333 results for “functional network”
Data from: Loss of functional connectivity in migration networks induces population decline in migratory birds
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Data from: Ditch network sustains functional connectivity and influences patterns of gene flow in an intensive agricultural landscape
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Systemic paralogy and function of retinal determination network homologs in arachnids
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Soil organic matter responses to nutrient enrichment in the Nutrient Network:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Soil nutrient analysis:Nutrient Network. A cross-site investigation of bottom-up control over herbaceous plant community dynamics and ecosystem function.
This experiment is one implementation of a globally distributed experiment, known as the Nutrient Network. At Cedar Creek, as in over 70 other sites in grasslands around the world, the experiment aims to describe impacts of increased nutrients (nitrogen, phosphorus, potassium, sulfur and other metals) and decreased herbivory (removal of mammals by fencing). Two overarching questions are being explored with these manipulations: 1. To what extent are plant production and diversity co-limited by multiple nutrients in herbaceous-dominated communities? 2. Under what conditions do grazers or fertilization control plant biomass, diversity, and composition? By utilizing identical protocols at diverse grassland sites around the world, NutNet aims to uncover both the generalities in ecosystem functioning, and the contingencies or differences which can obscure those common mechanisms. In addition to the standard NutNet protocol, e247 includes an additional low Nitrogen gradient (1 gram Nitrogen per meter squared per year and 5 grams Nitrogen per meter squared per year in addition to the standard 10 grams Nitrogen per meter squared per year).
Data from: Amyloid and cerebrovascular burden divergently influence brain functional network changes over time
Objective: To examine the effects of baseline Alzheimer's disease and cerebrovascular disease markers on longitudinal default mode network (DMN) and executive control network (ECN) functional connectivity (FC) changes in mild cognitive impairment (MCI) patients. Methods: We studied 30 amnestic (aMCI) and 55 subcortical vascular MCI (svMCI) patients with baseline Pittsburgh Compound B (PiB)–positron emission tomography (PET) scans and longitudinal magnetic resonance imaging (MRI) scans. Participants were followed up clinically with annual MR imaging for up to four years (aMCI: 26 with two time-points, 4 with three time-points; svMCI: 13 with two time-points, 16 with three time-points, 26 with four time-points). Results: Amyloid-β burden was associated with longitudinal DMN FC declines, while cerebrovascular burden was associated with longitudinal ECN FC changes. When patients were divided into PiB+ and PiB- groups, PiB+ patients showed longitudinal DMN FC declines, while svMCI patients showed longitudinal ECN FC increases. Direct comparisons between the two groups without mixed pathology (aMCI PiB+ and svMCI PiB-) recapitulated this divergent pattern: aMCI PiB+ patients showed steeper longitudinal DMN FC declines, while svMCI PiB- patients showed steeper longitudinal ECN FC increases. Finally, using baseline PiB uptake and lacune numbers as continuous variables, baseline PiB uptake showed inverse U-shape associations with longitudinal DMN FC changes in both MCI subtypes, while baseline lacune numbers showed both mainly inverse-U shape relationships with longitudinal ECN FC changes in svMCI patients. Conclusions: Our findings underscore the divergent effects of amyloid-β and cerebrovascular burden on longitudinal FC changes in the DMN and ECN in the pre-dementia stage, which reflect the underlying pathology and may be used to track early changes in Alzheimer's disease and cerebrovascular disease.
Data from: Choosing wavelet methods, filters, and lengths for functional brain network construction
Wavelet methods are widely used to decompose fMRI, EEG, or MEG signals into time series representing neurophysiological activity in fixed frequency bands. Using these time series, one can estimate frequency-band specific functional connectivity between sensors or regions of interest, and thereby construct functional brain networks that can be examined from a graph theoretic perspective. Despite their common use, however, practical guidelines for the choice of wavelet method, filter, and length have remained largely undelineated. Here, we explicitly explore the effects of wavelet method (MODWT vs. DWT), wavelet filter (Daubechies Extremal Phase, Daubechies Least Asymmetric, and Coiflet families), and wavelet length (2 to 24)—each essential parameters in wavelet-based methods—on the estimated values of graph metrics and in their sensitivity to alterations in psychiatric disease. We observe that the MODWT method produces less variable estimates than the DWT method. We also observe that the length of the wavelet filter chosen has a greater impact on the estimated values of graph metrics than the type of wavelet chosen. Furthermore, wavelet length impacts the sensitivity of the method to detect differences between health and disease and tunes classification accuracy. Collectively, our results suggest that the choice of wavelet method and length significantly alters the reliability and sensitivity of these methods in estimating values of metrics drawn from graph theory. They furthermore demonstrate the importance of reporting the choices utilized in neuroimaging studies and support the utility of exploring wavelet parameters to maximize classification accuracy in the development of biomarkers of psychiatric disease and neurological disorders.
Data from: Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish
According to the social decision-making (SDM) network hypothesis, SDM is encoded in a network of forebrain and midbrain structures in a distributed and dynamic fashion, such that the expression of a given social behaviour is better reflected by the overall profile of activation across the different loci rather than by the activity of a single node. This proposal has the implicit assumption that SDM relies on integration across brain regions, rather than on regional specialization. Here we tested the occurrence of functional localization and of functional connectivity in the SDM network. For this purpose we used zebrafish to map different social behaviour states into patterns of neuronal activity, as indicated by the expression of the immediate early genes c-fos and egr-1, across the SDM network. The results did not support functional localization, as some loci had similar patterns of activity associated with different social behaviour states, and showed socially driven changes in functional connectivity. Thus, this study provides functional support to the SDM network hypothesis and suggests that the neural context in which a given node of the network is operating (i.e. the state of its interconnected areas) is central to its functional relevance.
Data from: Large-scale functional networks identified from resting-state EEG using spatial ICA
Several methods have been applied to EEG or MEG signals to detect functional networks. In recent works using MEG/EEG and fMRI data, temporal ICA analysis has been used to extract spatial maps of resting-state networks with or without an atlas-based parcellation of the cortex. Since the links between the fMRI signal and the electromagnetic signals are not fully established, and to avoid any bias, we examined whether EEG alone was able to derive the spatial distribution and temporal characteristics of functional networks. To do so, we propose a two-step original method: 1) An individual multi-frequency data analysis including EEG-based source localisation and spatial independent component analysis, which allowed us to characterize the resting-state networks. 2) A group-level analysis involving a hierarchical clustering procedure to identify reproducible large-scale networks across the population. Compared with large-scale resting-state networks obtained with fMRI, the proposed EEG-based analysis revealed smaller independent networks thanks to the high temporal resolution of EEG, hence hierarchical organization of networks. The comparison showed a substantial overlap between EEG and fMRI networks in motor, premotor, sensory, frontal, and parietal areas. However, there were mismatches between EEG-based and fMRI-based networks in temporal areas, presumably resulting from a poor sensitivity of fMRI in these regions or artefacts in the EEG signals. The proposed method opens the way for studying the high temporal dynamics of networks at the source level thanks to the high temporal resolution of EEG. It would then become possible to study detailed measures of the dynamics of connectivity.
Data from: System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of Soybean (Glycine max)
Cellular interactome, in which genes and/or their products interact on several levels, forming transcriptional regulatory-, protein interaction-, metabolic-, signal transduction networks, etc., has attracted decades of research focuses. However, such a specific type of network alone can hardly explain the various interactive activities among genes. These networks characterize different interaction relationships, implying their unique intrinsic properties and defects, and covering different slices of biological information. Functional gene network (FGN), a consolidated interaction network that models fuzzy and more generalized notion of gene-gene relations, have been proposed to combine heterogeneous networks with the goal of identifying functional modules supported by multiple interaction types. There are yet no successful precedents of FGNs on sparsely studied non-model organisms, such as soybean (Glycine max), due to the absence of sufficient heterogeneous interaction data. We present an alternative solution for inferring the FGNs of soybean (SoyFGNs), in a pioneering study on the soybean interactome, which is also applicable to other organisms. SoyFGNs exhibit the typical characteristics of biological networks: scale-free, small-world architecture and modularization. Verified by co-expression and KEGG pathways, SoyFGNs are more extensive and accurate than an orthology network derived from Arabidopsis. As a case study, network-guided disease-resistance gene discovery indicates that SoyFGNs can provide system-level studies on gene functions and interactions. This work suggests that inferring and modelling the interactome of a non-model plant are feasible. It will speed up the discovery and definition of the functions and interactions of other genes that control important functions, such as nitrogen fixation and protein or lipid synthesis. The efforts of the study are the basis of our further comprehensive studies on the soybean functional interactome at the genome and microRNome levels. Additionally, a web tool for information retrieval and analysis of SoyFGNs can be accessed at SoyFN: http://nclab.hit.edu.cn/SoyFN.
TZO - Working memory performance in glioma patients is associated with functional connectivity between the right dorsolateral prefrontal cortex and default mode network
<p>Data files hosted on Figshare for "Working memory performance in glioma patients is associated with functional connectivity between the right dorsolateral prefrontal cortex and default mode network".</p> <p>Contains functional connectivity matrices, clinical variables, and working memory performance scores of 45 glioma patients.</p>
Dysfunctions-of-Multiscale-Dynamic-Brain-Functional-Networks-in-Subjective-Cognitive-Decline
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Figure 3 from: Datry T, Allen D, Argelich R, Barquin J, Bonada N, Boulton A, Branger F, Cai Y, Cañedo-Argüelles M, Cid N, Csabai Z, Dallimer M, de Araújo JC, Declerck S, Dekker T, Döll P, Encalada A, Forcellini M, Foulquier A, Heino J, Jabot F, Keszler P, Kopperoinen L, Kralisch S, Künne A, Lamouroux N, Lauvernet C, Lehtoranta V, Loskotová B, Marcé R, Martin Ortega J, Matauschek C, Miliša M, Mogyorósi S, Moya N, Müller Schmied H, Munné A, Munoz F, Mykrä H, Pal I, Paloniemi R, Pařil P, Pengal P, Pernecker B, Polášek M, Rezende C, Sabater S, Sarremejane R, Schmidt G, Senerpont Domis L, Singer G, Suárez E, Talluto M, Teurlincx S, Trautmann T, Truchy A, Tyllianakis E, Väisänen S, Varumo L, Vidal J-P, Vilmi A, Vinyoles D (2021) Securing Biodiversity, Functional Integrity, and Ecosystem Services in Drying River Networks (DRYvER). Research Ideas and Outcomes 7: e77750. https://doi.org/10.3897/rio.7.e77750
Figure 3 The DRYvER three-step workflow embedded within 7 Work Packages (WP) and the four main attributes of the DRYvER consortium (red ovals).
Figure 2 from: Datry T, Allen D, Argelich R, Barquin J, Bonada N, Boulton A, Branger F, Cai Y, Cañedo-Argüelles M, Cid N, Csabai Z, Dallimer M, de Araújo JC, Declerck S, Dekker T, Döll P, Encalada A, Forcellini M, Foulquier A, Heino J, Jabot F, Keszler P, Kopperoinen L, Kralisch S, Künne A, Lamouroux N, Lauvernet C, Lehtoranta V, Loskotová B, Marcé R, Martin Ortega J, Matauschek C, Miliša M, Mogyorósi S, Moya N, Müller Schmied H, Munné A, Munoz F, Mykrä H, Pal I, Paloniemi R, Pařil P, Pengal P, Pernecker B, Polášek M, Rezende C, Sabater S, Sarremejane R, Schmidt G, Senerpont Domis L, Singer G, Suárez E, Talluto M, Teurlincx S, Trautmann T, Truchy A, Tyllianakis E, Väisänen S, Varumo L, Vidal J-P, Vilmi A, Vinyoles D (2021) Securing Biodiversity, Functional Integrity, and Ecosystem Services in Drying River Networks (DRYvER). Research Ideas and Outcomes 7: e77750. https://doi.org/10.3897/rio.7.e77750
Figure 2 It shows how DRYvER will use this cyclic model as a structured loop embedded in a meta-system perspective to guide adaptive management of DRNs. DRYvER will translate climate projections into changes in flow intermittence patterns at multiple scales, including that of the strategically-selected focal DRNs. This physical setting will then be used to implement a dynamic meta-system perspective to understand the cascading changes in biodiversity, ecosystem functions and ecosystem services. This knowledge will be integrated to develop a multi-criteria decision framework combining scientific, management, socio-economic, legislative barriers and leverages to promote an adaptive management of DRNs.
Figure 4 from: Datry T, Allen D, Argelich R, Barquin J, Bonada N, Boulton A, Branger F, Cai Y, Cañedo-Argüelles M, Cid N, Csabai Z, Dallimer M, de Araújo JC, Declerck S, Dekker T, Döll P, Encalada A, Forcellini M, Foulquier A, Heino J, Jabot F, Keszler P, Kopperoinen L, Kralisch S, Künne A, Lamouroux N, Lauvernet C, Lehtoranta V, Loskotová B, Marcé R, Martin Ortega J, Matauschek C, Miliša M, Mogyorósi S, Moya N, Müller Schmied H, Munné A, Munoz F, Mykrä H, Pal I, Paloniemi R, Pařil P, Pengal P, Pernecker B, Polášek M, Rezende C, Sabater S, Sarremejane R, Schmidt G, Senerpont Domis L, Singer G, Suárez E, Talluto M, Teurlincx S, Trautmann T, Truchy A, Tyllianakis E, Väisänen S, Varumo L, Vidal J-P, Vilmi A, Vinyoles D (2021) Securing Biodiversity, Functional Integrity, and Ecosystem Services in Drying River Networks (DRYvER). Research Ideas and Outcomes 7: e77750. https://doi.org/10.3897/rio.7.e77750
Figure 4 DRYvER focal DRNs located in highly contrasted EU and CELAC biogeographic and climatic settings (red points), chosen to span the expected natural variability of drying processes and associated DRN responses.Mediterranean ecoregion: the Genal network, in Andalucía (Spain, Mediterranean climate), a dry region heavily impacted by climate change, where most rivers are already affected by drying (contact partner: UB);Alpine ecoregion: the Albarine network, in the Southern Jura (France, temperate climate), a region mildly impacted by climate change (the Albarine network is part of a national LTER project and monitored since 2006) (contact partner: INRAE);Continental ecoregion: the Velička network, in Morava (Czech Republic, continental climate), a region heavily impacted by climate change where many perennial rivers are shifting towards intermittent flow (contact partner: MU);Balkanic ecoregion: the Krka network, in the Dinaric Karst (Croatia, Mediterranean climate), a region where most rivers are already drying and heavily impacted by climate change (contact partner: UZ);Pannonian ecoregion: the Bükkösdi-víz network, in the Mecsek (Hungary, continental climate), a region moderately impacted by climate change, where DRNs are becoming common (contact partner: UP);Boreal ecoregion: the Vantaanjoki network, Helsinki-Uusimaa Region (Finland, boreal climate), region moderately impacted by climate change, where flow intermittence is currently rare (contact partner: SYKE);Pacific Lowlands: the Cube network, in the Andean-Choco region (Ecuador, tropical climate), a region where drying is very seasonal and increasing in duration and frequency (contact partner: USFQ);Central High Andes ecoregion: the Rio Chico network in the Sucre region (Bolivia, semi-arid climate), a dry area prone to desertification where political conflicts emerge due to water scarcity (contact partner: USFX);Caatinga ecoregion: the Jaguaribe network, in the Northeast Semiarid region (Brazil, semi-arid climate), the driest region in Brazil, already heavily impacted by climate change (contact partner: UFC).
Figure 1 from: Datry T, Allen D, Argelich R, Barquin J, Bonada N, Boulton A, Branger F, Cai Y, Cañedo-Argüelles M, Cid N, Csabai Z, Dallimer M, de Araújo JC, Declerck S, Dekker T, Döll P, Encalada A, Forcellini M, Foulquier A, Heino J, Jabot F, Keszler P, Kopperoinen L, Kralisch S, Künne A, Lamouroux N, Lauvernet C, Lehtoranta V, Loskotová B, Marcé R, Martin Ortega J, Matauschek C, Miliša M, Mogyorósi S, Moya N, Müller Schmied H, Munné A, Munoz F, Mykrä H, Pal I, Paloniemi R, Pařil P, Pengal P, Pernecker B, Polášek M, Rezende C, Sabater S, Sarremejane R, Schmidt G, Senerpont Domis L, Singer G, Suárez E, Talluto M, Teurlincx S, Trautmann T, Truchy A, Tyllianakis E, Väisänen S, Varumo L, Vidal J-P, Vilmi A, Vinyoles D (2021) Securing Biodiversity, Functional Integrity, and Ecosystem Services in Drying River Networks (DRYvER). Research Ideas and Outcomes 7: e77750. https://doi.org/10.3897/rio.7.e77750
Figure 1 Phases of flowing and drying alternate annually in the naturally intermittent Albarine River (France), a focal DRN of DRYvER. About half of EU's river channels now flow intermittently and this fraction is increasing. Photos: T. Datry.
Couple-Wise Functional Connectivity Similarity Between Auditory And Salience Network Predicts Marital Satisfaction
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AD-brain functional gene network
<p>AD-brain functional gene network</p>
Relationship Between Functional Health Status and Ventricular Performance After Fontan--Pediatric Heart Network
ClinicalTrials.gov study NCT00132782. IPD Sharing: Not stated. Countries: 0. Publications: 7.
Carotid Structure and Function in MPS Syndromes: A Multicenter Study of the Lysosomal Disease Network
ClinicalTrials.gov study NCT01586871. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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.