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539 results for “loss of function.”
Data and analysis supplement for: Functional imagery training versus motivational interviewing for weight loss: a randomised controlled trial of brief individual interventions for overweight and obesity.
<p>This submission provides the data and code for analyses reported in our publication.</p>
Implication of Folate Deficiency in CYP2U1 loss of function
<p>Hereditary spastic paraplegias are heterogeneous neurodegenerative disorders. Understanding of their pathogenic mechanisms remains sparse and therapeutic options are lacking. We characterized a mouse model lacking the Cyp2u1 gene, loss of which is known to be involved in a complex form of these diseases in Humans. We showed that this model partially recapitulated the clinical and biochemical phenotypes of patients. Using electron microscopy, lipidomic, and proteomic studies, we identified vitamin B2 as a substrate of the CYP2U1 enzyme, as well as coenzyme Q, neopterin, and interferon-alpha levels as putative biomarkers in mouse and in fluids obtained from the largest series of CYP2U1- mutated patients reported so far. We also confirmed brain calcifications as a potential biomarker in patients. Our results suggest that CYP2U1 deficiency disrupts mitochondrial function and impacts proper neurodevelopment, which could be prevented by folate supplementation in our mouse model, followed by a neurodegenerative process altering multiple neuronal and extra neuronal tissues.</p>
Characterization of a loss-of-function NAPB mutation in monozygotic triplets affected with epilepsy and autism using cortical neurons from proband-derived and CRISPR-corrected iPSC lines. Author names and affiliations
<p>RNA-seq data of matured cortical neurons (8-weeks old) derived from induced pluripoent stem cells (iPSC). There are three replicates (Rep1, Rep2, Rep3) for each sample with Forwad read (R1_001.fastq.gz) and reverse read (R2_001.fastq.gz).</p> <p>CtrlF: Control Father sample</p> <p>CtrlM: Control mother sample</p> <p>NDD_01: Proband sample</p> <p>NDD_04: Proband sample</p> <p>NDD_05: Proband sample</p>
Data from: Ecosystem functioning during biodiversity loss and recovery
<p>Anthropogenic biodiversity loss can impair ecosystem functioning. Human activities are often managed with the aim of reversing biodiversity loss and its associated functional impacts. However, it is currently unknown whether biodiversity–ecosystem function (BEF) relationships observed during biodiversity recovery are the same as those observed during biodiversity loss. This will depend on how species extirpation and recolonisation sequences compare and how different species influence ecosystem functioning. Using data from a marine benthic invertebrate community, we modelled how bioturbation potential – a proxy for benthic ecosystem functioning – changes along biodiversity loss and recovery sequences governed by species' sensitivity to physical disturbance and recolonisation capability, respectively. BEF relationships for biodiversity loss and recovery were largely the same despite species extirpation and recolonisation sequences being different. This held true irrespective of whether populations were assumed to exhibit compensatory responses as species were removed or added. These findings suggest that the functional consequences of local biodiversity loss can be reversed by alleviating its drivers, as different species present at comparable levels of species richness during biodiversity loss and recovery phases have similar functional effects. Empirically verifying and determining the generality of our model-based results are potential next steps for future research.</p>
FIGURE 4 in Taxonomic loss and functional reduction over time in the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River, Southern Brazil
FIGURE 4 | Two-dimensional functional space (PCoA) of the functional β-diversity of the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River (the transitional zone between 2006 and 2020).
FIGURE 3 in Taxonomic loss and functional reduction over time in the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River, Southern Brazil
FIGURE 3 | Two-dimensional functional space (PCoA) of the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River (transitional zone between 2006 and 2020). A, B, C, D = 2006. E, F, G, H = 2020. FRic = Functional richness; FEve = Functional evenness; FDiv = Functional divergence; FDis = Functional dispersion.
FIGURE 2 in Taxonomic loss and functional reduction over time in the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River, Southern Brazil
FIGURE 2 | Non-metric multidimensional scaling (NMDS) of the ichthyofauna composition of the Taquaruçu Reservoir, lower Paranapanema River (the transitional zone between 2006 and 2020).
FIGURE 1 in Taxonomic loss and functional reduction over time in the ichthyofauna of the Taquaruçu Reservoir, lower Paranapanema River, Southern Brazil
FIGURE 1 | Location of the samplings points in the Taquaruçu Reservoir, lower Paranapanema River (transitional zone, 2020). Hydroelectric power plants: 1– Rosana; 2– Taquaruçu; 3– Capivara. MS = Mato Grosso do Sul State; PR = Paraná State; SP = São Paulo State.
Dataset related to article "Role of ultrastructural determinants of glomerular permeability in ultrafiltration function loss".
<p><em>The files contain the raw data related to the manuscript: "Role of ultrastructural determinants of glomerular permeability in ultrafiltration function loss" available at <a href="https://insight.jci.org/articles/view/137249">https://insight.jci.org/articles/view/13724</a>9.</em></p> <p><strong>Datasets:</strong></p> <p><strong>Scripts for CFD simulation of water passage through the glomerular filtration barrier (GFB) of Wistar, MWF and MWF-treated rats:</strong></p> <p><strong>STL_models</strong> - contains STL models of the unit cell of GFB reconstructed for the three groups of rats (i.e., WIST, MWF and MWFL). The dimensions assumed are presented in tables 2 and 4 in the main text and well explained in the Supplemental Material.</p> <p><strong>CFD_cases</strong> – contains cases in .rar archives for each group of rats; each case includes scripts which needed to run a CFD simulation of steady for incompressible, turbulent flow with porosity treatment, using the <strong><em>porousSimpleFoam</em></strong> solver in OpenFOAM. OpenFOAM version 6 (openfoam.org) was used for generating all data presented in this paper, but scripts should run well with updated versions.</p> <p><strong>Figure 1_Pores morphometrical analysis.xlsx </strong>- dataset for the calculation of distribution of slit pore size. These data are presented in Figure 1. </p> <p><strong>Figure 2_subpodocyte space morphometry.xlsx </strong>- dataset for the quantification of subpodocyte area. These data are presented in Figure 2. </p> <p><strong>Figure 5_CD151 and a3 integrin expression.xlsx </strong>- dataset related to the quantification of CD151, a3 integrin and their colocalization. These data are presented in Figure 5. </p> <p><strong>k_SupplTable2.xlsx</strong> – dataset for the calculation and total and relative permeability of each structural layer of GFB. These data are presented in Supplemental Table 2.</p> <p><strong>Neal-model_graphs_Figure4_SupplFigure3.xlsx</strong> - dataset for the calculation and of hydraulic resistances of GFB using the models of Neal et al. (2007). These data are presented in Figure 4 and Supplemental Figure 3.</p> <p><strong>Table 1_Systemic parameters.xlsx </strong>- dataset related to the systemic parameters. These data are presented in Table 1.</p> <p><strong>Table 2_Morphometric characterization.xlsx </strong>- dataset related to the morphometric characterization of epithelial slit pores and GBM. These data are presented in Table 2. </p> <p> </p> <p><strong>Abstract of the manuscript</strong></p> <p>The epithelial filtration slit is a crucial component of the glomerular capillary membrane, which is essential for maintaining glomerular filtration function. Though chronic kidney diseases are an immense clinical problem, the mechanisms through which structural alterations reduce glomerular water filtration have not yet been understood completely. To investigate the mechanisms underlying filtration function loss, we studied rats with spontaneously occurring progressive kidney disease, either treated with angiotensin II antagonist or untreated, combining high-resolution electron microscopy of the glomerular capillary wall with theoretical water filtration modeling. Under pathological conditions, epithelial filtration pores and the extension of the subpodocyte space were larger than in normal controls. Numerical analyses indicated that these ultrastructural changes increased hydraulic resistance of the glomerular capillary wall by extending coverage of the filtration barrier by the subpodocyte space, with the changes in hydrodynamic forces acting on podocytes likely being responsible for their detachment. Angiotensin II inhibition normalized the subpodocyte space's hydraulic resistance, restored mechanical podocyte load, and preserved CD151-α3 integrin complex assembly, improving podocyte adherence and survival. Our results show that ultrastructural changes in podocytes are major determinants of the hydraulic resistance of the glomerular capillary wall and highlight the mechanism of podocyte loss in kidney disease progression, as well as the mechanisms underlying angiotensin II inhibition.</p>
Data_Figure4_Loss of Claudin-3 Impairs Hepatic Metabolism, Biliary Barrier Function, and Cell Proliferation in the Murine Liver
<p>Data of Figure 4 from “Loss of Claudin-3 Impairs Hepatic Metabolism, Biliary Barrier Function, and Cell Proliferation in the Murine Liver”</p> <p>Dataset (doi: 10.1016/j.jcmgh.2021.04.003) contains the original publication as PDF-format (10.1038_s41598-020-59701-0). Corresponding raw data obtained from LC-MS/MS analysis provided as two files in CSV format (31003A-179400_10.1016j.jcmgh.2021.04.003_CGC_4-1.csv, 31003A-179400_10.1016j.jcmgh.2021.04.003_CGC_4-2.csv). All further experiment related information provided as two meta-data-files (31003A-179400_10.1016j.jcmgh.2021.04.003_CGC _4_1-2_M_1.PDF, 31003A-179400_10.1016j.jcmgh.2021.04.003_CGC _4_1-2_M_2.PDF) as PDF format.</p>
Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"
<p>This dataset provides the predictions of the protein quality<br> assessment method Q_epsilon with respect to CASP13 and CASP14, as well<br> as a snapshot of the github repository providing the code for the<br> method.<br> The format of the file is as follows: The first column represents the<br> target and decoy names in the format <target name>_<decoy name>. The<br> second column is the true GDTTS, and the third column represents the<br> predicted GDTTS by Q_epsilon.</p>
The global loss of avian functional and phylogenetic diversity from anthropogenic extinctions
Open the record for dataset details and reuse information.
Data from: Ecosystem functioning during biodiversity loss and recovery
Open the record for dataset details and reuse information.
Input data for the analysis of changes in functional structures of Japanese tree species by species loss simulation
<p>The dataset was used in Kusumoto, Shiono & Kubota (2020). It includes functional structure indices (community means, functional richness, and Rao's quadratic entropy) for 514 Japanese timber and non-timber tree species at 10-km grid cell level. The community means were based on specific leaf area and leaf nitrogen content, respectively. Functional richness and Rao's Q were based on wood density and tree height. There functional metrics were calculated for the observed species assemblages and simulated assemblages at 10-km grid cell level. The simulated assemblages were computed by removing species in each grid cell at 5 levels of species loss (10%, 20%, 30%, 40% and 50%) with two scenarios: random loss and ordered loss depending on species successional niche score (i.e. later successinal species are preferentially lost). See "README" sheet for detailed explanations of the contents.</p> <p>Kusumoto, Shiono & Kubota (2020) Ethnobotany-informed trait ecology: measuring vulnerability of timber provisioning services across forest biomes in Japan. Biodiversity and Conservation. DOI: 10.1007/s10531-020-01974-y</p>
Experimental facilitation of heat loss affects work rate and innate immune function in a breeding passerine bird
The capacity to get rid of excess heat produced during hard work is a possible constraint on parental effort during reproduction (heat dissipation limit [HDL] theory). We released hard-working blue tits (Cyanistes caeruleus) from this constraint by experimentally removing ventral plumage. We then assessed if this changed their reproductive effort (feeding rate and nestling size) and levels of self-maintenance (change in body mass and innate immune function). Feather-clipped females reduced the number of feeding visits and increased levels of constitutive innate immunity compared to unclipped females but did not fledge smaller nestlings. Thus, they increased self-maintenance without compromising current reproductive output. In contrast, feather-clipping did not affect the number of feeding visits or innate immune function in males, despite increased heat loss rate. Our results show that analyses of physiological parameters, such as constitutive innate immune function, can be important when trying to understand sources of variation in investment in self-maintenance versus reproductive effort and that risk of overheating can influence innate immune function during reproduction.
Data for One Earth publication "Breaching planetary boundaries: Over half of global land area suffers critical losses in functional biosphere integrity"
<p>This repository contains data and processing scripts for the study: Stenzel et al. 2025, One Earth, "Breaching planetary boundaries: Over half of global land area suffers critical losses in functional biosphere integrity".</p>
Trait-based mechanistic approach highlights global patterns and losses of herbivore biomass functional diversity
<ol> <li>Mammalian herbivores play a pivotal role in Earth System processes by affecting biogeochemical cycles and ecosystem functioning, potentially leading to significant repercussions on atmosphere-biosphere feedbacks. Global dynamic models of mammalian populations can improve our understanding of their ecological role at large scales and the consequences of their extinctions. However, such models are still lacking and mammals are poorly integrated in Earth System science.</li> <li>We developed a mechanistic global model of terrestrial herbivore populations simulated with 37 functional groups defined through the analysis of eco-physiological traits across all extant herbivores (2599 species). We coupled this model with a global vegetation model to predict herbivores' maximum potential biomass in pre-industrial and at present-day and to study the environmental drivers explaining the distribution of herbivore biomass. Present-day biomass was estimated by accounting for anthropogenic activity causing habitat and range losses.</li> <li>We show that natural ecosystems could have sustained a potential wild herbivore wet biomass of 330 Mt [95% CI 245–417], comprised of 193 Mt [95% CI 177–208] by large species (body mass > 1–10 kg, depending on functional group) and 138 Mt [95% CI 68-209] by small species. We estimate that the remaining present-day large herbivores biomass is 82 Mt [95% CI 32–133], reduced by 57% due to anthropogenic activity; consequently, small herbivores currently dominate global herbivore biomass with 98 Mt (95% CI 91–106, -29%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline.</li> <li>Actual evapotranspiration is the most important driver of total, large, and small herbivore biomass and explains 64%, 59%, and 49% of its variation, respectively. Distribution of modeled and observed large herbivores' biomass suggested a high dependency on energy and water with more biomass in hot and wet areas. These results challenge the notion that large herbivore biomass peaks primarily in ecosystems with intermediate precipitation levels such as savannas.</li> <li>Outside Africa and the Tropics, pre-industrial biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species biomass in certain areas. These herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System science and models.</li> </ol>
The hidden legacy of megafaunal extinction: loss of functional diversity and resilience over the late Quaternary at Hall's Cave
<p>This dataset contains trait data and R code used in the analysis for the paper "Hedberg, C.P., Lyons S.K., & Smith F.A. (2021). THe Hidden Legacy of megafaunal extinction: loss of functional diversity and resilience over the Late Quaternary at Hall's Cave. Global Ecology and Biogeography. https://doi.org/10.1111/geb.13428"</p> <p>We collected data for eight functional traits (mass, diet, arboreality, cursoriality, soil disturbance, group size, activity period, migration habit) that collectively describe a species' ecological role and influence on ecosystem processes. With these data, we investigated changes in functional diversity and redundancy of a local mammal community over time at Hall's Cave, a site in Central Texas with a continuous record from 21,000 years ago to the present. Additionally, we included several common introduced and domestic species to the modern community to test whether they restore some lost ecological function. </p> <p>We found that declines in functional diversity were greater than expected given the decrease in species richness, implying lost taxa contributed higher than average distinct ecological function. Functional distances between remaining species increased through time leading to lowered functional redundancy in younger communities. However, recently introduced taxa increased functional diversity to levels similar to the Holocene and partially restored functional space occupied by Late Pleistocene fauna. Our local-scale analysis demonstrates how prolonged biodiversity erosion not only leads to functionally depauperate communities, but critically lowers ecological resilience to future disturbance.</p>
Data from: Natural Zeitgebers under temperate conditions cannot compensate for the loss of a functional circadian clock in timing of a vital behavior in Drosophila
<p><span>The adaptive significance of adjusting behavioral activities to the right time of the day seems obvious but is under debate. Our data provides evidence that proper timing of eclosion, a vital behavior of the fruit fly <em>Drosophila melanogaster</em>, requires a functional molecular clock under quasi-natural conditions. </span></p> <p><span>We compared eclosion profiles and assessed eclosion rhythmicity in wildtype flies (CS) and clock-related mutant strains <em>(per<sup>01</sup></em>, <em>pdf<sup>01</sup></em>, <em>han<sup>5304</sup></em>) under laboratory and outdoor conditions. In the laboratory, flies were entrained in either light-dark cycle (LD12:12) or warm (25°C)-cold (16°C) cycle (WC12:12), and tested under entrainment or constant conditions using TriKinetics Drosophila Eclosion Monitors. For outdoor assays, a WEclMon system was used and experiments were performed between July-Octobre 2014 and July-Octobre 2016. </span></p> <p><span>Flies with a defective molecular clock showed impaired rhythmicity and gating under natural temperate conditions in Würzburg/Germany even in the presence of a full complement of abiotic Zeitgebers. We also found that eclosion rhythmicity cannot be entrained by daily cycles in relative humidity. Low relative humidity also did not or only weakly affect the ability of the flies to eclose and unfold their wings.</span></p> <p><span>Our results suggest that the presence of natural Zeitgebers is not sufficient, and a functional molecular clock is required to induce stable temporal eclosion patterns in flies under temperate conditions with considerable day-today variation in light intensity and temperature. Temperate Zeitgebers are, however, sufficient to functionally rescue a loss of PDF-signalling.</span></p> <p><span>The data set belongs to the publication:</span></p> <p><em><span>Ruf F, Mitesser O, Mungwa ST, Horn M, Rieger D, Hovestadt T, and Wegener C (2021) Natural Zeitgebers Under Temperate Conditions Cannot Compensate for the Loss of a Functional Circadian Clock in Timing of a Vital Behavior in Drosophila. </span>Journal of Biological Rhythms 36: 271–285. DOI: 10.1177/0748730421998112.</em></p>
Data from: Forest loss and treeless matrices cause the functional impoverishment of sapling communities in old-growth forest patches across tropical regions
<p>Landscape-level disturbances, such as forest loss, can profoundly alter the functional composition and diversity of biotic assemblages. In fact, the landscape-moderated functional trait selection (LMFTS) hypothesis states that landscape-level disturbances may act as environmental filters that select a set of species with disturbance-adapted attributes while causing the loss of species with disturbance-sensitive attributes, ultimately compromising ecosystem functioning. However, the impact of landscape patterns on the functional composition and diversity of tropical regenerating trees (saplings) is unknown.</p> <p>Using a multiscale approach to identify the best spatial scale (i.e. the scale of effect), we tested the effect of forest cover, matrix openness and forest patch density (fragmentation) on functional composition and functional diversity of tree saplings in old-growth forest patches (n = 59) in three Mexican rainforest regions with different degree of deforestation. For 368 species and ~23,000 individuals, we compiled information from global and national databases on six functional traits related to seed dispersal and plant establishment and calculated their community abundance-weighted mean (CWMs) and three complementary functional diversity indices.</p> <p>Forest loss and matrix openness reduced functional richness and evenness, but only in the two most deforested regions. Overall, fragmentation had contrasting effects on functional diversity and composition, but correlated negatively with some functional traits in the most deforested region. Importantly, in the regions with high-to-intermediate degree of deforestation, functional composition experienced major changes: maximum height, seed mass, fruit size and wood density decreased, and SLA increased, in forest patches surrounded by open matrices in highly deforested and fragmented landscapes. This caused a shift of community traits towards more disturbed-adapted attributes.</p> <p><em>Synthesis and applications</em>. In agreement with the LMFTS hypothesis, our results confirm that landscape modifications in regions undergoing high and long-lasting deforestation greatly impoverish the functional composition and diversity of sapling communities. The shift from communities composed mainly by conservative attributes towards communities with a higher prevalence of disturbance-adapted attributes disrupts the future community structure and jeopardizes critical ecosystem functions. Management practices focused on preventing deforestation, increasing forest cover, and promoting treed matrices are necessary to preserve the functionality of these species-rich but increasingly threatened rainforests.</p>
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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.