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2,135 results for “stabling”
Ratio of 18O to 16O Stable Isotopes in Tree Stem Cores at HJA, HFR, NWT, CWT, LUQ, and Barro Colorado Island
Patterns of biodiversity, such as the increase toward the tropics and the peaked curve during ecological succession, are fundamental phenomena for ecology. Such patterns have multiple, interacting causes, but temperature emerges as a dominant factor across organisms from microbes to trees and mammals, and across terrestrial, marine, and freshwater environments. However, there is little consensus on the underlying mechanisms, even as global temperatures increase and the need to predict their effects becomes more pressing. The purpose of this project is to generate and test theory for how temperature impacts biodiversity through its effect on biochemical processes and metabolic rate. A combination of standardized surveys in the field and controlled experiments in the field and laboratory measure diversity of three taxa -- trees, invertebrates, and microbes -- and key biogeochemical processes of decomposition in seven forests distributed along a geographic gradient of increasing temperature from cold temperate to warm tropical. The most abundant tree species (by basal area) were sampled at each experimental site (HJA, HFR, NWT, CWT, LUQ, and Barro Colorado Island) for ratio of stable isotopes of 18 Oxygen to 16 Oxygen in parts per million from ground and homogenized tree stem cores as part of a macrosystems biodiversity and latitude project supported by the National Science Foundation under Cooperative Agreement DEB#1065836. .
System data - Enabling inter-area reserves exchanges through stable benefit allocation mechanisms
<p>Appendix for paper 'Enabling inter-area reserves exchanges through stable benefit allocation mechanisms' </p> <p>This repository contains the system data for the case study presented in the paper.</p> <p>This is a joint work by Orcun Karaca, Stefanos Delikaraoglou, Gabriela Hug and Maryam Kamgarpour</p>
Data from: Gene editing to induce FOXP3 expression in human CD4+ T cells leads to a stable regulatory phenotype and function.
<p>Thymic regulatory T cells (tTreg) are potent inhibitors of autoreactive immune responses and loss of tTreg function results in fatal autoimmune disease. Defects in Treg number or function are also implicated in multiple autoimmune diseases, leading to growing interest in use of Treg as cell therapies to establish immune tolerance. Because tTreg are present at low numbers in circulating blood and may be challenging to purify and expand, and also inherently defective in some subjects, we designed an alternative strategy to creating autologous Treg-like cells from bulk CD4+ T cells. We utilized homology-directed-repair (HDR)-based gene-editing to enforce FOXP3 expression. Targeted insertion of a robust enhancer/promoter proximal to the first coding exon bypassed epigenetic silencing, permitting stable, high level endogenous FOXP3 expression. HDR-edited T cells, edTreg, manifested a transcriptional program leading to sustained expression of canonical markers and suppressive activity of tTreg. Both human and murine edTreg mediated immunosuppression in vivo in models of inflammatory disease. Further, this engineering strategy permitted generation of antigen-specific edTreg with robust in vitro and in vivo functional activity. Finally, edTreg could be enriched and expanded at scale using clinically-relevant methods. Together, these finding suggest edTreg production may permit broad future clinical application.</p>
Data from: Applied use of alternate stable state modeling in restoration ecology
<p>The concept of alternate stable states is important in ecological theory and models, but the application and implementation of these models have the potential to make significant future advances in the field of patterned landscapes. The bi-stable, ridge and slough landscape is a central feature of Everglades restoration and provides an important opportunity to test stable state theory with multistate transition models. We used these models to estimate environmental parameters associated with state changes (water depths, edaphic factors, etc.) to develop a quantitative method to measure resilience and stability. The multistate model indicates that long-term, local hydrology (15-year mean maximums and 15-year mean amplitude) and edaphic factors control the local scale shifts between ridge and slough states. We show that multistate models can provide hydrologic envelopes for managers, produce a tool to help assess future water management scenarios, and address issues of sustainability, resilience, and restoration for any bi-stable system.</p>
Generation of stable mammalian cell lines for the expression of proteins related to COVID-19 through random integration
<p>Scientists centred around University of Oxford came together in the current COVID-19 pandemic to contribute to relevant studies collaboratively. Researchers with no prior experience in virology studies, myself included, had volunteered our time to contribute whichever way we can based on our field of expertise. The Biotech team of SGC Oxford, headed by Nicola Burgess-Brown had taken up the role of producing proteins used in serological assays, basic research to understand COVID-19 pathophysiology and hunt for treatment compounds. The initial production of these proteins was based on transient transfection of expression construct DNA into mammalian cells. This approach was laborious and consumed large amounts of plasmid DNA. Therefore, I volunteered to generate stable expression cell lines that will negate the constant need for transfection.</p> <p>I aimed to stably integrate the expression constructs into the genome of Expi293F human cells commonly used in large scale protein production. The expression constructs carried neomycin marker for selection in mammalian cells. Toxicity to the cells is not a concern in this case because the expressed proteins are secreted into the medium and do not build up in the cells. The expression constructs are randomly integrated into the genome mainly via non-homologous end-joining (NHEJ). An advantage of this approach is that molecular sub-cloning is not necessary.</p> <p>In order to maximise the rate of correct integration of the expression constructs, restriction digestion was performed to cut once between the expression cassette and antibiotic resistance cassette (refer to cartoon in Figure 1). Without this step, the construct DNA will be broken at a random position during the integration step, potentially disrupting the expression cassette. I have also tested the effect of actively creating double strand breaks (DSBs) in the genome of the cells on the integration efficiency. More DSBs in the genome might increase the incidence of NHEJ and integration of our constructs. This was achieved by co-transfection of AAVS1 CRISPR/eSpCas9(1.1) construct (refer to cartoon in Figure 1). The eSpCas9(1.1)_No_FLAG_AAVS1_T2 construct was a gift from Yannick Doyon (Addgene plasmid # 79888 ; http://n2t.net/addgene:79888 ; RRID:Addgene_79888)</p> <p> </p> <p>Please refer to my SGC opennotebook post for my other research work unrelated to the pandemic.</p> <p>https://openlabnotebooks.org/generation-of-stable-mammalian-cell-lines-for-the-expression-of-proteins-related-to-covid-19-through-random-integration/</p>
Stable carbon, oxygen and nitrogen isotopes in tree rings from temperate forests within long-term monitoring network in the UK
<p>Supporting dataset for the paper "Climate and atmospheric deposition effects on forest water‑use efficiency and nitrogen availability across Britain" by Guerrieri et al. 2020 Scientific Reports DOI is 10.1038/s41598-020-67562-w (<a href="https://www.nature.com/articles/s41598-020-67562-w">https://www.nature.com/articles/s41598-020-67562-w</a>)</p> <p>The dataset includes carbon, oxygen and nitrogen stable isotope composition measured in tree rings for four species at twelve forests across climate and atmospheric deposition gradients in Britain. Data were used to i) investigate spatial and temporal (over 30‑years) changes in tree intrinsic water use efficiency (iWUE, i.e., the ratio between CO<sub>2</sub> assimilation - A, and stomatal conductance- g<sub>s</sub>); ii) assess the possible species-specific physiological mechanisms (changes in A and/or g<sub>s</sub>) evaluate whether sites receiving high Ndep experience increase in ecosystem N availability and N saturation (using tree-ring nitrogen isotope composition as a proxy); iv) elucidate drivers of spatial and temporal changes in the isotope-derived physiological and ecological processes (i.e., relative contribution of climate vs. changes in atmospheric CO<sub>2</sub> and nitrogen and sulfur deposition). </p> <p>The following files are available:</p> <ul> <li>CSV file including: a) Site names; b) Species; c) Latitude; d) Longitude; e) Investigated years (1980-2010); f) Measured isotope-related parameters and tree ring nitrogen %. Isotope-related parameters included in the dataset are: 1) delta13C, 2) carbon isotope discrimination (Delta13C), 3) intercellular CO2 concentration (ci) and the ratio of intercellular to atmospheric CO2 concentrations (ci/ca), delta18O, estimated delta18O in precipitation (delta18OP) according to Barbour et al. 2001 (see Method in Guerrieri et al. 2020 Scientific Reports), oxygen isotope discrimination above the source water (Delta18O), delta15N. </li> <li>PDF file reporting the equations used to calculate the isotope-derived parameters, which can also be found in the paper by Guerrieri et al. 2020 Scientific Reports (accepted)</li> </ul>
Codes and datasets associated with the paper "Addressing the Grid-size Sensitivity Issue in Large-eddy Simulations of Stable Boundary Layers"
<p>From here, you will find some of the codes, simulation data in the article: </p> <p>Dai, Y., Basu, S., Maronga, B. and de Roode, S.R., 2020. Addressing the Grid-size Sensitivity Issue in Large-eddy Simulations of Stable Boundary Layers. <em>arXiv preprint arXiv:2003.09463</em>.</p> <p><strong>Simulation results from DALES: </strong></p> <p>within the folder of DALES, D52 denotes default scheme of Deardorff, H52 denotes the revised Deardorff scheme. Numbers of each fold indicates the grid number in each direction. </p> <p><strong>Simulation results from MATLES:</strong></p> <p>file name: MATLES/variable.out</p> <p>Example: MATLES/aT.out, the potential temperature data (2D, time and height) from MATLES</p> <p><strong>Python code for plotting: </strong></p> <p>dalesfunc.py is the function file used to process data</p> <p>DALES_plotting.py is the code file used for plotting the simulation results from DALES and MATLES</p> <p><strong>DALES input:</strong></p> <p>namoptions in each folder is the file for DALES options input</p>
Supplementary material 3 from: Hill KGW, Nielson KE, Tyler JJ, McInerney FA, Doubleday ZA, Frankham GJ, Johnson RN, Gillanders BM, Delean S, Cassey P (2020) Pet or pest? Stable isotope methods for determining the provenance of an invasive alien species. NeoBiota 59: 21-37. https://doi.org/10.3897/neobiota.59.53671
Figure S1. Results from a carbon decision tree
Supplementary material 4 from: Hill KGW, Nielson KE, Tyler JJ, McInerney FA, Doubleday ZA, Frankham GJ, Johnson RN, Gillanders BM, Delean S, Cassey P (2020) Pet or pest? Stable isotope methods for determining the provenance of an invasive alien species. NeoBiota 59: 21-37. https://doi.org/10.3897/neobiota.59.53671
Table S4.1. Determining confidence in status assignment
Resilience and alternative stable states after desert wildfires
<p>Improving models of community change is a fundamental goal in ecology and has renewed importance during global change and increasing human disturbance of the biosphere. Using the Mojave Desert (southwestern USA) as a model system, invaded by non-native plants and subject to wildfire disturbances, we examined models of resilience, alternative stable states, and convergent-divergent trajectories for 36 years of plant community change after 31 wildfires in communities dominated by the native shrubs <i>Larrea</i> <i>tridentata </i>or <i>Coleogyne</i> <i>ramosissima</i>. Perennial species richness on average was fully resilient within 23 years after disturbance in both community types. Perennial cover was fully resilient within 25 years in the <i>Larrea</i> community, but recovery was projected to require 52 years in the <i>Coleogyne</i> community. Species composition shifts were persistent, and in the <i>Coleogyne</i> community, the projected compositional recovery time of 550 years and increasing resembled a deflected trajectory toward potential alternative states. Disturbed sites contained a perennial species composition of predominately short-statured forbs, subshrubs, and grasses, contrasting with the larger-statured shrub and tree structure of undisturbed sites. Auxiliary datasets characterizing species recruitment, annual plants including non-native grasses, biocrust communities, and soils showed persistent differences between disturbed and undisturbed sites consistent with positive feedbacks potentially contributing to alternative stable states. Resprouting produced limited resilience for the large shrubs <i>Larrea tridentata</i> and <i>Yucca</i> spp. important to population persistence, but did not forestall long-term reduced abundance of the species. The non-native annual grass <i>Bromus rubens</i> increased on disturbed sites over time, suggesting persistently abundant non-native plant fuels and reburn potential. Biocrust cover on disturbed sites was half and species richness a third of amounts on undisturbed sites. Soil nitrogen was 30% greater on disturbed sites and no significant trend was evident for it to decline on even the oldest burns. Disturbed desert plant communities simultaneously supported all three models of resilience, alternative stable states, and convergent-divergent trajectories among community measures (e.g., species richness, composition), timeframes since disturbance, and spatial resolutions. Accommodating expression within ecosystems of multiple models, including those opposing each other, may help broaden theoretical models of ecosystem change.</p>
Ionic and water stable isotope composition of different Mendoza River basin (Argentina) water sources
<p>Samples obtained in a high temporal resolution from different water sources of the upper Mendoza River basin (Argentinean Central Andes). Ionic and water stable isotopes compositions are expressed and electric conductivity, pH and mean catchments altitudes. Decimal positions are expressed with comma.</p>
Informatics and statistics for: Stable coexistence or competitive exclusion? Fern endophytes demonstrate rapid turnover favoring a dominant fungus
<p>Fungal endophytes are critical members of the plant microbiome, but their community dynamics throughout an entire growing season are underexplored. Additionally, most fungal endophyte research has centered on seed-reproducing hosts, while spore-reproducing plants spend a significant proportion of their lifecycle in a haploid state and may filter vertically-transmitted fungi. In order to examine annual fungal endophyte community dynamics in a spore-reproducing host, we examined endophytes in a single population of ferns, <i>Polystichum munitum</i>, in the Pacific Northwest. Through culture-independent sequencing, we characterized the community assembly and temporal turnover of foliar endophytes throughout a growing season. From these results, we selected endophytes with outsized representations in sequence data and performed <i>in vitro</i> competition assays. Finally, we inoculated sterile fern gametophytes with dominant fungi observed in the field and determined their effects on host performance. Sequencing demonstrated that ferns were colonized by a diverse community of fungal endophytes in newly-emerged tissue, but diversity decreased throughout the season leading to the preponderance of a single fungus in later sampling months. This previously-undescribed endophyte appears to form specialized associations with the fern. While competition assays on a variety of media types failed to demonstrate that the dominant fungus was competitive against other fungi isolated from the same hosts, inoculation onto sterile fern gametophytes resulted in increased host growth suggesting mutualistic effects. When considering the potential for other fungi to act antagonistically on ferns in nature, the presence of this fungus may drive host success within the study site and possibly throughout its growing range.</p>
Stable isotope signatures of soil nitrogen on an environmental-geomorphic gradient within the Congo Basin
<p>Stable isotope signatures of soil N of three different forest types within the Congo Basin. </p>
Using stable isotopes to estimate migratory connectivity for a patchily distributed, wetland-associated Neotropical migrant
<p>Estimates of migratory connectivity are needed for full annual cycle population models of migratory bird species experiencing rapid declines in abundance. One technique to determine migratory connectivity is through stable isotope analysis. This low-resolution method may be influenced by how data are calibrated between isotopes measured in precipitation and those measured in feathers, and can be informed by incorporating relative abundance into the assignment model. eBird abundance maps are a new tool combining citizen science data into a predictive species distribution model. In the Prothonotary Warbler (Protonotaria citrea), a wetland-associated songbird with a patchy breeding distribution, we sought to use stable-hydrogen isotope analysis informed by a species-specific calibration equation and eBird abundance data to determine the strength of migratory connectivity. We developed a species-specific calibration equation using known-origin samples from the breeding grounds and found that stable-hydrogen isotope values measured in precipitation explained 50% of the variation in stable-hydrogen isotope values among feathers. We found that the assignment model incorporating eBird abundance data correctly identified the true origins of 66% of individuals, and that the average assignment area (as a measure of precision) was 64% of the breeding distribution. These results represented a 7% increase in precision and a 3% decrease in accuracy when compared to a model that was not informed by abundance. Based on these models, wintering populations from 6 countries represented a mix of likely breeding origins, suggesting low migratory connectivity for Prothonotary Warblers. We found evidence that wintering latitude was related to likely breeding origin, with individuals at western wintering locations more likely to have southern breeding origins, but this relationship was weak. These results corroborate studies using archival light-level geolocators and high-resolution genetic markers, which also demonstrated weak migratory connectivity in this species. For patchily distributed species, eBird abundance data may not provide a useful increase in precision and accuracy for isotope assignments.</p>
Chromium reduction and associated stable isotope fractionation restricted to anoxic shelf waters in the Peruvian Oxygen Minimum Zone
<p>Full research data accompanying the publication</p>
Dataset of the hydrometrics and stable isotopes of water in Schwingbach Environmental Observatory, Germany
<p>Dataset includes the following variables for Aug-Dec 2018 and Apr-Oct 2019 :</p> <ul> <li>Precipitation</li> <li>Air temperature</li> <li>soil moisture at 5, 30 and 70 cm depths</li> <li>stable isotopes of stream water</li> <li>stable isotopes of precipitation</li> </ul> <p> </p> <p> </p>
Data from: Widespread variation in stable isotope trophic position estimates: patterns, causes, and potential consequences
<p>Stable isotope analysis is one of the most widely used techniques to estimate trophic position and provides fundamental insight into the structure and management of ecological communities. To account for the effects of geographic variation in isotope levels, trophic position is typically estimated relative to an isotope "baseline" (i.e., material representing geographic variation) using a methodology such as a formula or statistical analysis. There is, however, remarkable variation in the baselines and methodologies used to estimate trophic position from stable isotopes. The consequences of this lack of standardization are unknown but could result in biased or erroneous conclusions. We conducted a literature review to quantify the variation in baselines and methodologies used to estimate trophic position from stable isotopes. Next, we assessed the consequences of this variation on individual species estimates and food web structure by extracting published trophic positions and applying various baselines and methodologies to existing datasets. We identified ten baselines and eight methodologies, the use of which varied by ecosystem studied. Moreover, we found that different baselines and methodologies yield significantly different trophic position estimates for individual species, as well as different conclusions about food web structure. Authors should avoid biological interpretations of absolute, stand-alone trophic positions (as these are prone to a number of biases). We recommend pairing stable isotope analysis with other techniques for more robust conclusions. Increased sample size may mitigate some of the variation caused by different baselines and methodologies; however, an alarmingly large proportion of studies collected only one sample in at least one trophic group (41% of all reviewed studies). Authors should collect a minimum of five samples per trophic group (but ten for best-practices) from as many trophic groups as possible to increase statistical power and redundancy in comparisons. When sample size is unavoidably constrained, we recommend using compound-specific isotope analysis with a taxon-specific trophic discrimination factor, because it may be more accurate and require fewer samples to maintain appropriate statistical power. Implementing our recommendations will increase the robustness and accuracy of conclusions based on stable isotopes, resulting in better management decisions and a more accurate understanding of ecological communities.</p>
Lipid content and stable isotopes of zooplankton during five winters around the northern Antarctic Peninsula
<p>The Southern Ocean zooplankton community is diverse, yet most species are understudied, especially with respect to their overwinter feeding ecologies. This dataset describes body condition and trophic biomarker data (lipid content and stable isotopes of carbon and nitrogen) from 19 zooplankton species collected over five consecutive winters (August and September 2012 – 2016) around the northern Antarctic Peninsula. To complement these data and provide context for interpretation, we report environmental data (percent sea-ice cover, sea-ice type, water temperature, salinity, and integrated chlorophyll-a (to 100 m)) as well as species abundance data at each sampling location. For most species, these are the first winter measurements or time series of body condition, trophic position, and abundance in relation to environmental variables around the northern Antarctic Peninsula. </p>
Stable leaders pave the way for cooperation under time-dependent exploration rates
<p>The exploration of different behaviors is part of the adaptation repertoire of individuals to new environments. Here, we explore how the evolution of cooperative behavior is affected by the interplay between exploration dynamics and social learning, in particular when individuals engage on the Prisoner's Dilemma along the edges of a social network. We show that when the population undergoes a transition from strong to weak exploration rates a decline in the overall levels of cooperation is observed. However, both constant and variable exploration rates are shown to be beneficial for cooperation as long as leaders (highly connected individuals) adopt lower exploration rates than followers (less connected individuals). This result suggests that noisy decision-making at the periphery of social networks may, in some cases, translate into major benefits at the population level. </p>
Data from: Stable producer–scrounger dynamics in wild birds: sociability and learning speed covary with scrounging behaviour
There has been extensive game-theoretic modelling of conditions leading to equilibria of producer–scrounger dichotomies in groups. However there is a surprising paucity of experimental evidence in wild populations. Here, we examine producer–scrounger games in five subpopulations of birds feeding at a socially learnt foraging task. Over four weeks, a bimodal distribution of producers and scroungers emerged in all areas, with pronounced and consistent individual tactic specialization persisting over 3 years. Tactics were unrelated to exploratory personality, but correlated with latency to contact and learn the foraging task, with the late arrivers and slower learners more likely to adopt the scrounging role. Additionally, the social environment was also important: at the broad scale, larger subpopulations with a higher social density contained proportionally more scroungers, while within subpopulations scroungers tended to be central in the social network and be observed in larger foraging flocks. This study thus provides a rare example of a stable, dimorphic distribution of producer–scrounger tactics in a wild population. It further gives support across multiple scales for a major prediction of social foraging theory; that the frequency of scroungers increases with group size.
ScienceDex guides
Understand access before you commit
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.