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1,355 results for “manipulation”
Ecosystem-Scale Rainfall Manipulation in a Piñon-Juniper Forest at the Sevilleta National Wildlife Refuge, New Mexico: Soil Temperature Data (2006-2013)
Climate models predict that water limited regions around the world will become drier and warmer in the near future, including southwestern North America. We developed a large-scale experimental system that allows testing of the ecosystem impacts of precipitation changes. Four treatments were applied to 1600 m2 plots (40 m × 40 m), each with three replicates in a piñon pine (Pinus edulis) and juniper (Juniper monosperma) ecosystem. These species have extensive root systems, requiring large-scale manipulation to effectively alter soil water availability.  Treatments consisted of: 1) irrigation plots that receive supplemental water additions, 2) drought plots that receive 55% of ambient rainfall, 3) cover-control plots that receive ambient precipitation, but allow determination of treatment infrastructure artifacts, and 4) ambient control plots. Our drought structures effectively reduced soil water potential and volumetric water content compared to the ambient, cover-control, and water addition plots. Drought and cover control plots experienced an average increase in maximum soil and air temperature at ground level of 1-4° C during the growing season compared to ambient plots, and concurrent short-term diurnal increases in maximum air temperature were also observed directly above and below plastic structures. Our drought and irrigation treatments significantly influenced tree predawn water potential, sap-flow, and net photosynthesis, with drought treatment trees exhibiting significant decreases in physiological function compared to ambient and irrigated trees. Supplemental irrigation resulted in a significant increase in both plant water potential and xylem sap-flow compared to trees in the other treatments. This experimental design effectively allows manipulation of plant water stress at the ecosystem scale, permits a wide range of drought conditions, and provides prolonged drought conditions comparable to historical droughts in the past – drought events for whi
Ecosystem-Scale Rainfall Manipulation in a Piñon-Juniper Forest at the Sevilleta National Wildlife Refuge, New Mexico: Water Potential Data (2006-2013)
Climate models predict that water limited regions around the world will become drier and warmer in the near future, including southwestern North America. We developed a large-scale experimental system that allows testing of the ecosystem impacts of precipitation changes. Four treatments were applied to 1600 m2 plots (40 m × 40 m), each with three replicates in a piñon pine (Pinus edulis) and juniper (Juniper monosperma) ecosystem. These species have extensive root systems, requiring large-scale manipulation to effectively alter soil water availability.  Treatments consisted of: 1) irrigation plots that receive supplemental water additions, 2) drought plots that receive 55% of ambient rainfall, 3) cover-control plots that receive ambient precipitation, but allow determination of treatment infrastructure artifacts, and 4) ambient control plots. Our drought structures effectively reduced soil water potential and volumetric water content compared to the ambient, cover-control, and water addition plots. Drought and cover control plots experienced an average increase in maximum soil and air temperature at ground level of 1-4° C during the growing season compared to ambient plots, and concurrent short-term diurnal increases in maximum air temperature were also observed directly above and below plastic structures. Our drought and irrigation treatments significantly influenced tree predawn water potential, sap-flow, and net photosynthesis, with drought treatment trees exhibiting significant decreases in physiological function compared to ambient and irrigated trees.  Supplemental irrigation resulted in a significant increase in both plant water potential and xylem sap-flow compared to trees in the other treatments. This experimental design effectively allows manipulation of plant water stress at the ecosystem scale, permits a wide range of drought conditions, and provides prolonged drought conditions comparable to historical droughts in the past – drought events for w
Ecosystem-Scale Rainfall Manipulation in a Piñon-Juniper Forest at the Sevilleta National Wildlife Refuge, New Mexico: Sap Flow Data (2006-2013)
Climate models predict that water limited regions around the world will become drier and warmer in the near future, including southwestern North America. We developed a large-scale experimental system that allows testing of the ecosystem impacts of precipitation changes. Four treatments were applied to 1600 m2 plots (40 m × 40 m), each with three replicates in a piñon pine (Pinus edulis) and juniper (Juniper monosperma) ecosystem. These species have extensive root systems, requiring large-scale manipulation to effectively alter soil water availability.  Treatments consisted of: 1) irrigation plots that receive supplemental water additions, 2) drought plots that receive 55% of ambient rainfall, 3) cover-control plots that receive ambient precipitation, but allow determination of treatment infrastructure artifacts, and 4) ambient control plots. Our drought structures effectively reduced soil water potential and volumetric water content compared to the ambient, cover-control, and water addition plots. Drought and cover control plots experienced an average increase in maximum soil and air temperature at ground level of 1-4° C during the growing season compared to ambient plots, and concurrent short-term diurnal increases in maximum air temperature were also observed directly above and below plastic structures. Our drought and irrigation treatments significantly influenced tree predawn water potential, sap-flow, and net photosynthesis, with drought treatment trees exhibiting significant decreases in physiological function compared to ambient and irrigated trees.  Supplemental irrigation resulted in a significant increase in both plant water potential and xylem sap-flow compared to trees in the other treatments. This experimental design effectively allows manipulation of plant water stress at the ecosystem scale, permits a wide range of drought conditions, and provides prolonged drought conditions comparable to historical droughts in the past – drought events for w
Drought Impact on Desert Ecosystems, Drought Network precipitation manipulation experiment in desert grasslands
Climate change amplifies the global water cycle, making droughts more frequent and more severe. The hot deserts of the U.S. rely on the stability and frequency of water availability in order to sustain biological communities, making these ecosystems incredibly vulnerable to anticipated alterations in the water cycle. This project seeks to understand which biotic and abiotic variables are principle in determining desert ecosystem sensitivity to drought? To answer these questions, we have installed a drought manipulation that will simulate an extreme drought event by reducing annual precipitation by 66% in seven desert sites. Plant abundance data are collected annually to track changes in the plant community. Data collection began in Spring 2018. Treatments at three Sevilleta sites began in Fall 2018 after data collection in October 2018. Treatments started at four sites in Arizona and California in March and April of 2019 and spring pretreatment data collection. The treatments will last for four years.
Benthic Chlorophyll and Macroalgae on an Experimentally-manipulated Tidal Flat on the Virginia Coast, 2016-2017
In 2016 a Before-After-Control-Impact experimental design was used to test if the removal of macroalgae from a heavily vegetated mudflat would result in an increase in MPB biomass (Smith 2002). Data Table 1 (BCL_BACIexpa.csv):Benthic chlorophyll samples collected from mudflat where experimental macroalgal removal was conducted. Samples collected haphazardly from 3500 m^2 plots. Sediment cores were 1 cm inner diameter and 2 cm deep. Data Table 2 (BCL_MAMPBa.csv):Survey data where macroalgal mats were sampled and sediment beneath mats sampled for benthic chlorophyll. This data table contains benthic chlorophyll data. Corresponding macroalgal mass data found in MAmass_MAMPBa.csv. Sediment cores were 1 cm inner diameter and 2 cm deep. Three subsamples taken (A,B,C). Data Table 3 (MAmass_MAMPBa.csv): Survey data where macroalgal mats were sampled and sediment beneath mats sampled for benthic chlorophyll. This data table contains macroalgal mass data. Corresponding chlorophyll data found in BCL_MAMPBa.csv
Magnetic manipulation of intracellular signals
<p>In the context of the MAGNEURON project we have developed magnetic tools to manipulate intracellular proteins involved in intracellular signaling processes. We focused on the manipulation of the subdomain DHPH of ITSN1 in order to control the activity of CDC42.</p> <p>To control the activity of CDC42 we produced a fusion protein consisting in the DHPH domain of ITSN1, the mCherry fluorescent protein and a nanobody against GFP (aGFPnb).</p> <p>The manipulations were done either using a magnetic tip or magnetic micropillars done with soft magnetic material (Nickel Iron alloy). Nanoparticles were first injected in the cytoplasm of the cell. After a delay of at least ten minutes, the survival of the cell was controlled and the manipulation could start.<br> We monitored the fluorescence of the reporter (IRFP-NWASP) and the formation of protrusion/filopodia as markers of a biological response to the manipulation.</p> <p>We observed protrusion formation as well as NWASP activity when attracting the nanoparticles, but control experiments (Manipulation of particles without ITSN1-mcherry-aGFPnb) also showed increase of fluorescence of the NWASP reporter at the point of attraction of the particles.</p> <p>In addition, if compared to optogenetic manipulation of the similar ITSN1-DHPH domain, the formation of protrusion was very limited. We concluded that magnetic manipulation of intracellular signals was not efficient to hijack signaling pathways.</p> <p>We publish here the raw data of some experiments that were produced in the lab.</p> <p>Each experiment has a README file describing the parameter of the recording and what can be observe on the video</p>
Individual skyrmion manipulation by local magnetic field gradients - Dataset
<p>Dataset for the article: Casiraghi A, Corte-León H, Vafaee M, Garcia-Sanchez F, Durin G, Pasquale M, Jakob G, Kläui M and Kazakova O 2019 Individual skyrmion manipulation by local magnetic field gradients 25–7. DOI: 10.1038/s42005-019-0242-5.</p> <p>The data is divided in figures and for each figure we report the raw data and the python code to analyse it.</p>
Acoustic Hologram Enhanced Phased Arrays for Particle Manipulation Data
<p>All data relating to figures and statistics uploaded in the paper entitled "Acoustic Hologram Enhanced Phased Arrays for Particle Manipulation"</p>
When fiction becomes fact: exaggerating host manipulation by parasites
<p>In an era where some find fake news around every corner, the use of sensationalism has inevitably found its way into the scientific literature. This is especially the case for host manipulation by parasites, a phenomenon in which a parasite causes remarkable change in the appearance or behaviour of its host. This concept, which has deservedly garnered popular interest throughout the world in recent years, is nearly 50-years old. In the past two decades, the use of scientific metaphors, including anthropomorphisms and science fiction, to describe host manipulation has become more and more prevalent. It is possible that the repeated use of such catchy, yet misleading words in both the popular media and the scientific literature could unintentionally hamper our understanding of the complexity and extent of host manipulation, ultimately shaping its narrative in part or in full. In this commentary, the impacts of exaggerating host manipulation are brought to light by examining trends in the use of embellishing words. By looking at key examples of exaggerated claims from widely reported host-parasite systems found in the recent scientific literature, it would appear that some of the fiction surrounding host manipulation has since become fact.</p>
Data from: Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe
<p><em><span>Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants <i>Solidago canadensis </i>and <i>S. gigantea</i>,<i> </i>we tested whether such differentiation might have happened through heritable epigenetic changes in cytosine methylation. In a two-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in </span></em><em><i><span>S. canadensis</span></i></em><em><span>, but three genetic clusters in </span></em><em><i><span>S. gigantea</span></i></em><em><span>. </span></em><em><i><span>Solidago canadensis</span></i></em><em><span> showed latitudinal clines in flowering phenology and growth. In </span></em><em><i><span>S. gigantea</span></i></em><em><span>, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, likely through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.</span></em></p>
Sex-specific patterns of senescence in artificial insect populations varying in sex-ratio to manipulate reproductive effort
<p><strong>Background:</strong> The disposable soma theory of ageing assumes that organisms optimally trade-off limited resources between reproduction and longevity to maximize fitness. Early reproduction should especially trade-off against late reproduction and longevity because of reduced investment into somatic protection, including immunity. Moreover, as optimal reproductive strategies of males and females differ, sexually dimorphic patterns of senescence may evolve. In particular, as males gain fitness through mating success, sexual competition should be a major factor accelerating male senescence. In a single experiment, we examined these possibilities by establishing artificial populations of the mealworm beetle, <em>Tenebrio molitor</em>, in which we manipulated the sex-ratio to generate variable levels of investment into reproductive effort and sexual competition in males and females.</p> <p><strong>Results:</strong> As predicted, variation in sex-ratio affected male and female reproductive efforts, with contrasted sex-specific trade-offs between lifetime reproduction, survival and immunity. High effort of reproduction accelerated mortality in females, without affecting immunity, but high early reproductive success was observed only in balanced sex-ratio condition. Male reproduction was costly on longevity and immunity, mainly because of their investment into copulations rather than in sexual competition.</p> <p><strong>Conclusions:</strong> Our results suggest that <em>T. molitor</em> males, like females, maximize fitness through enhanced longevity, partly explaining their comparable longevity. </p>
Selective extinctions resulting from random habitat destruction lead to under‐estimates of local and regional biodiversity loss in a manipulative field experiment
<p>Land-use change is a significant cause of anthropogenic extinctions, which are likely to continue and accelerate as habitat conversion proceeds in most biomes. One way to understand the effects of habitat loss on biodiversity is through improved tools for predicting the number and identity of species losses in response to habitat loss. There are relatively few methods for predicting extinctions and even fewer opportunities for rigorously assessing the quality of these predictions. In this paper we address these issues by applying a new method based on rarefaction to predict species losses after random, but aggregated, habitat loss. We compare predictions from three rarefaction models, individual-based, sample-based, and spatially-clustered, to those derived from a commonly-used extinction estimation method, the Species-Area Relationship (SAR). We apply each method to a mesocosm experiment, in which we aim to predict species richness and extinctions of arthropods immediately following 50% habitat loss. While each model produced strikingly accurate predictions of species richness immediately after the habitat loss disturbance, each model significantly underestimated the number of extinctions occurring at both the local (within-mesocosm) and regional (treatment-wide) scales. Despite the stochastic nature of our small-scale, short-term, and randomly applied habitat loss experiment, we found surprisingly clear evidence for extinction selectivity, for example when abundant species with low extinction probabilities were extirpated following habitat loss. The important role played by selective extinction even in this contrived experimental system suggests that ecologically driven, trait-based extinctions play an equally important role to stochastic extinction, even when the disturbance itself has no clear selectivity. As a result, neutrally stochastic null models such as the SAR and rarefaction are likely to underestimate extinctions caused by habitat loss. Nevertheless, given the difficulty of predicting extinctions, null models provide useful benchmarks for conservation planning by providing minimum estimates and probabilities of species extinctions.</p>
Datasets for the manipulator trials during WP7
<p>These data were produced acquired by the AML Group at UPAT for the needs of CompInnova’s (H2020 FETOPEN, Grant Agreement No. 665238) for the laser module trials during WP7 "Integration and validation of the prototype system and performance trials"</p> <p>The files are in easy read formats as office files, pdf and jpeg. Also raw files are included.</p> <p>The requirement of third-party usage of this database will be the referencing of this database and the publications made under the CompInnova project, as referenced under the licensing terms. </p> <p>The data were used in the deliverable D7.3</p>
Data from: Soil heterogeneity increases plant diversity after twenty years of manipulation during grassland restoration
The 'environmental heterogeneity hypothesis' predicts that variability in resources promotes species coexistence, but few experiments support this hypothesis in plant communities. A previous 15-y test of this hypothesis in a prairie restoration experiment demonstrated a weak effect of manipulated soil resource heterogeneity on plant diversity. This response was attributed to a transient increase in richness following a post-restoration supplemental propagule addition, occasionally higher diversity under nutrient enrichment, and reduced cover of a dominant species in a subset of soil treatments. Here, we report community dynamics under continuous propagule addition in the same experiment, corresponding to 16-20 y of restoration, in response to altered availability and heterogeneity of soil resources. We also quantified traits of newly added species to determine if heterogeneity increases the amount and variety of niches available for new species to exploit. The heterogeneous treatment contained a factorial combination of altered nutrient availability and soil depth; control plots had no manipulations. Total diversity and richness were higher in the heterogeneous treatment during this 5 y study due to higher cover, diversity, and richness of previously established forbs, particularly in the N-enriched subplots. All new species added to the experiment exhibited unique trait spaces, but there was no evidence that heterogeneous plots contained a greater variety of new species representing a wider range of trait spaces relative to the control treatment. The richness and cover of new species was higher in N-enriched soil, but the magnitude of this response was small. Communities assembling under long-term N addition were dominated by different species among subplots receiving added N, leading to greater dispersion of communities among the heterogeneous relative to control plots. Contrary to the deterministic mechanism by which heterogeneity was expected to increase diversity (greater variability in resources for new species to exploit), higher diversity in the heterogeneous plots resulted from destabilization of formerly grass-dominated communities in N-enriched subplots. While we do not advocate increasing available soil N at large scales, we conclude that the positive effect of environmental heterogeneity on diversity can take decades to materialize and depend on development of stochastic processes in communities with strong establishment limitation.
Data from: Large-scale manipulation of the acoustic environment can alter the abundance of breeding birds: evidence from a phantom natural gas field
1. Altered animal distributions are a consequence of human expansion and development. Anthropogenic noise can be an important predictor of abundance declines near human infrastructure, yet more information is needed to understand noise impacts at the spatial and temporal scales necessary to alter populations. 2. Energy development and associated anthropogenic noise are globally pervasive, and expanding. For example, 600,000 new natural gas wells have been drilled across central North America in less than twenty years. 3. We experimentally broadcast energy sector noise (recordings of compressor engines) in Southwest Idaho (USA). We placed arrays of speakers creating a "phantom natural gas field" in a large-scale experiment, and tested the effects of noise alone on breeding songbird abundance. To examine variation in human-caused noise, we broadcast two types of compressor noise, one with a slightly higher sound intensity and greater bandwidth than the other. 4. Our phantom natural gas field encompassed approximately 100 km2. We broadcast noise for over three continuous months, for each of two seasons, and quantified over 20,000 hours of background sound levels. 5. Brewer's sparrows (Spizella breweri) were affected by our narrowband playback, declining 30% 50 m from the speaker arrays. During our broadband playback, all species combined and Brewer's sparrows decreased 20% and 33% respectively at the scale of our sites (~0.5 km2; up to 400 m from speaker arrays). 6. Our results show the importance of incorporating the acoustic structure of noise when estimating the cost of noise exposure for populations and suggest an urgent need for noise mitigation, such as quieting compressor station noise, in energy extraction fields and natural areas broadly.
Manipulation of trait expression and pollination regime reveal the adaptive significance of spur length
<p class="Standardmedindrag">Understanding the mechanisms of adaptive population differentiation requires that both the functional and adaptive significance of divergent traits are characterized in contrasting environments. Here, we (a) determined the effects of floral spur length on pollen removal and receipt using plants with artificial spurs representing the species-wide variation in length, and (b) quantified pollinator-mediated selection on spur length and three traits contributing to floral display in two populations each of the short-spurred and the long-spurred ecotype of the orchid <i>Platanthera bifolia</i>. Both pollen receipt and removal reached a maximum at 28-29 mm long spurs in a short-spurred population visited by short-tongued moths. In contrast, pollen receipt increased linearly across the tested range (4-52 mm) and pollen removal was unrelated to spur length in a long-spurred population predominantly visited by a long-tongued moth. The experimentally documented effects on pollen transfer were not reflected in pollinator-mediated selection through female fitness or pollen removal indicating that the natural within-population variation in spur length was insufficient to result in detectable variation in pollen limitation. Our study illustrates how combining trait manipulation with analysis of causes and strength of phenotypic selection can illuminate the functional and adaptive significance of trait expression when trait variation is limited.</p>
GenomicInteractions: an R/Bioconductor package for manipulating and investigating chromatin interaction data.
<p>Files required to regenerate figures in main text of paper, using existing Supplemental R Markdown files. </p>
Flow-Guided Warping for Image-Based Shape Manipulation
<p>Dataset relative to the following publication:</p> <p>Vergne, R., Barla P., Bonneau, G.-P. and R. W. Fleming (2016). Flow-Guided Warping for Image-Based Shape Manipulation. <em>ACM Transactions on Graphics (Proceedings of SIGGRAPH 2016), 35(4)</em>: 93.</p> <p>Each folder contains *.mat files with the data from the experiments presented in Figure 12 of the article (Experiment 1: cg results, Experiment 2: photo results) and a text file with comments.</p>
Manipulation of complex objects dataset - Rhythmic Cup Task experiment
<p>This dataset contains raw data from a behavioral neuroscience experiment conducted at Northeastern University, Boston, MA, USA.</p> <p>Ten participants rhythmically manipulated a virtual cup containing a ball via a robotic manipulandum which controlled the cup position and provided haptic feedback of the force applied by the ball. The cup movement was constrained to 1 dimension. Participants were free to choose the frequency of oscillation, while the amplitude was imposed by visual constraints. The cup and ball system was represented mathematically by a cart and pendulum system. The following dimensions were used for the experiment: pendulum length = 0.45m, pendulum mass = 0.6kg, cart mass = 2.4kg.</p> <p>Each participant performed 5 blocks of 10 trials. For each data file, the first 2 letters identify (anonymously) a participant, the first number identifies the block and the second number identifies the trial within the block.</p> <p>The data are in Matlab data format. "RackPosition" (resp. Velocity, Acceleration) corresponds to the cart position (resp. velocity, acceleration). Y is the axis of the movement. "BallTheta" and "BallOmega" are the pendulum angular position and velocity. Please note that in this dataset angles are positive in clockwise direction (contrary to usual mechanical conventions). "BallForce" is the force applied by the pendulum on the cart.</p> <p>This experimental dataset was confronted to simulation results obtained with two different models. One ("Uncoupled Model") only simulates the dynamics of a cart and pendulum system (Matlab script "cup_task_uncoupled_model_inverde_dynamics.m" and "simulation_cup_task_uncoupled_model_inverse_dynamics.m"). Simulations of this Uncoupled Model are run using inverse dynamics, assuming a sinusoidal trajectory of the cart. The second model ("Coupled Model") includes a simplified model of hand dynamics, represented by an ideal force generator in parallel with a spring and a damper to simulate hand impedance (Matlab and Simulink scripts "cup_task_coupled_model.slx" and "simulation_coupled_model_forward_dynamics.m"). Simulations of this Coupled Model are run using forward dynamics</p> <p> </p>
Decoupling of growth, physiological state, and subsequent performance in a developmentally manipulated songbird
<p class="MsoNormal"><span>It is generally assumed that larger juveniles are more physiologically mature, hence their overall condition and subsequent performance are higher. Yet, some taxa face extreme workload transitions during development (e.g., nest departure in birds), which may select for non-linear growth profiles that decouple relationships between body size and physiological state, making associations between development<span> </span>and juvenile performance uncertain. We manipulated perceived mass in European starlings approaching fledging using 4.0 g weighted backpacks, measuring subsequent growth trajectories (mass, wing length) and physiological state (aerobic capacity, energy state, oxidative status) to test whether body size and physiology are developmentally coupled during a non-linear growth phase (pre-fledging mass recession). Nanotag radio transmitters were then used to track post-fledging performance (activity, activity-slope, dispersal). Weighted nestlings had greater pre-fledging mass recession and lower oxidative status than controls, but equal aerobic capacity and energy state. Haemoglobin and dROMs, as well as metrics of growth and body size, predicted post-fledging performance in control birds, whereas weighted birds showed no correlation between fledgling state and performance. Our data suggest mass-independent development of some physiological traits in species with non-linear growth profiles, potentially with a context-dependent oxidative cost, and that physiology (not just body size) may predict post-fledging performance.</span></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.