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1,355 results for “manipulation”
Natural history and ecological effects on the establishment and fate of Florida carpenter ant cadavers infected by the parasitic-manipulator Ophiocordyceps camponoti-floridani
<p class="MsoNormal">1. <em>Ophiocordyceps</em> fungi manipulate the behavior of their ant hosts to produce a summit disease phenotype, thereby establishing infected ant cadavers onto vegetation at elevated positions suitable for fungal growth and transmission. Multiple environmental and ecological factors have been proposed to shape the timing, positioning, and outcome of these manipulations.</p> <p class="MsoNormal">2. We conducted a long-term field study of <em>Ophiocordyceps</em> <em>camponoti-floridani</em> infections of <em>Camponotus floridanus</em> ants – the Florida zombie ants. We propose and refine hypotheses on the factors that shape infection outcomes by tracking the occurrence of fungal growth from hundreds of ant cadavers. We modeled and report these data in relation to weather, light, vegetation, and attack by mycoparasites.</p> <p class="MsoNormal">3. We investigated environmental factors that could affect the occurrence and location of newly manipulated ant cadavers. New cadavers were positively correlated with epiphytic <em>Tillandsia </em>bromeliads, canopy openness, and weather conditions (an interactive effect of temperature, humidity, and precipitation) with an increased occurrence during the sub-tropical summer. We further suggest that incident light at the individual cadaver level may reflect microhabitat choice by manipulated ants or selective pressure on cadaver maintenance for conditions improving fungal survival.</p> <p class="MsoNormal">4. We also sought to connect fungal fitness to environmental conditions. Continued fungal development of reproductive structures and putative transmission increased with moist weather conditions (interaction of humidity and precipitation) and canopy openness, while being reduced by attack by mycoparasites. Moreover, under the most open canopy conditions, we found an atypical <em>Ophiocordyceps</em> growth morphology that could represent a plastic response to conditions influenced by high light levels.</p> <p class="MsoNormal">5. Taken together, we explore general trends and the effects of various ecological conditions on host and parasite disease outcomes in the Florida zombie ant system. These insights from the field can be used to inform experimental laboratory setups that directly test the effects of biotic and abiotic factors on fungus-ant interactions or aim to uncover underlying molecular mechanisms.</p>
Co-manipulation of soft-materials estimating deformation from depth images
<p>Video describing our work on Co-manipulation of soft-materials estimating deformation from depth images</p>
Dataset of human manipulation actions
<p>This dataset consists of nine object manipulation actions performed by 12 humans: pick and place, put on top/take down, put inside/take out, hide/uncover, and push/pull with a total of 7,652 movement examples.</p> <p>See the README.md file for more information.</p>
Data for: Plant and herbivorous insect communities respond in complex ways to rainfall manipulation in an oak savanna grassland
<p>Changes in precipitation due to climate change will have consequences for plant and herbivorous insect communities alike. Multiple hypotheses explain how changes in plant diversity and productivity can lead to changes in herbivore community composition. Yet as rainfall patterns change, the bottom-up effects on the relationships between plant and herbivore communities are less well understood. Using a long-term rainfall manipulation experiment in a remnant patch of Garry oak (<em>Quercus garryana</em>) savanna, we examined how plant diversity and productivity have responded to variation in soil moisture over six years. This highly endangered ecosystem is predicted to experience significantly wetter springs and drier summers by 2080. We also investigated plant-mediated, indirect effects of manipulated rainfall on herbivore diversity and abundance, drawing on multiple hypotheses describing the relationships between plant and herbivore communities. For example, the more individuals hypothesis predicts that increased plant productivity results in increased herbivore abundance which in turn results in increased herbivore diversity. We found that plant productivity was influenced by soil moisture, but the direction and magnitude of the response varied across years, and no support for plant diversity influencing productivity. We also found that the cover and productivity of grasses increased significantly with increasing precipitation. In addition to a significant direct effect on herbivore diversity, soil moisture had a significant indirect negative effect on herbivore abundance, via the negative effect of plant productivity on abundance, contradicting the more individuals hypothesis.</p> <p>Synthesis: Our results highlight that not only can drought result in significant reductions in plant productivity in this threatened ecosystem, but that these changes will also result in increases in herbivore abundance. In contrast, where soil moisture is higher, grasses will become more dominant resulting in decreased abundance. Ultimately, predicting how this system responds to changes in precipitation will depend on the ability to predict whether growing season soil moisture will be consistently drier or wetter in the future, a significant challenge. Going forward, investigating how variation in precipitation due to climate change affects the links between trophic levels, including how herbivores affect plant communities, remains critical for understanding ecosystem processes and stability.</p>
Androgen and prolactin manipulation do not induce changes in gene expression in the telencephalon in parental male bluegill (Lepomis macrochirus) during parental care
<p>Transcriptome of the prosencephalon of 11-KT, prolactin and placebo implanted fish.</p>
Effects of thermal fluctuations on biological processes: A meta-analysis of experiments manipulating thermal variability
<p>Thermal variability is a key driver of ecological processes, affecting organisms and populations across multiple temporal scales. Despite the ubiquity of variation, biologists lack a quantitative synthesis of the observed ecological consequences of thermal variability across a wide range of taxa, phenotypic traits, and experimental designs. Here, we conduct a meta-analysis to investigate how properties of organisms, their experienced thermal regime, and whether thermal variability is experienced in either the past (prior to an assay) or present (during the assay) affect performance, relative to the performance of organisms experiencing constant thermal environments. Our results – which draw upon 1,712 effect sizes from 75 studies – indicate that the effects of thermal variability are not unidirectional and become more negative as mean temperature and fluctuation range increase. Exposure to variation in the past decreases performance to a greater extent than variation experienced in the present and increases the costs to performance more than diminishing benefits across a broad set of empirical studies. Further, we identify life history attributes that predictably modify the ecological response to variation. Our findings demonstrate that effects of thermal variability on performance are context-dependent, yet negative outcomes may be heightened in warmer, more variable climates.</p>
Data from: Aging and memory are altered by genetically manipulating lactate dehydrogenase in the neurons or glia of flies
<p>The astrocyte-neuron lactate shuttle hypothesis posits that glial-generated lactate is transported to neurons to fuel metabolic processes required for long-term memory. Although studies in vertebrates have revealed that lactate shuttling is important for cognitive function, it is uncertain if this form of metabolic coupling is conserved in invertebrates or is influenced by age. Lactate dehydrogenase (Ldh) is a rate-limiting enzyme that interconverts lactate and pyruvate. Here we genetically manipulated expression of <em>Drosophila</em> <em>melanogaster</em> lactate dehydrogenase (dLdh) in neurons or glia to assess the impact of altered lactate metabolism on invertebrate aging and long-term courtship memory at different ages. We also assessed survival, negative geotaxis, brain-neutral lipids (the core component of lipid droplets), and whole head metabolites. Both upregulation and downregulation of dLdh in neurons resulted in decreased survival and memory impairment with age. Glial downregulation of dLdh expression caused age-related memory impairment without altering survival, while upregulated glial dLdh expression lowered survival without disrupting memory. Both neuronal and glial dLdh upregulation increased neutral lipid accumulation. We provide evidence that altered lactate metabolism with age affects the tricarboxylic acid (TCA) cycle, 2-hydroxyglutarate (2HG), and neutral lipid accumulation. Collectively, our findings indicate that the direct alteration of lactate metabolism in either glia or neurons affects memory and survival but only in an age-dependent manner. </p>
Targeted Surface Manipulation of Cu/Zn/Ag coatings and Ag/Cu particles based on Sacrificial Element Selection by Electrodeposition and Redox replacement
<p>Dataset Targeted Surface Manipulation of Cu/Zn/Ag coatings and Ag/Cu particles based on Sacrificial Element Selection by Electrodeposition and Redox replacement</p>
Data Collection and Manipulation Template for MAED (Model for Analysis of Energy Demand)
<p>A Data Collection and Manipulation Template for MAED (Model for Analysis of Energy Demand). </p>
Immunohistochemistry of wild type and hjv-/- iron manipulated mouse livers and spleens treated with LPS or Hepcidin
<p><span>The iron hormone hepcidin is transcriptionally activated by iron or inflammation via distinct, partially overlapping pathways. We addressed how iron affects inflammatory hepcidin levels and the ensuing hypoferremic response. Dietary iron overload did not mitigate hepcidin induction in LPS-treated wt mice but prevented effective inflammatory hypoferremia. Likewise, LPS modestly decreased serum iron in hepcidin-deficient Hjv-/- mice, model of hemochromatosis. Synthetic hepcidin triggered hypoferremia in control but not iron-loaded wt animals. Furthermore, it dramatically decreased hepatic and splenic ferroportin in Hjv-/- mice on standard or iron-deficient diet, but only triggered hypoferremia in the latter. Mechanistically, iron antagonized hepcidin responsiveness by inactivating IRPs in the liver and spleen, to stimulate ferroportin mRNA translation. Prolonged LPS treatment eliminating ferroportin mRNA permitted hepcidin-mediated hypoferremia in iron-loaded mice. Thus, de novo ferroportin synthesis is critical determinant of serum iron and finetunes hepcidin-dependent functional outcomes. Our data uncover a crosstalk between hepcidin and IRE/IRP systems that controls tissue ferroportin expression and determines serum iron levels. Moreover, they suggest that hepcidin supplementation therapy is more efficient combined with iron depletion.</span></p>
Co-manipulation of soft-materials estimating deformation from depth images [Dataset]
<p>The dataset and training results used in the paper "Co-manipulation of soft-materials estimating deformation from depth images" G. Nicola, E. Villagrossi, N.Pedrocchi submitted at Robotics and Computer Integrated Manufacturing.</p>
Experimental manipulation of scavenger and herbivore functional role and their effects on plant communities following mass mortality events
<p>We designed an experiment to measure the relative importance of bottom-up forces (nutrient addition) and top-down forces (impairment of obligate scavenger and herbivore functional roles) generated by experimental carrion deployment to simulate mass mortality events on the local plant community. In our experimental plots, we measured changes in plant functional groups before and for three years after experimental carrion deployment. Additionally, we monitored cherrybark oak (<em>Quercus pagoda</em>) seedlings' growth and survival three years after being transplanted in the experimental plots. </p>
Supplemental data for: Visualization of rank-citation curves for fast detection of possible manipulations with the h-index of the university
<p>This dataset consists of papers of universities in the top 30 Scopus Ranking of Ukrainian Universities (May 2023). The data was obtained from Scopus using the search query "AF-ID (“university name”) AND PUBYEAR < 2023 AND PUBYEAR > 2002". Rank-citation curves were also generated for the publications of each university. In this analysis, the rank of publications was plotted along the horizontal axis, while the corresponding citation counts were depicted on the left axis. All types of documents were included in the dataset.</p>
Data Collection and Manipulation Template for FlexTool
<p>This repository includes the following files:</p> <p><strong>1) FlexTool_Data_Collection_template.xlsx: </strong>Workbook for inserting raw data, manipulating it and preparing FlexTool input sheets. The data collection and manipulation template for IRENA FlexTool 2.0 serves as a quick and standardized methodology for putting together a single-node country model in FlexTool.<br> <strong>2) FlexTool_Starter_template.xlsm: </strong>Template FlexTool input file structured to receive the input sheets, as prepared in the FlexTool_Data_Collection_template.xlsx<br> <strong>3) Data Collection Template for IRENA FlexTool.pdf</strong>: Guidelines for preparing a FlexTool model based on the Data Collection and Manipulation template. </p> <p><strong>4) OSeMOSYS and FlexTool data sharing</strong>: Instructions on how to populate the FlexTool input file from the OSeMOSYS SAND file<br> FlexTool data file population:</p> <p><strong>5) Instructions on how to populate the FlexTool Data Collection File from the OSeMOSYS Data Collection File</strong>.</p>
Motion Planning Integration on ABB Robot Manipulator for Robot Welding
<p>Integration of Motion Planning based on Moveit Robot Operating System (ROS) on ABB Robot Manipulator for Robot Welding. Stochastic Trajectory Optimization for Motion Planning (STOMP) and Rapidly exploring Random Tree Star (RRT*) are used in this implementation. STOMP is used as primary path planner as it has less computation time whereas RRT* is used as failsafe if STOMP fails to compute a plan.</p>
Multi-contact loco-manipulation trajectories for the ANYmal robot with a 6-DoF Arm
<p>Loco-manipulation planning skills are pivotal for expanding the utility of robots in everyday environments. These skills can be assessed based on a system's ability to coordinate complex holistic movements and multiple contact interactions when solving different tasks. However, existing approaches have been merely able to shape such behaviors with hand-crafted state machines, densely engineered rewards, or pre-recorded expert demonstrations. Here, we propose a minimally-guided framework that automatically discovers whole-body trajectories jointly with contact schedules for solving general loco-manipulation tasks in pre-modeled environments. The key insight is that multi-modal problems of this nature can be modeled within the context of integrated Task and Motion Planning (TAMP), resulting in a tractable bilevel optimization formulation. An effective bilevel search strategy is achieved owing to the fusion of domain-specific rules with the well-established strengths of different planning techniques: trajectory optimization and informed graph search, coupled with sampling-based planning. We showcase emergent behaviors for a quadrupedal mobile manipulator exploiting both prehensile and non-prehensile interactions to perform real-world tasks such as opening/closing heavy dishwashers and traversing spring-loaded doors. These behaviors are also deployed on the real system using a two-layer whole-body tracking controller.</p>
2019 nitrogen-by-pH field manipulation experiment physiology dataset and code
<p>Updated analyses, now only including <em>A. saccharum</em> in main analyses. Models including all species are now shuttled to the supplemental information (originally part of main analyses in v1.0).</p> <p>Updates included part of manuscript being submitted to <em>Functional Ecology</em>.</p>
Interdimensional radial discrete diffraction in Mathieu photonic lattices - Control and manipulation of light in complex photonic systems (CompsLight)
<p>Experimental and numerical data from the journal paper published in Optics Express Vol. 31, Issue 18, pp. 28946-28953 (2023) (https://doi.org/10.1364/OE.497795). Experimental data contains original results in .jpg format, presenting intensity distributions of probe beam after propagation in a 2cm long Mathieu photonic lattices optically induced in cerium doped strontium barium niobate (Ce:SBN61) crystal. Numerical data are intensity distributions (I) that correspond to experimental data as Matlab files (.m format) as well as contain information about numerical space in micrometers (x, y). Data for Figure 5 contains probe beam intensity distributions (I) and lattice intensity distributions (L). </p> <p>We demonstrate transitional dimensionality of discrete diffraction in radial-elliptical photonic lattices. Varying the order, characteristic structure size, and ellipticity of the Mathieu beams used for the photonic lattices generation, we control the shape of discrete diffraction distribution over the combination of the radial direction with the circular, elliptic, or hyperbolic. We also investigate the transition from one-dimensional to two-dimensional discrete diffraction by varying the input probe beam position. The most pronounced discrete diffraction is observed along the crystal anisotropy direction.</p>
Files for training purposes - Protein structure manipulation training session @BIOI2
<p>AlphaFold2 prediction of ORF1 Nter dimer (using ColabFold v1.5)</p>
Creation and manipulation of Schrödinger cat states of a nuclear spin qudit in silicon
<p>High-dimensional quantum systems are a valuable resource for quantum information processing. They can be used to encode error-correctable logical qubits, for instance in continuous-variable states of oscillators such as microwave cavities or the motional modes of trapped ions. Powerful encodings include 'Schrödinger cat' states, and superpositions of widely displaced coherent states, which also embody the challenge of quantum effects at the large scale. Alternatively, recent proposals suggest encoding logical qubits in high-spin atomic nuclei, which can host hardware-efficient versions of continuous-variable codes on a finite-dimensional system. Here we demonstrate the creation and manipulation of Schrödinger cat states using the spin-7/2 nucleus of a single antimony (<sup>123</sup>Sb) atom, embedded and operated within a silicon nanoelectronic device. We use a coherent multi-frequency control scheme to produce spin rotations that preserve the SU(2) symmetry of the qudit, and constitute logical Pauli operations for logical qubits encoded in the Schrödinger cat states. The Wigner function of the cat states exhibits parity oscillations with a contrast up to 0.982(5), and state fidelities up to 0.913(2). These results demonstrate high-fidelity preparation of nonclassical resource states and logical control in a single atomic-scale object, opening up applications in quantum information processing and quantum error correction within a scalable, manufacturable semiconductor platform.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.