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7,228 results for “modules”
Tutorial Photonics Explorer Module 3 part 1: lenses, imaging rules, optical setups and telescopes
<p>Photonics Austria (PhAu) has conducted Teacher Training Programmes about Photonics - the Photonics Explorer- in order to promote the potential of photonics to enliven physics lessons. This video tutorial contains several experiments designed to illustrate imaging equation and the laws of lenses.</p>
Dataset supplementing "Marx, S., & Einhäuser, W. (2015). Reward modulates perception in binocular rivalry. Journal of Vision, 15(1):11, 1–13, http://www.journalofvision.org/content/15/1/11, doi:10.1167/15.1.11."
<p>These data supplement the publication</p> <p>Marx, S., & Einhäuser, W. (2015). Reward modulates perception in binocular rivalry. Journal of Vision, 15(1):11, 1–13, http://www.journalofvision.org/content/15/1/11, doi:10.1167/15.1.11.</p> <p>and be used freely for scientific purposes provided the aforementioned paper is appropriately cited.</p> <p>exp1_data.mat contains data of experiment 1</p> <p>exp2_data.mat contains data of experiment 2</p> <p>figure2_3.m and figure4_5.m exemplify usage of the data and reproduce the figures 2-5 of the aforementioned article.</p>
Context modulation of learned attention deployment.
<p>Eye tracking data and statistical analysis of:</p> <p>Uengoer, M., Pearce, J. M., Lachnit, H., & Koenig, S. (2017). Context modulation of learned attention deploymentReward draws the eye, uncertainty holds the eye: Associative learning modulates distractor interference in visual search. Learning & Behavior. doi:10.3758/s13420-017-0277-y</p> <p>Abstract: In three experiments, we investigated the contextual control of attention in human discrimination learning. In each experiment, participants initially received discrimination training in which the cues from Dimension Awere relevant in Context 1 but irrelevant in Context 2, whereas the cues from Dimension B were irrelevant in Context 1 but relevant in Context 2. In Experiment 1, the same cues from each dimension were used in Contexts 1 and 2, whereas in Experiments 2 and 3, the cues from each dimension were changed across contexts. In each experiment, participants were subsequently shifted to a transfer discrimination involving novel cues from either dimension, to assess the contextual control of attention. In Experiment 1, measures of eye gaze during the transfer discrimination revealed that Dimension A received more attention than Dimension B in Context 1, whereas the reverse occurred in Context 2. Corresponding results indicating the contextual control of attention were found in Experiments 2 and 3, in which we used the speed of learning (associability) as an indirect marker of learned attentional changes. Implications of our results for current theories of learning and attention are discussed.</p> <p><br> Please see related identifier 10.5281/zenodo.583223 for analysis of:<br> Koenig, S., Uengoer, M., & Lachnit, H. (2017). Attentional bias for uncertain cues of shock in human fear conditioning: Evidence for attentional learning theory. Frontiers in Human Neuroscience. doi: 10.3389/fnhum.2017.00266.</p> <p>Please see related identifier 10.5281/zenodo.583233 for analysis of:<br> Koenig, S., Kadel, H., Uengoer, M., Schubö, A., & Lachnit, H. (2017). Reward Draws the Eye, Uncertainty Holds the Eye: Associative Learning Modulates Distractor Interference in Visual Search. Frontiers in Behavioral Neuroscience,11, 128. doi: 10.3389/fnbeh.2017.00128.</p> <p> </p> <p> </p>
Modeling and measuring how codon usage modulates the relationship between burden and yield during protein overexpression in bacteria
<p>Additional data from experiments associated with paper revisions.</p> <p>Also added codon optimizer script.</p>
Amyloid-motif-dependent tau self-assembly is modulated by isoform sequence context
<p><span>The microtubule-associated protein tau is implicated in neurodegenerative diseases characterized by amyloid formation. Mutations associated with frontotemporal dementia increase tau aggregation propensity and disrupt its endogenous microtubule-binding activity. However, the structural relationship between aggregation propensity and biological activity remains unclear. We employed a multi-disciplinary approach, including computational modeling, NMR, cross-linking mass spectrometry, and cell models to engineer tau sequences that modulate its structural ensemble. Our findings show that substitutions near the conserved 'PGGG' </span><span>β</span><span>-turn motif informed by tau isoform context reduce tau aggregation in vitro and cells and can even counteract aggregation from disease-associated proline-to-serine mutations. Engineered tau sequences maintain microtubule binding and explain why 3R isoforms exhibit reduced pathogenesis compared to 4R. We propose a simple mechanism to reduce the formation of pathogenic tau species while preserving biological function, thus offering insights for therapeutic strategies aimed at reducing tau protein misfolding in neurodegenerative diseases.</span></p> <p><strong>Description of Source Data and Supplementary Data</strong>: All MD, NMR (peptide and tauRD), ThT, XL-MS, MT stabilization, MT:tau modeling, and cell-based aggregation data are available in the Source_Data directory as Data S1, Data S2, Data S3, Data S4, Data S5, Data S6, Data S7, and Data S8, respectively. Supplementary Data for raw MD trajectory files, structure files for MSM modeling and validation file, and tau:MT modeling are available as "Supplementary_Data_MD_Trajectories_Structures", "Supplementary_Data_MSM_models_Structures" and "Supplementary_Data_MT-tau_complex_models", respectively."</p>
Allosteric Modulation of YAP/TAZ-TEAD Interaction by Palmitoylation and Small Molecule Inhibitors
<p>The tar file contains 3 directories, each of which contains all of the simulation input files (pdb, prmtop, inpcrd) and trajectory files (nc) for the simulations run. </p><ol><li>TEAD_Only: Simulations of the TEAD protein in the apo, inhibitor(inh)-bound, palmitate(plt)-bound, or palmitic acid(plm)-bound form </li><li>YAP-TEAD: Simulations of the YAP-TEAD heterodimer in the apo, inhibitor(inh)-bound, palmitate(plt)-bound, or palmitic acid(plm)-bound form </li><li>TAZ-TEAD: Simulations of the TAZ-TEAD heterodimer in the apo, inhibitor(inh)-bound, palmitate(plt)-bound, or palmitic acid(plm)-bound form </li></ol>
Collective synchrony of mating signals modulated by ecological cues and social signals in bioluminescent sea fireflies
<p><span>Individuals often employ simple rules that can emergently synchronise behaviour. Some collective behaviours are intuitively beneficial, but others like mate signalling in leks occur across taxa despite theoretical individual costs. Whether disparate instances of synchronous signalling are similarly organised is unknown, largely due to challenges observing many individuals simultaneously. Recording field collectives and <em>ex situ</em> playback experiments, we describe principles of synchronous bioluminescent signals produced by marine ostracods (Crustacea; Luxorina) that seem behaviorally convergent with terrestrial fireflies, and with whom they last shared a common ancestor over 500 mya. Like synchronous fireflies, groups of signalling males use visual cues (intensity and duration of light) to decide when to signal. Individual ostracods also modulate their signal based on the distance to nearest neighbours. During peak darkness, luminescent "waves" of synchronous displays emerge and ripple across the sea floor every ~60 seconds, but such periodicity decays within and between nights after the full moon. Our data reveal these bioluminescent aggregations are sensitive to both ecological and social light sources. Because the function of collective signals is difficult to dissect, evolutionary convergence, like in the synchronous visual displays of diverse arthropods, provides natural replicates to understand the generalities that produce emergent group behaviour.</span></p>
Landscape structure and farming management interacts to modulate pollination supply and crop production in blueberries
<p><span>Pollination services are affected by landscape context, farming management, and pollinator community structure, all of which impact flower visitation rates, pollen deposition and final production. We studied these processes in Argentina for Highbush Blueberry crops which depend on pollinators to produce marketable yields. </span></p> <p><span>We studied how land cover and honeybee stocking influence the abundance of wild and managed pollinators in blueberry crops, using structural equation modeling to disentangle the cascading effects through which pollinators contribute to blueberry fruit number, size, nutritional content and overall yield. </span></p> <p><span>All pollinator functional groups responded to landscape changes at a spatial scale under 1000 m, and the significance or direction of the effects were modulated by the field-level deployment of honeybee hives. </span></p> <p><span>Fruit diameter increased with pollen deposited, but decreased with honeybee abundance, which, had indirect effects on fruit acidity and sugar content. Honeybees had a positive effect on the number of fruit produced by the plants and also benefited the overall yield (kg plant</span><sup><span>-1</span></sup><span>) through independent effects on both the quality and quantity components of fruit production.</span></p> <p><span><em>Synthesis and applications:</em> </span></p> <p><span>Deployment of beehives in blueberry fields can buffer, but not compensate for the negative effects on honeybee abundance produced by surrounding large scale none-flowering crops. Such compensation would require high-quality beehives by monitoring their health and strength.</span> <span>The </span><span>contribution of honeybees to crop production is not equal across production metrics. That is, higher abundance of honeybees increases the number of berries produced, but at the cost of smaller and more acidic fruits, potentially reducing market value. Growers must consider this trade-off between fruit quantity and quality when actively managing honeybee abundance. </span></p>
Body size modulates the extent of seasonal diet switching by large mammalian herbivores in Yellowstone National Park
<div> <p><span>Large mammalian herbivores vary their diets markedly with changes in resource availability yet the ways that seasonal changes in individual foraging behaviors scale up to reconfigure complex trophic networks are poorly understood. Two years of dietary DNA data enabled us to quantify fine-grained dietary variation within and among populations of five large herbivore species at Yellowstone National Park, revealing remarkably strong and significant correlations between body size and five key indicators of diet seasonality (R<sup>2</sup> = 0.71–0.80). Data from GPS collars implicated seasonal changes in each species' movement- and habitat-use patterns as potential determinants of foraging constraints and specializations that give rise to the strong allometry in diet composition. Bison and elk showed relatively muted seasonal changes compared to smaller species that exhibited stronger switches. Whereas the taxonomic breadth of individual diets contracted for all species in winter, larger species generally consumed a greater functional diversity of plants and thus maintained more unique dietary niches under resource limitations.</span></p> </div>
Simulation dataset and plotting scripts used for journal article "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024)
<p>Simulation data underlying all figures presented in "Impact of acidity and surface modulated acid dissociation on cloud response to organic aerosol" by Sengupta et al. (2024). DOI: 10.5194/acp-24-1467-2024</p> <p>The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.</p>
Data used in "The Complex Role of Storms in Modulating Air-Sea CO2 Fluxes in the sub-Antarctic Southern Ocean"
<p>The data included in this repository were used to generate the figures for the paper "The Complex Role of Storms in Modulating Air-Sea CO2 Fluxes in the sub-Antarctic Southern Ocean" in Geophysical Research Letter.</p> <p>Abstract:</p> <p>"The intra-seasonal CO<sub>2</sub> flux (FCO<sub>2</sub>) variability across the Southern Ocean is poorly understood due to sparse observations at the required temporal and spatial scales. Twinned Waveglider-Seaglider experiments were used to investigate how storms influence FCO<sub>2</sub> through both the gas transfer velocity (k<sub>w</sub>) and the air-sea gradient in partial pressure of CO<sub>2</sub> (ΔpCO<sub>2</sub>) in the sub-Antarctic zone. Winter-spring storms caused ΔpCO<sub>2</sub> to weaken (by 15-55 μatm) due to mixing/entrainment and weaker stratification. This response in ΔpCO<sub>2</sub> was in phase with k<sub>w</sub> resulting in a counteractive weakening in FCO<sub>2</sub> (by 6.6 - 26.5% per storm), despite the wind-driven increase in k<sub>w</sub>. Stronger stratification during summer explained the weaker sensitivity of ΔpCO<sub>2</sub> to storms, instead its thermal drivers dominated the ΔpCO<sub>2 </sub>variability. These results highlight the importance of observing synoptic-scale variability in ΔpCO<sub>2</sub>, the absence of which may propagate significant biases to the mean annual FCO<sub>2</sub> estimates from large-scale observing programmes and reconstructions."</p> <p>The data collected from the Wave Glider, such as the concentration of CO<sub>2</sub> in the atmosphere (xCO<sub>2air</sub>) and in the ocean (xCO<sub>2sea</sub>), surface temperature and salinity were used to calculate the different parameters of the bulk CO<sub>2</sub> flux formula (FCO<sub>2</sub> = k<sub>w</sub> x ko x ΔpCO<sub>2</sub>). Note that the meteorological weather station of one of the Wave Gliders was faulty and the wind speed, wind direction and wind stress data was replaced by hourly ERA5 data provided by ECMWF available at <a href="https://doi.org/10.24381/cds.bd0915c6">https://doi.org/10.24381/cds.bd0915c6</a>. </p> <p>The temperature, pressure and salinity data collected by the Seaglider were used to calculate the Mixed Layer Depth and the Brunt Vaisala Frequency of the first 300m of the ocean.</p>
Food and social cues modulate reproductive development but not migratory behavior in a nomadic songbird, the Pine Siskin (Pinus spinus)
<p>Many animals rely on photoperiodic and non-photoperiodic environmental cues to gather information and appropriately time life history stages across the annual cycle, such as reproduction, molt, and migration. Here, we experimentally demonstrate that the reproductive physiology, but not migratory behavior, of captive Pine Siskins responds to both food and social cues during the spring migratory-breeding period. Pine Siskins are a nomadic finch with a highly flexible breeding schedule and, in the spring, free-living Pine Siskins can wander large geographic areas and opportunistically breed. To understand the importance of non-photoperiodic cues to the migratory-breeding transition, we maintained individually housed birds on either a standard or enriched diet in the presence of group-housed heterospecifics or conspecifics experiencing either the standard or enriched diet type. We measured body condition and reproductive development of all Pine Siskins and, among individually housed Pine Siskins, quantified nocturnal migratory restlessness. In group-housed birds, the enriched diet caused increases in body condition and, among females, promoted reproductive development. Among individually housed birds, female reproductive development differed between treatment groups whereas male reproductive development did not. Specifically, individually housed females showed greater reproductive development when presented with conspecifics compared to heterospecifics. The highest rate of female reproductive development, however, was observed amongst individually housed females provided the enriched diet and maintained with group-housed conspecifics on an enriched diet. Changes in nocturnal migratory restlessness did not vary by treatment group or sex. By manipulating both the physical and social environment, this study demonstrates how multiple environmental cues can affect the timing of transitions between life history stages with differential responses between sexes and between migratory and reproductive systems.</p>
Pneumatic elastostatics of multi-functional inflatable lattices: Realization of extreme specific stiffness with active modulation and deployability
<p>Supplementary codes and data: Elastostatics of multi-functional inflatable lattices: Realization of extreme specific stiffness with active modulation and deployability</p>
Dataset The Lactate Receptor HCAR1: a Key Modulator of Epileptic Seizure Activity
<p>This dataset is related to the study: </p> <p>The Lactate Receptor HCAR1: a Key Modulator of Epileptic Seizure Activity</p> <p>by Maxime Alessandri (1), Alejandro Osorio-Forero (1), Anita Luthi (1) & Jean-Yves Chatton* (1)</p> <p><span>(1) Department of Fundamental Neurosciences, University of Lausanne, 1005 Lausanne, Vaud, Switzerland.</span></p>
Simulation dataset and plotting scripts used for journal article "Surface modulated dissociation of organic aerosol acids and bases in different atmospheric environments" by Sengupta and Prisle (2024)
<p>Simulation data underlying all figures presented in "Surface modulated dissociation of organic aerosol acids and bases in different atmospheric environments" by Sengupta and Prisle (2024) <a href="http://dx.doi.org/10.1080/02786826.2024.2323641" target="_blank" rel="noopener noreferrer">http://dx.doi.org/10.1080/02786826.2024.2323641</a>. </p> <p>The data for each figure and the plotting scripts are included in a zip file labelled by the figure number as presented in the paper and accompanying supplement.</p>
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module, this module consists of two clearly separated sections, each consisting of two long tanks (2 × 0.2 × 0.2 m) designed to accommodate hatching boxes, a filtration tank and an independent water circulation pump with a cooling unit and UV sterilizer. This allows simultaneous monitoring of 16 batches of eggs.
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of larvae hatching module, this installation was used to determine the optimum larvae load during the rearing process and provided additional space for rearing several thousand larvae. It consists of nine 20-litre tanks with a glass panel along the front. They are fitted with an inlet supplying filtrated water at a rate of 100 l/h and an individual air inlet.
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of hatching module in Zoug jars, this system consists of a 300-litre temperature-controlled isothermal enclosure containing 10 one-litre Zoug jars, each able to accommodate several hundred eggs. An ascending current holds the eggs in suspension and carries the larvae to the surface. Another bottle connected to this device collects the larvae. The water circulating in the jars is independent of that used in the filtration circuit. A cooling unit and UV sterilizer complete the installation.
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Bottom of DR1 tank, the sides of the module are fitted with glass panels which allow natural light from a window to enter the tank, and the observer to view the behaviour of the broodstock. This device ensures easy viewing and checking of the broodstock, facilitates management of feeding and allows effective monitoring of reproduction.
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day. in Reproduction of Zingel asper (Linnaeus, 1758) in controlled conditions: an assessment of the experiences realized since 2005 at the Besançon Natural History Museum
Operating diagram of DR1/DR2 double riffle; it consists of two independent sections (DR1 and DR2), each containing 630 litres of water and measuring 2.5 x 0.6 m. Each section contains a filtration system separate from the fish, a cooling unit and an ultraviolet sterilizer. An 80 W UQL lamp completes the lighting of the module lit during the day.
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.