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1,742 results for “activity data”
Data and code for the publication of "Fluctuating hydrodynamics of chiral active fluids"
<p>We provide all the data used to make the plots in main figures, extended figures and supplementary figures in our paper "Fluctuating hydrodynamics of chiral active fluids". </p> <p> </p> <p>We also provide codes to reproduce the simulation results shown in the paper</p>
Data related to the manuscript "Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor"
<p>These are the data that are related to the manuscript "Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor" by </p> <p>Eike K. Mahlandt<sup>1,*</sup>, Janine J. G. Arts<sup>1,2</sup>,Werner J. van der Meer<sup>1</sup>, Franka H. van der Linden<sup>1</sup>, Simon Tol<sup>2</sup>, Jaap D. van Buul<sup>1,2</sup>, Theodorus W. J. Gadella Jr.<sup>1</sup>, Joachim Goedhart<sup>1,*</sup></p> <p><sup>1</sup> Swammerdam Institute for Life Sciences, Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands</p> <p><sup>2</sup> Molecular Cell Biology Lab at Dept. Molecular Hematology, Sanquin Research and Landsteiner Laboratory, Amsterdam, The Netherlands</p>
Data from: Ongoing habenular activity is driven by forebrain networks and modulated by olfactory stimuli
<p>The data was collected using volumetric two-photon calcium imaging of the forebrain and habenula of juvenile zebrafish expressing a transgenic calcium indicator. The data provided is organized according to the figures of our manuscript and contains the necessary codes and data to replicate the figures presented. In short, included repository contains 6 datasets of experiments. Data structure includes neuronal data as normalised to the baseline fluorescence for each neuron over time (DF/F), 2 or 3 dimensional coordinates of each cell and information about duration and samplings rate of experiments, and appropriate information about stimulation either microstimulation or odor stimulation (if any was performed within the experiment).</p>
Supplementary data: "Secondary control activation analysed and predicted with explainable AI"
<p>This repository contains processed data and result files for the paper <a href="https://arxiv.org/abs/2109.04802">Secondary control activation analysed and predicted with explainable AI</a> . The code for producing the processed data and the results is <a href="https://github.com/johkruse/XAI-for-aFRR-activation">available at github</a>.</p> <p><strong>Data</strong></p> <p>The data folder contains the feature and target data used to train the ML model. The data for Germany comprises the following folders and files:</p> <ul> <li><em>raw_input_data.h5</em><strong> </strong>:<strong> </strong>The aggregated external features without additional engineered features.</li> <li><em>inputs_<model_type>.h5 </em><em>:</em> The input features for the different model types used in the paper including the engineered features. Depending on the model type, the input files also contain the IGCC features.</li> <li><em>outputs.h5 </em>: The activated aFRR volumes in Germany.</li> <li><em>version_2021-08-20</em>: Folder containing the training and test sets used for the results.</li> <li><em>documentation_of_data_download</em>: Information files concerning the ENTSO-E raw data and its aggregation.</li> </ul> <p>In addition to the German time series, the data folder contains the raw input data for the remaining IGCC states. Note that the results contain more model types as actually discussed in the paper.</p> <p><strong>Data sources</strong></p> <p>The data for input features (<em>raw_input_data.h5</em> and <em>input_<model_type>.h5</em>) is derived from ENTSO-E Transparency Platform data [1]. The target data (<em>outputs.h5</em>) is based on publicly available data from the German Transmission System Operators (TSOs) [2].</p> <p><strong>Results</strong></p> <p>The result folder comprises the results of hyper-parameter optimization, model prediction and interpretation via SHAP. The model type, the loss function to train the model and the data set for prediction/interpretation were varied.</p> <ul> <li><em>cv_results_<model_type>_<loss_function>.csv</em> : Performance results for each combination in the hyper-parameter grid search.</li> <li><em>cv_best_params_<model_type>_<loss_function>.csv</em> : Hyper-parameters used in the final (optimized) model.</li> <li><em>shap_values_<data_set>_<model_type>_<loss_function>.npy</em> : First-order SHAP values calculated on different data sets: The train set, the randomized test set and the continuous test set.</li> <li><em>y_pred_<data_set>.h5</em> : Predictions of daily profile predictor and Machine Learning models.</li> </ul> <p><strong>Disclaimer</strong></p> <p>The data might be subject to copyright or related rights. Please consult the primary data owner.</p>
Supporting Data for "Actively Searching: Inverse Design of Novel Molecules with Simultaneously Optimized Properties" Manuscript
<p>Training data and xTB calculated properties of sampled structures from the generative active learning experiments reported in the manuscript.</p>
Data from: First evidence of wasp brood development inside active nests of a termite with the description of a previously unknown potter wasp species
<p>Potter wasps (Vespidae: Eumeninae) are known to exhibit not only sophisticated preying strategies but also a remarkable ability to manipulate clay during nest building. Due to a mixture of plasticity in building behaviour and flexibility in substrate preferences during nest-building, the group has been reported nesting in a variety of places, including decaying nests abandoned by termite species. Yet, evidence of wasps nesting inside senescent termite mounds is poorly reported and, to date, accounts confirming their presence inside active colonies of termites are absent. Here, we address a novel intriguing association between two species from the Brazilian Cerrado: a previously unknown potter wasp (nest invader) and a termite species (nest builder). Besides scientifically describing <i>Montezumia termitophila</i> sp. nov. (Vespidae: Eumeninae), named after its association with the termite <i>Constrictotermes cyphergaster</i> (Silvestri, 1901) (Termitidae: Nasutitermitinae), we provide preliminary information about the new species' bionomics by including (i) a hypothetical life cycle based on the evidence we collected and (ii) a footage showing the first interaction between a recently ecloded wasp and a group of termites. In doing so, we attempt to provoke relevant discussions in the field and, perhaps, motivate further studies with the group. Finally, we describe a solution to efficiently detect and sample termitophilous species from termite nests, an intrinsic yet challenging task of any studies dealing with such a cryptic biological system.Potter wasps (Vespidae: Eumeninae) are known to exhibit not only sophisticated preying strategies but also a remarkable ability to manipulate clay during nest building. Due to a mixture of plasticity in building behaviour and flexibility in substrate preferences during nest-building, the group has been reported nesting in a variety of places, including decaying nests abandoned by termite species. Yet, evidence of wasps nesting inside senescent termite mounds is poorly reported and, to date, accounts confirming their presence inside active colonies of termites are absent. Here, we address a novel intriguing association between two species from the Brazilian Cerrado: a previously unknown potter wasp (nest invader) and a termite species (nest builder). Besides scientifically describing <i>Montezumia termitophila</i> sp. nov. (Vespidae: Eumeninae), named after its association with the termite <i>Constrictotermes cyphergaster</i> (Silvestri, 1901) (Termitidae: Nasutitermitinae), we provide preliminary information about the new species' bionomics by including (i) a hypothetical life cycle based on the evidence we collected and (ii) a footage showing the first interaction between a recently ecloded wasp and a group of termites. In doing so, we attempt to provoke relevant discussions in the field and, perhaps, motivate further studies with the group. Finally, we describe a solution to efficiently detect and sample termitophilous species from termite nests, an intrinsic yet challenging task of any studies dealing with such a cryptic biological system.</p>
Data from: Effectiveness of signs of activity as relative abundance indices for wild boar
<p><span>Population growth in wild boars and feral pigs (</span><i><span>Sus scrofa</span></i><span>) has negative environmental and economic implications worldwide. Accordingly, it is necessary to monitor population trends for appropriate management. Despite the potential for bias, relative abundance indices based on signs of activity </span><span><span>have the potential to be </span></span><span>practical, low-cost monitoring tools for data collection at a local scale and over large areas. However, few studies have examined the effectiveness of specific signs as measures of relative wild boar abundance </span><span><span>in comparison with reliable density estimates.</span></span><span> In this study, we examined whether three activity signs (digging marks, rubbing marks, and fecal pellet groups) could be used as relative abundance indices for wild boar. In particular, we conducted transect surveys for signs of activity as well as camera trap surveys from September 2017 to January 2018 at six sites in Hyogo Prefecture and eight sites in Chiba Prefecture, Japan. We modeled the relations between the number of activity signs and wild boar densities or </span><span><span>abundances</span></span><span> estimated from camera trap data </span><span><span>in a hierarchical framework</span></span><span>. Fecal pellet counts are a well-established method for estimating the abundance of herbivores, including wild boar; however, we found few fecal pellet groups in our study area, and the counts were not related to wild boar densities. Instead, we found that digging marks were strongly associated with estimates of wild boar density. Although fluctuations in the number of digging marks may be affected by factors other than boar density, including environmental conditions and seasonality, our results suggest that digging marks are an effective relative abundance index for evaluations of the spatial patterns of wild boar in Japan.</span></p>
Data and code for Mitonuclear interactions affect locomotor activity and sleep in Drosophila melanogaster
<p>Data and R code for Mitonuclear interactions affect locomotor activity and sleep in Drosophila melanogaster</p>
Code and Data to recreate figures from: Activation of immune receptor Rx1 triggers distinct immune-responses culminating in cell death after four hours.
<p>Code and Data to recreate figures from: Activation of immune receptor Rx1 triggers distinct immune-responses culminating in cell death after four hours.</p> <p><a href="https://doi.org/10.1111/mpp.12776">https://doi.org/10.1111/mpp.12776</a></p> <p> </p> <p>These files are also on Github:</p> <p>https://github.com/MolPlantPathology/PMID-30537296-</p>
All Data Used in "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks"
<p>This dataset submission contains the data necessary to reproduce any and all results presented in the paper "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks", set to be submitted for publication in the coming days.</p>
All Data Used in "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks"
<p>These files contain all the data necessary to fully reproduce any and all results presented in the paper "The effects of Time-Variable Absorption due to Gamma-Ray Bursts In Active Galactic Nuclei Accretion Disks", set to be submitted to MNRAS in the coming days. </p>
All data support the published articel "Loop-optimization of Trichoderma reesei endoglucanases for balancing the activity–stability trade-off through cross-strategy between machine learning and the B-factor analysis"
<p><em>Trichoderma reesei</em> endoglucanases (EGs) have limited industrial applications due to its low thermostability and activity. Here, we aimed to improve the thermostability of EGs from<em> T.reesei</em> without reducing its activity counteracting the activity-stability trade-off. A cross-strategy combination of machine learning and B-factor analysis was used to predict beneficial amino acid substitution in EG loop optimization. Experimental validation showed single-site mutated EG concomitantly improved enzymatic activity and thermal properties by 17.21%–18.06% and 49.85%–62.90%, respectively, compared with wild-type EGs. Furthermore, the mechanism explained mutant variants had lower RMSD values and a more stable overall structure than the wild type. According to this study, EGs loop optimization is crucial for balancing the activity-stability trade-off, which may provide new insights into how loop region function interacts with enzymatic characteristics. Moreover, the cross-strategy between machine learning and B-factor analysis improved superior enzyme activity-stability performance, which integrated structure-dependent and sequence-dependent information.</p>
Raw data for the paper "Cobalamin co-limits phytoplankton and bacterial biomass and activity in Eastern Mediterranean coastal waters"
<p>Raw data for the paper "Cobalamin co-limits phytoplankton and bacterial biomass and activity in Eastern Mediterranean coastal waters".</p> <p> </p>
Data From: Active sinking particles: Flow and transport dynamics due to sessile suspension feeders on sinking aggregates
<p>Sinking or sedimentation of biological aggregates plays a critical role in carbon sequestration in the ocean and in vertical material fluxes in waste-water treatment plants. In both these contexts, the sinking aggregates are "active," since they are biological hot-spots and are densely colonized by microorganisms including bacteria and sessile protists, some of which generate feeding currents. However, the effect of these feeding currents on the sinking rates, trajectories, and mass transfer to these "active sinking particles," has not previously been studied. Here we use a novel scale-free vertical-tracking microscope (a.k.a. Gravity Machine, Krishnamurthy et al. "Scale-free vertical tracking microscopy." Nature Methods (2020)) to follow model sinking aggregates (agar spheres) with attached protists (<em>Vorticella convallaria</em>), sinking over long distances while simultaneously measuring local flows. We find that activity due to attached \vortc causes significant changes to the flow around aggregates in a dynamic manner and reshapes mass transport boundary layers. Furthermore, we find that activity-mediated local flows along with sinking modify the encounter and plume cross-sections of the aggregate and induce sustained aggregate rotations. Overall our work shows the important role of biological activity in shaping the near-field flows around aggregates with potentially important effects on aggregate fate and material fluxes.</p>
Source data for "Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting".
<p>Contains numeric data for figures 16-18 and supplementary fig 6 linked with the publication: Panwar, J., Autour, A. & Merten, C.A. Design and construction of a microfluidics workstation for high-throughput multi-wavelength fluorescence and transmittance activated droplet analysis and sorting. <em>Nat Protoc</em> (2023). <a href="https://doi.org/10.1038/s41596-022-00796-2">https://doi.org/10.1038/s41596-022-00796-2</a></p>
Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"
<p>Data explanation for Manuscript "'An optimized hydroponic pipeline for large-scale identification of wheat genotypes with resilient biological nitrification inhibition (BNI) activity'"</p>
Data for: Ongoing and visually evoked activity in the zebrafish optic tectum and adjacent brain structures
<p>The ongoing activity of neuronal populations represents an internal brain state that influences how sensory information is processed to control behaviour. Conversely, external sensory inputs perturb network dynamics, resulting in lasting effects that persist beyond the duration of the stimulus. However, the relationship between these dynamics and circuit architecture and their impact on sensory processing, cognition and behaviour are poorly understood. By combining cellular-resolution calcium imaging with mechanistic network modelling, we aimed to infer the spatial and temporal network interactions in the zebrafish optic tectum that shape its ongoing activity and state-dependent responses to visual input. We showed that a simple recurrent network architecture, wherein tectal dynamics are dominated by fast, short range, excitation countered by long-lasting, activity-dependent suppression, was sufficient to explain multiple facets of population activity including intermittent bursting, trial-to-trial sensory response variability and spatially-selective response adaptation. Moreover, these dynamics also predicted behavioural trends such as selective habituation of visually evoked prey-catching responses. Overall, we demonstrate that a mechanistic circuit model, built upon a uniform recurrent connectivity motif, can estimate the incidental state of a dynamic neural network and account for experience-dependent effects on sensory encoding and visually guided behaviour.</p>
Data for: Low protease activity in B cell follicles promotes retention of intact antigens after immunization
<p>The structural integrity of vaccine antigens is critical to the generation of protective antibody responses, but the impact of protease activity on vaccination in vivo is poorly understood. We characterized protease activity in lymph nodes and found that antigens were rapidly degraded in the subcapsular sinus, paracortex, and interfollicular regions, whereas low protease activity and antigen degradation rates were detected in the vicinity of follicular dendritic cells (FDCs). Correlated with these findings, immunization regimens designed to target antigen to FDCs led to germinal centers dominantly targeting intact antigen, whereas traditional immunizations led to much weaker responses that equally targeted the intact immunogen and antigen breakdown products. Thus, spatially compartmentalized antigen proteolysis affects humoral immunity and can be exploited.</p>
Data for: Inflammation differentially controls transport of depolarizing Nav versus hyperpolarizing Kv channels to drive rat nociceptor activity
<p>Inflammation causes pain by shifting the balance of ionic currents in nociceptors towards depolarization, leading to hyperexcitability. The ensemble of ion channels within the plasma membrane is regulated by processes including biogenesis, transport, and degradation. Thus, alterations in ion channel trafficking may influence excitability. Sodium channel Na<sub>V</sub>1.7 and potassium channel K<sub>V</sub>7.2 promote and oppose excitability in nociceptors, respectively. We used live-cell imaging to investigate mechanisms by which inflammatory mediators modulate the abundance of these channels at axonal surfaces through transcription, vesicular loading, axonal transport, exocytosis, and endocytosis. Inflammatory mediators induced a Na<sub>V</sub>1.7-dependent increase in activity in distal axons. Further, inflammation increased the abundance of Na<sub>V</sub>1.7, but not of K<sub>V</sub>7.2, at axonal surfaces by selectively increasing channel loading into anterograde transport vesicles and insertion at the membrane, without affecting retrograde transport. These results uncover a cell-biological mechanism for inflammatory pain and suggest Na<sub>V</sub>1.7 trafficking as a potential therapeutic target.</p>
Supplementary data for: Pevonedistat, a Nedd8-activating enzyme inhibitor, in combination with ibrutinib in patients
<p>In a clinical trial to evaluate a NEDD8-activating enzyme inhibitor in treating a mantle cell lymphoma patient, peripheral blood mononuclear cells (PBMCs) were collected from the patient at baseline and after 3 and 24 hours after drug infusion. Then, single-cell RNA-seq was conducted on the collected PBMCs. The pre-processed data was saved as a Seurat object.</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.