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29,897 results for “activism”
Multi-Omics Visible Drug Activity Prediction with a Biologically Informed Neural Network Model
<p>Drug discovery is a challenging task, it takes several years for a drug to be introduced on the market, with most of<br> the studied drugs not even passing the first phase. The understanding of the mechanisms influencing response to drugs<br> can reduce failures and accelerate drug development. Virtual drug screening, based on Machine Learning models, is a<br> promising field for the prediction of the outcome of a treatment. However, the complex relationships between the features<br> learned by these models are still poorly understood and not easy to interpret.<br> We have designed a Neural Network model for drug sensitivity prediction that leverages a Visible Neural Network, an<br> easily interpretable model, due to its biologically informed nature. The trained model can be inspected to study which<br> biological processes were fundamental for the prediction and to identify the drug properties that affect sensitivity. It<br> combines multi-omics data from various types of tumor tissues and drug representations based on molecular descriptors.<br> The mechanisms learned from the network can also be exploited to find candidate drugs for synergy to predict the effect<br> of combined therapies. We consider the unbalanced nature of public drug screening datasets and show that our model<br> outperforms state-of-the-art visible machine learning models.</p>
Recordings of electrical activity from the colonies of S. commune
<p>Exemplar data for the paper:</p> <p>Multiscalar electrical spiking in <em>Schizophyllum commune</em></p> <p>Andrew Adamatzky, Ella Schunselaar, Han A. B. Wösten, Phil Ayres</p> <p>doi: https://doi.org/10.1101/2023.04.20.537646</p>
Dataset supporting the paper "Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities"
<p>Datasets involved in the construction and benchmarking of the CollecTRI-derived regulons as presented in the paper "Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities".</p>
Not only hedgerows, but also flower fields can enhance bat activity in intensively used agricultural landscapes
<p>Agri-environment schemes (AES) have become important tools for farmland biodiversity conservation, providing suitable habitats, resources, and connectivity within agricultural landscapes. Bats are rarely studied in relation to AES effectiveness in contrast to birds, even though their presence and activity as biological control agents on insects, especially pest species, can be important for agricultural crops. While the role of hedgerows for bat occurrence and activity, as well as for their prey's diversity and abundance has been widely studied, the role of other AESs such as flower fields remains unclear. We monitored the activity of the main functional groups (edge, narrow and open space foragers) using ultrasound recorders, as well as potential prey abundances using light traps, across 35 study sites representing different AES in Central Germany from late July to September 2018. The sampled AES consisted of annual flower fields, mixed flower fields (with annual and biennial vegetation), perennial flower fields (sown every 5 years), hedgerows (surrounded by meadows and agricultural fields), and were compared to winter wheat (control) in a balanced design. Bat activity over hedgerows increased threefold for edge space foragers and sevenfold for narrow space foragers compared to wheat fields. Compared to wheat fields, narrow space forager activity increased fourfold over perennial flower fields, threefold over annual and twofold over mixed flower fields. This group's activity over hedgerows also increased almost threefold compared to mixed flower fields. However, the number of feeding buzzes and prey abundance did not differ significantly between AES. We detected foraging group-specific differences in bat activity between the studied AES. Thus, to promote bats in agricultural landscapes and to ensure their biological control services, it is important to establish more AES, such as hedgerows and flower fields, to increase their diversity and connectivity in intensively used agricultural landscapes.</p>
Fig. 10. A in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 10. A Sunda palm civet in Surabaya's Bratang wildlife market on 20 July 2018. Photograph: Angie Appel.
Fig. 7. A in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 7. A, Sunda palm civet on a dyke on 17 October 2018; B, nocturnal activity pattern of the Sunda palm civet.
Fig. 9 in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 9. Activity overlaps of species pairs with coefficients of overlapping activity patterns (Δ̂1 (95% confidence interval)). Level of overlap is shaded in grey.
Fig. 4. A in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 4. A, Javan mongoose in a pond at low tide on 20 September 2018; B, diurnal activity pattern of the Javan mongoose.
Fig. 3. A in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 3. A, small Indian civet foraging in a silted-up area inside a pond on 3 August 2018; B, activity pattern of the small Indian civet.
Fig. 5. A in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 5. A, Sunda leopard cat on a dyke on 18 September 2018; B, activity pattern of the Sunda leopard cat.
Fig. 2 in Small carnivores (Mammalia: Carnivora) in the Wonorejo Mangroves, Jawa Timur, Indonesia: habitat use and activity patterns
Fig. 2. Abandoned pond in the Wonorejo Mangroves with silted-up area in the background. Photograph: Angie Appel.
Figures 2–5 in One size doesn′t fit all: Singularities in bat species richness and activity patterns in wind-energy complexes in Brazil and implications for environmental assessment
Figures 2–5. Bat activity based on the pooled number of echolocation pulses per hour in four wind-energy complexes in northeastern Brazil, from September 2015 to January 2017: (2) Curva dos Ventos, municipality of Caetité, state of Bahia; (3) Cristal, municipality of Morro do Chapéu, state of Bahia; (4) Modelo, municipality of João Câmara, state of Rio Grande do Norte; (5) Fonte dos Ventos, municipality of Tacaratu, state of Pernambuco.
Figure 1 in One size doesn′t fit all: Singularities in bat species richness and activity patterns in wind-energy complexes in Brazil and implications for environmental assessment
Figure 1. Wind-energy complexes in northeastern Brazil studied for the presence and activity of insectivorous bats from September 2015 to January 2017.
Site occupancy of Dasypus novemcinctus (Mammalia, Cingulata) and daily activity of four armadillo species in the Uruguayan Savanna and southern Atlantic Forest
<p>Datasets and R code for the research article "Site occupancy of Dasypus novemcinctus (Mammalia, Cingulata) and daily activity of four armadillo species in the Uruguayan Savanna and southern Atlantic Forest", published in Mammalian Biology. <a href="https://doi.org/10.1007/s42991-023-00366-3">https://doi.org/10.1007/s42991-023-00366-3</a></p>
Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling
<p>Failure to clear damaged mitochondria via mitophagy disrupts physiological function and may initiate damage signaling via inflammatory cascades, though how these pathways intersect remains unclear. We discovered that NF-κB essential regulator NEMO is recruited to damaged mitochondria in a Parkin-dependent manner in a time-course similar to recruitment of the structurally-related mitophagy adaptor, OPTN. Upon recruitment, NEMO partitions into phase-separated condensates distinct from OPTN, but colocalizing with p62/SQSTM1. NEMO recruitment in turn recruits the active catalytic IKK component phospho-IKKb, initiating NF-κB signaling and the upregulation of inflammatory cytokines. Consistent with a potential neuroinflammatory role, NEMO is recruited to mitochondria in primary astrocytes upon oxidative stress. These findings suggest that damaged, ubiquitinated mitochondria serve as an intracellular platform to initiate innate immune signaling, promoting the formation of activated IKK complexes sufficient to activate NF-kB signaling. We propose that mitophagy and NF-κB signaling are initiated as parallel pathways in response to mitochondrial stress. </p>
Data from: Beyond rhythm - a framework for understanding the frequency spectrum of neural activity
<p>Cognitive and behavioral processes are often accompanied by changes within well-defined frequency bands of the local field potential (LFP i.e., the voltage induced by neuronal activity). These changes are detectable in the frequency domain using the Fourier transform and are often interpreted as neuronal oscillations. However, aside some well-known exceptions, the processes underlying such changes are difficult to track in time, making their oscillatory nature hard to verify. In addition, many non-periodic neural processes can also have spectra that emphasize specific frequencies. Thus, the notion that spectral changes reflect oscillations is likely too restrictive. In this study, we use a simple yet versatile framework to understand the frequency spectra of neural recordings. Using simulations, we derive the Fourier spectra of periodic, quasi-periodic and non-periodic neural processes having diverse waveforms, illustrating how these attributes shape their spectral signatures. We then show how neural processes sum their energy in the local field potential in simulated and real-world recording scenarios. We find that the spectral power of neural processes is essentially determined by two aspects: 1) the distribution of neural events in time and 2) the waveform of the voltage induced by single neural events. Taken together, this work guides the interpretation of the Fourier spectrum of neural recordings and indicates that power increases in specific frequency bands do not necessarily reflect periodic neural activity.</p>
Logistic Activity Recognition Challenge (LARa Version 03) – A Motion Capture and Inertial Measurement Dataset
<p><strong>LARa</strong><strong> Version 03</strong> is a freely accessible logistics-dataset for human activity recognition. In the “Innovationlab Hybrid Services in Logistics” at TU Dortmund University, two picking and one packing scenarios with 16 subjects were recorded using an optical marker-based Motion Capturing system (OMoCap), Inertial Measurement Units (IMUs), and an RGB camera. Each subject was recorded for one hour (960 minutes in total). All the given data have been labelled and categorised into eight activity classes and 19 binary coarse-semantic descriptions, also called attributes. In total, the dataset contains 221 unique attribute representations.</p> <p>The <strong>dataset was created according to the guideline</strong> of the following paper: “A Tutorial on Dataset Creation for Sensor-based Human Activity Recognition”, PerCom, 2023 DOI: <a href="http://dx.doi.org/10.1109/PerComWorkshops56833.2023.10150401">10.1109/PerComWorkshops56833.2023.10150401</a></p> <p>The LARa Version 03 contains a <strong>new Annotation tool </strong>for OMoCap and RGB Videos, namely, the <strong>S</strong>equence <strong>A</strong>ttribute <strong>R</strong>etrieval <strong>A</strong>nnotator (<strong>SARA</strong>). SARA, developed and modified based on the LARa Version 02 annotation tool, includes desirable features and attempts to overcome limitations as found in the LARa annotation tool. Furthermore, few features were included based on the explorative study of previously developed annotation tools, see journal. In alignment with the LARa annotation tool, SARA focuses on OMoCap and video annotations. However, it is to be noted that SARA was not intended to be a video annotation tool with features such as subject tracking and multiple subject annotations. Here, the video is considered to be a supporting input to the OMoCap annotation. We would recommend other tools for pure video-based multiple-human activity annotation, including subject tracking, segmentation, and pose estimation. There are different ways of <strong>installing the annotation tool</strong>: Compiled binaries (executable files) for Windows and Mac can be directly downloaded from here. Python users can install the tool from https://pypi.org/project/annotation-tool/ (PyPi): “pip install annotation-tool”. For more information, please refer to the “Annotation Tool - Installation and User Manual”.</p> <p><strong>Upgrade:</strong></p> <ul> <li>Annotation tool (<strong>SARA</strong>) added (for Windows and MacOS, including an installation and user manual)</li> <li>Neural Networks updated (can be used with the annotation tool)</li> <li>OMoCap data: <ul> <li>Annotation errors corrected</li> <li>Annotations reformatted, fitting the SARA annotation tool</li> <li>“additional annotated data” extended</li> <li>“Markers_Exports” added</li> </ul> </li> <li>IMU data (MbientLab and MotionMiners Sensors) <ul> <li>Annotation errors corrected</li> </ul> </li> <li>README file (protocol) updated and extended</li> </ul> <p> </p> <p><strong>If you use this dataset for research, please cite the following paper: “LARa: Creating a Dataset for Human Activity Recognition in Logistics Using Semantic Attributes</strong><strong>”, Sensors 2020, DOI: <a href="https://doi.org/10.3390/s20154083">10.3390/s20154083</a>.</strong></p> <p><strong>If you use the Mbientlab Networks, please cite the following paper: “From Human Pose to On-Body Devices for Human-Activity Recognition”, 25th International Conference on Pattern Recognition (ICPR), 2021, DOI: </strong><a href="https://doi.org/10.1109/ICPR48806.2021.9412283"><strong>10.1109/ICPR48806.2021.9412283</strong></a><strong>.</strong></p> <p>For any questions about the dataset, please contact Friedrich Niemann at friedrich.niemann@tu-dortmund.de.</p>
Dataset for "Active buckling of pressurized spherical shells : Monte Carlo simulation"
<p>We study the buckling of pressurized spherical shells by <br> Monte Carlo simulations in which the<br> detailed balance is explicitly broken -- thereby driving the shell<br> active, out of thermal equilibrium.<br> Such a shell typically has either higher (active) or<br> lower (quiescent) fluctuations<br> compared to one in thermal equilibrium depending on how the detailed balance<br> is broken.<br> We show that, for the same set of elastic parameters, a shell<br> that is not buckled in thermal equilibrium can be buckled if turned<br> active. Similarly a shell that is buckled in thermal equilibrium<br> can unbuckle if turned quiescent.<br> Based on this result, we suggest that it is possible to experimentally design<br> microscopic elastic shells whose buckling can be optically controlled.</p>
Data and code for: Wildfire activity in northern Rocky Mountain subalpine forests still within millennial-scale range of variability
<p>Increasing area burned across western North America raises questions about the precedence and magnitude of changes in fire activity, relative to the historical range of variability (HRV) that ecosystems experienced over recent centuries and millennia. Paleoecological records of past fire occurrence provide context for contemporary changes in ecosystems characterized by infrequent, high-severity fire regimes. Here we present a network of 12 fire-history records derived from macroscopic charcoal preserved in sediments of small subalpine lakes within a c. 10,000 km<sup>2</sup> landscape in the U.S. northern Rocky Mountains (Northern Rockies). We used this network to characterize landscape-scale burning over the past 2500 yr and evaluate the precedence of widespread regional burning experienced in the early 20<sup>th</sup> and 21<sup>st </sup>centuries. We further compare the Northern Rockies fire history to a previously published network of fire-history records in the Southern Rockies. In Northern Rockies subalpine forests, widespread fire activity was strongly linked to seasonal climate conditions, in contemporary, historical, and paleo records. The average estimated fire rotation period (FRP) over the past 2500 years was 164 yr (HRV: 127-225 yr), while the contemporary FRP from 1900-2021 CE was 215 yr. Thus, extensive regional burning in the early 20<sup>th</sup> century (e.g., 1910 CE) and in recent decades was within the HRV of recent millennia. Results from the Northern Rockies contrast with the Southern Rockies, which burned with less frequency on average over the past 2500 yr, and where 21<sup>st</sup>-century burning has exceeded the HRV. Our results support expectations that Northern Rockies fire activity will continue to increase with climatic warming, surpassing historical burning if more than one exceptional fire year akin to 1910 occurs within the next several decades. The societal and ecological consequences of climatic warming in subalpine forests will depend, in large part, on the magnitude of fire-regime changes relative to the past.</p>
Fig. 2. Feeding activity during the 2021 in Vantage point surveys of cetaceans (Mammalia, Cetacea) and their interactions with marine birds
Fig. 2. Feeding activity during the 2021 observations at Cape Emine - white dot; blue – T. t. ponticus, green – P. p. relicta, red – D. d. ponticus, yellow - vantage - point.
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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.