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Annex to paper entitled From Collective Action to Civil Disorder: Comparative Analysis of Pandemic-ridden Czechia and Slovakia. From: March 1, 2020; To: March 1, 2022

This databasis draws on ACLED DATA PROJECT. It was elaborated for the research project Civil Disorder in Pandemic-ridden European Union. The latter was financially supported by the National Science Centre, Poland [grant number 2021/43/B/HS5/00290].

Fractiformers: A New Paradigm in AI Architecture – Whitepapers, Prototypes, and Industry Call-to-Action

This record introduces Fractiformers, a pioneering architecture that redefines traditional transformer models by incorporating fractal-based attention mechanisms, recursive processing, quantum-inspired superposition, and adaptive context management. Developed to address the limitations of transformer-based models in handling long-range dependencies, context adaptation, and computational efficiency, Fractiformers represent a leap forward in AI’s ability to manage complex, dynamic data at scale.   Included in this record are detailed whitepapers that outline the theoretical framework, potential applications, and comparative advantages of Fractiformers over traditional transformers. These whitepapers also serve as a call-to-action for GPU manufacturers and AI developers, encouraging collaboration to build hardware and applications optimized for Fractiformers. A prototype implementation is also provided to demonstrate the architecture’s practical benefits, showcasing how Fractiformers outperform conventional models in resource efficiency, contextual coherence, and adaptability.   Key Features:   • Whitepapers: Comprehensive analysis of Fractiformer architecture, including comparisons with transformers and a breakdown of its unique recursive, fractal, and adaptive components. • Prototype Code: A demonstration prototype to showcase Fractiformers’ performance advantages in handling complex, long-range contexts. • Industry Call-to-Action: An open letter urging GPU manufacturers and AI developers to collaborate on Fractiformer-compatible hardware, with an invitation to participate in joint research and development initiatives.   Applications: This record is valuable for AI researchers, GPU manufacturers, and developers aiming to push the boundaries of AI architecture, particularly in fields that demand high-performance, contextually adaptive models such as conversational AI, autonomous systems, and advanced NLP applications.

BioAgora D3.1 Annex - BDS2020 actionable information elements

Table from BioAgora D3.1. Annex 3 c.  First attempt of extraction and classification of information elements (IE) from the Support to the Evaluation of the EU biodiversity strategy to 2020, and follow-up: final evaluation report (European Commission: Directorate-General for Environment, 2022) document, which helped to build the framework and identify actionable information types.

BioAgora D3.1 Annex - BDS 2020 vs BDS 2030 Actions

Table from BioAgora D3.1. Annex 4  Comparison between BDS 2020 and BDS 2030 Actions. Green areas indicate the occurrence of a match between two Actions of the strategies. This may indicate continuity, also in terms of actionable information produced for the previous strategy that could be transferred or updated.

opencc-zeroDec 2016View details →

Data from: Effects of gene action, marker density, and time since selection on the performance of landscape genomic scans of local adaptation

Genomic "scans" to identify loci that contribute to local adaptation are becoming increasingly common. Many methods used for such studies have assumed that local adaptation is created by loci experiencing antagonistic pleiotropy and that the selected locus itself is assayed, and few consider how signals of selection change through time. However, most empirical data sets have marker density too low to assume that a selected locus itself is assayed, researchers seldom know when selection was first imposed, and many locally adapted loci likely experience not antagonistic pleiotropy but conditional neutrality. We simulated data to evaluate how these factors affect the performance of tests for genotype-environment association. We found that three types of regression-based analyses (linear models, mixed linear models, and latent factor mixed models) and an implementation of BayEnv all performed well, with high rates of true positives and low rates of false positives, when the selected locus experienced antagonistic pleiotropy, and when the selected locus was assayed directly. However, all tests had reduced power to detect loci experiencing conditional neutrality, and the probability of detecting associations was sharply reduced when physically linked rather than causative loci were sampled. Antagonistic pleiotropy also maintained detectable genotype-environment associations much longer than conditional neutrality. Our analyses suggest that if local adaptation is often driven by loci experiencing conditional neutrality, genome-scan methods will have limited capacity to find loci responsible for local adaptation.

opencc-zeroDec 2015View details →

Data from: Patterns of mammalian population decline inform conservation action

1. Evaluations of wildlife population dynamics have the potential to convey valuable information on the type of pressure affecting a population and could help predict future changes in the population's trajectory. Greater understanding of different patterns of population declines could provide a useful mechanism for assessing decline severity in the wild and identifying those populations that are more likely to exhibit severe declines. 2. We identified 93 incidences of decline within 75 populations of mammalian species using a time-series analysis method. These included: linear, quadratic convex (accelerating) declines, exponential concave (decelerating) declines, and quadratic concave declines (representing recovering populations). Excluding linear declines left a dataset of 85 declines to model the relationship between each decline-curve type and a range of biological, anthropogenic, and time-series descriptor explanatory variables. 3. None of the decline-curve types were spatially or phylogenetically clustered. The only characteristic that could be consistently associated with any curve-type was the time at which they were more likely to occur within a time-series. Quadratic convex declines were more likely to occur at the start of the time-series, while recovering curve shapes (quadratic concave declines) were more likely at the end of the time-series. 4. Synthesis and applications: The ability to link certain factors with specific decline dynamics across a number of mammalian populations is useful for management purposes as it provides decision-makers with potential triggers upon which to base their conservation actions. We propose that the identification of quadratic convex declines could be used as an early-warning signal of potentially severe decline dynamics. For such populations, increased population monitoring effort should be deployed to diagnose the cause of its decline and avert possible extinctions. Conversely, the presence of a quadratic concave decline suggests that the population has already undergone a period of serious decline but is now in the process of recovery. Such populations will require different types of conservation actions, focussed on enhancing their chances of recovery.

opencc-zeroJun 2021View details →

Consequences of migratory coupling of predators and prey when mediated by human actions

Aim: Animal migrations influence ecosystem structure, dynamics, and persistence of predator and prey populations. The theory of migratory coupling postulates that aggregations of migrant prey can induce large-scale synchronized movements in predators, and this coupling is consequential for the dynamics of ecological communities. The degree to which humans influence these interactions remains largely unknown. We tested whether the creation of large resource pulses by humans such as seasonal herding of reindeer Rangifer tarandus and hunting of moose, Alces alces, can induce migratory coupling with Golden Eagles, Aquila chrysaetos, and if these lead to demographic consequences for the eagles. Location: Fennoscandia Methods: We used movement data from 32 tracked Golden Eagles spanning 125 annual migratory cycles over eight years. We obtained reindeer distribution data through collaboration with reindeer herders based on satellite tracking of reindeer, and moose harvest data from the national hunting statistics for Sweden. We assessed demographic consequences for eagles from ingesting lead from ammunition fragments in moose carcasses through survival estimates and their links with lead concentrations in eagles' blood. Results: In spring, eagles migrated hundreds of kilometers to be spatially and temporally coupled with calving reindeer, whereas in autumn, eagles matched their distribution with the location and timing of moose hunt. Juveniles were more likely to couple with reindeer calving, whereas adults were particularly drawn to areas of higher moose harvest. Due to this coupling, eagles ingested lead from spent ammunition in moose offal and carcasses and the resulting lead-toxicity increased the risk of mortality by 3.4 times. Main conclusions: We show how migratory coupling connects landscape processes and that human actions can influence migratory coupling over large spatial scales and increase demographic risks for predators. We provide vital knowledge towards resolving human wildlife conflicts and the conservation of protected species over a large spatial and temporal scale.

opencc-zeroJun 2021View details →

The role of action potential changes in depolarization-induced failure of excitation contraction coupling in mouse skeletal muscle

Excitation-contraction coupling (ECC) is the process by which electrical excitation of muscle is converted into force generation. Depolarization of skeletal muscle resting potential contributes to failure of ECC in diseases such as periodic paralysis, intensive care unit acquired weakness and possibly fatigue of muscle during vigorous exercise. When extracellular K+ is raised to depolarize the resting potential, failure of ECC occurs suddenly, over a narrow range of resting potentials. Intracellular recordings of action potentials (APs) in individual mouse skeletal muscle fibers during depolarization of the resting potential revealed small APs are still generated at resting potentials at which force production has failed. Simultaneous imaging of Ca2+ transients and recording of APs demonstrated failure to generate Ca2+ transients when APs peaked at potentials more negative than -30 mV. An AP property that closely correlated with failure of the Ca2+ transient was the integral of AP voltage with respect to time. Simultaneous recording of Ca2+ transients and APs with electrodes separated by 1.6 mm revealed AP conduction fails when APs peak below -21 mV. We hypothesize propagation of APs and generation of Ca2+ transients are governed by distinct AP properties: AP conduction is governed by AP peak, whereas Ca2+ release from the sarcoplasmic reticulum is governed by AP integral of voltage with respect to time. The reason distinct AP properties may govern separate steps of ECC is the kinetics of the ion channels involved in the different steps of ECC. Na channels, which govern propagation, have rapid kinetics such that propagation is insensitive to AP width (and integral) whereas Ca2+ release is governed by movement of gating charges in Cav1.1 channels, which have slower kinetics such that Ca2+ release is sensitive to AP width (and integral). The quantitative relationships established between resting potential, AP properties, AP conduction and Ca2+ transients provide the foundation for future studies of failure of ECC induced by depolarization of the resting potential.

opencc-by-4.0Jul 2021View details →

High-Speed Atomic Force Microscopy Highlights New Molecular Mechanism of Daptomycin Action

Data underlying the figures in the publication “High-speed atomic force microscopy highlights new molecular mechanism of daptomycin action”, published in Nat Commun, 2020, 11, 6312. <a href="https://doi.org/10.1038/s41467-020-19710-z">https://doi.org/10.1038/s41467-020-19710-z</a> Table of contents: 1. Movie 1; HS-AFM movie of the first minutes after exposure to sub-MIC Dap on a POPG supported membrane. Guides to the eye highlights those oligomers identifiable. Movie parameters: frame rate 33 ms; full image of 90 nm x 65 nm and 256x180 pixels; colour depth 8bit (256 values); full colour scale 4 nm. 2. Movie 2; HS-AFM movie after tens of minutes after exposure to sub-MIC Dap that shows diffusing dimples on a POPG supported membrane which interact by swinging trajectories. Movie parameters: frame rate 83 ms; full image of 150nm x 150nm and 256x256 pixels; colour depth 8bit (256 values); full colour scale 4 nm. 3. Movie 3; HS-AFM movie of the first minutes after exposure to over-MIC of a POPG supported membrane. A flow of material is visualized thanks to the motion of the ripples, it starts at the lm3m cubic phase (left) and ends at a tubulation (right). Movie parameters: frame rate 456 ms; full image of 400nm x 400nm and 300x300 pixels; colour depth 8bit (256 values); full colour scale 16 nm. 4. Movie 4; HS-AFM movie of the cyclic accumulation of material in the pores created on TOCL/POPG supported membranes under the exposure of the outer leaflet to supplementary quantities of Dap added to the imaging solution. The process seems to eject material out of the membrane; see the material that appears next to the pore at 1.30s. Movie parameters: frame rate 260 ms; zoom of a full image of 140nm x 100nm and 256x180 pixels; colour 29 depth 8bit (256 values); full colour scale 3 nm.

opencc-by-4.0Jan 2021View details →

Volitional Action Control and Depression in Chronic Pain: Does Action versus State Orientation Moderate the Relations of Pain-Related Cognitions to Depression?

The rationale of this study was to better understand the interplay between content- and function-focused variables that are assumed to contribute to depression due to motivational and volitional deficits. Therefore, we stepwise examined the conditional indirect and direct relations of pain-related cognitions to depression. Subjective helplessness was included as presumably mediating the relations of catastrophizing and thought suppression to depression due to motivational deficits. In addition, moderating effects of dispositional action versus state orientation were analyzed, whereby state orientation indicates volitional deficits in coping with distress. The data acquisition for this project was funded by the German Pension Insurance (Deutsche Rentenversicherung Bund) and the Federal Ministry of Education and Research (BMBF) within the research priority “Chronic diseases and patient orientation” - Grant number: 0421-FSCP-0529.

opennotspecifiedNov 2011View details →

Figure 3 in Action of the saproxylic scarab larva Cetonia aurataeformis (Coleoptera: Scarabaeoidea: Cetoniidae) on woody substrates

Figure 3. FTIR spectra of litter (L), Betula alba wood (BW) and Quercus pyrenaica wood (QW), normalized with the band about 1028 cm−1.

opennotspecifiedNov 2011View details →

Figure 2 in Action of the saproxylic scarab larva Cetonia aurataeformis (Coleoptera: Scarabaeoidea: Cetoniidae) on woody substrates

Figure 2. Thermal curves of (A) Betula alba wood (BW) and frass (BF), (B) Quercus pyrenaica wood (QW) and frass (QF), (C) litter (L) and frass (LF). Y-axis shows the mass change in respect to temperature (dm/dt: derivation of mass in respect to temperature).

opencc-zeroAug 2021View details →

Data from: Poor endometrial proliferation after clomiphene is associated with altered estrogen action

Context: Suboptimal endometrial thickening is associated with lower pregnancy rates and occurs in some infertile women treated with clomiphene. Objective: To examine cellular and molecular differences in the endometrium of women with suboptimal versus optimal endometrial thickening following clomiphene. Design: Translational prospective cohort study from 2018-2020. Setting: University-affiliated clinic. Patients or Participants: Reproductive age women with unexplained infertility treated with 100mg of clomiphene cycle days 3-7 who developed optimal (≥8mm; n=6, controls) or suboptimal (<6mm; n=7, subjects) endometrial thickness. Interventions: Pre-ovulatory blood and endometrial sampling. Main outcome measures: Endometrial tissue architecture, abundance and location of specific proteins, RNA expression, ERa binding. Results: The endometrium of suboptimal subjects compared to optimal controls was characterized by a reduced volume of glandular epithelium (16% vs 24%, P=0.01), decreased immunostaining of markers of proliferation (PCNA, ki67) and angiogenesis (PECAM-1), increased immunostaining of pan-leukocyte marker CD45 and ERb, but decreased ERa immunostaining (all P<0.05). RNASeq identified 398 differentially expressed genes between groups. Pathway analysis of differentially expressed genes indicated reduced proliferation (Z-score= -2.2, P<0.01), decreased angiogenesis (Z-score = -2.87, P<0.001), increased inflammation (Z-score= +2.2, P<0.01), and ERb activation (Z-score= +1.6, P<0.001) in suboptimal subjects. ChIP-seq identified 6 genes bound by ERα that were differentially expressed between groups (P<0.01), some of which may play a role in implantation. Conclusions: Women with suboptimal endometrial thickness after clomiphene exhibit aberrant estrogen receptor expression patterns, architectural changes and altered gene and protein expression, suggesting reduced proliferation and angiogenesis in the setting of increased inflammation.

opencc-by-4.0Oct 2021View details →

Nigrostriatal dopamine signals sequence-specific action-outcome prediction errors

Data for Hollon et al. (2021) Nigrostriatal dopamine signals sequence-specific action-outcome prediction errors. Current Biology

opencc-by-4.0Oct 2022View details →

Cooperative virulence via the collective action of secreted pathogen effectors

Barcode sequence data. Unique barcode sequences were incorporated into the effector plasmids to confirm that all individual effector clones within the metaclone were present throughout infection and that the overall diversity of the metaclones remained unchanged (Extended Data Fig. 4).

openother-atDec 2022View details →

Material from a collaborative analysis with young people. Insights into the analysis process of R&I Action #2 Youth Employment of the CoAct project

The collaborative data analysis presented in this document was undertaken in the context of the research project CoAct (Co-designing Citizen Social Science for Collective Action) as part of the R&I Action #2 on Youth Employment. In this R&I Action, using Citizen Social Science as a research approach, young people aged between 15 and 21 years in employment measures in Vienna/Austria participated in collaborative social research activities. The visualisation of data analysis in the form of posters, is a selection of the collaborative analysis of qualitative expert interviews using the the “Stop and Go” (Harrasser, 2017) method. Following this method, audio recording of interviews, done by the young co-researchers themselves, are listened to and summarized as well as connected to the co-researchers’ own experience. The Creative Commons license and a recommendation regarding the citation of the material are provided in the document. For more information please contact veronika.woehrer@univie.ac.at

opencc-by-4.0Jul 2021View details →

MPOSE2021: a Dataset for Short-Time Pose-Based Human Action Recognition

This repository contains the MPOSE2021 Dataset for short-time pose-based Human Action Recognition (HAR). MPOSE2021 is specifically designed to perform short-time Human Action Recognition. MPOSE2021 is developed as an evolution of the MPOSE Dataset [1-3]. It is made by human pose data detected by <a href="https://github.com/CMU-Perceptual-Computing-Lab/openpose">OpenPose</a> [4] and <a href="https://github.com/tensorflow/tfjs-models/tree/master/posenet">Posenet</a> [11] on popular datasets for HAR, i.e. Weizmann [5], i3DPost [6], IXMAS [7], KTH [8], UTKinetic-Action3D (RGB only) [9] and UTD-MHAD (RGB only) [10], alongside original video datasets, i.e. ISLD and ISLD-Additional-Sequences [1]. Since these datasets have heterogenous action labels, each dataset labels are remapped to a common and homogeneous list of actions. Generated sequences have a number of frames between 20 and 30. Sequences are obtained by cutting the so-called Precursor videos (video from the above-mentioned datasets), with non-overlapping sliding windows. Frames where OpenPose/PoseNet cannot detect any subject are automatically discarded. Resulting samples contain one subject at the time, performing a fraction of a single action. Overall, MPOSE2021 contains 15429 samples, divided into 20 actions, performed by 100 subjects. More information about the dataset can be found in the <a href="https://github.com/PIC4SeRCentre/MPOSE2021_Dataset">MPOSE2021 repository</a>, also providing a user-friendly Python package to import and use the dataset by just running the command <pre><code>pip install mpose</code></pre>   Data Structure The repository contains 3 datasets for each pose extractor (namely 1, 2 and 3) which consist of the same data divided in different train/test splits. Each dataset contains X and y numpy arrays for both training and testing. X has the following shape: <pre>(B, T, K, C)</pre> where <ul> <li>B is the batch number;</li> <li>T (= 30) is the duration of the sequences in frames (zero-padded in the case of shorter sequences);</li> <li>K (= 17 for PoseNet and 25 for OpenPose) is the number of pose keypoints;</li> <li>C (= 3) is the number of channels, comprehending 2D keypoint coordinates (x,y) in the original video reference frame and the keypoint confidence (p <= 1)</li> </ul> The .txt files specifying the metadata associated with the split samples are also included. References MPOSE2021 is part of a <a href="https://authors.elsevier.com/a/1eH6s77nKcvmg">paper published by the Pattern Recognition Journal</a> (Elsevier), and is intended for scientific research purposes. If you want to use MPOSE2021 for your research work, please also cite [1-11]. <pre><code>@article{mazzia2021action, title={Action Transformer: A Self-Attention Model for Short-Time Pose-Based Human Action Recognition}, author={Mazzia, Vittorio and Angarano, Simone and Salvetti, Francesco and Angelini, Federico and Chiaberge, Marcello}, journal={Pattern Recognition}, pages={108487}, year={2021}, publisher={Elsevier} } </code></pre> [1] Angelini, F., Fu, Z., Long, Y., Shao, L., & Naqvi, S. M. (2019). 2D Pose-Based Real-Time Human Action Recognition With Occlusion-Handling. IEEE Transactions on Multimedia, 22(6), 1433-1446. [2] Angelini, F., Yan, J., & Naqvi, S. M. (2019, May). Privacy-preserving Online Human Behaviour Anomaly Detection Based on Body Movements and Objects Positions. In ICASSP 2019-2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) (pp. 8444-8448). IEEE. [3] Angelini, F., & Naqvi, S. M. (2019, July). Joint RGB-Pose Based Human Action Recognition for Anomaly Detection Applications. In 2019 22th International Conference on Information Fusion (FUSION) (pp. 1-7). IEEE. [4] Cao, Z., Hidalgo, G., Simon, T., Wei, S. E., & Sheikh, Y. (2019). OpenPose: Realtime Multi-Person 2D Pose Estimation Using Part Affinity Fields. IEEE transactions on pattern analysis and machine intelligence, 43(1), 172-186. [5] Gorelick, L., Blank, M., Shechtman, E., Irani, M., & Basri, R. (2007). Actions as Space-Time Shapes. IEEE transactions on pattern analysis and machine intelligence, 29(12), 2247-2253. [6] Starck, J., & Hilton, A. (2007). Surface Capture for Performance-Based Animation. IEEE computer graphics and applications, 27(3), 21-31. [7] Weinland, D., Özuysal, M., & Fua, P. (2010, September). Making Action Recognition Robust to Occlusions and Viewpoint Changes. In European Conference on Computer Vision (pp. 635-648). Springer, Berlin, Heidelberg. [8] Schuldt, C., Laptev, I., & Caputo, B. (2004, August). Recognizing Human Actions: a Local SVM Approach. In Proceedings of the 17th International Conference on Pattern Recognition, 2004. ICPR 2004. (Vol. 3, pp. 32-36). IEEE. [9] Xia, L., Chen, C. C., & Aggarwal, J. K. (2012, June). View Invariant Human Action Recognition using Histograms of 3D Joints. In 2012 IEEE computer society conference on computer vision and pattern recognition workshops (pp. 20-27). IEEE. [10] Chen, C., Jafari, R., & Kehtarnavaz, N. (2015, September). UTD-MHAD: A Multimodal Dataset for Human Action Recognition utilizing a Depth Camera and a Wearable Inertial Sensor. In 2015 IEEE International conference on image processing (ICIP) (pp. 168-172). IEEE. [11] Papandreou, G., Zhu, T., Chen, L. C., Gidaris, S., Tompson, J., & Murphy, K. (2018). Personlab: Person Pose Estimation and Instance Segmentation with a Bottom-Up, Part-Based, Geometric Embedding Model. In Proceedings of the European Conference on Computer Vision (ECCV) (pp. 269-286).

opencc-by-4.0Jan 2023View details →

Safe cardiac action potential test (www.scaptest.com): a database describing the in silico cardiac safety profile of drugs and their propensity to induce early afterdepolarization

The aim of the present database is to describe the in silico cardiac safety profile of drugs and their propensity to induce early afterdepolarization.  This is based on the study of the effects of drugs on the non-failing human ventricular myocyte action potential (endo-, mid- and epicardial subtypes) reconstructed by computational simulation (O’Hara-Rudy dynamic algorithm) in order to identify cardiac action potential abnormalities such as high variations and/or occurrence of resting membrane potential, action potential amplitude, maximal rate of action potential rise, action potential duration, triangulation, early afterdepolarization, transmural dispersion of repolarization, reverse use dependence, qNet or minimal rate of action potential decrease at early afterdepolarization take-off voltage. These various parameters are useful in order to assume a more accurate predictability of pro-arrhythmic liabilities of new drug candidate in the cardiac safety pharmacology screening process, which is the aim of the comprehensive in vitro pro-arrhythmia assay (CiPA) initiative. The in silico cardiac safety profile of each drug (150 drugs described in this first version) is illustrated by a separate page describing the effects induced by each compound on these various parameters. The results are summarized regarding the expected pro-arrhythmia profile of the various compounds as described by the CredibleMeds classification evaluating their propensity to induce torsade de pointes.

opencc-by-4.0Feb 2023View details →

Scheib_Stoll_Randerath_Frontiers_Does Aging Amplify the Rule-based Efficiency Effect in Action Selection_Dataset

Dataset belongs to publication in Frontiers in Psychology, section Cognition Title: Does Aging Amplify the Rule-based Efficiency Effect in Action Selection? Authors: Jean P. P. Scheib 1; Sarah E. M. Stoll 1,2; Jennifer Randerath 3,2,1 Affiliations: 1: University of Konstanz, Konstanz, Germany, 2: Lurija Institute for Rehabilitation Science and Health Research, Kliniken Schmieder, Allensbach, Germany 3: University of Vienna, Vienna, Austria