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Results and code associated with «Predictability of ecological and evolutionary dynamics in a changing world»
<p>Below you'll find results and code associated with the following article (*):</p> <p>Bozzuto, C, Ives, AR (2024): Predictability of ecological and evolutionary dynamics in a changing world. <em>Proceedings of the Royal Society B</em>, <strong>291</strong>: 20240980. https://doi.org/10.1098/rspb.2024.0980</p> <p>ABSTRACT: Ecological and evolutionary predictions are being increasingly employed to inform decision-makers confronted with intensifying pressures on biodiversity. For these efforts to effectively guide conservation actions, knowing the limit of predictability is pivotal. In this study, we provide realistic expectations for the enterprise of predicting changes in ecological and evolutionary observations through time. We begin with an intuitive explanation of predictability (the extent to which predictions are possible) employing an easy-to-use metric, predictive power <em>PP</em>(<em>t</em>). To illustrate the challenge of forecasting, we then show that among insects, birds, fishes and mammals, (i) 50% of the populations are predictable at most 1 year in advance and (ii) the median 1-year-ahead predictive power corresponds to a prediction <em>R</em><sup>2</sup> of only 20%. Predictability is not an immutable property of ecological systems. For example, different harvesting strategies can impact the predictability of exploited populations to varying degrees. Moreover, incorporating explanatory variables, accounting for time trends and considering multivariate time series can enhance predictability. To effectively address the challenge of biodiversity loss, researchers and practitioners must be aware of the information within the available data that can be used for prediction and explore efficient ways to leverage this knowledge for environmental stewardship.</p> <p>(*) previously a preprint on <em>bioRxiv</em>: https://doi.org/10.1101/2023.11.01.565089</p>
FIGURE 2. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 2. CMM-V-10108, a Miocene pathological cetacean vertebra associated with the one shown in Figures 5 and 6. A. Anterior view showing a major shear-compression fracture with comminution. B. right lateral view, and C. posterior view showing the intact fused epiphysis.
FIGURE 3. CMM-V-10108 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 3. CMM-V-10108, shear-fractured Miocene cetacean lumbar vertebra in three transverse CT-scan images. These CT-scan images cut through the vertebra in an anterodorsal-posteroventral direction. A. CT-scan image through the anterior portion of the vertebra showing the wide-open lumen of the shear-compression fracture. B. CT-scan image from approximately 1 cm behind A, showing the thickness of the periosteal reactive bone layer. C. CT-image at about the midpoint in the length of the vertebra showing the posterior-most part of the sheared base of the centrum compressed (telescoped) into the body of the centrum.
FIGURE 7. CMM-V-8522 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 7. CMM-V-8522, Otodus megalodon lower anterior tooth in labial view. This tooth was found touching one of the two pathological vertebrae (CMM-V-10108). Notice the spall-fracture marking the tip of the tooth. White scale bar equals 10 mm.
FIGURE 6. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 6. CMM-V-10108, a second Miocene pathological cetacean vertebra (also shown in Figure 5) associated with the one shown in Figures 2-4. A. CT-scan image towards the anterior end of the vertebra. B. CT-scan image at about the midpoint in the length of the vertebra showing the thickness of the periosteal reactive bone.
FIGURE 8 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 8. One possible way in which the shear-compression fracture occurred in CMM-V-10108. The posterior vertebral column was severely hyperflexed to such a degree that at least one of its vertebrae experienced a shear-compression fracture, and the periosteum was pulled away from most of the sides of both vertebrae. Artwork by Clarence (Shoe) Schumaker (CMM).
FIGURE 5. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 5. CMM-V-10108, a second Miocene pathological cetacean vertebra (CT-scans shown in Figure 6) associated with the one shown in Figures 2-4. A. Posterior view showing that the neural spine is incomplete and that the sides of the centrum are covered with periosteal reactive bone. B. ventral view to highlight the periosteal reactive bone. In B, the anterior end of the centrum is up.
FIGURE. 1 in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE. 1. The site along Calvert Cliffs where the two pathological cetacean vertebrae (CMM-V-10108) and associated Otodus megalodon tooth (CMM-V-8522) were found in situ in Shattuck-Zone 12. Looking north along the cliffs at Warrior's Rest. Photo by M. Ellwood.
FIGURE 4. CMM-V-10108, a in A Miocene cetacean vertebra showing a partially healed longitudinal shear-compression fracture, possibly the result of domoic acid toxicity or failed predation
FIGURE 4. CMM-V-10108, a single CT-scan image in the sagittal plane of a Miocene pathological cetacean vertebra in left lateral view showing the broken lower portion of the centrum, the displaced piece of bone, and the new bone growth (periosteal reactive bone ventrally).
Precalculated results for "An image processing pipeline for electron cryo-tomography in RELION-5"
<p>RELION workspace containing the results presented in the article "An image processing pipeline for electron cryo-tomography in RELION-5"</p>
Carbon sequestration potential in hedgerow soils: Results from 23 sites in Germany
<p>Dataset to the manuscript: Drexler, S. & Don, A. (2024). Carbon sequestration potential in hedgerow soils: Results from 23 sites in Germany. Geoderma. <a href="https://doi.org/10.1016/j.geoderma.2024.116878">https://doi.org/10.1016/j.geoderma.2024.116878</a></p> <ul> <li>Drexler_Don_2024_Data: contains the lab data for all samples</li> <li>Drexler_Don_2024_SOC_Stock_Per_Core: contains the calculated SOC stocks per soil core</li> </ul>
IoT Application Generation Module Expert Review Documents and Results
<p>The ZIP file contains all study documents that have been used to perform an expert review of the IoT Application Generation Module which has been developed as an extension to the eSPACE end-user authoring tool.</p> <p>It also contains the results of our study which has been performed with 6 participants (see Expert Review Results Data.pdf).</p>
OPTIMADE compliant results database + Detailed input/outputs of VASP calculations as BSON mongodump and JSON formats
<p>This dataset that contains the results presented in the journal article entitled "SurfFlow: High-throughput surface energy calculations for arbitrary crystals" that was published in Volume 234 of the Elsevier journal Computational Materials Science.</p> <p>The dataset consists of a dump of a MongoDB database with two collections; an OPTIMADE compliant results collection, and a supplementary collection that contains detailed data on the VASP calculations performed. Each entry in the OPTIMADE-compliant results collection contains an id, and every VASP calculation that was involved in the calculation of surface energies of that entry can be found by filtering for the same id matching the "optimade_id" in the VASP data collection.</p> <p>The data is served in two different formats; a BSON mongodump folder that can be restored to a MongoDB instance using the mongorestore tool, and additionally as simple .json files. The contents are identical and the users are encouraged to choose the format that is convenient to them.</p> <p>Here's a simple tree-view of the uncompressed attachment:</p> <p>./surfflow-bson/surfflow:<br>2.2M optimade.bson.gz<br> 153 optimade.metadata.json.gz<br> 40M vasp_data.bson.gz<br> 154 vasp_data.metadata.json.gz</p> <p>./surfflow-json:<br> 27M optimade.json<br>346M vasp_data.json</p>
The Why and What of AI Deployment and Innovation in Companies – Results and Learnings from a Systematic Literature Research
<p>These appendices are made available online as a critical part of the research paper accepted for publication at ISPIM 2024 in Tallinn on 10-12June 2024.</p> <p><strong>Abstract:</strong> Despite vast and growing investments in Artificial Intelligence, only a tiny fraction of companies report achieving tangible results. To fill this gap and establish a baseline for companies, we conducted Systematic Literature Research on the status of AI deployment in companies. We analyzed and synthesized 99 peer-reviewed articles for objectives, approaches, results, and learnings. This research confirms that AI is still at the pre-deployment stage in companies. Developing the capability to deploy AI is more challenging and takes more time, concerted effort, innovation, and learning than generally thought. Through the results and the conceptual framework, this research increases understanding of AI deployment and emphasizes the importance of the pre-deployment stages from theoretical and practical viewpoints. The Sensing stage of the dynamic capabilities theory aligns well with the developed pre-deployment stages. More real-life case research is needed, and existing theories verified to deploy AI knowledgeably for business and stakeholder benefits. </p>
Data and results for "A corpus-based study to triangulating experimental evidence regarding verb-noun association for action verbs"
<p>This repository provides spreadsheets containing the results of corpus-based and experimental studies for my undergraduate thesis titled "A corpus-based study to triangulating experimental evidence regarding verb-noun association for action verbs" (supervised by Gede Primahadi Wijaya Rajeg, PhD [main] and Ketut Santi Indriani, M.Hum. [associate]) in the Bachelor of English Literature (BoEL) program, Faculty of Humanities, Udayana University. The thesis explores convergences/divergences between different methods and data types for a set of verb-noun collocations for several action verbs and their synonyms. The description of the dataset is as follows:</p> <ol> <li>"data-raw": A raw dataset containing the results of an experiment conducted using Gorilla Experiment Builder. This consists of responses regarding verb-noun collocation co-occurrences from 17 participants into one. Link to Gorilla Experiment: (https://app.gorilla.sc/openmaterials/622948).</li> <li>"Corpus Analysis Results": A compiled data containing search results of frequencies found in the Corpus of Contemporary American English (COCA). The frequencies were compiled into tables for the five main verbs showing the number of co-occurrences of specific verb-noun collocations.</li> <li>"Experiment Results (1)": A compiled data containing the experiment results calculated as a total, showing the number of co-occurrences of specific verb-noun collocations across five verbs from the participant responses.</li> </ol> <p>The thesis is part of the pedagogical outcome of the <a title="CompLexico" href="https://www.cirhss.org/complexico/" target="_blank" rel="noopener"><em>CompLexico</em></a> research group at <a title="CIRHSS" href="https://www.cirhss.org/" target="_blank" rel="noopener"><em>CIRHSS</em></a>, and the Psycholinguistics course I took with I Made Sena Darmasetiyawan, PhD at BoEL, both in the Faculty of Humanities, Udayana University.</p>
Data for: Field data and simulation results of the Seoul Halloween crowd-crush
<div> <div>This data contains field data and simulation results related to the Seoul Halloween crowd-crush that occurred in Itaewon, Seoul, in 2022. The dataset includes original mobile LTE data from the event, conversations between pedestrians and police, and simulation codes and results. The simulations were conducted using MATLAB and Fortran to analyze crowd dynamics and potential safety measures.</div> </div>
Tensile tests results on artificially aged aluminum-magnesium-silicon alloy blanks subjected to different localized heat treatment strategies
<p>Tensile tests results on artificially aged aluminum-magnesium-silicon alloy blanks subjected to different localized heat treatment strategies </p>
Aero-engine NOx emissions in case of electrochemical suppression technique application (experimental results)
<p><span>Results of the mini engine exhaust tests with various excitation discharge type and energy application</span></p>
Results of MD simulations of collision cascades in hcp Zr at 600 K.
<p>This is a database consisting of pre- and post-processing scripts, input files and results from molecular dynamics (MD) simulations of collision cascades in LAMMPS. The database is associated with the paper: <a href="https://arxiv.org/abs/2405.03332">Molecular dynamics simulations of neutron induced collision cascades in Zr</a>. The material studied was hcp Zr at the temperature of 600 K. A detailed description of the record can be found in the <code>pdf</code> file, as well as in Emacs <code>org</code> and Jupyter notebooks (<code>ipynb</code>). Files also include Python code describing how to access and process the data.</p>
Template for HFLAV results in Zenodo
The data corresponding to a specific release of results from HFLAV
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.