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1,952 results for “actionality”
Muller's Ratchet in Action: The Erosion of Sexual Reproduction Genes in Domesticated Cassava (Manihot esculenta)
<p>Data Files for research study on Cassava gene evolutionary selection.</p>
Supporting MD trajectories for the paper "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae"
<p>Source data and molecular dynamic trajectories for the article "In Situ Captured Antibacterial Action of Membrane-Incising Peptide Lamellae"</p> <p>New compounds with unique mechanisms of action are needed to combat the growing issue of antimicrobial resistance. Supramolecular assemblies, which combine the complex membrane attacking mechanisms of natural host defense peptides with the improved biostability of non-natural compounds offer a promising alternative to current small molecule antibiotics. However, for such membrane-targeting compounds the direct visual insight on the toxic agents in bacteria is still lacking. To this end, we employed a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular peptide structures triggered by bacterial cell surface lipopolysaccharides (LPS). Inspired by the alternating chirality backbone pattern of some effective peptide antimicrobials, we designed lysine-rich heterochiral β3-peptides, termed lamellin-2K and lamellin-3K, with optimal residual spacing for enhanced coordination on the phosphate groups of LPS. Combined molecular dynamics simulations (MD), EM and bacterial assays confirmed that the phosphate-induced conformational change of these lamellins led to the formation of thin, striped lamellar layers, where each stripe represents double arrays of H-bonded peptide molecules that are interconnected by phosphate ions. EM micrographs of Gram-negative bacteria show that the lamellae incised the cell envelope, while leakage and antibacterial activity assays prove that growth inhibition starts already at submicromolar concentrations. Detailed image analysis demonstrated that the lamellae penetrating deep into the bacterial cell have a rather uniform size distribution and, surprisingly, only a few of these supramolecules are sufficient to cause major cell wall damage making them efficient in destroying target cells. Our findings also provide a missing mechanistic link for membrane-targeting agents, connecting how the antibiotic mechanism is built up from individual molecules through on-site formation of the active supramolecules that lead to bactericidal activity.</p> <p>Molecular dynamics trajectories from the production runs of single beta-peptide strands in water + 150 mM NaCl + 50:1 MePO4^(2-):peptide. Altogether 8 runs were performed, each one starting from a different helical conformation (H10, H12 and H14, both positive and negative winding) of the peptide. In the first half (500 ns) of the simulation, the intra-chain hydrogen bonds responsible for the actual helix were kept together by distance restraints. In the second half (again 500 ns), these restraints were instantaneously lifted and the system was left to evolve from the same state. In all cases the helical structure unwound in a very short time (under 100 ns), and did not refold in any helix.</p>
Assessing Multiple Values of Nature in National Biodiversity Strategies and Action Plans: Coded Data
<p>We coded eleven National Biodiversity Strategies and Action Plans (NBSAPs) for the human values for nature (instrumental, instrinsic, and relational) expressed in the NBSAPs. The 11 country NBSAPs coded were: Angola, Australia, Bhutan, Czech Republic, Egypt, Germany, Guyana, Malaysia, Russia, Saint Vincent and the Grenadines, and Turkey. Each sentence, <span>defined as an orthographic unit beginning with a capital letter and ending with a full stop, was provided a value code (instrumental, intrinsic, relational, unspecified, ‘not value orientation statement', or uncertain) depending on the value orientation of the statement. Coding criteria for each code is given below: </span></p> <p><span><span> </span></span></p> <table> <tbody> <tr> <td> <p><strong><span>Code</span></strong></p> </td> <td> <p><strong><span>Description</span></strong></p> </td> </tr> <tr> <td> <p><span>Instrumental</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Nature is described as valuable or useful for humans ends</span></p> <p><span><span>●<span> </span></span></span><span>Mentions of provisioning services, regulating services, economic benefits, natural capital, stocks and harvests, use of nature (tourism/recreation was tagged as instrumental unless an explicit relational aspect mentioned)</span></p> </td> </tr> <tr> <td> <p><span>Intrinsic</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Nature is described as valuable regardless of humans</span></p> <p><span><span>●<span> </span></span></span><span>Nature is valuable for natural (nonhuman) ends (e.g., forests must be preserved as habitats for animals)</span></p> <p><span><span>●<span> </span></span></span><span>Nature as having a right to exist undisturbed by humans</span></p> </td> </tr> <tr> <td> <p><span>Relational</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Meaningful relationships with nature </span></p> <p><span><span>●<span> </span></span></span><span>Links between nature and culture, identity, traditions, traditional knowledge, fairness, environmental justice and rights, sharing, future generations, heritage, responsibilities, human beings as a part of nature, and quality of life</span></p> <p><span><span>●<span> </span></span></span><span>References to personified nature (e.g. “Mother Earth”)</span></p> </td> </tr> <tr> <td> <p><span>Unspecified</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Value or importance of nature is implied, but no direct link to instrumental, intrinsic, or relational values (e.g., “our coastal and marine areas house important ecosystems”; “we have safeguarded all our key ecosystems, species and genetic diversity”)</span></p> </td> </tr> <tr> <td> <p><span>Not value orientation statement</span></p> </td> <td> <p><span><span>●<span> </span></span></span><span>Sentence does not imply value, or value statement does not link to nature. Purely biophysical language that is only descriptive (e.g., “There are an estimated 15,000 species of plants in the country”).</span></p> </td> </tr> </tbody> </table> <p> </p> <p>For a detailed overview of the methods, please refer the paper published in People and Nature.</p>
Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic alterations, TMB, and PD-L1
<p>Wallen ZD, Ko H, Nesline MK, Tierno M, Roos A, Schnettler E, Husain H, Sathyan P, Caveney B, Eisenberg M, Severson EA, Ramkissoon SH. <strong>Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic.</strong> <em>Front Oncol.</em> 2024 Nov 5;14:1473327. doi: <a href="https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2024.1473327">10.3389/fonc.2024.1473327</a>.</p> <p><strong>ABSTRACT</strong></p> <p><strong>Introduction: </strong>Matching patients to an effective targeted therapy or immunotherapy is a challenge for <br>advanced and metastatic non-small cell lung cancer (NSCLC), especially when relying on assays that test one <br>marker at a time. Unlike traditional single marker tests, comprehensive genomic profiling (CGP) can <br>simultaneously assess NSCLC tumors for hundreds of genomic biomarkers and markers for immunotherapy <br>response, leading to quicker and more precise matches to therapeutics. <strong>Methods: </strong>In this study, we performed <br>CGP on 7,606 patients with advanced or metastatic NSCLC using the Illumina TruSight Oncology 500 (TSO <br>500) CGP assay to show its coverage and utility in detecting known and novel features of NSCLC. <strong>Results: </strong><br>Testing revealed distinct genomic profiles of lung adenocarcinoma and squamous cell carcinomas and <br>detected variants with a current targeted therapy or clinical trial in >72% of patient tumors. Known associations <br>between genomic alterations and immunotherapy markers were observed including significantly lower TMB <br>levels in tumors with therapy-associated alterations and significantly higher PD-L1 levels in tumors with ALK, <br>MET, BRAF, or ROS1 driver mutations. Co-occurrence analysis followed by network analysis with gene <br>module detection revealed known and novel co-occurrences between genomic alterations. Further, certain <br>modules of genes with co-occurring genomic alterations had dose-dependent relationships with histology and <br>increasing or decreasing levels of PD-L1 and TMB, suggesting a complex relationship between PD-L1, TMB, <br>and genomic alterations in these gene modules. <strong>Discussion:</strong> This study is the largest clinical study to date <br>utilizing the TSO 500. It provides an opportunity to further characterize the landscape of NSCLC using this <br>newer technology and show its clinical utility in detecting known and novel facets of NSCLC to inform treatment <br>decision-making.</p> <p><strong>DATA AVAILABILITY</strong></p> <p>The data and code presented in the study are deposited in this Zenodo repository, accession number <br>13137232 (<a href="https://zenodo.org/record/13137232">https://zenodo.org/record/13137232</a>). Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Further data inquiries can be directed to the corresponding <br>author. </p>
Community Tapestry: An Actionable Tool to Track Turnover and Diversity in OSS
Open the record for dataset details and reuse information.
Establishing Technical Debt Management - A Five-Step Workshop Approach and an Action Research Study
<div> <div>The additional material for the paper "Establishing Technical Debt Management - A Five-Step Workshop Approach and an Action Research Study" comprises the following documents:</div> <div> </div> <div>* Guideline_to_Use_TD-SAGAT.docx (.pdf)</div> <div> A short guideline on how to use the TD-SAGAT method.</div> <div>* SAGAT_for_TD_from_Goals_to_Queries.pdf</div> <div> Determination of survey questions by following the SAGAT approach of following the hierarchy of goals, subgoals, decisions, requirements, and queries </div> <div>* WIKI page on technical debt.pdf</div> <div> The teams' wiki page on TD management written by the TD manager</div> <div>* AzureTDTickets_Template.pdf</div> <div> Screenshot of the backlog's TD item template as presented in the paper for better readability.</div> <div>* OverviewOfActionCycles_ExtendedTable5.xlsx</div> <div> Table 5 (Overview of actions cycles with workshop topics, TD activities, actions taken, and learning) as an Excel sheet with additional information on actions and learning, which we did not put into the paper</div> <div> </div> <div>* Workshops/workshop_slides/TDMGuide_<x>_Workshop.pptx</div> <div> Slides for each of the six workshops </div> <div>* Workshops/workshop_slides/TDMGuide_0_InitTalk_35Min_EN.pptx</div> <div> The initial one-hour introduction into the TD topic (~40 min. talk + 20 min. for a short discussion) </div> <div> </div> <div>* Workshops/workshop_flipcharts/WS<No.>_<explanation>.jpg</div> <div> Six anonymized flipchart photos to give an impression of the workshops, particularly of the kick-off workshop (other workshops made less use of flipcharts).</div> <div> Translations are directly included in the photos, except for ...</div> <div>* Workshops/workshop_flipcharts/WS1_Topic Cache - Translation.txt</div> <div> Translation of the German topic cache in an extra file, as there were too many topics to translate in the photo</div> <div> </div> <div>* Workshops/Workshop Agendas.pdf</div> <div>Agendas for the kick-off workshop and a general agenda for further workshops, each with a detailed agenda for workshop moderators and a rough agenda for participants.</div> <div> </div> <div>* Workshops/ TD_Energy_Matrix.xlsx</div> <div> Matrix where participants mark their own, the teams, and the companies' (assumed) level of willingness to invest in a TDM versus their (assumed) evaluation of TDM's importance. Used in kickoff workshop</div> <div> </div> <div> </div> <div>* Evaluations/Backlog_Evaluations_and_Figures.xlsx</div> <div>- Backlog data from the 5th workshop (for 6th workshop, we used the PowerBI Visualization instead)</div> <div>- Evaluation of this data comprising </div> <div>- priority calculations based on priority risk and </div> <div>- priority calculations based on priority risk based on ROI</div> <div> </div> <div>* Evaluations/Meetings_Overview_Observations_Evaluation_Figures.xlsx</div> <div>- Overview of all meetings plus information on length, participants, whether a video exists and was used for evaluation</div> <div>- Filled out observation protocols from different meetings</div> <div>- Summation, evaluations, and resulting figures</div> <div> </div> <div>* Evaluations/TD-SAGAT_Survey_and_SurveyResults_Figures.xlsx</div> <div>- Survey questions for TD-SAGAT plus results</div> <div>- Evaluation plus figures</div> <div> </div> <div>* Evaluations/Workshop_Survey_and_SurveyResults_Figures.xlsx</div> <div>- Survey questions for Workshops plus results</div> <div>- Evaluation plus figures</div> <div> </div> <div>* Evaluations/Kickoff_Survey_and_SurveyResults.xlsx</div> <div>- Survey questions for Kickoff Workshops (incl. questions on current TDM process) plus results</div> <div>- Evaluation in Workshop_Survey_and_SurveyResults_Figures.xslx</div> <div> </div> <div> </div> <div>* Visualizations/V<No.>_<adopted|mockup>_<explanation>.png</div> <div>- "adopted" visualizations are similarly presented in the paper in Fig. 2.</div> <div>- "mockup" visualizations were presented during the workshops but not adopted in this form. </div> <div>If a respective "adopted" visualization for this No. exists, the visualisation was replaced by a more suitable one. </div> <div>If no respective "adopted" visualization for this No. exists, the visualisation was discarded.</div> <div> </div> <div> </div> <div>* Visualizations/Dashboard <Manager|Team>.png</div> <div>- shows the dashboard mockups for the manager and the team, respectively. </div> <div>Visualizations presented in the dashboards that were not adopted by the team were removed or replaced by the improved visualizations in the final dashboard versions.</div> <div> </div> <div> </div> <div> </div> <div> </div> </div>
Dataset for Learning in Continuous Action Space for Developing High Dimensional Potential Energy Models
<p>The NN potentials developed in this study and the other available MLIP methods such as GAP, SNAP, qSNAP, and MEGNET used for benchmarking.</p>
Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement
<p>Volition - the sense of control or agency over one's voluntary actions - is widely recognized as the basis of both human subjective experience and natural behavior in non-human animals. To date, several human studies have found peaks in neural activity preceding voluntary actions, e.g. the readiness potential (RP), and some have shown upcoming actions could be decoded even before awareness. While these findings may pose a challenge to traditional accounts of human volition, some have proposed that random processes underlie and explain pre-movement neural activity. Here we seek to address part of this controversy by evaluating whether pre-movement neural activity in mice contains structure beyond that present in random neural activity. Implementing a self-initiated water-rewarded lever pull paradigm in mice while recording widefield [Ca++] neural activity we find that cortical activity changes in variance seconds prior to movement and that upcoming lever pulls or spontaneous body movements could be predicted between 1 second to more than 10 seconds prior to movement, similar to but even earlier than in human studies. We show that mice, like humans, are biased towards initiation of voluntary actions during specific phases of neural activity oscillations but that the pre-movement neural code in mice changes over time and is widely distributed as behavior prediction improved when using all vs single cortical areas. These findings support the presence of structured multi-second neural dynamics preceding voluntary action beyond that expected from random processes. Our results also suggest that neural mechanisms underlying self-initiated voluntary action could be preserved between mice and humans.</p>
An action potential initiation mechanism in distal axons for the control of dopamine release
<p>Data table for An action potential initiation mechanism in distal axons for the control of dopamine release</p>
Data table for an action potential initiation mechanism in distal axons for the control of dopamine release
<p>Data table for the article: An action potential initiation mechanism in distal axons for the control of dopamine release</p>
Source Data For: "Focused ultrasound excites action potentials in mammalian peripheral neurons in part through the mechanically gated ion channel Piezo2"
<p>Source Data For: "Focused ultrasound excites action potentials in mammalian peripheral neurons in part through the mechanically gated ion channel Piezo2"</p>
Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program
<p>Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (<em>Sarcophilus harrisii</em>) within the insurance metapopulation and across the species' range (64,519 km<sup>2</sup>). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumour disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for "resistance" alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012-2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.</p>
Rapid decline of carbon monoxide emissions in the Fenwei Plain in China during the Three-year Action Plan on Defending the Blue Sky
<p>The Fenwei Plain is one of China’s most polluted regions, with poor atmospheric dispersion conditions and an outdated energy structure. After implementing multiple policies in recent years, significant reductions in air pollutant concentrations were observed. We inferred high-resolution carbon monoxide (CO) emissions of the Fenwei Plain by inversion of observed atmospheric concentrations and analyzed the causes for variations in CO emissions, especially the effect of the “Three-year Action Plan on Defending the Blue Sky” (TAPDBS). Before the policy went into action, CO emissions temporarily increased and the overall decrease in CO emissions per unit of Gross Domestic Product (GDP) slowed down. When the policy was implemented, CO emission fluxes declined sharply, with an average drop of 28%, accompanied by an even higher 37% decrease of the CO emission per GDP. Thus, the TAPDBS has brought a breakthrough in both economic development and air quality protection in the Fenwei Plain.</p>
How 2 and 4 year old children coordinate joint actions with peers
<p>The interaction engine hypothesis postulates a uniquely human ability and motivation for social interaction. A crucial juncture in the ontogeny of the interaction engine could be around 2-4 years of age, but observational studies of children in natural contexts are lacking. Moreover, data on the ontogenetic development of joint action coordination can provide critical human data for comparative research investigating the phylogenetic roots of the interaction engine. In this study we report on focal observations on 31 children aged 2 and 4 years old in 4 preschools (approximately 20h per child). Interactions were videotaped, transcribed and coded for the presence and duration of joint actions, their type (e.g., play, conflict) and the partners involved, as well as the presence and duration of entry, exit and main body phases of those joint actions. Children interact with a wide range of partners, many infrequently, but with one or two close friends. 4 year olds engage in cooperative joint actions more often than 2 year olds, and fight less than 2 year olds. Conversations and playing with objects are the most frequent action types. Joint actions are relatively brief (28s on average) and shorter than those of great apes in comparable studies. Their joint actions feature entry and exit phases about two-thirds of the time, less frequently than great apes. However, children interact with many more partners than great apes do, about 20% of their joint actions are multiparty and overall they engage in joint actions more frequently than great apes (on average 13 distinct joint actions per hour). The results support the interaction engine hypothesis, suggesting that, at a very young age humans already manifest a remarkable motivation and ability for fast-paced, flexible social interaction with multiple partners.</p>
Action-based predictions affect visual perception, neural processing, and pupil size, regardless of temporal predictability
<p>Data supporting the findings in:</p> <p>Lubinus, C., Einhäuser, W., Schiller, F., Kircher, T., Straube, B., & van Kemenade, B. M. (2022). Action-based predictions affect visual perception, neural processing, and pupil size, regardless of temporal predictability. <em><strong>NeuroImage</strong>. DOI: XXX</em></p> <p>Details are specified in the readme file.</p>
Interest in insect die-off and intention for action using Google trends
<p><span>1. The publication of "More than 75 percent decline over 27 years in total flying insect biomass in protected areas" by Hallmann et al. in October 2017 gained vast media coverage in Germany. The insect crisis as conservation topic has received little attention among the public before, but since media influences people's awareness, we investigated i) whether the study publication induced </span><span>increased awareness among the German public for insect die-off, and ii) whether it contributed to people's intentions to undertake insect protecting actions. </span></p> <p><span>2. We used Google Trends to examine the people's internet activity in terms of keywords relevant to our research question.</span></p> <p><span>3. A high peak in Google searches for insect die-off (Insektensterben) was indeed visible just after the study publication, and search volume remained significantly higher for the following six months, confirming that the topic gained attention. </span></p> <p><span>4. Searches for the three keywords insect hotel, bee friendly and bee meadow increased significantly over the summers of the years 2017 to 2019. This suggests that intentions to undertake these simple insect protecting actions rose as well. The results propose that media should use the window of opportunity opened by shocking news about a crisis to spread information on feasible counteractions. </span></p> <p><span>5. </span><span>Due to the prevailing topicality in the media and the already increased awareness and willingness to action among the population, conservation organizations can take advantage of the situation by communicating practical conservation measures to the general public in cooperation with media agencies or via own channels such as press releases and social media campaigns.</span></p> <div> <div> <div class="msocomtxt"></div> </div> </div>
Towards a Generic Grasp Planning Pipeline using End-Effector Specific Primitive Grasping Actions
<p>In the past few years, several robotic end-effectors based on diverse kinematics and actuation principles have been developed to provide grasping and manipulation functionalities. To ease the control and application of these wide-ranging end-effectors, the development of effective reusable tools that can facilitate the end-effector motion planning and control is necessary. In this work, we introduce a generic grasp planner that leverages on the concept of the primitive grasping actions. Given the specific characteristics of an end-effector, including its kinematic and actuation arrangements, a number of primitive grasping actions are extracted and employed by the proposed grasp planner to autonomously plan and synthesize more complex grasping behaviours. The grasp planner is validated through experimental trials involving the HERI II robotic hand, a four-fingers tendon-driven under-actuated hand. The results of these experiments demonstrate the efficacy of the proposed method to generate appropriate planning actions enabling to grasp objects of different shapes.</p>
Figure 5 in Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
Figure 5. The Wallich Catalogue. Screenshot of Wallich Catalogue hosted by Royal Botanic Garden Edinburgh showing popup for stable URI containing information hosted at Botanic Garden and Botanical Museum Berlin-Dahlem.
Figure 4 in Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
Figure 4. The CETAF Specimen URI Tester provides for any given Specimen URI an overview of the redirection process as well as a preview of machine-readable and human-readable data associated with the URI.
Figure 3 in Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects
Figure 3. CETAF stable HTTP URIs in the GBIF data portal. The Global Biodiversity Information Facility (GBIF) publishes CETAF stable HTTP URIs via their data portal.
ScienceDex guides
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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.