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Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees
<p>It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes.</p>
Multi-sensor dataset for testing merge of Hyperspectral, HD and 3D cloud information for image recognition
<p>This data contain multisensor image dataset constructed for benchmarking purposes. It contains multiple images of the constructed scenes -- on which objects made of different materials are placed to test image recognition scenarios. The scene is recorded from various angles by imagining sensors, i.e. HSI camera, HD camera on mobile chassis and MS Kinect to provide complete information.<br> </p> <p><strong>Equipment</strong><br> The imaging was performed with use of three devices for three different approaches to data. Those three devices' imaging characteristics are widely different when it comes to angle and resolution which required them to be separately positioned to acquire the matching images. Therefore while HD camera was being transferred on the moving platform (chassis), both Kinect and SOC710 were placed on a stationary position which was moved between the frames by hand.</p> <p><em>Hyperspectral data</em></p> <p><br> Hyperspectral data acquisition was performed with Surface Optics SOC710 camera. This camera records spectra at VNIR range $377-1046$ nm; the output image has dimensions $696 \times 520$ with 128 bands and $12$ bit dynamic range.</p> <p>The camera is equipped with sensor line translation unit and can be used from static stand as a conventional camera (i.e. it does not require mechanical translation of the observed sample or rotary stand, as in traditional ‘push broom’ hyperspectral cameras). The lighting was provided with four ambient lamps and adjusted for each scenario separately, so that most of the dynamic range of the camera was used and image saturation is avoided. Captured hyperspectral images were subject to a standard calibration procedure, including: the removal of a dark frame, spectral and radiometric calibration as well as reflectance normalization using the calibration panel. </p> <p><em>3D point clouds</em></p> <p><br> The Kinect sensor incorporates several advanced sensing hardware. The depth sensor consists of the IR projector combined with the IR camera, which is a monochrome complementary metaloxide semiconductor (CMOS) sensor. The IR projector is an IR laser that passes through a diffraction grating and turns into a set of IR dots. The relative geometry between the IR projector and the IR camera as well as the projected IR dot pattern are known. If we can match a dot observed in an image with a dot in the projector pattern, we can reconstruct it in 3D using triangulation. Because the dot pattern is relatively random, the matching between the IR image and the projector pattern can be done in a straightforward way by comparing small neighborhoods using, for example, normalized cross correlation. The depth value is encoded with gray values; the darker a pixel, the closer the point is to the camera in space. The black pixels indicate that no depth values are available for those pixels. This might happen if the points are too far (and the depth values cannot be computed accurately), are too close (there is a blind region due to limited fields of view for the projector and the camera), are in the cast shadow of the projector (there are no IR dots), or reflect poor IR lights </p> <p><em>HD Images</em></p> <p><br> The HD images were acquired using 5 Megapixel HD camera mounted on a mobile chassis made by Dawn Robotics, that allowed the camera to be moved freely on the scene. Both camera and mobile chassis was controlled by a Raspberry PI unit which was also responsible to position the camera in accord to the data being collected by other sources. <br> </p> <p><strong>Data</strong></p> <p>The dataset consists of three scenes consisting of various objects -- minerals, fruit, wood plastic and metal -- placed on a stand. The objects, depending on the view are partially covered and seen from different perspective. Each scene is captured from 8 different angles.</p> <p>Scene 1 (denoted <em>SceneEagle</em>) uses mostly inorganic materials, such as wood, metal, plastic and glass all placed on the vertical stand.<br> Scene 2 (<em>SceneFruit</em>) uses fruits normal and artificial, that are similar on HD photography and 3D cloud of point, but differs in hyperspectral image.<br> Scene 3 (<em>SceneFruit2</em>) uses the fruits but also includes printed full colour images of same fruits that are 2-dimensional.</p> <p> </p> <p>The data are formatted as follows:<br> - The HIS images are available in both \text{*.hdr} and \text{*.cube} formats. The separate files with calibrating panel is provided for each frame.<br> - Kinect clouds are provided in \text{*.obj} format, typical for Kinect output files.<br> - Matched Hyperspectral clouds are also provided as \text{*.obj} files<br> - HD photo files are provided in \text{*.jpg} files.<br> </p> <p><br> <strong>Acknowledgements</strong></p> <p>This work has been supported by the National Science Centre, based on decision no. DEC2012/07/N/ST6/03656.</p> <p> </p>
Detecting and Tracking Drift in Quantum Information Processors
<p>This is supplemental data and code for:<strong> </strong>T. Proctor et al, <a href="https://www.nature.com/articles/s41467-020-19074-4"><em>Detecting and tracking drift in quantum information processors</em></a>, Nat. Comm. 11, 5396 (2020).</p> <p>Please direct any questions to Timothy Proctor (tjproct@sandia.gov).</p> <p>This folder contains all the data and the analysis code to generate the results presented in that paper. The core data analysis routines use PyGSTi, which can be found at <a href="https://github.com/pyGSTio/pyGSTi">https://github.com/pyGSTio/pyGSTi</a>.</p> <p>The analysis was run using pyGSTi commit 7c6ddd1de209b795ea39bfb69d010b687e812d07. This code does <em>not</em> work on the latest full release of pyGSTi (0.9.9). It is anticipated that it will work with the next full release of pyGSTi (0.9.10).</p> <p>Below is a basic guide to navigating this SI:</p> <p><strong>Time-resolved Ramsey tomography on experimental data.</strong></p> <p><em>Directory: ramsey/experiment</em></p> <p>This folder contains the data and analysis code for the time-resolved Ramsey experiment, the results of which are presented in Figure 1 of the paper. The folder contains a single Jupyter notebook, which runs all of the data analysis.</p> <p><strong>Time-resolved randomized benchmarking (RB) on simulated data.</strong></p> <p><em>Directory: rb/simulation</em></p> <p>This folder contains the data and analysis code for the simulation of time-resolved RB, the results of which are presented in Figure 2 of the paper. The folder contains a single Jupyter notebook, which runs all of the data analysis on the simulated data, and which can be used to run new simulations with the same noise model.</p> <p><strong>Time-resolved gate set tomography (GST) on simulated data.</strong></p> <p><em>Directory: gst/simulation</em></p> <p>This contains the data and analysis code for the simulation of time-resolved GST, the results of which are presented in Figure 2 of the paper. The raw simulated data is contained in the "data" folder. All the code is contained in the "analysis" folder. This contains the following code files:</p> <ul> <li>create_simulated_data.py : this generates the simulated data. This was run using MPI on 20 cores.</li> <li>drift.ipynb : this contains the general circuit-agnostic drift analysis.</li> <li>trgst_fit.py : this contains the TR-GST model-fitting code. This was run using MPI on 20 cores.</li> <li>tdmodel.py : encodes the general time-dependent model that the data is fit to.</li> </ul> <p><strong>Time-resolved gate set tomography (GST) on experimental data.</strong></p> <p><em>Directory: gst/experiments</em></p> <p>This folder contains the data and analysis code for the two time-resolved GST experiments, the results of which are presented in Figure 3 of the paper. The raw data is contained in the two folders "data/1" and "data/2", corresponding to the first and second experiment, respectively. All analysis code is contained in the "analysis" folder. This contains the following code files:</p> <ul> <li>drift.ipynb : this contains the general circuit-agnostic drift analysis.</li> <li>gst.ipynb : this contains the standard GST analysis, used to inform the TR-GST analysis.</li> <li>trgst_fit.py : this contains the TR-GST model-fitting code. This was run using MPI on 20 cores.</li> <li>trgst_plotting.ipnyb : this contains code that analyzes the results of the TR-GST fit.</li> <li>tdmodel.py : encodes the general time-dependent model that the data is fit to.</li> </ul>
Supplementary information to the article by van Beijnum et al. "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment"
<p>Supplementary information to the article "Integrating phenotypic search and phosphoproteomic profiling of active kinases for optimization of drug mixtures for RCC treatment".</p> <p><strong>Judy R. van Beijnum<sup>1</sup>, Andrea Weiss<sup>2, 3</sup>, Robert H. Berndsen<sup>1,2 </sup>, Tse J. Wong<sup>1</sup>, Louise C. Reckman<sup>1</sup>, Sander R. Piersma<sup>4,5</sup>, Marloes Zoetemelk<sup>2,3</sup>, Richard de Haas<sup>1,4,5</sup>, Olivier Dormond<sup>6</sup>, Axel Bex<sup>7,8</sup>, Alexander A. Henneman<sup>4,5</sup>, Connie R. Jimenez<sup>4,5</sup>, Arjan W. Griffioen<sup>1</sup>, Patrycja Nowak-Sliwinska<sup>2,3,9</sup>*</strong></p> <p> </p> <p><sup>1</sup> Angiogenesis Laboratory, Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands;</p> <p><sup>2</sup> Molecular Pharmacology Group, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland*;</p> <p><sup>3 </sup>Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland</p> <p><sup>4 </sup>Department of Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands</p> <p><sup>5</sup> OncoProteomics Laboratory, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands</p> <p><sup>6</sup> Department of Visceral surgery, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland<sup> </sup> </p> <p><sup>7</sup> Royal Free London NHS Foundation Trust, Renal Cancer Centre, UCL Division of Surgical and Interventional Science, London, UK</p> <p><sup>8</sup> Netherlands Cancer Institute, Amsterdam, The Netherlands</p> <p><sup>9 </sup> Translational Research Centre in Oncohaematology, Geneva, Switzerland</p> <p> Correspondence: <a href="mailto:Patrycja.Nowak-Sliwinska@unige.ch">Patrycja.Nowak-Sliwinska@unige.ch</a></p>
Supplementary information for: The effects of geographic range size and abundance on extinction during a time of 'sluggish' evolution
<p>Geographic range size and abundance are important determinants of extinction risk in fossil and extant taxa. However, the relationship between these variables and extinction risk has not been tested extensively during evolutionarily 'quiescent' times of low extinction and speciation in the fossil record. Here we examine the influence of geographic range size and abundance on extinction risk during the late Paleozoic (Mississippian–Permian), a time of 'sluggish' evolution when global rates of origination and extinction were roughly half those of other Paleozoic intervals. Analyses used spatio-temporal occurrences for 164 brachiopod species from the North American midcontinent. We found abundance to be a better predictor of extinction risk than measures of geographic range size. Moreover, species exhibited reductions in abundance prior to their extinction, but did not display contractions in geographic range size. The weak relationship between geographic range size and extinction in this time and place may reflect the relative preponderance of larger-ranged taxa, combined with the physiographic conditions of the region that allowed for easy habitat tracking that dampened both extinction and speciation. These conditions led to a prolonged period (19 – 25 Myr) during which standard macroevolutionary rules did not apply.</p>
Bilingual Dataset for Information Retrieval and Question Answering over the Spanish Workers Statute
<p>A bilingual dataset of questions and answers over a key document in Spanish labor law legislation is presented. The document contains 150 questions and their respective answers in the form of one part number from the 130 parts in which the Workers Statute is divided (articles and other provisions), and with the most relevant excerpt of information for the answer.</p>
Data from: Spatial and temporal patterns of environmental DNA detection to inform sampling protocols in lentic and lotic systems.
<p>The development of efficient sampling protocols for the capture of environmental DNA (eDNA) could greatly help improve accuracy of occupancy monitoring for species that are difficult to detect. However, the process of developing a protocol in situ is complicated for rare species by the fact that animal locations are often unknown. We tested sampling designs in lake and stream systems to determine the most effective eDNA sampling protocols for two rare species: the Sierra Nevada yellow-legged frog (<i>Rana sierrae</i>) and the foothill yellow-legged frog (<i>R. boylii</i>). We varied water volume, spatial sampling, and seasonal timing in lakes and streams; in lakes we also tested multiple filter types. We found that filtering 2 L versus 1 L increased the odds of detection in streams 5.42X (95% CI: 3.2-9.19X) in our protocol, from a probability of 0.51 to 0.85 per technical replicate. Lake sample volumes were limited by filter clogging and we found no effect of volume or filter type. Sampling later in the season increased the odds of detection in streams by 1.96X for every 30 days (95% CI: 1.3 - 2.97X) but there was no effect for lakes. Spatial autocorrelation of the quantity of yellow-legged frog eDNA captured in streams between 100 and 200 m, indicating that sampling at close intervals is important.</p>
Mining Detailed Information from Description for App functions comparison
<p>The corresponding Dataset and Source-Code for the paper named "Mining Detailed Information from Description for App functions comparison"</p>
Supplementary materials for article focused on traffic information enrichment: Animation and complete overview of all road segments on which basis summary test results were calculated
<p><strong>Supplementary materials </strong>(Appendix A and B) for the article:</p> <p>Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints</p> <p><em>Abstract: </em>Traffic speed prediction for a selected road segment from a short-term and long-term perspective is among the fundamental issues of intelligent transportation systems (ITS). During the course of the past two decades, many artefacts (e.g., models) have been designed dealing with traffic speed prediction. However, no satisfactory solution has been found for the issue of a long-term prediction for days and weeks using the vast spatial and temporal data. This article aims to introduce a long-term traffic speed prediction ensemble model using country-scale historic traffic data from 37,002 km of roads, which constitutes 66% of all roads in the Czech Republic. The designed model comprises three submodels and combines parametric and nonparametric approaches in order to acquire a good-quality prediction that can enrich available real-time traffic information. Furthermore, the model is set into a conceptual design which expects its usage for the improvement of navigation through waypoints (e.g., delivery service, goods distribution, police patrol) and the estimated arrival time. The model validation is carried out using the same network of roads, and the model predicts traffic speed in the period of 1 week. According to the performed validation of average speed prediction at a given hour, it can be stated that the designed model achieves good results, with mean absolute error of 4.67 km/h. The achieved results indicate that the designed solution can effectively predict the long-term speed information using large-scale spatial and temporal data, and that this solution is suitable for use in ITS.</p> <p>Simunek, M., & Smutny, Z. (2021). Traffic Information Enrichment: Creating Long-Term Traffic Speed Prediction Ensemble Model for Better Navigation through Waypoints. <em>Applied Sciences</em>, 11(1), 315. <a href="https://doi.org/10.3390/app11010315">https://doi.org/10.3390/app11010315</a></p> <p> </p> <p><strong>Appendix A</strong><br> Examples of the deviation between the average speed and the FreeFlowSpeed for selected hours.</p> <p> </p> <p><strong>Appendix B</strong><br> The text file provides a complete overview of all road segments on which basis summary test results were calculated in Section 6 of the article.</p>
Full information on the eORCA1 grid (mesh_mask) used in IPSL-CM6A-LR configuration
<p>This file contains all relevant information on the ORCA1 grid. See https://www.nemo-ocean.eu/wp-content/uploads/NEMO_book.pdf for more details on the grid.</p>
Supplementary Information for "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"
<p>Data and code to reproduce the analyses in "Resolution and the Detection of Cultural Dispersals: development and application of spatiotemporal methods in Lowland South America"</p> <p> </p> <p><strong>Abstract</strong></p> <p>Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.Inferring episodes of expansion, admixture, diffusion, and/or migration in prehistory is at present undergoing a resurgence in macro-scale archaeological interpretation. In parallel to this renewed popularity, expanding access to computational tools and datasets has seen the use of aggregated radiocarbon datasets for the study of dispersals also increasing. This paper advocates for developing reflexive practice in the application of radiocarbon dates to prehistoric dispersals, by reflecting on the quality and qualities of the underlying data, particularly chronometric uncertainty, and framing dispersals explicitly in terms of hypothesis testing. This paper draws on cultural expansions within South America and employs two emblematic examples, the Arauquinoid and Tupiguarani traditions, to develop an analytical solution that not only incorporates chronometric uncertainty in bivariate regression but, importantly, tests whether the datasets provide statistically significant evidence for a dispersal process. The analysis, which the paper provides the means to replicate, identifies fundamental issues with resolution and data quality that impede identification of pre-Columbian cultural dispersals through simple spatial gradients of radiocarbon data. The results suggest that reflexivity must be fed back into theoretical frameworks of prehistoric mobility for the study of dispersals, in turn informing the construction of more critical statistical null models. As a first step, alternative models of cultural expansion should be formally considered alongside demographic models.</p>
Annex - Information Technology as Enabler of Transparency in Food Supply Chains
<p>This is the Annex of the paper: Information Technology as Enabler of Transparency in Food Supply Chains</p>
Mimicry in motion and morphology: do information limitation, trade-offs or compensation relax selection for mimetic accuracy?
<p>Many animals mimic dangerous or undesirable prey as a defence from predators. We would expect predators to reliably and exclusively avoid animals that closely resemble dangerous prey, yet imperfect mimics are common. There have been many hypotheses suggested to explain imperfect mimicry, but comparative tests across multiple mimicry systems are needed to determine which are applicable, and which—if any—represent general principles of imperfect mimicry. We tested four hypotheses on Australian ant mimics and found support for only one of them: the information limitation hypothesis. A predator with incomplete information will be unable to discriminate some poor mimics from their models. We also show that since predators must make decisions while they are learning, they are likely to never sample broadly enough to gain and utilise the full information needed to discriminate poor mimics from their models. We found no evidence that one accurate mimetic trait can compensate for another, or that rapid movement reduces selection pressure for good mimicry. Based on our results, we argue that information limitation is likely to be a general principle behind imperfect mimicry of any complex traits, while interactions between components of mimicry may apply to some mimicry systems but not others.</p>
Diversity of response and effect traits provides complementary information about avian community dynamics linked to ecological function
<p>Functional diversity metrics based on species traits are widely used to investigate ecosystem functioning. In theory, such metrics have different implications depending on whether they are calculated from traits mediating responses to environmental change (response traits) or those regulating function (effect traits), yet trait choice in diversity metrics is rarely scrutinized. Here, we compile effect and response traits for British bird species supplying two key ecological services – seed dispersal and insect predation – to assess the relationship between functional diversity and both mean and stability of community abundance over time. As predicted, functional diversity correlates with stability in community abundance of seed dispersers when calculated using response traits. However, we found a negative relationship between functional diversity and mean community abundance of seed dispersers when calculated using effect traits. Subsequently, when combining all traits together, we found inconsistent results with functional diversity correlating with reduced stability in insectivores, but greater stability in seed dispersers. Our findings suggest that trait choice should be considered more carefully when applying such metrics in ecosystem management.</p>
Data from: Making Brexit work for the environment and livelihoods: delivering a stakeholder informed vision for agriculture and fisheries
1. The UK's decision to leave the EU has far-reaching implications for agriculture and fisheries. To ensure the future sustainability of UK agricultural and fisheries systems, we argue that it is essential to grasp the opportunity that Brexit is providing to develop integrated policies that improve the management and protection of the natural environments, upon which these industries rely. 2. This article advances a stakeholder informed vision of the future design of UK agriculture and fisheries policies. We assess how currently emerging UK policy will need to be adapted in order to implement this vision. Our starting point is that Brexit provides the opportunity to redesign current unsustainable practices and can in principle deliver a sustainable future for agriculture and fisheries. 3. Underpinning policies with an ecosystem approach, with explicit inclusion of public goods provision, and social welfare equity were found to be central to the success of this endeavour. Recognition of the needs of, and innovative practices in, the devolved UK nations is also required as the new policy and regulatory landscape is established. 4. Achieving our proposed vision will necessitate drawing on best practice and creating more coherent and integrated food, environment and rural and coastal economy policies. Sustainable prosperity should and can form the core of future post-Brexit environmental policy thinking and our findings demonstrate the "bottom-up" and co-production approaches that will be key to the development of more environmentally sustainable agricultural and fisheries policies.
Logical inferences from visual and auditory information in ruffed lemurs and sifakas
<p>Inference by exclusion, or the ability to select a correct course of action by systematically excluding other potential alternatives, is a form of logical inference that allow individuals to solve problems without complete information. Current comparative research shows that several bird, mammal, and primate species can find hidden food through inference by exclusion. Yet there is also wide variation in how successful different species are, as well kinds of sensory information they can use to do so. An important question is therefore why some species are better at engaging in logical inference than others. Here, we investigate the evolution of logical reasoning abilities by comparing two strepsirrhine primate species that vary in dietary ecology: frugivorous ruffed lemur (<em>Varecia</em> spp.) and folivorous Coquerel's sifakas (<em>Propithecus coquereli</em>). Across two studies, we examined their abilities to locate food using direct information versus inference from exclusion and using both visual and auditory information. In Study 1, we assessed whether these lemurs could make inferences when full visual and auditory information about the two potential locations of food were provided. In Study 2, we then compared their ability to make direct inferences versus inferences by exclusion in both the visual and auditory domains. We found that both lemur species can use visual information to find food, but that only ruffed lemurs were also able to use auditory cues, mirroring differences in the complexity of their wild ecology. We further found that, unlike many anthropoid species tested to date, both strepsirrhine species failed to make inferences by exclusion. These results highlight the importance of natural history in understanding the evolution of logical inference, and help reconstruct the deeper phylogeny of primate cognition.</p>
On the use of private versus social information in oviposition site choice decisions by Drosophila melanogaster females
<p>Individuals are faced with decisions throughout their lifetimes, and the choices they make often have important consequences towards their fitness. Being able to discern which available option is best to pursue often incurs sampling costs, which may be largely avoided by copying the behaviour and decisions of others. Although social learning and copying behaviours are widespread, much remains unknown about how effective and adaptive copying behaviour is, as well as the factors that underlie its expression. Recently, it has been suggested that since female fruit flies (<i>Drosophila melanogaster</i>) appear to rely heavily on public information when selecting oviposition sites, they are a promising model system for researching patch-choice copying, and more generally, the mechanisms that control decision-making. Here, we set out to determine how well female distinguish between socially-produced cues, and whether females are using 'relevant' signals when choosing an oviposition site. We found that females showed a strong preference for ovipositing on media patches that had been previously occupied by ovipositing females of the same species and diet over other female outgroups. However, in a separate assay, we observed that females favoured ovipositing on media patches that previously housed virgin males over those exhibiting alternative conspecific signals. Our results confirm that females use cues left behind by other flies when choosing between potential oviposition sites, though their prioritization of these signals raises serious questions as to whether fruit flies are employing copying behaviour, or are instead responding to signals that may not be of relevance to oviposition site suitability.</p>
An Improved Global Catalog LU1319373 of Lunar Craters (≥1 km) with 3D Morphometric Information of Craters
<p>A global crater catalog LU1319373 that includes approximately 1.32 million lunar craters with diameters ≥ 1 km. The crater catalog also include 3D morphometric data on the craters.</p> <p>This first version of the crater catalog LU1319373 includes the following information for each crater:</p> <ul> <li>Longitude and latitude coordinates of the center;</li> <li>Crater diameter;</li> <li>Crater depth (other morphometric data will be provided in future versions).</li> </ul> <p>Please cite the following reference for using the crater catalog LU1319373.</p> <p>Wang, Y., Wu, B., Xue, H., Li, X., & Ma, J. (2021). An improved global catalog of lunar impact craters (≥1 km) with 3D morphometric information and updates on global crater analysis. Journal of Geophysical Research: Planets, 126, e2020JE006728.</p>
Science to inform policy: linking population dynamics to habitat for a threatened species in Canada
<p>Abstract</p> <p>1. Boreal forests provide numerous ecological services, including the ability to store large amounts of carbon, and are of significance to global biodiversity. Increases in industrial activities in boreal landscapes since the mid-20th century have added to concerns over biodiversity loss and climate change. Boreal forests are home to dwindling populations of boreal caribou (Rangifer tarandus caribou) in Canada, a species at risk that requires large, undisturbed landscapes for persistence. In 2012, the Canadian government defined critical habitat for boreal caribou by relating calf recruitment to disturbances. Some have questioned whether the recruitment-relationship can be extrapolated beyond the environmental conditions represented in the analysis.</p> <p>2. We examined the effects of human disturbances and fire (alone and in combination) on variation in recruitment and adult female survival using data from 58 study areas in Canada. Top models were used in aspatial scenarios of landscape change to evaluate the efficacy of the critical habitat definition in achieving the recovery objectives for boreal caribou in two contrasting landscapes: Little Smoky, dominated by high levels of human disturbances, and SK1, dominated by fire.</p> <p>3. The top recruitment model suggested the negative effect of fire was 3-4 times smaller than human disturbances. The top adult female survival model included human disturbances only. These results re-affirm that human disturbances are the primary factor contributing to boreal caribou declines.</p> <p>4. Our aspatial scenarios suggested that undisturbed habitat would have to increase to ≥68% for Little Smoky to maintain a self-sustaining population of boreal caribou with some degree of certainty. In contrast, the SK1 population was self-sustaining with 40% undisturbed habitat when fire disturbance predominates, but could become vulnerable with increases in human disturbances (8–9%). 5. Policy implications: Our results suggest that the 65% undisturbed critical habitat designation may serve as a reasonable proxy for achieving boreal caribou recovery in landscapes dominated by human disturbances. However, some populations may be less or more vulnerable, as illustrated by the SK1 scenarios. Continued population monitoring will be essential to assessing the effectiveness of land management strategies developed for boreal caribou recovery, especially with climate change.</p>
Data from: Combining role-play with interactive simulation to motivate informed climate action: evidence from the World Climate simulation
Climate change communication efforts grounded in the information deficit model have largely failed to close the gap between scientific and public understanding of the risks posed by climate change. In response, simulations have been proposed to enable people to learn for themselves about this complex and politically charged topic. Here we assess the impact of a widely-used simulation, World Climate, which combines a socially and emotionally engaging role-play with interactive exploration of climate change science through the C-ROADS climate simulation model. Participants take on the roles of delegates to the UN climate negotiations and are challenged to create an agreement that meets international climate goals. Their decisions are entered into C-ROADS, which provides immediate feedback about expected global climate impacts, enabling them to learn about climate change while experiencing the social dynamics of negotiations. We assess the impact of World Climate by analyzing pre- and post-survey results from >2,000 participants in 39 sessions in eight nations. We find statistically significant gains in three areas: (i) knowledge of climate change causes, dynamics and impacts; (ii) affective engagement including greater feelings of urgency and hope; and (iii) a desire to learn and do more about climate change. Contrary to the deficit model, gains in urgency were associated with gains in participants' desire to learn more and intent to act, while gains in climate knowledge were not. Gains were just as strong among American participants who oppose government regulation of free markets - a political ideology that has been linked to climate change denial in the US - suggesting the simulation's potential to reach across political divides. The results indicate that World Climate offers a climate change communication tool that enables people to learn and feel for themselves, which together have the potential to motivate action informed by science.
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.