Find research datasets worth reusing

opencc-by-4.0Oct 2016View details →

Visual perception of shape altered by inferred causal history

Dataset and stimuli relative to the following publication: Spröte, P., Schmidt, F., & Fleming, R. W. (2016). Visual perception of shape altered by inferred causal history. Scientific Reports, 6, 36245. <a href="http://dx.doi.org/10.1038/srep36245"> http://dx.doi.org/10.1038/srep36245</a> Each folder contains the data and stimuli relative to one experiment and a text file with comments.

opencc-by-4.0Dec 2016View details →

Data files for: Structural variation shapes the landscape of recombination in mouse

Supplementary data files for the manuscript "Structural variation shapes the landscape of recombination in mouse."

Parallel Body Shape Divergence in the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) Along Elevational Gradients of the Western Slopes of the Ecuadorian Andes

TPS files for geometric morphometric analysis of body shape data of Rhoadsia spp. (Teleostei: Characidae) collected in western Ecuador.

Parallel Body Shape Divergence in the Neotropical Fish Genus Rhoadsia (Teleostei: Characidae) Along Elevational Gradients of the Western Slopes of the Ecuadorian Andes

Morphological data collected from specimens of Rhoadsia spp. (Teleostei: Characidae) in western Ecuador. Excel file with individual standard length (SL), body depth (BD), size-adjusted fineness ratio (Adj_FR), and size-adjusted canonical variates analysis scores on axes 1 and 2 (Adj_CV1, Adj_CV2).

Inferring the stiffness of unfamiliar objects from optical, shape and motion cues

Dataset relative to the following publication: Schmidt, F., Paulun, V. C., van Assen, J. J. R., & Fleming, R. W. (2017). Inferring the stiffness of unfamiliar objects from optical, shape, and motion cues. Journal of Vision, 17(3):18, 1-17. <a href="http://dx.doi.org/10.1167/17.3.18">http://dx.doi.org/10.1167/17.3.18 </a> Each folder contains the stimuli and data relative to one experiment and a text file with comments. The folder of Experiment 1 (Material) also contains the Maxwell (NextLimit Technologies, Madrid, Spain) material files that were used to render the stimuli in all experiments.

Figure 6. - Commonest shape of the rostrum. Palaemoncarteri (a MPEG 787), Palaemonivonicus (b INPA 128) and Palaemonyuna sp. n. (c CCDB 4866).

Figure 5. - Commonest shape of the antennular peduncle. Palaemoncarteri (a MPEG 787), Palaemonivonicus (b INPA 128) and Palaemonyuna sp. n. (c CCDB 4866).

Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.

Figure 10. - Maximum-likelihood phylogeny of Epicephala species based on sequences of the COI, ArgK and EF1α genes. Numbers above nodes are maximum-likelihood bootstrap support values based on 1,000 replications. The Japanese Epicephala species are marked in blue. Symbols right to species names donate ovipositor morphology: inverted U-shape, rounded apically; inverted V-shape, acute apically.

Flow-Guided Warping for Image-Based Shape Manipulation

Dataset relative to the following publication: Vergne, R., Barla P., Bonneau, G.-P. and R. W. Fleming (2016). Flow-Guided Warping for Image-Based Shape Manipulation. ACM Transactions on Graphics (Proceedings of SIGGRAPH 2016), 35(4): 93. Each folder contains *.mat files with the data from the experiments presented in Figure 12 of the article (Experiment 1: cg results, Experiment 2: photo results) and a text file with comments.

Bent out of shape: The visual inference of non-rigid shape transformations applied to objects

Dataset relative to the following publication: Spröte, P., & Fleming, R. W. (2016). Bent out of shape: The visual inference of non-rigid shape transformations applied to objects. Vision research, 126, 330-346. <a href="https://doi.org/10.1016/j.visres.2015.08.009">https://doi.org/10.1016/j.visres.2015.08.009</a> Each folder contains the data relative to one experiment and a text file with comments.

Low-Amplitude Textures Explored with the Bare Finger: Roughness Judgments Follow an Inverted U-Shaped Function of Texture Period Modified by Texture Type

Roughness is probably the most salient dimension pertaining to the perception of textures by touch and has been widely investigated. There is a controversy on how roughness relates to the texture’s spatial period and which factors influence this relation. Here, roughness during bare finger exploration of coarse textures is studied for different types of textures with elements of low height (0.3 mm). Participants were presented with square-wave gratings that were defined along one dimension and sine-wave gratings that were defined along one or two dimensions. Textures of each type varied in their spatial half period between 0.25 and 5.17 mm. Participants explored the textures by a lateral movement or a stationary finger contact. In all conditions judged roughness increased with spatial period up to a peak roughness and then decreased again. The exact function depended on the texture type, but hardly on exploration mode. We conclude that roughness is an inverted U-shaped function of texture period, if the textures are of low amplitude. The effects are explained by the interplay of two components contributing to the spatial code to roughness: variability in skin deformation due to the finger’s intrusion into the texture, which increases with the textures’ period up to a maximum (when the skin contacts the texture’s ground), and variability associated with the spatial frequency of the deformation, which decreases with spatial period. Drewing, K. (2016). Low-Amplitude Textures Explored with the Bare Finger: Roughness Judgments Follow an Inverted U-Shaped Function of Texture Period Modified by Texture Type. Haptics: Perception, Devices, Control, and Applications (pp. 206-217). Springer: Heidelberg. The file DataPerTrialAndVp_Zenodo.txt contains all data relative to the publication. A description of the variables is contained in the file VARIABLE_CODES.txt

opencc-by-4.0Aug 2017View details →

Perceiving animacy from shape

Dataset relative to the following publication: Schmidt, F., Hegele, M., & Fleming, R. W. (2017). Perceiving animacy from shape. Journal of Vision, 17, 10. <a href="http://dx.doi.org/10.1167/17.11.10">http://dx.doi.org/10.1167/17.11.10</a> Each folder contains the data relative to one experiment and a text file with comments.

opencc-by-4.0Sep 2024View details →

Crops and Climate: Shaping Pakistan's Economic Future

The project, Crops and Climate: Shaping Pakistan’s Economic Future, aims to address the challenges posed by climate variability and unsustainable agricultural practices in Pakistan. Agriculture plays a crucial role in the country’s economy, contributing between 19% and 20% of its GDP and employing approximately 38% of the labor force (Government of Pakistan, 2022). However, the sector is vulnerable to unpredictable weather patterns, fluctuating crop yields, and a lack of data-driven decision-making. To mitigate these challenges, the project proposes developing an AI-powered Climate and Crop Economic Analysis System. This system will utilize machine learning algorithms and real-time data analytics to forecast crop yields for key crops such as wheat, rice, cotton, maize, and sugarcane, taking into account historical agricultural data, climate patterns, and production trends. It will provide agricultural stakeholders, policymakers, and industry leaders with informed decision-making tools, thus optimizing resource allocation, enhancing food security, and promoting sustainable agricultural practices. The expected outcome is a modernized agricultural sector that contributes to economic stability, reduces reliance on imports, and increases export potential.By incorporating climate adaptation strategies, the project also aligns with global efforts to mitigate the impacts of climate change on food production (FAO, 2020).

opencc-by-4.0Oct 2023View details →

Identification of structural and regulatory cell-shape determinants in Haloferax volcanii

Archaea are key players in various processes, yet little is known about their cell biology, including cell-shape determination. Haloferax volcanii is a haloarchaeon that can form both rod- and disk-shaped cells, depending on growth conditions. In this study, we used proteomics, genetics, and live-cell imaging to identify mutants that are defective in rod or disk formation. Diverse proteins were implicated to be important for cell-shape determination, including predicted transporters, transducers, signaling molecules, and transcriptional regulators. We identified and phenotypically characterized two deletion strains, strains missing rod-determining factor A (RdfA) and disk-determining factor A (DdfA), which are required for rod and disk formation, respectively. We also identified an actin homolog, volactin, which we characterized with live-cell imaging and determined to be dynamic and important for disk-shape determination. This Zenodo project includes the CellProfiler pipeline (.cpproj file) used for analyzing and quantifying cell-shape images. Additionally, the cell-shape images taken during the proteomics sample collection (comparing H53, ∆rdfA, and ∆ddfA at early- and late-log growth phases) are provided. This project also includes whole genome sequencing Illumina files for H53, ∆rdfA, ∆sph3, ∆ddfA, JK3, and JK5. These data accompany: Schiller, H., Hong, Y., Kouassi, J., Rados, T., Kwak, J., DiLucido, A., Safer, D., Marchfelder, A., Pfeiffer, F., Bisson, A., Schulze, S., and Pohlschroder, M. 2024. Identification of structural and regulatory cell-shape determinants in Haloferax volcanii. Nat Commun 15(1):1414. https://doi.org/10.1038/s41467-024-45196-0.

opencc-zeroOct 2023View details →

Data from: How far can I extrapolate my species distribution model? Exploring Shape, a novel method

Species distribution and ecological niche models (hereafter SDMs) are popular tools with broad applications in ecology, biodiversity conservation, and environmental science. Many SDM applications require projecting models in environmental conditions non-analog to those used for model training (extrapolation), giving predictions that may be statistically unsupported and biologically meaningless. We introduce a novel method, Shape, a model-agnostic approach that calculates the extrapolation degree for a given projection data point by its multivariate distance to the nearest training data point. Such distances are relativized by a factor that reflects the dispersion of the training data in environmental space. Distinct from other approaches, Shape incorporates an adjustable threshold to control the binary discrimination between acceptable and unacceptable extrapolation degrees. We compared Shape's performance to five extrapolation metrics based on their ability to detect analog environmental conditions in environmental space and improve SDMs suitability predictions. To do so, we used 760 virtual species to define different modeling conditions determined by species niche tolerance, distribution equilibrium condition, sample size, and algorithm. All algorithms had trouble predicting species niches. However, we found a substantial improvement in model predictions when model projections were truncated independently of extrapolation metrics. Shape's performance was dependent on extrapolation threshold used to truncate models. Because of this versatility, our approach showed similar or better performance than the previous approaches and could better deal with all modeling conditions and algorithms. Our extrapolation metric is simple to interpret, captures the complex shapes of the data in environmental space, and can use any extrapolation threshold to define whether model predictions are retained based on the extrapolation degrees. These properties make this approach more broadly applicable than existing methods for creating and applying SDMs. We hope this method and accompanying tools support modelers to explore, detect, and reduce extrapolation errors to achieve more reliable models.

opencc-zeroOct 2023View details →

Data from: Predator-driven behavioral shifts in a common lizard shape resource-flow from marine to terrestrial ecosystems

We conducted a field experiment to assess foraging niche dynamics of semiarboreal brown anole lizards in the presence/absence of predatory ground-dwelling curly tailed lizards in a replicated set of island ecosystems. Data used in this study includes ecological infomration for the replicated islands of study (i.e. relative arthropod and seaweedabundances) together with phenotypic data of the lizards studied (body mass, size, body condition, as well as behavioral traits describing risk-taking behavior) as well as habitat use data and marine component of diet as a surrogate of the diet of these lizards. One year after experimental translocation, brown anoles exposed to these predators increased perch height and reduced consumption of marine-derived food resources. We also use this dataset to investigate if this foraging niche shift altered marine-to-terrestrial resource-flow dynamics and persisted in the diets of the first-generation offspring. Finally, we also assessed if lizards that displayed more risk-taking behaviors consumed more marine prey on islands with predators present.

opencc-by-4.0Nov 2023View details →

Bioenergy cropping systems shape ant community composition and functional roles

R code and partial data for Haan, Helms, & Landis 2023, Bioenergy cropping systems shape ant community composition and functional roles, to be published in Frontiers in Conservation Science. The ant species list we use to generate the species matrix was uploaded previously (10.5281/zenodo.8215581) in association with another manuscript (Haan et al. 2023, Science Advances, Contrasting effects of bioenergy crops on biodiversity). Therefore here we include a small table with trait information for each species along with the R code used specifically for this manuscript.

opencc-zeroNov 2023View details →

Hybrid dynamic model for shape memory alloy linear and unimorph actuators

Shape memory alloy morphing actuators are a type of soft actuator with many attractive properties. These actuators exhibit large deformation, small form factor, self-sense ability, and physical reservoir computing potential, while also being inexpensive. These morphing actuators are composed of active shape memory alloy wires and a passive base layer that is used to magnify the overall deflection. Although morphing actuators have great potential, the modeling of shape memory alloy actuators is difficult due to both shape memory alloy characteristics and the nonlinearity of the passive layer. Here, a hybrid dynamical model is proposed that couples the phase kinetics & thermal modeling for the shape memory alloy with a dynamic Cosserat nonlinear beam model. This hybrid model is benchmarked against linear and morphing experimental actuators. The model resulted in a root mean squared error of 1.48 mm and 1.63 mm for the morphing actuator configuration for two different actuators. This model can expand the capability and design of novel morphing actuators for a designed deformation profile for use in soft robotics.

opencc-zeroNov 2023View details →

Interests, beliefs, experience, and perceptions shape tolerance towards impacts of recovering predators

<ol> <li>The modification of landscapes is increasing the interface between humans and wildlife, while conflicts concerning predator impacts on human activities persist. Some previously persecuted but now protected predator species are experiencing recovery and range expansion.</li> <li>Tolerance is considered essential for achieving coexistence between humans and wildlife; however, its conceptualisation remains unresolved. Little is known about tolerance in the context of recovering predators, particularly which drivers are relevant to all or specific species and human interests.</li> <li>Using an online questionnaire survey shared with members of organisations with interests in rural land-based activities, we collected data on interests and beliefs, and attitudes, perceptions, experience, and management preferences for six recovering vertebrate predators in the UK (n=819). We created a species tolerance score representing the management choices of the respondents in different conflict scenarios, which differed in the degree of impact on the predator population.</li> <li>Our species tolerance score was characterized by a complex combination of the interests and beliefs of the respondents about wildlife management, perceptions and experience of that species (perceived benefits, population trend, positive and negative experience, indirect negative experience) and negative experience of other recovering predators. </li> <li>We found a tolerance gradient between interest groups with notable overlap between groups with primary interests in wildlife conservation, shooting, farming, and fishing. Although higher perceived benefits consistently corresponded to higher tolerance, having a negative experience of the species dampened the effect of perceived benefits on tolerance. When both negative personal and indirect experiences were reported, tolerance was dramatically reduced. The classification of species from least to most tolerated was consistent between interest groups. </li> <li>The application of our species tolerance score as the normative dimension (i.e., acceptability) in Brenner and Metcalf's (2020) Social Tolerance of Wildlife Framework highlights that tolerance (negative attitude-high acceptability) is potentially rare and more positive attitudes must be achieved before acceptance of the impacts of species can increase. </li> <li>Our findings highlight that considering only primary interests may hinder debates concerning recovering predators. Strategies to reduce negative experiences or change how they are perceived could significantly increase tolerance in combination with increasing positive experiences.</li> </ol>