Find research datasets worth reusing

opencc-by-4.0Mar 2020View details →

Data set for all Bifurcation diagrams of 'Two-dimensional patterns in dip coating - first steps on the continuation path'

Data set for all bifurcation diagrams of  'Two-dimensional patterns in dip coating - first steps on the continuation path' by Phong-Minh Timmy Ly, Kevin David Joachim Mitas, Uwe Thiele, Svetlana V. Gurevich published as Physica D 409, 132485 (2020).  DOI: <a href="http://doi.org/10.1016/j.physd.2020.132485">10.1016/j.physd.2020.132485</a> Specifically: Figures 1, 2, 5, 6 and 7

opencc-zeroAug 2020View details →

Data from: Incorporating alternative interaction modes, forbidden links and trait-based mechanisms increases the minimum trait dimensionality of ecological networks

<ol> <li>Individual-level traits mediate interaction outcomes and community structure. It is important, therefore, to identify the minimum number of traits that characterise ecological networks, i.e. their 'minimum dimensionality'. Existing methods for estimating minimum dimensionality often lack three features associated with increased trait numbers: alternative interaction modes (e.g. feeding strategies such as active vs. sit-and-wait feeding), trait-mediated 'forbidden links' and a mechanistic description of interactions. Omitting these features can underestimate the trait numbers involved, and therefore, minimum dimensionality. We develop a 'minimum mechanistic dimensionality' measure, accounting for these three features.</li> <li>The only input our method requires is the network of interaction outcomes. We assume how traits are mechanistically involved in alternative interaction modes. These unidentified traits are contrasted using pairwise performance inequalities between interacting species. For example, if a predator feeds upon a prey species via a typical predation mode, in each step of the predation sequence the predator's performance must be greater than the prey's. We construct a system of inequalities from all observed outcomes, which we attempt to solve with mixed integer linear programming. The number of traits required for a feasible system of inequalities provides our minimum dimensionality estimate.</li> <li>We applied our method to 658 published empirical ecological networks including primary consumption, predator–prey, parasitism, pollination, seed dispersal and animal dominance networks, to compare with minimum dimensionality estimates when the three focal features are missing. Minimum dimensionality was typically higher when including alternative interaction modes (54% of empirical networks), 'forbidden interactions' as trait-mediated interaction outcomes (92%), or a mechanistic perspective (81%), compared to estimates missing these features. Additionally, we tested minimum dimensionality estimates on simulated networks with known dimensionality. Our method typically estimated a higher minimum dimensionality, closer to the actual dimensionality, while avoiding the overestimation associated with a previous method.</li> <li>Our method can reduce the risk of omitting traits involved in different interaction modes, in failure outcomes, or mechanistically. More accurate estimates will allow us to parameterise models of theoretical networks with more realistic structure at the interaction outcome level. Thus, we hope our method can improve predictions of community structure and structure-dependent dynamics.</li> </ol>

opencc-zeroSep 2020View details →

Three dimensional dataset combining gait and full body movement of children with autism spectrum disorders collected by Kinect v2 camera

To the best of our knowledge, this is the maiden attempt to build a three-dimensional dataset that combines gait and body movement analysis of children with Autism Spectrum Disorders (ASD) in controlled environments for fifty children with autism children and fifty typical children. A 3D dataset includes 3D joints positions, the corresponding skeleton movement video, joints trajectories video captured by Kinect v2, and color videos captured by Samsung Note 9 rear camera. On the other hand, color videos for 9 children suffer from severe autism is also included for scientific benefit. Finally, the dataset includes 700 folders (350 for typical children, 350 for children with ASD) which include 3D files of tracked joints, angles between joints, and skeleton tracking video related to the augmentation of the original dataset based on seven transformations described in the paper.

opencc-by-4.0Sep 2020View details →

Three-dimensional reconstructed canopies of apple cultivars grafted on different interstocks

Canopy architecture is important for a range of orchard ecosystem processes, including radiation interception and distribution within canopy, flowering, carbon assimilation, fruit yield and quality and pest and pathogen attacks in fruit trees. The canopy of fruit tree varies greatly from cultivar to cultivar, and can be manipulated by horticultural practices, such as rootstock, pruning, training etc. We collected canopy architectural data in ‘Fuji’ and ‘Gala’ apple cultivars which were grafted onto two rootstock/interstock combinations: M. micromalus/M. domestica cv. ‘Qinguan’, a vigorous interstock and M. micromalus/M26, a dwarf interstock. Allometric relationships at leaf and shoot scale were determined for all shoot types before harvests in 2011 and 2012, including bourse, bourse short shoot, bourse long shoot, vegetative short shoot, and vegetative long shoot. A dataset of 4351 records of leaf Euler angles were digitized for all shoot types. For 19 trees, their 3D distribution of the foliage within canopy was reconstructed by combining both the spatial locations of shoots (as measured from 3D digitizing) and foliage reconstruction based on allometric relationships and leaf angle distributions. We believe this dataset is a valuable resource for studies and models that require leaf angles and detailed 3D virtual canopies.

opencc-zeroOct 2020View details →

Dental molds from: Three-dimensional dental topography and feeding ecology in the extinct cave bear

The cave bear (Ursus spelaeus s.l.) is an iconic extinct bear that inhabited the Pleistocene of Eurasia whose extinction causes are controversial. To identify the actual causes of the cave bear extinction, it is crucial to understand their feeding preferences. Here, we quantify shape descriptor metrics (DNE, RFI and OPCR) in three dimensional (3D) models of cave bear upper teeth (P4-M2) to make inferences on its controversial feeding behaviour. We use a comparative sample including representatives of all living bear species with known diets as a template. Our topographic analyses evidence that the complexity of upper tooth rows in living bears is more associated with the mechanical properties of the items consumed than with the type of food. Cave bears exhibit intermediate values on topographic metrics between those exhibited by the bamboo-feeder giant panda (Ailuropoda melanoleuca) and those taken by specialists in hard-mast consumption (Ursus arctos and Ursus thibetanus). The crown topography of cave bear upper teeth suggests a high efficiency to chew on tough vegetal resources of lower-quality, and no living bear is currently exploiting it. Our results align with a climatic-driven hypothesis to explain demise in cave bear populations during the late Pleistocene.

opencc-by-4.0Dec 2020View details →

Data and code for comparison of different machine learning methods and dimensionality reduction for classification astrocytoma and glioblastoma tissues by mass spectra

This upload contains all replication material for "Comparison of different machine learning methods and dimensionality reduction for classification astrocytoma and glioblastoma tissues by mass spectra" (forthcoming). Authors: E.S. Zhvansky, A.A. Sorokin, V.A. Shurkhay, V.A. Eliferov, D.S. Bormotov, D.G. Ivanov, D.S. Zavorotnyuk, A.A. Potapov. Code and data are located within data_and_code.zip. Code is written in Python 3.7.7 using Jupyter Notebook, MATLAB R2019b, and Python 3.5.2. Please find the readme.txt for code using and the code to replicate the main findings of the paper described below: <ul> <li>venn_diagramm.py for Venn diagram figures.</li> <li>SSM.m for SSM calculation and visualization.</li> <li>DR_ML.ipynb for dimensionality reduction and machine learning algorithms comparing on the datasets.</li> </ul>

opencc-zeroDec 2020View details →

Multi-dimensional biodiversity hotspots and the future of taxonomic, ecological, and phylogenetic diversity: a case study of North American rodents

Aim: We investigate geographic patterns across taxonomic, ecological, and phylogenetic diversity to test for spatial (in)congruency and identify aggregate diversity hotspots in relation to present land-use and future climate. Simulating extinctions of imperiled species, we demonstrate where losses across diversity dimensions and geography are predicted. Location: North America Time period: Present-day, future Major taxa studied: Rodentia Methods: Using geographic range maps for rodent species, we quantified spatial patterns for eleven dimensions of diversity: taxonomic (species, range-weighted), ecological (body size, diet, habitat), phylogenetic (mean, variance, and nearest-neighbor patristic distances, phylogenetic distance, genus-to-species ratio) and phyloendemism. We tested for correlations across dimensions and used spatial residual analyses to illustrate regions of pronounced diversity. We aggregated diversity hotspots in relation to land-use and climate-change predictions and recalculated metrics following extinctions of IUCN-listed imperiled species. Results: Topographically-complex western North America hosts high diversity across multiple dimensions: phyloendemism and ecological diversity exceed predictions based on taxonomic richness and phylogenetic variance patterns indicate steep gradients in phylogenetic turnover. While an aggregate diversity hotspot emerges in the west, spatial incongruence exists across diversity dimensions at the continental scale. Notably, phylogenetic metrics are uncorrelated with ecological diversity. Diversity hotspots overlap with land-use and climate change, and extinctions predicted by IUCN status are unevenly distributed across space, phylogeny, or ecological groups. Main conclusions: Comparison of taxonomic, ecological, and phylogenetic diversity patterns for North American rodents clearly shows the multifaceted nature of biodiversity. Testing for geographic patterns and (in)congruency across dimensions of diversity facilitates investigation into underlying ecological and evolutionary processes. The geographic scope of this analysis suggests that several explicit regional challenges face North American rodent fauna in the future. Simultaneous consideration of multidimensional biodiversity allows us to assess what critical functions or evolutionary history we might lose with future extinctions and maximize the potential of our conservation efforts.

opencc-by-4.0Dec 2020View details →

Flow through a submerged canopy partially covering the bed: spatial flow pattern, multi-dimensional vortices and junction momentum exchange

The dataset (including videos) are uploaded to support the research study Flow through a submerged canopy partially covering the bed: spatial flow pattern, multi-dimensional vortices and junction momentum exchange (submitted to Water Resources Research)

opencc-zeroDec 2020View details →

Data from: A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian saber-tooth

Morphological convergence can be assessed through a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here we introduce a new method to chart patterns of convergence on three-dimensional models, deployed with the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well-known case study, the saber-tooth morphotype which has evolved independently among distinct mammalian clades, from placentals to metatherians. Although previous authors have concluded that saber-tooths kill using a stabbing 'bite' to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the saber-tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among saber-tooths than for any other taxa. We found that the morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence implies similarity in function among these phylogenetically distant species. In our view this function is most likely the killing of relatively large prey by a stabbing bite.

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-8 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-6 week

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-control group

Datasets for "Insight into ductular reaction in obstructive biliary disease from a three-dimensional perspective using ex vivo X-ray phase contrast computed tomography"

Phase-contrast CT of BDL rats liver-4 week

opencc-zeroDec 2013View details →

Data from: A method for analysis of phenotypic change for phenotypes described by high-dimensional data

The analysis of phenotypic change is important for several evolutionary biology disciplines, including phenotypic plasticity, evolutionary developmental biology, morphological evolution, physiological evolution, evolutionary ecology and behavioral evolution. It is common for researchers in these disciplines to work with multivariate phenotypic data. When phenotypic variables exceed the number of research subjects—data called 'high-dimensional data'—researchers are confronted with analytical challenges. Parametric tests that require high observation to variable ratios present a paradox for researchers, as eliminating variables potentially reduces effect sizes for comparative analyses, yet test statistics require more observations than variables. This problem is exacerbated with data that describe 'multidimensional' phenotypes, whereby a description of phenotype requires high-dimensional data. For example, landmark-based geometric morphometric data use the Cartesian coordinates of (potentially) many anatomical landmarks to describe organismal shape. Collectively such shape variables describe organism shape, although the analysis of each variable, independently, offers little benefit for addressing biological questions. Here we present a nonparametric method of evaluating effect size that is not constrained by the number of phenotypic variables, and motivate its use with example analyses of phenotypic change using geometric morphometric data. Our examples contrast different characterizations of body shape for a desert fish species, associated with measuring and comparing sexual dimorphism between two populations. We demonstrate that using more phenotypic variables can increase effect sizes, and allow for stronger inferences.

opencc-zeroDec 2014View details →

Data from: Computed tomography, anatomical description and three-dimensional reconstruction of the lower jaw of Eusthenopteron foordi Whiteaves, 1881 from the Upper Devonian of Canada

The cranial anatomy of the iconic early tetrapod Eusthenopteron foordi is probably the best understood of all fossil fishes. In contrast, the anatomy of the lower jaw – crucial for both phylogenetics and biomechanical analyses – has been only superficially described. Computed tomography data of three Eusthenopteron skulls were segmented using visualization software to digitally separate bone from matrix and individual bones from each other. Here, we present a new description of the lower jaw of Eusthenopteron based on microcomputed tomography data, including the following: detailed description of sutural morphology and the mandibular symphysis; confirmed occurrence of pre- and intercoronoid fossae on the dorsal aspect of the lower jaw; and the arrangement of the submandibular bones. Furthermore, we identify a novel dermal ossification, the postsymphysial, present on the anteromedial aspect of the lower jaw in Eusthenopteron and describe its distribution in other stem tetrapod taxa. Sutural morphology is used to infer load regimes and, along with overall skull and lower jaw morphology, suggests that Eusthenopteron may have used biting along with suction feeding to capture and consume large prey. Finally, visualization software was used to repair and reconstruct the lower jaw, resulting in a three-dimensional digital reconstruction.

opencc-zeroDec 2012View details →

Data from: Taphonomy of the Ediacaran fossil Pteridinium simplex preserved three-dimensionally in mass flow deposits, Nama Group, Namibia

Ediacara-type fossils are found in a diverse array of preservational styles, implying that multiple taphonomic mechanisms might have been responsible for their preservational expression. For many Ediacara fossils, the "death mask" model has been invoked as the primary taphonomic pathway. The key to this preservational regime is the replication or sealing of sediments around the degrading organisms by microbially induced precipitation of authigenic pyrite, leading toward fossil preservation along bedding planes. Nama-style preservation, on the other hand, captures Ediacaran organisms as molds and three-dimensional casts within coarse-grained mass flow beds, and has been previously regarded as showing little or no evidence of a microbial preservational influence. To further understand these two seemingly distinct taphonomic pathways, we investigated the three-dimensionally preserved Ediacaran fossil Pteridinium simplex from mass flow deposits of the upper Kliphoek Member, Dabis Formation, Kuibis Subgroup, southern Namibia. Our analysis, using a combination of petrographic and micro-analytical methods, shows that Pteridinium simplex vanes are replicated with minor pyrite, but are most often represented by open voids that can be filled with secondary carbonate material; clay minerals are also found in association with the vanes, but their origin remains unresolved. The scarcity of pyrite and the development of voids are likely related to oxidative weathering and it is possible that microbial activities and authigenic pyrite may have contributed to the preservation of Pteridinium simplex; however, any microbes growing on P. simplex vanes within mass flow deposits were unlikely to have formed thick mats as envisioned in the death mask model. Differential weathering of replicating minerals and precipitation of secondary minerals greatly facilitate fossil collection and morphological characterization by allowing Pteridinium simplex vanes to be parted from the massive hosting sandstone.

opencc-zeroDec 2012View details →

Data from: Short-term disturbance by a commercial two-dimensional seismic survey does not lead to long-term displacement of harbour porpoises

Assessments of the impact of offshore energy developments are constrained because it is not known whether fine-scale behavioral responses to noise lead to broader-scale displacement of protected small cetaceans. We used passive acoustic monitoring and digital aerial surveys to study changes in the occurrence of harbour porpoises across a 2000 km2 study area during a commercial 2-D seismic survey in the North Sea. Acoustic and visual data provided evidence of group responses to air-gun noise from the 470 cu inch array over ranges of 5-10 km, at received peak-to-peak sound pressure levels of 165-172 dB re 1 µPa and sound exposure levels of 145-151 dB re. 1µPa2 s. However, animals were typically detected again at affected sites within a few hours, and the level of response declined through the 10 day survey. Overall, acoustic detections decreased significantly during the survey period in the impact area compared to a control area, but this effect was small in relation to natural variation. These results demonstrate that prolonged seismic survey noise did not lead to broader-scale displacement into sub-optimal or higher-risk habitats, and suggest that impact assessments should focus on sub-lethal effects resulting from changes in foraging performance of animals within affected sites.

opencc-zeroDec 2016View details →

Data from: Intraspecific variation in cephalopod conchs changes during ontogeny: perspectives from three-dimensional morphometry of Nautilus pompilius

Intraspecific variation of organisms is of great importance to correctly carry out taxonomic work, which is a prerequisite for important disciplines in paleontology such as community paleoecology, biostratigraphy, and biogeography. However, intraspecific variation is rarely studied in ectocochleate cephalopods (ammonoids and nautiloids), in which an excessive number of taxa were established during the past centuries. Since intraspecific variation of fossilized organisms suffers from various biases (time averaging and taphonomy), an extant example is needed for actualistic comparison. We applied 3D morphometry to 93 specimens of Nautilus pompilius from three different geographic populations. This dataset was used to examine the intraspecific variation throughout ontogeny in detail. Although there are slight differences between the populations as well as some measurement biases, a common pattern of intraspecific variation appears to be present. High variation appears early in ontogeny and then decreases gradually in the following ontogenetic stages. Subsequently, the variation shows an increase again before maturity until a sharp increase or decrease occurs towards the end of ontogeny. Comparison with intraspecific variation of ammonoids and belemnites illustrated that some groups have ontogenetic patterns of intraspecific variation, which are similar to that of N. pompilius. This implies that the above-mentioned ontogenetic pattern of intraspecific variation might be common in some major cephalopod clades.

opencc-zeroDec 2015View details →

Data from: Disentangling visual and olfactory signals in mushroom-mimicking Dracula orchids using realistic three-dimensional printed flowers

Flowers use olfactory and visual signals to communicate with pollinators. Disentangling the relative contributions and potential synergies between signals remains a challenge. Understanding the perceptual biases exploited by floral mimicry illuminates the evolution of these signals. Here, we disentangle the olfactory and visual components of Dracula lafleurii, which mimics mushrooms in size, shape, color and scent, and is pollinated by mushroom-associated flies. To decouple signals, we used three-dimensional printing to produce realistic artificial flower molds that were color matched and cast using scent-free surgical silicone, to which we could add scent. We used GC-MS to measure scents in co-occurring mushrooms, and related orchids, and used these scents in field experiments. By combining silicone flower parts with real floral organs, we created chimeras that identified the mushroom-like labellum as a source of volatile attraction. In addition, we showed remarkable overlap in the volatile chemistry between D. lafleurii and co-occurring mushrooms. The characters defining the genus Dracula – a mushroom-like, 'gilled' labellum and a showy, patterned calyx – enhance pollinator attraction by exploiting the visual and chemosensory perceptual biases of drosophilid flies. Our techniques for the manipulation of complex traits in a nonmodel system not conducive to gene silencing or selective breeding are useful for other systems.