Find research datasets worth reusing

opencc-by-4.0Sep 2021View details →

A novel big data mining framework for reconstructing large-scale daily MAIAC AOD across China from 2000 to 2020

This dataset contains the mean reconstructed MAIAC AOD and mean percentage of coverage of reconstructed MAIAC AOD across China from 2000 to 2020.

opencc-by-4.0Sep 2021View details →

Experimental data for "A Novel Clinical-Driven Design for Robotic Hand Rehabilitation: Combining Sensory Training, Effortless Setup and Large Range of Motion in a Palmar Device"

Experimental data for the interaction force benchmark test of the PRIDE haptic hand rehabilitation device.

opencc-zeroOct 2021View details →

Trait-habitat associations explain novel bird assemblages mixing native and alien species across New-Zealand landscapes

Aim: Species introductions have reshaped island faunas for the last 200 years, often threatening native biodiversity. Approximately equal numbers of native and alien species currently co-occur in the New Zealand avifauna, but they show distinct habitat use. Antagonistic interactions, habitat affinities and legacies of introduction history may concur to explain their segregation along habitat gradients. To investigate these processes, we explored how habitat, ecological traits and introduction history relate with the current composition of bird assemblages. Location: New Zealand Taxon: Birds Methods: We analysed 917 bird point counts spread along habitat and elevation gradients in the Canterbury region, South Island, and related 10 ecological traits to landscape composition using a three-table ordination method known as 'RLQ analysis', accounting for spatial autocorrelation and phylogeny. We tested whether alien species' positions in the RLQ were related to proxies of introduction history. Results: Eighteen endemic, 11 native and 19 alien species were distributed along a gradient from forest to open-habitat assemblages, in relation to foraging mode, nesting site and body size. A second gradient segregated species between native and exotic forests according to territoriality, sedentarity and diet. Traits accounted for the separation of native and alien bird species in forests, but not in open habitats. Phylogenetic signals emerged from the separation of native and alien species by forest type, and spatial structures suggested a landscape-level, rather than regional or local determinism. These correlations were independent of introduction history, although open-habitat assemblages tended to host alien species introduced later in time. Main conclusions: Habitat type and resource availability explain the spatial partitioning of New Zealand bird assemblages between native and alien species more consistently than competitive exclusion. We conclude that trait-mediated ecological differences among species have likely played a predominant role in species' segregation among landscapes, while maintaining endemic bird assemblages in native forests.

opencc-by-4.0Nov 2018View details →

Novel and Disappearing Climates 2050 SRES A2

This dataset contains two metrics for climate change exposure using downscaled climate projections with the SRES A2 emissions scenario (Tabor and Williams, 2007).The metrics represent dissimilarity measurements of the squared Euclidean distance between seasonal (June–August and December–February) temperature and precipitation variables in the 20th century climate and mid-21st century climate. (1) disappearing climate risk -  measure of dissimilarity between a pixel’s late 20th century climate and its closest matching pixel in the global set of 21st-century climates  (2) novel climate risk - measure of dissimilarity between a pixel’s future climate and its closest matching pixel in the global set of late 20th-century climates. The data are in arcASCII format. All data are in units of standard Euclidean distance and multiplied by 1000. This is the original data. To scale the data similar to Tabor et al. (2018), remove outliers above the 99th percentile distribution before rescaling from 0-1.  Unprojected  number of columns 2160 number of rows 857 Lower Left X Center -179.917 Lower Left Y Center -59.084 Cell size 0.166667 decimal degrees (10 minutes or ~17 km)

opencc-zeroOct 2022View details →

Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish

The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra, Astyanax mexicanus, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations of A. mexicanus have independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use of A. mexicanus has led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application of A. mexicanus. The optimization of husbandry protocols that maximize high-nutrient feed, smaller tank densities, and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high-protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of A. mexicanus as a genetic model.

opencc-by-4.0Oct 2022View details →

Data in support to the manuscript: Testing a novel sensor design to jointly measure cosmic-ray neutrons, muons and gamma rays for non-invasive soil moisture estimation by Gianessi et al. (2024)

The files contain data presented and discussed in the manuscript: Testing a novel sensor design to jointly measure cosmic-ray neutrons, muons and gamma rays for non-invasive soil moisture estimation by Gianessi et al. (2024). <div> <div>Gianessi, Stefano, Matteo Polo, Luca Stevanato, Marcello Lunardon, Till Francke, Sascha E. Oswald, Hami Said Ahmed, et al. “Testing a Novel Sensor Design to Jointly Measure Cosmic-Ray Neutrons, Muons and Gamma Rays for Non-Invasive Soil Moisture Estimation.” Geoscientific Instrumentation, Methods and Data Systems 13, no. 1 (January 16, 2024): 9–25. <a href="https://doi.org/10.5194/gi-13-9-2024">https://doi.org/10.5194/gi-13-9-2024</a>.</div> </div>

opencc-zeroNov 2022View details →

Data for: Whole Animal Feed FLat (WAFFL): A complete and comprehensive validation of a novel high-throughput fly experimentation system

Non-mammalian model organisms have been essential for our understanding of the mechanisms that control development, disease, and physiology, but they are underutilized in pharmacological and toxicological phenotypic screening assays due to their low throughput in comparison with cell-based screens. To increase the utility of using Drosophila melanogaster in screening, we designed the Whole Animal Feeding FLat (WAFFL), a novel, flexible, and complete system for feeding, monitoring, and assaying flies in a high-throughput format. Our 3-D printed system is compatible with inexpensive and readily available, commercial 96-well plate consumables and equipment. Experimenters can change the diet at will during the experiment and video record for behavior analysis, enabling precise dosing, measurement of feeding, and analysis of behavior in 96-well plate format.

opencc-zeroNov 2022View details →

Severe environmental conditions create severe conflicts? A novel ecological pathway to extreme coyote attacks on humans

1) Identifying the circumstances and causes of carnivore attacks on humans is important for prevention of future incidents as well as employing effective wildlife management strategies. Cape Breton Highlands National Park (CBHNP) in Nova Scotia has experienced multiple attacks by coyotes (Canis latrans) on humans, including a fatal attack on an adult in 2009. 2) Here we use a combination of data on space use and diet collected from 2011–2013 to reveal that limited resources and a reliance on a large ungulate (moose, Alces americanus) as the mechanism leading to aggression by coyotes in CBHNP. 3) Resident coyotes exhibited large home range sizes (mean=77.5 km2) indicative of limited resources and spatiotemporal avoidance of human activity. Carbon (d13C) and nitrogen (d15N) isotope values of sub-sampled coyote whiskers (n=32), which provide a longitudinal record of diet over the months before collection, revealed little intra- and inter-individual variation with nearly all individuals specializing on moose, a pattern that agrees with indices of natural resource availability. Specifically, stable isotope mixing models show that moose was the most important prey for most coyotes (25/32), representing between 41% and 78% of dietary inputs. Only four coyotes exhibited use of anthropogenic resources (food), and only one of seven coyotes involved in attacks on people had been consuming human foods before the attacks. 4) Synthesis and Applications: We have described a unique ecological system in which a generalist carnivore has expanded its niche to specialize on a large prey species, with the unfortunate consequence of also expanding pathways to conflicts with people. Our results suggest extreme unprovoked predatory attacks by coyotes on people are likely to be quite rare and associated with unique ecological characteristics. Extreme management actions such as bounties are unnecessary, but managers may need to employ hazing or lethal removal earlier in the conflict process than under normal circumstances. Also, users of these areas should be made aware of the risks coyotes pose and encouraged to take precautions.

opencc-by-4.0Dec 2022View details →

Expanding the host-range of functional metagenomics reveals resistance threats to novel antibiotics

Expanding the host-range of functional metagenomics reveals resistance threats to novel antibiotics. Sequences.

Normative behavioral data from the novel One Trail Trace escape reaction task (OTTER)

We designed a behavioral task where rats learn to associate two temporally distinct but close-in-time events by means of incidental one-trial learning. The task takes advantage of two competing motivations - to avoid light places and to avoid painful stimuli (foot shock) predicted by an acoustic signal. Motivation to avoid a bright light is constant throughout the experiment and is manifested by rats preferring a dark compartment in a light/dark shuttle box. Motivation to stay in the dark is overridden (1) during the training session: when foot-shock (US) (preceded by the acoustic stimulus (CS)) is presented; and (2) during the testing session: when CS, that predicts US, is presented. The latter case occurs when rats successfully form an association between CS and US in the training session and the rat escapes into the light compartment ('responders'). The rats that do not escape ('non-responders' appear to lack this memory as even non-specific fear response (freezing) was absent. Generally, >50% of rats escape into the lit compartments following CS on the testing day. Importantly, rats do not show a contextual association measured by freezing behavior and preference for a light compartment on the testing day. Moreover, we observed that several putative details in the setup affect the probability of the successful formation of a one-trial trace association. Compared to similar tasks, the OTTER task tests incidental learning with no requirement for pre-training. Moreover, the memory formed in the OTTER task consists of two events that do not overlap in time: a characteristic of many episodic memories. The OTTER task presents high-throughput means to study neuronal substrates of incidental temporal binding.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders and are not optimized for the RTA clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41,845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

opencc-zeroJan 2023View details →

A novel camera trapping method for individually identifying pumas by facial features

Camera traps (CTs), used in conjunction with capture-mark-recapture analyses (CMR; photo-CMR), are a valuable tool for estimating abundances of rare and elusive wildlife. However, a critical requirement of photo-CMR is that individuals are identifiable in CT images (photo-ID). Thus, photo-CMR is generally limited to species with conspicuous pelage patterns (e.g., stripes or spots) using lateral-view images from CTs stationed along travel paths. Pumas (Puma concolor) are an elusive species for which CTs are highly effective at collecting image data, but their suitability to photo-ID is controversial due to their lack of pelage markings. For a wide range of taxa, facial features are useful for photo-ID, but this method has generally been limited to images collected with traditional handheld cameras. Here we evaluate the feasibility of using puma facial features for photo-ID in a CT framework. We consider two issues: 1) the ability to capture puma facial images using CTs, and 2) whether facial images improve human ability to photo-ID pumas. We tested a novel CT accessory that used light and sound to attract the attention of pumas, thereby collecting face images for use in photo-ID. Face captures rates increased at CTs that included the accessory (n = 208, χ2 = 43.23, P ≤ 0.001). To evaluate if puma faces improve photo-ID, we measured the inter-rater agreement of 5 independent assessments of photo-ID for 16 of our puma face capture events. Agreement was moderate to good (Fleiss' kappa = 0.54, 95% CI = 0.48–0.60), and was 92.90% greater than a previously published kappa using conventional CT methods. This study is the first time such a technique has been used for photo-ID, and we believe a promising demonstration of how photo-ID may be feasible for an elusive but unmarked species.

opencc-by-4.0Jan 2023View details →

Solution, Crystal and in-Silico Structures of the Organometallic Vitamin B12-Derivative Acetylcobalamin and of its Novel Rhodium-Analogue Acetylrhodibalamin

Cartesian coordinates of all calculated structures discussed in the paper.

opencc-by-4.0Dec 2021View details →

Artifact for "MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software"

This artifact is for the paper entitled “MAAT: A Novel Ensemble Approach to Addressing Fairness and Performance Bugs for Machine Learning Software”, which is accepted by ESEC/FSE 2022. MAAT is a novel ensemble approach to improving the fairness-performance trade-off for ML software. It outperforms state-of-the-art bias mitigation methods. The artifact has also been placed on GitHub (https://github.com/chenzhenpeng18/FSE22-MAAT) under the Apache License, publicly accessible to other researchers. In this artifact, we provide the source code of MAAT and other existing bias mitigation methods that we use in our study, as well as the intermediate results, the installation instructions, and a replication guideline (included in the README). The replication guideline provides detailed steps to replicate all the results for all the research questions.

On the fast track: Hybrids adapt more rapidly than parental populations in a novel environment

Rates of hybridization are predicted to increase due to climate change and human activity that cause redistribution of species and bring previously isolated populations into contact. At the same time, climate change leads to rapid changes in the environment, requiring populations to adapt rapidly in order to survive. A few empirical cases suggest hybridization can facilitate adaptation despite its potential for incompatibilities and deleterious fitness consequences. Here we use simulations and Fisher's Geometric model to evaluate the conditions and time frame of adaptation via hybridization in both diploids and haplodiploids. We find that hybrids adapt faster to new environments compared to parental populations in nearly all simulated scenarios, generating a fitness advantage that can offset intrinsic incompatibilities and last for tens of generations, regardless of whether the population was diploid or haplodiploid. Our results highlight the creative role of hybridization and suggest that hybridization may help contemporary populations adapt to the changing climate. However, adaptation by hybrids may well happen at the cost of reduced biodiversity, if previously isolated lineages collapse into one.

opencc-by-4.0Jan 2023View details →

DATASET: Water Phantom Characterization of a Novel Optical Fiber Sensor for LDR Brachytherapy

Dataset for the journal article "Water Phantom Characterization of a Novel Optical Fiber Sensor for LDR Brachytherapy"

opencc-zeroFeb 2023View details →

Biomass potential via light interception of novel miscanthus hybrids from field trials

New biomass crop hybrids for bioeconomic expansion require yield projections to determine their potential for strategic land use planning in the face of global challenges. Our biomass growth simulation incorporates radiation interception and conversion efficiency. Models often use leaf area to predict interception which is demanding to determine accurately, so instead, we use low-cost rapid light interception measurements using a simple lab-made line ceptometer and relate the dynamics of canopy closure to thermal time, and to measurements of biomass. We apply the model to project the European biomass potentials of new market-ready hybrids for 2020–30. Field measurements are easier to collect, the calibration is seasonally dynamic and reduces influence of weather variation between field sites. The model obtained is conservative, being calibrated by crops of varying establishment and varying maturity on less productive (marginal) land. This results in conservative projections of miscanthus hybrids for 2020-30 based on 10% land use conversion of the least (productive) grassland and arable for farm diversification, which show a European potential of 80.7–89.7 Mt y-1 biomass, with potential for 1.2-1.3 EJ y-1 energy and 36.3–40.3 Mt y-1 carbon capture, with seeded M. sacchariflorus x sinensis displaying highest yield potential. Simulated biomass projections must be viewed in light of the field measurements on less productive land with high soil water deficits. We are attempting to model results from an ambitious and novel project combining new hybrids across Europe with agronomy which has not been perfected on less productive sites. Nevertheless, at a time of energy sourcing issues, seed-propagated miscanthus hybrids for the upscaled provision of bioenergy offer an alternative source of renewable energy. If European countries provide incentives for growers to invest, seeded hybrids can improve product availability and biomass yields over the current commercial miscanthus variety.

openmit-licenseJul 2018View details →

EuroSAT: A Novel Dataset and Deep Learning Benchmark for Land Use and Land Cover Classification

EuroSAT is a land use and land cover classification dataset. The dataset is based on Sentinel-2 satellite imagery covering 13 spectral bands and consists of 10 LULC classes with a total of 27,000 labeled and geo-referenced images. The dataset is associated with the publications "<a href="https://ieeexplore.ieee.org/abstract/document/8519248">Introducing EuroSAT: A Novel Dataset and Deep Learning Benchmark for Land Use and Land Cover Classification</a>" and "<a href="https://ieeexplore.ieee.org/abstract/document/8736785">EuroSAT: A Novel Dataset and Deep Learning Benchmark for Land Use and Land Cover Classification</a>". EuroSAT_RGB.zip contains the RGB version of the dataset, which includes the optical R, G and B frequency bands encoded as JPEG images. EuroSAT_MS.zip contains the multi-spectral version of the EuroSAT dataset, which includes all 13 Sentinel-2 bands in the original value range.

opencc-zeroMar 2023View details →

Seed limitation interacts with biotic and abiotic factors to constrain novel species' impact on community biomass and richness

Seed limitation can narrow down the number of coexisting plant species, limit plant community productivity, and can also constrain community responses to changing environmental and biotic conditions. In a 10-year full-factorial experiment of seed addition, fertilisation, warming, and herbivore exclusion, we tested how seed addition alters community richness and biomass, and how its effects depend on seed origin and biotic and abiotic context. We found that seed addition increased species richness in all treatments, and increased plant community biomass depending on nutrient addition and warming. Novel species, originally absent from the communities, increased biomass the most, especially in fertilised plots and in the absence of herbivores, while adding seeds of local species did not affect biomass. Our results show that seed limitation constrains both community richness and biomass, and highlight the importance of considering trophic interactions and soil nutrients when assessing novel species immigrations and their effects on community biomass.

Phylogenomics of novel ploeotid taxa contribute to the backbone of the euglenid tree

Euglenids are a diverse group of flagellates that inhabit most environments and exhibit many different nutritional modes. The most prominent euglenids are phototrophs, but phagotrophs constitute the majority of phylogenetic diversity of euglenids. They are pivotal to our understanding of euglenid evolution, yet we are only starting to understand relationships amongst phagotrophs, with the backbone of the tree being the most elusive. Ploeotids make up most of this backbone diversity—yet despite their morphological similarities, SSU rDNA analyses and multigene analyses show they are non-monophyletic. As more ploeotid diversity is sampled, known taxa have coalesced into some subgroups (e.g. Alistosa), but the relationships between these are not always supported and some taxa remain unsampled for multigene phylogenetics. Here, we used light microscopy and single-cell transcriptomics to characterize five ploeotid euglenids and place them into a multigene phylogenetic framework. Our analyses place Decastava in Alistosa; while Hemiolia branches with Liburna, establishing the novel clade Karavia. We describe Hemiolia limna, a freshwater-dwelling species in an otherwise marine clade. Intriguingly, two undescribed ploeotids are found to occupy pivotal positions in the tree: Chelandium granulatum nov. gen. nov. sp. branches as sister to Olkasia, and Gaulosia striata nov. gen. nov. sp. remains an orphan taxon.