Find research datasets worth reusing

opencc-by-4.0Dec 2020View details →

Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite"

Dataset and Jupyter worksheet interpreting the (results from) small- and wide-angle scattering data from a series of boehmite/epoxy nanocomposites. Accompanies the publication "Competition of nanoparticle-induced mobilization and immobilization effects on segmental dynamics of an epoxy-based nanocomposite", by Paulina Szymoniak, Brian R. Pauw, Xintong Qu, and Andreas Schönhals. Datasets are in three-column ascii (processed and azimuthally averaged data) from a Xenocs NanoInXider SW instrument. Monte-Carlo analyses were performed using McSAS 1.3.1, other analyses are in the Python 3.7 worksheet. Graphics and result tables are output by the worksheet.

opencc-zeroDec 2020View details →

Data from: Maximum cardiac performance of Antarctic fishes that lack haemoglobin and myoglobin: exploring the effect of warming on nature's natural knockouts

Comparisons among related species provide valuable insight into the functional consequences of natural genetic mutations. We assessed cardiac function at ambient and elevated temperatures in Antarctic notothenioids with contrasting levels of the oxygen binding proteins, haemoglobin (Hb) and myoglobin (Mb), to elucidate changes in cardiac performance that may compensate for impaired O2 transport. Notothenia coriiceps (Hb+Mb+) at 1oC had the highest maximum cardiac work rate (WC) and pressure generating capacity, but lowest relative ventricular mass and maximum cardiac output (Q̇) when compared with two icefish species, Chionodraco rastrospinosus (Hb-Mb+) and Chaenocephalus aceratus (Hb-Mb-). Cardiomegaly associated with absence of Hb generated an exceptionally large maximum stroke volume (VS) and Q̇, but a lower WC. However, C. rastrospinosus had a larger ventricle, a higher intrinsic heart rate (fH), and greater maximum VS and Q̇ than C. aceratus, suggesting that cardiac Mb has functional relevance. Warming to 4oC increased fH, but only increased maximum Q̇ in icefishes, while maximum WC and pressure development increased in N. coriiceps (both ~2.5x that of C. aceratus). The Hb+Mb+ myocardium generated considerable Q̇ against raised afterload, unlike icefish hearts. The presence of Hb and Mb enhances cardiac performance, and likely resilience to near-future ocean warming.

opencc-zeroJan 2021View details →

Effects of plant hydraulic traits on the flammability of live fine canopy fuels in 62 Australian plant species

<ol> <li>Plant species vary in how they regulate moisture and this has implications for their flammability during wildfires. We explored how fuel moisture is shaped by variation within six hydraulic traits: saturated moisture content, cell wall rigidity, cell solute potential, symplastic water fraction and tissue capacitance.</li> <li>Using pressure-volume curves, we measured these hydraulic traits distal shoots (i.e. twigs + leaves) in 62 plant species across four wooded communities in south-eastern Australia. For a subset of 30 of those species, we also measured hydraulic traits of twigs using moisture-release curves. Moisture content of fine fuels was then estimated for circumstances typical of fire weather. These projections were made assuming that under the hot, dry, windy conditions typical of large wildfires, leaves and fine twigs would function at internal water pressures close to wilting point (i.e. turgor loss point, TLP). The effect of different moisture contents at TLP on ignition time was then modelled using a fully mechanistic, finite element model of biomass ignition based on standard principles of physical chemistry.</li> <li>We also measured predawn water potential, an indication of plant access to soil water that is influenced by root architecture. These data were used to model how root traits influence fuel moisture and ignition time.</li> </ol>

opencc-zeroJan 2022View details →

Data from: Telomere heritability and parental age at conception effects in a wild avian population

Individual variation in telomere length is predictive of health and mortality risk across a range of species. However, the relative influence of environmental and genetic variation on individual telomere length in wild populations remains poorly understood. Heritability of telomere length has primarily been calculated using parent–offspring regression which can be confounded by shared environments. To control for confounding variables, quantitative genetic 'animal models' can be used, but few studies have applied animal models in wild populations. Furthermore, parental age at conception may also influence offspring telomere length, but most studies have been cross-sectional. We investigated within- and between- parental age at conception effects and heritability of telomere length in the Seychelles warbler using measures from birds caught over 20 years and a multi-generational pedigree. We found a weak negative within-paternal age at conception effect (as fathers aged, their offspring had shorter telomeres) and a weak positive between-maternal age at conception effect (females that survived to older ages had offspring with longer telomeres). Animal models provided evidence that heritability and evolvability of telomere length was low in this population, and that variation in telomere length was not driven by early-life effects of hatch period or parental identities. qPCR plate had a large influence on telomere length variation and not accounting for it in the models would have underestimated heritability. Our study illustrates the need to include and account for technical variation in order to accurately estimate heritability, as well as other environmental effects, on telomere length in natural populations.

Raw Data related to Research Article: Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects, Optics Express, volume 29, issue 3, 2021

These are the plotted and raw data used to obtain figures shown in: P. Tiwari, P. Wen, D. Caimi, S. Mauthe, N. Vico Triviño, M. Sousa, and K. E. Moselund, Scaling of metal-clad InP nanodisk lasers: optical performance and thermal effects., Optics Express, volume 29, issue 3, 2021 Please comply with copyright rules of the Optical Society of America under the terms of the OSA Open Access Publishing Agreement.: https://www.osapublishing.org/library/license_v1.cfm#VOR-OA

opencc-by-4.0Dec 2020View details →

Data and material for the manuscript "Mutation testing and self/peer assessment: analyzing their effect on students in a software testing course"

This repository is composed of two different parts: <ul> <li><a href="https://zenodo.org/record/4464300/files/Assessment%20data%20and%20Mutation%20Scores.xlsx?download=1">Assessment data and Mutation Scores</a> file contains the student-generated data used in the experience.</li> <li><a href="https://zenodo.org/record/4464300/files/experience-material.zip?download=1">Experience-material</a> file contains the files to be able to reproduce the experience.</li> </ul>   The <a href="https://zenodo.org/record/4464300/files/experience-material.zip?download=1">Experience-material</a> file for the lab is used in two sessions: Session 1: Development and assessment of test suites In this session, the student has to develop a test suite for a program under test. At the end of the session, the test suite will be evaluated against a set of assessment criteria regarding the quality of the developed test suite. Files for this session: <ul> <li>VVS-Lab6-S1 pdf file , with the description of this session.</li> <li>Material-S1 zip file, with the files required to complete this session.</li> </ul> Session 2: Evaluation applying mutation testing with MuCPP In this session, the test cases designed in the first part of this lab will be evaluated based on the mutation adequacy criterion. This will be done by using the <a href="https://ucase.uca.es/mucpp/">MuCPP mutation tool</a>. Files for this session: <ul> <li>VVS-Lab6-S2 pdf file, with the description of this session.</li> <li>Material-S2 zip file, with the files required to complete this session.</li> </ul> The source code files family.[cpp|hpp] have been adapted from a listing in [1]. Note that, while considered to be fault free in this lab, these source files are used in other sessions where students are expected to detect some defects in them. [1] S. Wiener and L. J. Pinson, The C++ Workbook. USA: Addison-Wesley Longman Publishing Co., Inc., 1990.

opencc-by-4.0Nov 2020View details →

Effects of wind on honeybee and bumblebee foraging behaviour on multiple plant species

Dataset of results used for two publications. It shows the foraging behaviours of honeybees and bumblebees on multiple plant species in different wind speeds,

Silver Nanoparticles Alter Cell Viability Ex Vivo and in Vitro and Induce Proinflammatory Effects in Human Lung Fibroblasts

Dataset for data generated and presented in following article by Löfdahl et al in Nanomaterials 2020, 10, 1868. doi:10.3390/nano10091868

Detection of ultra-weak laser pulses by free-running single-photon detectors: modeling dead time and dark counts effects

In quantum communication systems, the precise estimation of the detector´s response to the incoming light is necessary to avoid security breaches. The typical working regime uses a free-running single-photon avalanche diode in combination with attenuated laser pulses at telecom wavelength for encoding information. We demonstrate the validity of an analytical model for this regime which considers the effects of dark counts and dead time on the measured count rate. For the purpose of gaining a better understanding of these effects, the photon detections were separated from the dark counts via a software-induced gating mechanism. The model was verified by experimental data for mean photon numbers covering three orders of magnitude as well as for laser repetition frequencies below and above the inverse dead time. Consequently, our model would be of interest for predicting the detector response not only in the field of quantum communications, but also in any other quantum physics experiment where high detection rates are needed.

GREENER Project official video: InteGRated systems for Effective ENvironmEntal Remediation

Find out more about the GREENER's goals and technologies applied, aiming to remediate a range of organic and inorganic pollutants of high concern, while producing useful end-products, such as bioelectricity and harmless metabolites.

opencc-zeroJun 2021View details →

Far-field effects of impulsive noise on coastal bottlenose dolphins

Increasing levels of anthropogenic underwater noise have caused concern over their potential impacts on marine life. Offshore renewable energy developments and seismic exploration can produce impulsive noise which is especially hazardous for marine mammals because it can induce auditory damage at shorter distances and behavioural disturbance at longer distances. However, far-field effects of impulsive noise remain poorly understood, causing a high level of uncertainty when predicting the impacts of offshore energy developments on marine mammal populations. Here we used a 10-year dataset on the occurrence of coastal bottlenose dolphins over the period 2009-2019 to investigate far-field effects of impulsive noise from offshore activities undertaken in three different years. Activities included a 2D seismic survey and the pile installation at two offshore wind farms, 20-75 km from coastal waters known to be frequented by dolphins. We collected passive acoustic data in key coastal areas and used a Before-After Control-Impact design to investigate variation in dolphin detections in areas exposed to different levels of impulsive noise from these offshore activities. We compared dolphin detections at two temporal scales, comparing years and days with and without impulsive noise. Passive acoustic data confirmed that dolphins continued to use the impact area throughout each offshore activity period, but also provided evidence of short-term behavioural responses in this area. Unexpectedly, and only at the smallest temporal scale, a consistent increase in dolphin detections was observed at the impact sites during activities generating impulsive noise. We suggest that this increase in dolphin detections could be explained by changes in vocalization behaviour. Marine mammal protection policies focus on the near-field effects of impulsive noise; however, our results emphasize the importance of investigating the far-field effects of anthropogenic disturbances to better understand the impacts of human activities on marine mammal populations.

opencc-zeroJun 2021View details →

Difference in effect of pheromone for monitoring the European spruce bark beetle

In recent decades there have been an increasing number of outbreaks of the European spruce bark beetle (Ips typographus) in Europe. A large amount of sanitary felling has taken place, with significant economic and ecological consequences. In order to anticipate such large-scale outbreaks, an effective monitoring system should be set up. One important aspect of monitoring is the decision on which pheromone to use. We suggest a framework for selecting an effective pheromone with few side effects and implemented it on five different pheromones under different disturbance conditions: Pheroprax, IT Ecolure, Ipstyp, Ipsowit and Typosan. We set 50 traps in two areas with sites that were disturbed and undisturbed by wind storms. We collected bark beetles from traps every one to two weeks from the end of March until the end of September in 2019. We investigated the number of bark beetles caught, bark beetle dynamics, amount of bycatch and predators, the taxonomic groups of the bycatch and the overall costs of the monitoring system. We found that Pheroprax, IT Ecolure and Ipsowit caught the most bark beetles and best showed the population dynamics. There was a low amount of bycatch (less than 6% of the total catch) and predators (a few individuals), but some groups seem to prefer certain pheromones. The cost of the pheromones increased with their effectiveness. However, pheromone costs are low relative to the personnel costs involved in setting traps and collecting bark beetles. The framework and the results will help professionals to decide which pheromones to purchase for their bark beetle monitoring system.

opencc-zeroDec 2016View details →

Data from: Multimodal in situ datalogging quantifies inter-individual variation in thermal experience and persistent origin effects on gaping behavior among intertidal mussels (Mytilus californianus)

In complex habitats, environmental variation over small spatial scales can equal or exceed larger-scale gradients. This small-scale variation may allow motile organisms to mitigate stressful conditions by choosing benign microhabitats, whereas sessile organisms may rely on other behaviors to cope with environmental stresses in these variable environments. We developed a monitoring system to track body temperature, valve gaping behavior, and posture of individual mussels (Mytilus californianus) in field conditions in the rocky intertidal zone. Neighboring mussels' body temperatures varied by up to 14°C during low tides. Valve gaping during low tide and postural adjustments, which could theoretically lower body temperature, were not commonly observed. Rather, gaping behavior followed a tidal rhythm at a warm, high intertidal site; this rhythm shifted to a circadian period at a low intertidal site and for mussels continuously submerged in a tidepool. However, individuals within a site varied considerably in time spent gaping when submerged. This behavioral variation could be attributed in part to persistent effects of mussels' developmental environment. Mussels originating from a wave-protected, warm site gaped more widely, and they remained open for longer periods during high tide than mussels from a wave-exposed, cool site. Variation in behavior was modulated further by recent wave heights and body temperatures during the preceding low tide. These large ranges in body temperatures and durations of valve closure events - which coincide with anaerobic metabolism - support the conclusion that individuals experience "homogeneous" aggregations such as mussel beds in dramatically different fashion, ultimately contributing to physiological variation among neighbors.

opencc-zeroDec 2017View details →

Data from: Temperature dependent effects of cutaneous bacteria on a frog's tolerance of fungal infection

Defense against pathogens is one of many benefits that bacteria provide to animal hosts. A clearer understanding of how changes in the environment affect the interactions between animals and their microbial benefactors is needed in order to predict the impact and dynamics of emerging animal diseases. Due to its dramatic effects on the physiology of animals and their pathogens, temperature may be a key variable modulating the level of protection that beneficial bacteria provide to their animal hosts. Here we investigate how temperature and the makeup of the skin microbial community impact the susceptibility of amphibian hosts to infection by Batrachochytrium dendrobatidis, one of two fungal pathogens known to cause the disease chytridiomycosis. To do this, we manipulated the skin bacterial communities of susceptible hosts, northern cricket frogs (Acris crepitans), prior to exposing these animals to Batrachochytrium dendrobatidis under two different ecologically relevant temperatures. Our manipulations included one treatment where antibiotics were used to reduce the skin bacterial community, one where the bacterial community was augmented with the antifungal bacterium, Stenotrophomonas maltophilia, and one in which the frog's skin bacterial community was left intact. We predicted that frogs with reduced skin bacterial communities would be more susceptible (i.e., less resistant to and/or tolerant of Bd infection), and frogs with skin bacterial communities augmented with the known antifungal bacterium would be less susceptible to Bd infection and chytridiomycosis. However, we also predicted that this interaction would be temperature-dependent. We found a strong effect of temperature but not of skin microbial treatment on the probability and intensity of infection in Bd-exposed frogs. Whether temperature impacted survival, however, differed among our skin microbial treatment groups, with animals having more S. maltophilia on their skin surviving longer at 14 but not at 26 °C. Our results suggest that temperature was the predominant factor influencing Bd's ability to colonize the host (i.e., resistance) but that the composition of the cutaneous bacterial community was important in modulating the host's ability to survive (i.e., tolerate) a heavy Bd infection.

opencc-zeroDec 2018View details →

Data from: Soil organic carbon stability in forests: distinct effects of tree species identity and traits

Rising atmospheric CO2 concentrations have increased interest in the potential for forest ecosystems and soils to act as carbon (C) sinks. While soil organic C contents often vary with tree species identity, little is known about if, and how, tree species influence the stability of C in soil. Using a 40‐year‐old common garden experiment with replicated plots of eleven temperate tree species, we investigated relationships between soil organic matter (SOM) stability in mineral soils and 17 ecological factors (including tree tissue chemistry, magnitude of organic matter inputs and their turnover, microbial community descriptors, and soil physico‐chemical properties). We measured five SOM stability indices, including heterotrophic respiration, C in aggregate‐occluded particulate organic matter (POM) and mineral‐associated SOM, and bulk SOM δ15N and ∆14C. The stability of SOM varied substantially among tree species and this variability was independent of the amount of organic C in soils. Thus, when considering forest soils as C sinks, the stability of C stocks must be considered in addition to their size. Further, our results suggest tree species regulate soil C stability via the composition of their tissues, especially roots. Stability of SOM appeared to be greater (as indicated by higher δ15N and reduced respiration) beneath species with higher concentrations of nitrogen and lower amounts of acid‐insoluble compounds in their roots, while SOM stability appeared to be lower (as indicated by higher respiration and lower proportions of C in aggregate‐occluded POM) beneath species with higher tissue calcium contents. The proportion of C in mineral‐associated SOM and bulk soil ∆14C, though, were negligibly dependent on tree species traits, likely reflecting an insensitivity of some SOM pools to decadal‐scale shifts in ecological factors. Strategies aiming to increase soil C stocks may thus focus on particulate C pools, which can more easily be manipulated and are most sensitive to climate change.

opencc-zeroOct 2019View details →

Data from: Diversification rates have no effect on the convergent evolution of foraging strategies in the most speciose genus of bats, Myotis

Adaptive radiations are defined as rapid diversification with phenotypic innovation led by colonization to new environments. Notably, adaptive radiations can occur in parallel when habitats with similar selective pressures are accessible promoting convergent adaptions. While convergent evolution appears to be a common process, it is unclear what are the main drivers leading the reappearance of morphologies or ecological roles. We explore this question in Myotis bats, the only Chiropteran genus with a worldwide distribution. Three foraging strategies –gleaning, trawling, and aerial netting– repeatedly evolved in several regions of the world, each linked to characteristic morphologies recognized as ecomorphs. Phylogenomic, morphometric, and comparative approaches were adopted to investigate convergence of such foraging strategies and skull morphology as well as factors that explain diversification rates. Genomic and morphometric data were analyzed from ~80% extant taxa. Results confirm that the ecomorphs evolved multiple times, with trawling evolving more often and foliage gleaning most recently. Skull morphology does not reflect common ancestry, evolves convergently with foraging strategy. While diversification rates have been roughly constant across the genus, speciation rates are area-dependent in taxa with temperate distributions. Results suggest that in this species-rich group of bats, first, stochastic processes have led divergence into multiple lineages. Then, natural selection in similar niches has promoted repeated adaptation of phenotypes and foraging strategies. Myotis bats are thus a remarkable case of ecomorphological convergence and an emerging model system for investigating the genomic basis of parallel adaptive radiation.

opencc-zeroNov 2014View details →

Data from: Effect of culling on individual badger (Meles meles) behaviour: potential implications for bovine tuberculosis transmission

1. Culling wildlife as a form of disease management can have unexpected and sometimes counterproductive outcomes. In the UK, badgers (Meles meles) are culled in efforts to reduce badger-to-cattle transmission of Mycobacterium bovis, the causative agent of bovine tuberculosis (TB). However, culling has previously been associated with both increased and decreased incidence of M. bovis infection in cattle. 2. The adverse effects of culling have been linked to cull-induced changes in badger ranging, but such changes are not well documented at the individual level. Using GPS-collars, we characterised individual badger behaviour within an area subjected to widespread industry-led culling, comparing it with the same area before culling and with three unculled areas. 3. Culling was associated with a 61% increase (95% CI 27-103%) in monthly home range size, a 39% increase (95% CI 28-51%) in nightly maximum distance from the sett, and a 17% increase (95% CI 11-24%) in displacement between successive GPS-collar locations recorded at 20-minute intervals. Despite travelling further, we found a 91.2 minute (95% CI 67.1-115.3 minute) reduction in the nightly activity time of individual badgers associated with culling. These changes became apparent while culls were ongoing and persisted after culling ended. 4. Expanded ranging in culled areas was associated with individual badgers visiting 45% (95% CI 15-80%) more fields each month, suggesting that surviving individuals had the opportunity to contact more cattle. Moreover, surviving badgers showed a 19.9-fold increase (95% CI 10.8-36.4 increase) in the odds of trespassing into neighbouring group territories, increasing opportunities for intergroup contact. 5. Synthesis and Applications: Badger culling was associated with behavioural changes among surviving badgers which potentially increased opportunities for both badger-to-badger and badger-to-cattle transmission of M. bovis. Furthermore, by reducing the time badgers spent active, culling may have reduced badgers' accessibility to shooters, potentially undermining subsequent population control efforts. Our results specifically illustrate the challenges posed by badger behaviour to cull-based TB control strategies and furthermore, they highlight the negative impacts culling can have on integrated disease control strategies.

opencc-zeroFeb 2020View details →

Time spent in distinct life-history stages has sex-specific effects on reproductive fitness in wild Atlantic salmon

In species with complex life cycles, life history theory predicts that fitness is affected by conditions encountered in previous life history stages. Here, we use a four-year pedigree to investigate if time spent in two distinct life history stages has sex-specific reproductive fitness consequences in anadromous Atlantic salmon (Salmo salar). We determined the amount of years spent in fresh water as juveniles (freshwater age, FW, measured in years), and years spent in the marine environment as adults (sea age, SW, measured in sea winters) on 264 sexually mature adults collected on a river spawning ground. We then estimated reproductive fitness as the number of offspring (reproductive success) and the number of mates (mating success) using genetic parentage analysis (>5000 offspring). Sea age is significantly and positively correlated with reproductive and mating success of both sexes whereby older and larger individuals gained the highest reproductive fitness benefits (females: 62.2% increase in offspring/SW and 34.8% increase in mate number/SW; males: 201.9% offspring/SW and 60.3% mates/SW). Younger freshwater age was significantly related to older sea age and thus increased reproductive fitness, but only among females (females: -33.9% offspring/FW and -32.4% mates/FW). This result implies that females can obtain higher reproductive fitness by transitioning to the marine environment earlier. In contrast, male mating and reproductive success was unaffected by freshwater age and more males returned at a younger age than females despite the reproductive fitness advantage of later sea age maturation. Our results show that the timing of transitions between juvenile and adult phases has a sex-specific consequence on female reproductive fitness, demonstrating a life-history trade-off between maturation and reproduction in wild Atlantic salmon.

opencc-zeroOct 2019View details →

Data from: Species-specific effects of passive warming in an Antarctic moss system

Polar systems are experiencing rapid climate change and the high sensitivity of these Arctic and Antarctic ecosystems make them especially vulnerable to accelerated ecological transformation. In Antarctica, warming regions result in a mosaic of ice-free terrestrial habitats dominated by a diverse assemblage of cryptogamic plants (i.e. mosses and lichens). Although these plants provide key habitat for a wide array of microorganisms and invertebrates, we have little understanding of the interaction between trophic levels in this terrestrial ecosystem, and whether there are functional effects of plant species on higher trophic levels that may alter with warming. Here, we used Open Top Chambers (OTCs) on Fildes Peninsula, King George Island, Antarctica, to examine the effects of passive warming and moss species on the abiotic environment and ultimately on higher trophic levels. For the dominate mosses, Polytrichastrum alpinum and Sanionia georgicouncinata, we found species-specific effects on the abiotic environment, including moss canopy temperature and soil moisture. Additionally, we found distinct reproductive shifts in P. alpinum plants under warming compared to mosses without warming, and invertebrate communities in this moss species were strongly correlated with plant reproduction. Mosses under warming had substantially larger total invertebrate communities, and some invertebrate taxa were influenced differentially by moss species. However, warmed moss plants showed lower fungal biomass than control moss plants, and fungal biomass differed between moss species. Our results indicate that continued warming will differentially impact the reproductive output of Antarctic moss species, potentially altering terrestrial ecosystems dynamics from the bottom up. Understanding these effects requires clarifying the foundational, mechanistic role that individual plant species play in mediating complex interactions in Antarctica's terrestrial food-webs.