Find research datasets worth reusing

opencc-zeroJun 2023View details →

Reversing declines in farmland birds: how much agri-environment provision is needed at farm and landscapes scales?

1) Agri-environment schemes (AES) are the primary policy mechanism for addressing farmland biodiversity declines across Europe. Despite previous studies on the impacts of AES on biodiversity, there is little empirical evidence on the scale of provision required to reverse declines. 2) Across three regions of lowland England with contrasting farm systems (arable, pastoral, mixed) we estimated avian Population Growth Rates (PGRs) on farmland with high AES provision ('higher-tier': average bird-friendly option cover = 7.4%), low AES provision ('lower-tier': 2.3%), and no bird-friendly AES ('no AES'). Ten-year PGRs were derived for 24 species and three multi-species groups comprising farmland-associated species ('farmland birds'), species of conservation concern ('priority birds'), and species restricted to farmland ('specialist birds'). We used PGRs to simulate the proportion of the regional farmland landscape that would have to be assigned to higher- and lower-tier agreements to stabilise or increase populations. 3) In the arable and pastoral regions, 13/23 and 13/22 species respectively had more positive PGRs under higher-tier AES than on no AES farmland (none had more negative PGRs), compared to 4/22 (positive) and 1/22 (negative) in the mixed region. Only 2-4 species per region exhibited more positive PGRs under lower-tier AES compared to no AES farmland. 4) Multi-species PGRs in the arable and pastoral regions increased from no AES (strong decline), to lower-tier (decline or stability) to higher-tier (moderate or strong increase). There was no overall AES effect in the mixed region. 5) To increase regional farmland bird populations by 10% over 10-years, 47% and 26% of the farmed landscape would need to be devoted to higher-tier agreements in arable and pastoral landscapes respectively. This falls to 34% and 17% when higher-tier is targeted at localities supporting higher abundances of target species, and to 29% and 10% when 30% of the farmed landscape is also devoted to lower-tier. Priority and specialist birds require higher provision levels. 6) Policy implications. Where farmland bird recovery is an AES objective, farms should prioritise higher-tier agreement delivery over lower-tier. Farmland bird responses to AES provision are likely to vary regionally but careful targeting will reduce the amount needed in the landscape.

opencc-zeroJun 2023View details →

Data from: Heteroaggregation of virions with microplastics reduces the number of active bacteriophages in aqueous environments

The objective of this study is to explore the effects of microplastics on the viability of the bacteriophages in an aqueous environment. Bacteriophages (phages), i.e., viruses of bacteria, are essential in homeostasis. It is estimated that phages cause up to 40% of the death of all bacteria daily. Any factor affecting phage activity is vital for the whole food chain and the ecology of numerous niches. We hypothesize that the number of active phages decreases due to the virions' adsorption on microplastic particles or by the released leachables from additives used in the production of plastic, e.g., stabilizers, plasticizers, colorants, and reinforcements. We exposed three diverse phages, namely T4 (tailed), MS2 (icosahedral), and M13 (filamentous), to 1 mg/mL suspension of twelve industrial-grade plastics [acrylonitrile butadiene styrene (ABS), high-impact polystyrene (HIPS), poly-ε-caproamide (PA6), polycarbonate (PC), polyethylene (PE), polyethylene terephthalate (PET), poly(methyl methacrylate) (PMMA), polypropylene (PP), polystyrene (PS), polytetrafluoroethylene (PTFE), polyurethane (PUR), polyvinyl chloride (PVC)] shredded to obtain microparticles of radius ranging from 2 to 50 µm. The effect of leachables was measured upon exposure of phages not to particles themselves but to the buffer pre-incubated with microplastics. A double-overlay plaque counting method was used to assess phage titers. We employed a classical linear regression model to verify which physicochemical parameters (65 variables were tested) govern the decrease of phage titers. The key finding is that adsorption mechanisms result in up to complete scavenging of virions, whereas leachables deactivate up to 50% of phages. This study reveals microplastic pollution's plausible and unforeseen ecotoxicological effect causing phage deactivation. Also, phage transmission through adsorption can alter the balance of the food chain in the new environment. The effect depends mainly on the zeta potentials of the polymers and the phage type.

opencc-by-4.0Jun 2023View details →

Dataset: A new working fluid for condensation particle counters for use in sensitive working environments

Dataset used for the puplication in Aerosol-Research: A new working fluid for condensation particle counters for use in sensitive working environments

opencc-by-4.0Feb 2021View details →

BQE WIM Data Year 4 Project (Implementation and Effectiveness of Autonomous Enforcement of Overweight Trucks in an Urban Infrastructure Environment)

BQE (Brooklyn-Queens Expressway) WIM Data for QB (Queens Bound) and SIB (Staten Island Bound)

opencc-zeroJun 2023View details →

Novel environments induce variability in fitness-related traits

Environmental change from anthropogenic activities threatens individual organisms, the persistence of populations, and entire species. Rapid environmental change puts organisms in a double bind, they are forced to contend with novel environmental conditions but with little time to respond. Phenotypic plasticity can act quickly to promote establishment and persistence of individuals and populations in novel or altered environments. In typical environmental conditions, fitness-related traits can be buffered, reducing phenotypic variation in expression of traits, and allowing underlying genetic variation to accumulate without selection. In stressful conditions, buffering mechanisms can break down, exposing underlying phenotypic variation and permitting the expression of phenotypes that may allow populations to persist in the face of altered or otherwise novel environments. Using reciprocal transplant experiments of freshwater snails, we demonstrate that novel conditions induce higher variability in growth rates and, to a lesser degree, morphology (area of the shell opening) relative to natal conditions. Our findings suggest a potentially important role of phenotypic plasticity in population persistence as organisms face a rapidly changing, human-altered world.

Variation in oxidative status, but not structural and physiological development, associated with changing ontogenetic environments

Despite the potential for temporally-dependent relationships between trait values and fitness (e.g., as juveniles approach life-stage transitions such as fledging), how developmental stage affects canalization (a measure of robustness to environmental variation) of morphological and physiological traits is rarely considered. To test the sensitivity of morphological and physiological traits to environmental variation in two developmental stages, we manipulated brood size at hatch in European starlings (Sturnus vulgaris) and cross-fostered chicks between enlarged and reduced broods approaching fledging. We measured body size (mass, tarsus, wing length) and physiological state (aerobic capacity, oxidative status) at asymptotic mass on day 15, then cross-fostered chicks between 'high' and 'low' quality environments and assessed the same traits again on day 20, after five days of pre-fledging mass recession. Chicks in reduced broods were heavier at asymptotic mass and had lower reactive oxygen metabolites than enlarged broods, while structural size, aerobic capacity, and antioxidant capacity were unaffected by experimental brood size. The observed canalization of structural and physiological traits during early development was maintained after cross-fostering, during late development. However, in contrast to early development, antioxidant capacity approaching fledging appeared sensitive to environmental conditions, as trajectories varied by cross-fostering treatment. Elevated reactive oxygen metabolites observed after early development in enlarged brood chicks were maintained after cross-fostering, suggesting canalized development in low-quality environments could produce oxidative costs that carry over between life-stages, even when conditions improve. These data reveal trait-specific relationships between environmental conditions and development and highlight how natal environment effects may vary by developmental stage.

Morphological variability decreases in populations living in less suitable environments and close to the range edges

Aim: Geographic range expansion depends on ecological and evolutionary processes that may hamper local adaptations in populations living at range edges by constraining phenotypic variability. This study investigates the spatial patterns of the intraspecific variability of skull traits throughout the geographic range of a marsupial from the Brazilian Atlantic Forest. We aimed to answer whether the distance from the range edge and the environmental suitability explain the geographic variation of morphological variability of the species. Location: Atlantic Forest, Brazil. Taxon: Marmosops incanus (Didelphimorphia, Didelphidae). Methods: We analysed adult specimens deposited in the main biological collections in southeastern Brazil. The morphological variability extent and integration within populations were characterised by 13 linear measures of the skull, using a multivariate approach. Environmental suitability for the species' occurrence was estimated by Ecological Niche Models, using climatic and vegetation productivity as predictors and three different modelling methods. Distance from the range edge was calculated based on the minimum linear distance between populations and the closest range limit. We fitted linear regressions and selected the best models that explained the spatial variation of morphological variability based on the Akaike information criterion. Results: The extent of morphological variability of M. incanus is positively correlated with morphological integration and increases with local environmental suitability and distance from the range edges. However, the relationship between morphological variability and environmental suitability depends on the niche modelling method. Main conclusions: Unfavourable environmental conditions constrain morphological variability within populations of the Gray slender opossum and may hamper local adaptation in peripheral populations living in less suitable environments. In addition to environmental conditions, geographic location of populations also plays an important role in phenotypic variability among populations. We stress the boundary effect of the species range on the local adaptation of peripheral populations and its possible consequences for the range expansion dynamics.

opencc-by-4.0Jul 2023View details →

An ontology for defining and characterizing Demonstration Environments

Demonstration Environments (DE) refer to all facilities and environments for technology development including testing, prototyping and confronting technology with different usage situations (e.g. testbed, pilot plant, living lab, sandbox, etc.). This DE Ontology is proposed to define, conceptualise and characterise DEs from various perspectives including their application domains, characteristics, network components and measurable values like lifespan. It enables different types of DEs to be situated on the same level for comparison and benchmarking. It also provides a standardisation of terminologies related to DEs which solves heterogeneity in the description of various names of DEs across domains, and provides a common understanding of DEs through a systematic framework which is the ontology.

Data from: Mother knows best: Nest-site choice homogenizes embryo thermal environments among populations in a widespread ectotherm

Species with large geographic ranges provide an excellent model of how different populations respond to dissimilar local conditions, particularly variation in climate. Maternal effects, such as oviposition-site choice greatly affect offspring phenotypes and survival. Thus, maternal behavior has the potential to mitigate the effects of divergent climatic conditions across a species' range. We delineated natural nesting areas of six populations of painted turtles (Chrysemys picta) that span a broad latitudinal range and quantified spatial and temporal variation in nest characteristics. To quantify microhabitats available for females to choose, we also identified sites within the nesting area of each location that were representative of available thermal microhabitats. Across the range females nested non-randomly and targeted microhabitats that generally had less canopy cover and thus higher nest temperatures. Nest microhabitats differed among locations but did not predictably vary with latitude or historic mean air temperature during embryonic development. In conjunction with other studies of these populations, nest-site choice appears to be homogenizing nest environments, buffering embryos from thermally-induced selection, which could stymie evolution of embryonic traits. Thus, although effective at a macroclimatic scale, nest-site choice may be unable to compensate for novel stressors that rapidly increase local temperatures.

opencc-by-4.0May 2022View details →

Fig. 6 in Red wood Ants (Formica rufa-group) prefer mature pine forests in Variscan granite environments (Hymenoptera: Formicidae)

Fig. 6 – Preferred terrain exposure of RWA nests in a, MG (n=2,328) and b, FB (n=2,829) study area.

opencc-zeroDec 2022View details →

Data from: Parallel shifts in trout feeding morphology suggest rapid adaptation to alpine lake environments

Eco-evolutionary interactions following ecosystem change provide critical insight into the ability of organisms to adapt to shifting resource landscapes. Here we explore evidence for the rapid parallel evolution of trout feeding morphology following eco-evolutionary interactions with zooplankton in alpine lakes stocked at different points in time in the Wind River Range (Wyoming, USA). In this system, trout predation has altered the zooplankton species community and driven a decrease in average zooplankton size. In some lakes that were stocked decades ago, we find shifts in gill raker traits consistent with the hypothesis that trout have rapidly adapted to exploit available smaller-bodied zooplankton more effectively. We explore this morphological response in multiple lake populations across two species of trout (cutthroat trout, Oncorhynchus clarkii, and golden trout Oncorhynchus aguabonita) and examine the impact of resource availability on morphological variation in gill raker number among lakes. Furthermore, we present genetic data to provide evidence that historically stocked cutthroat trout populations likely derive from multiple population sources, and incorporate variation from genomic relatedness in our exploration of environmental predictors of feeding morphology. These findings describe rapid adaptation and eco-evolutionary interactions in trout and document an evolutionary response to novel, contemporary ecosystem change.

opencc-by-4.0Jul 2023View details →

Embedded machine learning to promote detection of unsafe environments

Datasets used to train and validate the devices and model described in the paper "Embedded machine learning of IoT streams to promote early detection of unsafe environments"

Data for: Developmental plasticity in anurans: meta-analysis reveals effects of larval environments on size at metamorphosis and timing of metamorphosis

Many anuran amphibians (frogs and toads) rely on aquatic habitats during their larval stage. The quality of this environment can significantly impact the overall lifetime fitness and dynamics of the population. Over 450 studies have been published on the impact of the environment on anuran developmental plasticity, yet we lack a synthesis of these effects across different environments. We conducted a meta-analysis and used a comparative approach to understand whether developmental plasticity in response to different larval environments produces predictable changes in metamorphic phenotypes. We analyzed data from 124 studies spanning 80 anuran species and six larval environments and showed that interspecific variation in mass at metamorphosis and the duration of the larval period is partly explained by the type of environment experienced during the larval period. Phylogenetic relationships among species were not associated with variation in mass at metamorphosis plasticity or duration of the larval period plasticity. Larval environments tended to reduce mass at metamorphosis relative to control conditions, with the degree of change depending on the identity and severity of environmental change. Higher temperatures and lower water levels shortened the duration of the larval period, whereas less food and higher densities increased the duration of the larval period. Our results provide a foundation for future studies on developmental plasticity, especially in response to global changes. This study provides motivation for additional work that links developmental plasticity with fitness consequences within and across life stages, as well as how the outcomes described here are altered in compounding environments.

opencc-by-4.0Oct 2022View details →

Inertial self-propelled particles in anisotropic environments

Supplementary data for the following manuscript: Alexander R. Sprenger, Christian Scholz, Anton Ldov, Raphael Wittkowski, and Hartmut Löwen, "Inertial self-propelled particles in anisotropic environments".

opencc-by-4.0Jun 2023View details →

Data from: Changes in environment and management practices improve foot health in zoo-housed flamingos

Summary This dataset accompanies the publication "Changes in Environment and Management Practices Improve Foot Health in Zoo-Housed Flamingos" published in Animals. This study tracked changes in foot lesions for an individual flock of Chilean flamingos (97 birds) at Dublin Zoo (Ireland) over an 18-month period in response to management and substrate changes . Photos of each flamingo's feet were taken on May 6th 2021, when all flamingos had access to their outdoor habitat (Time Point A). Photos were taken again on 16th April 2022, following a six month period when the flamingos were restricted to their indoor habitat due to a Government order to prevent the spread of Avian Influenza (Time Point B). Final photos were taken on 9th November 2022, six months following the release of the birds back into their outdoor habitat (Time Point C). Further details can be found in the corresponding publication.  Scoring was undertaken blindly by two independent and trained evaluators. These scores reflect the scoring metric developed by Nielsen et al. 2010, and include the four types of common flamingo foot lesion: hyperkeratosis, fissures, nodular lesions, and papillomatous growths. The independently calculated foot scores were subsequently compared, and in instances where the foot scores did not match, a consensus was sought between both evaluators to provide a final value for subsequent analysis. The data presented here reflects the consensus values used in the analysis. Discrepancies in the foot scores between both evaluators are reported and discussed in the corresponding publication.  Description of the Dataset One file is provided in .csv format. The file contains the following 11 columns:  <ul> <li>Time_Point: The Time Point at which photos were taken (A = 6th May 2021, B = 16th April 2022, and C = 9th November 2022).   </li> <li>Animal_Identifier: An anonymous code used to identify individual flamingos (n = 97).</li> <li>Hyperkeratosis_Total: The total hyperkeratosis score for that flamingo at that Time Point (considering both feet).</li> <li>Fissures_Total: The total fissures score for that flamingo at that Time Point (considering both feet).</li> <li>Nodular_Lesions_Total: The total nodular lesions score for that flamingo at that Time Point (considering both feet).</li> <li>Papillomatous_Growths_Total: The total papillomatous growths score for that flamingo at that Time Point (considering both feet).</li> <li>L_Total: The total left foot lesions score for that flamingo at that Time Point (considering all types of foot lesion).</li> <li>R_Total: The total right foot lesions score for that flamingo at that Time Point (considering all types of foot lesion).</li> <li>Overall_Total: The total foot lesions score for that flamingo at that Time Point (considering both feet and all types of foot lesion).</li> <li>Sex: The sex of the flamingo (Male or Female) </li> <li>Age: The age of the flamingo (Years)</li> </ul>   Acknowledgements We acknowledge and thank all Dublin Zoo staff and volunteers for their support and assistance throughout the project. Additionally, we thank Dr. Laura Kane for her technical assistance and support.      Disclaimer Despite our best efforts at screening the data for errors and inconsistencies, some information could be erroneous.    Credit If you use this dataset, please cite the corresponding publication: Mooney, A., McCall, K., Bastow, S., & Rose, P. (2023). Changes in Environment and Management Practices Improve Foot Health in Zoo-Housed Flamingos. Animals, 13(15), 2483. <a href="https://doi.org/10.3390/ani13152483">https://doi.org/10.3390/ani13152483</a>

opencc-by-4.0Aug 2023View details →

Human-Actions-in-Diverse-Environments-HAR-Approach

#### HADE Dataset - Collected and curated for the foundation of the HAR system, comprising 1500+ videos - Preprocessing techniques for suitable data format. - Raw data from smartphone cameras saved as .mp4 video files. - Videos: 4-5 seconds duration, 30 fps. - Frames organized by subject and action names.   After manual annotation, and pre-processing, we obtained the following frames/samples #### Actions in HADE Dataset | Action # | Action Name   | # of Samples | |----------|---------------|--------------| | 1        | Clapping      | 178          | | 2        | Sitting Down  | 171          | | 3        | Standing Up   | 171          | | 4        | Walking       | 178          | | **Total**|               | **699**      | - HADE dataset includes Clapping, Sitting Down, Standing Up, and Walking actions. - Total of 699 samples. #### Dataset Diversity and Comparison - HADE dataset stands out for broader action range and environmental diversity. - Enhanced model generalizability and adaptability.

opencc-by-4.0Aug 2023View details →

Stage-specific genotype-by-environment interactions determine yield components in wheat

The tables (climate_data.csv, and Yield_data.csv) include the recorded climatic and measured yield components data from multi-environment field trails (2014-2017). The table (soil_water_data.csv) presents the simulated water content for the experiments. The tables (Coefficients_data.csv, and multiple_regression_coefficients_data.csv) present the log p-values of comparing models M1, M2, and M3 and their coefficients. All the necessary information to read these datasets is provided in the table (read_me.csv).

opencc-zeroAug 2023View details →

Codes for: A numerical model supports the evolutionary advantage of recombination plasticity in shifting environments

Numerous empirical studies have witnessed an increase in meiotic recombination rate in response to physiological stress imposed by unfavorable environmental conditions. Thus, inherited plasticity in recombination rate is hypothesized to be evolutionarily advantageous in changing environments. Previous theoretical models proceeded from the assumption that organisms increase their recombination rate when the environment becomes more stressful and demonstrated the evolutionary advantage of such a form of plasticity. Here, we numerically explore a complementary scenario – when the plastic increase in recombination rate is triggered by the environmental shifts. Specifically, we assume increased recombination in individuals developing in a different environment than their parents and optionally, also in offspring of such individuals. We show that such shift-inducible recombination is always superior when the optimal constant recombination implies an intermediate rate. Moreover, under certain conditions, plastic recombination may appear beneficial also when the optimal constant recombination is either zero or free. The advantage of plastic recombination was better predicted by the range of the population's mean fitness over the period of environmental fluctuations, compared to the geometric mean fitness. These results hold for both panmixia and partial selfing, with faster dynamics of recombination modifier alleles under selfing. We think that recombination plasticity can be acquired under the control of environmentally responsive mechanisms such as chromatin epigenetics remodeling.

opencc-by-4.0May 2023View details →

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"

Community assembly amplicon sequences, with pipeline to get asv table for "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities"   compressed FASTA files for 16s amplicon sequences relating to two separate projects,  "Spatial structure drives compositional convergence between nutrient environments in experimental microbial communities" and "Habitat filtering leads to phylogenetic clustering in synthetic microbial communities". DADA22 pipeline is included, which pools all samples for better accuracy. A Julia script bioinfo.jl is then used to select only the samples relevant to spatial structure project.   All csv filenames are appended with "_q" indicating an increase in the stringency of quality filtering parameters (also increasing minimum hamming distance used in DADA2 algorithm to 5) to produce a taxa table with a sensible number of ASVs (given a known number of input strains) with each ASV uniquely aligning to an individual sequence from colony PCR of said input strains.