Find research datasets worth reusing

opencc-by-4.0Dec 2020View details →

Clustered Embedding using Deep Learning to Analyze Urban Mobility based on Complex Transportation Data

The subset of the anonymized dataset for personalized POI embedding.

opencc-by-4.0Dec 2020View details →

Output Files from Reactive Transport Models (supplement to Solid Earth Manuscript 'se-2020-99')

This repository includes the output files (in Tecplot format) of the numerical models in the paper entitled "Understanding controls on hydrothermal dolomitisation: insights from 3D Reactive Transport Modelling of geothermal convection". A key to the output data provided here is summarised in Data_Benjakul_et_al_2020.xlsx.   We used TOUGHREACT, a numerical simulation program developed by the Lawrence Berkeley National Laboratory (LBNL) which is available at: <a href="https://tough.lbl.gov/licensing-download/toughreact-licensing-download/">https://tough.lbl.gov/licensing-download/toughreact-licensing-download/</a> to numerically model the convection of seawater in a single fault within carbonate-hosted system. The parameters used in the numerical models are given in the paper. <a href="https://doi.org/10.5194/se-11-2439-2020">https://doi.org/10.5194/se-11-2439-2020</a> The output files from TOUGHREACT (in Tecplot format) are visualised using trexplot, a python script developed by Hamish Robertson which can be found at: <a href="https://github.com/hammytheham/trexplot">https://github.com/hammytheham/trexplot</a> (last access: 5 December 2020).   Please contact me via the following e-mail addresses in case you have any questions: <a href="mailto:rb17526@bristol.ac.uk">rb17526@bristol.ac.uk</a> or <a href="mailto:rbenjaku@gmail.com">rbenjaku@gmail.com</a>

opencc-zeroDec 2018View details →

Data from: Promiscuious pollinators - evidence from an Afromontane sunbird-plant pollen transport network

Sunbirds play a major role in the pollination of Old World nectiverous plants. However, with the exception of the Cape Floristic Region there is a major knowledge gap around African nectivore interaction networks- a stark contrast from the abundance of neotropical hummingbird-plant networks. Here we describe a sunbird pollen transfer network (PTN) which we use in conjunction with a sunbird- flower visitation network (FVN) to explore levels of sunbird specialization within an Afromontane forest habitat. Both networks were generalised compared with similar sized hummingbird networks, reflecting the wide range of flower types visited, the generalist diet and bill characteistics of sunbirds. Three sunbird species from the genus Cinnyris accounted for 85% of flower visits and 77% of all pollen transported. Of the 17 plant species across both networks, 15 are predominantly pollinated by insects while Anthonotha noldeae (Fabaceae- Caesalpinoidie) and Globimetula braunii (Loranthaceae) depend on sunbirds for seed set. Sunbird species average bill lengths varied between 14.5 mm (the variable sunbird) to 23.6 mm (the green headed sunbird) but while more pollen was carried on longer bills we found no evidence for a relationship between bill length and type of flower visited. Both networks were nested. Some specialization was observed in both networks although this does not appear to be driven much by sunbird –flower trait matching. Overall, our results suggest that in contrast to nectivores elsewhere, factors such as phenology and/or environment, rather than morphology may play important roles in limiting potential sunbird-flower interactions and need further investigation.

opencc-zeroJul 2019View details →

Data from: Wildfire alters the structure and seasonal dynamics of nocturnal pollen-transport networks

Wildfires drive global biodiversity patterns and affect plant–pollinator interactions, and are expected to become more frequent and severe under climate change. Post‐fire plant communities often have increased floral abundance and diversity, but the effects of wildfires on the ecological process of pollination are poorly understood. Nocturnal moths are globally important pollinators, but no previous study has examined the effects of wildfire on nocturnal pollination interactions. We investigated the effects of wildfire on nocturnal pollen‐transport networks. We analysed the abundance and species richness of moths and flowers, and the structure of these networks, at three burned and three unburned sites in Portugal for two years, starting eight months after a large fire. Nocturnal pollen‐transport networks had lower complexity and robustness following the fire than at nearby unburned sites. Overall, 70% of individual moths carried pollen, and moths were found to be transporting pollen from 83% of the flower species present. Burned sites had significantly more abundant flowers, but less abundant and species‐rich moths. Individual moths transported more pollen in summer at burned sites, but less in winter; however, total pollen transport by the moth assemblage at burned sites was just 20% of that at unburned sites. Interaction turnover between burned and unburned networks was high. Negative effects of fire upon moths will likely permeate to other taxa through loss of mutualisms. Therefore, if wildfires become more frequent under climate change, community resilience may be eroded. Understanding the responses of ecological networks to wildfire can inform management that promotes resilience and facilitates whole‐ecosystem conservation.

opencc-zeroDec 2015View details →

Data from: Anthropogenic transport of species across native ranges: unpredictable genetic and evolutionary consequences

Human activities are responsible for the translocation of vast amounts of organisms, altering natural patterns of dispersal and gene flow. Most research to date has focused on the consequences of anthropogenic transportation of non-indigenous species within introduced ranges, with little research focusing on native species. Here, we compared genetic patterns of the sessile marine invertebrate, Ciona intestinalis, which has highly restricted dispersal capabilities. We collected individuals in a region of the species' native range where human activities that are known to facilitate the artificial spread of species are prevalent. Using microsatellite markers, we revealed highly dissimilar outcomes. First, we found low levels of genetic differentiation among sites separated by both short and large geographical distances, indicating the presence of anthropogenic transport of genotypes, and little influence of natural geographical barriers. Second, we found significant genetic differentiation in pairwise comparisons among certain sites, suggesting that other factors besides artificial transport (e.g. natural dispersal, premodern population structure) may be shaping genetic patterns. Taken together, we found dissimilar patterns of population structure in a highly urbanized region that could not be predicted by artificial transport alone. We conclude that anthropogenic activities alter genetic composition of native ranges, with unknown consequences for species' evolutionary trajectories.

opencc-zeroDec 2012View details →

Data from: Downscaling pollen-transport networks to the level of individuals

1. Most plant-pollinator network studies are conducted at species level whereas little is known about network patterns at the individual level. In fact, nodes in traditional species-based interaction networks are aggregates of individuals establishing the actual links observed in nature. Thus, emergent properties of interaction networks might be the result of mechanisms acting at the individual level. 2. Pollen loads carried by insect flower-visitors from two mountain communities were studied to construct pollen-transport networks. For the first time, these community-wide pollen-transport networks were downscaled from species-species (sp-sp) to individuals-species (i-sp) in order to explore specialization, network patterns and niche variation at both interacting levels. We used a null model approach to account for network size differences inherent to the downscaling process. Specifically, our objectives were: (i) to investigate whether network structure changes with downscaling, (ii) to evaluate the incidence and magnitude of individual specialization in pollen use, and (iii) to identify potential ecological factors influencing the observed degree of individual specialization. 3. Network downscaling revealed a high specialization of pollinator individuals, which was masked and unexplored in sp-sp networks. The average number of interactions per node, connectance, interaction diversity and degree of nestedness decreased in i-sp networks, because generalized pollinator species were composed of specialized and idiosyncratic conspecific individuals. An analysis with 21 pollinator species representative of two communities showed that mean individual pollen resource niche was only c. 46% of the total species niche. 4.The degree of individual specialization was associated to inter- and intraspecific overlap in pollen use and it was higher for abundant than for rare species. Such niche heterogeneity depends on individual differences in foraging behaviour and likely has implications for community dynamics and species stability. 5. Our findings highlight the importance of taking inter-individual variation into account when studying higher–order structures such as interaction networks. We argue that exploring individual-based networks will improve our understanding of species-based networks and will enhance the link between network analysis, foraging theory and evolutionary biology.

Data from: Atrazine transport through a soil-epikarst system

Row crop and livestock production contaminate soils and groundwater of the karst aquifers within south-central Kentucky's Pennyroyal Plateau. Transport of atrazine from field application to the epikarstic drainage system beneath a field with active row-crop farming was investigated. The Crumps Cave study site is a shallow autogenic drainage system with a recharge area of ∼1 ha that contains two epikarst drains (WF-1 and WF-2) which were monitored for atrazine, deethylatrazine (DEA), and deisopropylatrazine (DIA) concentrations from January 2011 to May 2012. Atrazine concentrations in both drains did not increase above winter background levels for nearly 2 mo after application when levels suddenly spiked and reached peak concentrations for the study during an event in May 2011. Atrazine, DEA, and DIA were detected in 100% of samples, and metabolites accounted for 54 to 94% of the monthly total loads, except in May 2011. Median dealkylated metabolite/atrazine ratios (DMAR) were ∼5:1 at both sites, and seasonal DMAR patterns corresponded with changes in soil temperature. These data support the hypothesis that a combination of sorption and degradation in the soil column above the epikarst controlled the transport of atrazine and its metabolites. This resulted in delayed atrazine transport after application and prolonged transport of atrazine and its weakly sorbed metabolites to the epikarst aquifer. Management practices that reduce herbicide inputs, such as diverse crop rotations, cover crops, and use of low-rate and strong-sorbing herbicides, would improve groundwater quality in areas of the Corn Belt with intensive row cropping on karst topography.

Data from: An alternative water transport system in land plants

The evolution of vascular tissue is a key innovation enabling plants to inhabit terrestrial environments. Here, we demonstrate extra-vascular water transport in a giant, prop-rooted monocot from Lord Howe Island. Pandanus forsteri (Pandanaceae) produces gutter-like leaves that capture rainwater, which is then couriered along a network of channels to the tips of aerial roots, where it is stored by absorptive tissue. This passive mechanism of water acquisition, transport, and storage is critical to the growth of aerial prop roots that cannot yet attain water via vascular conduction. This species therefore sheds light on the elaborate means by which plants have evolved to attain water.

opencc-zeroDec 2016View details →

Data from: Argentine ants (Linepithema humile) use adaptable transportation networks to track changes in resource quality

Transportation networks play a crucial role in human and animal societies. For a transportation network to be efficient, it must have adequate capacity to meet traffic demand. Network design becomes increasingly difficult in situations where traffic demand can change unexpectedly. In humans, network design is often constrained by path dependency because it is difficult to move a road once it is built. A similar issue theoretically faces pheromone-trail-laying social insects; once a trail has been laid, positive feedback makes re-routing difficult because new trails cannot compete with continually reinforced pre-existing trails. In the present study, we examined the response of Argentine ant colonies and their trail networks to variable environments where resources differ in quality and change unexpectedly. We found that Argentine ant colonies effectively tracked changes in food quality such that colonies allocated the highest proportion of foragers to the most rewarding feeder. Ant colonies maximised access to high concentration feeders by building additional trails and routes connecting the nest to the feeder. Trail networks appeared to form via a pruning process in which lower traffic trails were gradually removed from the network. At the same time, we observed several instances where new trails appear to have been built to accommodate a surge in demand. The combination of trail building when traffic demand is high and trail pruning when traffic demand is low results in a demand-driven network formation system that allows ants to monopolise multiple dynamic resources.

opencc-zeroJan 2020View details →

The neural basis of tadpole transport in poison frogs

The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental care in a typically male uniparental species, the Dyeing Poison Frog (Dendrobates tinctorius). We first characterized hormone levels and whole brain gene expression across parental care stages during sex-typical care. Surprisingly, hormonal changes and brain gene expression differences associated with active parental behavior in males were mirrored in their non-caregiving female partners. To further explore the disconnect between neuroendocrine patterns and behavior, we characterized hormone levels and neural activity patterns in females performing sex-reversed parental care. In contrast to hormone and gene expression patterns, we found that patterns of neural activity were linked to the active performance of parental behavior, with sex-reversed tadpole transporting females exhibiting neural activity patterns more similar to those of transporting males than non-caregiving females. We suggest that parallels in hormones and brain gene expression in active and observing parents are related to females' ability to flexibly take over parental care in the absence of their male partners.The occasional reversal of sex-typical behavior suggests that many of the neural circuits underlying behavior are conserved between males and females and can be activated in response to the appropriate social condition or stimulus. Most poison frog species (Family Dendrobatidae) exhibit male uniparental care, but flexible compensation has been observed in some species, where females will take over parental care duties when males disappear. We investigated hormonal and neural correlates of sex-typical and sex-reversed parental care in a typically male uniparental species, the Dyeing Poison Frog (Dendrobates tinctorius). We first characterized hormone levels and whole brain gene expression across parental care stages during sex-typical care. Surprisingly, hormonal changes and brain gene expression differences associated with active parental behavior in males were mirrored in their non-caregiving female partners. To further explore the disconnect between neuroendocrine patterns and behavior, we characterized hormone levels and neural activity patterns in females performing sex-reversed parental care. In contrast to hormone and gene expression patterns, we found that patterns of neural activity were linked to the active performance of parental behavior, with sex-reversed tadpole transporting females exhibiting neural activity patterns more similar to those of transporting males than non-caregiving females. We suggest that parallels in hormones and brain gene expression in active and observing parents are related to females' ability to flexibly take over parental care in the absence of their male partners.

opencc-zeroDec 2015View details →

Data from: Explaining high-diversity death assemblages: undersampling of the living community, out-of-habitat transport, time-averaging of rare taxa, and local extinction

Molluscan benthic assemblages provide unique opportunities for understanding both spatial and temporal patterns of biodiversity. Species richness in the shell remains found at a site (i.e. the death assemblage) is typically several times higher than in the counterpart living assemblage, reflecting a complex history of settlement, dissemination and decomposition post-mortem. We used high-density temporal and spatial sampling (>37'000 individuals representing 196 taxa) of a shallow (5-8 m) nearshore sandy habitat off the coast of south-east Sardinia (Italy, Mediterranean Sea) to study the factors responsible for differences in the relative diversity of living and death assemblages. We found that death assemblages at all sites were considerably more diverse than living communities (1.5-3.5x more dead than living taxa after sample-size standardization), with 78% of all taxa solely recovered as empty shells, resulting in low live-dead agreement. By carefully filtering the raw data and combining them with habitat information extracted from the literature, we disentangled the major causes of this discordance and quantified their individual effects. Increased dead diversities could not be attributed to undersampling of the living community, but instead resulted from three phenomena of decreasing importance: the post-mortem, out-of-habitat transport of non-indigenous taxa (57% of dead-only taxa were allochthonous), the time-averaged presence of rare indigenous taxa (40% of dead-only taxa), and the likely local extirpation of a small number of species (3% of dead-only taxa). Our approach demonstrates how ecological inferences based on death assemblages can be improved by restricting analyses to demonstrably indigenous taxa, and highlights how mollusc shell remains can be used to provide information over both ecological and evolutionary timescales.

Data from: Repeat variants for the SbMATE transporter protect sorghum roots from aluminum toxicity by transcriptional interplay in cis and trans

Acidic soils, where aluminum (Al) toxicity is a major agricultural constraint, are globally widespread and are prevalent in developing countries. In sorghum, the root citrate transporter SbMATE confers Al tolerance by protecting root apices from toxic Al3+, but can exhibit reduced expression when introgressed into different lines. We show that allele-specific SbMATE transactivation occurs and is caused by factors located away from SbMATE. Using expression-QTL mapping and -GWAS, we establish that SbMATE transcription is controlled in a bipartite fashion, primarily in cis but also in trans. Multi-allelic promoter transactivation and ChIP analyses demonstrated that intermolecular effects on SbMATE expression arise from a WRKY and a zinc finger-DHHC transcription factor (TF) that bind to and trans-activate the SbMATE promoter. A haplotype analysis in sorghum RILs indicate that the TFs influence SbMATE expression and Al tolerance. Variation in SbMATE expression likely results from changes in tandemly repeated cis sequences flanking a transposable element (MITE) insertion in the SbMATE promoter, which are recognized by the Al3+-responsive TFs. According to our model, repeat expansion in Al-tolerant genotypes increases TF recruitment and, hence, SbMATE expression, which is, in turn, lower in Al-sensitive genetic backgrounds due to lower TF expression and fewer binding sites. We thus show that even dominant cis regulation of an agronomically-important gene can be subjected to precise intermolecular fine-tuning. These concerted cis/trans interactions, which allow the plant to sense and respond to environmental cues, such as Al3+ toxicity, can now be used to increase yields and food security on acidic soils.

opencc-zeroDec 2015View details →

Data from: Effects of a novel fish transport system on the health of adult fall Chinook salmon

Movement past hydroelectric dams and related in-river structures has important implications for habitat connectivity and population persistence in migratory fish. A major problem is that many of these structures lack effective fish passage facilities, which can fragment spawning and rearing areas and negatively impact recruitment. While traditional fish passage facilities (e.g., ladders, trap and haul) can effectively enable fish to pass over barriers, their capital or operational costs can be significant. We evaluated the utility of a novel transport device that utilizes a flexible tube with differential internal air pressure to pass fish around in-river barriers. A total of N = 147 adult fall Chinook salmon (Oncorhynchus tshawytscha) nearing maturation were apportioned to three treatments and a control group. In two of the treatments, adult fall Chinook salmon were transported through the device via two lengths of tube (12 or 77 m) and their injury, stress, and immune system responses and reproductive function were compared to a third treatment where fish were moved by a standard trap and haul method and also to a control group. We observed no significant differences among the treatment or control groups in post-treatment adult survival, injury or stress. Indicators of immune system response and reproductive readiness were also not significantly different among the four groups. Egg survival was significantly different among the groups, with the highest survival in the eggs from females transported 77 m and lowest in the control group; the differences were highly variable within groups and not consistent with the duration of treatment or degree of handling. Taken together, the results suggest the device did not injure or alter normal physiological functioning of adult fall Chinook salmon nearing maturation and may provide an effective method for transporting such fish around in-river barriers during their spawning migration.

opencc-zeroDec 2014View details →

Data from: The multilayer temporal network of public transport in Great Britain

Despite the widespread availability of information concerning public transport coming from different sources, it is extremely hard to have a complete picture, in particular at a national scale. Here, we integrate timetable data obtained from the United Kingdom open-data program together with timetables of domestic flights, and obtain a comprehensive snapshot of the temporal characteristics of the whole UK public transport system for a week in October 2010. In order to focus on multi-modal aspects of the system, we use a coarse graining procedure and define explicitly the coupling between different transport modes such as connections at airports, ferry docks, rail, metro, coach and bus stations. The resulting weighted, directed, temporal and multilayer network is provided in simple, commonly used formats, ensuring easy access and the possibility of a straightforward use of old or specifically developed methods on this new and extensive dataset.

opencc-zeroDec 2014View details →

Data from: Food spoilage, storage, and transport: implications for a sustainable future

Human societies have always faced temporal and spatial fluctuations in food availability. The length of time that food remains edible and nutritious depends on temperature, moisture, and other factors that affect the growth rates of organisms that cause spoilage. Some storage techniques, such as drying, salting, and smoking, date back to ancient hunter–gatherer and early agricultural societies and use relatively low energy inputs. Newer technologies developed since the industrial revolution, such as canning and compressed-gas refrigeration, require much greater energy inputs. Coincident with the development of storage technologies, the transportation of food helped to overcome spatial and temporal fluctuations in productivity, culminating in today's global transport system, which delivers fresh and preserved foods worldwide. Because most contemporary humans rely on energy-intensive technologies for storing and transporting food, there are formidable challenges for feeding a growing and increasingly urbanized global population as finite supplies of fossil fuels rapidly deplete.

opencc-by-4.0Jun 2021View details →

Figures of Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes

Figures of the article "Conductivity Transitions of La0.7Sr0.3MnO3±d andLa0.6Sr0.4Co0.2Fe0.8O3-d in Ce0.9Gd0.1O2-d Matrix for Dual-Phase Oxygen Transport Membranes"

opencc-zeroOct 2019View details →

Predicting barrier effects of transportation networks on Asian elephants: Implications for environmental impact assessment

The rapid proliferation of transportation networks (TNs) is a threat to wide–ranged animals through habitat erosion, road–kill, and indirect socio–ecological interaction. In most cases, environmental impact assessments of TNs about animals are descriptive and targeted to direct impacts of the "linear features", while indirect and cumulative impacts are relatively neglected. Using spatially explicit data of elephant–caused damage during 2012–2015 in China, we quantified barrier effects of TN on Asian elephants and predicted the effects under a TN expansion scenario using maximum entropy algorithms. We found that TN acted as a strong barrier even for the elephants that have inhabited highly fragmented landscapes for years, with only 18% of the damage occurred on the crossed side of roads. Also, the TN expansion will reduce elephant habitats, exacerbating herd isolation and human–elephant conflict locally. Thus, we suggest that mitigation of the conflicts should be integrated into future environmental impact assessments.

opencc-zeroDec 2014View details →

Data from: A genetic discontinuity in moose (Alces alces) in Alaska corresponds with fenced transportation infrastructure

The strength and arrangement of movement barriers can impact the connectivity among habitat patches. Anthropogenic barriers (e.g. roads) are a source of habitat fragmentation that can disrupt these resource networks and can have an influence on the spatial genetic structure of populations. Using microsatellite data, we evaluated whether observed genetic structure of moose (Alces alces) populations were associated with human activities (e.g. roads) in the urban habitat of Anchorage and rural habitat on the Kenai Peninsula, Alaska. We found evidence of a recent genetic subdivision among moose in Anchorage that corresponds to a major highway and associated infrastructure. This subdivision is most likely due to restrictions in gene flow due to alterations to the highway (e.g. moose-resistant fencing with one-way gates) and a significant increase in traffic volume over the past 30 years; genetic subdivision was not detected on the Kenai Peninsula in an area not bisected by a major highway. This study illustrates that anthropogenic barriers can substructure wildlife populations within a few generations and highlights the value of genetic assessments to determine the effects on connectivity among habitat patches in conjunction with behavioral and ecological data.

Data from: Field observations of turbulence, sand suspension and cross-shore transport under spilling and plunging breakers

Measurements of wave orbital velocity, near-bed turbulence levels and sediment suspension were obtained under plunging and spilling breakers in the outer surf zone on the beach at Vejers, Denmark. For the same range of relative wave heights and indicators of wave nonlinearity, we observed significantly larger suspended sediment concentrations and onshore-directed rates of suspended sediment transport under (long-period) plunging breakers, compared to (short-period) spilling breakers. This is consistent with the long-held understanding that, for a given beach slope, onshore transport and beach accretion is associated with longer-period waves and offshore transport and erosion is associated with shorter-period waves. An intra-wave analysis of hydrodynamics and sediment suspension revealed that the main reason for the larger suspended sediment transport rates under plunging waves was i) larger time-averaged suspended sediment loads under plunging waves, and ii) a larger difference in cumulated sediment load under the wave crest phase compared to the wave trough phase for plunging breakers. This latter difference was due to an earlier arrival at the seabed of higher levels of turbulent kinetic energy (TKE) under plunging waves compared to spilling waves. Hence, both magnitude and timing within the wave cycle of TKE production is important in a quantification of sediment transport under breaking waves. For ensemble-averaged intense suspension events, contributing roughly 50% of the total sediment suspension during individual records, we found that instantaneous near-bed sediment load was linearly related to instantaneous levels of Froude-scaled TKE.