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opencc-by-4.0Sep 2019View details →

Data: Transsaccadic integration benefits are not limited to the saccade target

Dataset for article "Transsaccadic integration benefits are not limited to the saccade target". doi:10.1152/jn.00420.2019.

opencc-by-4.0Jun 2019View details →

Data supplementing the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities" K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal

These data supplement the article "Diatom DNA metabarcoding for biomonitoring : strategies to avoid major taxonomical and bioinformatical biases limiting molecular indices capacities"  K. Tapolczai, F. Keck, A. Bouchez, F. Rimet, M. Kahlert and V. Vasselon submitted to "Frontiers in Ecology and Evolution" journal. The directory contains the following files: 464_samples_fastq_files_(mothur).rar - contains the 464 fastq files proceed together during the Mothur bioinformatics treatments to produce the OTUs and ISUs tables. As the contig and the demultiplexing steps were performed by the sequencing platform, there is 1 fastq file per sample. From this 464 samples OTU/ISU tables, only information regarding 76 samples were used in this study and are listed in the "76_samples_list_(mothur).xlsx" file. 76_samples_list_(mothur).xlsx - contains the information regarding the 76 samples used to create the OTUs and ISUs tables presented in the paper. 76_samples_R1_R2_fastq_files(DADA2).rar - contains the raw demultiplexed fastq files (R1.fastq and R2.fastq) for each of the 76 samples used in this study to produce the ESVs table using the DADA2 bioinformatics pipeline.

opencc-by-4.0Apr 2024View details →

Data for: Synergistic mechanisms of plant phosphorus (P) resorption and microbial P-limitation affecting soil P during grassland vegetation succession

Data for: Synergistic mechanisms of plant phosphorus (P) resorption and microbial P-limitation affecting soil P during grassland vegetation succession

opencc-by-4.0Sep 2024View details →

Supporting Data for "Why Half‐Cell Samples Provide Limited Insight Into the Aging Mechanisms of Potassium Batteries"

This dataset provides the raw data to the manuscript "Why Half‐Cell Samples Provide Limited Insight Into the Aging Mechanisms of Potassium Batteries" published in Advanced Energy Materials, 2024, DOI 10.1002/aenm.202403811 <a href="https://doi.org/10.1002/aenm.202403811">Link to Publisher</a>   Comments: <ul> <li>HAXPES synchrotron data is provided as IGOR file (IGOR Pro (v6.37, WaveMaterics Inc.). The file contains the original 2D data and the converted 1D datasets used for analysis</li> <li>In-House XPS data is provided with corresponding peak fits as excel spreadsheet</li> <li>peak data (binding energy (after referencing), intensity, area, FWHM and at.%) is provided in separate excel spreadsheet.</li> </ul>

opencc-by-4.0Oct 2024View details →

Data for: `Limits on planetary-mass primordial black holes from the OGLE high-cadence survey of the Magellanic Clouds'

This repository contains data presented in the paper "Limits on planetary-mass primordial black holes from the OGLE high-cadence survey of the Magellanic Clouds".

opencc-by-4.0Oct 2024View details →

Supplementary material for the paper "Data-Limited Continuous Experimentation (dlCE): A Literature Review"

This is supplementary material for a paper, "Data-Limited Continuous Experimentation (DLC): A Literature Review", published at the 15th International Conference on Software Business (ICSOB 2024). It contains a list of included papers from a literature review, their experimentation cases and extracted data related to contextual and experimentation factors, as well as their relevance to dlCE scenarios.

opencc-zeroMay 2020View details →

Data from: Limited biomass recovery from gold mining in Amazonian forests

<ol> <li>Gold mining has rapidly increased across the Amazon Basin in recent years, especially in the Guiana shield, where it is responsible for >90% of total deforestation. However, the ability of forests to recover from gold mining activities remains largely unquantified. </li> <li>Forest inventory plots were installed on recently abandoned mines in two major mining regions in Guyana, and re-censused 18 months later, to provide the first ground-based quantification of gold mining impacts on Amazon forest biomass recovery. </li> <li>We found that woody biomass recovery rates on abandoned mining pits and tailing ponds are amongst the lowest ever recorded for tropical forests, with close to no woody biomass recovery after 3-4 years. </li> <li>On the overburden sites (i.e. areas not mined but where excavated soil is deposited), however, aboveground biomass recovery rates (0.4 - 3.5 Mg ha-1 yr-1) were within the range of those recorded in other secondary forests across the Neotropics following abandonment of pastures and agricultural lands. </li> <li>Our results suggest that forest recovery is more strongly limited by severe mining-induced depletion of soil nutrients, especially nitrogen, than by mercury contamination, due to slowing of growth in nutrient-stripped soils. </li> <li>We estimate that the slow recovery rates in mining pits and ponds currently reduce carbon sequestration across Amazonian secondary forests by ~21,000 t C yr-1, compared to the carbon that would have accumulated following more traditional land uses such as agriculture or pasture. </li> <li> Synthesis and applications. To achieve large-scale restoration targets, Guyana and other Amazonian countries will be challenged to remediate previously mined lands. The recovery process is highly dependent on nitrogen availability rather than mercury contamination, affecting woody biomass regrowth. The significant recovery in overburden zones indicates that one potential active remediation strategy to promote biomass recovery may be to back-fill mining pits and ponds with excavated soil. </li> </ol>

opencc-zeroAug 2019View details →

Data from: Usefulness and limitations of thermal performance curves in predicting ectotherm development under global change

1. Thermal performance curves (TPCs) have been estimated in multiple temperate ectotherm species and used to predict the effect of global warming. However, TPCs are typically assessed under constant temperature regimes, so their reliability for predicting thermal responses in the wild where temperature fluctuates diurnally and seasonally remains poorly documented. 2. Here we use distant latitudinal populations of five species of sepsid flies (Diptera: Sepsidae) from the temperate region (Europe, North Africa, North America) to compare estimates derived from constant TPCs with observed development rate under fluctuating temperatures in laboratory and field conditions. 3. TPCs changed across gradients in that flies originating from higher latitudes or altitudes showed accelerated development, an adaptive response. TPCs were then used to predict development rates observed under fluctuating temperatures; these predictions were relatively accurate in the laboratory but not in the field. Interestingly, the precision of TPC-predictions depended not only on the resolution of temperature data, with diurnal and overall temperature summing performing better than hourly temperature summing, but also on the frequency of temperatures falling below the estimated critical minimum temperature. Hourly temperature resolution most strongly underestimated actual development rates, because flies apparently either did not stop growing when temperatures dropped below this threshold, or they speed up their growth when the temperature rises again, thus most severely reflecting this error. 4. We conclude that when flies do not encounter cold temperatures, TPC-predictions based on constant temperatures can accurately reflect performance under fluctuating temperatures if adequately adjusted for non-linearities, but when they encounter cold temperatures this method is more error-prone. 5. Our study emphasizes the importance of the resolution of temperature data and cold temperatures in shaping thermal reaction norms, thus improving predictions of the responses of ectotherms to climate change in the age of big data and citizen science.

opencc-zeroDec 2017View details →

Data from: Potential limits to the benefits of admixture during biological invasion

Species introductions often bring together genetically divergent source populations, resulting in genetic admixture. This geographic reshuffling of diversity has the potential to generate favorable new genetic combinations, facilitating the establishment and invasive spread of introduced populations. Observational support for the superior performance of admixed introductions has been mixed, however, and the broad importance of admixture to invasion questioned. Under most underlying mechanisms, admixture's benefits should be expected to increase with greater divergence among and lower genetic diversity within source populations, though these effects have not been quantified in invaders. We experimentally crossed source populations differing in divergence in the invasive plant Centaurea solstitialis. Crosses resulted in many positive (heterotic) interactions, but fitness benefits declined and were ultimately negative at high source divergence, with patterns suggesting cyto-nuclear epistasis. We explored the literature to assess whether such negative epistatic interactions might be impeding admixture at high source population divergence. Admixed introductions reported for plants came from sources with a wide range of genetic variation, but were disproportionately absent where there was high genetic divergence among native populations. We conclude that while admixture is common in species introductions and often happens under conditions expected to be beneficial to invaders, these conditions may be constrained by predictable negative genetic interactions, potentially explaining conflicting evidence for admixture's benefits to invasion.

opencc-zeroJul 2021View details →

Data from: Can conflicting selection from pollinators and nectar-robbing antagonists drive adaptive pollen limitation? A conceptual model and empirical test

Pollen limitation is widespread, despite predictions that it shouldn't be. We propose a novel mechanism generating pollen limitation: conflicting selection by pollinators and antagonists on pollinator attraction traits. We introduce a heuristic model demonstrating antagonist-induced adaptive pollen limitation, and present a field study illustrating its occurrence in a wild population. For antagonist-induced adaptive pollen limitation to occur, four criteria must be met: 1) correlated attraction of pollinators and antagonists, 2) greater response by antagonists than pollinators to altered investment in attraction traits, 3) reduced investment in pollinator attraction leading to pollen limitation, and 4) higher fitness for plants with reduced investment in pollinator attraction. We surveyed nectar robbery and reproductive output for 109 Odontonema cuspidatum (Acanthaceae) plants in a pollen-limited population over two years and used experimental floral arrays to evaluate how flower number affects pollination and nectar robbery. Both pollinators and nectar robbers preferred larger floral displays, and nectar robbery reduced reproductive output, suggesting conflicting selection. Survey and experimental data agreed closely on the optimum flower number under antagonist-induced pollen limitation; this number was substantially overrepresented in the population. While criteria for antagonist-induced adaptive pollen limitation are restrictive, the necessary conditions may often be realized. Considering interactions beyond the plant-pollinator dyad illuminates previously overlooked mechanisms generating pollen limitation.

opencc-zeroAug 2021View details →

Data from: Within-species trait variation can lead to size limitations in seed dispersal of small-fruited plants

The inability of small-gaped animals to consume very large fruits may limit seed dispersal of the respective plants. This has often been shown for large-fruited plant species that remain poorly dispersed when large-gaped animal species are lost due to anthropogenic pressure. Little is known about whether gape-size limitations similarly influence seed dispersal of small-fruited plant species that can show a large variation in fruit size within species. In this study, fruit sizes of 15 plant species were compared with the gape sizes of their 41 animal dispersers in the temperate, old-growth Białowieża Forest, Poland. The effect of gape-size limitations on fruit consumption was assessed at the plant species level, and for a subset of nine plant species, also at the individual level, and subindividual level (i.e., fruits of the same plant individual). In addition, for the species subset, fruit-seed trait relationships were investigated to determine whether a restricted access of small-gaped animals to large fruits results in the dispersal of fewer or smaller seeds per fruit. Fruit sizes widely varied among plant species (74.2%), considerably at the subindividual level (17.1%), and to the smallest extent among plant individuals (8.7%). Key disperser species should be able to consume fruits of all plant species and all individuals (except those of the largest-fruited plant species), even if they are able to consume only 28-55% of available fruits. Fruit and seed traits were positively correlated in eight out of nine plant species, indicating that gape size limitations will result in 49% fewer (in one plant species) or 16-21% smaller seeds (in three plant species) dispersed per fruit by small-gaped than by large-gaped main dispersers, respectively. Our results show that a large subindividual variation in fruit size is characteristic for small-fruited plant species, and increases their connectedness with frugivores at the level of plants species and individuals. Simultaneously, however, the large variation in fruit size leads to gape-size limitations that may induce selective pressures on fruit size if large-gaped dispersers become extinct. This study emphasizes the mechanisms by which gape-size limitation at the species, individual and subindividual level shape plant-frugivore interactions and the co-evolution of small-fruited plants.

opencc-zeroAug 2021View details →

Data from: Predicting range shifts of pikas (Mammalia, Ochotonidae) in China under scenarios incorporating land-use change, climate change, and dispersal limitations

Two of the most important forces affecting biodiversity are land-use change (LUC) and global climate change (GCC). Previous studies have modeled their impacts on species separately and together, but few have done so for multiple species with dispersal limitations incorporated into the models. We integrate species distribution models plus a dispersal model to predict LUC and GCC impacts on the ranges of five species of pikas in the Qinghai-Tibet Plateau region of China. Pikas are sensitive to land-use and climate change, and have limited dispersal abilities. The predicted impacts of LUC and GCC on pikas vary between species as well as between LUC and GCC projections. Incorporation of dispersal limitations appreciably restricts the amount of colonized habitat. For all five species, the amount of habitat abandoned or colonized when LUC and GCC are modeled together is less than the sum of LUC and GCC modeled separately. Three of the five species experience a net increase in occupied habitat by 2080 relative to their current ranges under all modeled projections. However, relative to a "Dispersal Only" baseline scenario that assumes no environmental change but continued range expansion into suitable, unoccupied habitat, all five species suffer a net loss of occupied habitat by 2080 under some or all projections. Predictions of future distributions of species based solely on LUC or GCC, as well as predictions assuming additive impacts, can be misleading. Inclusion of dispersal limitations in models markedly alters predicted future distributions of species. The use of a "Dispersal Only" scenario provides a different and perhaps more accurate way to gauge net impacts to species. Future work should consider incorporating all these parameters to better predict the impacts of LUC and GCC on biodiversity.

opencc-zeroDec 2020View details →

Limitations of using surrogates for behaviour classification of accelerometer data: refining methods using random forest models in Caprids

Animal-attached devices can be used on cryptic species to measure their movement and behaviour, enabling unprecedented insights into fundamental aspects of animal ecology and behaviour. However, direct observations of subjects are often still necessary to translate biologging data accurately into meaningful behaviours. As many elusive species cannot easily be observed in the wild, captive or domestic surrogates are typically used to calibrate data from devices. However, the utility of this approach remains equivocal. Here, we assess the validity of using captive conspecifics, and phylogenetically-similar domesticated counterparts (surrogate species) for calibrating behaviour classification. Tri-axial accelerometers and tri-axial magnetometers were used with behavioural observations to build random forest models to predict the behaviours. We applied these methods using captive Alpine ibex (Capra ibex) and a domestic counterpart, pygmy goats (Capra aegagrus hircus), to predict the behaviour including terrain slope for locomotion behaviours of captive Alpine ibex. Behavioural classification of captive Alpine ibex and domestic pygmy goats was highly accurate (> 98%). Model performance was reduced when using data split per individual, i.e., classifying behaviour of individuals not used to train models (mean ± sd = 56.1 ± 11%). Behavioural classifications using domestic counterparts, i.e., pygmy goat observations to predict ibex behaviour, however, were not sufficient to predict all behaviours of a phylogenetically similar species accurately (> 55%). We demonstrate methods to refine the use of random forest models to classify behaviours of both captive and free-living animal species. We suggest there are two main reasons for reduced accuracy when using a domestic counterpart to predict the behaviour of a wild species in captivity; domestication leading to morphological differences and the terrain of the environment in which the animals were observed. We also identify limitations when behaviour is predicted in individuals that are not used to train models. Our results demonstrate that biologging device calibration needs to be conducted using: (i) with similar conspecifics, and (ii) in an area where they can perform behaviours on terrain that reflects that of species in the wild.

opencc-zeroOct 2022View details →

Data for: Flowers that self-shade reduce heat stress and pollen limitation

Premise: Plants are facing increased risk of heat stress with global climate change. Reproductive tissues are particularly sensitive which can result in lower plant fitness. Floral shading and closure are possible mechanisms to limit heat stress although most previous work on petal orientation has considered adaptations to raise temperatures. We hypothesized that floral shading could reduce temperature and increase reproductive success. Results: Individual flowers of all four species that shaded their pistils experienced temperatures 3 – 8 oC lower than those that remained open and unshaded. In our wiring experiment, unencumbered R. coulteri controls were 40% more likely to produce seeds than flowers that were either permanently open or closed. Without added pollen, control flowers produced 2x more seeds than flowers wired open and 8x more than those wired closed. However, pollen addition eliminated the effects of wiring and increased capsule weight and seed production. This suggests that pollen limitation was responsible for observed differences in the wiring treatments. Pollinators may prefer control flowers over those that were wired open or closed; petal shading may make flowers cooler and more attractive to pollinators. Conclusions: Petal shading may be a behavior that allows flowers to reduce heat stress and increases their chances of pollination and seed set.

opencc-by-4.0Oct 2022View details →

Supplemental data for "Applications and Limitations of Portable Density Meter Measurements Of Na-Ca-Mg-K-Cl-SO4 Brines"

Geochemistry, brine density measurements, environmental observations and geochemical modeling of the Bonneville Salt Flats and surrounding area.

Supporting data for: Limited genetic differentiation of Mycetomoellerius mikromelanos in Parc National Soberanía, Panama: Implications for queen dispersal

The coevolutionary relationship between fungus-growing ants (Formicidae: Attini: Attina) and their symbionts has been well-studied in the Panamanian rainforests. To further understand the ecological context of these evolutionary relationships, we have examined the population genetic structure of the fungus-growing ant species Mycetomoellerius mikromelanos Cardenas, Schultz, & Adams 2021, in the Panama Canal Zone. We specifically investigated the presence of population structure, the significance of geographic features (i.e., creeks) limiting gene flow, and relatedness between ant colonies. To accomplish this, we genotyped 85 ant colonies from nine creeks across an approximately 30 km transect in Parque National Soberanía, Panama using double digest restriction-site associated DNA sequencing. We did not find distinct population structures using two genetic clustering methods; however, we did detect an effect of isolation by distance. Furthermore, related colonies were frequently detected on the same creek or neighboring creeks, and some at further geographic distances. Collectively, these findings demonstrate that new colonies tend to establish on natal creeks and occasionally on distant creeks following long-distance dispersal events. We discuss how population genetic patterns reveal the natural history of M. mikromelanos in Parque National Soberanía and how these results fit into the context of fungus-growing ant mutualisms.

Data for: Phosphorus limitation of early growth differs between nitrogen-fixing and non-fixing dry tropical forest tree species

Tropical forests are often characterized by low soil phosphorus (P) availability, suggesting that P limits plant performance. However, how seedlings from different functional types respond to soil P availability is poorly known but important for understanding and modeling forest dynamics under changing environmental conditions. We grew four nitrogen (N)-fixing Fabaceae and seven diverse non-N-fixing tropical dry forest tree species in a shade house under three P fertilization treatments, and evaluated carbon (C) allocation responses, P demand, P-use, investment in P acquisition traits, and correlations among P acquisition traits. N-fixers grew larger with increasing P addition in contrast to non-N-fixers, which showed fewer responses in C allocation and P-use. Foliar P increased with P addition for both functional types, while P acquisition strategies did not vary among treatments but differed between functional types, with N-fixers showing higher root phosphatase activity (RPA) than non-fixers. Growth responses suggest that N-fixers are limited by P, but non-fixers may be limited by other resources. However, regardless of limitation, P acquisition traits such as mycorrhizal colonization and RPA were non-plastic across a steep P gradient. Differential limitation among plant functional types has implications for forest succession and earth system models.

Data for: Single-blind determination of methane detection limits and quantification accuracy using aircraft-based LiDAR

Methane detection limits, emission rate quantification accuracy, and potential cross-species interference are assessed for Bridger Photonics' Gas Mapping LiDAR (GML) system utilizing data collected during laboratory testing and single-blind controlled release testing. Laboratory testing identified no significant interference in the path-integrated methane measurement from the gas species tested (ethylene, ethane, propane, n-butane, i-butane, and carbon dioxide). The controlled release study, comprised of 650 individual measurement passes, represents the largest dataset collected to date to characterize GML with respect to point-source emissions. Binomial regression is utilized to create detection curves illustrating the likelihood of detecting an emission of a given size under different wind conditions and for different flight altitudes. Wind-normalized methane detection limits (90% detection rate) of 0.25 (kg/h)/(m/s) and 0.41 (kg/h)/(m/s) are observed at a flight altitude of 500 feet and 675 feet above ground level, respectively. Quantification accuracy is also assessed for emissions ranging from 0.15 to 1400 kg/h. When emission rate estimates were generated using wind from High-Resolution Rapid Refresh (HRRR) model (the primary wind source that Bridger uses for their commercial operations), linear regression indicates bias of 8.1% (R2 = 0.89). For 95% of controlled releases above Bridger's stated production-sector detection sensitivity (3 kg/h with 90% probability of detection), accuracy of individual emission rate estimates produced using HRRR wind ranged from -64.1% to 87.0%. Across all controlled releases 38.1% of estimates had error within +/- 20%, and 87.3% of measurements were within a factor of two (-50% to +100% error). At low wind speed (less than 2 m/s) and low emission rates (less than 3 kg/h) emission estimates are biased high; however, when removed do not impact the regression significantly. The aggregate quantification error including all detected emission events was +8.2% using the HRRR wind source. The resulting detection curves and quantification accuracy illustrate important implications which must be considered when using measurements from GML or other remote emission measurement techniques to inform or validate inventory models, or to audit reported emission levels from oil and gas systems.

Data from: eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system

In their natural environment, most bacteria preferentially live as complex surface-attached multicellular colonies called biofilms. Biofilms begin with a few cells adhering to a surface, where they multiply to form a mature colony. When conditions deteriorate, cells can leave the biofilm. This dispersion is thought to be an important process that modifies the overall biofilm architecture and that promotes colonization of new environments. In Caulobacter crescentus biofilms, extracellular DNA (eDNA) is released upon cell death and prevents newborn cells from joining the established biofilm. Thus, eDNA promotes the dispersal of newborn cells and the subsequent colonization of new environments. These observations suggest that eDNA is a cue for sensing detrimental environmental conditions in the biofilm. Here we show that the toxin-antitoxin system (TAS) ParDE4 stimulates cell death in areas of a biofilm with decreased O2 availability. In conditions where O2 availability is low, eDNA concentration is correlated with cell death. Cell dispersal away from biofilms is decreased when parDE4 is deleted, probably due to the lower local eDNA concentration. Expression of parDE4 is positively regulated by O2 and the expression of this operon is decreased in biofilms where O2 availability is low. Thus, a programmed cell death mechanism using an O2-regulated TAS stimulates dispersal away from areas of a biofilm with decreased O2 availability and favors colonization of a new, more hospitable environment.