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opencc-by-4.0Mar 2018View details →

Model-based analysis of postprandial glycemic response dynamics for different types of food

Background & aims Knowledge of postprandial glycemic response (PPGR) dynamics is important in nutrition management and diabetes research, care and (self)management. In daily life, food intake is the most important factor influencing the occurrence of hyperglycemia. However, the large variability in PPGR dynamics to different types of food is inadequately predicted by existing glycemic measures. The objective of this study was therefore to quantitatively describe PPGR dynamics using a systems approach. Methods Postprandial glucose and insulin data were collected from literature for many different food products and mixed meals. The predictive value of existing measures, such as the Glycemic Index, was evaluated. A physiology-based dynamic model was used to reconstruct the full postprandial response profiles of both glucose and insulin simultaneously. Results We collected a large range of postprandial glucose and insulin dynamics for 53 common food products and mixed meals. Currently available glycemic measures were found to be inadequate to describe the heterogeneity in postprandial dynamics. By estimating model parameters from glucose and insulin data, the physiology-based dynamic model accurately describes the measured data whilst adhering to physiological constraints. Conclusions The physiology-based dynamic model provides a systematic framework to analyze postprandial glucose and insulin profiles. By changing parameter values the model can be adjusted to simulate impaired glucose tolerance and insulin resistance.

opencc-by-4.0Dec 2019View details →

Investigation of Dynamic Fracture of Elastomers - IIa

These set of experiments are the continuation of the investigation of dynamic fracture of Poly-Urethane elastomer; the details of which can be found <a href="https://doi.org/10.5281/zenodo.4034638">here</a>. Currently, a different geometry has been investigated to study the effect of geometry on the crack speeds when inertial effects cannot be neglected. The data consists of images from a High Resolution (HR) camera and a High Speed (HS) camera. The test protocol is similar to the one from the above link and the specimen is 200 mm long, 20 mm tall and 3 mm thick. The name of the folder corresponds to the stretch level of the specimen before the introduction of a crack.

Dataset related to 'Pedagogy matters: Experience-dependent spatiotemporal brain network dynamics'

System Diversity (SD) and Spatio-Temporal Diversity (STD) values (as defined in [Vohryzek2020]) estimated on two groups of children (6-12 y.o.) from Montessori and traditional schools. We provide the values for the two groups and values from 1000 permutations between groups.

opencc-zeroSep 2019View details →

Data from: Evolution alters post-invasion temporal dynamics in experimental communities.

1. The causes and consequences of temporal variation in the abundance of organisms constitute central themes in ecological inquiry. Rapid evolution can occur over ecological time scales, potentially resulting in altered temporal variation in abundance and complicating inferences about the consequences of temporal variation. 2. We assessed whether evolution altered the temporal variability in species' abundances in simple assemblages of species. We then compared experimental results to predictions from two-species models to better understand our results in the context of competitive and predator-prey interactions. 3. We compared founder populations and their evolved descendants in experimental communities of ciliates and rotifers. Using a series of orthogonal contrasts, we then evaluated whether: 1) evolutionary history of invaders or 2) residents, 3) coevolution among invaders and residents, and 4) invasion itself altered temporal variability in species abundances following invasion by a novel species. Using two-species competition and predator-prey models, we also generated predictions to better understand the effects of evolution on temporal variation in the abundances of interacting species. Finally, we compared experimental and modeling results to aid in the interpretation of which interspecific interactions might be affected by ongoing evolution in our communities. 4. In experimental populations, differing evolutionary histories resulted in significant differences among treatments in abundances and temporal variation in abundances of both resident and invading species. For the contrasts, we found evidence that evolutionary history of the invader and residents, coevolution among invaders and residents, and invasion itself affected temporal variability in abundance, but the importance of each differed for the two communities and the species within those communities. When comparing experimental results to model predictions, the increased abundance and decreased temporal variation of one invader, Euplotes daidaleos, are potentially consistent with evolution resulting in reduced attack rates in the novel community. 5. Evolutionary history alone can affect temporal variation in the abundances of species, generating important consequences for interspecific interactions among species and complicating inferences about the consequences of temporal variability in biological communities.

Artificial nightlight alters the predator-prey dynamics of an apex carnivore

Artificial nightlight is increasingly recognized as an important environmental disturbance that influences the habitats and fitness of numerous species. However, its effects on wide-ranging vertebrates and their interactions remain unclear. Light pollution has the potential to amplify land-use change, and as such, answering the question of how this sensory stimulant affects behavior and habitat use of species valued for their ecological roles and economic impacts is critical for conservation and land-use planning. Here, we combined satellite-derived estimates of light pollution, with GPS-data from cougars (Puma concolor; n = 56), mule deer (Odocoileus hemionus; n = 263), and locations of cougar-killed deer (n = 1,562 carcasses), to assess the effects of light exposure on mammal behavior and predator-prey relationships across wildland-urban gradients in the southwestern United States. Our results indicate that deer used the anthropogenic environments to access forage and were more active at night than their wildland conspecifics. Despite higher nightlight levels, cougars killed deer at the wildland-urban interface, but hunted them in the relatively darkest locations. Light had the greatest effect of all covariates on where cougars killed deer at the wildland-urban interface. Both species exhibited functional responses to light pollution at fine scales; individual cougars and deer with less light exposure increasingly avoided illuminated areas when exposed to greater radiance, whereas deer living in the wildland-urban interface selected elevated light levels. We conclude that integrating estimates of light pollution into ecological studies provides crucial insights into how the dynamic human footprint can alter animal behavior and ecosystem function across spatial scales.

opencc-zeroSep 2020View details →

Rainfall pulses mediate long-term plant community compositional dynamics in a semi-arid rangeland

1. Semi-arid rangelands, comprising more than 40% of the Earth's land surface, provide critical ecosystem services. Worldwide, these ecosystems are experiencing rapid degradation due to overgrazing and precipitation changes. However, how plants respond to these interacting factors remains relatively unexplored, and precisely which and how rainfall factors determine plant community dynamics in rangelands has not been well developed. 2. We used a long-term (1953‒2018) dataset from semi-arid rangeland to investigate coupled effects of grazing intensity and rainfall intensity (the total amount of precipitation) on different groups of plant cover (herbaceous, woody, and cacti plants) using linear mixed-effects models, redundancy analysis and structural equation models. We examined how rainfall intensity influenced plant cover dynamics according to pulse size (intensity over time) categories, which we analyzed at three scales: yearly, within the wet season only (June to September), and within the dry season only (October to May). 3. Plant community cover showed a humpbacked trend in the last six decades, mostly through changes in woody plants. Although both grazing intensity and rainfall presented similar humpbacked trends with plant community cover, our models demonstrated that the reduction of plant cover from the 1990s has been mainly caused by a decrease of rainfall rather than grazing intensity, particularly due to profound reductions of the intensity of relatively small rainfall pulses (e.g., 5.1 ~ 15 mm·day-1) during the dry season. Specifically, these small rainfall pulses can increase plant cover of all subgroups of woody and herbaceous species, thereby increasing plant community cover. Moreover, rainfall pulses during the wet season had negative effects on herbaceous species and positive effects on woody plants. These results suggest a phenological niche partitioning between woody plants and herbaceous in subtropical rangelands. 4. Synthesis and applications. Our results show how critical seasonal rainfall pulses are for regulating plant community compositional dynamics, which has significant implications for rangeland management and our ability to adapt and mitigate amplified climate influences in semi-arid ecosystems.

Dataset for "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism"

This record is the dataset for Figures 4, 5, 6, 7, 8 and 9 in the journal article "Sorption, anomalous water transport and dynamic porosity in cement paste: A spatially localised 1H NMR relaxation study and a proposed mechanism" published in Cement and Concrete Research, Volume 133, July 2020, 106045, https://doi.org/10.1016/j.cemconres.2020.106045. Abstract: The link between anomalous water sorption and dynamic porosity in cement pastes is explored using spatially resolved GARField1H nuclear magnetic resonance (NMR) relaxation analysis. A model is developed in which the effective capillary diffusion coefficient is dependent on the instantaneous pore size distribution. This and earlier data show changes in pore size distribution resultant from changes in saturation that do not occur instantaneously with changes in degree of saturation. Therefore, it is assumed that the pore size distribution is always relaxing exponentially towards a (saturation dependent) equilibrium. It follows that the diffusivity is sample history (i.e. time) dependent as well as saturation dependent. This is sufficient to explain anomalies in rapid capillary water sorption. The same concepts are applied to slow drying. In this case, porosity changes occur on a timescale much shorter than drying so the system is always in dynamic equilibrium and anomalies are therefore not seen.

Data: Using environmental DNA and occupancy modeling to estimate rangewide metapopulation dynamics

We demonstrate the power of combining two emergent tools for resolving rangewide metapopulation dynamics. First, we employed environmental DNA (eDNA) surveys to efficiently generate multi-season rangewide site occupancy histories. Second, we developed a novel dynamic, spatial multiscale occupancy model to estimate metapopulation dynamics. The model incorporates spatial relationships, explicitly accounts for non-detection bias and allows direct evaluation of the drivers of extinction and colonization. We applied these tools to examine metapopulation dynamics of endangered tidewater goby, a species endemic to California estuarine habitats. We analyzed rangewide eDNA data from 190 geographically isolated sites (813 total water samples) surveyed from two years (2016 and 2017). Rangewide estimates of the proportion of sites that were occupied varied little between 2016 (0.52) and 2017 (0.51). However, there was evidence of extinction and colonization dynamics. The probability of extinction of an occupied site (0.106) and probability of colonization of an unoccupied site (0.085) were nearly equal. Stability in site occupancy proportions combined with nearly equal rates of extinction and colonization suggests a dynamic equilibrium between the two years surveyed. Assessment of covariate effects revealed that colonization probability increased as the number of occupied neighboring sites increased and as distance between occupied sites decreased. We show that eDNA surveys can rapidly provide a snapshot of a species distribution over a broad geographic range, and when these surveys are paired with occupancy modeling, can uncover metapopulation dynamics and their drivers.

Dataset for "Strain induced electrochemical behaviours of ionic liquid electrolytes in an electric double layer capacitor: Insights from molecular dynamics simulations"

The datafile contains molecular dynamics simulation results for analysing the electrochemical behaviour of ionic liquid based EDLC under compression and tension.

opencc-zeroSep 2020View details →

The scale and dynamics of COVID-19 epidemics across Europe

The number of COVID-19 deaths reported from European countries has varied more than 100-fold. In terms of coronavirus transmission, the relatively low death rates in some countries could be due to low intrinsic (e.g. low population density) or imposed contact rates (e.g. non-pharmaceutical interventions) among individuals, or because fewer people were exposed or susceptible to infection (e.g. smaller populations). Here we develop a flexible empirical model (skew-logistic) to distinguish among these possibilities. We find that countries reporting fewer deaths did not generally have intrinsically lower rates of transmission and epidemic growth, and flatter epidemic curves. Rather, countries with fewer deaths locked down earlier, had shorter epidemics that peaked sooner, and smaller populations. Consequently, as lockdowns are eased we expect, and are starting to see, a resurgence of COVID-19 across Europe.

The dynamics and stoichiometry of dissolved organic carbon release by kelp: Carbon fixation, DOC release and nutrient uptake data

Canopy-forming kelps are foundational species in coastal ecosystems, fixing tremendous amounts of carbon, yet we know little about the ecological and physiological determinants of dissolved organic carbon (DOC) release by kelps. We examined DOC release by the bull kelp, Nereocystis luetkeana, in relation to carbon fixation, nutrient uptake, tissue nitrogen content, and light availability. DOC release was approximately 3.5 times greater during the day than at night. During the day, N. luetkeana blades released an average of 16.2% of fixed carbon as DOC. Carbon fixation increased with light availability but DOC release did not, leading to a lower proportion of fixed carbon released as DOC at high light levels. We found no relationship between carbon fixation and DOC release rates measured concurrently. Rather, DOC release by N. luetkeana blades declined with marginal significance as blade tissue nitrogen content increased and with experimental nitrate addition, supporting the role of stoichiometric relationships in DOC release. Using a stable isotope (13C) tracer method, we demonstrated that inorganic carbon is rapidly fixed and released by N. luetkeana blades as 13DOC, within hours. However, recently fixed carbon (13DOC) comprised less than 20% of the total DOC released, indicating that isotope studies that rely on tracer production alone may underestimate total DOC release, as it is decoupled from recent kelp productivity. Comparing carbon and nitrogen assimilation dynamics of the annual kelp N. luetkeana with the perennial kelp Macrocystis pyrifera revealed that N. luetkeana had significantly higher carbon fixation, DOC production and nitrogen uptake rates per unit dry mass. Both kelp species were able to perform light-independent carbon fixation at night. Carbon fixation by the annual kelp N. luetkeana is as high as 2.35 kg C m-2 yr-1, but an average of 16% of this carbon (376 g C m-2 yr-1) is released as DOC. As kelp forests are increasingly viewed as vehicles for carbon sequestration, it is important to consider the fate of this substantial quantity of DOC released by canopy-forming kelps.

Python Script used in: Evolution of nuptial gifts and its coevolutionary dynamics with male-like persistence traits of females for multiple mating

Many male animals donate nutritive materials during courtship or mating to their female mates. Donation of large-sized gifts, though costly to prepare, can result in increased sperm transfer during mating and delayed remating of the females, resulting in a higher paternity. Nuptial gifting sometimes causes severe female-female competition for obtaining gifts (i.e., sex-role reversal in mate competition) and female polyandry, changing the intensity of sperm competition and the resultant paternity gains. We built a theoretical model to analyze such coevolutionary feedbacks between nuptial gift size (male trait) and propensity for multiple mating (female trait). Our genetically explicit, individual-based computer simulations demonstrate that a positive correlation between donated gift size and the resultant paternity gain is a requisite for the co-occurrence of large-sized gifts and females' competitive multiple mating for the gifts. When gift donation imposes monandry, exaggeration of nuptial gift size also occurs under the assumption that the last male monopolizes paternity, although it reduces mating opportunities, also occurs under the assumption that the last male monopolizes paternity. We also analyzed the causes and consequences of the evolution of a female persistence trait in trading of nuptial gifts, that is, double receptacles for nuptial gifts known to occur in an insect group with a "female penis" (Neotrogla spp.).

opencc-zeroSep 2020View details →

Perturbation drives changing metapopulation dynamics in a top marine predator

Metapopulation theory assumes a balance between local decays/extinctions and local growth/new colonisations. Here we investigate whether recent population declines across part of the UK harbour seal range represent normal metapopulation dynamics or are indicative of perturbations potentially threatening the metapopulation viability, using 20 years of population trends, location tracking data ( n = 380), and UK-wide, multi-generational population genetic data ( n = 269). First, we use microsatellite data to show that two genetic groups previously identified are distinct metapopulations: northern and southern. Then, we characterize the northern metapopulation dynamics in two different periods, before and after the start of regional declines (pre-/peri-perturbation). We identify source–sink dynamics across the northern metapopulation, with two putative source populations apparently supporting three likely sink populations, and a recent metapopulation-wide disruption of migration coincident with the perturbation. The northern metapopulation appears to be in decay, highlighting that changes in local populations can lead to radical alterations in the overall metapopulation's persistence and dynamics.

opencc-zeroDec 2016View details →

Data from: Mammal diversity and metacommunity dynamics in urban green spaces: implications for urban wildlife conservation

As urban growth expands and natural environments fragment, it is essential to understand the ecological roles fulfilled by urban green spaces. To evaluate how urban green spaces function as wildlife habitat, we estimated mammal diversity and metacommunity dynamics in city parks, cemeteries, golf courses, and natural areas throughout the greater Chicago, IL, USA region. We found similar a-diversity (with the exception of city parks), but remarkably dissimilar communities in different urban green spaces. Additionally, the type of urban green space greatly influenced species colonization and persistence rates. For example, coyotes (Canis latrans) had the highest, but white-tailed deer (Odocoileus virginianus) the lowest, probability of persistence in golf courses compared to other green space types. Further, most species had a difficult time colonizing city parks even when sites were seemingly available. Our results indicate that urban green spaces contribute different, but collectively important, habitats for maintaining and conserving biodiversity in cities.

opencc-by-4.0Jan 2020View details →

Vibrational Spectra of a N719-Chromophore/Titania Interface from Empirical-Potential Molecular-Dynamics Simulation, Solvated by a Room Temperature Ionic Liquid

A dye-sensitized solar cell was solvated by RTILs; using optimized empirical potentials, a molecular dynamics simulation was applied to compute vibrational properties. The obtained vibrational spectra were compared with experiment and ab initio molecular dynamics; various empirical potential spectra show how partial-charge charge parameterization of the ionic liquid affects vibrational spectra prediction.

Data from: Temporal dynamics of competitive fertilization in social groups of red junglefowl (Gallus gallus) shed new light on avian sperm competition

Studies of birds have made a fundamental contribution to elucidating sperm competition processes, experimentally demonstrating the role of individual mechanisms in competitive fertilisation. However, the relative importance of these mechanisms and the way in which they interact under natural conditions remain largely unexplored. Here, we conduct a detailed behavioural study of freely-mating replicate groups of red junglefowl, Gallus gallus, to predict the probability that competing males fertilise individual eggs over the course of 10-day trials. Remating frequently with a female and mating last increased a male's probability of fertilisation, but only for eggs ovulated in the last days of a trial. Conversely, older males, and those mating with more polyandrous females, had consistently lower fertilisation success. Similarly, resistance to a male's mating attempts, particularly by younger females, reduced fertilisation probability. After considering these factors, male social status, partner relatedness and the estimated state of a male extragonadal sperm reserves did not predict sperm competition outcomes. These results shed new light on sperm competition dynamics in taxa such as birds, with prolonged female sperm storage and staggered fertilisations.

Neural population dynamics in motor cortex are different for reach and grasp

Low-dimensional linear dynamics are observed in neuronal population activity in primary motor cortex (M1) when monkeys make reaching movements. This population-level behavior is consistent with a role for M1 as an autonomous pattern generator that drives muscles to give rise to movement. In the present study, we examine whether similar dynamics are also observed during grasping movements, which involve fundamentally different patterns of kinematics and muscle activations. Using a variety of analytical approaches, we show that M1 does not exhibit such dynamics during grasping movements. Rather, the grasp-related neuronal dynamics in M1 are similar to their counterparts in somatosensory cortex, whose activity is driven primarily by afferent inputs rather than by intrinsic dynamics. The basic structure of the neuronal activity underlying hand control is thus fundamentally different from that underlying arm control.Low-dimensional linear dynamics are observed in neuronal population activity in primary motor cortex (M1) when monkeys make reaching movements. This population-level behavior is consistent with a role for M1 as an autonomous pattern generator that drives muscles to give rise to movement. In the present study, we examine whether similar dynamics are also observed during grasping movements, which involve fundamentally different patterns of kinematics and muscle activations. Using a variety of analytical approaches, we show that M1 does not exhibit such dynamics during grasping movements. Rather, the grasp-related neuronal dynamics in M1 are similar to their counterparts in somatosensory cortex, whose activity is driven primarily by afferent inputs rather than by intrinsic dynamics. The basic structure of the neuronal activity underlying hand control is thus fundamentally different from that underlying arm control.

Response of lion demography and dynamics to the loss of preferred larger prey

Large carnivores are experiencing range contraction and population declines globally. Prey depletion due to illegal offtake is considered a major contributor, but the effects of prey depletion on large carnivore demography are rarely tested. We measured African lion density and tested the factors that affect survival using mark-recapture models fit to six years of data from known individuals in Kafue National Park (KNP), Zambia. KNP is affected by prey depletion, particularly for large herbivores that were preferred prey for KNP lions a half-century ago. This provides a unique opportunity to test whether variables that explain local prey density also affect lion survival. Average lion density within our study area was 3.43 individuals per 100 km2 (95% CI: 2.79 – 4.23), which was much lower than lion density reported for another miombo ecosystem with similar vegetation structure and rainfall that was less affected by prey depletion. Despite this, comparison to other lion populations showed that age- and sex-specific survival rates for KNP lions were generally good, and factors known to correlate with local prey density had small effects on lion survival. In contrast, recruitment of cubs was poor and average pride size was small. In particular, the proportion of the population comprised of 2nd year cubs was low, indicating that few cubs are recruited into the sub adult age class. Our findings suggest that low recruitment might be a better signal of low prey density than survival. Thus, describing a lion population's age structure in addition to average pride size may be a simple and effective method of initially evaluating whether a lion population is affected by prey depletion. These dynamics should be evaluated for other lion populations and other large carnivore species. Increased resource protection and reducing the underlying drivers of prey depletion are urgent conservation needs for lions and other large carnivores as their conservation is increasingly threatened by range contraction and population declines.

Dynamic evolution and scenario simulation of habitat quality under the impact of land-use change in the Huaihe River Economic Belt, China

1. Land-use data Meaning of the value in the layers: 11: Paddy field  12: Dry land 21: Forestland 22: Shrubland 23: Sparse woodland 24: Other woodland 31: High coverage grassland 32: Medium coverage grassland 33: Low coverage grassland 41: River canal 42: Lake 43: Reservoir and pond 44: Permanent glacial snow 45: Coastal mud flat  46: Inland tidal flat 51: Urban land 52: Rural residential land 53: Industrial and traffic land 61: Dene 62: Gobi Desert 63: Saline and alkaline land 64: Marshland 65: Bare land 66: Bare rock 67: Other unused land 2. GDP data (Meaning of the value in the layer: yuan/km2) 3. Population density data (Meaning of the value in the layer: person/km2) 4. Meteorological data temperature data (unit: ℃) perception data(unit:mm) 5. Terrain data including elevation, slope and aspect 6. Vector data including railways, highways, national roads, provincial roads and county roads