Understanding Uncertainties in Non-Linear Population Trajectories: A Bayesian Semi-Parametric Hierarchical Approach to Large-Scale Surveys of Coral Cover

Recently, attempts to improve decision making in species management have focussed on uncertainties associated with modelling temporal fluctuations in populations. Reducing model uncertainty is challenging; while larger samples improve estimation of species trajectories and reduce statistical errors, they typically amplify variability in observed trajectories. In particular, traditional modelling approaches aimed at estimating population trajectories usually do not account well for nonlinearities and uncertainties associated with multi-scale observations characteristic of large spatio-temporal surveys. We present a Bayesian semi-parametric hierarchical model for simultaneously quantifying uncertainties associated with model structure and parameters, and scale-specific variability over time. We estimate uncertainty across a four-tiered spatial hierarchy of coral cover from the Great Barrier Reef. Coral variability is well described; however, our results show that, in the absence of additional model specifications, conclusions regarding coral trajectories become highly uncertain when considering multiple reefs, suggesting that management should focus more at the scale of individual reefs. The approach presented facilitates the description and estimation of population trajectories and associated uncertainties when variability cannot be attributed to specific causes and origins. We argue that our model can unlock value contained in large-scale datasets, provide guidance for understanding sources of uncertainty, and support better informed decision making

Turbulence measurements in a shallow tidal estuary : analysis based on triple decomposition

In an estuary, mixing and dispersion are the result of the combination of large scale advection and small scale turbulence which are both complex to estimate. A field study was conducted in a small sub-tropical estuary in which high frequency (50 Hz) turbulent data were recorded continuously for about 48 hours. A triple decomposition technique was introduced to isolate the contributions of tides, resonance and turbulence in the flow field. A striking feature of the data set was the slow fluctuations which exhibited large amplitudes up to 50% the tidal amplitude under neap tide conditions. The triple decomposition technique allowed a characterisation of broader temporal scales of high frequency fluctuation data sampled during a number of full tidal cycles.

Hydrological consequences of land-cover change: Quantifying the influence of plants on soil moisture with time-lapse electrical resistivity

Electrical resistivity of soils and sediments is strongly influenced by the presence of interstitial water. Taking advantage of this dependency, electrical-resistivity imaging (ERI) can be effectively utilized to estimate subsurface soil-moisture distributions. The ability to obtain spatially extensive data combined with time-lapse measurements provides further opportunities to understand links between land use and climate processes. In natural settings, spatial and temporal changes in temperature and porewater salinity influence the relationship between soil moisture and electrical resistivity. Apart from environmental factors, technical, theoretical, and methodological ambiguities may also interfere with accurate estimation of soil moisture from ERI data. We have examined several of these complicating factors using data from a two-year study at a forest-grassland ecotone, a boundary between neighboring but different plant communities.At this site, temperature variability accounts for approximately 20-45 of resistivity changes from cold winter to warm summer months. Temporal changes in groundwater conductivity (mean=650 S/cm =57.7) and a roughly 100-S/cm spatial difference between the forest and grassland had only a minor influence on the moisture estimates. Significant seasonal fluctuations in temperature and precipitation had negligible influence on the basic measurement errors in data sets. Extracting accurate temporal changes from ERI can be hindered by nonuniqueness of the inversion process and uncertainties related to time-lapse inversion schemes. The accuracy of soil moisture obtained from ERI depends on all of these factors, in addition to empirical parameters that define the petrophysical soil-moisture/resistivity relationship. Many of the complicating factors and modifying variables to accurately quantify soil moisture changes with ERI can be accounted for using field and theoretical principles.

Decision making in social neurobiological systems modeled as transitions in dynamic pattern formation

Extant models of decision making in social neurobiological systems have typically explained task dynamics as characterized by transitions between two attractors. In this paper, we model a three-attractor task exemplified in a team sport context. The model showed that an attacker–defender dyadic system can be described by the angle x between a vector connecting the participants and the try line. This variable was proposed as an order parameter of the system and could be dynamically expressed by integrating a potential function. Empirical evidence has revealed that this kind of system has three stable attractors, with a potential function of the form V(x)=−k1x+k2ax2/2−bx4/4+x6/6, where k1 and k2 are two control parameters. Random fluctuations were also observed in system behavior, modeled as white noise εt, leading to the motion equation dx/dt = −dV/dx+Q0.5εt, where Q is the noise variance. The model successfully mirrored the behavioral dynamics of agents in a social neurobiological system, exemplified by interactions of players in a team sport.

Temporal characteristics of melanopsin inputs to the human pupil light reflex

Rods, cones and melanopsin containing intrinsically photosensitive retinal ganglion cells (ipRGCs) operate in concert to regulate pupil diameter. The temporal properties of intrinsic ipRGC signalling are distinct to those of rods and cones, including longer latencies and sustained signalling after light offset. We examined whether the melanopsin mediated post-illumination pupil response (PIPR) and pupil constriction were dependent upon the inter-stimulus interval (ISI) between successive light pulses and the temporal frequency of sinusoidal light stimuli. Melanopsin excitation was altered by variation of stimulus wavelength (464 nm and 638 nm lights) and irradiance (11.4 and 15.2 log photons cm(-2) s(-1)). We found that 6s PIPR amplitude was independent of ISI and temporal frequency for all melanopsin excitation levels, indicating complete summation. In contrast to the PIPR, the maximum pupil constriction increased with increasing ISI with high and low melanopsin excitation, but time to minimum diameter was slower with high melanopsin excitation only. This melanopsin response to briefly presented pulses (16 and 100 ms) slows the temporal response of the maximum pupil constriction. We also demonstrate that high melanopsin excitation attenuates the phasic peak-trough pupil amplitude compared to conditions with low melanopsin excitation, indicating an interaction between inner and outer retinal inputs to the pupil light reflex. We infer that outer retina summation is important for rapidly controlling pupil diameter in response to short timescale fluctuations in illumination and may occur at two potential sites, one that is presynaptic to extrinsic photoreceptor input to ipRGCs, or another within the pupil control pathway if ipRGCs have differential temporal tuning to extrinsic and intrinsic signalling.

Understanding the effects of complex seasonality on suburban daily transit ridership

Fluctuations in transit ridership pattern over the year have always concerned transport planners, operators and researchers. Predominantly, metrological elements have been specified to explain variability in ridership volume. However, the outcome of this research points to new direction to explain ridership fluctuation in Brisbane. It explored the relationship between daily bus ridership, seasonality and weather variables for a one-year period, 2012. Rather than segregating the entire year’s ridership into the four calendar seasons (summer, autumn, spring, and winter), this analysis distributed the yearly ridership into nine complex seasonality blocks. These represent calendar season, school/university (academic) period and their corresponding holidays, as well as other observant holidays such as Christmas. The dominance of complex seasonality over typical calendar season was established through analysis and using Multiple Linear Regression (MLR). This research identified a very strong association between complex seasonality and bus ridership. Furthermore, an expectation that Brisbane’s subtropical summer is unfavourable to transit usage was not supported by the findings of this study. A nil association of precipitation and temperature was observed in this region. Finally, this research developed a ridership estimation model, capable of predicting daily ridership within very limited error range. Following the application of this developed model, the estimated annual time series data of each suburb was analysed using Fourier Transformation to appreciate whether any cyclical effects remained, compared with the original data.

Turbulence and Mixing in the Environment: Multi-Device Study in a Sub-tropical Estuary

In an estuary, mixing and dispersion result from a combination of large-scale advection and smallscale turbulence, which are complex to estimate. The predictions of scalar transport and mixing are often inferred and rarely accurate, due to inadequate understanding of the contributions of these difference scales to estuarine recirculation. A multi-device field study was conducted in a small sub-tropical estuary under neap tide conditions with near-zero fresh water discharge for about 48 hours. During the study, acoustic Doppler velocimeters (ADV) were sampled at high frequency (50 Hz), while an acoustic Doppler current profiler (ADCP) and global positioning system (GPS) tracked drifters were used to obtain some lower frequency spatial distribution of the flow parameters within the estuary. The velocity measurements were complemented with some continuous measurement of water depth, conductivity, temperature and some other physiochemical parameters. Thorough quality control was carried out by implementation of relevant error removal filters on the individual data set to intercept spurious data. A triple decomposition (TD) technique was introduced to access the contributions of tides, resonance and ‘true’ turbulence in the flow field. The time series of mean flow measurements for both the ADCP and drifter were consistent with those of the mean ADV data when sampled within a similar spatial domain. The tidal scale fluctuation of velocity and water level were used to examine the response of the estuary to tidal inertial current. The channel exhibited a mixed type wave with a typical phase-lag between 0.035π– 0.116π. A striking feature of the ADV velocity data was the slow fluctuations, which exhibited large amplitudes of up to 50% of the tidal amplitude, particularly in slack waters. Such slow fluctuations were simultaneously observed in a number of physiochemical properties of the channel. The ensuing turbulence field showed some degree of anisotropy. For all ADV units, the horizontal turbulence ratio ranged between 0.4 and 0.9, and decreased towards the bed, while the vertical turbulence ratio was on average unity at z = 0.32 m and approximately 0.5 for the upper ADV (z = 0.55 m). The result of the statistical analysis suggested that the ebb phase turbulence field was dominated by eddies that evolved from ejection type process, while that of the flood phase contained mixed eddies with significant amount related to sweep type process. Over 65% of the skewness values fell within the range expected of a finite Gaussian distribution and the bulk of the excess kurtosis values (over 70%) fell within the range of -0.5 and +2. The TD technique described herein allowed the characterisation of a broader temporal scale of fluctuations of the high frequency data sampled within the durations of a few tidal cycles. The study provides characterisation of the ranges of fluctuation required for an accurate modelling of shallow water dispersion and mixing in a sub-tropical estuary.

Estimate of Lagrangian integral scales in shallow tidal water using high resolution GPS-tracked drifters

In estuaries and natural water channels, the estimate of velocity and dispersion coefficients is critical to the knowledge of scalar transport and mixing. This estimate is rarely available experimentally at sub-tidal time scale in shallow water channels where high frequency is required to capture its spatio-temporal variation. This study estimates Lagrangian integral scales and autocorrelation curves, which are key parameters for obtaining velocity fluctuations and dispersion coefficients, and their spatio-temporal variability from deployments of Lagrangian drifters sampled at 10 Hz for a 4-hour period. The power spectral densities of the velocities between 0.0001 and 0.8 Hz were well fitted with a slope of 5/3 predicted by Kolmogorov’s similarity hypothesis within the inertial subrange, and were similar to the Eulerian power spectral previously observed within the estuary. The result showed that large velocity fluctuations determine the magnitude of the integral time scale, TL. Overlapping of short segments improved the stability of the estimate of TL by taking advantage of the redundant data included in the autocorrelation function. The integral time scales were about 20 s and varied by up to a factor of 8. These results are essential inputs for spatial binning of velocities, Lagrangian stochastic modelling and single particle analysis of the tidal estuary.

A functional MRI study of the relationship between naming treatment outcomes and resting state functional connectivity in post-stroke aphasia

Background: The majority of studies investigating the neural mechanisms underlying treatment in people with aphasia have examined task-based brain activity. However, the use of resting-state fMRI may provide another method of examining the brain mechanisms responsible for treatment-induced recovery, and allows for investigation into connectivity within complex functional networks Methods: Eight people with aphasia underwent 12 treatment sessions that aimed to improve object naming. Half the sessions employed a phonologically-based task, and half the sessions employed a semantic-based task, with resting-state fMRI conducted pre- and post-treatment. Brain regions in which the amplitude of low frequency fluctuations (ALFF) correlated with treatment outcomes were used as seeds for functional connectivity (FC) analysis. FC maps were compared from pre- to post-treatment, as well as with a group of 12 healthy older controls Results: Pre-treatment ALFF in the right middle temporal gyrus (MTG) correlated with greater outcomes for the phonological treatment, with a shift to the left MTG and supramarginal gyrus, as well as the right inferior frontal gyrus, post-treatment. When compared to controls, participants with aphasia showed both normalization and up-regulation of connectivity within language networks post-treatment, predominantly in the left hemisphere Conclusions: The results provide preliminary evidence that treatments for naming impairments affect the FC of language networks, and may aid in understanding the neural mechanisms underlying the rehabilitation of language post-stroke.

Large variations in the Holocene marine radiocarbon reservoir effect reflect ocean circulation and climatic changes

Accurate radiocarbon dating of marine samples requires knowledge of the marine radiocarbon reservoir effect. This effect for a particular site/region is generally assumed constant through time when calibrating marine 14C ages. However, recent studies have shown large temporal variations of several hundred to a couple of thousand years in this effect for a number of regions during the late Quaternary and Holocene. Here we report marine radiocarbon reservoir correction (ΔRΔR) for Heron Reef and Moreton Bay in southwestern (SW) Pacific for the last 8 ka derived from 14C analysis of 230Th-dated corals. Most of our ΔRΔR for the last ∼5.4 ka agree well with their modern value, but large ΔRΔR variability of ∼410 yr (from trough to peak) with possible decadal/centennial fluctuations is evident for the period ∼5.4–8 ka. The latter time interval also has significant variations with similar features in previously published ΔRΔR values for other sites in the Pacific, including southern Peru–northern Chile in southeastern (SE) Pacific, the South China Sea, Vanuatu and Papua New Guinea, with the largest magnitude of ∼920 yr from SE Pacific. The mechanisms for these large ΔRΔR variations across the Pacific during the mid-Holocene are complex processes involving (1) changes in the quantity and 14C content of upwelled waters in tropical east Pacific (TEP) (frequency and intensity of ocean upwelling in the TEP, and contribution of Subantarctic Mode Water to the upwelled waters, which is influenced by the intensity and position of southern westerly winds), and (2) variations in ocean circulation associated with climate change (La Niña/El Niño conditions, intensity of easterly trade winds, positions of the Intertropical Convergence Zone and the South Pacific Convergence Zone), which control the spreading of the older upwelled surface waters in the TEP to the western sites. Our results imply the need for employing temporal changes in ΔRΔR values, instead of constant (modern) values, for age calibration of Holocene marine samples not only for the SW Pacific sites but also for other tropical and subtropical sites in the Pacific.

High connectivity in rastrelliger kanagurta: Influence of historical signatures and migratory behaviour inferred from mtDNA Cytochrome b

Phylogeographic patterns and population structure of the pelagic Indian mackerel, Rastrelliger kanagurta were examined in 23 populations collected from the Indonesian-Malaysian Archipelago (IMA) and the West Indian Ocean (WIO). Despite the vast expanse of the IMA and neighbouring seas, no evidence for geographical structure was evident. An indication that R. kanagurta populations across this region are essentially panmictic. This study also revealed that historical isolation was insufficient for R. kanagurta to attain migration drift equilibrium. Two distinct subpopulations were detected between the WIO and the IMA (and adjacent populations); interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the IMA and WIO regions suggest historical isolation as a result of fluctuations in sea levels during the late Pleistocene. This occurrence resulted in the evolution of a phylogeographic break for this species to the north of the Andaman Sea.

Cuff tear arthropathy: Evidence of functional variation in pyrophosphate metabolism genes

We investigated the role of two genes, ANKH and TNAP, in patients with cuff tear arthropathy. These genes encode proteins which regulate the extracellular concentration of inorganic pyrophosphate, fluctuations of which can lead to calcium crystal formation. Variants were detected by direct sequencing of DNA and their frequencies compared with healthy controls. The effect of variants on protein function was further studied by in vitro approaches. Variant genotypes were observed more frequently in the cases when compared with controls in ANKH (45% and 20%) and TNAP (32% and 9%). Variants in ANKH altered inorganic pyrophosphate (PPi) concentrations in transfected human chondrocytes. There was a higher mean serum concentration of TNAP detected in female patients compared with normal ranges. Cuff tear arthropathy is associated with variants in ANKH and TNAP that alter extracellular inorganic pyrophosphate concentrations causing calcium crystal deposition. This supports a theory that genetic variants predispose patients to primary crystal deposition which when combined with a massive rotator cuff tear leads to the development of arthritis.

Human body stability in floodwaters: The 2011 flood in Brisbane CBD

The flooding of urbanised areas constitutes a hazard to the population and infrastructure. Floods through inundated urban environments have been studied recently and the potential impact of flowing waters on pedestrians is not well known. Herein the stability of individuals in floodwaters is reviewed based upon the re-analysis of detailed field measurements in an inundated section of the central business district of the City of Brisbane (Australia) during the 2011 flood. Detailed water elevation and velocity data were recorded. On-site observations showed some hydrodynamic instability linked to local topographic effects, in the form of a combination of fast turbulent fluctuations and (very) slow fluctuations of water level and velocity associated with surges. The flow conditions in Gardens Point Road was unsafe for individuals and a review of past guidelines suggests that many previous recommendations are over-optimistic and unsafe in real floodwaters.

Wavelet-based multiresolution analysis of Wivenhoe Dam water temperatures

Water temperature measurements from Wivenhoe Dam offer a unique opportunity for studying fluctuations of temperatures in a subtropical dam as a function of time and depth. Cursory examination of the data indicate a complicated structure across both time and depth. We propose simplifying the task of describing these data by breaking the time series at each depth into physically meaningful components that individually capture daily, subannual, and annual (DSA) variations. Precise definitions for each component are formulated in terms of a wavelet-based multiresolution analysis. The DSA components are approximately pairwise uncorrelated within a given depth and between different depths. They also satisfy an additive property in that their sum is exactly equal to the original time series. Each component is based upon a set of coefficients that decomposes the sample variance of each time series exactly across time and that can be used to study both time-varying variances of water temperature at each depth and time-varying correlations between temperatures at different depths. Each DSA component is amenable for studying a certain aspect of the relationship between the series at different depths. The daily component in general is weakly correlated between depths, including those that are adjacent to one another. The subannual component quantifies seasonal effects and in particular isolates phenomena associated with the thermocline, thus simplifying its study across time. The annual component can be used for a trend analysis. The descriptive analysis provided by the DSA decomposition is a useful precursor to a more formal statistical analysis.

Hypoxic corneal changes following 8 hours of scleral contact lens wear

- Purpose To examine the change in corneal thickness and posterior curvature following 8 hours of miniscleral contact lens wear. - Methods Scheimpflug imaging (Pentacam HR, Oculus) was captured before, and immediately following, 8 hours of miniscleral contact lens wear for 15 young (mean age 22 ± 3 years), healthy participants with normal corneae. Natural diurnal variations were considered by measuring baseline corneal changes obtained on a separate control day without contact lens wear. - Results Over the central 6 mm of the cornea, a small, but highly statistically significant amount of edema was observed following 8 hours of miniscleral lens wear, after accounting for normal diurnal fluctuations (mean ± standard deviation percentage swelling 1.70 ± 0.98%, p < 0.0001). Posterior corneal topography remained stable following lens wear (-0.01 ± 0.07 mm steepening over the central 6 mm, p = 0.60). The magnitude of posterior corneal topographical changes following lens wear did not correlate with the extent of lens-related corneal edema (r = -0.16, p = 0.57). Similarly, the initial central corneal vault (maximum post-lens tear layer depth) was not associated with corneal swelling following lens removal (r = 0.27, p = 0.33). - Conclusions While a small amount of corneal swelling was induced following 8 hours of miniscleral lens wear (on average <2%), modern high Dk miniscleral contact lenses that vault the cornea do not induce clinically significant corneal edema or hypoxic related posterior corneal curvature changes during short-term wear. Longer-term studies of compromised eyes (e.g. corneal ectasia) are still required to inform the optimum lens and fitting characteristics for safe scleral lens wear to minimize corneal hypoxia.