Type-1 error inflation in the traditional by-participant analysis to metamemory accuracy: a generalized mixed-effects model perspective

In order to examine metacognitive accuracy (i.e., the relationship between metacognitive judgment and memory performance), researchers often rely on by-participant analysis, where metacognitive accuracy (e.g., resolution, as measured by the gamma coefficient or signal detection measures) is computed for each participant and the computed values are entered into group-level statistical tests such as the t-test. In the current work, we argue that the by-participant analysis, regardless of the accuracy measurements used, would produce a substantial inflation of Type-1 error rates, when a random item effect is present. A mixed-effects model is proposed as a way to effectively address the issue, and our simulation studies examining Type-1 error rates indeed showed superior performance of mixed-effects model analysis as compared to the conventional by-participant analysis. We also present real data applications to illustrate further strengths of mixed-effects model analysis. Our findings imply that caution is needed when using the by-participant analysis, and recommend the mixed-effects model analysis.

Evidence of a topographic signal in surface soil moisture derived from ENVISAT ASAR wide swath data

The susceptibility of a catchment to flooding is affected by its soil moisture prior to an extreme rainfall event. While soil moisture is routinely observed by satellite instruments, results from previous work on the assimilation of remotely sensed soil moisture into hydrologic models have been mixed. This may have been due in part to the low spatial resolution of the observations used. In this study, the remote sensing aspects of a project attempting to improve flow predictions from a distributed hydrologic model by assimilating soil moisture measurements are described. Advanced Synthetic Aperture Radar (ASAR) Wide Swath data were used to measure soil moisture as, unlike low resolution microwave data, they have sufficient resolution to allow soil moisture variations due to local topography to be detected, which may help to take into account the spatial heterogeneity of hydrological processes. Surface soil moisture content (SSMC) was measured over the catchments of the Severn and Avon rivers in the South West UK. To reduce the influence of vegetation, measurements were made only over homogeneous pixels of improved grassland determined from a land cover map. Radar backscatter was corrected for terrain variations and normalized to a common incidence angle. SSMC was calculated using change detection. To search for evidence of a topographic signal, the mean SSMC from improved grassland pixels on low slopes near rivers was compared to that on higher slopes. When the mean SSMC on low slopes was 30–90%, the higher slopes were slightly drier than the low slopes. The effect was reversed for lower SSMC values. It was also more pronounced during a drying event. These findings contribute to the scant information in the literature on the use of high resolution SAR soil moisture measurement to improve hydrologic models.

Langmuir turbulence and deeply penetrating jets in an unstratified mixed layer

The influence of surface waves and an applied wind stress is studied in an ensemble of large eddy simulations to investigate the nature of deeply penetrating jets into an unstratified mixed layer. The influence of a steady monochromatic surface wave propagating parallel to the wind direction is parameterized using the wave-filtered Craik-Leibovich equations. Tracer trajectories and instantaneous downwelling velocities reveal classic counterrotating Langmuir rolls. The associated downwelling jets penetrate to depths in excess of the wave's Stokes depth scale, δs. Qualitative evidence suggests the depth of the jets is controlled by the Ekman depth scale. Analysis of turbulent kinetic energy (tke) budgets reveals a dynamical distinction between Langmuir turbulence and shear-driven turbulence. In the former, tke production is dominated by Stokes shear and a vertical flux term transports tke to a depth where it is dissipated. In the latter, tke production is from the mean shear and is locally balanced by dissipation. We define the turbulent Langmuir number Lat = (v*/Us)0.5 (v* is the ocean's friction velocity and Us is the surface Stokes drift velocity) and a turbulent anisotropy coefficient Rt = /( + ). The transition between shear-driven and Langmuir turbulence is investigated by varying external wave parameters δs and Lat and by diagnosing Rt and the Eulerian mean and Stokes shears. When either Lat or δs are sufficiently small the Stokes shear dominates the mean shear and the flow is preconditioned to Langmuir turbulence and the associated deeply penetrating jets.

Isolating the signal of ocean global warming

Identifying the signature of global warming in the world's oceans is challenging because low frequency circulation changes can dominate local temperature changes. The IPCC fourth assessment reported an average ocean heating rate of 0.21 ± 0.04 Wm−2 over the period 1961–2003, with considerable spatial, interannual and inter-decadal variability. We present a new analysis of millions of ocean temperature profiles designed to filter out local dynamical changes to give a more consistent view of the underlying warming. Time series of temperature anomaly for all waters warmer than 14°C show large reductions in interannual to inter-decadal variability and a more spatially uniform upper ocean warming trend (0.12 Wm−2 on average) than previous results. This new measure of ocean warming is also more robust to some sources of error in the ocean observing system. Our new analysis provides a useful addition for evaluation of coupled climate models, to the traditional fixed depth analyses.

Characteristics of Langmuir Turbulence in the Ocean Mixed Layer

This study uses large-eddy simulation (LES) to investigate the characteristics of Langmuir turbulence through the turbulent kinetic energy (TKE) budget. Based on an analysis of the TKE budget a velocity scale for Langmuir turbulence is proposed. The velocity scale depends on both the friction velocity and the surface Stokes drift associated with the wave field. The scaling leads to unique profiles of nondimensional dissipation rate and velocity component variances when the Stokes drift of the wave field is sufficiently large compared to the surface friction velocity. The existence of such a scaling shows that Langmuir turbulence can be considered as a turbulence regime in its own right, rather than a modification of shear-driven turbulence. Comparisons are made between the LES results and observations, but the lack of information concerning the wave field means these are mainly restricted to comparing profile shapes. The shapes of the LES profiles are consistent with observed profiles. The dissipation length scale for Langmuir turbulence is found to be similar to the dissipation length scale in the shear-driven boundary layer. Beyond this it is not possible to test the proposed scaling directly using available data. Entrainment at the base of the mixed layer is shown to be significantly enhanced over that due to normal shear turbulence.

On the climate response of the low-latitude Pacific Ocean to changes in the global freshwater cycle

Under global warming, the predicted intensification of the global freshwater cycle will modify the net freshwater flux at the ocean surface. Since the freshwater flux maintains ocean salinity structures, changes to the density-driven ocean circulation are likely. A modified ocean circulation could further alter the climate, potentially allowing rapid changes, as seen in the past. The relevant feedback mechanisms and timescales are poorly understood in detail, however, especially at low latitudes where the effects of salinity are relatively subtle. In an attempt to resolve some of these outstanding issues, we present an investigation of the climate response of the low-latitude Pacific region to changes in freshwater forcing. Initiated from the present-day thermohaline structure, a control run of a coupled ocean-atmosphere general circulation model is compared with a perturbation run in which the net freshwater flux is prescribed to be zero over the ocean. Such an extreme experiment helps to elucidate the general adjustment mechanisms and their timescales. The atmospheric greenhouse gas concentrations are held constant, and we restrict our attention to the adjustment of the upper 1,000 m of the Pacific Ocean between 40°N and 40°S, over 100 years. In the perturbation run, changes to the surface buoyancy, near-surface vertical mixing and mixed-layer depth are established within 1 year. Subsequently, relative to the control run, the surface of the low-latitude Pacific Ocean in the perturbation run warms by an average of 0.6°C, and the interior cools by up to 1.1°C, after a few decades. This vertical re-arrangement of the ocean heat content is shown to be achieved by a gradual shutdown of the heat flux due to isopycnal (i.e. along surfaces of constant density) mixing, the vertical component of which is downwards at low latitudes. This heat transfer depends crucially upon the existence of density-compensating temperature and salinity gradients on isopycnal surfaces. The timescale of the thermal changes in the perturbation run is therefore set by the timescale for the decay of isopycnal salinity gradients in response to the eliminated freshwater forcing, which we demonstrate to be around 10-20 years. Such isopycnal heat flux changes may play a role in the response of the low-latitude climate to a future accelerated freshwater cycle. Specifically, the mechanism appears to represent a weak negative sea surface temperature feedback, which we speculate might partially shield from view the anthropogenically-forced global warming signal at low latitudes. Furthermore, since the surface freshwater flux is shown to play a role in determining the ocean's thermal structure, it follows that evaporation and/or precipitation biases in general circulation models are likely to cause sea surface temperature biases.

Evaluating the efficacy of planktonic foraminifer calcite and 18O data for sea surface temperature reconstruction for the Late Miocene

This study examines the efficacy of published δ18O data from the calcite of Late Miocene surface dwelling planktonic foraminifer shells, for sea surface temperature estimates for the pre-Quaternary. The data are from 33 Late Miocene (Messinian) marine sites from a modern latitudinal gradient of 64°N to 48°S. They give estimates of SSTs in the tropics/subtropics (to 30°N and S) that are mostly cooler than present. Possible causes of this temperature discrepancy are ecological factors (e.g. calcification of shells at levels below the ocean mixed layer), taphonomic effects (e.g. diagenesis or dissolution), inaccurate estimation of Late Miocene seawater oxygen isotope composition, or a real Late Miocene cool climate. The scale of apparent cooling in the tropics suggests that the SST signal of the foraminifer calcite has been reset, at least in part, by early diagenetic calcite with higher δ18O, formed in the foraminifer shells in cool sea bottom pore waters, probably coupled with the effects of calcite formed below the mixed layer during the life of the foraminifera. This hypothesis is supported by the markedly cooler SST estimates from low latitudes—in some cases more than 9 °C cooler than present—where the gradients of temperature and the δ18O composition of seawater between sea surface and sea bottom are most marked, and where ocean surface stratification is high. At higher latitudes, particularly N and S of 30°, the temperature signal is still cooler, though maximum temperature estimates overlap with modern SSTs N and S of 40°. Comparison of SST estimates for the Late Miocene from alkenone unsaturation analysis from the eastern tropical Atlantic at Ocean Drilling Program (ODP) Site 958—which suggest a warmer sea surface by 2–4 °C, with estimates from oxygen isotopes at Deep Sea Drilling Project (DSDP) Site 366 and ODP Site 959, indicating cooler than present SSTs, also suggest a significant impact on the δ18O signal. Nevertheless, much of the original SST variation is clearly preserved in the primary calcite formed in the mixed layer, and records secular and temporal oceanographic changes at the sea surface, such as movement of the Antarctic Polar Front in the Southern Ocean. Cooler SSTs in the tropics and sub-tropics are also consistent with the Late Miocene latitude reduction in the coral reef belt and with interrupted reef growth on the Queensland Plateau of eastern Australia, though it is not possible to quantify absolute SSTs with the existing oxygen isotope data. Reconstruction of an accurate global SST dataset for Neogene time-slices from the existing published DSDP/ODP isotope data, for use in general circulation models, may require a detailed re-assessment of taphonomy at many sites.

Modelling the movement and survival of the root-feeding clover weevil, Sitona lepidus, in the root-zone of white clover

White clover (Trifolium repens) is an important pasture legume but is often difficult to sustain in a mixed sward because, among other things, of the damage to roots caused by the soil-dwelling larval stages of S. lepidus. Locating the root nodules on the white clover roots is crucial for the survival of the newly hatched larvae. This paper presents a numerical model to simulate the movement of newly hatched S. lepidus larvae towards the root nodules, guided by a chemical signal released by the nodules. The model is based on the diffusion-chemotaxis equation. Experimental observations showed that the average speed of the larvae remained approximately constant, so the diffusion-chernotaxis model was modified so that the larvae respond only to the gradient direction of the chemical signal but not its magnitude. An individual-based lattice Boltzmann method was used to simulate the movement of individual larvae, and the parameters required for the model were estimated from the measurement of larval movement towards nodules in soil scanned using X-ray microtomography. The model was used to investigate the effects of nodule density, the rate of release of chemical signal, the sensitivity of the larvae to the signal, and the random foraging of the larvae on the movement and subsequent survival of the larvae. The simulations showed that the most significant factors for larval survival were nodule density and the sensitivity of the larvae to the signal. The dependence of larval survival rate on nodule density was well fitted by the Michealis-Menten kinetics. (c) 2005 Elsevier B.V All rights reserved.

Characterization and identification of mixed-metal phosphates in soils: the application, of Raman spectroscopy

The development of protocols for the identification of metal phosphates in phosphate-treated, metal-contaminated soils is a necessary yet problematical step in the validation of remediation schemes involving immobilization of metals as phosphate phases. The potential for Raman spectroscopy to be applied to the identification of these phosphates in soils has yet to be fully explored. With this in mind, a range of synthetic mixed-metal hydroxylapatites has been characterized and added to soils at known concentrations for analysis using both bulk X-ray powder diffraction (XRD) and Raman spectroscopy. Mixed-metal hydroxylapatites in the binary series Ca-Cd, Ca-Pb, Ca-Sr and Cd-Pb synthesized in the presence of acetate and carbonate ions, were characterized using a range of analytical techniques including XRD, analytical scanning electron microscopy (SEM), infrared spectroscopy (IR), inductively coupled plasma-atomic emission spectrometry (ICP-AES) and Raman spectroscopy. Only the Ca-Cd series displays complete solid solution, although under the synthesis conditions of this study the Cd-5(PO4)(3)OH end member could not be synthesized as a pure phase. Within the Ca-Cd series the cell parameters, IR active modes and Raman active bands vary linearly as a function of Cd content. X-ray diffraction and extended X-ray absorption fine structure spectroscopy (EXAFS) suggest that the Cd is distributed across both the Ca(1) and Ca(2) sites, even at low Cd concentrations. In order to explore the likely detection limits for mixed-metal phosphates in soils for XRD and Raman spectroscopy, soils doped with mixed-metal hydroxylapatites at concentrations of 5, 1 and 0.5 wt.% were then studied. X-ray diffraction could not confirm unambiguously the presence or identity of mixed-metal phosphates in soils at concentrations below 5 wt.%. Raman spectroscopy proved a far more sensitive method for the identification of mixed-metal hydroxylapatites in soils, which could positively identify the presence of such phases in soils at all the dopant concentrations used in this study. Moreover, Raman spectroscopy could also provide an accurate assessment of the degree of chemical substitution in the hydroxylapatites even when present in soils at concentrations as low as 0.1%.

Evaluating the efficacy of planktonic foraminifer calcite and 18O data for sea surface temperature reconstruction for the Late Miocene

This study examines the efficacy of published δ18O data from the calcite of Late Miocene surface dwelling planktonic foraminifer shells, for sea surface temperature estimates for the pre-Quaternary. The data are from 33 Late Miocene (Messinian) marine sites from a modern latitudinal gradient of 64°N to 48°S. They give estimates of SSTs in the tropics/subtropics (to 30°N and S) that are mostly cooler than present. Possible causes of this temperature discrepancy are ecological factors (e.g. calcification of shells at levels below the ocean mixed layer), taphonomic effects (e.g. diagenesis or dissolution), inaccurate estimation of Late Miocene seawater oxygen isotope composition, or a real Late Miocene cool climate. The scale of apparent cooling in the tropics suggests that the SST signal of the foraminifer calcite has been reset, at least in part, by early diagenetic calcite with higher δ18O, formed in the foraminifer shells in cool sea bottom pore waters, probably coupled with the effects of calcite formed below the mixed layer during the life of the foraminifera. This hypothesis is supported by the markedly cooler SST estimates from low latitudes—in some cases more than 9 °C cooler than present—where the gradients of temperature and the δ18O composition of seawater between sea surface and sea bottom are most marked, and where ocean surface stratification is high. At higher latitudes, particularly N and S of 30°, the temperature signal is still cooler, though maximum temperature estimates overlap with modern SSTs N and S of 40°. Comparison of SST estimates for the Late Miocene from alkenone unsaturation analysis from the eastern tropical Atlantic at Ocean Drilling Program (ODP) Site 958—which suggest a warmer sea surface by 2–4 °C, with estimates from oxygen isotopes at Deep Sea Drilling Project (DSDP) Site 366 and ODP Site 959, indicating cooler than present SSTs, also suggest a significant impact on the δ18O signal. Nevertheless, much of the original SST variation is clearly preserved in the primary calcite formed in the mixed layer, and records secular and temporal oceanographic changes at the sea surface, such as movement of the Antarctic Polar Front in the Southern Ocean. Cooler SSTs in the tropics and sub-tropics are also consistent with the Late Miocene latitude reduction in the coral reef belt and with interrupted reef growth on the Queensland Plateau of eastern Australia, though it is not possible to quantify absolute SSTs with the existing oxygen isotope data. Reconstruction of an accurate global SST dataset for Neogene time-slices from the existing published DSDP/ODP isotope data, for use in general circulation models, may require a detailed re-assessment of taphonomy at many sites.

Modelling the movement and survival of the root-feeding clover weevil, Sitona lepidus, in the root-zone of white clover

White clover (Trifolium repens) is an important pasture legume but is often difficult to sustain in a mixed sward because, among other things, of the damage to roots caused by the soil-dwelling larval stages of S. lepidus. Locating the root nodules on the white clover roots is crucial for the survival of the newly hatched larvae. This paper presents a numerical model to simulate the movement of newly hatched S. lepidus larvae towards the root nodules, guided by a chemical signal released by the nodules. The model is based on the diffusion-chemotaxis equation. Experimental observations showed that the average speed of the larvae remained approximately constant, so the diffusion-chernotaxis model was modified so that the larvae respond only to the gradient direction of the chemical signal but not its magnitude. An individual-based lattice Boltzmann method was used to simulate the movement of individual larvae, and the parameters required for the model were estimated from the measurement of larval movement towards nodules in soil scanned using X-ray microtomography. The model was used to investigate the effects of nodule density, the rate of release of chemical signal, the sensitivity of the larvae to the signal, and the random foraging of the larvae on the movement and subsequent survival of the larvae. The simulations showed that the most significant factors for larval survival were nodule density and the sensitivity of the larvae to the signal. The dependence of larval survival rate on nodule density was well fitted by the Michealis-Menten kinetics. (c) 2005 Elsevier B.V All rights reserved.

Coupled simulations of the Indian monsoon intraseasonal oscillation using a fine-resolution mixed-layer ocean model

The intraseasonal variability (ISV) of the Indian summer monsoon is dominated by a 30–50 day oscillation between “active” and “break” events of enhanced and reduced rainfall over the subcontinent, respectively. These organized convective events form in the equatorial Indian Ocean and propagate north to India. Atmosphere–ocean coupled processes are thought to play a key role the intensity and propagation of these events. A high-resolution, coupled atmosphere–mixed-layer-oceanmodel is assembled: HadKPP. HadKPP comprises the Hadley Centre Atmospheric Model (HadAM3) and the K Profile Parameterization (KPP) mixed-layer ocean model. Following studies that upper-ocean vertical resolution and sub-diurnal coupling frequencies improve the simulation of ISV in SSTs, KPP is run at 1 m vertical resolution near the surface; the atmosphere and ocean are coupled every three hours. HadKPP accurately simulates the 30–50 day ISV in rainfall and SSTs over India and the Bay of Bengal, respectively, but suffers from low ISV on the equator. This is due to the HadAM3 convection scheme producing limited ISV in surface fluxes. HadKPP demonstrates little of the observed northward propagation of intraseasonal events, producing instead a standing oscillation. The lack of equatorial ISV in convection in HadAM3 constrains the ability of KPP to produce equatorial SST anomalies, which further weakens the ISV of convection. It is concluded that while atmosphere–ocean interactions are undoubtedly essential to an accurate simulation of ISV, they are not a panacea for model deficiencies. In regions where the atmospheric forcing is adequate, such as the Bay of Bengal, KPP produces SST anomalies that are comparable to the Tropical Rainfall Measuring Mission Microwave Imager (TMI) SST analyses in both their magnitude and their timing with respect to rainfall anomalies over India. HadKPP also displays a much-improved phase relationship between rainfall and SSTs over a HadAM3 ensemble forced by observed SSTs, when both are compared to observations. Coupling to mixed-layer models such as KPP has the potential to improve operational predictions of ISV, particularly when the persistence time of SST anomalies is shorter than the forecast lead time.

Comprehension of wh-questions in a case of mixed dementia

We investigated processing of wh-questions and declarative sentences with differing syntactic complexity in a case of mixed dementia (FA). FA was impaired in her ability to understand syntactically complex declarative sentences and syntactically complex wh-questions beginning with which but not complex who questions. This profile, novel in dementia, is similar to that reported for people with agrammatic aphasia and discerns a ‘‘fault line’’ of the language system along a syntactic/semantic parameter

Thermopile radiometer signal conditioning for surface atmospheric radiation measurements

A highly stable microvolt amplifier for use with atmospheric broadband thermopile radiometers is described. The amplifier has a nominal gain of 500, for bipolar input signals in the range +/- 10 mV from a floating source. The noise level at the input is less than 5 mu V (at 100 k Omega input impedance), permitting instantaneous diffuse solar radiation measurements to 0.5 W m(-2) resolution with 12 bit analog to digital conversion. The temperature stability of gain is better than 5 ppm/degrees C (-4 to 20 degrees C). Averaged over a decade of use, the long term drift of the amplifier gain is less than similar to 0.02%/yr. As well as radiometers measuring solar and terrestrial radiations, the amplifier has also been successfully used with low level signals from thermocouples and ground heat flux plates.