Maternally expressed gene1 is a novel maize endosperm transfer cell-specific gene with a maternal parent-of-origin pattern of expression

Growth of the maize (Zea mays) endosperm is tightly regulated by maternal zygotic and sporophytic genes, some of which are subject to a parent-of-origin effect. We report here a novel gene, maternally expressed gene1 (meg1), which shows a maternal parent-of-origin expression pattern during early stages of endosperm development but biallelic expression at later stages. Interestingly, a stable reporter fusion containing the meg1 promoter exhibits a similar pattern of expression. meg1 is exclusively expressed in the basal transfer region of the endosperm. Further, we show that the putatively processed MEG1 protein is glycosylated and subsequently localized to the labyrinthine ingrowths of the transfer cell walls. Hence, the discovery of a parent-of-origin gene expressed solely in the basal transfer region opens the door to epigenetic mechanisms operating in the endosperm to regulate certain aspects of nutrient trafficking from the maternal tissue into the developing seed.

Increases in prefrontal cortex activity when regulating negative emotion predicts symptom severity trajectory over six months in depression

Context: Emotion regulation is critically disrupted in depression and use of paradigms tapping these processes may uncover essential changes in neurobiology during treatment. In addition, as neuroimaging outcome studies of depression commonly utilize solely baseline and endpoint data – which is more prone to week-to week noise in symptomatology – we sought to use all data points over the course of a six month trial. Objective: To examine changes in neurobiology resulting from successful treatment. Design: Double-blind trial examining changes in the neural circuits involved in emotion regulation resulting from one of two antidepressant treatments over a six month trial. Participants were scanned pretreatment, at 2 months and 6 months posttreatment. Setting: University functional magnetic resonance imaging facility. Participants: 21 patients with Major Depressive Disorder and without other Axis I or Axis II diagnoses and 14 healthy controls. Interventions: Venlafaxine XR (doses up to 300mg) or Fluoxetine (doses up to 80mg). Main Outcome Measure: Neural activity, as measured using functional magnetic resonance imaging during performance of an emotion regulation paradigm as well as regular assessments of symptom severity by the Hamilton Rating Scale for Depression. To utilize all data points, slope trajectories were calculated for rate of change in depression severity as well as rate of change of neural engagement. Results: Those depressed individuals showing the steepest decrease in depression severity over the six months were those individuals showing the most rapid increases in BA10 and right DLPFC activity when regulating negative affect over the same time frame. This relationship was more robust than when using solely the baseline and endpoint data. Conclusions: Changes in PFC engagement when regulating negative affect correlate with changes in depression severity over six months. These results are buttressed by calculating these statistics which are more reliable and robust to week-to-week variation than difference scores.

A Lagrangian model of air-mass photochemistry and mixing using a trajectory ensemble: the Cambridge Tropospheric Trajectory model of Chemistry And Transport (CiTTyCAT) version 4.2

A Lagrangian model of photochemistry and mixing is described (CiTTyCAT, stemming from the Cambridge Tropospheric Trajectory model of Chemistry And Transport), which is suitable for transport and chemistry studies throughout the troposphere. Over the last five years, the model has been developed in parallel at several different institutions and here those developments have been incorporated into one "community" model and documented for the first time. The key photochemical developments include a new scheme for biogenic volatile organic compounds and updated emissions schemes. The key physical development is to evolve composition following an ensemble of trajectories within neighbouring air-masses, including a simple scheme for mixing between them via an evolving "background profile", both within the boundary layer and free troposphere. The model runs along trajectories pre-calculated using winds and temperature from meteorological analyses. In addition, boundary layer height and precipitation rates, output from the analysis model, are interpolated to trajectory points and used as inputs to the mixing and wet deposition schemes. The model is most suitable in regimes when the effects of small-scale turbulent mixing are slow relative to advection by the resolved winds so that coherent air-masses form with distinct composition and strong gradients between them. Such air-masses can persist for many days while stretching, folding and thinning. Lagrangian models offer a useful framework for picking apart the processes of air-mass evolution over inter-continental distances, without being hindered by the numerical diffusion inherent to global Eulerian models. The model, including different box and trajectory modes, is described and some output for each of the modes is presented for evaluation. The model is available for download from a Subversion-controlled repository by contacting the corresponding authors.

Quantification of chemical and physical processes influencing ozone during long-range transport using a trajectory ensemble

During long-range transport, many distinct processes – including photochemistry, deposition, emissions and mixing – contribute to the transformation of air mass composition. Partitioning the effects of different processes can be useful when considering the sensitivity of chemical transformation to, for example, a changing environment or anthropogenic influence. However, transformation is not observed directly, since mixing ratios are measured, and models must be used to relate changes to processes. Here, four cases from the ITCT-Lagrangian 2004 experiment are studied. In each case, aircraft intercepted a distinct air mass several times during transport over the North Atlantic, providing a unique dataset and quantifying the net changes in composition from all processes. A new framework is presented to deconstruct the change in O3 mixing ratio (Δ O3) into its component processes, which were not measured directly, taking into account the uncertainty in measurements, initial air mass variability and its time evolution. The results show that the net chemical processing (Δ O3chem) over the whole simulation is greater than net physical processing (Δ O3phys) in all cases. This is in part explained by cancellation effects associated with mixing. In contrast, each case is in a regime of either net photochemical destruction (lower tropospheric transport) or production (an upper tropospheric biomass burning case). However, physical processes influence O3 indirectly through addition or removal of precursor gases, so that changes to physical parameters in a model can have a larger effect on Δ O3chem than Δ O3phys. Despite its smaller magnitude, the physical processing distinguishes the lower tropospheric export cases, since the net photochemical O3 change is −5 ppbv per day in all three cases. Processing is quantified using a Lagrangian photochemical model with a novel method for simulating mixing through an ensemble of trajectories and a background profile that evolves with them. The model is able to simulate the magnitude and variability of the observations (of O3, CO, NOy and some hydrocarbons) and is consistent with the time-average OH following air-masses inferred from hydrocarbon measurements alone (by Arnold et al., 2007). Therefore, it is a useful new method to simulate air mass evolution and variability, and its sensitivity to process parameters.

The role of hydrological transience in peatland pattern formation

The sloping flanks of peatlands are commonly patterned with non-random, contour-parallel stripes of distinct microhabitats such as hummocks, lawns and hollows. Patterning seems to be governed by feedbacks among peatland hydrological processes, plant micro-succession, plant litter production and peat decomposition. An improved understanding of peatland patterning may provide important insights into broader aspects of the long-term development of peatlands and their likely response to future climate change.

Grouping of 24 apple cultivars on the basis of starch degradation rate and their fruit pattern

The ripening processes of 24 apple cultivars were examined in the United Kingdom National Fruit Collection in 2010. Basically the starch content, and additionally ground colour, water-soluble solids content and flesh firmness were studied during ripening. The degradation of the starch content was evaluated using a 0–10 scale. A starch degradation value of 50% was taken to be the optimum harvest date, with harvest beginning at a value of 40% and finishing at 60%. Depending on the cultivar, this represented a harvest window of 9 to 21 days. Later ripening cultivars matured more slowly, leading to a longer harvesting period, with the exception of cv. Feuillemorte. Pronounced differences were observed among the cultivars on the basis of the starch degradation pattern, allowing them to be divided into four groups. Separate charts were elaborated for each group that are recommended for use in practice.

Problems with binary pattern measures for flood model evaluation

As the calibration and evaluation of flood inundation models are a prerequisite for their successful application, there is a clear need to ensure that the performance measures that quantify how well models match the available observations are fit for purpose. This paper evaluates the binary pattern performance measures that are frequently used to compare flood inundation models with observations of flood extent. This evaluation considers whether these measures are able to calibrate and evaluate model predictions in a credible and consistent way, i.e. identifying the underlying model behaviour for a number of different purposes such as comparing models of floods of different magnitudes or on different catchments. Through theoretical examples, it is shown that the binary pattern measures are not consistent for floods of different sizes, such that for the same vertical error in water level, a model of a flood of large magnitude appears to perform better than a model of a smaller magnitude flood. Further, the commonly used Critical Success Index (usually referred to as F<2 >) is biased in favour of overprediction of the flood extent, and is also biased towards correctly predicting areas of the domain with smaller topographic gradients. Consequently, it is recommended that future studies consider carefully the implications of reporting conclusions using these performance measures. Additionally, future research should consider whether a more robust and consistent analysis could be achieved by using elevation comparison methods instead.

The influence of distractors on saccade­ target selection: saccade trajectory effects

It has long been known that the path (trajectory) taken by the eye to land on a target is rarely straight (Yarbus, 1967). Furthermore, the magnitude and direction of this natural tendency for curvature can be modulated by the presence of a competing distractor stimu­ lus presented along with the saccade target. The distractor­related modulation of saccade trajectories provides a subtle measure of the underlying competitive processes involved in saccade target selection. Here we review some of our own studies into the effects distract­ ors have on saccade trajectories, which can be regarded as a way of probing the competit­ ive balance between target and distractor salience.

Attribution of the spatial pattern of CO2-forced sea level change to ocean surface flux changes

Climate models taking part in the coupled model intercomparison project phase 5 (CMIP5) all predict a global mean sea level rise for the 21st century. Yet the sea level change is not spatially uniform and differs among models. Here we evaluate the role of air–sea fluxes of heat, water and momentum (windstress) to find the spatial pattern associated to each of them as well as the spread they can account for. Using one AOGCM to which we apply the surface flux changes from other AOGCMs, we show that the heat flux and windstress changes dominate both the pattern and the spread, but taking the freshwater flux into account as well yields a sea level change pattern in better agreement with the CMIP5 ensemble mean. Differences among the CMIP5 control ocean temperature fields have a smaller impact on the sea level change pattern.

Relationship of dayside auroral precipitations to the open-closed separatrix and the pattern of convective flow

The implications are discussed of acceleration of magnetospheric ions by reflection off two magnetopause Alfvén waves, launched by the reconnection site into the inflow regions on both sides of the boundary. The effects of these waves on the ion populations, predicted using the model described by Lockwood et al. [1996], offer a physical interpretation of all the various widely used classifications of precipitation into the dayside ionosphere, namely, central plasma sheet, dayside boundary plasma sheet (BPS), void, low-latitude boundary layer (LLBL), cusp, mantle, and polar cap. The location of the open-closed boundary and the form of the convection flow pattern are discussed in relation to the regions in which these various precipitations are typically found. Specifically, the model predicts that both the LLBL and the dayside BPS precipitations are on newly opened field lines and places the convection reversal within the LLBL, as is often observed. It is shown that this offers solutions to a number of paradoxes and problems that arise if the LLBL and BPS precipitations are thought of as being on closed field lines. This model is also used to make quantitive predictions of the longitudinal extent and latitudinal width of the cusp, as a function of solar wind density.

Analysis of the regional pattern of sea level change due to ocean dynamics and density changes for 1993-2099 in observations and CMIP5 AOGCMs

Predictions of twenty-first century sea level change show strong regional variation. Regional sea level change observed by satellite altimetry since 1993 is also not spatially homogenous. By comparison with historical and pre-industrial control simulations using the atmosphere–ocean general circulation models (AOGCMs) of the CMIP5 project, we conclude that the observed pattern is generally dominated by unforced (internal generated) variability, although some regions, especially in the Southern Ocean, may already show an externally forced response. Simulated unforced variability cannot explain the observed trends in the tropical Pacific, but we suggest that this is due to inadequate simulation of variability by CMIP5 AOGCMs, rather than evidence of anthropogenic change. We apply the method of pattern scaling to projections of sea level change and show that it gives accurate estimates of future local sea level change in response to anthropogenic forcing as simulated by the AOGCMs under RCP scenarios, implying that the pattern will remain stable in future decades. We note, however, that use of a single integration to evaluate the performance of the pattern-scaling method tends to exaggerate its accuracy. We find that ocean volume mean temperature is generally a better predictor than global mean surface temperature of the magnitude of sea level change, and that the pattern is very similar under the different RCPs for a given model. We determine that the forced signal will be detectable above the noise of unforced internal variability within the next decade globally and may already be detectable in the tropical Atlantic.

Models agree on forced response pattern of precipitation and temperature extremes

Model projections of heavy precipitation and temperature extremes include large uncertainties. We demonstrate that the disagreement between individual simulations primarily arises from internal variability, whereas models agree remarkably well on the forced signal, the change in the absence of internal variability. Agreement is high on the spatial pattern of the forced heavy precipitation response showing an intensification over most land regions, in particular Eurasia and North America. The forced response of heavy precipitation is even more robust than that of annual mean precipitation. Likewise, models agree on the forced response pattern of hot extremes showing the greatest intensification over midlatitudinal land regions. Thus, confidence in the forced changes of temperature and precipitation extremes in response to a certain warming is high. Although in reality internal variability will be superimposed on that pattern, it is the forced response that determines the changes in temperature and precipitation extremes in a risk perspective.

Beyond description to pattern: The contribution of Batesonian epistemology to critical realist research

This paper proposes a limitation to epistemological claims to theory building prevalent in critical realist research. While accepting the basic ontological and epistemological positions of the perspective as developed by Roy Bhaskar, it is argued that application in social science has relied on sociological concepts to explain the underlying generative mechanisms, and that in many cases this has been subject to the effects of an anthropocentric constraint. A novel contribution to critical realist research comes from the work and ideas of Gregory Bateson. This is in service of two central goals of critical realism, namely an abductive route to theory building and a commitment to interdisciplinarity. Five aspects of Bateson’s epistemology are introduced: (1) difference, (2) logical levels of abstraction, (3) recursive causal loops, (4) the logic of metaphor, and (5) Bateson’s theory of mind. The comparison between Bateson and Bhaskar’s ideas is seen as a form of double description, illustrative of the point being raised. The paper concludes with an appeal to critical realists to start exploring the writing and outlook of Bateson himself.

Dynamic game soundtrack generation in response to a continously varying emotional trajectory

Dynamic soundtracking presents various practical and aesthetic challenges to composers working with games. This paper presents an implementation of a system addressing some of these challenges with an affectively-driven music generation algorithm based on a second order Markov-model. The system can respond in real-time to emotional trajectories derived from 2-dimensions of affect on the circumplex model (arousal and valence), which are mapped to five musical parameters. A transition matrix is employed to vary the generated output in continuous response to the affective state intended by the gameplay.