Revealing ensemble state transition patterns in multi-electrode neuronal recordings using hidden Markov models

In order to harness the computational capacity of dissociated cultured neuronal networks, it is necessary to understand neuronal dynamics and connectivity on a mesoscopic scale. To this end, this paper uncovers dynamic spatiotemporal patterns emerging from electrically stimulated neuronal cultures using hidden Markov models (HMMs) to characterize multi-channel spike trains as a progression of patterns of underlying states of neuronal activity. However, experimentation aimed at optimal choice of parameters for such models is essential and results are reported in detail. Results derived from ensemble neuronal data revealed highly repeatable patterns of state transitions in the order of milliseconds in response to probing stimuli.

Community patterns of soil bacteria and nematodes in relation to geographic distance

Ecosystems consist of aboveground and belowground subsystems and the structure of their communities is known to change with distance. However, most of this knowledge originates from visible, aboveground components, whereas relatively little is known about how soil community structure varies with distance and if this variability depends on the group of organisms considered. In the present study, we analyzed 30 grasslands from three neighboring chalk hill ridges in southern UK to determine the effect of geographic distance (1e198 km) on the similarity of bacterial communities and of nematode communities in the soil. We found that for both groups, community similarity decayed with distance and that this spatial pattern was not related to changes either in plant community composition or soil chemistry. Site history may have contributed to the observed pattern in the case of nematodes, since the distance effect depended on the presence of different nematode taxa at one of the hill ridges. On the other hand, site-related differences in bacterial community composition alone could not explain the spatial turnover, suggesting that other factors, such as biotic gradients and local dispersal processes that we did not include in our analysis, may be involved in the observed pattern. We conclude that, independently of the variety of causal factors that may be involved, the decay in similarity with geographic distance is a characteristic feature of both communities of soil bacteria and nematodes.

Characterising North Atlantic weather patterns for climate-optimal aircraft routing

Daily weather patterns over the North Atlantic are classified into relevant types: typical weather patterns that may characterize the range of climate impacts from aviation in this region, for both summer and winter. The motivation is to provide a set of weather types to facilitate an investigation of climate-optimal aircraft routing of trans-Atlantic flights (minimizing the climate impact on a flight-by-flight basis). Using the New York to London route as an example, the time-optimal route times are shown to vary by over 60 min, to take advantage of strong tailwinds or avoid headwinds, and for eastbound routes latitude correlates well with the latitude of the jet stream. The weather patterns are classified by their similarity to the North Atlantic Oscillation and East Atlantic teleconnection patterns. For winter, five types are defined; in summer, when there is less variation in jet latitude, only three types are defined. The types can be characterized by the jet strength and position, and therefore the location of the time-optimal routes varies by type. Simple proxies for the climate impact of carbon dioxide, ozone, water vapour and contrails are defined, which depend on parameters such as the route time, latitude and season, the time spent flying in the stratosphere, and the distance over which the air is supersaturated with respect to ice. These proxies are then shown to vary between weather types and between eastbound and westbound routes.

Spatial patterns of office employment in the New York region

This study analyzes the regional spatial dynamics of the New York region for a period of roughly twenty years and places the effects of the 9/11 terrorist attacks in the context of longer-term regional dynamics. The analysis reveals that office-using industries are still heavily concentrated in Manhattan despite ongoing decentralization in many of these industries over the last twenty years. Financial services tend to be highly concentrated in Manhattan whereas administrative and support services are the least concentrated of the six major office-using industry groups. Although office employment has been by and large stagnant in Manhattan for at least two decades, growth of output per worker has outpaced the CMSA as well as the national average. This productivity differential is mainly attributable to competitive advantages of office-using industries in Manhattan and not to differences in industry composition. Finally, the zip-code level analysis of the Manhattan core area yielded further evidence of the existence of significant spillover effects at the small-scale level.

The North Atlantic jet stream under climate change and its relation to the NAO and EA patterns

This paper describes recent variations of the North Atlantic eddy-driven jet stream and analyzes the mean response of the jet to anthropogenic forcing in climate models. Jet stream changes are analyzed both using a direct measure of the near-surface westerly wind maximum and using an EOF-based approach. This allows jet stream changes to be related to the widely used leading patterns of variability: the North Atlantic Oscillation (NAO) and East Atlantic (EA) pattern. Viewed in NAO–EA state space, isolines of jet latitude and speed resemble a distorted polar coordinate system, highlighting the dependence of the jet stream quantities on both spatial patterns. Some differences in the results of the two methods are discussed, but both approaches agree on the general characteristics of the climate models. While there is some agreement between models on a poleward shift of the jet stream in response to anthropogenic forcing, there is still considerable spread between different model projections, especially in winter. Furthermore, the model responses to forcing are often weaker than their biases when compared to a reanalysis. Diagnoses of jet stream changes can be sensitive to the methodologies used, and several aspects of this are also discussed.

Are patterns of growth adaptive?

Models which define fitness in terms of per capita rate of increase of phenotypes are used to analyse patterns of individual growth. It is shown that sigmoid growth curves are an optimal strategy (i.e. maximize fitness) if (Assumption 1a) mortality decreases with body size; (2a) mortality is a convex function of specific growth rate, viewed from above; (3) there is a constraint on growth rate, which is attained in the first phase of growth. If the constraint is not attained then size should increase at a progressively reducing rate. These predictions are biologically plausible. Catch-up growth, for retarded individuals, is generally not an optimal strategy though in special cases (e.g. seasonal breeding) it might be. Growth may be advantageous after first breeding if birth rate is a convex function of G (the fraction of production devoted to growth) viewed from above (Assumption 5a), or if mortality rate is a convex function of G, viewed from above (Assumption 6c). If assumptions 5a and 6c are both false, growth should cease at the age of first reproduction. These predictions could be used to evaluate the incidence of indeterminate versus determinate growth in the animal kingdom though the data currently available do not allow quantitative tests. In animals with invariant adult size a method is given which allows one to calculate whether an increase in body size is favoured given that fecundity and developmental time are thereby increased.