Essay - The role of ecological theory in microbial ecology

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Red-shifts and red herrings in geographical ecology

I draw attention to the need for ecologists to take spatial structure into account more seriously in hypothesis testing. If spatial autocorrelation is ignored, as it usually is, then analyses of ecological patterns in terms of environmental factors can produce very misleading results. This is demonstrated using synthetic but realistic spatial patterns with known spatial properties which are subjected to classical correlation and multiple regression analyses. Correlation between an autocorrelated response variable and each of a set of explanatory variables is strongly biased in favour of those explanatory variables that are highly autocorrelated - the expected magnitude of the correlation coefficient increases with autocorrelation even if the spatial patterns are completely independent. Similarly, multiple regression analysis finds highly autocorrelated explanatory variables "significant" much more frequently than it should. The chances of mistakenly identifying a "significant" slope across an autocorrelated pattern is very high if classical regression is used. Consequently, under these circumstances strongly autocorrelated environmental factors reported in the literature as associated with ecological patterns may not actually be significant. It is likely that these factors wrongly described as important constitute a red-shifted subset of the set of potential explanations, and that more spatially discontinuous factors (those with bluer spectra) are actually relatively more important than their present status suggests. There is much that ecologists can do to improve on this situation. I discuss various approaches to the problem of spatial autocorrelation from the literature and present a randomisation test for the association of two spatial patterns which has advantages over currently available methods.

Hierarchical Bayesian models in ecology: Reconstructing species interaction networks from non-homogeneous species abundance data

The relationships among organisms and their surroundings can be of immense complexity. To describe and understand an ecosystem as a tangled bank, multiple ways of interaction and their effects have to be considered, such as predation, competition, mutualism and facilitation. Understanding the resulting interaction networks is a challenge in changing environments, e.g. to predict knock-on effects of invasive species and to understand how climate change impacts biodiversity. The elucidation of complex ecological systems with their interactions will benefit enormously from the development of new machine learning tools that aim to infer the structure of interaction networks from field data. In the present study, we propose a novel Bayesian regression and multiple changepoint model (BRAM) for reconstructing species interaction networks from observed species distributions. The model has been devised to allow robust inference in the presence of spatial autocorrelation and distributional heterogeneity. We have evaluated the model on simulated data that combines a trophic niche model with a stochastic population model on a 2-dimensional lattice, and we have compared the performance of our model with L1-penalized sparse regression (LASSO) and non-linear Bayesian networks with the BDe scoring scheme. In addition, we have applied our method to plant ground coverage data from the western shore of the Outer Hebrides with the objective to infer the ecological interactions. (C) 2012 Elsevier B.V. All rights reserved.

Spatial and temporal ecology of Scots pine ectomycorrhizas

Spatial analysis was used to explore the distribution of individual species in an ectomycorrhizal (ECM) fungal community to address: whether mycorrhizas of individual ECM fungal species were patchily distributed, and at what scale; and what the causes of this patchiness might be. Ectomycorrhizas were extracted from spatially explicit samples of the surface organic horizons of a pine plantation. The number of mycorrhizas of each ECM fungal species was recorded using morphotyping combined with internal transcribed spacer (ITS) sequencing. Semivariograms, kriging and cluster analyses were used to determine both the extent and scale of spatial autocorrelation in species abundances, potential interactions between species, and change over time. The mycorrhizas of some, but not all, ECM fungal species were patchily distributed and the size of patches differed between species. The relative abundance of individual ECM fungal species and the position of patches of ectomycorrhizas changed between years. Spatial and temporal analysis revealed a dynamic ECM fungal community with many interspecific interactions taking place, despite the homogeneity of the host community. The spatial pattern of mycorrhizas was influenced by the underlying distribution of fine roots, but local root density was in turn influenced by the presence of specific fungal species.

A retrospective study of the behavioural and psychological symptoms of mid and late phase Alzheimer's disease

To document the behavioural and psychological symptoms in patients with a diagnosis of established Alzheimer's disease (AD) for at least 3 years.

The effects of winter ice cover on the trophic ecology of whitefish (Coregonus lavaretus L.) in subarctic lakes

Lakes in Arctic and subarctic regions display extreme levels of seasonal variation in light, temperature and ice cover. Comparatively little is known regarding the effects of such seasonal variation on the diet and resource use of fish species inhabiting these systems. Variation in the diet of European whitefish Coregonus lavaretus (L.) during periods of ice cover in this region is often regarded as 'common knowledge'; however, this aspect of the species' ecology has not been examined empirically. Here, we outline the differences in invertebrate community structure, fish activity, and resource use of monomorphic whitefish populations between summer (August-September) and winter (February-March) in three subarctic lakes in Finnish Lapland. Benthic macroinvertebrate densities did not exhibit measurable differences between summer and winter. Zooplankton diversity and abundance, and activity levels of all fish species (measured as catch per unit effort) were lower in winter. The summer diet of C. lavaretus was typical of a generalist utilising a variety of prey sources. In winter, its dietary niche was significantly reduced, and the diet was dominated by chironomid larvae in all study sites. Pelagic productivity decreases during winter, and fish species inhabiting these systems are therefore restricted to feeding on benthic prey. Sampling time has strong effect on our understanding of resource utilisation by whitefish in subarctic lakes and should be taken into account in future studies of these systems. © 2012 John Wiley & Sons A/S.

Behavioural skeletons in GCM: autonomic management of grid components

Autonomic management can be used to improve the QoS provided by parallel/distributed applications. We discuss behavioural skeletons introduced in earlier work: rather than relying on programmer ability to design “from scratch” efficient autonomic policies, we encapsulate general autonomic controller features into algorithmic skeletons. Then we leave to the programmer the duty of specifying the parameters needed to specialise the skeletons to the needs of the particular application at hand. This results in the programmer having the ability to fast prototype and tune distributed/parallel applications with non-trivial autonomic management capabilities. We discuss how behavioural skeletons have been implemented in the framework of GCM(the Grid ComponentModel developed within the CoreGRID NoE and currently being implemented within the GridCOMP STREP project). We present results evaluating the overhead introduced by autonomic management activities as well as the overall behaviour of the skeletons. We also present results achieved with a long running application subject to autonomic management and dynamically adapting to changing features of the target architecture.
Overall the results demonstrate both the feasibility of implementing autonomic control via behavioural skeletons and the effectiveness of our sample behavioural skeletons in managing the “functional replication” pattern(s).

Judging pain in infants:behavioural, contextual, and developmental determinants

Caretakers intuitively use various sources of evidence when judging infant pain, but the relative importance of salient cues has received little attention. This investigation examined the predictive significance for judgements of painful discomfort in preterm and full-term neonates of behavioural (facial activity and body movement), contextual (invasiveness of the procedure), and developmental (gestational age) information. Judges viewed videotapes showing infants varying in the foregoing characteristics undergoing heel incisions for routine blood sampling purposes. Findings indicated all but the contextual information contributed uniquely to judgements of pain, with facial activity accounting for the most unique variance (35%), followed by bodily activity and gestational age, each accounting for 3% and 1% of the judgmental variance, respectively. Generally, 71% of the variance in ratings of pain could be predicted using facial activity alone, compared to 30% of the variance using bodily activity alone, 19% by relying on context alone, and 8% by referring to gestational age alone. Noteworthy was the tendency to judge early preterm infants to be experiencing less pain even though they were subjected to the same invasive procedure as the older infants. This finding also runs counter to evidence from developmental neurobiology which indicates that preterm newborns may be hypersensitive to invasive procedures.

Pain in the preterm neonate:behavioural and physiological indices

The impact of invasive procedures on preterm neonates has received little systematic attention. We examined facial activity, body movements, and physiological measures in 56 preterm and full-term newborns in response to heel lancing, along with comparison preparatory and recovery intervals. The measures were recorded in special care and full-term nurseries during routine blood sampling. Data analyses indicated that in all measurement categories reactions of greatest magnitude were to the lancing procedure. Neonates with gestational ages as short as 25-27 weeks displayed physiological responsivity to the heel lance, but only in the heart rate measure did this vary with gestational age. Bodily activity was diminished in preterm neonates in general, relative to full-term newborns. Facial activity increased with the gestational age of the infant. Specificity of the response to the heel lance was greatest on the facial activity measure. Identification of pain requires attention to gestational age in the preterm neonate.

The spatial ecology of the whiskered bat (Myotis mystacinus) at the western extreme of its range provides evidence of regional adaptation

Although widespread, the ecology of the whiskered bat, Myotis mystacinus in Europe remains poorly understood. Ireland is positioned at the most western extreme of this species' range. To ascertain the ecology of M. mystacinus at its geographic range extreme, the roosting behaviour, home range and habitat use of females in a maternity roost in Ireland was investigated by radio-tracking. M. mystacinus were active in a diversity of habitats: namely, mixed woodland, riparian vegetation, arable land and rough grassland. However, only mixed woodland and riparian habitats were selected as core foraging areas. This is in contrast to a previous study from Britain where only pasture was utilised but is in agreement with data from Slovakia, where woodland was also selected, whilst riparian areas were also utilised by this species in Germany. A high degree of overlap in the foraging areas of individuals was observed. A total of seven roosts were utilised by tracked bats and roost switching behaviour was observed. We discuss our contrasting results in respect to range limitations, regional variability in landscape structure and the composition of bat communities. The present results have implications for the conservation of M. mystacinus within Ireland and other parts of its range, highlighting the need for range wide ecological studies. Regional variability in the ecology of bats related to landscape factors is an important consideration for bat conservation and therefore must be incorporated into future management plans. (C) 2012 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.

Group Trauma-Focused Cognitive-Behavioural Therapy with Former Child Soldiers and other War-affected Boys in the DR Congo: A Randomised Controlled Trial.

Background: The Democratic Republic of Congo (DRC) has been home to the world’s deadliest con?ict since World War II and is reported to have the largest number of child soldiers in the world. Despite evidence of the debilitating impact of war, no group-based mental health or psychosocial intervention has been evaluated in a randomised controlled trial for psychologically distressed former child soldiers.

Method: A randomised controlled trial involving 50 boys, aged 13–17, including former child soldiers (n = 39) and other war-affected boys (n = 11). They were randomly assigned to an intervention group, or wait-list control group. The intervention group received a 15-session, group-based, culturally adapted Trauma-Focused Cognitive–Behavioural Therapy (TF-CBT) intervention. Assessment interviews were completed at baseline, postintervention and 3-month follow-up (intervention group).

Results: Analysis of Covariance (ANCOVA) demonstrated that, in comparison to the wait-list control group, the TF-CBT intervention group had highly signi?cant reductions in posttraumatic stress symptoms, overall psychosocial distress, depression or anxiety-like symptoms, conduct problems and a signi?cant increase in prosocial behaviour (p < .001 for all). Effect sizes were higher when former child soldier scores were separated for sub-analysis. Three-month follow-up of the intervention group found that treatment gains were maintained.

Conclusions: A culturally modi?ed, group-based TF-CBT intervention was effective in reducing posttraumatic stress and psychosocial distress in former child soldiers and other war-affected boys.

Determinants of neuropsychological and behavioural outcomes in early childhood survivors of congenital heart disease

To evaluate the relative effect of cyanosis, surgical interventions and family processes on neuropsychological and behavioural outcomes in 4-year-old survivors of serious congenital heart disease (CHD).

A long-term follow-up of cognitive, emotional, and behavioural sequelae to Reye syndrome

Eighteen adolescents who had survived Reye syndrome (RS) in early childhood were assessed on cognitive, emotional, and behavioural variables in a second follow-up study tracking this group. Siblings were used as controls. The entire group with RS had survived with no obvious neurological damage at the first follow-up study. Indeed, current findings suggested that long-term cognitive, emotional, and behavioural functioning was comparable to siblings in approximately half of the group with RS. However, two factors were associated with a less favourable outcome. Cognitive, emotional, and behavioural functioning were significantly poorer in the subgroup of survivors whose illness had occurred in the first year of life. In addition, loss of consciousness, although the association with poor outcome was not as noticeable, was also associated with relative deficits on some scales of cognitive ability. Many of these deficits had not been obvious at the first follow-up and the importance of neurodevelopmental factors are considered. Finally, the implications of these findings for research and interventions in RS and other such encephalopathies are discussed.