Simona M. Hapca

Adaptive-window indicator kriging: A thresholding method for computed tomography images of porous media

Image segmentation is a crucial step in understanding the structure of porous materials, subsequent analyses being profoundly dependent upon segmentation accuracy. Computed tomography images of naturally occurring heterogeneous materials such as soils are particularly challenging to segment reliably, due to the prevalence of partial volume effects, noise, and other artefacts induced during the image acquisition process. As a result, boundaries between classes of objects, typically pore versus solid in the case of soil, are difficult to identify. Indicator kriging can address these problems in a robust fashion but the computational cost can be very great under some circumstances; this is particularly true under conditions that occur regularly in images of soil. The kriging window size parameter is decisive in obtaining a good quality result at reasonable cost, but is difficult to estimate for an image exhibiting significant heterogeneity. This work demonstrates that, allowing the kriging window size to adapt locally throughout the image provides a very efficient solution. Moreover, it is shown that this can be achieved using a conceptually simple mechanism that involves negligible extra processing cost. The adaptive-window indicator kriging method described in this study achieves easily an order of magnitude improvement in computational performance over a fixed size window implementation without sacrificing quality. In addition, it is shown that, by improving the locality of estimation, the new method is robust when applied to soil images.

Anomalous diffusion of heterogeneous populations characterized by normal diffusion at the individual level

The characterization of the dispersal of populations of non-identical individuals is relevant to most ecological and epidemiological processes. In practice, the movement is quantified by observing relatively few individuals, and averaging to estimate the rate of dispersal of the population as a whole. Here, we show that this can lead to serious errors in the predicted movement of the population if the individuals disperse at different rates. We develop a stochastic model for the diffusion of heterogeneous populations, inspired by the movement of the parasitic nematode Phasmarhabditis hermaphrodita. Direct observations of this nematode in homogeneous and heterogeneous environments reveal a large variation in individual behaviour within the population as reflected initially in the speed of the movement. Further statistical analysis shows that the movement is characterized by temporal correlations and in a heterogeneously structured environment the correlations that occur are of shorter range compared with those in a homogeneous environment. Therefore, by using the first-order correlated random walk techniques, we derive an effective diffusion coefficient for each individual, and show that there is a significant variation in this parameter among the population that follows a gamma distribution. Based on these findings, we build a new dispersal model in which we maintain the classical assumption that individual movement can be described by normal diffusion, but due to the variability in individual dispersal rates, the diffusion coefficient is not constant at the population level and follows a continuous distribution. The conclusions and methodology presented are relevant to any heterogeneous population of individuals with widely different diffusion rates.

Reverse engineering of biochar

This study underpins quantitative relationships that account for the combined effects that starting biomass and peak pyrolysis temperature have on physico-chemical properties of biochar. Meta-data was assembled from published data of diverse biochar samples (n=102) to (i) obtain networks of intercorrelated properties and (ii) derive models that predict biochar properties. Assembled correlation networks provide a qualitative overview of the combinations of biochar properties likely to occur in a sample. Generalized Linear Models are constructed to account for situations of varying complexity, including: dependence of biochar properties on single or multiple predictor variables, where dependence on multiple variables can have additive and/or interactive effects; non-linear relation between the response and predictors; and non-Gaussian data distributions. The web-tool Biochar Engineering implements the derived models to maximize their utility and distribution. Provided examples illustrate the practical use of the networks, models and web-tool to engineer biochars with prescribed properties desirable for hypothetical scenarios.

Three-Dimensional Mapping of Soil Chemical Characteristics at Micrometric Scale by Combining 2D SEM-EDX Data and 3D X-Ray CT Images

There is currently a significant need to improve our understanding of the factors that control a number of critical soil processes by integrating physical, chemical and biological measurements on soils at microscopic scales to help produce 3D maps of the related properties. Because of technological limitations, most chemical and biological measurements can be carried out only on exposed soil surfaces or 2-dimensional cuts through soil samples. Methods need to be developed to produce 3D maps of soil properties based on spatial sequences of 2D maps. In this general context, the objective of the research described here was to develop a method to generate 3D maps of soil chemical properties at the microscale by combining 2D SEM-EDX data with 3D X-ray computed tomography images. A statistical approach using the regression tree method and ordinary kriging applied to the residuals was developed and applied to predict the 3D spatial distribution of carbon, silicon, iron, and oxygen at the microscale. The spatial correlation between the X-ray grayscale intensities and the chemical maps made it possible to use a regression-tree model as an initial step to predict the 3D chemical composition. For chemical elements, e.g., iron, that are sparsely distributed in a soil sample, the regression-tree model provides a good prediction, explaining as much as 90% of the variability in some of the data. However, for chemical elements that are more homogenously distributed, such as carbon, silicon, or oxygen, the additional kriging of the regression tree residuals improved significantly the prediction with an increase in the R2 value from 0.221 to 0.324 for carbon, 0.312 to 0.423 for silicon, and 0.218 to 0.374 for oxygen, respectively. The present research develops for the first time an integrated experimental and theoretical framework, which combines geostatistical methods with imaging techniques to unveil the 3-D chemical structure of soil at very fine scales. The methodology presented in this study can be easily adapted and applied to other types of data such as bacterial or fungal population densities for the 3D characterization of microbial distribution.

Surfactants expressed by soil pseudomonads alter local soil-water distribution, suggesting a hydrological role for these compounds.

Several biological roles have been demonstrated for surfactants expressed by soil and rhizosphere Pseudomonas spp., but the impact of these powerful surface-active agents on the local soil-water distribution within the partially saturated soil pore network has not been examined. To investigate this potential hydrological role, the liquid surface tension (γ)-reducing activities (LSTRA) of 72 pseudomonads isolated from a sandy loam soil by tensiometry of culture supernatants were characterized. Of these, 67% exhibited LSTRA, reducing γ to a minimum (γ(Min)) of 24 mN m(-1) established by individual distribution identification analysis. Soil microcosms were then used to examine the impact of surfactant expression on the local soil-water distribution. The volumetric water content (θ) of soil microcosms was significantly lowered (0.78 ×) by Pseudomonas fluorescens SBW25 expressing the surfactant viscosin compared with a surfactant-deficient mutant (P<0.002). Six of 15 soil pseudomonad isolates examined were found to have a similar impact on θ when compared with sterile microcosms (P<0.05). These findings indicate that surfactant-expressing pseudomonads could modify the local soil-water distributions and that surfactants may therefore play a significant hydrological role in soils, in addition to their recognized biological activities.

Influence of substrate on the body-waving behaviour of nematodes

The soil-dwelling nematodes Steinernema carpocapsae, S. scapterisci, S. feltiae, S. glaseri, Heterorhabditis bacteriophora, H. megidis, Phasmarhabditis hermaphrodita and Caenorhabditis elegans were placed on agar plates each containing four substrates (peat, sand, sandy loam and leaf litter). The body-waving behaviour of infective juveniles was recorded over a 10-day period in the presence or absence of an insect, Galleria mellonella , a susceptible host of some species. Body-waving behaviour differed amongst species and varied significantly in relation to substrate, time and the presence of G. mellonella. Steinernema carpocapsae showed body-waving behaviour more than other species and this tendency increased significantly with time. More S. carpocapsae were seen body waving on peat and leaf litter than on either sandy loam or sand. Conversely, sand promoted body waving in S. scapterisci . Body waving by C. elegans was more common on peat than on any of the other substrates. Heterorhabditis megidis , not previously known to body wave, did so in low numbers on peat and sandy loam. The remaining four species did not body wave. Previous work has shown that the presence of S. glaseri increases body waving by S. carpocapsae. We investigated whether substrate influenced this interaction and also included S. scapterisci in the study. The presence of S. glaseri significantly altered rates of body waving in S. carpocapsae and S. scapterisci in a way that was substrate-dependent. Our data suggest that body-waving behaviour is determined by substrate quality and differing body-waving behaviours may be a mechanism by which nematodes avoid competition.

Epidemiology and outcomes of people with dementia, delirium, and unspecified cognitive impairment in the general hospital: prospective cohort study of 10,014 admissions

BackgroundCognitive impairment of various kinds is common in older people admitted to hospital, but previous research has usually focused on single conditions in highly-selected groups and has rarely examined associations with outcomes. This study examined prevalence and outcomes of cognitive impairment in a large unselected cohort of people aged 65+ with an emergency medical admission.MethodsBetween January 1, 2012, and June 30, 2013, admissions to a single general hospital acute medical unit aged 65+ underwent a structured specialist nurse assessment (n = 10,014). We defined ‘cognitive spectrum disorder’ (CSD) as any combination of delirium, known dementia, or Abbreviated Mental Test (AMT) score < 8/10. Routine data for length of stay (LOS), mortality, and readmission were linked to examine associations with outcomes.ResultsA CSD was present in 38.5% of all patients admitted aged over 65, and in more than half of those aged over 85. Overall, 16.7% of older people admitted had delirium alone, 7.9% delirium superimposed on known dementia, 9.4% known dementia alone, and 4.5% unspecified cognitive impairment (AMT score < 8/10, no delirium, no known dementia). Of those with known dementia, 45.8% had delirium superimposed. Outcomes were worse in those with CSD compared to those without – LOS 25.0 vs. 11.8 days, 30-day mortality 13.6% vs. 9.0%, 1-year mortality 40.0% vs. 26.0%, 1-year death or readmission 62.4% vs. 51.5% (all P < 0.01). There was relatively little difference by CSD type, although people with delirium superimposed on dementia had the longest LOS, and people with dementia the worst mortality at 1 year.ConclusionsCSD is common in older inpatients and associated with considerably worse outcomes, with little variation between different types of CSD. Healthcare systems should systematically identify and develop care pathways for older people with CSD admitted as medical emergencies, and avoid only focusing on condition-specific pathways such as those for dementia or delirium alone.

Analysis of physical pore space characteristics of two pyrolytic biochars and potential as microhabitat

Background and AimsBiochar amendment to soil is a promising practice of enhancing productivity of agricultural systems. The positive effects on crop are often attributed to a promotion of beneficial soil microorganisms while suppressing pathogens e.g. This study aims to determine the influence of biochar feedstock on (i) spontaneous and fungi inoculated microbial colonisation of biochar particles and (ii) physical pore space characteristics of native and fungi colonised biochar particles which impact microbial habitat quality.MethodsPyrolytic biochars from mixed woods and Miscanthus were investigated towards spontaneous colonisation by classical microbiological isolation, phylogenetic identification of bacterial and fungal strains, and microbial respiration analysis. Physical pore space characteristics of biochar particles were determined by X-ray μ-CT. Subsequent 3D image analysis included porosity, surface area, connectivities, and pore size distribution.ResultsMicroorganisms isolated from Wood biochar were more abundant and proliferated faster than those from the Miscanthus biochar. All isolated bacteria belonged to gram-positive bacteria and were feedstock specific. Respiration analysis revealed higher microbial activity for Wood biochar after water and substrate amendment while basal respiration was on the same low level for both biochars. Differences in porosity and physical surface area were detected only in interaction with biochar-specific colonisation. Miscanthus biochar was shown to have higher connectivity values in surface, volume and transmission than Wood biochars as well as larger pores as observed by pore size distribution. Differences in physical properties between colonised and non-colonised particles were larger in Miscanthus biochar than in Wood biochar.ConclusionsVigorous colonisation was found on Wood biochar compared to Miscanthus biochar. This is contrasted by our findings from physical pore space analysis which suggests better habitat quality in Miscanthus biochar than in Wood biochar. We conclude that (i) the selected feedstocks display large differences in microbial habitat quality as well as physical pore space characteristics and (ii) physical description of biochars alone does not suffice for the reliable prediction of microbial habitat quality and recommend that physical and surface chemical data should be linked for this purpose.

The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness

Experimental evolution studies are used to investigate bacterial adaptive radiation in simple microcosms. In the case of the Wrinkly Spreader, a class of biofilm-forming adaptive mutants of Pseudomonas fluorescens SBW25, the current paradigm is that they are only evolutionarily successful in static microcosms where they outcompete other lineages for O2 at the air-liquid interface. However, we have isolated Wrinkly Spreaders from drip-fed glass bead columns as an example of parallel evolution. These mutants are adaptive, with competitive fitness advantages on columns of 1.28-1.78. This might be explained by the enhanced attachment characteristically shown by Wrinkly Spreaders, allowing them to resist liquid flow through the column pore network. A comparison of column and static microcosm-isolated Wrinkly Spreaders showed that many aspects of wrinkleality, including colony reversion, microcosm growth, biofilm strength and attachment, as well as fitness in static microcosms, were significantly different within and between the two groups of mutants. These findings indicate that the two environments had selected for Wrinkly Spreaders with subtly differing degrees of wrinkleality and fitnesses, suggesting that aspects of the Wrinkly Spreader phenotype may have different relative values in static microcosms and drip-fed columns.

Movement of the nematode, Phasmarhabditis hermaphrodita, in a structurally heterogeneous environment

We consider the effect of structural heterogeneity on the movement of the slug-parasitic nematode, Phasmarhabditis hermaphrodita. The study involves image recording and analysis of nematode movement on a homogeneous layer of technical agar compared to movement of nematodes in a structurally heterogeneous environment that was created by adding sand particles to the plates of agar. Features of nematode trail, such as speed, turning angle distribution, fractal dimension and mean square displacement, were calculated for each treatment. The presence of sand particles significantly reduced the speed of nematodes and affected the distribution of the turning angle with an increased tendency for moving forward or radically changing the direction of movement. Also, the power-law pattern of the mean square displacement changed, suggesting that nematode dispersal capacity became slower, from super-diffusive in homogeneous agar to sub-diffusive in the presence of sand particles. Further, the correlation in step length and turning angles was computed as a function of lags between steps and used to identify memory effects on nematode movement. While in the homogeneous environment movement was characterised by strong temporal correlations; the impact of sand particles was to reduce these correlations between steps. The results suggest that the presence of structural heterogeneity introduces a new bias into the movement, which plays an important role in complex environments where the nematode movement may be obstructed by soil particles.