Accounting for management costs in sensitivity analyses of matrix population models

Traditional sensitivity and elasticity analyses of matrix population models have been used to inform management decisions, but they ignore the economic costs of manipulating vital rates. For example, the growth rate of a population is often most sensitive to changes in adult survival rate, but this does not mean that increasing that rate is the best option for managing the population because it may be much more expensive than other options. To explore how managers should optimize their manipulation of vital rates, we incorporated the cost of changing those rates into matrix population models. We derived analytic expressions for locations in parameter space where managers should shift between management of fecundity and survival, for the balance between fecundity and survival management at those boundaries, and for the allocation of management resources to sustain that optimal balance. For simple matrices, the optimal budget allocation can often be expressed as simple functions of vital rates and the relative costs of changing them. We applied our method to management of the Helmeted Honeyeater (Lichenostomus melanops cassidix; an endangered Australian bird) and the koala (Phascolarctos cinereus) as examples. Our method showed that cost-efficient management of the Helmeted Honeyeater should focus on increasing fecundity via nest protection, whereas optimal koala management should focus on manipulating both fecundity and survival simultaneously. These findings are contrary to the cost-negligent recommendations of elasticity analysis, which would suggest focusing on managing survival in both cases. A further investigation of Helmeted Honeyeater management options, based on an individual-based model incorporating density dependence, spatial structure, and environmental stochasticity, confirmed that fecundity management was the most cost-effective strategy. Our results demonstrate that decisions that ignore economic factors will reduce management efficiency. ©2006 Society for Conservation Biology.

GPU accelerated algorithms for computing matrix function vector products with applications to exponential integrators and fractional diffusion

The efficient computation of matrix function vector products has become an important area of research in recent times, driven in particular by two important applications: the numerical solution of fractional partial differential equations and the integration of large systems of ordinary differential equations. In this work we consider a problem that combines these two applications, in the form of a numerical solution algorithm for fractional reaction diffusion equations that after spatial discretisation, is advanced in time using the exponential Euler method. We focus on the efficient implementation of the algorithm on Graphics Processing Units (GPU), as we wish to make use of the increased computational power available with this hardware. We compute the matrix function vector products using the contour integration method in [N. Hale, N. Higham, and L. Trefethen. Computing Aα, log(A), and related matrix functions by contour integrals. SIAM J. Numer. Anal., 46(5):2505–2523, 2008]. Multiple levels of preconditioning are applied to reduce the GPU memory footprint and to further accelerate convergence. We also derive an error bound for the convergence of the contour integral method that allows us to pre-determine the appropriate number of quadrature points. Results are presented that demonstrate the effectiveness of the method for large two-dimensional problems, showing a speedup of more than an order of magnitude compared to a CPU-only implementation.

Modelling intermittent microwave convective drying (IMCD) of food materials

This thesis develops comprehensive mathematical models for an advanced drying technology Intermittent Microwave Convective Drying (IMCD). The models provide an improved physical understanding of the heat and mass transport during the drying process, which will help to improve the quality of dried food and energy efficiency of the process, as well as will increase the ability of automation and optimization. The final model in this thesis represents the most comprehensive fundamental multiphase model for IMCD that considers 3D electromagnetics coupled with multiphase porous media transport processes. The 3D electromagnetics considers Maxwell's equation and multiphase transport model considers three different phases: solid matrix, liquid water and gas consisting water vapour and air. The multiphase transport includes pressure-driven flow, capillary diffusion, binary diffusion, and evaporation. The models developed in this thesis were validated with extensive experimental investigations.

Hierarchical clustering of the genetic connectivity matrix reveals the network topology of gene action on brain microstructure: An N=531 twin study

Genetic correlation (rg) analysis determines how much of the correlation between two measures is due to common genetic influences. In an analysis of 4 Tesla diffusion tensor images (DTI) from 531 healthy young adult twins and their siblings, we generalized the concept of genetic correlation to determine common genetic influences on white matter integrity, measured by fractional anisotropy (FA), at all points of the brain, yielding an NxN genetic correlation matrix rg(x,y) between FA values at all pairs of voxels in the brain. With hierarchical clustering, we identified brain regions with relatively homogeneous genetic determinants, to boost the power to identify causal single nucleotide polymorphisms (SNP). We applied genome-wide association (GWA) to assess associations between 529,497 SNPs and FA in clusters defined by hubs of the clustered genetic correlation matrix. We identified a network of genes, with a scale-free topology, that influences white matter integrity over multiple brain regions.

Stabilization of stormwater biofilters: Impacts of wetting and drying phases and the addition of organic matter to filter media

Ripening period refers to a phase of stabilization in sand filters in water treatment systems that follows a new installation or cleaning of the filter. Intermittent wetting and drying, a unique property of stormwater biofilters, would similarly be subjected to a phase of stabilization. Suspended solids, is an important parameter that is often used to monitor the stabilization of sand filters in water treatment systems. Stormwater biofilters however, contain organic material that is added to the filter layer to enhance nitrate removal, the dynamics of which is seldom analysed in stabilization of stormwater biofilters. Therefore, in this study of stormwater biofiltration in addition to suspended solids (Turbidity), organic matter (TOC, DOC, TN and TKN) was also monitored as a parameter for stabilization of the stormwater biofilter. One Perspex bioretention column (94 mm internal diameter) was fabricated with filter layer that contained 8% organic material and fed with tapwater with different antecedent dry days (0 – 40 day) at 100 mL/min. Samples were collected from the outflow at different time intervals between 2 – 150 minutes and were tested for Total Organic Carbon, Dissolved Organic Carbon, Total Nitrogen, Total Kjeldhal Nitrogen and Turbidity. The column was observed to experience two phases of stabilization, one at the beginning of each event that lasted for 30 minutes while the other phase was observed across subsequent events that related to the age of filter.

An exploratory study into managing value creation in tourism service firms: Understanding value creation phases at the intersection of the tourism service firm and their customers

To satisfy customers, managers of tourism services need to understand their customers' value requirements and then develop a unique service value offering based on those requirements. This understanding underpins their effort to provide superior value to customers and deliver the proposed services through employees. Problematically, previous work on value creation (i.e. customer value) has focused separately on either the firm or customer. This theoretical separation does not allow investigation of whether there may be discrepancies between what value firms offer and what value customers perceive they have received. We bring tourism service firms (manager and employee) and customers together and examine the nature of a tourism service provider's value proposition, its contribution to the value offering, and subsequent impact on customers' perceived-value-in-use. We focus on the important role that employees play as boundary spanning workers in the value creation phases, linking the tourism service provider and customer.

Mathematical modelling of gas production and compositional shift of a CSG (coal seam gas) field: Local model development

In this work we discuss the development of a mathematical model to predict the shift in gas composition observed over time from a producing CSG (coal seam gas) well, and investigate the effect that physical properties of the coal seam have on gas production. A detailed (local) one-dimensional, two-scale mathematical model of a coal seam has been developed. The model describes the competitive adsorption and desorption of three gas species (CH4, CO2 and N2) within a microscopic, porous coal matrix structure. The (diffusive) flux of these gases between the coal matrices (microscale) and a cleat network (macroscale) is accounted for in the model. The cleat network is modelled as a one-dimensional, volume averaged, porous domain that extends radially from a central well. Diffusive and advective transport of the gases occurs within the cleat network, which also contains liquid water that can be advectively transported. The water and gas phases are assumed to be immiscible. The driving force for the advection in the gas and liquid phases is taken to be a pressure gradient with capillarity also accounted for. In addition, the relative permeabilities of the water and gas phases are considered as functions of the degree of water saturation.

Geographical and morphological variation within and between colour phases in Coris julis (L. 1758), a protogynous marine fish

The possible differences between sexes in patterns of morphological variation in geographical space have been explored only in gonochorist freshwater species. We explored patterns of body shape variation in geographical space in a marine sequential hermaphrodite species, Coris julis (L. 1758), analyzing variation both within and between colour phases, through the use of geometric morphometrics and spatially-explicit statistical analyses. We also tested for the association of body shape with two environmental variables: temperature and chlorophyll a concentration, as obtained from time-series of satellite-derived data. Both colour phases showed a significant morphological variation in geographical space and patterns of variation divergent between phases. Although the morphological variation was qualitatively similar, individuals in the initial colour phase showed a more marked variation than individuals in the terminal phase. Body shape showed a weak but significant correlation with environmental variables, which was more pronounced in primary specimens.

High threshold of β1 integrin inhibition required to block collagen I-induced membrane type-1 matrix metalloproteinase (MT1-MMP) activation of matrix metalloproteinase 2 (MMP-2)

Background Matrix metalloproteinase-2 (MMP-2) is an endopeptidase that facilitates extracellular matrix remodeling and molecular regulation, and is implicated in tumor metastasis. Type I collagen (Col I) regulates the activation of MMP-2 through both transcriptional and post-transcriptional means; however gaps remain in our understanding of the involvement of collagen-binding ?1 integrins in collagen-stimulated MMP-2 activation. Methods Three ?1 integrin siRNAs were used to elucidate the involvement of ?1 integrins in the Col I-induced MMP-2 activation mechanism. ?1 integrin knockdown was analyzed by quantitative RT-PCR, Western Blot and FACS analysis. Adhesion assay and collagen gel contraction were used to test the biological effects of ?1 integrin abrogation. MMP-2 activation levels were monitored by gelatin zymography. Results All three ?1 integrin siRNAs were efficient at ?1 integrin knockdown and FACS analysis revealed commensurate reductions of integrins ?2 and ?3, which are heterodimeric partners of ?1, but not ?V, which is not. All three ?1 integrin siRNAs inhibited adhesion and collagen gel contraction, however only the siRNA showing the greatest magnitude of ?1 knockdown inhibited Col I-induced MMP-2 activation and reduced the accompanying upregulation of MT1-MMP, suggesting a dose response threshold effect. Re-transfection with codon-swapped ?1 integrin overcame the reduction in MMP-2 activation induced by Col-1, confirming the ?1 integrin target specificity. MMP-2 activation induced by TPA or Concanavalin A (Con A) was not inhibited by ?1 integrin siRNA knockdown. Conclusion Together, the data reveals that strong abrogation of ?1 integrin is required to block MMP-2 activation induced by Col I, which may have implications for the therapeutic targeting of ?1 integrin.

Effect of decellularization on the load-bearing characteristics of articular cartilage matrix

The application of decellularized extracellular matrices to aid tissue regeneration in reconstructive surgery and regenerative medicine has been promising. Several decellularization protocols for removing cellular materials from natural tissues such as heart valves are currently in use. This paper evaluates the feasibility of potential extension of this methodology relative to the desirable properties of load bearing joint tissues such as stiffness, porosity and ability to recover adequately after deformation to facilitate physiological function. Two decellularization protocols, namely: Trypsin and Triton X-100 were evaluated against their effects on bovine articular cartilage, using biomechanical, biochemical and microstructural techniques. These analyses revealed that decellularization with trypsin resulted in severe loss of mechanical stiffness including deleterious collapse of the collagen architecture which in turn significantly compromised the porosity of the construct. In contrast, triton X-100 detergent treatment yielded samples that retain mechanical stiffness relative to that of the normal intact cartilage sample, but the resulting construct contained ruminant cellular constituents. We conclude that both of these common decellularization protocols are inadequate for producing constructs that can serve as effective replacement and scaffolds to regenerate articular joint tissue.

Stabilization of exotic minority phases in a multicomponent self-assembled molecular network

Trimesic acid (TMA) and alcohols were recently shown to self-assemble into a stable, two-component linear pattern at the solution/highly oriented pyrolytic graphite (HOPG) interface. Away from equilibrium, the TMA/alcohol self-assembled molecular network (SAMN) can coexist with pure-TMA networks. Here, we report on some novel characteristics of these non-equilibrium TMA structures, investigated by scanning tunneling microscopy (STM). We observe that both the chicken-wire and flower-structure TMA phases can host 'guest' C60 molecules within their pores, whereas the TMA/alcohol SAMN does not offer any stable adsorption sites for the C60 molecules. The presence of the C60 molecules at the solution/solid interface was found to improve the STM image quality. We have taken advantage of the high-quality imaging conditions to observe unusual TMA bonding geometries at domain boundaries in the TMA/alcohol SAMN. Boundaries between aligned TMA/alcohol domains can give rise to doubled TMA dimer rows in two different configurations, as well as a tripled-TMA row. The boundaries created between non-aligned domains can create geometries that stabilize TMA bonding configurations not observed on surfaces without TMA/alcohol SAMNs, including small regions of the previously predicted 'super flower' TMA bonding geometry and a tertiary structure related to the known TMA phases. These structures are identified as part of a homologic class of TMA bonding motifs, and we explore some of the reasons for the stabilization of these phases in our multicomponent system.

Feasibility of autologous bone marrow mesenchymal stem cell-derived extracellular matrix scaffold for cartilage tissue engineering

Extracellular matrix (ECM) materials are widely used in cartilage tissue engineering. However, the current ECM materials are unsatisfactory for clinical practice as most of them are derived from allogenous or xenogenous tissue. This study was designed to develop a novel autologous ECM scaffold for cartilage tissue engineering. The autologous bone marrow mesenchymal stem cell-derived ECM (aBMSC-dECM) membrane was collected and fabricated into a three-dimensional porous scaffold via cross-linking and freeze-drying techniques. Articular chondrocytes were seeded into the aBMSC-dECM scaffold and atelocollagen scaffold, respectively. An in vitro culture and an in vivo implantation in nude mice model were performed to evaluate the influence on engineered cartilage. The current results showed that the aBMSC-dECM scaffold had a good microstructure and biocompatibility. After 4 weeks in vitro culture, the engineered cartilage in the aBMSC-dECM scaffold group formed thicker cartilage tissue with more homogeneous structure and higher expressions of cartilaginous gene and protein compared with the atelocollagen scaffold group. Furthermore, the engineered cartilage based on the aBMSC-dECM scaffold showed better cartilage formation in terms of volume and homogeneity, cartilage matrix content, and compressive modulus after 3 weeks in vivo implantation. These results indicated that the aBMSC-dECM scaffold could be a successful novel candidate scaffold for cartilage tissue engineering.

Discussion of “Generalized estimating equations: Notes on the choice of the working correlation matrix”

Objective To discuss generalized estimating equations as an extension of generalized linear models by commenting on the paper of Ziegler and Vens "Generalized Estimating Equations. Notes on the Choice of the Working Correlation Matrix". Methods Inviting an international group of experts to comment on this paper. Results Several perspectives have been taken by the discussants. Econometricians have established parallels to the generalized method of moments (GMM). Statisticians discussed model assumptions and the aspect of missing data Applied statisticians; commented on practical aspects in data analysis. Conclusions In general, careful modeling correlation is encouraged when considering estimation efficiency and other implications, and a comparison of choosing instruments in GMM and generalized estimating equations, (GEE) would be worthwhile. Some theoretical drawbacks of GEE need to be further addressed and require careful analysis of data This particularly applies to the situation when data are missing at random.

Applicability of pebble matrix filtration for the pre-treatment of surface waters containing high turbidity and NOM

Purification of drinking water is routinely achieved by use of conventional coagulants and disinfection procedures. However, there are instances such as flood events when the level of turbidity reaches extreme levels while NOM may be an issue throughout the year. Consequently, there is a need to develop technologies which can effectively treat water of high turbidity during flood events and natural organic matter (NOM) content year round. It was our hypothesis that pebble matrix filtration potentially offered a relatively cheap, simple and reliable means to clarify such challenging water samples. Therefore, a laboratory scale pebble matrix filter (PMF) column was used to evaluate the turbidity and natural organic matter (NOM) pre-treatment performance in relation to 2013 Brisbane River flood water. Since the high turbidity was only a seasonal and short term problem, the general applicability of pebble matrix filters for NOM removal was also investigated. A 1.0 m deep bed of pebbles (the matrix) partly in-filled with either sand or crushed glass was tested, upon which was situated a layer of granular activated carbon (GAC). Turbidity was measured as a surrogate for suspended solids (SS), whereas, total organic carbon (TOC) and UV Absorbance at 254 nm were measured as surrogate parameters for NOM. Experiments using natural flood water showed that without the addition of any chemical coagulants, PMF columns achieved at least 50% turbidity reduction when the source water contained moderate hardness levels. For harder water samples, above 85% turbidity reduction was obtained. The ability to remove 50% turbidity without chemical coagulants may represent significant cost savings to water treatment plants and added environmental benefits accrue due to less sludge formation. A TOC reduction of 35-47% and UV-254 nm reduction of 24-38% was also observed. In addition to turbidity removal during flood periods, the ability to remove NOM using the pebble matrix filter throughout the year may have the benefit of reducing disinfection by-products (DBP) formation potential and coagulant demand at water treatment plants. Final head losses were remarkably low, reaching only 11 cm at a filtration velocity of 0.70 m/h.