Agent-based computational modeling of wounded epithelial cell monolayers

Computational modeling of biological systems, or ‘in silico biology’ is an emerging tool for understanding structure and order in biological tissues. Computational models of the behavior of epithelial cells in monolayer cell culture have been developed and used to predict the healing characteristics of scratch wounds made to urothelial cell cultures maintained in low and physiological [Ca2+] environments. Both computational models and in vitro experiments demonstrated that in low exogenous [Ca2+], the closure of 500mm scratch wounds was achieved primarily by cell migration into the denuded area. The wound healing rate in low (0.09mM) [Ca2+] was approximately twice as rapid as in physiological (2mM) [Ca2+]. Computational modeling predicted that in cell cultures that are actively proliferating, no increase in the fraction of cells in S-phase would be expected, and this conclusion was supported experimentally in vitro by BrdU incorporation assay. We have demonstrated that a simple rule-based model of cell behavior, incorporating rules relating to contact inhibition of proliferation and migration, is sufficient to qualitatively predict the calcium-dependent pattern of wound closure observed in vitro. Differences between the in vitro and in silico models suggest a role for wound-induced signaling events in urothelial cell cultures

Inquiring Systems in Approaches to Information Systems Development

The initial assertion of this paper is that information systems development (ISD) failures can best be addressed through a systems approach. Such an approach is characterised by Linstone’s Multiple Viewpoints or Checkland’s Soft System Methodology (SSM), both of which are supported by Singerian inquiring systems. The paper notes that these approaches are both forms of action research and therefore examines the support given to other forms of action research by Singerian inquiring systems. Organisations which recognise that they are not perfect when it comes to ISD and wish to do something about it can be considered as Learning Organisations. Senge’s approach to Learning Organisations is seen as being generic. In the context of ISD, it is contrasted with SSM. In particular, the support required by these approaches from the classical inquiring systems is being considered. Further, the implications of what any resolution might mean for ISD is also considered. The final focus is to consider the framework of ISD as a social construct and examine the benefits of a non-classical inquiring system, based on the philosophy of Rorty

Hydropyrolysis: implications for radiocarbon pre-treatment and characterization of Black Carbon

Charcoal is the result of natural and anthropogenic burning events, when biomass is exposed to elevated temperatures under conditions of restricted oxygen. This process produces a range of materials, collectively known as pyrogenic carbon, the most inert fraction of which is known as Black Carbon (BC). BC degrades extremely slowly, and is resistant to diagenetic alteration involving the addition of exogenous carbon making it a useful target substance for radiocarbon dating particularly of more ancient samples, where contamination issues are critical. We present results of tests using a new method for the quantification and isolation of BC, known as hydropyrolysis (hypy). Results show controlled reductive removal of non-BC organic components in charcoal samples, including lignocellulosic and humic material. The process is reproducible and rapid, making hypy a promising new approach not only for isolation of purified BC for 14C measurement but also in quantification of different labile and resistant sample C fractions

The Epitheliome: agent-based modelling of the social behaviour of cells

We have developed a new computational modelling paradigm for predicting the emergent behaviour resulting from the interaction of cells in epithelial tissue. As proof-of-concept, an agent-based model, in which there is a one-to-one correspondence between biological cells and software agents, has been coupled to a simple physical model. Behaviour of the computational model is compared with the growth characteristics of epithelial cells in monolayer culture, using growth media with low and physiological calcium concentrations. Results show a qualitative fit between the growth characteristics produced by the simulation and the in vitro cell models

Erosion-Corrosion in Pipe Flows of Particle-Laden Liquids

The transmission of particle-bearing liquids in pipes has motivated continuing research into erosion mechanisms and the distribution of erosion rates over wetted surfaces. This chapter covers these initiatives with particular reference to erosion-corrosion modelling within bends and straight sections of cylindrical pipes manufactured in a variety of materials and transporting a variety of liquids. Erosion-corrosion modelling techniques such as submerged slurry jets and rotating cylinder electrodes have been used to study factors influencing material degradation. Improvements in computational fluid dynamics (CFD), such as the development of a moving deforming mesh (MDM) have improved the accuracy of CFD models in predicting pipe wall erosion rates. Combined discrete phase tracking approaches such as the CFD-DPM-DEM (discrete phase-discrete element model) have helped improve computational efficiency. Wall impact erosion models are calibrated using laboratory scale tests. Validation of CFD models using full-scale test data is rare, meaning their accuracy is still largely unreported. Material testing has helped to identify the resilience of prospective pipeline materials to erosion-corrosion, while modifications to internal geometry and pipe section have shown potential to improve erosion-corrosion resistance

The development, landscapes and habitats of the village of Allithwaite - a representative of overlooked lowlands of the English Lake District

Allithwaite consisted of only a few farms and cottages from the seventeenth until the mid-nineteenth centuries, and maps of the development through the centuries are given. In the next 40 years, a large hall, church, vicarage and school were built followed by about 20 residences. In the twentieth Century, over 170 new buildings were added, mainly in small estates but all were contained in the central area of the village because of effective planning control. Apart from the residential area in the centre of the village, the landscapes have therefore remained little changed since the nineteenth century and vary from the open tidal margins of Morecambe Bay to a patchwork of small fields, except for one area of open grassland on a low limestone hill. The landscapes are described together with the associated habitats using a standard classification. The field boundaries were mapped and are also shown and consist mainly of hedgerows but with walls on the shallow limestone soils and the habitats vary from small deciduous woodlands to limestone grassland

Statistical mechanics of topological phase transitions in networks

We provide a phenomenological theory for topological transitions in restructuring networks. In this statistical mechanical approach energy is assigned to the different network topologies and temperature is used as a quantity referring to the level of noise during the rewiring of the edges. The associated microscopic dynamics satisfies the detailed balance condition and is equivalent to a lattice gas model on the edge-dual graph of a fully connected network. In our studies -- based on an exact enumeration method, Monte-Carlo simulations, and theoretical considerations -- we find a rich variety of topological phase transitions when the temperature is varied. These transitions signal singular changes in the essential features of the global structure of the network. Depending on the energy function chosen, the observed transitions can be best monitored using the order parameters Phi_s=s_{max}/M, i.e., the size of the largest connected component divided by the number of edges, or Phi_k=k_{max}/M, the largest degree in the network divided by the number of edges. If, for example the energy is chosen to be E=-s_{max}, the observed transition is analogous to the percolation phase transition of random graphs. For this choice of the energy, the phase-diagram in the [,T] plane is constructed. Single vertex energies of the form E=sum_i f(k_i), where k_i is the degree of vertex i, are also studied. Depending on the form of f(k_i), first order and continuous phase transitions can be observed. In case of f(k_i)=-(k_i+c)ln(k_i), the transition is continuous, and at the critical temperature scale-free graphs can be recovered.Comment: 12 pages, 12 figures, minor changes, added a new refernce, to appear in PR

School-based mental health supports during COVID-19: School professional perspectives

The present study explored the ways school professionals adapted school-based mental health supports and services for remote delivery during the coronavirus disease 2019 (COVID-19) pandemic. We surveyed 81 school professionals (e.g., counselors, psychologists, and social workers) and conducted in-depth interviews with a subsample of professionals (n = 14) to explore their perceptions and experiences of supporting youth with mental health concerns and suicide-related risk during the fall and winter of the 2020–2021 school year. Commonly endorsed school-based mental health interventions (e.g., counseling services and checking in), ways of communicating (phone and email), and individuals delivering support and services to students with suicide-related risk (e.g., counselors and teachers) were identified based on school professional survey responses. Qualitative findings point to facilitators (e.g., specific platforms for connecting with students and families) and barriers (e.g., limited communication) to successful service delivery during COVID-19. Findings highlight the creative ways school support professionals adapted to provide school-based mental health supports. Implications for remote school-based mental health services during and following the pandemic are discussed