Models of collective cell spreading with variable cell aspect ration: a motivation for degenerate diffusion models

Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multiscale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (PME). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the PME to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models

Application of a continuum theory to vertical vibrations of a layer of granular material

Many interesting phenomena have been observed in layers of granular materials subjected to vertical oscillations; these include the formation of a variety of standing wave patterns, and the occurrence of isolated features called oscillons, which alternately form conical heaps and craters oscillating at one-half of the forcing frequency. No continuum-based explanation of these phenomena has previously been proposed. We apply a continuum theory, termed the double-shearing theory, which has had success in analyzing various problems in the flow of granular materials, to the problem of a layer of granular material on a vertically vibrating rigid base undergoing vertical oscillations in plane strain. There exists a trivial solution in which the layer moves as a rigid body. By investigating linear perturbations of this solution, we find that at certain amplitudes and frequencies this trivial solution can bifurcate. The time dependence of the perturbed solution is governed by Mathieu’s equation, which allows stable, unstable and periodic solutions, and the observed period-doubling behaviour. Several solutions for the spatial velocity distribution are obtained; these include one in which the surface undergoes vertical velocities that have sinusoidal dependence on the horizontal space dimension, which corresponds to the formation of striped standing waves, and is one of the observed patterns. An alternative continuum theory of granular material mechanics, in which the principal axes of stress and rate-of-deformation are coincident, is shown to be incapable of giving rise to similar instabilities

Comprehensive Family Hygiene Promotion in Peri-Urban Cape Town: Reduction of Respiratory Illness in Children Under Five

Background: Examination with Cone Beam CT (CBCT) is common for localizing maxillary canines with eruption disturbance. The benefits and costs of these examinations are unclear. Objectives: To measure: 1. the proportion of orthodontists' treatment decisions that were different based on intraoral and panoramic radiography (M1) compared with CBCT and panoramic radiography (M2); and 2. the costs of producing different treatment plans, regarding patients with maxillary canines with eruption disturbance. Subjects and methods: Orthodontists participated in a web-based survey and were randomly assigned to denote treatment decisions and the level of confidence in this decision for four patient cases presented with M1 or M2 at two occasions for the same patient case. Results: One hundred and twelve orthodontists made 445 assessments based on M1 and M2, respectively. Twenty-four per cent of the treatment decisions were different depending on which method the raters had access to, whereof one case differed significantly from all other cases. The mean total cost per examination was €99.84 using M1 and €134.37 using M2, resulting in an incremental cost per examination of €34.53 for M2. Limitations: Benefits in terms of number of different treatment decisions must be considered as an intermediate outcome for the effectiveness of a diagnostic method and should be interpreted with caution. Conclusions: For the patient cases presented in this study, most treatment decisions were the same irrespective of radiological method. Accordingly, this study does not support routine use of CBCT regarding patients with maxillary canine with eruption disturbance

Mean exit time for diffusion on irregular domains

Many problems in physics, biology, and economics depend upon the duration of time required for a diffusing particle to cross a boundary. As such, calculations of the distribution of first passage time, and in particular the mean first passage time, is an active area of research relevant to many disciplines. Exact results for the mean first passage time for diffusion on simple geometries, such as lines, discs and spheres, are well--known. In contrast, computational methods are often used to study the first passage time for diffusion on more realistic geometries where closed--form solutions of the governing elliptic boundary value problem are not available. Here, we develop a perturbation solution to calculate the mean first passage time on irregular domains formed by perturbing the boundary of a disc or an ellipse. Classical perturbation expansion solutions are then constructed using the exact solutions available on a disc and an ellipse. We apply the perturbation solutions to compute the mean first exit time on two naturally--occurring irregular domains: a map of Tasmania, an island state of Australia, and a map of Taiwan. Comparing the perturbation solutions with numerical solutions of the elliptic boundary value problem on these irregular domains confirms that we obtain a very accurate solution with a few terms in the series only. Matlab software to implement all calculations is available on GitHub.Comment: 31pages, 12 figure

Discrete and continuous mathematical models of sharp-fronted collective cell migration and invasion

Mathematical models describing the spatial spreading and invasion of populations of biological cells are often developed in a continuum modelling framework using reaction-diffusion equations. While continuum models based on linear diffusion are routinely employed and known to capture key experimental observations, linear diffusion fails to predict well-defined sharp fronts that are often observed experimentally. This observation has motivated the use of nonlinear degenerate diffusion, however these nonlinear models and the associated parameters lack a clear biological motivation and interpretation. Here we take a different approach by developing a stochastic discrete lattice-based model incorporating biologically-inspired mechanisms and then deriving the reaction-diffusion continuum limit. Inspired by experimental observations, agents in the simulation deposit extracellular material, that we call a substrate, locally onto the lattice, and the motility of agents is taken to be proportional to the substrate density. Discrete simulations that mimic a two--dimensional circular barrier assay illustrate how the discrete model supports both smooth and sharp-fronted density profiles depending on the rate of substrate deposition. Coarse-graining the discrete model leads to a novel partial differential equation (PDE) model whose solution accurately approximates averaged data from the discrete model. The new discrete model and PDE approximation provides a simple, biologically motivated framework for modelling the spreading, growth and invasion of cell populations with well-defined sharp frontsComment: 47 Pages, 8 Figure

Identification of Violence in the Home - Pediatric and Parental Reports

Objectives: To compare the rates of domestic violence reported by mothers with those identified by physicians, to compare the rates of harsh discipline practices reported by mothers with the rates of abuse identified by physicians, and to examine the relationship between reported domestic violence and harsh discipline practices. Design: Interviews with parents and pediatricians to compare pediatric detection of domestic violence and child abuse with parental reports of domestic violence and harsh discipline practices. Setting: Community-based pediatric practices in the 13-town greater New Haven, Conn, area. Participants: Of the 23 practices invited, 19 agreed to participate. Of the 2006 parents of eligible 4- to 8-year-olds asked to participate, 1886 (94%) completed the Child Behavior Checklist. Of those invited into the interview portion, 1148 (83%) completed the 90-minute in-person interview. Main Outcome Measures: Percentages of cases of domestic violence identified by pediatricians and reported by mothers. Percentages of cases of child abuse detected by pediatricians and percentages of mothers reporting that they have hit their children and left a mark. Results: Pediatricians detected domestic violence in 0.3% of the cases, but parents reported domestic violence in 4.2% (kappa = 0.106 [95% confidence interval, -0.007 to 0.219]). Pediatricians identified physical abuse of children in 0.5% of the cases, while mothers reported hitting their children and leaving a mark in 21.6% (kappa = 0.003 [95% confidence interval, -0.018 to 0.024]). Mothers reporting domestic violence were significantly more likely to report hitting hard enough to leave a mark (relative risk, 1.6 ([95% confidence interval, 1.09-2.38]) compared with those not reporting domestic violence. Physicians identifying domestic violence were not significantly more likely to report child abuse than those not identifying domestic violence. Conclusions: Parents report more cases of violence than pediatricians detect. Pediatricians should ask parents directly about domestic violence and harsh discipline

Implicit reconstructions of thin leaf surfaces from large, noisy point clouds

Thin surfaces, such as the leaves of a plant, pose a significant challenge for implicit surface reconstruction techniques, which typically assume a closed, orientable surface. We show that by approximately interpolating a point cloud of the surface (augmented with off-surface points) and restricting the evaluation of the interpolant to a tight domain around the point cloud, we need only require an orientable surface for the reconstruction. We use polyharmonic smoothing splines to fit approximate interpolants to noisy data, and a partition of unity method with an octree-like strategy for choosing subdomains. This method enables us to interpolate an N-point dataset in O(N) operations. We present results for point clouds of capsicum and tomato plants, scanned with a handheld device. An important outcome of the work is that sufficiently smooth leaf surfaces are generated that are amenable for droplet spreading simulations

Beaten into Submissiveness? An Investigation into the Protective Strategies used by Survivors of Domestic Abuse

This is a pre-copyedited, author-produced pdf of an article accepted for publication in Journal of Interpersonal Violence following peer review. Laura Irving & Ben Chi-pun Liu, 'Beaten into Submissiveness? An investigation Into the Protective Strategies Used by Survivors of Domestic Abuse', Journal of Interpersonal Violence, first published online 14 December 2016, available online at doi: 10.1177/0886260516682520 © The Author(s) 2016 Published by SAGEThe aim of the study was to identify the prevalence and perceived helpfulness of a variety of protective strategies that were used by female survivors of domestic abuse and to explore factors that may have influenced strategy usage. Forty participants were recruited from a voluntary sector domestic abuse service, commissioned by an outer London local authority in the UK. The measurement tools used were the Intimate Partner Violence Strategies Index and the CAADA Domestic Abuse, Stalking and ‘Honour’-Based Violence (DASH) Risk Assessment Checklist. The average age was 33 (SD=7.9, range: 20-57), half reported to be of Asian ethnicity, 37.5% White and 12.5% Black or Mixed ethnicity. The average DASH score was 9.8 (SD=13.2, range: 0-18) and an average of 18 (SD=6.7, range: 1-29) protective strategies were utilised by each participant. All of the most commonly used strategies were from the Placating category. Though Safety Planning strategies were rated as the most helpful by all participants, Placating strategies were also rated as helpful by two-thirds of participants. Stepwise multiple regression showed that Placating was the only significant predictor of DASH score (β=0.375, p<0.05) and accounted for 14% of the variance of DASH score. Findings showed that women utilized a diverse range of protective strategies with placating strategies being most intensely used and rated as helpful. However, placating strategy usage could be a risk factor as opposed to a protective factor. This study has also demonstrated that greater placating strategies were used by White than South Asian women, and women who were employed used more formal strategies. This research has extended the knowledge base of protective strategies that professionals can draw from to underpin decisions and interventions when working with domestic abuse survivors.Peer reviewedFinal Accepted Versio

Identification and validation of genetic variants predictive of gait in standardbred horses

Several horse breeds have been specifically selected for the ability to exhibit alternative patterns of locomotion, or gaits. A premature stop codon in the gene DMRT3 is permissive for “gaitedness” across breeds. However, this mutation is nearly fixed in both American Standardbred trotters and pacers, which perform a diagonal and lateral gait, respectively, during harness racing. This suggests that modifying alleles must influence the preferred gait at racing speeds in these populations. A genome-wide association analysis for the ability to pace was performed in 542 Standardbred horses (n = 176 pacers, n = 366 trotters) with genotype data imputed to ~74,000 single nucleotide polymorphisms (SNPs). Nineteen SNPs on nine chromosomes (ECA1, 2, 6, 9, 17, 19, 23, 25, 31) reached genome-wide significance (p < 1.44 x 10−6). Variant discovery in regions of interest was carried out via whole-genome sequencing. A set of 303 variants from 22 chromosomes with putative modifying effects on gait was genotyped in 659 Standardbreds (n = 231 pacers, n = 428 trotters) using a high-throughput assay. Random forest classification analysis resulted in an out-of-box error rate of 0.61%. A conditional inference tree algorithm containing seven SNPs predicted status as a pacer or trotter with 99.1% accuracy and subsequently performed with 99.4% accuracy in an independently sampled population of 166 Standardbreds (n = 83 pacers, n = 83 trotters). This highly accurate algorithm could be used by owners/trainers to identify Standardbred horses with the potential to race as pacers or as trotters, according to the genotype identified, prior to initiating training and would enable fine-tuning of breeding programs with designed matings. Additional work is needed to determine both the algorithm’s utility in other gaited breeds and whether any of the predictive SNPs play a physiologically functional role in the tendency to pace or tag true functional alleles