Entrainment and Control of Bacterial Populations: An in Silico Study over a Spatially Extended Agent Based Model

This is the author accepted manuscript. The final version is available from American Chemical Society via the DOI in this record.We extend a spatially explicit agent based model (ABM) developed previously to investigate entrainment and control of the emergent behavior of a population of synchronized oscillating cells in a microfluidic chamber. Unlike most of the work in models of control of cellular systems which focus on temporal changes, we model individual cells with spatial dependencies which may contribute to certain behavioral responses. We use the model to investigate the response of both open loop and closed loop strategies, such as proportional control (P-control), proportional-integral control (PI-control) and proportional-integral-derivative control (PID-control), to heterogeinities and growth in the cell population, variations of the control parameters and spatial effects such as diffusion in the spatially explicit setting of a microfluidic chamber setup. We show that, as expected from the theory of phase locking in dynamical systems, open loop control can only entrain the cell population in a subset of forcing periods, with a wide variety of dynamical behaviors obtained outside these regions of entrainment. Closed-loop control is shown instead to guarantee entrainment in a much wider region of control parameter space although presenting limitations when the population size increases over a certain threshold. In silico tracking experiments are also performed to validate the ability of classical control approaches to achieve other reference behaviors such as a desired constant output or a linearly varying one. All simulations are carried out in BSim, an advanced agent-based simulator of microbial population which is here extended ad hoc to include the effects of control strategies acting onto the population.The authors declare no competing interests. We thank Dr. Nigel J. Savery at the University of Bristol for useful discussions around the subject of GRNs and for his help in developing the original ABM model. We also wish to thank Dr Gianfranco Fiore at the University of Bristol and the anonymous reviewers for reading the revised manuscript carefully and providing insightful comments that led to a consistent revision of the original manuscript. P.M. was supported by EPSRC Grant EP/E501214/1 and K.T.-A. by EPSRC Grant EP/I018638/1. The funders had no role in study design, data collection, and analysis, decision to publish, or preparation of the manuscript. This work was carried out using the computational facilities of the Advanced Computing Research Centre, University of Bristol, http://www.bris.ac.uk/acrc/

Dynamics of symmetric dynamical systems with delayed switching

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this record.We study dynamical systems that switch between two different vector fields depending on a discrete variable and with a delay. When the delay reaches a problem-dependent critical value so-called event collisions occur. This paper classifies and analyzes event collisions, a special type of discontinuity induced bifurcations, for periodic orbits. Our focus is on event collisions of symmetric periodic orbits in systems with full reflection symmetry, a symmetry that is prevalent in applications. We derive an implicit expression for the Poincare map near the colliding periodic orbit. The Poincare map is piecewise smooth, finite-dimensional, and changes the dimension of its image at the collision. In the second part of the paper we apply this general result to the class of unstable linear single-degree-of-freedom oscillators where we detect and continue numerically collisions of invariant tori. Moreover, we observe that attracting closed invariant polygons emerge at the torus collision.The research of JS and PK was partially supported by EPSRC grant GR/R72020/0

Cardiosphere-derived cells suppress allogeneic lymphocytes by production of PGE2 acting via the EP4 receptor

derived cells (CDCs) are a cardiac progenitor cell population, which have been shown to possess cardiac regenerative properties and can improve heart function in a variety of cardiac diseases. Studies in large animal models have predominantly focussed on using autologous cells for safety, however allogeneic cell banks would allow for a practical, cost-effective and efficient use in a clinical setting. The aim of this work was to determine the immunomodulatory status of these cells using CDCs and lymphocytes from 5 dogs. CDCs expressed MHC I but not MHC II molecules and in mixed lymphocyte reactions demonstrated a lack of lymphocyte proliferation in response to MHC-mismatched CDCs. Furthermore, MHC-mismatched CDCs suppressed lymphocyte proliferation and activation in response to Concanavalin A. Transwell experiments demonstrated that this was predominantly due to direct cell-cell contact in addition to soluble mediators whereby CDCs produced high levels of PGE2 under inflammatory conditions. This led to down-regulation of CD25 expression on lymphocytes via the EP4 receptor. Blocking prostaglandin synthesis restored both, proliferation and activation (measured via CD25 expression) of stimulated lymphocytes. We demonstrated for the first time in a large animal model that CDCs inhibit proliferation in allo-reactive lymphocytes and have potent immunosuppressive activity mediated via PGE2

Improving education in primary care: development of an online curriculum using the blended learning model

<p>Abstract</p> <p>Background</p> <p>Standardizing the experiences of medical students in a community preceptorship where clinical sites vary by geography and discipline can be challenging. Computer-assisted learning is prevalent in medical education and can help standardize experiences, but often is not used to its fullest advantage. A blended learning curriculum combining web-based modules with face-to-face learning can ensure students obtain core curricular principles.</p> <p>Methods</p> <p>This course was developed and used at The Case Western Reserve University School of Medicine and its associated preceptorship sites in the greater Cleveland area. Leaders of a two-year elective continuity experience at the Case Western Reserve School of Medicine used adult learning principles to develop four interactive online modules presenting basics of office practice, difficult patient interviews, common primary care diagnoses, and disease prevention. They can be viewed at <url>http://casemed.case.edu/cpcp/curriculum</url>. Students completed surveys rating the content and technical performance of each module and completed a Generalist OSCE exam at the end of the course.</p> <p>Results</p> <p>Participating students rated all aspects of the course highly; particularly those related to charting and direct patient care. Additionally, they scored very well on the Generalist OSCE exam.</p> <p>Conclusion</p> <p>Students found the web-based modules to be valuable and to enhance their clinical learning. The blended learning model is a useful tool in designing web-based curriculum for enhancing the clinical curriculum of medical students.</p

Psychometric evaluation of the Italian Revised Exercise Addiction Inventory (EAI-R) among Italian speaking exercisers: confirmatory factor analysis

Background: The Exercise Addiction Inventory (EAI) is a valid and reliable instrument and has been used in numerous contexts and research studies. The EAI was recently revised (EAI-R), but the psychometric properties of the EAI-R have yet to be examined in an Italian context. Therefore, the present study aimed to validate the EAI-R among Italian-speaking exercisers. Methods: The sample comprised 200 Italian-speaking exercisers (62% females, 38% male; mean age = 35 years, SD±11.42), who completed a survey including the EAI-R, Depression Anxiety and Stress Scale-21 (DASS-21), Rosenberg's Self-Esteem Scale (RSES), and Exercise Dependence Scale-Revised (EDS-R). Results: Confirmatory factor analysis (CFA) showed the EAI-R had good psychometric characteristics (Cronbach's α = 0.90) and confirmed the scale's unidimensional properties. Scores on the EAI-R were positively correlated with EDS-R scores, the number of weekly hours of exercise, and DASS-21 scores. Conversely, EAI-R scores were negatively correlated with the RSES scores and age. Conclusion: The EAI-R is a psychometrically reliable and valid measure for assessing the risk of exercise addiction among Italian adults. The study expands the literature on exercise addiction and demonstrates important associational factors in the Italian context

Eight common genetic variants associated with serum dheas levels suggest a key role in ageing mechanisms

Dehydroepiandrosterone sulphate (DHEAS) is the most abundant circulating steroid secreted by adrenal glands-yet its function is unknown. Its serum concentration declines significantly with increasing age, which has led to speculation that a relative DHEAS deficiency may contribute to the development of common age-related diseases or diminished longevity. We conducted a meta-analysis of genome-wide association data with 14,846 individuals and identified eight independent common SNPs associated with serum DHEAS concentrations. Genes at or near the identified loci include ZKSCAN5 (rs11761528; p = 3.15×10-36), SULT2A1 (rs2637125; p = 2.61×10-19), ARPC1A (rs740160; p = 1.56×10-16), TRIM4 (rs17277546; p = 4.50×10-11), BMF (rs7181230; p = 5.44×10-11), HHEX (rs2497306; p = 4.64×10-9), BCL2L11 (rs6738028; p = 1.72×10-8), and CYP2C9 (rs2185570; p = 2.29×10-8). These genes are associated with type 2 diabetes, lymphoma, actin filament assembly, drug and xenobiotic metabolism, and zinc finger proteins. Several SNPs were associated with changes in gene expression levels, and the related genes are connected to biological pathways linking DHEAS with ageing. This study provides much needed insight into the function of DHEAS

NF-κB2 signalling in enteroids modulates enterocyte responses to secreted factors from bone marrow-derived dendritic cells

Alternative pathway NF-κB signalling regulates susceptibility towards developing inflammatory bowel disease (IBD), colitis-associated cancer and sepsis-associated intestinal epithelial cell apoptosis and shedding. However, the cell populations responsible for the perturbed alternative pathway NF-κB signalling in intestinal mucosal pathology remain unclear. In order to investigate the contribution of the epithelial compartment, we have tested whether NF-κB2 regulated transcription in intestinal epithelial cells controls the intestinal epithelial response to cytokines that are known to disrupt intestinal barrier permeability. Enteroids were generated from the proximal, middle and distal regions of small intestine (SI) from C57BL/6J wild-type mice and displayed region-specific morphology that was maintained during sub-culture. Enteroids treated with 100 ng/mL TNF were compared with corresponding regions of SI from C57BL/6J mice treated systemically with 0.33 mg/kg TNF for 1.5 h. TNF-induced apoptosis in all regions of the intestine in vitro and in vivo but resulted in Paneth cell degranulation only in proximal tissue-derived SI and enteroids. TNF also resulted in increased enteroid sphericity (quantified as circularity from two-dimensional bright field images). This response was dose and time-dependent and correlated with active caspase-3 immunopositivity. Proximal tissue-derived enteroids generated from Nfκb2−/− mice showed a significantly blunted circularity response following the addition of TNF, IFNγ, lipopolysaccharide (LPS) activated C57BL/6J-derived bone marrow-derived dendritic cells (BMDC) and secreted factors from LPS-activated BMDCs. However, Nfκb1−/− mouse-derived enteroids showed no significant changes in response to these stimuli. In conclusion, the selection of SI region is important when designing enteroid studies as region-specific identity and response to stimuli such as TNF are maintained in culture. Intestinal epithelial cells are at least partially responsible for regulating their own fate by modulating NF-κB2 signalling in response to stimuli known to be involved in multiple intestinal and systemic diseases. Future studies are warranted to investigate the therapeutic potential of intestinal epithelial NF-κB2 inhibition

Wizard CD Plus and ProTaper Universal: analysis of apical transportation using new software

OBJECTIVE: This study has two aims: 1) to evaluate the apical transportation of the Wizard CD Plus and ProTaper Universal after preparation of simulated root canals; 2) to compare, with Adobe Photoshop, the ability of a new software (Regeemy) in superposing and subtracting images. MATERIAL AND METHODS: Twenty five simulated root canals in acrylic-resin blocks (with 20º curvature) underwent cone beam computed tomography before and after preparation with the rotary systems (70 kVp, 4 mA, 10 s and with the 8×8 cm FoV selection). Canals were prepared up to F2 (ProTaper) and 24.04 (Wizard CD Plus) instruments and the working length was established to 15 mm. The tomographic images were imported into iCAT Vision software and CorelDraw for standardization. The superposition of pre- and post-instrumentation images from both systems was performed using Regeemy and Adobe Photoshop. The apical transportation was measured in millimetres using Image J. Five acrylic resin blocks were used to validate the superposition achieved by the software. Student's t-test for independent samples was used to evaluate the apical transportation achieved by the rotary systems using each software individually. Student's t-test for paired samples was used to compare the ability of each software in superposing and subtracting images from one rotary system per time. RESULTS: The values obtained with Regeemy and Adobe Photoshop were similar to rotary systems (P>0.05). ProTaper Universal and Wizard CD Plus promoted similar apical transportation regardless of the software used for image's superposition and subtraction (P>0.05). CONCLUSION: Wizard CD Plus and ProTaper Universal promoted little apical transportation. Regeemy consists in a feasible software to superpose and subtract images and appears to be an alternative to Adobe Photoshop

Applying Bayesian model averaging for uncertainty estimation of input data in energy modelling

Background Energy scenarios that are used for policy advice have ecological and social impact on society. Policy measures that are based on modelling exercises may lead to far reaching financial and ecological consequences. The purpose of this study is to raise awareness that energy modelling results are accompanied with uncertainties that should be addressed explicitly. Methods With view to existing approaches of uncertainty assessment in energy economics and climate science, relevant requirements for an uncertainty assessment are defined. An uncertainty assessment should be explicit, independent of the assessor&#8217;s expertise, applicable to different models, including subjective quantitative and statistical quantitative aspects, intuitively understandable and be reproducible. Bayesian model averaging for input variables of energy models is discussed as method that satisfies these requirements. A definition of uncertainty based on posterior model probabilities of input variables to energy models is presented. Results The main findings are that (1) expert elicitation as predominant assessment method does not satisfy all requirements, (2) Bayesian model averaging for input variable modelling meets the requirements and allows evaluating a vast amount of potentially relevant influences on input variables and (3) posterior model probabilities of input variable models can be translated in uncertainty associated with the input variable. Conclusions An uncertainty assessment of energy scenarios is relevant if policy measures are (partially) based on modelling exercises. Potential implications of these findings include that energy scenarios could be associated with uncertainty that is presently neither assessed explicitly nor communicated adequately