Learning differential equation models from stochastic agent-based model simulations

Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology, and epidemiology. Analysis of the model dynamics can be challenging due to their inherent stochasticity and heavy computational requirements. Common approaches to the analysis of agent-based models include extensive Monte Carlo simulation of the model or the derivation of coarse-grained differential equation models to predict the expected or averaged output from the agent-based model. Both of these approaches have limitations, however, as extensive computation of complex agent-based models may be infeasible, and coarse-grained differential equation models can fail to accurately describe model dynamics in certain parameter regimes. We propose that methods from the equation learning field provide a promising, novel, and unifying approach for agent-based model analysis. Equation learning is a recent field of research from data science that aims to infer differential equation models directly from data. We use this tutorial to review how methods from equation learning can be used to learn differential equation models from agent-based model simulations. We demonstrate that this framework is easy to use, requires few model simulations, and accurately predicts model dynamics in parameter regions where coarse-grained differential equation models fail to do so. We highlight these advantages through several case studies involving two agent-based models that are broadly applicable to biological phenomena: a birth-death-migration model commonly used to explore cell biology experiments and a susceptible-infected-recovered model of infectious disease spread

Evolving a puncture black hole with fixed mesh refinement

We present an algorithm for treating mesh refinement interfaces in numerical relativity. We detail the behavior of the solution near such interfaces located in the strong field regions of dynamical black hole spacetimes, with particular attention to the convergence properties of the simulations. In our applications of this technique to the evolution of puncture initial data with vanishing shift, we demonstrate that it is possible to simultaneously maintain second order convergence near the puncture and extend the outer boundary beyond 100M, thereby approaching the asymptotically flat region in which boundary condition problems are less difficult and wave extraction is meaningful.Comment: 18 pages, 12 figures. Minor changes, final PRD versio

Palatability and chemical defenses of sponges from the western Antarctic Peninsula

The present study surveyed the palatability of all sponge species that could be collected in sufficient quantities in a shallow-water area along the western Antarctic Peninsula. Of 27 species assayed, 78% had outermost tissues that were significantly unpalatable to the sympatric, omnivorous sea star Odontaster validus. Of those species with unpalatable outer tissues, 62% had inner tissues that were also unpalatable to the sea stars. Sea stars have often been considered as the primary predators of sponges in other regions of Antarctica, and their extra-oral mode of feeding threatens only the outermost sponge tissues. The observation that many of the sponges allocate defenses to inner tissues suggests the possibility that biting predators such as mesograzers, which could access inner sponge layers, may also be important in communities along the Antarctic Peninsula. In feeding bioassays with extracts from 12 of the unpalatable species in artificial foods, either lipophilic or hydrophilic extracts were deterrent in each species. These data indicate an overall level of chemical defenses in these Antarctic sponges that is comparable to, and slightly greater than, that found in a previous survey of tropical species

Training Practices of Academy Rugby League and their alignment to Physical Qualities deemed important for Current and Future Performance

This study aimed to investigate rugby league coaches’ perceptions of physical qualities for current and future performance, while also establishing the training practices of Under-16 and Under-19 players. Twenty-four practitioners (rugby coach, strength and conditioning coach) working within nine Super League clubs completed a questionnaire. The questionnaire required practitioners to rank eleven physical qualities (i.e., strength, power, acceleration, maximum speed, aerobic endurance, change of direction, agility, height, body mass, lean mass and fat mass) by importance for current performance, future performance and career longevity according to playing position (forwards, backs, hookers & halves). Practitioners were asked to provide detail on the frequency and duration of each type of training session completed during a typical week throughout each phase of the season; pre-season, in-season (early), in-season (mid), and in-season (late). Typically, practitioners ranked strength, power and acceleration qualities highest, and endurance and anthropometric qualities lowest. The importance of physical qualities varied according to each playing level and position. Training practices of U16 and U19 players differed during each phase of the season, with U19 players undertaking greater training volumes than U16s players. Overall, the physical qualities coaches perceived as most important were not reflected within their training practices. Rugby league practitioners can use this information as a reference source to design long term athletic development plans, prescribe training and during player development procedures. Moreover, these data can inform and improve training practices while influencing the design of pre-season preparatory phases and in-season periods

Biologically-informed neural networks guide mechanistic modeling from sparse experimental data

Biologically-informed neural networks (BINNs), an extension of physics-informed neural networks [1], are introduced and used to discover the underlying dynamics of biological systems from sparse experimental data. In the present work, BINNs are trained in a supervised learning framework to approximate in vitro cell biology assay experiments while respecting a generalized form of the governing reaction-diffusion partial differential equation (PDE). By allowing the diffusion and reaction terms to be multilayer perceptrons (MLPs), the nonlinear forms of these terms can be learned while simultaneously converging to the solution of the governing PDE. Further, the trained MLPs are used to guide the selection of biologically interpretable mechanistic forms of the PDE terms which provides new insights into the biological and physical mechanisms that govern the dynamics of the observed system. The method is evaluated on sparse real-world data from wound healing assays with varying initial cell densities [2]

Adolescent decision making about participation in a hypothetical HIV vaccine trial

Purpose The purpose of this study was to examine the process of adolescent decision-making about participation in an HIV vaccine clinical trial, comparing it to adult models of informed consent with attention to developmental differences. Methods As part of a larger study of preventive misconception in adolescent HIV vaccine trials, we interviewed 33 male and female 16–19-year-olds who have sex with men. Participants underwent a simulated HIV vaccine trial consent process, and then completed a semistructured interview about their decision making process when deciding whether or not to enroll in and HIV vaccine trial. An ethnographic content analysis approach was utilized. Results Twelve concepts related to adolescents' decision-making about participation in an HIV vaccine trial were identified and mapped onto Appelbaum and Grisso's four components of decision making capacity including understanding of vaccines and how they work, the purpose of the study, trial procedures, and perceived trial risks and benefits, an appreciation of their own situation, the discussion and weighing of risks and benefits, discussing the need to consult with others about participation, motivations for participation, and their choice to participate. Conclusion The results of this study suggest that most adolescents at high risk for HIV demonstrate the key abilities needed to make meaningful decisions about HIV vaccine clinical trial participation

Ozone depletion, greenhouse gases, and climate change

This symposium was organized to study the unusual convergence of a number of observations, both short and long term that defy an integrated explanation. Of particular importance are surface temperature observations and observations of upper atmospheric temperatures, which have declined significantly in parts of the stratosphere. There has also been a dramatic decline in ozone concentration over Antarctica that was not predicted. Significant changes in precipitation that seem to be latitude dependent have occurred. There has been a threefold increase in methane in the last 100 years; this is a problem because a source does not appear to exist for methane of the right isotopic composition to explain the increase. These and other meteorological global climate changes are examined in detail

The Gendered Way of Hooking Up among College Students

This study explores gender differences in sexual socialization as a determinant of hooking up by college students. Survey results for 469 respondents show both generic (alcohol consumption and sexual socialization through pornography) and gender specific (gender-related attitudes) mechanisms that explain men’s higher rates of hooking up. Men engage in the generic behavioral correlates of hooking up more often than women. Women with patriarchal attitudes report more hooking up and men with rape supportive attitudes report more hooking up. Efforts by college administrators to reduce rates of hooking up should take into consideration alcohol consumption, pornography, and gender related attitudes

Draft genome sequence of Neurospora crassa strain FGSC 73

Citation: Baker, S. E., Schackwitz, W., Lipzen, A., Martin, J., Haridas, S., LaButti, K., . . . McCluskey, K. (2016). Draft genome sequence of Neurospora crassa strain FGSC 73. Genome Announcements, 3(2). doi:10.1128/genomeA.00074-15Citation: Baker, S., Schackwitz, W., Lipzen, A., . . . McCluskey, K. (2015). Draft Genome Sequence of Neurospora crassa Strain FGSC 73. Genome Announcements, 3(2), e00074-15. https://doi.org/10.1128/genomeA.00074-15We report the elucidation of the complete genome of the Neurospora crassa (Shear and Dodge) strain FGSC 73, a mat-a, trp-3 mutant strain. The genome sequence around the idiotypic mating type locus represents the only publicly available sequence for a mat-a strain. 40.42 Megabases are assembled into 358 scaffolds carrying 11,978 gene models. © 2015 Baker et al