A modified Oster-Murray-Harris mechanical model of morphogenesis

There are two main modeling paradigms for biological pattern formation in developmental biology: chemical prepattern models and cell aggregation models. This paper focuses on an example of a cell aggregation model, the mechanical model developed by Oster, Murray, and Harris [Development, 78 (1983), pp. 83--125]. We revisit the Oster--Murray--Harris model and find that, due to the infinitesimal displacement assumption made in the original version of this model, there is a restriction on the types of boundary conditions that can be prescribed. We derive a modified form of the model which relaxes the infinitesimal displacement assumption. We analyze the dynamics of this model using linear and multiscale nonlinear analysis and show that it has the same linear behavior as the original Oster--Murray--Harris model. Nonlinear analysis, however, predicts that the modified model will allow for a wider range of parameters where the solution evolves to a bounded steady state. The results from both analyses are verified through numerical simulations of the full nonlinear model in one and two dimensions. The increased range of boundary conditions that are well-posed, as well as a wider range of parameters that yield bounded steady states, renders the modified model more applicable to, and more robust for, comparisons with experiments

Multiple Imputation to Correct for Measurement Error in Admixture Estimates in Genetic Structured Association Testing

Objectives: Structured association tests ( SAT), like any statistical model, assumes that all variables are measured without error. Measurement error can bias parameter estimates and confound residual variance in linear models. It has been shown that admixture estimates can be contaminated with measurement error causing SAT models to suffer from the same afflictions. Multiple imputation (MI) is presented as a viable tool for correcting measurement error problems in SAT linear models with emphasis on correcting measurement error contaminated admixture estimates. Methods: Several MI methods are presented and compared, via simulation, in terms of controlling Type I error rates for both non-additive and additive genotype coding. Results: Results indicate that MI using the Rubin or Cole method can be used to correct for measurement error in admixture estimates in SAT linear models. Conclusion: Although MI can be used to correct for admixture measurement error in SAT linear models, the data should be of reasonable quality, in terms of marker informativeness, because the method uses the existing data to borrow information in which to make the measurement error corrections. If the data are of poor quality there is little information to borrow to make measurement error corrections. Copyright © 2009 S. Karger AG, Base

Post-Dieselgate : Evidence of NOx Emission Reductions Using On-Road Remote Sensing

The Dieselgate scandal which broke in September 2015 demonstrated that vehicle manufacturers, such as the Volkswagen Group (VWG), engaged in software-based manipulation which led to vehicles passing laboratory-based emission testing limits but were far more polluting while being driven on roads. Using 23 000 on-road remote sensing measurements of light-duty Euro 5 diesel vehicles in the United Kingdom between 2012 and 2018, VWG vehicles with the "Dieselgate-affected" EA189 engine demonstrated anomalous NOx emission behavior between the pre- and post-Dieselgate periods which was not observed in other vehicle makes or models. These anomalous changes can be explained by voluntary VWG hardware and software fixes which have led to improved NOx emission control. The VGW 1.6 L vehicles, with a simple hardware fix and a software upgrade, resulted in a 36% reduction in NOx, whereas the 2.0 L vehicles that required a software-only fix showed a 30% reduction in NOx once controlled for ambient temperature effects. These results show that even minor changes or upgrades can considerably reduce NOx emissions, which has implications for future emission control activities and local air quality

Comparing self-reported ethnicity to genetic background measures in the context of the Multi-Ethnic Study of Atherosclerosis (MESA)

<p>Abstract</p> <p>Background</p> <p>Questions remain regarding the utility of self-reported ethnicity (SRE) in genetic and epidemiologic research. It is not clear whether conditioning on SRE provides adequate protection from inflated type I error rates due to population stratification and admixture. We address this question using data obtained from the Multi-Ethnic Study of Atherosclerosis (MESA), which enrolled individuals from 4 self-reported ethnic groups. We compare the agreement between SRE and genetic based measures of ancestry (GBMA), and conduct simulation studies based on observed MESA data to evaluate the performance of each measure under various conditions.</p> <p>Results</p> <p>Four clusters are identified using 96 ancestry informative markers. Three of these clusters are well delineated, but 30% of the self-reported Hispanic-Americans are misclassified. We also found that MESA SRE provides type I error rates that are consistent with the nominal levels. More extensive simulations revealed that this finding is likely due to the multi-ethnic nature of the MESA. Finally, we describe situations where SRE may perform as well as a GBMA in controlling the effect of population stratification and admixture in association tests.</p> <p>Conclusions</p> <p>The performance of SRE as a control variable in genetic association tests is more nuanced than previously thought, and may have more value than it is currently credited with, especially when smaller replication studies are being considered in multi-ethnic samples.</p

Explorations, Vol. 3, No. 1

Cover: Debouche, a thermo-formed acrylic sculpture, by Deborah de Moulpied, Associate Professor of Art at the University of Maine, (from the collection of Barbara Heldt and Gerald Smith, Oxford, England); photograph by Dale and Nedra Van Volkinburg. Articles include: Biotechnology, by Michael R. Gross The Search for Tom Swift or Some Reflections on One of America\u27s Best-Known Cultural Heroes, by David K. Vaughan ENDO-EXO 1 Sculpture in Motion Communication is Not Just Saying Words; It is Creating True Understanding, by Marisue Pickering Maine Outreach: Teaching Success, by Richard A. Hale and James F. Philp Through Cloud and Fog, Hunting the Elusive pH, by Richard Jagels Ocean Basin with a Past A Cryptic History: Breaking the Code Discerning a Future, by Detmar Schnitker We Stand Corrected in Volume II, Number 2, of EXPLORATIONS Dialogue: Letters [to the Editor] Updates from the Dispatch Cas

Placenta-specific Slc38a2/SNAT2 knockdown causes fetal growth restriction in mice

Fetal growth restriction (FGR) is a complication of pregnancy that reduces birth weight, markedly increases infant mortality and morbidity and is associated with later-life cardiometabolic disease. No specific treatment is available for FGR. Placentas of human FGR infants have low abundance of sodium-coupled neutral amino acid transporter 2 (Slc38a2/SNAT2), which supplies the fetus with amino acids required for growth. We determined the mechanistic role of placental Slc38a2/SNAT2 deficiency in the development of restricted fetal growth, hypothesizing that placenta-specific Slc38a2 knockdown causes FGR in mice. Using lentiviral transduction of blastocysts with a small hairpin RNA (shRNA), we achieved 59% knockdown of placental Slc38a2, without altering fetal Slc38a2 expression. Placenta-specific Slc38a2 knockdown reduced near-term fetal and placental weight, fetal viability, trophoblast plasma membrane (TPM) SNAT2 protein abundance, and both absolute and weight-specific placental uptake of the amino acid transport System A tracer, 14C-methylaminoisobutyric acid (MeAIB). We also measured human placental SLC38A2 gene expression in a well-defined term clinical cohort and found that SLC38A2 expression was decreased in late-onset, but not early-onset FGR, compared with appropriate for gestational age (AGA) control placentas. The results demonstrate that low placental Slc38a2/SNAT2 causes FGR and could be a target for clinical therapies for late-onset FGR

ROTATIONAL-DYNAMICS OF SOLID C-70 - A NEUTRON-SCATTERING STUDY

PMID: 10011126PMID: 10011126 This work at the University of Sussex at supported by the Science and Engineering Research Council, U.K.PMID: 10011126 This work at the University of Sussex at supported by the Science and Engineering Research Council, U.K.PMID: 10011126 This work at the University of Sussex at supported by the Science and Engineering Research Council, U.K.We report the results of neutron-diffraction and low-energy neutron-inelastic-scattering experiments on high-purity solid C-70 between 10 and 640 K. Thermal hysteresis effects are found to accompany structural changes both on cooling and on heating. The observed diffuse scattering intensity does not change with temperature. At 10 K broad librational peaks are observed at 1.82(16) meV [full width at half maximum=1.8(5) meV]. The peaks soften and broaden further with increasing temperature. At and above room temperature, they collapse into a single quasielastic line. At 300 K, the diffusive reorientational motion appears to be somewhat anisotropic, becoming less so with increasing temperature. An isotropic rotational diffusion model, in which the motions of adjacent molecules are uncorrelated, describes well the results at 525 K. The temperature dependence of the rotational diffusion constants is consistent with a thermally activated process having an activation energy of 32(7) meV.This work at the University of Sussex at supported by the Science and Engineering Research Council, U.K

The use of plasmodes as a supplement to simulations: A simple example evaluating individual admixture estimation methodologies

With the advent of powerful computers, simulation studies are becoming an important tool in statistical methodology research. However, computer simulations of a specific process are only as good as our understanding of the underlying mechanisms. An attractive supplement to simulations is the use of plasmode datasets. Plasmodes are data sets that are generated by natural biologic processes, under experimental conditions that allow some aspect of the truth to be known. The benefit of the plasmode approach is that the data are generated through completely natural processes, thus circumventing the common concern of the realism and accuracy of computer simulated data. The estimation of admixture, or the proportion of an individual’s genome that originates from different founding populations, is a particularly difficult research endeavor that is well suited to the use of plasmodes. Current methods have been tested with simulations of complex populations where the underlying mechanisms such as the rate and distribution of recombination are not well understood. To demonstrate the utility of this method data derived from mouse crosses is used to evaluate the effectiveness of several admixture estimation methodologies. Each cross shares a common founding population so that the ancestry proportion for each individual is known, allowing for the comparison of true and estimated individual admixture values. Analysis shows that the different estimation methodologies (Structure, AdmixMap and FRAPPE) examined all perform well with simple datasets. However, the performance of the estimation methodologies varied greatly when applied to a plasmode consisting of three founding populations. The results of these examples illustrate the utility of plasmodes in the evaluation of statistical genetics methodologies