Variability of Internally Generated Turbulence in an Estuary, from 100 Days of Continuous Observations

We present detailed observations of internally generated turbulence in a sheared, stratified natural flow, as well as an analysis of the external factors leading to its generation and temporal variability. Multi-month time series of vertical profiles of velocity, acoustic backscatter (0.5 Hz), and turbulence parameters were collected with two moored acoustic Doppler current profilers (ADCPs) in the Hudson River estuary, and estuary-long transects of water density were collected 30 times. ADCP backscatter is used for visualization of coherent turbulent structures and evaluation of surface wave biases to the turbulence measurements. Benefits of the continuous long-term turbulence record include our capturing: (1) the seasonality of turbulence due to changing riverflow, (2) hysteresis in stratification and turbulence over the fortnightly cycle of tidal range, and (3) intermittent events such as breaking internal waves. Internal mixing layers (IMLs) are defined as turbulent regions above the logarithmic velocity layer, and the bottom boundary layer (BBL) is defined as the continuously turbulent range of heights above the bed. A cross-correlation analysis reveals how IML and BBL turbulence vary with stratification and external forcing from tidal range, river flow, and winds. Turbulence in both layers is maximal at spring tide and minimal when most stratified, with one exception IML turbulence at a site with changing channel depth and width is maximal at times of maximum stratification and freshwater input

Models of Type Theory Based on Moore Paths

This paper introduces a new family of models of intensional Martin-L\"of type theory. We use constructive ordered algebra in toposes. Identity types in the models are given by a notion of Moore path. By considering a particular gros topos, we show that there is such a model that is non-truncated, i.e. contains non-trivial structure at all dimensions. In other words, in this model a type in a nested sequence of identity types can contain more than one element, no matter how great the degree of nesting. Although inspired by existing non-truncated models of type theory based on simplicial and cubical sets, the notion of model presented here is notable for avoiding any form of Kan filling condition in the semantics of types.Comment: This is a revised and expanded version of a paper with the same name that appeared in the proceedings of the 2nd International Conference on Formal Structures for Computation and Deduction (FSCD 2017

Analysis of signalling pathways using the prism model checker

We describe a new modelling and analysis approach for signal transduction networks in the presence of incomplete data. We illustrate the approach with an example, the RKIP inhibited ERK pathway [1]. Our models are based on high level descriptions of continuous time Markov chains: reactions are modelled as synchronous processes and concentrations are modelled by discrete, abstract quantities. The main advantage of our approach is that using a (continuous time) stochastic logic and the PRISM model checker, we can perform quantitative analysis of queries such as if a concentration reaches a certain level, will it remain at that level thereafter? We also perform standard simulations and compare our results with a traditional ordinary differential equation model. An interesting result is that for the example pathway, only a small number of discrete data values is required to render the simulations practically indistinguishable

Evaluation by simulation of interpolation and acceleration algorithms for Stepper Motors

Stepper motors are used to control CNC machines for many applications. As well as following the required path precisely, it is also important that the motion be smooth and that the surface speed be controllable. Improved interpolation algorithms for individual straight lines and circular arcs have been developed using distance as a parameter [Chow et al, 2002], [Chow, 2003]. The algorithms control the motor by means of pulses and the generation of the pulse timings is based on the geometry of the shape. For high speeds it is necessary to allow smooth acceleration at the beginning and similar smooth deceleration at the end. Thus, appropriate acceleration and deceleration algorithms have been developed for use with the new interpolation algorithms. This paper describes how simulation has been used to evaluate the new algorithms and compare them with previous algorithms. The algorithms are described for the 2D case but the principle can be extended to 3D

A structured approach for the engineering of biochemical network models, illustrated for signalling pathways

http://dx.doi.org/10.1093/bib/bbn026Quantitative models of biochemical networks (signal transduction cascades, metabolic pathways, gene regulatory circuits) are a central component of modern systems biology. Building and managing these complex models is a major challenge that can benefit from the application of formal methods adopted from theoretical computing science. Here we provide a general introduction to the field of formal modelling, which emphasizes the intuitive biochemical basis of the modelling process, but is also accessible for an audience with a background in computing science and/or model engineering. We show how signal transduction cascades can be modelled in a modular fashion, using both a qualitative approach { Qualitative Petri nets, and quantitative approaches { Continuous Petri Nets and Ordinary Differential Equations. We review the major elementary building blocks of a cellular signalling model, discuss which critical design decisions have to be made during model building, and present ..

Mixture effects at very low doses with combinations of anti-androgenic pesticides, antioxidants, industrial pollutant and chemicals used in personal care products

This article has been made available through the Brunel Open Access Publishing Fund.Many xenobiotics have been identified as in vitro androgen receptor (AR) antagonists, but information about their ability to produce combined effects at low concentrations ismissing. Such data can reveal whether joint effects at the receptor are induced at low levels andmay support the prioritisation of in vivo evaluations and provide orientations for the grouping of anti-androgens in cumulative risk assessment. Combinations of 30 AR antagonists from a wide range of sources and exposure routes (pesticides, antioxidants, parabens, UV-filters, synthetic musks, bisphenol-A, benzo(a)pyrene, perfluorooctane sulfonate and pentabromodiphenyl ether) were tested using a reporter gene assay (MDA-kb2). Chemicalswere combined at threemixture ratios, equivalent to single components' effect concentrations that inhibit the action of dihydrotesterone by 1%, 10% or 20%. Concentration addition (CA) and independent action were used to calculate additivity expectations. We observed complete suppression of dihydrotestosterone effects when chemicals were combined at individual concentrations eliciting 1%, 10% or 20% AR antagonistic effect. Due to the large number of mixture components, the combined AR antagonistic effects occurred at very low concentrations of individual mixture components. CA slightly underestimated the combined effects at all mixture ratios. In conclusion, large numbers of AR antagonists froma wide variety of sources and exposure routes have the ability of acting together at the receptor to produce joint effects at very low concentrations. Significant mixture effects are observed when chemicals are combined at concentrations that individually do not induce observable AR antagonistic effects. Cumulative risk assessment for AR antagonists should apply grouping criteria based on effects where data are available, rather than on criteria of chemical similarity

In-work poverty in the East Midlands

Research that explores the nature and scale of in-work poverty in the East Midlands, using several established measures

SCIENCE AND PUBLIC POLICY OF EARTHQUAKE HAZARD MITIGATION IN THE NEW MADRID SEISMIC ZONE

In the central United States, undefined earthquake sources, long earthquake recurrence intervals and uncertain ground motion attenuation models have contributed to an overstatement of regional seismic hazard for the New Madrid Seismic Zone on the National Seismic Hazard Maps. This study examined concerns regarding scientific uncertainties, overly stringent seismic mitigation policies and depressed local economy in western Kentucky through a series of informal interviews with local businessmen, public officials, and other professionals in occupations associated with seismic mitigation. Scientific and relative economic analyses were then performed using scenario earthquake models developed with FEMA’s Hazus-MH software. Effects of the 2008 Wenchuan earthquake in central China and seismic mitigation policies in use there were considered for potential parallels and learning opportunities. Finally, suggestions for continued scientific research, additional educational opportunities for laymen and engineering professionals, and changes in the application of current earthquake science to public policy in the central United States were outlined with the goal of easing western Kentucky economic issues while maintaining acceptable public safety conditions

A dispersive wave pattern on Jupiter's fastest retrograde jet at 20∘20^\circS

A compact wave pattern has been identified on Jupiter's fastest retrograding jet at 20S (the SEBs) on the southern edge of the South Equatorial Belt. The wave has been identified in both reflected sunlight from amateur observations between 2010 and 2015, thermal infrared imaging from the Very Large Telescope and near infrared imaging from the Infrared Telescope Facility. The wave pattern is present when the SEB is relatively quiescent and lacking large-scale disturbances, and is particularly notable when the belt has undergone a fade (whitening). It is generally not present when the SEB exhibits its usual large-scale convective activity ('rifts'). Tracking of the wave pattern and associated white ovals on its southern edge over several epochs have permitted a measure of the dispersion relationship, showing a strong correlation between the phase speed (-43.2 to -21.2 m/s) and the longitudinal wavelength, which varied from 4.4-10.0 deg. longitude over the course of the observations. Infrared imaging sensing low pressures in the upper troposphere suggest that the wave is confined to near the cloud tops. The wave is moving westward at a phase speed slower (i.e., less negative) than the peak retrograde wind speed (-62 m/s), and is therefore moving east with respect to the SEBs jet peak. Unlike the retrograde NEBn jet near 17N, which is a location of strong vertical wind shear that sometimes hosts Rossby wave activity, the SEBs jet remains retrograde throughout the upper troposphere, suggesting the SEBs pattern cannot be interpreted as a classical Rossby wave. Cassini-derived windspeeds and temperatures reveal that the vorticity gradient is dominated by the baroclinic term and becomes negative (changes sign) in a region near the cloud-top level (400-700 mbar) associated with the SEBs, suggesting a baroclinic origin for this meandering wave pattern. [Abr]Comment: 19 pages, 11 figures, article accepted for publication in Icaru

Bioinformatics tools for analysing viral genomic data

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing