The visual processing of text

The results of an investigation into the nature of the visual information obtained from pages of text and used in the visual processing of text during reading are reported. An initial investigation into the visual processing of text by applying a computational model of early vision (MIRAGE: Watt & Morgan, 1985; Watt, 1988) to pages of text (Computational Analysis 1) is shown to extract a range of features from a text image in the representation it delivers, which are organised across a range of spatial scales similar to those spanning human vision. The features the model extracts are capable of supporting a structured set of text processing tasks of the type required in reading. From the findings of this analysis, a series of psychophysical and computational studies are reported which exan-dne whether the type of information used in the human visual processing of text can be described by this modelled representation of information in text images. Using a novel technique to measure the 'visibility' of the information in text images, a second stage of investigation (Experiments 1-3) shows that information used to perform different text processing tasks of the type performed in reading is contained at different spatial scales of visual analysis. A second computational analysis of the information in text demonstrates how the spatial scale dependency of these text processing tasks can be accounted for by the model of early vision. In a third stage, two further experiments (Experiments 4-5) show how the pattern of text processing performance is determined by typographical parameters, and a third computational analysis of text demonstrates how changes in the pattern of text processing performance can be modelled by changes in the pattern of information represented by the model of vision. A fourth stage (Experiments 6-7 and Computational Analysis 4) examines the time-course of the visual processing of text. The experiments show how the duration required to reach a level of visual text processing performance varies as a function of typographical parameters, and comparison of these data with the model shows that this is consistent with a time-course of visual analysis based on a coarse-to-fine spatial scale of visual processing. A final experiment (Experiment 8) examines how reading performance varies with typographical parameters. It is shown how the pattern of reading performance and the pattern of visual text processing performance are related, and how the model of early vision might describe the visual processing of text in reading. The implications of these findings for theories of reading and theories of vision are finally discussed

IFIT3 and IFIT2/3 promote IFIT1-mediated translation inhibition by enhancing binding to non-self RNA.

Interferon-induced proteins with tetratricopeptide repeats (IFITs) are highly expressed during the cell-intrinsic immune response to viral infection. IFIT1 inhibits translation by binding directly to the 5' end of foreign RNAs, particularly those with non-self cap structures, precluding the recruitment of the cap-binding eukaryotic translation initiation factor 4F and ribosome recruitment. The presence of IFIT1 imposes a requirement on viruses that replicate in the cytoplasm to maintain mechanisms to avoid its restrictive effects. Interaction of different IFIT family members is well described, but little is known of the molecular basis of IFIT association or its impact on function. Here, we reconstituted different complexes of IFIT1, IFIT2 and IFIT3 in vitro, which enabled us to reveal critical aspects of IFIT complex assembly. IFIT1 and IFIT3 interact via a YxxxL motif present in the C-terminus of each protein. IFIT2 and IFIT3 homodimers dissociate to form a more stable heterodimer that also associates with IFIT1. We show for the first time that IFIT3 stabilizes IFIT1 protein expression, promotes IFIT1 binding to a cap0 Zika virus reporter mRNA and enhances IFIT1 translation inhibition. This work reveals molecular aspects of IFIT interaction and provides an important missing link between IFIT assembly and function.This work was supported by a joint Royal Society/Wellcome Trust Sir Henry Dale Fellowship (202471/Z/16/Z) and a Royal Society Research Grant (RG140708) to TRS. HVM is supported by a University of Cambridge, Department of Pathology PhD studentship. XYL is supported by a King’s Scholarship from the Malaysian government. TJS is supported by a Wellcome Trust PhD studentship (105389/Z/14/Z). RCF and DSM are supported by CAPES Computational Biology (23038.010048/2013-27). DSM is also supported by the Academy of Medical Sciences/UK (NAF004/1005). SCG is a Sir Henry Dale Fellow (098406/Z/12/Z) co-funded by the Wellcome Trust and Royal Society

Emergent global patterns of ecosystem structure and function from a mechanistic general ecosystem model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures

Ten Simple Rules for Effective Computational Research

<p>Ten Simple Rules for Effective Computational Research</p

Towards the rational design of synthetic cells with prescribed population dynamics

International audienceThe rational design of synthetic cell populations with prescribed behaviours is a long-standing goal of synthetic biology, with the potential to greatly accelerate the development of biotechnological applications in areas ranging from medical research to energy production. Achieving this goal requires well-characterized components, modular implementation strategies, simulation across temporal and spatial scales and automatic compilation of high-level designs to low-level genetic parts that function reliably inside cells. Many of these steps are incomplete or only partially understood , and methods for integrating them within a common design framework have yet to be developed. Here, we address these challenges by developing a prototype framework for designing synthetic cells with prescribed population dynamics. We extend the genetic engineering of cells (GEC) language, originally developed for programming intracellular dynamics, with cell population factors such as cell growth, division and dormancy, together with spatio-temporal simulation methods. As a case study, we use our framework to design synthetic cells with predator–prey interactions that, when simulated, produce complex spatio-temporal behaviours such as travelling waves and spatio-temporal chaos. An analysis of our design reveals that environmental factors such as density-dependent dormancy and reduced extracellular space destabilize the population dynamics and increase the range of genetic variants for which complex spatio-temporal behaviours are possible. Our findings highlight the importance of considering such factors during the design process. We then use our analysis of population dynamics to inform the selection of genetic parts, which could be used to obtain the desired spatio-temporal behaviours. By identifying, integrating and automating key stages of the design process, we provide a computational framework for designing synthetic systems, which could be tested in future laboratory studies

Data from: Emergent global patterns of ecosystem structure and function from a mechanistic General Ecosystem Model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global, and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g. growth rate), community (e.g. biomass turnover rates), ecosystem (e.g. trophic pyramids) and macro-ecological scales (e.g. global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures

Emergent global-level ecosystem properties.

<p>Properties emergent from the model after a 100-y global (65°N to 65°S) simulation using a grid-cell resolution of two degrees. (A) The spatial distribution of annual mean heterotroph biomass density; breaks in the colour scheme were based on quantiles in the data. (B, C) Latitudinal gradients in biomass density; solid lines represent means for each trophic level, and shading represents the range of values across all longitudes in each latitude band.</p

Study 4 - Global predictions

Outputs from the Madingley model for Study 4 of Table 3 of the manuscript. This study is comprised of one simulation over a global model grid at 2 degree by 2 degree resolution and extending from 65 degrees north to 65 degrees south, and from 180 degrees west to 180 degrees east. Outputs files are described in more detail in 'ReadMe.txt' and model setup files are described in 'ReadMe-ModelSetup.txt'