Literature-based priors for gene regulatory networks

Motivation: The use of prior knowledge to improve gene regulatory network modelling has often been proposed. In this paper we present the first research on the massive incorporation of prior knowledge from literature for Bayesian network learning of gene networks. As the publication rate of scientific papers grows, updating online databases, which have been proposed as potential prior knowledge in past rese-arch, becomes increasingly challenging. The novelty of our approach lies in the use of gene-pair association scores that describe the over-lap in the contexts in which the genes are mentioned, generated from a large database of scientific literature, harnessing the information contained in a huge number of documents into a simple, clear format. Results: We present a method to transform such literature-based gene association scores to network prior probabilities, and apply it to learn gene sub-networks for yeast, E. coli and Human organisms. We also investigate the effect of weighting the influence of the prior know-ledge. Our findings show that literature-based priors can improve both the number of true regulatory interactions present in the network and the accuracy of expression value prediction on genes, in comparison to a network learnt solely from expression data. Networks learnt with priors also show an improved biological interpretation, with identified subnetworks that coincide with known biological pathways. Contact

Extracting predictive models from marked-p free-text documents at the Royal Botanic Gardens, Kew, London

In this paper we explore the combination of text-mining, un-supervised and supervised learning to extract predictive models from a corpus of digitised historical floras. These documents deal with the nomenclature, geographical distribution, ecology and comparative morphology of the species of a region. Here we exploit the fact that portions of text in the floras are marked up as different types of trait and habitat. We infer models from these different texts that can predict different habitat-types based upon the traits of plant species. We also integrate plant taxonomy data in order to assist in the validation of our models. We have shown that by clustering text describing the habitat of different floras we can identify a number of important and distinct habitats that are associated with particular families of species along with statistical significance scores. We have also shown that by using these discovered habitat-types as labels for supervised learning we can predict them based upon a subset of traits, identified using wrapper feature selection

Small-scale field experiments accurately scale up to predict density dependence in reef fish populations at large scales

Field experiments provide rigorous tests of ecological hypotheses but are usually limited to small spatial scales. It is thus unclear whether these findings extrapolate to larger scales relevant to conservation and management. We show that the results of experiments detecting density-dependent mortality of reef fish on small habitat patches scale up to have similar effects on much larger entire reefs that are the size of small marine reserves and approach the scale at which some reef fisheries operate. We suggest that accurate scaling is due to the type of species interaction causing local density dependence and the fact that localized events can be aggregated to describe larger-scale interactions with minimal distortion. Careful extrapolation from small-scale experiments identifying species interactions and their effects should improve our ability to predict the outcomes of alternative management strategies for coral reef fishes and their habitats

Predators, Prey Refuges, and the Spatial Scaling of Density-Dependent Prey Mortality

We tested the biological cause of density-dependent mortality in the bridled goby (Coryphopterus glaucofraenum), a small coral reef fish, and evaluated whether this knowledge allowed us to detect density dependence at different spatial scales in natural habitats. To identify the biological cause of density dependence, we manipulated both population density and the availability of shelter (crevices used as refuges from predators) in small plots of continuous reef. We detected strong density-dependent mortality in plots with few refuges, but mortality was density independent in plots with abundant refuges, indicating that limited shelter causes density dependence. Predator density was unrelated to the density of gobies and refuges, suggesting that predators displayed a type III functional response in patches with few refuges. In a second experiment, we manipulated goby density within replicate plots of three sizes (4, 16, and 64 m2) that varied naturally in the availability of refuges. If refuge availability was ignored, mortality appeared to be density independent at all scales. If, however, plots were grouped by refuge availability, mortality was density dependent in plots with few refuges, but low and density independent in plots with many refuges at all spatial scales. Understanding the mechanism of density dependence (refuge shortage) was thus required to measure the strength of density dependence in natural, spatially variable, habitat. We suggest that density dependence was detectable in plots of different sizes because the relationships between the densities of gobies, refuges, and goby predators were similar across the spatial scales we studied. Our work demonstrates that identifying the biological interactions that cause density dependence, and characterizing the spatial domains at which those interactions operate, will be important to accurately assess the effects of density dependence on population dynamics

Some Aspects of the Farm Mortgage Situation in South Dakota and their Relation to a Future Land Use Policy

The purpose of this circular is to bring together in more available form some facts and figures regarding the development of the present farm mortgage situation in South Dakota and to point out their relationship to a future land use policy. It is hoped that each topic covered in the discussion will contribute something to a better understanding of farm mortgage credit conditions in the state, More knowledge of the present situation is essential if an intelligent attack is to be made on this important problem. It has not been possible to analyze thoroughly each problem considered. Such conclusions as are offered will therefore have to be considered as more or less tentative. If the discussion that follows will be of assistance in furnishing some background for intelligent action on these timely and most important problems the undertaking will have served its main purpose

Human response to vibration in residential environments (NANR209), executive summary

The aim of the Defra-funded project NANR209 ‘Human response to vibration in residential environments’ was to develop exposure-response relationships for vibration experienced in residential environments from sources outside of the residents’ control. The project was performed at the University of Salford between January 2008 and March 2011. The final report was published on the Defra website on 6th September 2012. The NANR209 Final Report consists of the following documents: • Executive summary • Final project report • Technical report 1: Measurement of vibration exposure • Technical report 2: Measurement of response • Technical report 3: Calculation of vibration exposure • Technical report 4: Measurement and calculation of noise exposure • Technical report 5: Analysis of the social survey findings • Technical report 6: Determination of exposure-response relationships This document is the Executive summary

Quantum transport in carbon nanotubes

Carbon nanotubes are a versatile material in which many aspects of condensed matter physics come together. Recent discoveries, enabled by sophisticated fabrication, have uncovered new phenomena that completely change our understanding of transport in these devices, especially the role of the spin and valley degrees of freedom. This review describes the modern understanding of transport through nanotube devices. Unlike conventional semiconductors, electrons in nanotubes have two angular momentum quantum numbers, arising from spin and from valley freedom. We focus on the interplay between the two. In single quantum dots defined in short lengths of nanotube, the energy levels associated with each degree of freedom, and the spin-orbit coupling between them, are revealed by Coulomb blockade spectroscopy. In double quantum dots, the combination of quantum numbers modifies the selection rules of Pauli blockade. This can be exploited to read out spin and valley qubits, and to measure the decay of these states through coupling to nuclear spins and phonons. A second unique property of carbon nanotubes is that the combination of valley freedom and electron-electron interactions in one dimension strongly modifies their transport behaviour. Interaction between electrons inside and outside a quantum dot is manifested in SU(4) Kondo behavior and level renormalization. Interaction within a dot leads to Wigner molecules and more complex correlated states. This review takes an experimental perspective informed by recent advances in theory. As well as the well-understood overall picture, we also state clearly open questions for the field. These advances position nanotubes as a leading system for the study of spin and valley physics in one dimension where electronic disorder and hyperfine interaction can both be reduced to a very low level.Comment: In press at Reviews of Modern Physics. 68 pages, 55 figure

A novel design process of low cost 3D printed ambidextrous finger designed for an ambidextrous robotic hand

This paper presents the novel mechanical design of an ambidextrous finger specifically designed for an ambidextrous anthropomorphic robotic hand actuated by pneumatic artificial muscles. The ambidextrous nature of design allows fingers to perform both left and right hand movements. The aim of our design is to reduce the number of actuators, increase the range of movements with best possible range ideally greater than a common human finger. Four prototypes are discussed in this paper; first prototype is focused on the choice of material and to consider the possible ways to reduce friction. Second prototype is designed to investigate the tendons routing configurations. Aim of third and fourth prototype is to improve the overall performance and to maximize the grasping force. Finally, a unified design (Final design) is presented in great detail. Comparison of all prototypes is done from different angles to evaluate the best design. The kinematic features of intermediate mode have been analysed to optimize both the flexibility and the robustness of the system, as well as to minimize the number of pneumatic muscles. The final design of an ambidextrous finger has developed, tested and 3D printed