Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network.

Traditional Chinese Medicine (TCM) has received increasing attention as a complementary approach or alternative to modern medicine. However, experimental methods for identifying novel targets of TCM herbs heavily relied on the current available herb-compound-target relationships. In this work, we present an Herb-Target Interaction Network (HTINet) approach, a novel network integration pipeline for herb-target prediction mainly relying on the symptom related associations. HTINet focuses on capturing the low-dimensional feature vectors for both herbs and proteins by network embedding, which incorporate the topological properties of nodes across multi-layered heterogeneous network, and then performs supervised learning based on these low-dimensional feature representations. HTINet obtains performance improvement over a well-established random walk based herb-target prediction method. Furthermore, we have manually validated several predicted herb-target interactions from independent literatures. These results indicate that HTINet can be used to integrate heterogeneous information to predict novel herb-target interactions

A virtual environment to support the distributed design of large made-to-order products

An overview of a virtual design environment (virtual platform) developed as part of the European Commission funded VRShips-ROPAX (VRS) project is presented. The main objectives for the development of the virtual platform are described, followed by the discussion of the techniques chosen to address the objectives, and finally a description of a use-case for the platform. Whilst the focus of the VRS virtual platform was to facilitate the design of ROPAX (roll-on passengers and cargo) vessels, the components within the platform are entirely generic and may be applied to the distributed design of any type of vessel, or other complex made-to-order products

Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition

The DNA Damage Response (DDR) pathway represents a signalling mechanism that is activated in eukaryotic cells following DNA damage and comprises of proteins involved in DNA damage detection, DNA repair, cell cycle arrest and apoptosis. This pathway consists of an intricate network of signalling interactions driving the cellular ability to recognise DNA damage and recruit specialised proteins to take decisions between DNA repair or apoptosis. ATM and ATR are central components of the DDR pathway. The activities of these kinases are vital in DNA damage induced phosphorylational induction of DDR substrates. Here, firstly we have experimentally determined DDR signalling network surrounding the ATM/ATR pathway induced following double stranded DNA damage by monitoring and quantifying time dependent inductions of their phosphorylated forms and their key substrates. We next involved an automated inference of unsupervised predictive models of time series data to generate in silico (molecular) interaction maps. We characterized the complex signalling network through system analysis and gradual utilisation of small time series measurements of key substrates through a novel network inference algorithm. Furthermore, we demonstrate an application of an assumption-free reverse engineering of the intricate signalling network of the activated ATM/ATR pathway. We next studied the consequences of such drug induced inductions as well as of time dependent ATM kinase inhibition on cell survival through further biological experiments. Intermediate and temporal modelling outcomes revealed the distinct signaling profile associated with ATM kinase activity and inhibition and explained the underlying signalling mechanism for dual ATM functionality in cytotoxic and cytoprotective pathways

Space syntax and spatial cognition: or why the axial line?

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Synthesis of variable dancing styles based on a compact spatiotemporal representation of dance

Dance as a complex expressive form of motion is able to convey emotion, meaning and social idiosyncrasies that opens channels for non-verbal communication, and promotes rich cross-modal interactions with music and the environment. As such, realistic dancing characters may incorporate crossmodal information and variability of the dance forms through compact representations that may describe the movement structure in terms of its spatial and temporal organization. In this paper, we propose a novel method for synthesizing beatsynchronous dancing motions based on a compact topological model of dance styles, previously captured with a motion capture system. The model was based on the Topological Gesture Analysis (TGA) which conveys a discrete three-dimensional point-cloud representation of the dance, by describing the spatiotemporal variability of its gestural trajectories into uniform spherical distributions, according to classes of the musical meter. The methodology for synthesizing the modeled dance traces back the topological representations, constrained with definable metrical and spatial parameters, into complete dance instances whose variability is controlled by stochastic processes that considers both TGA distributions and the kinematic constraints of the body morphology. In order to assess the relevance and flexibility of each parameter into feasibly reproducing the style of the captured dance, we correlated both captured and synthesized trajectories of samba dancing sequences in relation to the level of compression of the used model, and report on a subjective evaluation over a set of six tests. The achieved results validated our approach, suggesting that a periodic dancing style, and its musical synchrony, can be feasibly reproduced from a suitably parametrized discrete spatiotemporal representation of the gestural motion trajectories, with a notable degree of compression