WordCloud: a Cytoscape plugin to create a visual semantic summary of networks

<p>Abstract</p> <p>Background</p> <p>When biological networks are studied, it is common to look for clusters, i.e. sets of nodes that are highly inter-connected. To understand the biological meaning of a cluster, the user usually has to sift through many textual annotations that are associated with biological entities.</p> <p>Findings</p> <p>The WordCloud Cytoscape plugin generates a visual summary of these annotations by displaying them as a tag cloud, where more frequent words are displayed using a larger font size. Word co-occurrence in a phrase can be visualized by arranging words in clusters or as a network.</p> <p>Conclusions</p> <p>WordCloud provides a concise visual summary of annotations which is helpful for network analysis and interpretation. WordCloud is freely available at <url>http://baderlab.org/Software/WordCloudPlugin</url></p

Minimalistic control of biped walking in rough terrain

Toward our comprehensive understanding of legged locomotion in animals and machines, the compass gait model has been intensively studied for a systematic investigation of complex biped locomotion dynamics. While most of the previous studies focused only on the locomotion on flat surfaces, in this article, we tackle with the problem of bipedal locomotion in rough terrains by using a minimalistic control architecture for the compass gait walking model. This controller utilizes an open-loop sinusoidal oscillation of hip motor, which induces basic walking stability without sensory feedback. A set of simulation analyses show that the underlying mechanism lies in the “phase locking” mechanism that compensates phase delays between mechanical dynamics and the open-loop motor oscillation resulting in a relatively large basin of attraction in dynamic bipedal walking. By exploiting this mechanism, we also explain how the basin of attraction can be controlled by manipulating the parameters of oscillator not only on a flat terrain but also in various inclined slopes. Based on the simulation analysis, the proposed controller is implemented in a real-world robotic platform to confirm the plausibility of the approach. In addition, by using these basic principles of self-stability and gait variability, we demonstrate how the proposed controller can be extended with a simple sensory feedback such that the robot is able to control gait patterns autonomously for traversing a rough terrain.National Science Foundation (U.S.) (grant 0746194)Swiss National Science Foundation (grant PBZH2-114461)Swiss National Science Foundation (grant PP00P2_123387/1

Influence of simulated neuromuscular noise on movement variability and fall risk in a 3D dynamic walking model

People at risk of falling exhibit increased gait variability, which may predict future falls. However, the causal mechanisms underlying these correlations are not well known. Increased neuronal noise associated with aging likely leads to increased gait variability, which could in turn lead to increased fall risk. This paper presents a model of how changes in neuromuscular noise independently affect gait variability and probability of falling, and aims to determine the extent to which changes in gait variability directly predict fall risk. We used a dynamic walking model that incorporates a lateral step controller to maintain lateral stability. Noise was applied to this controller to approximate neuromuscular noise in humans. Noise amplitude was varied between low amplitudes that did not induce falls and high amplitudes for which the model always fell. With increases in noise amplitude, the model fell more often and after fewer steps. Gait variability increased with noise amplitude and predicted increased probability of falling. Importantly, these relationships were not linear. At either low gait variability or very high gait variability, small increases in noise and variability affected probability of falling very little. Conversely, at intermediate noise and/or variability levels, the same small increases resulted in large increases in probability of falling. Our results validate the idea that age-related increases in neuromuscular noise likely play a direct contributing role in increasing fall risk. However, neuromuscular noise remains only one of many important factors that need to be considered. These findings have important implications for fall prevention research and practice

Design, synthesis and cytotoxic activity of novel sulfonylurea derivatives of podophyllotoxin

Three series of novel sulfonylurea podophyllotoxin derivatives were designed, synthesized, and evaluated for in vitro cytotoxicity against four tumor cell lines (A-549, DU-145, KB and KBvin). Compounds 14c (IC(50:) 1.41–1.76 μM) and 14e (IC(50): 1.72–2.01 μM) showed superior cytotoxic activity compared with etoposide (IC(50): 2.03– >20μM), a clinically available anticancer drug. Significantly, most of the compounds exhibited comparable cytotoxicity against the drug-resistant tumor cell line KBvin, while etoposide lost activity completely. Preliminary structure-activity relationship (SAR) correlations indicated that the 4′-O-methyl functionality in podophyllotoxin analogues may be essential to maintain cytotoxic activity, while an arylsulfonylurea side chain at podophyllotoxin’s 4β position can significantly improve cytotoxic activity