Graffinity: Visualizing Connectivity in Large Graphs

Multivariate graphs are prolific across many fields, including transportation and neuroscience. A key task in graph analysis is the exploration of connectivity, to, for example, analyze how signals flow through neurons, or to explore how well different cities are connected by flights. While standard node‐link diagrams are helpful in judging connectivity, they do not scale to large networks. Adjacency matrices also do not scale to large networks and are only suitable to judge connectivity of adjacent nodes. A key approach to realize scalable graph visualization are queries: instead of displaying the whole network, only a relevant subset is shown. Query‐based techniques for analyzing connectivity in graphs, however, can also easily suffer from cluttering if the query result is big enough. To remedy this, we introduce techniques that provide an overview of the connectivity and reveal details on demand. We have two main contributions: (1) two novel visualization techniques that work in concert for summarizing graph connectivity; and (2) Graffinity, an open‐source implementation of these visualizations supplemented by detail views to enable a complete analysis workflow. Graffinity was designed in a close collaboration with neuroscientists and is optimized for connectomics data analysis, yet the technique is applicable across domains. We validate the connectivity overview and our open‐source tool with illustrative examples using flight and connectomics data.     

The low process yield of some PNP power transistors

A study is presented of the symptoms of the devices in a slice of PNP power transistors with a poor yield. The failure modes over the slice are analysed. In specific areas the electrical characteristics and optical appearance of the devices were studied and failure statistics are presented. The low yield is ascribed to cracks in the phosphosilicate glass used for the base diffusion. The effect of these cracks is just visible in the optical and scanning electron microscope.     

Revised Estimates of Dimension and Exercise Variance Components in Assessment Center Postexercise Dimension Ratings.

The authors reanalyzed assessment center (AC) multitrait-multimethod (MTMM) matrices containing correlations among postexercise dimension ratings (PEDRs) reported by F. Lievens and J. M. Conway (2001). Unlike F. Lievens and J. M. Conway, who used a correlated dimension-correlated uniqueness model, we used a different set of confirmatory-factor-analysis-based models (1-dimension-correlated Exercise and 1-dimension-correlated uniqueness models) to estimate dimension and exercise variance components in AC PEDRs. Results of reanalyses suggest that, consistent with previous narrative reviews, exercise variance components dominate over dimension variance components after all. Implications for AC construct validity and possible redirections of research on the validity of ACs are discussed. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Progress in protein structure prediction

If protein structure prediction methods are to make any impact on the impending onerous task of analyzing the large numbers of unknown protein sequences generated by the ongoing genome-sequencing projects, it is vital that they make the difficult transition from computational 'gedankenexperiments' to practical software tools. This has already happened in the field of comparative modelling and is currently happening in the threading field. Unfortunately, there is little evidence of this transition happening in the field of ab initio tertiary-structure prediction.     

Using neural networks to learn hand-eye co-ordination

The work presented in this paper shows how the association of proprioceptive and exteroceptive stimuli can enable a Kohonen neural network, controlling a robot arm, to learn hand-eye co-ordination so that the arm can reach for and track a visually presented target. The approach presented in this work assumes no a priorimodel of arm kinematics or of the imaging characteristics of the cameras. No explicit representation, such as homogeneous transformations, is used for the specification of robot pose, and camera calibration and triangulation are done implicitly as the system adapts and learns its hand-eye co-ordination by experience. This research is validated on physical devices and not by simulation.     

Mutation of herpesvirus thymidine kinase to generate ganciclovir-specific kinases for use in cancer gene therapies

Understanding the functional and mechanistic properties of themulti-substrate herpes simplex virus type-1 thymidine kinase(HSV-1 TK) remains critical to defining its role as a majorpharmacological target in herpesvirus and gene therapies forcancer. An inherent limitation of the activity of HSV-TK isthe >70-fold difference in the K_ms for phosphorylation ofthymidine over the pro-drug ganciclovir (GCV). To engineer anHSV-1 TK isoform that is specific for GCV as the preferred substrate,16 site-specific mutants were generated. The mutations wereconcentrated at conserved residues involved in nucleoside basebinding, Gln125 and near sites 3 and 4 involved in catalysisand substrate binding. The substrate preferences of each mutantenzyme were compared with wild-type HSV-1 TK. One mutant, termedQ7530 TK, had a lower K_m for GCV than thymidine. Expressionof the Q7530 TK in tumor cells indicated comparable metabolismto and improved sensitivity to GCV over wild-type HSV-1 TK,with minimal thymidine phosphorylation activity. A molecularmodeling simulation of the different HSV-1 TK active-sites wasdone for GCV and thymidine binding. It was concluded that mutationsat Gln125 and near site 4, especially at Ala168, were responsiblefor loss of deoxypyrimidine substrate binding.     

A measurement of the NBS electrical watt in SI units

The National Bureau of Standards (NBS) electric watt in SI units to be: W_NBS/W=K_W =1-(16.69±1.33) p.p.m. The uncertainty of 1.33 p.p.m. has the significance of a standard deviation and includes the best estimate of random and known or suspected systematic uncertainties. The mean time of the measurement is May 15, 1988. Combined with the measurement of the NBS ohm in SI units: Ω_NBS/Ω=K_Ω =1-(1.593±0.022) p.p.m., this leads to a Josephson frequency/voltage quotient of E_J=E₀[1+(7.94±0.67) p.p.m.] where E₀=483, 594 GHz/V