Fast training of self organizing maps for the visual exploration of molecular compounds

Visual exploration of scientific data in life science area is a growing research field due to the large amount of available data. The Kohonen’s Self Organizing Map (SOM) is a widely used tool for visualization of multidimensional data. In this paper we present a fast learning algorithm for SOMs that uses a simulated annealing method to adapt the learning parameters. The algorithm has been adopted in a data analysis framework for the generation of similarity maps. Such maps provide an effective tool for the visual exploration of large and multi-dimensional input spaces. The approach has been applied to data generated during the High Throughput Screening of molecular compounds; the generated maps allow a visual exploration of molecules with similar topological properties. The experimental analysis on real world data from the National Cancer Institute shows the speed up of the proposed SOM training process in comparison to a traditional approach. The resulting visual landscape groups molecules with similar chemical properties in densely connected regions.

Neocolonialism and international law, with specific reference to customary counterterrorism obligations and the principle of self-defence

Has international law ever, and, if it has not, can it ever, truly freed itself from the strictures of neocolonialism and the drive by a privileged elite to dominate the world scene? This article begins by inquiring into the nature of neocolonialism and, in so doing, pays particular attention to the writings of former Ghanaian President Kwame Nkrumah. It then proceeds to determine how neocolonialist designs surface in international law today by briefly looking at two aspects of international law in particular, namely customary international law, with specific reference to the counterterrorism context, and the principle of self-defence. In the final analysis, this article argues for a necessary and eternal scepticism of international law and the agendas of its privileged gatekeepers. Like classic State power, it opens itself to, and often operates as, neocolonial overreach, and to quote Nkrumah, “[t]he cajolement, the wheedlings, the seductions and the Trojan horses of neo-colonialism must be stoutly resisted, for neo-colonialism is a latter-day harpy, a monster which entices its victims with sweet music.”

Toughness, the shearing of self-mated junctions and friction

Since ductile fracture (rupture) is the process by which junctions are separated and which prevents ever-increasing plasticity and junction growth, it is argued that models of friction ought to include toughness as well as yield strength. An expression for the coefficient of sliding friction is derived using ductile fracture mechanics. The predictions are quite reasonable.

What neuroimaging and perceptions of self-other similarity can tell us about the mechanism underlying mentalizing

Carruthers' "mindreading is prior" model postulates one unitary mindreading mechanism working identically for self and other. While we agree about shared mindreading mechanisms, there is also evidence from neuroimaging and mentalizing about dissimilar others that suggest factors that differentially affect self-versus-other mentalizing. Such dissociations suggest greater complexity than the mindreading is prior model allows.

A simulation model of self-organising evolvability in software systems

The evolvability of a software artifact is its capacity for producing heritable or reusable variants; the inverse quality is the artifact's inertia or resistance to evolutionary change. Evolvability in software systems may arise from engineering and/or self-organising processes. We describe our 'Conditional Growth' simulation model of software evolution and show how, it can be used to investigate evolvability from a self-organisation perspective. The model is derived from the Bak-Sneppen family of 'self-organised criticality' simulations. It shows good qualitative agreement with Lehman's 'laws of software evolution' and reproduces phenomena that have been observed empirically. The model suggests interesting predictions about the dynamics of evolvability and implies that much of the observed variability in software evolution can be accounted for by comparatively simple self-organising processes.

Detection of neural correlates of self-paced motor activity using empirical mode decomposition phase locking analysis

Transient episodes of synchronisation of neuronal activity in particular frequency ranges are thought to underlie cognition. Empirical mode decomposition phase locking (EMDPL) analysis is a method for determining the frequency and timing of phase synchrony that is adaptive to intrinsic oscillations within data, alleviating the need for arbitrary bandpass filter cut-off selection. It is extended here to address the choice of reference electrode and removal of spurious synchrony resulting from volume conduction. Spline Laplacian transformation and independent component analysis (ICA) are performed as pre-processing steps, and preservation of phase synchrony between synthetic signals. combined using a simple forward model, is demonstrated. The method is contrasted with use of bandpass filtering following the same preprocessing steps, and filter cut-offs are shown to influence synchrony detection markedly. Furthermore, an approach to the assessment of multiple EEG trials using the method is introduced, and the assessment of statistical significance of phase locking episodes is extended to render it adaptive to local phase synchrony levels. EMDPL is validated in the analysis of real EEG data, during finger tapping. The time course of event-related (de)synchronisation (ERD/ERS) is shown to differ from that of longer range phase locking episodes, implying different roles for these different types of synchronisation. It is suggested that the increase in phase locking which occurs just prior to movement, coinciding with a reduction in power (or ERD) may result from selection of the neural assembly relevant to the particular movement. (C) 2009 Elsevier B.V. All rights reserved.

Compression of polymer brushes: quantitative comparison of self-consistent field theory with experiment

The self-consistent field theory (SCFT) prediction for the compression force between two semi-dilute polymer brushes is compared to the benchmark experiments of Taunton et al. [Nature, 1988, 332, 712]. The comparison is done with previously established parameters, and without any fitting parameters whatsoever. The SCFT provides a significant quantitative improvement over the classical strong-stretching theory (SST), yielding excellent quantitative agreement with the experiment. Contrary to earlier suggestions, chain fluctuations cannot be ignored for normal experimental conditions. Although the analytical expressions of SST provide invaluable aids to understanding the qualitative behavior of polymeric brushes, the numerical SCFT is necessary in order to provide quantitatively accurate predictions.

Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

The 5'-cap-structures of higher eukaryote mRNAs are ribose 2'-O-methylated. Likewise, a number of viruses replicating in the cytoplasm of eukayotes have evolved 2'-O-methyltransferases to modify autonomously their mRNAs. However, a defined biological role of mRNA 2'-O-methylation remains elusive. Here we show that viral mRNA 2'-O-methylation is critically involved in subversion of type-I-interferon (IFN-I) induction. We demonstrate that human and murine coronavirus 2'-O-methyltransferase mutants induce increased IFN-I expression, and are highly IFN-I sensitive. Importantly, IFN-I induction by 2'-O-methyltransferase-deficient viruses is dependent on the cytoplasmic RNA sensor melanoma differentiation-associated gene 5 (MDA5). This link between MDA5-mediated sensing of viral RNA and mRNA 2'-O-methylation suggests that RNA modifications, such as 2'-O-methylation, provide a molecular signature for the discrimination of self and non-self mRNA.

Hydrogelation of self-assembling RGD-based peptides

The self-assembly of tripeptides based on the RGD cell adhesion motif is investigated. Two tripeptides containing the Fmoc [N-(fluorenyl)-9-methoxycarbonyl] aromatic unit were synthesized, Fmoc-RGD and a control peptide containing a scrambled sequence, Fmoc-GRD. The Fmoc is used to control selfassembly via aromatic stacking interactions. The self-assembly and hydrogelation properties of the two Fmoc-tripeptides are compared. Both form well defined amyloid fibrils (as shown by cryo-TEM and SAXS) with b-sheet features in their circular dichroism and FTIR spectra. Both peptides form selfsupporting hydrogels, the dynamic shear modulus of which was measured. Preliminary cell culture experiments reveal that Fmoc-RGD can be used as a support for bovine fibroblasts, but not Fmoc- GRD, consistent with the incorporation of the cell adhesion motif in the former peptide.

The challenge of self-regulation in commercial property leasing: a study of lease codes in the UK.

Purpose – UK Government policy to address perceived market failure in commercial property leasing has largely been pursued through industry self-regulation. Yet, it is proving difficult to assess whether self-regulation on leasing has been a “success”, or even to determine how to evaluate this. The purpose of this paper is to provide a framework for this and a clearer understanding of self-regulation in commercial leasing. Design/methodology/approach – A literature review suggests key criteria to explain the (in)effectiveness of self-regulation. UK lease codes are analysed in the light of this literature, drawing on previous research carried out by the authors on the operation of these codes. Findings – Lease codes appear to be failing as an effective system of self-regulation. While there are influential market actors championing them, the fragmentation of the leasing process lessens this influence. The structures are not there to ensure implementation, monitor compliance and record views of affected stakeholders. Research limitations/implications – This work adds to the literature on self-regulation in general, and provides an insight into its operation in a previously unexplored industry. Research is needed into the experience of other countries in regulating the property industry by voluntary means. Social implications – There are institutional limitations to self-regulation within the property industry. This has implications for policy makers in considering the advantages and limitation of using a voluntary solution to achieve policy aims within the commercial leasing market. Originality/value – This paper provides a first step in considering the lease codes in the wider context of industry self-regulation and is relevant to policy makers and industry bodies.