The IBMAP approach for Markov networks structure learning

In this work we consider the problem of learning the structure of Markov networks from data. We present an approach for tackling this problem called IBMAP, together with an efficient instantiation of the approach: the IBMAP-HC algorithm, designed for avoiding important limitations of existing independence-based algorithms. These algorithms proceed by performing statistical independence tests on data, trusting completely the outcome of each test. In practice tests may be incorrect, resulting in potential cascading errors and the consequent reduction in the quality of the structures learned. IBMAP contemplates this uncertainty in the outcome of the tests through a probabilistic maximum-a-posteriori approach. The approach is instantiated in the IBMAP-HC algorithm, a structure selection strategy that performs a polynomial heuristic local search in the space of possible structures. We present an extensive empirical evaluation on synthetic and real data, showing that our algorithm outperforms significantly the current independence-based algorithms, in terms of data efficiency and quality of learned structures, with equivalent computational complexities. We also show the performance of IBMAP-HC in a real-world application of knowledge discovery: EDAs, which are evolutionary algorithms that use structure learning on each generation for modeling the distribution of populations. The experiments show that when IBMAP-HC is used to learn the structure, EDAs improve the convergence to the optimum

Quantum and Thermal Fluctuations in Field Theory

Blocking transformation is performed in quantum field theory at finite temperature. It is found that the manner temperature deforms the renormalized trajectories can be used to understand better the role played by the quantum fluctuations. In particular, it is conjectured that domain formation and mass parameter generation can be observed in theories without spontaneous symmetry breaking.Comment: 27pp+7 figures, MIT-CTP-214

Mononuclear lanthanide(III)-salicylideneaniline complexes: synthetic, structural, spectroscopic and magnetic studies

The reactions of hydrated lanthanide(III) [Ln(III)] nitrates and salicylideneaniline (salanH) have provided access to two families of mononuclear complexes depending on the reaction solvent used. In MeCN, the products are [Ln(NO3)3(salanH)2(H2O)]·MeCN, and, in MeOH, the products are [Ln(NO3)3(salanH)2(MeOH)]·(salanH). The complexes within each family are proven to be isomorphous. The structures of complexes [Ln(NO3)3(salanH)2(H2O)]·MeCN (Ln = Eu, 4·MeCN_Eu, Ln = Dy, 7·MeCN_Dy; Ln = Yb, 10·MeCN_Yb) and [Ln(NO3)3(salanH)2(MeOH)]·(salanH) (Ln = Tb, 17_Tb; Ln = Dy, 18_Dy) have been solved by single-crystal X-ray crystallography. In the five complexes, the LnIII center is bound to six oxygen atoms from the three bidentate chelating nitrato groups, two oxygen atoms from the two monodentate zwitterionic salanH ligands, and one oxygen atom from the coordinated H2O or MeOH group. The salanH ligands are mutually "cis" in 4·MeCN_Eu, 7·MeCN_Dy and 10·MeCN_Yb while they are "trans" in 17_Tb and 18_Dy. The lattice salanH molecule in 17_Tb and 18_Dy is also in its zwitterionic form with the acidic H atom being clearly located on the imine nitrogen atom. The coordination polyhedra defined by the nine oxygen donor atoms can be described as spherical tricapped trigonal prisms in 4·MeCN_Eu, 7·MeCN_Dy, and 10·MeCN_Yb and as spherical capped square antiprisms in 17_Tb and 18_Dy. Various intermolecular interactions build the crystal structures, which are completely different in the members of the two families. Solid-state IR data of the complexes are discussed in terms of their structural features. 1H NMR data for the diamagnetic Y(III) complexes provide strong evidence that the compounds decompose in DMSO by releasing the coordinated salanH ligands. The solid complexes emit green light upon excitation at 360 nm (room temperature) or 405 nm (room temperature). The emission is ligand-based. The solid Pr(III), Nd(III), Sm(III), Er(III), and Yb(III) complexes of both families exhibit LnIII-centered emission in the near-IR region of the electromagnetic spectrum, but there is probably no efficient salanH→LnIII energy transfer responsible for this emission. Detailed magnetic studies reveal that complexes 7·MeCN_Dy, 17_Tb and 18_Dy show field-induced slow magnetic relaxation while complex [Tb(NO3)3(salanH)2(H2O)]·MeCN (6·MeCN_Tb) does not display such properties. The values of the effective energy barrier for magnetization reversal are 13.1 cm−1 for 7·MeCN_Dy, 14.8 cm−1 for 17_Tb, and 31.0 cm−1 for 18_Dy. The enhanced/improved properties of 17_Tb and 18_Dy, compared to those of 6_Tb and 7_Dy, have been correlated with the different supramolecular structural features of the two families. The molecules [Ln(NO3)3(salanH)2(MeOH)] of complexes 17_Tb and 18_Dy are by far better isolated (allowing for better slow magnetic relaxation properties) than the molecules [Ln(NO3)3(salanH)2(H2O)] in 6·MeCN_Tb and 7·MeCN_Dy. The perspectives of the present initial studies in the Ln(III)/salanH chemistry are discussed

A preliminary analysis of in-depth accident data for powered two-wheelers and bicycles in Europe

Despite progress from scientific and technological advancements, road safety remains a major issue worldwide. Road accident impacts such as fatalities, injuries and property damage consist considerable costs borne not only by involved people but society as well. This study aims to present preliminary findings of in-depth accident analysis for two-wheelers (bicycles and powered two wheelers – PTWs) across six countries in Europe. Data regarding the conditions underlying accident occurrence are presented, including time and date, weather, vehicle and road conditions and rider-related parameters such as age, intoxication and use of protective equipment. In addition, a Two Step Cluster Analysis is implemented in order to explore any possible classification of the analysed cases. It appears that two clusters are formed: the first includes more favourable conditions (“no wind, no drugs, good lighting”) while the second consists of less favourable conditions for road safety (“windy, lighting, unknown DUI condition”). This hints at a meaningful separation of the examination of two-wheeler accidents when the influence of outside factors is considerable. The inclusion of different but representative areas across Europe offers robustness and transferability to the data and respective results

The fidelity of dynamic signaling by noisy biomolecular networks

This is the final version of the article. Available from Public Library of Science via the DOI in this record.Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error) can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.We acknowledge support from a Medical Research Council and Engineering and Physical Sciences Council funded Fellowship in Biomedical Informatics (CGB) and a Scottish Universities Life Sciences Alliance chair in Systems Biology (PSS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Two distinct repressive mechanisms for histone 3 lysine 4 methylation through promoting 3'-end antisense transcription

International audienceHistone H3 di- and trimethylation on lysine 4 are major chromatin marks that correlate with active transcription. The influence of these modifications on transcription itself is, however, poorly understood. We have investigated the roles of H3K4 methylation in Saccharomyces cerevisiae by determining genome-wide expression-profiles of mutants in the Set1 complex, COMPASS, that lays down these marks. Loss of H3K4 trimethylation has virtually no effect on steady-state or dynamically-changing mRNA levels. Combined loss of H3K4 tri- and dimethylation results in steady-state mRNA upregulation and delays in the repression kinetics of specific groups of genes. COMPASS-repressed genes have distinct H3K4 methylation patterns, with enrichment of H3K4me3 at the 3'-end, indicating that repression is coupled to 3'-end antisense transcription. Further analyses reveal that repression is mediated by H3K4me3-dependent 3'-end antisense transcription in two ways. For a small group of genes including PHO84, repression is mediated by a previously reported trans-effect that requires the antisense transcript itself. For the majority of COMPASS-repressed genes, however, it is the process of 3'-end antisense transcription itself that is the important factor for repression. Strand-specific qPCR analyses of various mutants indicate that this more prevalent mechanism of COMPASS-mediated repression requires H3K4me3-dependent 3'-end antisense transcription to lay down H3K4me2, which seems to serve as the actual repressive mark. Removal of the 3'-end antisense promoter also results in derepression of sense transcription and renders sense transcription insensitive to the additional loss of SET1. The derepression observed in COMPASS mutants is mimicked by reduction of global histone H3 and H4 levels, suggesting that the H3K4me2 repressive effect is linked to establishment of a repressive chromatin structure. These results indicate that in S. cerevisiae, the non-redundant role of H3K4 methylation by Set1 is repression, achieved through promotion of 3'-end antisense transcription to achieve specific rather than global effects through two distinct mechanisms