A novel and robust parameter training approach for HMMs under noisy and partial access to states

Cataloged from PDF version of article.This paper proposes a new estimation algorithm for the parameters of an HMM as to best account for the observed data. In this model, in addition to the observation sequence, we have partial and noisy access to the hidden state sequence as side information. This access can be seen as "partial labeling" of the hidden states. Furthermore, we model possible mislabeling in the side information in a joint framework and derive the corresponding EM updates accordingly. In our simulations, we observe that using this side information, we considerably improve the state recognition performance, up to 70%, with respect to the "achievable margin" defined by the baseline algorithms. Moreover, our algorithm is shown to be robust to the training conditions. (C) 2013 Elsevier B.V. All rights reserved

The Input Signal Step Function (ISSF), a Standard Method to Encode Input Signals in SBML Models with Software Support, Applied to Circadian Clock Models

LetterThis is the final version of the article. Available from SAGE Publications via the DOI in this record.Time-dependent light input is an important feature of computational models of the circadian clock. However, publicly available models encoded in standard representations such as the Systems Biology Markup Language (SBML) either do not encode this input or use different mechanisms to do so, which hinders reproducibility of published results as well as model reuse. The authors describe here a numerically continuous function suitable for use in SBML for models of circadian rhythms forced by periodic light-dark cycles. The Input Signal Step Function (ISSF) is broadly applicable to encoding experimental manipulations, such as drug treatments, temperature changes, or inducible transgene expression, which may be transient, periodic, or mixed. It is highly configurable and is able to reproduce a wide range of waveforms. The authors have implemented this function in SBML and demonstrated its ability to modify the behavior of publicly available models to accurately reproduce published results. The implementation of ISSF allows standard simulation software to reproduce specialized circadian protocols, such as the phase-response curve. To facilitate the reuse of this function in public models, the authors have developed software to configure its behavior without any specialist knowledge of SBML. A community-standard approach to represent the inputs that entrain circadian clock models could particularly facilitate research in chronobiology.K.S. was supported by the UK BBSRC grant BB/E015263/1. SynthSys Edinburgh is a Centre for Integrative Systems Biology (CISB) funded by BBSRC and EPSRC, reference BB/D019621/1

Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels

Cellular phenotypes underpinned by regulatory networks need to respond to evolutionary pressures to allow adaptation, but at the same time be robust to perturbations. This creates a conflict in which mutations affecting regulatory networks must both generate variance but also be tolerated at the phenotype level. Here, we perform mathematical analyses and simulations of regulatory networks to better understand the potential trade-off between robustness and evolvability. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics, through the creation of regions presenting sudden changes in phenotype with small changes in genotype. For genotypes embedding low levels of nonlinearity, robustness and evolvability correlate negatively and almost perfectly. By contrast, genotypes embedding nonlinear dynamics allow expression levels to be robust to small perturbations, while generating high diversity (evolvability) under larger perturbations. Thus, nonlinearity breaks the robustness-evolvability trade-off in gene expression levels by allowing disparate responses to different mutations. Using analytical derivations of robustness and system sensitivity, we show that these findings extend to a large class of gene regulatory network architectures and also hold for experimentally observed parameter regimes. Further, the effect of nonlinearity on the robustness-evolvability trade-off is ensured as long as key parameters of the system display specific relations irrespective of their absolute values. We find that within this parameter regime genotypes display low and noisy expression levels. Examining the phenotypic effects of mutations, we find an inverse correlation between robustness and evolvability that breaks only with nonlinearity in the network dynamics. Our results provide a possible solution to the robustness-evolvability trade-off, suggest an explanation for the ubiquity of nonlinear dynamics in gene expression networks, and generate useful guidelines for the design of synthetic gene circuits

Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data

Summary: Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors. Availability and implementation: BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

Lossless Text Compression Technique Using Syllable Based Morphology

In this paper, we present a new lossless text compression technique which utilizes syllable-based morphology of multi-syllabic languages. The proposed algorithm is designed to partition words into its syllables and then to produce their shorter bit representations for compression. The method has six main components namely source file, filtering unit, syllable unit, compression unit, dictionary file and target file. The number of bits in coding syllables depends on the number of entries in the dictionary file. The proposed algorithm is implemented and tested using 20 different texts of different lengths collected from different fields. The results indicated a compression of up to 43%

The interplay between consumer protection and competition law in India

The protection of the interests of consumers is a central aspect of all modern competition laws as well as a direct aim of consumer protection laws. However, despite being complementary in many ways, competition and consumer protection laws cover different issues and employ different methods to achieve their goals. While consumer protection rules are built upon the premise that consumers are the weaker party to transactions and should be directly protected for this reason in their dealings with traders through certain consumer rights, competition law only indirectly protects the consumers’ economic well-being by ensuring that the markets are subject to effective competition. This article explores the interplay between consumer protection and competition law in the Indian context with some comparison with the EU position, where relevant. After an examination of the relevant legislation and case law, the article finds that given that the mandate of the Competition Commission of India is to prevent practices having an adverse effect on competition, in cases of overlap between consumer protection and competition laws, the Authority should act only on the basis of adverse effects on competition. The treatment of ‘unfair trade practices’ is used to demonstrate the appropriateness of this approach

Magnetic properties of triethylene glycol coated CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's synthesized by polyol method

AbstractIn this study, we reported on the structural and magnetic properties of TEG-CoFe2O4 and TEG-Mn0.2Co0.8Fe2O4 nanocomposites produced by the glycothermal reaction (polyol). X-ray diffraction (XRD), transmission electron microscopy (TEM) and vibration sample magnetometer (VSM) analysis have been carried out in order to understand the effect of Mn2+ into CoFe2O4 and it was observed that the addition of Mn2+ tends to reduce the crystallite size, increase the ao (cell parameter) and increase the TB. The presence of adsorbed polyol entities on the surface of the CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's was also proven by TG measurements. FT-IR analysis suggested the presence of adsorbed TEG molecules on the surface of CoFe2O4 and Mn0.2Co0.8Fe2O4 NP's