Memory based on abstraction for dynamic fitness functions

Copyright @ Springer-Verlag Berlin Heidelberg 2008.This paper proposes a memory scheme based on abstraction for evolutionary algorithms to address dynamic optimization problems. In this memory scheme, the memory does not store good solutions as themselves but as their abstraction, i.e., their approximate location in the search space. When the environment changes, the stored abstraction information is extracted to generate new individuals into the population. Experiments are carried out to validate the abstraction based memory scheme. The results show the efficiency of the abstraction based memory scheme for evolutionary algorithms in dynamic environments.This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) of UK under Grant No. EP/E060722/1

Effects of edentulism in obstructive sleep apnea syndrome

Objectives: The purpose of this study was to investigate the effects of edentulism in obstructive sleep apnea syndrome (OSAS) patients.Materials and Methods: The study patients’ were selected from the Gaziantep University Sleep Clinic and Orthodontic Department archives between the years of 2009 and 2011. Study groups were determined according to age and edentulism, and the overall study population consisted of 42 (21 male, 21 female) OSAS patients. Data from 14 edentulous (Group I), 14 older dentate (Group II), and 14 middle‑aged dentate OSAS patients (Group III) were compared in this study. Polysomnographic parameters, which were measured and analyzed included: Sleep time, sleep efficiency, sleep stage 1, sleep stage 2, sleep stage 3, percentage of rapid eye movement sleep, apnea‑hypopnea index, oxygen saturation and arousal index. The Kruskal–Wallis and Mann–Whitney U statistical tests were used for comparing the differences between the three groups and subgroups.Results: Sleep time parameters showed significant differences between the groups (P < 0.05). Differences occurred between Group I and Group III in the sleep time parameter (P < 0.05), while the edentulous subjects showed lower mean sleep time values when compared to the older and middle‑aged dentate groups.Conclusion: According to our results, edentulism may not impact polysomnography parameters, with the exception of the sleep time parameter. Important attention should be given to edentulous individuals during sleep with their dentures to prevent OSAS complications. The use of dentures may prevent or protect patients from the predisposing factors of OSAS.Keywords: Dentures, edentulous, obstructive sleep apnea syndrome, polysomnograph

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

In the field of RNA, the technologies for studying the transcriptome have created a tremendous potential for deciphering the puzzles of the RNA biology. Along with the excitement, the unprecedented volume of RNA related omics data is creating great challenges in bioinformatics analyses. Here, we present the RNA Centric Annotation System (RCAS), an R package, which is designed to ease the process of creating gene-centric annotations and analysis for the genomic regions of interest obtained from various RNA-based omics technologies. The design of RCAS is modular, which enables flexible usage and convenient integration with other bioinformatics workflows. RCAS is an R/Bioconductor package but we also created graphical user interfaces including a Galaxy wrapper and a stand-alone web service. The application of RCAS on published datasets shows that RCAS is not only able to reproduce published findings but also helps generate novel knowledge and hypotheses. The meta-gene profiles, gene-centric annotation, motif analysis and gene-set analysis provided by RCAS provide contextual knowledge which is necessary for understanding the functional aspects of different biological events that involve RNAs. In addition, the array of different interfaces and deployment options adds the convenience of use for different levels of users. RCAS is available at http://bioconductor.org/packages/release/bioc/html/RCAS.html and http://rcas.mdc-berlin.de

HOT or not: examining the basis of high-occupancy target regions

High-occupancy target (HOT) regions are segments of the genome with unusually high number of transcription factor binding sites. These regions are observed in multiple species and thought to have biological importance due to high transcription factor occupancy. Furthermore, they coincide with house-keeping gene promoters and consequently associated genes are stably expressed across multiple cell types. Despite these features, HOT regions are solemnly defined using ChIP-seq experiments and shown to lack canonical motifs for transcription factors that are thought to be bound there. Although, ChIP-seq experiments are the golden standard for finding genome-wide binding sites of a protein, they are not noise free. Here, we show that HOT regions are likely to be ChIP-seq artifacts and they are similar to previously proposed 'hyper-ChIPable' regions. Using ChIP-seq data sets for knocked-out transcription factors, we demonstrate presence of false positive signals on HOT regions. We observe sequence characteristics and genomic features that are discriminatory of HOT regions, such as GC/CpG-rich k-mers, enrichment of RNA-DNA hybrids (R-loops) and DNA tertiary structures (G-quadruplex DNA). The artificial ChIP-seq enrichment on HOT regions could be associated to these discriminatory features. Furthermore, we propose strategies to deal with such artifacts for the future ChIP-seq studies

Testing timed systems modeled by stream X-machines

Stream X-machines have been used to specify real systems where complex data structures. They are a variety of extended finite state machine where a shared memory is used to represent communications between the components of systems. In this paper we introduce an extension of the Stream X-machines formalism in order to specify systems that present temporal requirements. We add time in two different ways. First, we consider that (output) actions take time to be performed. Second, our formalism allows to specify timeouts. Timeouts represent the time a system can wait for the environment to react without changing its internal state. Since timeous affect the set of available actions of the system, a relation focusing on the functional behavior of systems, that is, the actions that they can perform, must explicitly take into account the possible timeouts. In this paper we also propose a formal testing methodology allowing to systematically test a system with respect to a specification. Finally, we introduce a test derivation algorithm. Given a specification, the derived test suite is sound and complete, that is, a system under test successfully passes the test suite if and only if this system conforms to the specification

Modular logic gates: cascading independent logic gates via metal ion signals

Cataloged from PDF version of article.Abstract Systematic cascading of molecular logic gates is an important issue to be addressed for advancing research in this field. We have demonstrated that photochemically triggered metal ion signals can be utilized towards that goal. Thus, independent logic gates were shown to work together while keeping their identity in more complex logic designs. Communication through the intermediacy of ion signals is clearly inspired from biological processes modulated by such signals, and implemented here with ion responsive molecules. © 2014 The Royal Society of Chemistry.

Near-IR-Triggered, Remote-Controlled Release of Metal Ions: A Novel Strategy for Caged Ions

Cataloged from PDF version of article.A ligand incorporating a dithioethenyl moiety is cleaved into fragments which have a lower metal-ion affinity upon irradiation with low-energy red/near-IR light. The cleavage is a result of singlet oxygen generation which occurs on excitation of the photosensitizer modules. The method has many tunable factors that could make it a satisfactory caging strategy for metal ions

PiGx: reproducible genomics analysis pipelines with GNU Guix

In bioinformatics, as well as other computationally-intensive research fields, there is a need for workflows that can reliably produce consistent output, from known sources, independent of the software environment or configuration settings of the machine on which they are executed. Indeed, this is essential for controlled comparison between different observations or for the wider dissemination of workflows. Providing this type of reproducibility and traceability, however, is often complicated by the need to accommodate the myriad dependencies included in a larger body of software, each of which generally come in various versions. Moreover, in many fields (bioinformatics being a prime example), these versions are subject to continual change due to rapidly evolving technologies, further complicating problems related to reproducibility. Here, we propose a principled approach for building analysis pipelines and managing their dependencies with GNU Guix. As a case study to demonstrate the utility of our approach, we present a set of highly reproducible pipelines called PiGx for the analysis of RNA-seq, ChIP-seq, Bisulfite-seq, and single-cell RNA-seq. All pipelines process raw experimental data, and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables. Users may install these highly reproducible packages and apply them to their own datasets without any special computational expertise beyond the use of the command line. We hope such a toolkit will provide immediate benefit to laboratory workers wishing to process their own data sets or bioinformaticians seeking to automate all, or parts of, their analyses. In the long term, we hope our approach to reproducibility will serve as a blueprint for reproducible workflows in other areas. Our pipelines, along with their corresponding documentation and sample reports, are available at http://bioinformatics.mdc-berlin.de/pigx