Computing and visually analyzing mutual information in molecular co-evolution

<p>Abstract</p> <p>Background</p> <p>Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information -after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.</p> <p>Results</p> <p>To visually analyze mutual information we developed a matrix visualization tool that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to <it>Z</it>-scores with respect to the null model.</p> <p>Conclusions</p> <p>The new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users using the tool in real-world research. The software can also be used for visual analysis of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in <monospace>Java</monospace> and free for academic use under a GPL license.</p

BioPhysConnectoR: Connecting Sequence Information and Biophysical Models

<p>Abstract</p> <p>Background</p> <p>One of the most challenging aspects of biomolecular systems is the understanding of the coevolution in and among the molecule(s).</p> <p>A complete, theoretical picture of the selective advantage, and thus a functional annotation, of (co-)mutations is still lacking. Using sequence-based and information theoretical inspired methods we can identify coevolving residues in proteins without understanding the underlying biophysical properties giving rise to such coevolutionary dynamics. Detailed (atomistic) simulations are prohibitively expensive. At the same time reduced molecular models are an efficient way to determine the reduced dynamics around the native state. The combination of sequence based approaches with such reduced models is therefore a promising approach to annotate evolutionary sequence changes.</p> <p>Results</p> <p>With the <monospace>R</monospace> package <monospace>BioPhysConnectoR</monospace> we provide a framework to connect the information theoretical domain of biomolecular sequences to biophysical properties of the encoded molecules - derived from reduced molecular models. To this end we have integrated several fragmented ideas into one single package ready to be used in connection with additional statistical routines in <monospace>R</monospace>. Additionally, the package leverages the power of modern multi-core architectures to reduce turn-around times in evolutionary and biomolecular design studies. Our package is a first step to achieve the above mentioned annotation of coevolution by reduced dynamics around the native state of proteins.</p> <p>Conclusions</p> <p><monospace>BioPhysConnectoR</monospace> is implemented as an <monospace>R</monospace> package and distributed under GPL 2 license. It allows for efficient and perfectly parallelized functional annotation of coevolution found at the sequence level.</p

Using geographically weighted regression to explore neighborhood-level predictors of domestic abuse in the UK

Reducing domestic abuse has become a priority for both local and national governments in the UK, with its substantial human, social, and economic costs. It is an interdisciplinary issue, but to date there has been no research in the UK that has focused on neighborhood-level predictors of domestic abuse and their variation across space. This article uses geographically weighted regression to model the predictors of police-reported domestic abuse in Essex. Readily available structural and cultural variables were found to predict the domestic abuse rate and the repeat victimization rate at the lower super output area level and the model coefficients were all found to be non-stationary, indicating varying relationships across space. This research not only has important implications for victims' well being, but also enables policy makers to gain a better understanding of the geography of victimization, allowing targeted policy interventions and efficiently allocated resources

Geometric effects of sustainable auxetic structures integrating the particle swarm optimization and finite element method

The development of new materials based on industrial wastes has been the focus of much research for a sustainable world. The growing demand for tyres has been every year exacerbating environmental problems due to indiscriminate disposal in the nature, making a potentially harmful waste to public health. The incorporation of rubber particles from scrap tyres into polymeric composites has achieved high toughness and moderate mechanical properties. This work investigates the geometric effects (thickness, width and internal cell angle) of auxetic structures made of recycled rubber composites based on experimental and numerical data. The response surface models integrated with the swarm intelligence and finite element analysis were proposed in order to obtain a range of solutions that provides useful information to the user during the selection of geometric parameters for reentrant cells. The results revealed the cell thickness ranges from 39-40 mm and 5.98-6 mm, and the cell angle range from -0.01 to -0.06º maximize the ultimate strength. The same parameters were able to optimize the modulus of elasticity of rubber auxetic structures, excepting for the angle factor which must be set between -30º and 27.7º. The optimal Poisson's ratio was found when the cell angle ranged from -30º to -28.5º, cell width ranged from 5-5.6 mm and 2 mm in thickness

Service of devices working in can network problem on example of inclinometer

Artykuł przedstawia ogólne właściwości sieci CAN, a także podstawową specyfikację protokołu CANopen. W opracowaniu wyszczególnione są cechy charakterystyczne tego protokołu oraz problemy jakie można napotkać podczas implementacji sieci tej klasy. Przedstawiono problem identyfikacji węzła i adresowania wiadomości procesowych, odczyt zawartych w nich informacji (tzw. PDO-mapping) na przykładzie inklinometru. Na koniec opisano sposób reprezentacji danych na wyświetlaczu pracującego w standardzie sieci CAN.The article presents the general characteristics of the CAN network as well as the basic specification of the CANopen protocol. The paper lists the characteristics of this protocol and problems they may encounter during the implementation of this network. In the article a problem of node identification, addressing of processes message and read of contained information were presented. At the end authors described how to represent data on the display working in the CAN