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

Capability of modern tank floor scanning with Magnetic Flux Leakage

The article below depicts the current state of MFL technology utilized in testing of storage tanks floor. The main advantage of the MFL is the capability of locating and appraising the size of the defects on large areas in a fast and effective way. Similarly as with other testing methods there are limitations which can have influence on consistency and credibility of the reported defects, however quite often the MFL is considered to be an easy screening method, in which every competent inspector can easily interpret the results. There are many wrong opinions concerning MFL which are mainly caused by lack of knowledge or awareness. Additionally, the article will also cover the solutions used in MFL scanners available on the market that allow the users to obtain high resolutions of scanning as well as the making the distinction between faults and defects located on the surface from the tested side and those located on the opposite side.Niniejszy artykuł przedstawia obecny stan metody magnetycznego strumienia rozproszenia (MFL) wykorzystywanej do badania den zbiorników magazynowych. Podstawową zaletą MFL jest możliwość zlokalizowania i oszacowania wielkości defektów na dużych obszarach. Istnieją ograniczenia, które mogą mieć wpływ na spójność i wiarygodność raportowanych wad. Często metoda MFL jest traktowana jako prosta metoda przesiewowa, w której każdy kompetentny inspektor może łatwo interpretować wyniki. Istnieje wiele błędnych opinii dotyczących MFL, które wynikają głównie z braku wiedzy lub nieświadomości. W artykule zostaną przedstawione ograniczenia oraz wskazówki, w jaki sposób je zredukować. Omówione zostaną rozwiązania stosowane w skanerach MFL pozwalające na uzyskanie wysokich rozdzielczości skanowania oraz rozróżnienie wad na powierzchniach od strony badania od wad po przeciwległej stronie

Stress corrosion - when the defect depth is important

Scharakteryzowano zjawisko korozji naprężeniowej pod kątem możliwości detekcji klasycznymi metodami NDT. Opisano metodę wiroprądową z zastosowaniem sondy macierzowej w kontekście wykrywania niezgodności spowodowanych korozją naprężeniową. Zaprezentowano system kompensacji zmiany odległości cewki od powierzchni oraz możliwości wymiarowania. Przedstawiono charakterystykę przykładowej głowicy oraz przedstawiono wyniki pomiaru na elemencie referencyjnym i rzeczywistym. Przedstawione wyniki wykazują wysoką skuteczność w wykrywaniu niezgodności powstałych w wyniku korozji naprężeniowej. Ostatecznie dokonano porównania wyników uzyskanych metodą prezentowaną oraz metodami magnetyczno-proszkową i ultradźwiękową.The stress corrosion cracking phenomena has been characterized in terms of detection capabilities by classical NDT methods. An eddy current method using a array probe has been described in the context of detecting flaws caused by stress corrosion. A compensation system for changes of the probe lift-off distance and the dimensioning capability was presented. The characteristics of the sample head are shown and the measurement results are presented on the reference and real elements. The results shown are highly effective in detecting flaws caused by stress corrosion. Finally, the results obtained by the presented method with the ones of magnetic penetrant and ultrasonic methods were compared

Wykorzystanie technik zanurzeniowych UT dla optymalizacji akwizycji danych

Ascertaining the integrity of large steel structures such as storage tanks, pipes and vessels is a complex task. Silverwing (UK) Ltd have developed an inspection system based on a water immersion UT (ultrasonic testing) approach that can manage, present and generate reports for large volumes of data, from gigabytes to even terabytes that can be obtained from a single asset. This paper explores inspection efficiency at the data capture stage and shows examples towards illustrating how volumes of information is technically handled and how it can improve the efficiency of the overall inspection process, benefiting the inspection company, asset integrity engineer and asset owner.Określenie stanu dużych stalowych elementów takich jak zbiorniki magazynowe, rurociągi oraz zbiorniki ciśnieniowe to złożone zadanie. Firma Silverwing UK LTD opracowała system inspekcji oparty na technice zanurzeniowej UT (badania ultradźwiękowe), który umożliwia akwizycję, zarządzanie danymi oraz generowanie raportów nawet dla bardzo dużych ilości danych, od gigabajtów do nawet terabajtów, otrzymanych podczas badania jednej instalacji. W artykule dokonano oceny wydajności inspekcji na etapie akwizycji danych oraz przedstawiono przykłady przetwarzania różnych ilości danych oraz sposoby optymalizacji procesu inspekcji, na czym zyskają zarówno firmy przeprowadzające inspekcję, inżynierowie odpowiedzialni za stan techniczny oraz właściciele elementów poddawanych inspekcji