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

Non-Commutative Batalin-Vilkovisky Algebras, Homotopy Lie Algebras and the Courant Bracket

We consider two different constructions of higher brackets. First, based on a Grassmann-odd, nilpotent \Delta operator, we define a non-commutative generalization of the higher Koszul brackets, which are used in a generalized Batalin-Vilkovisky algebra, and we show that they form a homotopy Lie algebra. Secondly, we investigate higher, so-called derived brackets built from symmetrized, nested Lie brackets with a fixed nilpotent Lie algebra element Q. We find the most general Jacobi-like identity that such a hierarchy satisfies. The numerical coefficients in front of each term in these generalized Jacobi identities are related to the Bernoulli numbers. We suggest that the definition of a homotopy Lie algebra should be enlarged to accommodate this important case. Finally, we consider the Courant bracket as an example of a derived bracket. We extend it to the "big bracket" of exterior forms and multi-vectors, and give closed formulas for the higher Courant brackets.Comment: 42 pages, LaTeX. v2: Added remarks in Section 5. v3: Added further explanation. v4: Minor adjustments. v5: Section 5 completely rewritten to include covariant construction. v6: Minor adjustments. v7: Added references and explanation to Section

Hydrogen storage capacity of titanium met-cars

The adsorption of hydrogen molecules on the titanium metallocarbohedryne (met-car) cluster has been investigated by using the first-principles plane wave method. We have found that, while a single Ti atom at the corner can bind up to three hydrogen molecules, a single Ti atom on the surface of the cluster can bind only one hydrogen molecule. Accordingly, a Ti8C12 met-car can bind up to 16H2 molecules and hence can be considered as a high-capacity hydrogen storage medium. Strong interaction between two met-car clusters leading to the dimer formation can affect H2 storage capacity slightly. Increasing the storage capacity by directly inserting H 2 into the met-car or by functionalizing it with an Na atom have been explored. It is found that the insertion of neither an H2 molecule nor an Na atom could further promote the H2 storage capacity of a Ti8C12 cluster. We have also tested the stability of the H2-adsorbed Ti8C12 met-car with ab initio molecular dynamics calculations which have been carried out at room temperature. © 2006 IOP Publishing Ltd

Algorithms for Stable Matching and Clustering in a Grid

We study a discrete version of a geometric stable marriage problem originally proposed in a continuous setting by Hoffman, Holroyd, and Peres, in which points in the plane are stably matched to cluster centers, as prioritized by their distances, so that each cluster center is apportioned a set of points of equal area. We show that, for a discretization of the problem to an $n\times n$ grid of pixels with $k$ centers, the problem can be solved in time $O(n^2 \log^5 n)$, and we experiment with two slower but more practical algorithms and a hybrid method that switches from one of these algorithms to the other to gain greater efficiency than either algorithm alone. We also show how to combine geometric stable matchings with a $k$-means clustering algorithm, so as to provide a geometric political-districting algorithm that views distance in economic terms, and we experiment with weighted versions of stable $k$-means in order to improve the connectivity of the resulting clusters.Comment: 23 pages, 12 figures. To appear (without the appendices) at the 18th International Workshop on Combinatorial Image Analysis, June 19-21, 2017, Plovdiv, Bulgari

Generic temperature compensation of biological clocks by autonomous regulation of catalyst concentration

Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures, despite the expected Arrhenius form for the reaction coefficient. Observations have shown that the amplitude of the oscillation depends on the temperature but the period does not---this suggests that although not every reaction step is temperature independent, the total system comprising several reactions still exhibits compensation. We present a general mechanism for such temperature compensation. Consider a system with multiple activation energy barriers for reactions, with a common enzyme shared across several reaction steps with a higher activation energy. These reaction steps rate-limit the cycle if the temperature is not high. If the total abundance of the enzyme is limited, the amount of free enzyme available to catalyze a specific reaction decreases as more substrates bind to common enzyme. We show that this change in free enzyme abundance compensate for the Arrhenius-type temperature dependence of the reaction coefficient. Taking the example of circadian clocks with cyanobacterial proteins KaiABC consisting of several phosphorylation sites, we show that this temperature compensation mechanisms is indeed valid. Specifically, if the activation energy for phosphorylation is larger than that for dephosphorylation, competition for KaiA shared among the phosphorylation reactions leads to temperature compensation. Moreover, taking a simpler model, we demonstrate the generality of the proposed compensation mechanism, suggesting relevance not only to circadian clocks but to other (bio)chemical oscillators as well.Comment: 21 pages, 12 figure

First generation immigrant judgements of offence seriousness: evidence from the crime survey for England and Wales

This exploratory paper delves into differences and similarities in the rated seriousness of offences suffered by victims of different national origin. The issue is important because a mismatch between police and victim assessments of seriousness is likely to fuel discord. It was found that first generation immigrants did not differ in their rating of the seriousness of offences against the person from either the indigenous population or according to region of birth. However those of Asian origin rated vehicle and property crime they had suffered as more serious than did other groups about crimes they suffered. The anticipated higher seriousness rating of offences reported to the police r was observed for all groups. People of Asian origin reported to the police a smaller proportion of offences they rated trivial than did people in other groups. Analysis of seriousness judgements in victimization surveys represents a much-underused resource for understanding the nexus between public perceptions and criminal justice responses

Sketch-based interaction and modeling: where do we stand?

Sketching is a natural and intuitive communication tool used for expressing concepts or ideas which are difficult to communicate through text or speech alone. Sketching is therefore used for a variety of purposes, from the expression of ideas on two-dimensional (2D) physical media, to object creation, manipulation, or deformation in three-dimensional (3D) immersive environments. This variety in sketching activities brings about a range of technologies which, while having similar scope, namely that of recording and interpreting the sketch gesture to effect some interaction, adopt different interpretation approaches according to the environment in which the sketch is drawn. In fields such as product design, sketches are drawn at various stages of the design process, and therefore, designers would benefit from sketch interpretation technologies which support these differing interactions. However, research typically focuses on one aspect of sketch interpretation and modeling such that literature on available technologies is fragmented and dispersed. In this paper, we bring together the relevant literature describing technologies which can support the product design industry, namely technologies which support the interpretation of sketches drawn on 2D media, sketch-based search interactions, as well as sketch gestures drawn in 3D media. This paper, therefore, gives a holistic view of the algorithmic support that can be provided in the design process. In so doing, we highlight the research gaps and future research directions required to provide full sketch-based interaction support

Penile metastasis from primary transitional cell carcinoma of the renal pelvis: first manifestation of systemic spread

BACKGROUND: Almost one-third of all penile metastases are detected at the same time as a primary tumor, whereas the remaining two-thirds are detected a mean of 18 months after the discovery of the primary tumor. Cutaneous metastasis of transitional cell carcinoma (TCC) is extremely rare and generally accepted as the late manifestation of a systemic spread. CASE PRESENTATION: We report the first case of simultaneous penile and lung metastases from a primary TCC of the renal pelvis in a 76-year-old man, that occurred 8 years after a left nephroureterectomy. CONCLUSIONS: This case report underscores the importance of physical examinations of the skin of patients who undergo surgical procedures for TCC from bladder as well as from the upper urinary tract, including those seemingly without metastatic disease, because of the possibility of skin and penile metastatic spread