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Coalgebraic logic programming: from Semantics to Implementation (2016)

Komendantskaya, E., Power, J., Schmidt, M.

Oxford University Press

In: Journal of Logic and Computation

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Publication Date: 2016-03-30

Description: Coinductive definitions, such as that of an infinite stream, may often be described by elegant logic programs, but ones for which SLD-refutation is of no value as SLD-derivations fall into infinite loops. Such definitions give rise to questions of lazy corecursive derivations and parallelism, as execution of such logic programs can have both recursive and corecursive features at once. Observational and coalgebraic semantics have been used to study them abstractly. The programming developments have often occurred separately and have usually been implementation-led. Here, we give a coherent semantics-led account of the issues, starting with abstract category theoretic semantics, developing coalgebra to characterize naturally arising trees and proceeding towards implementation of a new dialect, CoALP, of logic programming, characterised by guarded lazy corecursion and parallelism.

Print ISSN: 0955-792X

Electronic ISSN: 1465-363X

Topics: Computer Science , Mathematics

Published by Oxford University Press

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Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins (2016)

Ziegler, Z., Schmidt, M., Gurry, T., Burger, V., Stultz, C. M.

Oxford University Press

In: Bioinformatics

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Publication Date: 2016-08-11

Description: : Intrinsically disordered proteins (IDPs) play central roles in many biological processes. Consequently, an accurate description of the disordered state is an important step towards a comprehensive understanding of a number of important biological functions. In this work we describe a new web server, Mollack, for the automated construction of unfolded ensembles that uses both experimental and molecular simulation data to construct models for the unfolded state. An important aspect of the method is that it calculates a quantitative estimate of the uncertainty in the constructed ensemble, thereby providing an objective measure of the quality of the final model. Overall, Mollack facilitates structure-function studies of disordered proteins. Availability and Implementation: http://cmstultz-mollack.mit.edu Contact: cmstultz@mit.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Print ISSN: 1367-4803

Electronic ISSN: 1460-2059

Topics: Biology , Computer Science , Medicine

Published by Oxford University Press

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Boric acid-dependent decrease in regulatory histone H3 acetylation is not mutagenic in yeast (2016)

Pointer, B. R., Schmidt, M.

Oxford University Press

In: FEMS Microbiology Letters

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Publication Date: 2016-06-02

Description: Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations . The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.

Keywords: Physiology & Biochemistry

Print ISSN: 0378-1097

Electronic ISSN: 1574-6968

Topics: Biology

Published by Oxford University Press

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Mean-convex Alexandrov embedded constant mean curvature tori in the 3-sphere (2016)

Hauswirth, L., Kilian, M., Schmidt, M. U.

Oxford University Press

In: Proceedings of the London Mathematical Society

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Publication Date: 2016-03-10

Description: We introduce the moduli space of spectral curves of constant mean curvature (CMC) cylinders of finite type in the round unit 3-sphere. The subset of spectral curves of mean-convex Alexandrov embedded cylinders is explicitly determined using a combination of integrable systems and geometric analysis techniques. We prove that these cylinders are surfaces of revolution. As a consequence, all mean-convex Alexandrov embedded CMC tori in the 3-sphere are surfaces of revolution.

Print ISSN: 0024-6115

Electronic ISSN: 1460-244X

Topics: Mathematics

Published by Oxford University Press

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Mt. Wendelstein imaging of the post-perihelion dust coma of 67P/Churyumov-Gerasimenko in 2015/2016 (2016)

Boehnhardt, H., Riffeser, A., Kluge, M., Ries, C., Schmidt, M., Hopp, U.

Oxford University Press

In: Monthly Notices of the Royal Astronomical Society

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Publication Date: 2016-12-29

Description: Comet 67P/Churyumov-Gerasimenko (67P) was imaged with the 2 m telescope at Mt. Wendelstein Observatory in the Alps. Coma and tail monitoring was performed during 51 nights between 2015 August 22 and 2016 May 9. The images through r and i Sloan Digital Sky Survey (SDSS) filters show the dust distribution around the comet, while images in the SDSS g filter also indicate the presence of coma gas in early 2015 September. The dust colour of 67P implies intrinsic reddening of 9 per cent/100 nm. After maximum, shortly after perihelion passage, the dust activity decreased with a heliocentric exponent of 4.1–4.2 from late 2015 September until 2016 May. The opposition surge during early 2016 can be explained by a linear light scattering phase function (β ~ 0.04) or an asteroid-like HG-type phase function ( G ~ 0.15). The radial brightness profile indicates a ‘quasi-steady-state’ dust coma from late September to the end of 2015. Dust fragmentation during about a month after perihelion may be responsible for radial coma profiles with slopes below unity, while dust accumulation due to very slow dust expansion velocity may result in steeper than unity profiles during 2016. Three fan-shape dust structures are characterized in the coma of 67P. A short dust ejection event on 2015 August 22–23 has produced a dust arc-let and jet feature in the coma. In 2015 September, the appearance of cometary dust tail is dominated by the young dust produced around perihelion. The older dust dominates the tail appearance as of 2015 mid-November.

Print ISSN: 0035-8711

Electronic ISSN: 1365-2966

Topics: Physics

Published by Oxford University Press

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Note on short-time behavior of semigroups associated to self-adjoint operators (2016)

Keller, M., Lenz, D., Münch, F., Schmidt, M., Telcs, A.

Oxford University Press

In: Bulletin of the London Mathematical Society

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Publication Date: 2016-12-30

Description: We present a simple observation showing that the heat kernel on a locally finite graph behaves for short times $t$ roughly like $t^d$ , where $d$ is the combinatorial distance. This is very different from the classical Varadhan-type behavior on manifolds. Moreover, this also gives that short-time behavior and global behavior of the heat kernel are governed by two different metrics whenever the degree of the graph is not uniformly bounded.

Print ISSN: 0024-6093

Electronic ISSN: 1469-2120

Topics: Mathematics

Published by Oxford University Press

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