The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-ray crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and [alpha]-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a [beta]-sheet arrangement reminiscent of the [beta]-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods

Automated Synthesis of a Finite Complexity Ordering for Saturation

We present in this paper a new procedure to saturate a set of clauses with respect to a well-founded ordering on ground atoms such that A < B implies Var(A) {\subseteq} Var(B) for every atoms A and B. This condition is satisfied by any atom ordering compatible with a lexicographic, recursive, or multiset path ordering on terms. Our saturation procedure is based on a priori ordered resolution and its main novelty is the on-the-fly construction of a finite complexity atom ordering. In contrast with the usual redundancy, we give a new redundancy notion and we prove that during the saturation a non-redundant inference by a priori ordered resolution is also an inference by a posteriori ordered resolution. We also prove that if a set S of clauses is saturated with respect to an atom ordering as described above then the problem of whether a clause C is entailed from S is decidable

Superposition frames for adaptive time-frequency analysis and fast reconstruction

In this article we introduce a broad family of adaptive, linear time-frequency representations termed superposition frames, and show that they admit desirable fast overlap-add reconstruction properties akin to standard short-time Fourier techniques. This approach stands in contrast to many adaptive time-frequency representations in the extant literature, which, while more flexible than standard fixed-resolution approaches, typically fail to provide efficient reconstruction and often lack the regular structure necessary for precise frame-theoretic analysis. Our main technical contributions come through the development of properties which ensure that this construction provides for a numerically stable, invertible signal representation. Our primary algorithmic contributions come via the introduction and discussion of specific signal adaptation criteria in deterministic and stochastic settings, based respectively on time-frequency concentration and nonstationarity detection. We conclude with a short speech enhancement example that serves to highlight potential applications of our approach.Comment: 16 pages, 6 figures; revised versio

Rapid Sampling for Visualizations with Ordering Guarantees

Visualizations are frequently used as a means to understand trends and gather insights from datasets, but often take a long time to generate. In this paper, we focus on the problem of rapidly generating approximate visualizations while preserving crucial visual proper- ties of interest to analysts. Our primary focus will be on sampling algorithms that preserve the visual property of ordering; our techniques will also apply to some other visual properties. For instance, our algorithms can be used to generate an approximate visualization of a bar chart very rapidly, where the comparisons between any two bars are correct. We formally show that our sampling algorithms are generally applicable and provably optimal in theory, in that they do not take more samples than necessary to generate the visualizations with ordering guarantees. They also work well in practice, correctly ordering output groups while taking orders of magnitude fewer samples and much less time than conventional sampling schemes.Comment: Tech Report. 17 pages. Condensed version to appear in VLDB Vol. 8 No.

Historical forest biomass dynamics modelled with Landsat spectral trajectories

Acknowledgements National Forest Inventory data are available online, provided by Ministerio de Agricultura, Alimentación y Medio Ambiente (España). Landsat images are available online, provided by the USGS.Peer reviewedPostprin