Clustering the annotation space of proteins

BACKGROUND: Current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas. RESULTS: Here we report a new approach, named CLAN, which clusters proteins according to both annotation and sequence similarity. This approach is extremely fast, clustering the complete SwissProt database within minutes. It is also accurate, recovering consistent protein families agreeing on average in more than 97% with sequence-based protein families from Pfam. Discrepancies between sequence- and annotation-based clusters were scrutinized and the reasons reported. We demonstrate examples for each of these cases, and thoroughly discuss an example of a propagated error in SwissProt: a vacuolar ATPase subunit M9.2 erroneously annotated as vacuolar ATP synthase subunit H. CLAN algorithm is available from the authors and the CLAN database is accessible at CONCLUSIONS: CLAN creates refined function-and-sequence specific protein families that can be used for identification and annotation of unknown family members. It also allows easy identification of erroneous annotations by spotting inconsistencies between similarities on annotation and sequence levels

Solitary and compact-like shear waves in the bulk of solids

We show that a model proposed by Rubin, Rosenau, and Gottlieb [J. Appl. Phys. 77 (1995) 4054], for dispersion caused by an inherent material characteristic length, belongs to the class of simple materials. Therefore, it is possible to generalize the idea of Rubin, Rosenau, and Gottlieb to include a wide range of material models, from nonlinear elasticity to turbulence. Using this insight, we are able to fine-tune nonlinear and dispersive effects in the theory of nonlinear elasticity in order to generate pulse solitary waves and also bulk travelling waves with compact support

The Cauchy Problem for a One Dimensional Nonlinear Peridynamic Model

This paper studies the Cauchy problem for a one-dimensional nonlinear peridynamic model describing the dynamic response of an infinitely long elastic bar. The issues of local well-posedness and smoothness of the solutions are discussed. The existence of a global solution is proved first in the sublinear case and then for nonlinearities of degree at most three. The conditions for finite-time blow-up of solutions are established.Comment: To appear in Journal of Differential Equations (added references, corrected typos, minor revision in Section 2, 18 pages

The Cauchy Problem for a One Dimensional Nonlinear Peridynamic Model

This paper studies the Cauchy problem for a one-dimensional nonlinear peridynamic model describing the dynamic response of an infinitely long elastic bar. The issues of local well-posedness and smoothness of the solutions are discussed. The existence of a global solution is proved first in the sublinear case and then for nonlinearities of degree at most three. The conditions for finite-time blow-up of solutions are established.Comment: To appear in Journal of Differential Equations (added references, corrected typos, minor revision in Section 2, 18 pages

Organic farming enhances parasitoid diversity at the local and landscape scales

1. The magnitude of the benefits derived from organic farming within contrasting managed landscapes remains unclear and, in particular, the potential scale-dependent response of insect parasitoids is relatively unexplored. Identifying the scale at which parasitoids are affected by organic farming will be an important step to enhance their conservation. 2. We sampled tachinid parasitoids at the centre and margin of arable and grassland fields on paired organic and conventional farms located in landscapes with different proportions of organic land. A total of 192 fields were sampled in two biogeographical regions of the UK. 3. We found that the positive effect of organic farming on tachinid parasitoid diversity can be observed at multiple spatial scales. At the local scale, we found higher abundance and species richness of tachinid parasitoids on organic than on conventional farms and on field margins than on field centres. At the landscape scale, the diversity of tachinids was higher in landscapes with higher proportions of organic land. At both scales, the positive effect of organic farming was clear for arable fields, while it was almost neutral for grasslands. 4. Synthesis and applications. Any attempt to enhance parasitoid diversity in agricultural landscapes needs to consider the local management in relation to the habitat type, location within the field and agricultural management in the surrounding landscape. To restore parasitoid diversity, the promotion of organic agriculture should aim to increase both the total extent of organic farming and the connectivity of individual farms. As the benefits of organic farming to biodiversity clearly spread beyond individual farm boundaries, any assessment of organic farming should consider these positive externalities

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

The BioCyc database collection is a set of 160 pathway/genome databases (PGDBs) for most eukaryotic and prokaryotic species whose genomes have been completely sequenced to date. Each PGDB in the BioCyc collection describes the genome and predicted metabolic network of a single organism, inferred from the MetaCyc database, which is a reference source on metabolic pathways from multiple organisms. In addition, each bacterial PGDB includes predicted operons for the corresponding species. The BioCyc collection provides a unique resource for computational systems biology, namely global and comparative analyses of genomes and metabolic networks, and a supplement to the BioCyc resource of curated PGDBs. The Omics viewer available through the BioCyc website allows scientists to visualize combinations of gene expression, proteomics and metabolomics data on the metabolic maps of these organisms. This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways present in these organisms, and the most frequently observed pathways. We seek scientists to adopt and curate individual PGDBs within the BioCyc collection. Only by harnessing the expertise of many scientists we can hope to produce biological databases, which accurately reflect the depth and breadth of knowledge that the biomedical research community is producing

The Cauchy problem for a class of two-dimensional nonlocal nonlinear wave equations governing anti-plane shear motions in elastic materials

This paper is concerned with the analysis of the Cauchy problem of a general class of two-dimensional nonlinear nonlocal wave equations governing anti-plane shear motions in nonlocal elasticity. The nonlocal nature of the problem is reflected by a convolution integral in the space variables. The Fourier transform of the convolution kernel is nonnegative and satisfies a certain growth condition at infinity. For initial data in $L^{2}$ Sobolev spaces, conditions for global existence or finite time blow-up of the solutions of the Cauchy problem are established.Comment: 15 pages. "Section 6 The Anisotropic Case" added and minor changes. Accepted for publication in Nonlinearit