Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers.

Human influenza occurs annually in most temperate climatic zones of the world, with epidemics peaking in the cold winter months. Considerable debate surrounds the relative role of epidemic dynamics, viral evolution, and climatic drivers in driving year-to-year variability of outbreaks. The ultimate test of understanding is prediction; however, existing influenza models rarely forecast beyond a single year at best.

River density and landscape roughness are universal determinants of linguistic diversity.

Global linguistic diversity (LD) displays highly heterogeneous distribution patterns. Though the origin of the latter is not yet fully understood, remarkable parallelisms with biodiversity distribution suggest that environmental variables should play an essential role in their emergence. In an effort to construct a broad framework to explain world LD and to systematize the available data, we have investigated the significance of 14 variables: landscape roughness, altitude, river density, distance to lakes, seasonal maximum, average and minimum temperature, precipitation and vegetation, and population density.

Role of demographic dynamics and conflict in the population-area relationship for human languages.

Many patterns displayed by the distribution of human linguistic groups are similar to the ecological organization described for biological species. It remains a challenge to identify simple and meaningful processes that describe these patterns. The population size distribution of human linguistic groups, for example, is well fitted by a log-normal distribution that may arise from stochastic demographic processes.

One hub-one process: a tool based view on regulatory network topology.

Background: The relationship between the regulatory design and the functionality of molecular networks is a key issue in biology. Modules and motifs have been associated to various cellular processes, thereby providing anecdotal evidence for performance based localization on molecular networks.

Results: To quantify structure-function relationship we investigate similarities of proteins which are close in the regulatory network of the yeast Saccharomyces Cerevisiae.

Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.

Background: The evolution of the full repertoire of proteins encoded in a given genome is mostly driven by gene duplications, deletions, and sequence modifications of existing proteins. Indirect information about relative rates and other intrinsic parameters of these three basic processes is contained in the proteome-wide distribution of sequence identities of pairs of paralogous proteins.

Results: We introduce a simple mathematical framework based on a stochastic birth-and-death model that allows one to extract some of this information and apply it to the set of all pairs of paralogous proteins in H.

Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles.

We have analyzed gene expression in different normal human tissues and different types of solid cancers derived from these tissues. The cancers analyzed include brain (astrocytoma and glioblastoma), breast, colon, endometrium, kidney, liver, lung, ovary, prostate, skin, and thyroid cancers. Comparing gene expression in each normal tissue to 12 other normal tissues, we identified 4,917 tissue-selective genes that were selectively expressed in different normal tissues.

Degree landscapes in scale-free networks.

We generalize the degree-organizational view of real-world networks with broad degree distributions in a landscape analog with mountains (high-degree nodes) and valleys (low-degree nodes). For example, correlated degrees between adjacent nodes correspond to smooth landscapes (social networks), hierarchical networks to one-mountain landscapes (the Internet), and degree-disassortative networks without hierarchical features to rough landscapes with several mountains. To quantify the topology, we here measure the widths of the mountains and the separation between different mountains.

Quantifying the benefits of translation regulation in the unfolded protein response.

Protein production can be regulated at the translation stage through modulation of mRNA activity and degradation. In the unfolded protein response in S. cerevisiae it works by regulating the conversion rate from a reservoir of passive mRNA to an active short-lived mRNA that is open for translation.

Improvement of hydrogen bond geometry in protein NMR structures by residual dipolar couplings--an assessment of the interrelation of NMR restraints.

We have examined how the hydrogen bond geometry in three different proteins is affected when structural restraints based on measurements of residual dipolar couplings are included in the structure calculations. The study shows, that including restraints based solely on (1)H(N)-(15)N residual dipolar couplings has pronounced impact on the backbone rmsd and Ramachandran plot but does not improve the hydrogen bond geometry. In the case of chymotrypsin inhibitor 2 the addition of (13)CO-(13)C(alpha) and (15)N-(13)CO one bond dipolar couplings as restraints in the structure calculations improved the hydrogen bond geometry to a quality comparable to that obtained in the 1.

Physical interpretation of residual dipolar couplings in neutral aligned media.

A novel method is described for rapidly calculating alignment tensors from hydrodynamic shape, required for the prediction of residual dipolar couplings in neutral aligned media. Simulations of alignment were used to show that for steric restriction at a planar surface, the alignment process is dependent on linear hydrodynamic length. However, as discussed, previous methods are not in agreement with this observation.