Virial statistical description of non-extensive hierarchical systems

In a first part the scope of classical thermodynamics and statistical mechanics is discussed in the broader context of formal dynamical systems, including computer programmes. In this context classical thermodynamics appears as a particular theory suited to a subset of all dynamical systems. A statistical mechanics similar to the one derived with the microcanonical ensemble emerges from dynamical systems provided it contains, 1) a finite non-integrable part of its phase space which is, 2) ergodic at a satisfactory degree after a finite time. The integrable part of phase space provides the constraints that shape the particular system macroscopical properties, and the chaotic part provides well behaved statistical properties over a relevant finite time. More generic semi-ergodic systems lead to intermittent behaviour, thus may be unsuited for a statistical description of steady states. Following these lines of thought, in a second part non-extensive hierarchical systems with statistical scale-invariance and power law interactions are explored. Only the virial constraint, consistent with their microdynamics, is included. No assumptions of classical thermodynamics are used, in particular extensivity and local homogeneity. In the limit of a large hierarchical range new constraints emerge in some conditions that depend on the interaction law range. In particular for the gravitational case, a velocity-site scaling relation is derived which is consistant with the ones empirically observed in the fractal interstellar medium.Comment: Based on the talk given at the Meeting on `Statistical Mechanics of Non-Extensive Systems', 24-25 Oct 05, Paris. To be published in a Special Issue of Les Comptes rendus de l'Academie des Sciences. 21 pages; 4 figure

Receiver design for the uplink of base station cooperation systems employing SC-FDE modulations

The presented paper considers the uplink transmission in base station (BS) cooperation schemes where mobile terminals (MTs) in adjacent cells share the same physical channel. We consider single-carrier with frequency-domain equalization (SC-FDE) combined with iterative frequency-domain receivers based on the iterative block decision feedback equalization (IB-DFE). We study the quantization requirements when sending the received signals, from different MTs, at different BSs to a central unit that performs the separation of different MTs using iterative frequency-domain receivers. Our performance results show that a relatively coarse quantization, with only 4 bits in the in-phase and quadrature components of the complex envelope already allows close-to-optimum macro-diversity gains, as well as an efficient separation of the transmitted signals associated with each MT

Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates

Shikimate kinase (SK; EC 2.7.1.71) catalyzes the fifth reaction of the shikimate pathway, which directs carbon from the central metabolism pool to a broad range of secondary metabolites involved in plant development, growth, and stress responses. In this study, we demonstrate the role of plant SK gene duplicate evolution in the diversification of metabolic regulation and the acquisition of novel and physiologically essential function. Phylogenetic analysis of plant SK homologs resolves an orthologous cluster of plant SKs and two functionally distinct orthologous clusters. These previously undescribed genes, shikimate kinase-like 1 (SKL1) and -2 (SKL2), do not encode SK activity, are present in all major plant lineages, and apparently evolved under positive selection following SK gene duplication over 400 MYA. This is supported by functional assays using recombinant SK, SKL1, and SKL2 from Arabidopsis thaliana (At) and evolutionary analyses of the diversification of SK-catalytic and -substrate binding sites based on theoretical structure models. AtSKL1 mutants yield albino and novel variegated phenotypes, which indicate SKL1 is required for chloroplast biogenesis. Extant SKL2 sequences show a strong genetic signature of positive selection, which is enriched in a protein–protein interaction module not found in other SK homologs. We also report the first kinetic characterization of plant SKs and show that gene expression diversification among the AtSK inparalogs is correlated with developmental processes and stress responses. This study examines the functional diversification of ancient and recent plant SK gene duplicates and highlights the utility of SKs as scaffolds for functional innovation

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Entrapment of Living Bacterial Cells in Low-Concentration Silica Materials Preserves Cell Division and Promoter Regulation

The entrapment of bacterial cells within inorganic silica materials was reported almost 20 years ago. However, almost all studies to date have shown that these entrapped cells are unable to divide and thus should be expected to have reduced promoter activity. In view of the importance of bacteria as model systems for both fundamental and applied biological studies, it is crucial that immobilized cells retain solutionlike properties, including the ability to divide and display normal promoter activity. Herein we report on a method to immobilize bacterial cells within low-density inorganic silica-based materials, where the cells retain both cell division and promoter activity. Sol gel processing was used to entrap Escherichia coli cells carrying a variety of green fluorescent protein-linked promoters into sodium silicate-derived materials that were formed in microwell plates. Using a series of assays, we were able to demonstrate that (1) the entrapped cells can divide within the pores of the silica matrix, (2) cellular pathways are regulated in a similar manner in both solution and the sol-gel-derived materials, and (3) promoters in entrapped cells can be specifically induced with small molecules (e.g., antimicrobial compounds) in a concentration-dependent manner to allow assessment of both potency and mode of action. This solid-phase assay system was tested using multiple antimicrobial pathways and should enable the development of solid-phase assays for the discovery of new small molecules that are active against bacteria