Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets

Motivation: To date, Gene Set Analysis (GSA) approaches primarily focus on identifying differentially expressed gene sets (pathways). Methods for identifying differentially coexpressed pathways also exist but are mostly based on aggregated pairwise correlations, or other pairwise measures of coexpression. Instead, we propose Gene Sets Net Correlations Analysis (GSNCA), a multivariate differential coexpression test that accounts for the complete correlation structure between genes.

Results: In GSNCA, weight factors are assigned to genes in proportion to the genes' cross-correlations (intergene correlations). The problem of finding the weight vectors is formulated as an eigenvector problem with a unique solution. GSNCA tests the null hypothesis that for a gene set there is no difference in the weight vectors of the genes between two conditions. In simulation studies and the analyses of experimental data, we demonstrate that GSNCA, indeed, captures changes in the structure of genes' cross-correlations rather than differences in the averaged pairwise correlations. Thus, GSNCA infers differences in coexpression networks, however, bypassing method-dependent steps of network inference. As an additional result from GSNCA, we define hub genes as genes with the largest weights and show that these genes correspond frequently to major and specific pathway regulators, as well as to genes that are most affected by the biological difference between two conditions. In summary, GSNCA is a new approach for the analysis of differentially coexpressed pathways that also evaluates the importance of the genes in the pathways, thus providing unique information that may result in the generation of novel biological hypotheses.

Intensive temperature and quantum correlations for refined quantum measurements

We consider the concept of temperature in a setting beyond the standard thermodynamics prescriptions. Namely, rather than restricting to standard coarse-grained measurements, we consider observers able to master any possible quantum measurement -a scenario that might be relevant at nanoscopic scales. In this setting, we focus on quantum systems of coupled harmonic oscillators and study the question of whether the temperature is an intensive quantity, in the sense that a block of a thermal state can be approximated by an effective thermal state at the same temperature as the whole system. Using the quantum fidelity as figure of merit, we identify instances in which this approximation is not valid, as the block state and the reference thermal state are distinguishable for refined measurements. Actually, there are situations in which this distinguishability even increases with the block size. However, we also show that the two states do become less distinguishable with the block size for coarse-grained measurements -thus recovering the standard picture. We then go further and construct an effective thermal state which provides a good approximation of the block state for any observables and sizes. Finally, we point out the role that entanglement plays in this scenario by showing that, in general, the thermodynamic paradigm of local intensive temperature applies whenever entanglement is not present in the system. Copyright (C) EPLA, 2012

New age estimates and climatostratigraphic correlations for the Borrobol and Penifiler Tephras: evidence from Abernethy Forest, Scotland

The emerging tephrostratigraphy of NW Europe spanning the last termination (ca. 15–9 ka) provides the potential for synchronizing marine, ice-core and terrestrial records, but is currently compromised by stratigraphic complications, geochemical ambiguity and imprecise age estimates for some layers. Here we present new tephrostratigraphic, radiocarbon and chironomid-based
palaeotemperature data from Abernethy Forest, Scotland, that refine the ages and stratigraphic positions of the Borrobol and Penifiler tephras. The Borrobol Tephra (14.14–13.95 cal ka BP) was deposited in a relatively warm period equated with Greenland Interstadial sub-stage GI-1e. The younger Penifiler Tephra (14.09–13.65 cal ka BP) is closely associated with a cold oscillation equated with GI-
1d. We also present evidence for a previously undescribed tephra layer that has a major-element chemical signature identical to the Vedde Ash. It is associated with the warming trend at the end of the Younger Dryas, and dates between 11.79 and 11.20 cal ka BP.

Angular distributions in two-colour two-photon ionization of He

We present R-Matrix with time dependence (RMT) calculations for the photoionization of helium irradiated by an EUV laser pulse and an overlapping IR pulse with an emphasis on the anisotropy parameters of the sidebands generated by the dressing laser field. We investigate how these parameters depend on the amount of atomic structure included in the theoretical model for two-photon ionization. To verify the accuracy of the RMT approach, our theoretical results are compared with experiment.

Non-Markovianity and system-environment correlations in a microscopic collision model

We show that the use of a recently proposed iterative collision model with interenvironment swaps displays a signature of strongly non-Markovian dynamics that is highly dependent on the establishment of system-environment correlations. Two models are investigated: one in which such correlations are canceled iteratively and one in which they are kept all across the dynamics. The degree of non-Markovianity, quantified using a measure based on the trace distance, is found to be much greater for all coupling strengths, when system-environment correlations are maintained.

Attenuation of urokinase activity during experimental ischaemia protects the cerebral barrier from damage through regulation of matrix metalloproteinase-2 and NAD(P)H oxidase

Ischaemic injury impairs the integrity of the blood-brain barrier (BBB). In this study, we investigated the molecular causes of this defect with regard to the putative correlations among NAD(P)H oxidase, plasminogen-plasmin system components, and matrix metalloproteinases. Hence, the activities of NAD(P)H oxidase, matrix metalloproteinase-2, urokinase-type plasminogen activator (uPA), and tissue-type plasminogen activator (tPA), and superoxide anion levels, were assessed in human brain microvascular endothelial cells (HBMECs) exposed to oxygen-glucose deprivation (OGD) alone or OGD followed by reperfusion (OGD + R). The integrity of an in vitro model of BBB comprising HBMECs and astrocytes was studied by measuring transendothelial electrical resistance and the paracellular flux of albumin. OGD with or without reperfusion (OGD ± R) radically perturbed barrier function while concurrently enhancing uPA, tPA and NAD(P)H oxidase activities and superoxide anion release in HBMECs. Pharmacological inactivation of NAD(P)H oxidase attenuated OGD ± R-mediated BBB damage through modulation of matrix metalloproteinase-2 and tPA, but not uPA activity. Overactivation of NAD(P)H oxidase in HBMECs via cDNA electroporation of its p22-phox subunit confirmed the involvement of tPA in oxidase-mediated BBB disruption. Interestingly, blockade of uPA or uPA receptor preserved normal BBB function by neutralizing both NAD(P)H oxidase and matrix metalloproteinase-2 activities. Hence, selective targeting of uPA after ischaemic strokes may protect cerebral barrier integrity and function by concomitantly attenuating basement membrane degradation and oxidative stress.

Modeling relativistic soliton interactions in overdense plasmas: A perturbed nonlinear Schrodinger equation framework

We investigate the dynamics of localized solutions of the relativistic cold-fluid plasma model in the small but finite amplitude limit, for slightly overcritical plasma density. Adopting a multiple scale analysis, we derive a perturbed nonlinear Schrodinger equation that describes the evolution of the envelope of circularly polarized electromagnetic field. Retaining terms up to fifth order in the small perturbation parameter, we derive a self-consistent framework for the description of the plasma response in the presence of localized electromagnetic field. The formalism is applied to standing electromagnetic soliton interactions and the results are validated by simulations of the full cold-fluid model. To lowest order, a cubic nonlinear Schrodinger equation with a focusing nonlinearity is recovered. Classical quasiparticle theory is used to obtain analytical estimates for the collision time and minimum distance of approach between solitons. For larger soliton amplitudes the inclusion of the fifth-order terms is essential for a qualitatively correct description of soliton interactions. The defocusing quintic nonlinearity leads to inelastic soliton collisions, while bound states of solitons do not persist under perturbations in the initial phase or amplitude

Toluene dioxygenase-catalysed oxidation route to angular cis-monohydrodiols and other bioproducts from bacterial metabolism of 1,2-dihydrobenzocyclobutene and derivatives

A mutant strain (UV4) of the soil bacterium Pseudomonas putida, containing toluene dioxygenase, has been used in the metabolic oxidation of 1,2-dihydrobenzocyclobutene 12 dagger and the related substrates 1,2-dihydrobenzocyclobuten-1-ol 13 and biphenylene 33. Stable angular cis-monohydrodiol metabolites (1R,2S)-bicyclo[4.2.0]octa-3,5-diene-1,2 7, (1S,2S,8S)-bicyclo[4.2.0]octa-3,5-diene-1,2,8-triol 8 and biphenylene-cis-1,8b-diol 9, isolated from each of these substrates, have been structurally and stereochemically assigned. The structure, enantiopurity and absolute configuration of the other cis-diol metabolites, (2R,3S)-bicyclo[4.2.0]octa-1(6),4-diene-2,3-diol 14 and cis-1,2-dihydroxy-1,2-dihydrobenzocyclobutene 16, and the benzylic oxidation bioproducts, 1,2-dihydrobenzocyclobuten-1-ol 13, 1,2-dihydrobenzocyclobuten-1-one 15 and 2-hydroxy-1,2-dihydrobenzocyclobuten-1-one 17, obtained from 1,2-dihydrobenzocyclobutene and 1,2-dihydrobenzocyclobuten-1-ol, have been determined with the aid of chiral stationary-phase HPLC, NMR and CD spectroscopy, and stereochemical correlation. X-Ray crystallographic methods have been used in the determination of absolute configuration of the di-camphanates 27 (from diol 7) and 32 (from diol 9), and the di-MTPA ester 29 (from diol 14) of the corresponding cis-diol metabolites. The metabolic sequence involved in the formation of bioproducts derived from 1,2-dihydrobenzocyclobutene 12 has been investigated.

Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype-phenotype correlations, codon bias and dominant-negative effects

The adaptor protein-2 sigma subunit (AP2sigma;2) is pivotal for clathrin-mediated endocytosis of plasma membrane constituents such as the calcium-sensing receptor (CaSR). Mutations of the AP2sigma;2 Arg15 residue result in familial hypocalciuric hypercalcaemia type 3 (FHH3), a disorder of extracellular calcium (Ca<inf>o</inf>²⁺) homeostasis. To elucidate the role of AP2sigma;2 in Ca<inf>o</inf>²⁺ regulation, we investigated 65 FHH probands, without other FHH-associated mutations, for AP2sigma;2 mutations, characterized their functional consequences and investigated the genetic mechanisms leading to FHH3. AP2sigma;2 mutations were identified in 17 probands, comprising 5 Arg15Cys, 4 Arg15His and 8 Arg15Leu mutations. A genotype-phenotype correlation was observed with the Arg15Leu mutation leading to marked hypercalcaemia. FHH3 probands harboured additional phenotypes such as cognitive dysfunction. All three FHH3-causing AP2sigma;2 mutations impaired CaSR signal transduction in a dominant-negative manner. Mutational bias was observed at the AP2sigma;2 Arg15 residue as other predicted missense substitutions (Arg15Gly, Arg15Pro and Arg15Ser), which also caused CaSR loss-of-function, were not detected in FHH probands, and these mutations were found to reduce the numbers of CaSR-expressing cells. FHH3 probands had significantly greater serum calcium (sCa) and magnesium (sMg) concentrations with reduced urinary calcium to creatinine clearance ratios (CCCR) in comparison with FHH1 probands with CaSR mutations, and a calculated index of sCa × sMg/100 × CCCR, which was ≥ 5.0, had a diagnostic sensitivity and specificity of 83 and 86%, respectively, for FHH3. Thus, our studies demonstrate AP2sigma;2 mutations to result in a more severe FHH phenotype with genotype-phenotype correlations, and a dominant-negative mechanism of action with mutational bias at the Arg15 residue.