Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

Synthesis of [3-C-13]-2,3-dihydroxy-4-methoxybenzaldehyde

An efficient synthesis of [3-13C]-2,3-dihydroxy-4-methoxybenzaldehyde, an isotopically labelled probe of a common intermediate used in the synthesis of a number of biologically relevant molecules, has been achieved in 9 steps from an acyclic, non-aromatic precursor. A 13C label for molecular imaging was introduced in a linear synthesis from the reaction of [13C]-labelled methyl iodide with glutaric monomethyl ester chloride. Cyclisation then aromatisation gave 1,3-dimethoxybenzene and an additional methoxy group was introduced by a formylation/Baeyer–Villiger/hydrolysis/methylation sequence. Subsequent ortho-formylation and selective demethylation yielded the desired [3-13C]-2,3-dihydroxy-4-methoxybenzaldehyde

Phase sensitive amplification in a highly nonlinear lead-silicate fibre

We experimentally demonstrate phase-sensitive amplification in a highly nonlinear lead-silicate W-type fibre. A phase-sensitive gain swing of 6dB was observed in a 1.56m sample of the fibre for a total launched power of 33dBm

Fine genetic mapping of a gene required for Rice yellow mottle virus cell-to-cell movement

International audienceThe very high resistance to rice yellow mottle virus observed in the two rice varieties Gigante (Oryza sativa) and Tog 5681 (O. glaberrima) is monogenic and recessive. Bulked segregant analysis was carried out to identify AFLP markers linked to the resistance gene. Mapping of PCR-specific markers, CAPS and microsatellite markers on 429 individuals of an IR64 × Gigante F 2 population pinpointed this resistance gene on the long arm of chromosome 4 in a 3.7-cM interval spanned by PCR markers. These markers also flanked the resistance gene of the O. glaberrima accession Tog 5681 and confirmed previous allelism tests. The rarity of this recessive natural resistance was in line with a resistance mechanism model based on point mutations of a host component required for cell-to-cell movement of the virus. Preliminary data on the genetic divergence between the two cultivated rice species in the vicinity of the resistance locus suggested that two different resistance alleles are present in Gigante and Tog 5681. A large set of recombinants is now available to envisage physical mapping and cloning of the gene

THE AMUNDSEN SEA LOW Variability, Change, and Impact on Antarctic Climate

The Amundsen Sea low (ASL) is a climatological low pressure center that exerts considerable influence on the climate of West Antarctica. Its potential to explain important recent changes in Antarctic climate, for example, in temperature and sea ice extent, means that it has become the focus of an increasing number of studies. Here, the authors summarize the current understanding of the ASL, using reanalysis datasets to analyze recent variability and trends, as well as ice-core chemistry and climate model projections, to examine past and future changes in the ASL, respectively. The ASL has deepened in recent decades, affecting the climate through its influence on the regional meridional wind field, which controls the advection of moisture and heat into the continent. Deepening of the ASL in spring is consistent with observed West Antarctic warming and greater sea ice extent in the Ross Sea. Climate model simulations for recent decades indicate that this deepening is mediated by tropical variability while climate model projections through the twenty-first century suggest that the ASL will deepen in some seasons in response to greenhouse gas concentration increases

New empirical fits to the proton electromagnetic form factors

Recent measurements of the ratio of the elastic electromagnetic form factors of the proton, G_Ep/G_Mp, using the polarization transfer technique at Jefferson Lab show that this ratio decreases dramatically with increasing Q^2, in contradiction to previous measurements using the Rosenbluth separation technique. Using this new high quality data as a constraint, we have reanalyzed most of the world e-p elastic cross section data. In this paper, we present a new empirical fit to the reanalyzed data for the proton elastic magnetic form factor in the region 0 < Q^2 < 30 GeV^2. As well, we present an empirical fit to the proton electromagnetic form factor ratio, G_Ep/G_Mp, which is valid in the region 0.1 < Q^2 < 6 GeV^2

Resonance Kondo Tunneling through a Double Quantum Dot at Finite Bias

It is shown that the resonance Kondo tunneling through a double quantum dot (DQD) with even occupation and singlet ground state may arise at a strong bias, which compensates the energy of singlet/triplet excitation. Using the renormalization group technique we derive scaling equations and calculate the differential conductance as a function of an auxiliary dc-bias for parallel DQD described by SO(4) symmetry. We analyze the decoherence effects associated with the triplet/singlet relaxation in DQD and discuss the shape of differential conductance line as a function of dc-bias and temperature.Comment: 11 pages, 6 eps figures include

Baryon Decuplet to Octet Electromagnetic Transitions in Quenched and Partially Quenched Chiral Perturbation Theory

We calculate baryon decuplet to octet electromagnetic transition form factors in quenched and partially quenched chiral perturbation theory. We work in the isospin limit of SU(3) flavor, up to next-to-leading order in the chiral expansion, and to leading order in the heavy baryon expansion. Our results are necessary for proper extrapolation of lattice calculations of these transitions. We also derive expressions for the case of SU(2) flavor away from the isospin limit.Comment: 16 pages, 3 figures, revtex

Quasi-Local Density Functional Theory and its Application within Extended Thomas-Fermi Approximation

A generalization of the Density Functional Theory is proposed. The theory developed leads to single-particle equations of motion with a quasi-local mean-field operator, which contains a quasi-particle position-dependent effective mass and a spin-orbit potential. The energy density functional is constructed using the Extended Thomas-Fermi approximation. Within the framework of this approach the ground-state properties of the doubly magic nuclei are considered. The calculations have been performed using the finite-range Gogny D1S force. The results are compared with the exact Hartree-Fock calculations

ADAMTS -1 and -4 are up-regulated following transient middle cerebral artery occlusion in the rat and their expression is modulated by TNF in cultured astrocytes

ADAMTS (a disintegrin and metalloproteinase with thrombospondin motifs) enzymes are a recently described group of metalloproteinases. The substrates degraded by ADAMTS-1, -4 and -5 suggests that they play a role in turnover of extracellular matrix in the central nervous system (CNS). ADAMTS-1 is also known to exhibit anti-angiogenic activity. Their main endogenous inhibitor is tissue inhibitor of metalloproteinases (TIMP)-3. The present study was designed to investigate ADAMTS-1, -4 and -5 and TIMP-3 expression after experimental cerebral ischaemia and to examine whether cytokines known to be up-regulated in stroke could alter their expression by astrocytes in vitro. Focal cerebral ischaemia was induced by transient middle cerebral artery occlusion in the rat using the filament method. Our results demonstrate a significant increase in expression of ADAMTS-1 and -4 in the occluded hemisphere but no significant change in TIMP-3. This was accompanied by an increase in mRNA levels for interleukin (IL)-1, IL-1 receptor antagonist (IL-1ra) and tumour necrosis factor (TNF). ADAMTS-4 mRNA and protein was up-regulated by TNF in primary human astrocyte cultures. The increased ADAMTS-1 and -4 in experimental stroke, together with no change in TIMP-3, may promote ECM breakdown after stroke, enabling infiltration of inflammatory cells and contribute to brain injury. In vitro studies suggest that the in vivo modulation of ADAMTS-1 and -4 may be controlled in part by TNF.</p