Multivariate Statistical Analysis Applied to an IL6 Signal Transduction Model in Hepatocytes

This paper introduces the application of linear multivariate statistical techniques, including partial least squares (PLS), canonical correlation analysis (CCA) and reduced rank regression (RRR), into the area of Systems Biology. This new approach aims to extract the important proteins embedded in complex signal transduction pathway models.The analysis is performed on a model of intracellular signalling along the janus-associated kinases/signal transducers and transcription factors (JAK/STAT) and mitogen activated protein kinases (MAPK) signal transduction pathways in interleukin-6 (IL6) stimulated hepatocytes, which produce signal transducer and activator of transcription factor 3 (STAT3).A region of redundancy within the MAPK pathway that does not affect the STAT3 transcription was identified using CCA. This is the core finding of this analysis and cannot be obtained by inspecting the model by eye. In addition, RRR was found to isolate terms that do not significantly contribute to changes in protein concentrations, while the application of PLS does not provide such a detailed picture by virtue of its construction.This analysis has a similar objective to conventional model reduction techniques with the advantage of maintaining the meaning of the states prior to and after the reduction process. A significant model reduction is performed, with a marginal loss in accuracy, offering a more concise model while maintaining the main influencing factors on the STAT3 transcription.The findings offer a deeper understanding of the reaction terms involved, confirm the relevance of several proteins to the production of Acute Phase Proteins and complement existing findings regarding cross-talk between the two signalling pathways.

Quantum chessboards in the deuterium molecular ion

We present a new algorithm for vibrational control in deuterium molecules that is feasible with current experimental technology. A pump mechanism is used for creating a coherent superposition of the D-2(+) vibrations. A short, intense infrared control pulse is applied after a chosen delay time to create selective interferences. A 'chessboard' pattern of states can be realized in which a set of even- or odd-numbered vibrational states can be selectively annihilated or enhanced. A technique is proposed for experimental realization and observation of this effect using 5 fs pulses of lambda = 790 nm radiation, with intermediate intensity (5 x 10(13) W cm(-2)).

Application of proton radiography in experiments of relevance to inertial confinement fusion

Multi-Mev proton beams generated by target normal sheath acceleration (TNSA) during the interaction of an ultra intense laser beam (Ia parts per thousand yen10(19) W/cm(2)) with a thin metallic foil (thickness of the order of a few tens of microns) are particularly suited as a particle probe for laser plasma experiments. The proton imaging technique employs a laser-driven proton beam in a point-projection imaging scheme as a diagnostic tool for the detection of electric fields in such experiments. The proton probing technique has been applied in experiments of relevance to inertial confinement fusion (ICF) such as laser heated gasbags and laser-hohlraum experiments. The data provides direct information on the onset of laser beam filamentation and on the plasma expansion in the hohlraum's interior, and confirms the suitability and usefulness of this technique as an ICF diagnostic.

Double-ionization dynamics of laser-driven helium

We report a new method which allows sequential and non-sequential double-ionization rates in laser-driven helium to be distinguished and calculated separately. The method is applied to calculate such rates for two laser pulses, one of 0.236 au frequency and 8.0 × 1015 W cm-2 peak intensity, the other of 1.0 au frequency and also of 8.0 × 1015 W cm-2 peak intensity.

Doppler cooling of gallium atoms: 2. Simulation in complex multilevel systems

This paper derives a general procedure for the numerical solution of the Lindblad equations that govern the coherences arising from multicoloured light interacting with a multilevel system. A systematic approach to finding the conservative and dissipative terms is derived and applied to the laser cooling of p-block elements. An improved numerical method is developed to solve the time-dependent master equation and results are presented for transient cooling processes. The method is significantly more robust, efficient and accurate than the standard method and can be applied to a broad range of atomic and molecular systems. Radiation pressure forces and the formation of dynamic dark states are studied in the gallium isotope 66Ga.

Hexyl Aminolaevulinate Is a More Effective Topical Photosensitiser Precursor than Methyl Aminolaevulinate and 5-Aminolaevulinic Acids When Applied in Equimolar Doses

Aminolaevulinic acid (ALA) is known to poorly penetrate into thick lesions, such as nodular basal cell carcinomas Short chain ALA esters, possessing increased lipophilicity relative to their hydrophilic parent, have previously been shown to be highly efficient at inducing protoporphyrin IX (PpIX) production in cell culture, at equimolar concentrations. In contrast, in vitro skin permeation and in vivo animal studies, which up to now have compared prodrugs on a % w/vv basis, have failed to demonstrate such benefits For the first time, equimolar concentrations of ALA, methyl-ALA (m-ALA) and hexyl-ALA (h-ALA) have been incorporated into an o/w cream preparation. In vitro penetration studies into excised porcine skin revealed that increased levels of h-ALA, compared to ALA and m-ALA were found in the upper skin layers, at all drug loadings studied. Topical application of the formulations to nude murine skin in vivo, revealed that creams containing h-ALA induced significantly higher levels of peak PpIX fluorescence (F-max = 289.0) at low concentrations compared to m-ALA (F-max = 159.2) and ALA (F-max = 191 9). Importantly, this study indicates that when compared on an equimolar basis, h-ALA has improved skin penetration, leading to enhanced PpIX production compared to the parent drug and m-ALA (C) 2010 Wiley-Liss, Inc and the American Pharmacists Association J Pharm Sci 99 3486-3498, 2010

Molecular diagnosis for heterogeneous genetic diseases with high-throughput DNA sequencing applied to retinitis pigmentosa

BACKGROUND:
The genetic heterogeneity of many Mendelian disorders, such as retinitis pigmentosa which results from mutations in over 40 genes, is a major obstacle to obtaining a molecular diagnosis in clinical practice. Targeted high-throughput DNA sequencing offers a potential solution and was used to develop a molecular diagnostic screen for patients with retinitis pigmentosa.
METHODS:
A custom sequence capture array was designed to target the coding regions of all known retinitis pigmentosa genes and used to enrich these sequences from DNA samples of five patients. Enriched DNA was subjected to high-throughput sequencing singly or in pools, and sequence variants were identified by alignment of up to 10 million reads per sample to the normal reference sequence. Potential pathogenicity was assessed by functional predictions and frequency in controls.
RESULTS AND CONCLUSIONS:
Known homozygous PDE6B and compound heterozygous CRB1 mutations were detected in two patients. A novel homozygous missense mutation (c.2957A?T; p.N986I) in the cyclic nucleotide gated channel ß1 (CNGB1) gene predicted to have a deleterious effect and absent in 720 control chromosomes was detected in one case in which conventional genetic screening had failed to detect mutations. The detection of known and novel retinitis pigmentosa mutations in this study establishes high-throughput DNA sequencing with DNA pooling as an effective diagnostic tool for heterogeneous genetic diseases.