Reliability of tissue microarrays in detecting protein expression and gene amplification in breast cancer

Tissue microarrays allow high throughput molecular profiling of diagnostic or predictive markers in cancer specimens and rapid validation of novel potential candidates identified from genomic and proteomic analyses in a large number of tumor samples. To validate the use of tissue microarray technology for all the main biomarkers routinely used to decide breast cancer prognostication and postsurgical adjuvant therapy, we constructed a tissue microarray from 97 breast tumors, with a single 0.6 mm core per specimen. Inummostaining; of tissue microarray sections and conventional full sections of each tumor were performed using well-characterized prognostic markers (estrogen receptor ER, progesterone receptor PR and c-erbB2). The full section versus tissue microarray concordance for these stains was 97% for ER, 98% for PR, and 97% for c-erbB2, respectively, with a strong statistical association (kappa value more than 0.90). Fluorescence in situ hybridization analysis for HER-2/neu gene amplification from the single-core tissue microarray was technically successful in about 90% (87/97) of the cases, with a concordance of 95% compared with parallel analyses with the full sections. The correlation with other pathological parameters was not significantly different between full-section and array-based results. It is concluded that the constructed tissue microarray with a single core per specimen ensures full biological representativeness to identify the associations between biomarkers and clinicopathological parameters, with no significant associated sampling bias.

Development and characterization of 10 polymorphic microsatellite loci for the blue shark, Prionace glauca, and their cross shark-species amplification.

Ten polymorphic nuclear microsatellite loci were developed from a microsatellite enriched genomic library of the blue shark, Prionace glauca. The utility of these markers for genetic studies of this globally distributed, heavily exploited, oceanic predator was assessed by screening 120 specimens sampled from six locations throughout the species’ range. Both moderately and highly polymorphic marker loci were identified. Three to 35 alleles were found to be segregating per locus (mean 10.1) with observed heterozygosities ranging from 24 to 91%. Evaluation of the cross-species amplification of these markers across 18 additional shark species indicates that these microsatellites are potentially useful for genetic studies of other species of conservation concern.

The RMT method for many-electron atomic systems in intense short-pulse laser light

We describe a new ab initio method for solving the time-dependent Schrödinger equation for multi-electron atomic systems exposed to intense short-pulse laser light. We call the method the R-matrix with time-dependence (RMT) method. Our starting point is a finite-difference numerical integrator (HELIUM), which has proved successful at describing few-electron atoms and atomic ions in strong laser fields with high accuracy. By exploiting the R-matrix division-of-space concept, we bring together a numerical method most appropriate to the multi-electron finite inner region (R-matrix basis set) and a different numerical method most appropriate to the one-electron outer region (finite difference). In order to exploit massively parallel supercomputers efficiently, we time-propagate the wavefunction in both regions by employing Arnoldi methods, originally developed for HELIUM.

Observation of plasma density dependence of electromagnetic soliton excitation by an intense laser pulse

The experimental evidence of the correlation between the initial electron density of the plasma and electromagnetic soliton excitation at the wake of an intense (10(19) W/cm(2)) and short (1 ps) laser pulse is presented. The spatial distribution of the solitons, together with their late time evolution into post-solitons, is found to be dependent upon the background plasma parameters, in agreement with published analytical and numerical findings. The measured temporal evolution and electrostatic field distribution of the structures are consistent with their late time evolution and the occurrence of multiple merging of neighboring post-solitons. (C) 2011 American Institute of Physics. [doi:10.1063/1.3625261]

Development and clinical validation of a loop-mediated isothermal amplification method for the rapid detection of Neisseria meningitidis

Loop-mediated isothermal amplification (LAMP) is an innovative technique that allows the rapid detection of target nucleic acid sequences under isothermal conditions without the need for complex instrumentation. The development, optimization, and clinical validation of a LAMP assay targeting the ctrA gene for the rapid detection of capsular Neisseria meningitidis were described. Highly specific detection of capsular N. meningitidis type strains and clinical isolates was demonstrated, with no cross-reactivity with other Neisseria spp. or with a comprehensive panel of other common human pathogens. The lower limit of detection was 6 ctrA gene copies detectable in 48 min, with positive reactions readily identifiable visually via a simple color change. Higher copy numbers could be detected in as little as 16 min. When applied to a total of 394 clinical specimens, the LAMP assay in comparison to a conventional TaqMan® based real-time polymerase chain reaction system demonstrated a sensitivity of 100% and a specificity of 98.9% with a ? coefficient of 0.942. The LAMP method represents a rapid, sensitive, and highly specific technique for the detection of N. meningitidis and has the potential to be used as a point-of-care molecular test and in resource-poor settings.

Optimization of double pulse pumping for Ni-like Sm x-ray lasers

We report a systematic study of double pulse pumping of the Ni-like Sm x-ray laser at 73 Angstrom, currently the shortest wavelength saturated x-ray laser. It is found that the Sm x-ray laser output can change by orders of magnitude when the intensity ratio of the pumping pulses and their relative delay are varied. Optimum pumping conditions are found and interpreted in terms of a simple model. (C) 1999 American Institute of Physics. [S0021-8979(99)07102-9].

A study to optimise the temporal drive pulse structure for efficient XUV lasing on the J=0-1, 19.6 nm line of Ge XXIII

Short pulses of 100 ps FWHM duration at 1.06 mu m wavelength are used as the pump source for driving the J = 0-1, 19.6 nm, Ne-like germanium X-ray laser. Different combinations of short pulses are investigated and quantitatively compared. Configurations investigated include a single pulse, double pulses at 400 ps and 800 ps separation, single pulses with prepulses and double pulses with prepulses. Data are presented in the form of integrated energy measurements, and supported by modelling. The most efficient short pulse configurations are shown to be orders of magnitude more effective than pumping with nanosecond duration pulses. (C) 1997 Elsevier Science B.V.