Detection of 1p19q Deletion by Real-Time Comparative Quantitative PCR

1p/19q (1p and/or 19q) deletions are prognostic factors in oligodendroglial tumors (OT) and predict better survival after both chemotherapy and radiotherapy. While studying 1p/19q status as a potential variable within multivariate prognosis models for OT, we have frequently encountered unknown 1p/19q status within our glioma sample database due to lack of paired blood samples for loss of heterozygosity (LOH) assay and/or failure to perform fluorescence in situ hybridization (FISH). We realized that a 1p and 19q deletion assay that could be reliably performed solely on tumor DNA samples would allow us to fill in these molecular biology data “holes”. We built recombinant DNA with fragments of the selected “marker” genes in 1p (E2F2, NOTCH2), and 19q (PLAUR) and “reference” genes (ERC2, SPOCK1, and SPAG16 ) and used it as quantification standard in real-time PCR to gain absolute ratios of marker/reference gene copy numbers in tumor DNA samples, thus called comparative quantitative PCR (CQ-PCR). Using CQ-PCR, we identified 1p and/ or 19q deletions in majority of pure low-grade oligodenroglioma (OG) tumors (17/21, 81%), a large portion of anaplastic oligodendroglioma (AO) tumors (6/15, 47%), but rarely found in mixed oligoastrcytomas (OA) tumors (1/8, 13%). These data are consistent with results of LOH and FISH assays generally reported for these tumor types. In addition, 15 out 18 samples showed concordant results between FISH and CQ-PCR. We conclude that CQ-PCR is a potential means to gain 1p/19q deletion information, which prognostic and predictive values of CQ-PCR-derived 1p/19q status will be determined in a future study

Motivation to study in Higher Education:a comparison between Germany and Great Britain

This article deals with reasons for the motivation to study in higher education. To find out about motives, around 200 A-level students in Germany and Great Britain were asked about their plans for the time after completion of their A-levels. Through socio-demographic data the authors could deploy facts about social backgrounds and the affiliations to socio-economic classes. There are some expected findings (e.g., British A-level students are more likely to study than their German comrades) and some pretty unexpected results (e.g., social classes do not seem to divide students into choosing university or not)

Detection and diversity of a putative novel heterogeneous polymorphic proline-glycine repeat (Pgr) protein in the footrot pathogen Dichelobacter nodosus

Dichelobacter nodosus, a Gram-negative anaerobic bacterium, is the essential causative agent of footrot in sheep. Currently, depending on the clinical presentation in the field, footrot is described as benign or virulent; D. nodosus strains have also been classified as benign or virulent, but this designation is not always consistent with clinical disease. The aim of this study was to determine the diversity of the pgr gene, which encodes a putative proline-glycine repeat protein (Pgr). The pgr gene was present in all 100 isolates of D. nodosus that were examined and, based on sequence analysis had two variants, pgrA and pgrB. In pgrA, there were two coding tandem repeat regions, R1 and R2: different strains had variable numbers of repeats within these regions. The R1 and R2 were absent from pgrB. Both variants were present in strains from Australia, Sweden and the UK, however, only pgrB was detected in isolates from Western Australia. The pgrA gene was detected in D. nodosus from tissue samples from two flocks in the UK with virulent footrot and only pgrB from a flock with no virulent or benign footrot for >10 years. Bioinformatic analysis of the putative PgrA protein indicated that it contained a collagen-like cell surface anchor motif. These results suggest that the pgr gene may be a useful molecular marker for epidemiological studies

Charged BTZ-like Black Holes in Higher Dimensions

Motivated by many worthwhile paper about (2 + 1)-dimensional BTZ black holes, we generalize them to to (n + 1)-dimensional solutions, so called BTZ-like solutions. We show that the electric field of BTZ-like solutions is the same as (2 + 1)-dimensional BTZ black holes, and also their lapse functions are approximately the same, too. By these similarities, it is also interesting to investigate the geometric and thermodynamics properties of the BTZ-like solutions. We find that, depending on the metric parameters, the BTZ-like solutions may be interpreted as black hole solutions with inner (Cauchy) and outer (event) horizons, an extreme black hole or naked singularity. Then, we calculate thermodynamics quantities and conserved quantities, and show that they satisfy the first law of thermodynamics. Finally, we perform a stability analysis in the canonical ensemble and show that the BTZ-like solutions are stable in the whole phase space.Comment: 5 pages, two column format, one figur

Shear viscosity of the Quark-Gluon Plasma from a virial expansion

We calculate the shear viscosity $\eta$ in the quark-gluon plasma (QGP) phase within a virial expansion approach with particular interest in the ratio of $\eta$ to the entropy density $s$, i.e. $\eta/s$. The virial expansion approach allows us to include the interactions between the partons in the deconfined phase and to evaluate the corrections to a single-particle partition function. In the latter approach we start with an effective interaction with parameters fixed to reproduce thermodynamical quantities of QCD such as energy and/or entropy density. We also directly extract the effective coupling \ga_{\rm V} for the determination of $\eta$. Our numerical results give a ratio $\eta/s\approx 0.097$ at the critical temperature $T_{\rm c}$, which is very close to the theoretical bound of $1/(4\pi)$. Furthermore, for temperatures $T\leq 1.8 T_{\rm c}$ the ratio $\eta/s$ is in the range of the present experimental estimates $0.1-0.3$ at RHIC. When combining our results for $\eta/s$ in the deconfined phase with those from chiral perturbation theory or the resonance gas model in the confined phase we observe a pronounced minimum of $\eta/s$ close to the critical temperature $T_{\rm c}$.Comment: Published in Eur. Phys. J. C, 7 pages, 2 figures, 3 tabl

The Japanese model in retrospective : industrial strategies, corporate Japan and the 'hollowing out' of Japanese industry

This article provides a retrospective look at the Japanese model of industrial development. This model combined an institutional approach to production based around the Japanese Firm (Aoki's, J-mode) and strategic state intervention in industry by the Japanese Ministry of International Trade and Industry (MITI). For a long period, the alignment of state and corporate interests appeared to match the wider public interest as the Japanese economy prospered. However, since the early 1990s, the global ambitions of the corporate sector have contributed to a significant 'hollowing out' of Japan's industrial base. As the world today looks for a new direction in economic management, we suggest the Japanese model provides policy-makers with a salutary lesson in tying the wider public interest with those of the corporate sector

Multiple locus VNTR analysis highlights that geographical clustering and distribution of Dichelobacter nodosus, the causal agent of footrot in sheep, correlates with inter-country movements

Dichelobacter nodosus is a Gram-negative, anaerobic bacterium and the causal agent of footrot in sheep. Multiple locus variable number tandem repeat (VNTR) analysis (MLVA) is a portable technique that involves the identification and enumeration of polymorphic tandem repeats across the genome. The aims of this study were to develop an MLVA scheme for D. nodosus suitable for use as a molecular typing tool, and to apply it to a global collection of isolates. Seventy-seven isolates selected from regions with a long history of footrot (GB, Australia) and regions where footrot has recently been reported (India, Scandinavia), were characterised. From an initial 61 potential VNTR regions, four loci were identified as usable and in combination had the attributes required of a typing method for use in bacterial epidemiology: high discriminatory power (D > 0.95), typeability and reproducibility. Results from the analysis indicate that D. nodosus appears to have evolved via recombinational exchanges and clonal diversification. This has resulted in some clonal complexes that contain isolates from multiple countries and continents; and others that contain isolates from a single geographic location (country or region). The distribution of alleles between countries matches historical accounts of sheep movements, suggesting that the MLVA technique is sufficiently specific and sensitive for an epidemiological investigation of the global distribution of D. nodosus

Statistics of the gravitational force in various dimensions of space: from Gaussian to Levy laws

We discuss the distribution of the gravitational force created by a Poissonian distribution of field sources (stars, galaxies,...) in different dimensions of space d. In d=3, it is given by a Levy law called the Holtsmark distribution. It presents an algebraic tail for large fluctuations due to the contribution of the nearest neighbor. In d=2, it is given by a marginal Gaussian distribution intermediate between Gaussian and Levy laws. In d=1, it is exactly given by the Bernouilli distribution (for any particle number N) which becomes Gaussian for N>>1. Therefore, the dimension d=2 is critical regarding the statistics of the gravitational force. We generalize these results for inhomogeneous systems with arbitrary power-law density profile and arbitrary power-law force in a d-dimensional universe

Structure of Fat Jets at the Tevatron and Beyond

Boosted resonances is a highly probable and enthusiastic scenario in any process probing the electroweak scale. Such objects when decaying into jets can easily blend with the cornucopia of jets from hard relative light QCD states. We review jet observables and algorithms that can contribute to the identification of highly boosted heavy jets and the possible searches that can make use of such substructure information. We also review previous studies by CDF on boosted jets and its measurements on specific jet shapes.Comment: invited review for a special "Top and flavour physics in the LHC era" issue of The European Physical Journal C, we invite comments regarding contents of the review; v2 added references and institutional preprint number