Genome sequence of human papillomavirus type 20, strain HPV-20/Lancaster/2015

The genome sequence of human papillomavirus type 20 (HPV-20; family Papillomaviridae, genus Betapapillomavirus, species Betapapillomavirus 1, type 20) was assembled by deep sequencing from nasopharyngeal swabs. The assembled genome is 0.37% divergent over its full length from the single complete genome of HPV-20 in GenBank (U31778). We named the strain HPV-20/Lancaster/2015

On Validating an Astrophysical Simulation Code

We present a case study of validating an astrophysical simulation code. Our study focuses on validating FLASH, a parallel, adaptive-mesh hydrodynamics code for studying the compressible, reactive flows found in many astrophysical environments. We describe the astrophysics problems of interest and the challenges associated with simulating these problems. We describe methodology and discuss solutions to difficulties encountered in verification and validation. We describe verification tests regularly administered to the code, present the results of new verification tests, and outline a method for testing general equations of state. We present the results of two validation tests in which we compared simulations to experimental data. The first is of a laser-driven shock propagating through a multi-layer target, a configuration subject to both Rayleigh-Taylor and Richtmyer-Meshkov instabilities. The second test is a classic Rayleigh-Taylor instability, where a heavy fluid is supported against the force of gravity by a light fluid. Our simulations of the multi-layer target experiments showed good agreement with the experimental results, but our simulations of the Rayleigh-Taylor instability did not agree well with the experimental results. We discuss our findings and present results of additional simulations undertaken to further investigate the Rayleigh-Taylor instability.Comment: 76 pages, 26 figures (3 color), Accepted for publication in the ApJ

Orbital Physics in the Perovskite Ti Oxides

In the perovskite Ti oxide RTiO3 (R=rare-earth ions), the Ti t2g orbitals and spins in the 3d^1 state couple each other through the strong electron correlations, resulting in a rich variety of orbital-spin phases. The origin and nature of orbital-spin states of these Mott insulators have been intensively studied. In this article, we review the studies on orbital physics in the perovskite titanates. We focus on the following three topics: (1) the origin and nature of the ferromagnetism as well as the orbital ordering in the compounds with relatively small R ions such as GdTiO3 and YTiO3, (2) the origin of the G-type antiferromagnetism and the orbital state in LaTiO3, and (3) the orbital-spin structures in other AFM(G) compounds with relatively large R ions (R=Ce, Pr, Nd and Sm). On the basis of these discussions, we discuss the whole phase diagram together with mechanisms of the magnetic phase transition. We also show that the Ti t2g degeneracy is inherently lifted in the titanates, which allows the single-band descriptions of the ground-state and low-energy electronic structures as a good starting point. Our analyses indicate that these compounds offer touchstone materials described by the single-band Hubbard model on the cubic lattice. From this insight, we also reanalyze the hole-doped titanates. Experimentally revealed filling-dependent and bandwidth-dependent properties and the critical behavior of the metal-insulator transitions are discussed in the light of theories based on the single-band Hubbard models.Comment: Review article, 26 pages, to appear in New Journal of Physic

A general reaction-diffusion model of acidity in cancer invasion

We model the metabolism and behaviour of a developing cancer tumour in the context of its microenvironment, with the aim of elucidating the consequences of altered energy metabolism. Of particular interest is the Warburg Effect, a widespread preference in tumours for cytosolic glycolysis rather than oxidative phosphorylation for glucose breakdown, as yet incompletely understood. We examine a candidate explanation for the prevalence of the Warburg Effect in tumours, the acid-mediated invasion hypothesis, by generalising a canonical non-linear reaction–diffusion model of acid-mediated tumour invasion to consider additional biological features of potential importance. We apply both numerical methods and a non-standard asymptotic analysis in a travelling wave framework to obtain an explicit understanding of the range of tumour behaviours produced by the model and how fundamental parameters govern the speed and shape of invading tumour waves. Comparison with conclusions drawn under the original system—a special case of our generalised system—allows us to comment on the structural stability and predictive power of the modelling framework

Expression of CD3-ζ on T-cells in primary cervical carcinoma and in metastasis-positive and -negative pelvic lymph nodes

Lymphocytic infiltrate is often present in cervical cancer lesions, possibly reflecting an ongoing, but ineffective, immune response to the tumour. Recently, evidence has accumulated for systemically impaired T-cell functions in cancer patients, associated with decreased expression of signal-transducing zeta (ζ) chain dimer molecules on circulating T-cells and NK-cells. Here, we report on the intralesional down-regulation of ζ chain expression on T-cells in cervical carcinoma. Paraffin-embedded or snap-frozen sections from 24 different cervical cancer specimens were studied. Paraffin-embedded tumour-positive (n = 7) and tumour-negative (n = 15) pelvic lymph nodes were also included in the study. Immunostaining was performed on consecutive sections with antibodies specific for CD3-ɛ or the CD3-associated ζ chain dimer. Antigen retrieval by sodium citrate/microwave treatment was essential for ζ staining of paraffin sections. The amount of ζ positive cells was quantitated and related to the number of CD3-ɛ+ cells in corresponding tumour areas. Of the 24 cervical cancer specimens studied, ζ chain dimer expression was reduced in seven cases and strongly reduced in the other 17 samples. In tonsil control sections, CD3-ɛ and CD3-ζ were always co-expressed in almost equal numbers. Also, both tumour-negative and -positive lymph nodes showed ζ chain expression which equalled that of CD3-ɛ expression. These data indicate that a decreased expression of signal-transducing ζ molecules on tumour-infiltrating T-cells is frequent in cervical cancer. The apparently unimpaired ζ chain expression within draining lymph nodes suggests that local tumour-derived factors at the primary site are instrumental in ζ chain down-regulation. © 1999 Cancer Research Campaig

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: the challenge ahead.

Lifestyle factors are responsible for a considerable portion of cancer incidence worldwide, but credible estimates from the World Health Organization and the International Agency for Research on Cancer (IARC) suggest that the fraction of cancers attributable to toxic environmental exposures is between 7% and 19%. To explore the hypothesis that low-dose exposures to mixtures of chemicals in the environment may be combining to contribute to environmental carcinogenesis, we reviewed 11 hallmark phenotypes of cancer, multiple priority target sites for disruption in each area and prototypical chemical disruptors for all targets, this included dose-response characterizations, evidence of low-dose effects and cross-hallmark effects for all targets and chemicals. In total, 85 examples of chemicals were reviewed for actions on key pathways/mechanisms related to carcinogenesis. Only 15% (13/85) were found to have evidence of a dose-response threshold, whereas 59% (50/85) exerted low-dose effects. No dose-response information was found for the remaining 26% (22/85). Our analysis suggests that the cumulative effects of individual (non-carcinogenic) chemicals acting on different pathways, and a variety of related systems, organs, tissues and cells could plausibly conspire to produce carcinogenic synergies. Additional basic research on carcinogenesis and research focused on low-dose effects of chemical mixtures needs to be rigorously pursued before the merits of this hypothesis can be further advanced. However, the structure of the World Health Organization International Programme on Chemical Safety 'Mode of Action' framework should be revisited as it has inherent weaknesses that are not fully aligned with our current understanding of cancer biology

First High-Convergence Cryogenic Implosion in a Near-Vacuum Hohlraum

Recent experiments on the National Ignition Facility [M. J. Edwards et al., Phys. Plasmas 20, 070501 (2013)] demonstrate that utilizing a near-vacuum hohlraum (low pressure gas-filled) is a viable option for high convergence cryogenic deuterium-tritium (DT) layered capsule implosions. This is made possible by using a dense ablator (high-density carbon), which shortens the drive duration needed to achieve high convergence: a measured 40% higher hohlraum efficiency than typical gas-filled hohlraums, which requires less laser energy going into the hohlraum, and an observed better symmetry control than anticipated by standard hydrodynamics simulations. The first series of near-vacuum hohlraum experiments culminated in a 6.8 ns, 1.2 MJ laser pulse driving a 2-shock, high adiabat (α ~ 3.5) cryogenic DT layered high density carbon capsule. This resulted in one of the best performances so far on the NIF relative to laser energy, with a measured primary neutron yield of 1.8×10[superscript 15] neutrons, with 20% calculated alpha heating at convergence ~27×